diff --git a/docs/____init_____8py.html b/docs/____init_____8py.html index 6648210e..d96adb6c 100644 --- a/docs/____init_____8py.html +++ b/docs/____init_____8py.html @@ -3,9 +3,9 @@ - + -EGS Brachy: /Users/marc/dev/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/eb_tests/__init__.py File Reference +EGS Brachy: /Users/marc/Developer/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/eb_tests/__init__.py File Reference @@ -30,7 +30,7 @@ - + @@ -30,7 +30,7 @@ - + +
-Generated by doxygen 1.9.5 +Generated by doxygen 1.9.8
diff --git a/docs/annotated.html b/docs/annotated.html index 898708b8..59437266 100644 --- a/docs/annotated.html +++ b/docs/annotated.html @@ -3,7 +3,7 @@ - + EGS Brachy: Class List @@ -30,7 +30,7 @@ - + @@ -30,7 +30,7 @@ - + @@ -30,7 +30,7 @@ - + +
-
/Users/marc/dev/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/array_sizes.h
+
/Users/marc/Developer/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/array_sizes.h
Go to the documentation of this file.
1/*
@@ -135,7 +140,7 @@
-Generated by doxygen 1.9.5 +Generated by doxygen 1.9.8
diff --git a/docs/brem__cyl_2____init_____8py.html b/docs/brem__cyl_2____init_____8py.html index 7e062b8f..69fdb4d0 100644 --- a/docs/brem__cyl_2____init_____8py.html +++ b/docs/brem__cyl_2____init_____8py.html @@ -3,9 +3,9 @@ - + -EGS Brachy: /Users/marc/dev/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/eb_tests/brem_cyl/__init__.py File Reference +EGS Brachy: /Users/marc/Developer/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/eb_tests/brem_cyl/__init__.py File Reference @@ -30,7 +30,7 @@
- + @@ -30,7 +30,7 @@ - + +
-Generated by doxygen 1.9.5 +Generated by doxygen 1.9.8
diff --git a/docs/brem__cyl_2test_8py.html b/docs/brem__cyl_2test_8py.html index d5c912e3..0c8b13d8 100644 --- a/docs/brem__cyl_2test_8py.html +++ b/docs/brem__cyl_2test_8py.html @@ -3,9 +3,9 @@ - + -EGS Brachy: /Users/marc/dev/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/eb_tests/brem_cyl/test.py File Reference +EGS Brachy: /Users/marc/Developer/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/eb_tests/brem_cyl/test.py File Reference @@ -30,7 +30,7 @@ - + @@ -30,7 +30,7 @@ - + +
Go to the documentation of this file.
1"""
2A test for ensuring x-ray sources mode is working. The test consists of a
-
31cm^2 beam of electrons incident on a thin cylindrical disc with dose
-
4being calculated in cylindrical slabs behind the target. The egs_brachy
-
5energy deposition doses are compared with values calculated by dosrznrc.
+
31cm^2 beam of electrons incident on a thin cylindrical disc with dose
+
4being calculated in cylindrical slabs behind the target. The egs_brachy
+
5energy deposition doses are compared with values calculated by dosrznrc.
6"""
-
7
-
8import csv
-
9import math
-
10import re
-
11
-
12from eb_tests.utils import doses_approx_equal, extract_all_doses
-
13
-
14EGSINP = "brem_cyl.egsinp"
-
15TIME_LIMIT_S_PER_MHZ = 20/2993. # s / MHz
-
16
-
17# doses calcualted using dosrz_brem_cyl.egsinp
-
18DOSRZ_NRC_DOSES = [
-
19 (3.0107E-013, 0.0002),
-
20 (1.0088E-016, 0.0040),
-
21 (5.6843E-017, 0.0042),
-
22 (3.8797E-017, 0.0041),
-
23]
-
24
-
25
-
26expected_doses = {
-
27 "tlen": [
+
7
+
8import csv
+
9import math
+
10import re
+
11
+
12from eb_tests.utils import doses_approx_equal, extract_all_doses
+
13
+
14EGSINP = "brem_cyl.egsinp"
+
15TIME_LIMIT_S_PER_MHZ = 20/2993. # s / MHz
+
16
+
17# doses calcualted using dosrz_brem_cyl.egsinp
+
18DOSRZ_NRC_DOSES = [
+
19 (3.0107E-013, 0.0002),
+
20 (1.0088E-016, 0.0040),
+
21 (5.6843E-017, 0.0042),
+
22 (3.8797E-017, 0.0041),
+
23]
+
24
+
25
+
26expected_doses = {
+
27 "tlen": [
28 (3.702E-16, 2.84),
29 (1.042E-16, 2.90),
30 (5.933E-17, 3.04),
@@ -119,7 +124,8 @@
40
41
42
-
43def compare_results(egslst, inp_name):
+
+
43def compare_results(egslst, inp_name):
44
45 actual = {
46 "tlen": [],
@@ -156,10 +162,12 @@
77 all_close = False
78
79 return all_close, actual, expected_doses
+
+
eb_tests.utils
Definition utils.py:1
-Generated by doxygen 1.9.5 +Generated by doxygen 1.9.8
diff --git a/docs/classBaseSpectrumScorer-members.html b/docs/classBaseSpectrumScorer-members.html index 9c17d199..3e75ade6 100644 --- a/docs/classBaseSpectrumScorer-members.html +++ b/docs/classBaseSpectrumScorer-members.html @@ -3,7 +3,7 @@ - + EGS Brachy: Member List @@ -30,7 +30,7 @@ - + + + + + + + + +
+
+ + + + + + +
+
EGS Brachy +
+
An egs++ user code for rapid brachytherapy calculations
+
+
+ + + + + + + + +
+
+ + +
+
+
+
+
+
Loading...
+
Searching...
+
No Matches
+
+
+
+
+ +
+
+
EB_UniformRunControl Member List
+
+
+ +

This is the complete list of members for EB_UniformRunControl, including all inherited members.

+ + + + + + + + + + + + + + + + +
appEB_UniformRunControlprotected
check_egsdatEB_UniformRunControlprotected
check_intervalsEB_UniformRunControlprotected
describeRCO()EB_UniformRunControl
EB_UniformRunControl(EB_Application *app, string egsdat_format)EB_UniformRunControl
finishSimulation()EB_UniformRunControl
ifirstEB_UniformRunControlprotected
iparEB_UniformRunControlprotected
millisecondsEB_UniformRunControlprotected
njobEB_UniformRunControlprotected
nparEB_UniformRunControlprotected
output_egsdat_formatEB_UniformRunControlprotected
startSimulation()EB_UniformRunControl
watcher_jobEB_UniformRunControlprotected
~EB_UniformRunControl()EB_UniformRunControlinline
+ +
+Generated by doxygen 1.9.8 +
+ + diff --git a/docs/classEB__UniformRunControl.html b/docs/classEB__UniformRunControl.html new file mode 100644 index 00000000..df249bb6 --- /dev/null +++ b/docs/classEB__UniformRunControl.html @@ -0,0 +1,506 @@ + + + + + + + +EGS Brachy: EB_UniformRunControl Class Reference + + + + + + + + + +
+
+ + + + + + +
+
EGS Brachy +
+
An egs++ user code for rapid brachytherapy calculations
+
+
+ + + + + + + + +
+
+ + +
+
+
+
+
+
Loading...
+
Searching...
+
No Matches
+
+
+
+
+ +
+
+
+Public Member Functions | +Protected Attributes | +List of all members
+
EB_UniformRunControl Class Reference
+
+
+ +

#include <egs_brachy.h>

+
+Inheritance diagram for EB_UniformRunControl:
+
+
Inheritance graph
+
[legend]
+
+Collaboration diagram for EB_UniformRunControl:
+
+
Collaboration graph
+
[legend]
+ + + + + + + + + + + + + +

+Public Member Functions

 EB_UniformRunControl (EB_Application *app, string egsdat_format)
 
 ~EB_UniformRunControl ()
 
void describeRCO ()
 
int startSimulation ()
 
int finishSimulation ()
 Uses 'watcher' jobs to determine if the simulation has finished.
 
+ + + + + + + + + + + + + + + + + + + + + + +

+Protected Attributes

EB_Application * app
 
string output_egsdat_format
 text or gzip
 
int milliseconds
 
int check_intervals
 
int njob
 
int npar
 
int ipar
 
int ifirst
 
bool check_egsdat
 
bool watcher_job
 
+

Detailed Description

+
+

Definition at line 520 of file egs_brachy.h.

+

Constructor & Destructor Documentation

+ +

◆ EB_UniformRunControl()

+ +
+
+ + + + + + + + + + + + + + + + + + +
EB_UniformRunControl::EB_UniformRunControl (EB_Application * app,
string egsdat_format 
)
+
+ +

Definition at line 2636 of file egs_brachy.cpp.

+ +
+
+ +

◆ ~EB_UniformRunControl()

+ +
+
+ + + + + +
+ + + + + + + +
EB_UniformRunControl::~EB_UniformRunControl ()
+ 		+inline
+
+ +

Definition at line 525 of file egs_brachy.h.

+ +
+
+

Member Function Documentation

+ +

◆ describeRCO()

+ +
+
+ + + + + + + +
void EB_UniformRunControl::describeRCO ()
+
+ +

Definition at line 2720 of file egs_brachy.cpp.

+ +
+
+ +

◆ finishSimulation()

+ +
+
+ + + + + + + +
int EB_UniformRunControl::finishSimulation ()
+
+ +

Uses 'watcher' jobs to determine if the simulation has finished.

+

If the current job is a 'watcher' job, it waits for some time before issuing the signal to recombine all available parallel jobs. These 'watcher' jobs can also produce intermediate results while waiting. If all jobs complete while waiting, the 'watcher' job combines all results and exits.

+ +

Definition at line 2747 of file egs_brachy.cpp.

+ +
+
+ +

◆ startSimulation()

+ +
+
+ + + + + + + +
int EB_UniformRunControl::startSimulation ()
+
+ +

Definition at line 2697 of file egs_brachy.cpp.

+ +
+
+

Member Data Documentation

+ +

◆ app

+ +
+
+ + + + + +
+ + + + +
EB_Application* EB_UniformRunControl::app
+ 		+protected
+
+ +

Definition at line 543 of file egs_brachy.h.

+ +
+
+ +

◆ check_egsdat

+ +
+
+ + + + + +
+ + + + +
bool EB_UniformRunControl::check_egsdat
+ 		+protected
+
+ +

Definition at line 557 of file egs_brachy.h.

+ +
+
+ +

◆ check_intervals

+ +
+
+ + + + + +
+ + + + +
int EB_UniformRunControl::check_intervals
+ 		+protected
+
+ +

Definition at line 550 of file egs_brachy.h.

+ +
+
+ +

◆ ifirst

+ +
+
+ + + + + +
+ + + + +
int EB_UniformRunControl::ifirst
+ 		+protected
+
+ +

Definition at line 556 of file egs_brachy.h.

+ +
+
+ +

◆ ipar

+ +
+
+ + + + + +
+ + + + +
int EB_UniformRunControl::ipar
+ 		+protected
+
+ +

Definition at line 555 of file egs_brachy.h.

+ +
+
+ +

◆ milliseconds

+ +
+
+ + + + + +
+ + + + +
int EB_UniformRunControl::milliseconds
+ 		+protected
+
+ +

Definition at line 547 of file egs_brachy.h.

+ +
+
+ +

◆ njob

+ +
+
+ + + + + +
+ + + + +
int EB_UniformRunControl::njob
+ 		+protected
+
+ +

Definition at line 553 of file egs_brachy.h.

+ +
+
+ +

◆ npar

+ +
+
+ + + + + +
+ + + + +
int EB_UniformRunControl::npar
+ 		+protected
+
+ +

Definition at line 554 of file egs_brachy.h.

+ +
+
+ +

◆ output_egsdat_format

+ +
+
+ + + + + +
+ + + + +
string EB_UniformRunControl::output_egsdat_format
+ 		+protected
+
+ +

text or gzip

+ +

Definition at line 545 of file egs_brachy.h.

+ +
+
+ +

◆ watcher_job

+ +
+
+ + + + + +
+ + + + +
bool EB_UniformRunControl::watcher_job
+ 		+protected
+
+ +

Definition at line 558 of file egs_brachy.h.

+ +
+
+
The documentation for this class was generated from the following files: +
+ +
+Generated by doxygen 1.9.8 +
+ + diff --git a/docs/classEB__UniformRunControl__coll__graph.dot b/docs/classEB__UniformRunControl__coll__graph.dot new file mode 100644 index 00000000..bc4d63b8 --- /dev/null +++ b/docs/classEB__UniformRunControl__coll__graph.dot @@ -0,0 +1,60 @@ +digraph "EB_UniformRunControl" +{ + // LATEX_PDF_SIZE + bgcolor="transparent"; + edge [fontname=Helvetica,fontsize=10,labelfontname=Helvetica,labelfontsize=10]; + node [fontname=Helvetica,fontsize=10,shape=box,height=0.2,width=0.4]; + rankdir="LR"; + Node1 [id="Node000001",label="EB_UniformRunControl",height=0.2,width=0.4,color="gray40", fillcolor="grey60", style="filled", fontcolor="black",tooltip=" "]; + Node2 -> Node1 [id="edge1_Node000001_Node000002",dir="back",color="steelblue1",style="solid",tooltip=" "]; + Node2 [id="Node000002",label="EGS_RunControl",height=0.2,width=0.4,color="gray40", fillcolor="white", style="filled",tooltip=" "]; + Node3 -> Node1 [id="edge2_Node000001_Node000003",dir="back",color="darkorchid3",style="dashed",tooltip=" ",label=" app",fontcolor="grey" ]; + Node3 [id="Node000003",label="EB_Application",height=0.2,width=0.4,color="gray40", fillcolor="white", style="filled",URL="$classEB__Application.html",tooltip="The main egs_brachy application class. See the Main Page for full documentation."]; + Node4 -> Node3 [id="edge3_Node000003_Node000004",dir="back",color="steelblue1",style="solid",tooltip=" "]; + Node4 [id="Node000004",label="EGS_AdvancedApplication",height=0.2,width=0.4,color="gray40", fillcolor="white", style="filled",tooltip=" "]; + Node5 -> Node3 [id="edge4_Node000003_Node000005",dir="back",color="darkorchid3",style="dashed",tooltip=" ",label=" escoring",fontcolor="grey" ]; + Node5 [id="Node000005",label="EnergyScoringStats",height=0.2,width=0.4,color="gray40", fillcolor="white", style="filled",URL="$classEnergyScoringStats.html",tooltip="a class to use for scoring information about total energy initialzed, escaping sources etc"]; + Node6 -> Node5 [id="edge5_Node000005_Node000006",dir="back",color="steelblue1",style="solid",tooltip=" "]; + Node6 [id="Node000006",label="Subscriber",height=0.2,width=0.4,color="gray40", fillcolor="white", style="filled",URL="$classSubscriber.html",tooltip=" "]; + Node7 -> Node3 [id="edge6_Node000003_Node000007",dir="back",color="darkorchid3",style="dashed",tooltip=" ",label=" recycle_opts",fontcolor="grey" ]; + Node7 [id="Node000007",label="RecycleOpts",height=0.2,width=0.4,color="gray40", fillcolor="white", style="filled",URL="$classRecycleOpts.html",tooltip=" "]; + Node8 -> Node3 [id="edge7_Node000003_Node000008",dir="back",color="darkorchid3",style="dashed",tooltip=" ",label=" phsp",fontcolor="grey" ]; + Node8 [id="Node000008",label="PHSPControl",height=0.2,width=0.4,color="gray40", fillcolor="white", style="filled",URL="$classPHSPControl.html",tooltip=" "]; + Node6 -> Node8 [id="edge8_Node000008_Node000006",dir="back",color="steelblue1",style="solid",tooltip=" "]; + Node9 -> Node3 [id="edge9_Node000003_Node000009",dir="back",color="darkorchid3",style="dashed",tooltip=" ",label=" ginfo",fontcolor="grey" ]; + Node9 [id="Node000009",label="GeomInfo",height=0.2,width=0.4,color="gray40", fillcolor="white", style="filled",URL="$classGeomInfo.html",tooltip="a container for organizing meta data about the geometries"]; + Node10 -> Node9 [id="edge10_Node000009_Node000010",dir="back",color="darkorchid3",style="dashed",tooltip=" ",label=" geom_tree",fontcolor="grey" ]; + Node10 [id="Node000010",label="Node",height=0.2,width=0.4,color="gray40", fillcolor="white", style="filled",URL="$classNode.html",tooltip=" "]; + Node11 -> Node3 [id="edge11_Node000003_Node000011",dir="back",color="darkorchid3",style="dashed",tooltip=" ",label=" gcr_phantom",fontcolor="grey" ]; + Node11 [id="Node000011",label="EB_Phantom",height=0.2,width=0.4,color="gray40", fillcolor="white", style="filled",URL="$classEB__Phantom.html",tooltip="A class to represent a single phantom for scoring dose in egs_brachy."]; + Node6 -> Node11 [id="edge12_Node000011_Node000006",dir="back",color="steelblue1",style="solid",tooltip=" "]; + Node12 -> Node11 [id="edge13_Node000011_Node000012",dir="back",color="darkorchid3",style="dashed",tooltip=" ",label=" publisher",fontcolor="grey" ]; + Node12 [id="Node000012",label="Publisher",height=0.2,width=0.4,color="gray40", fillcolor="white", style="filled",URL="$classPublisher.html",tooltip=" "]; + Node13 -> Node3 [id="edge14_Node000003_Node000013",dir="back",color="darkorchid3",style="dashed",tooltip=" ",label=" gen_vc_results\nsource_vc_results",fontcolor="grey" ]; + Node13 [id="Node000013",label="ebvolcor::Results",height=0.2,width=0.4,color="gray40", fillcolor="white", style="filled",URL="$structebvolcor_1_1Results.html",tooltip="Struct used to collect and output results about a volume correction run."]; + Node14 -> Node3 [id="edge15_Node000003_Node000014",dir="back",color="darkorchid3",style="dashed",tooltip=" ",label=" file_vc_results",fontcolor="grey" ]; + Node14 [id="Node000014",label="ebvolcor::FileResults",height=0.2,width=0.4,color="gray40", fillcolor="white", style="filled",URL="$structebvolcor_1_1FileResults.html",tooltip=" "]; + Node12 -> Node3 [id="edge16_Node000003_Node000012",dir="back",color="darkorchid3",style="dashed",tooltip=" ",label=" pevent_pub",fontcolor="grey" ]; + Node15 -> Node3 [id="edge17_Node000003_Node000015",dir="back",color="darkorchid3",style="dashed",tooltip=" ",label=" timing_blocks",fontcolor="grey" ]; + Node15 [id="Node000015",label="EB_TimingTree",height=0.2,width=0.4,color="gray40", fillcolor="white", style="filled",URL="$classEB__TimingTree.html",tooltip=" "]; + Node16 -> Node3 [id="edge18_Node000003_Node000016",dir="back",color="darkorchid3",style="dashed",tooltip=" ",label=" gz_data_out",fontcolor="grey" ]; + Node16 [id="Node000016",label="ogzstream",height=0.2,width=0.4,color="gray40", fillcolor="white", style="filled",URL="$classogzstream.html",tooltip=" "]; + Node17 -> Node16 [id="edge19_Node000016_Node000017",dir="back",color="steelblue1",style="solid",tooltip=" "]; + Node17 [id="Node000017",label="gzstreambase",height=0.2,width=0.4,color="gray40", fillcolor="white", style="filled",URL="$classgzstreambase.html",tooltip=" "]; + Node18 -> Node17 [id="edge20_Node000017_Node000018",dir="back",color="steelblue1",style="solid",tooltip=" "]; + Node18 [id="Node000018",label="std::ios",height=0.2,width=0.4,color="gray40", fillcolor="white", style="filled",tooltip=" "]; + Node19 -> Node17 [id="edge21_Node000017_Node000019",dir="back",color="darkorchid3",style="dashed",tooltip=" ",label=" buf",fontcolor="grey" ]; + Node19 [id="Node000019",label="gzstreambuf",height=0.2,width=0.4,color="gray40", fillcolor="white", style="filled",URL="$classgzstreambuf.html",tooltip=" "]; + Node20 -> Node19 [id="edge22_Node000019_Node000020",dir="back",color="steelblue1",style="solid",tooltip=" "]; + Node20 [id="Node000020",label="std::streambuf",height=0.2,width=0.4,color="gray40", fillcolor="white", style="filled",tooltip=" "]; + Node21 -> Node16 [id="edge23_Node000016_Node000021",dir="back",color="steelblue1",style="solid",tooltip=" "]; + Node21 [id="Node000021",label="std::ostream",height=0.2,width=0.4,color="gray40", fillcolor="white", style="filled",tooltip=" "]; + Node22 -> Node3 [id="edge24_Node000003_Node000022",dir="back",color="darkorchid3",style="dashed",tooltip=" ",label=" gz_data_in",fontcolor="grey" ]; + Node22 [id="Node000022",label="igzstream",height=0.2,width=0.4,color="gray40", fillcolor="white", style="filled",URL="$classigzstream.html",tooltip=" "]; + Node17 -> Node22 [id="edge25_Node000022_Node000017",dir="back",color="steelblue1",style="solid",tooltip=" "]; + Node23 -> Node22 [id="edge26_Node000022_Node000023",dir="back",color="steelblue1",style="solid",tooltip=" "]; + Node23 [id="Node000023",label="std::istream",height=0.2,width=0.4,color="gray40", fillcolor="white", style="filled",tooltip=" "]; + Node24 -> Node3 [id="edge27_Node000003_Node000024",dir="back",color="darkorchid3",style="dashed",tooltip=" ",label=" latch_control",fontcolor="grey" ]; + Node24 [id="Node000024",label="Latch",height=0.2,width=0.4,color="gray40", fillcolor="white", style="filled",URL="$classLatch.html",tooltip="A class for handling latch bits relevant to egs_brachy. The Latch class listens for particle events a..."]; + Node6 -> Node24 [id="edge28_Node000024_Node000006",dir="back",color="steelblue1",style="solid",tooltip=" "]; +} diff --git a/docs/classEB__UniformRunControl__inherit__graph.dot b/docs/classEB__UniformRunControl__inherit__graph.dot new file mode 100644 index 00000000..24eabae8 --- /dev/null +++ b/docs/classEB__UniformRunControl__inherit__graph.dot @@ -0,0 +1,10 @@ +digraph "EB_UniformRunControl" +{ + // LATEX_PDF_SIZE + bgcolor="transparent"; + edge [fontname=Helvetica,fontsize=10,labelfontname=Helvetica,labelfontsize=10]; + node [fontname=Helvetica,fontsize=10,shape=box,height=0.2,width=0.4]; + Node1 [id="Node000001",label="EB_UniformRunControl",height=0.2,width=0.4,color="gray40", fillcolor="grey60", style="filled", fontcolor="black",tooltip=" "]; + Node2 -> Node1 [id="edge1_Node000001_Node000002",dir="back",color="steelblue1",style="solid",tooltip=" "]; + Node2 [id="Node000002",label="EGS_RunControl",height=0.2,width=0.4,color="gray40", fillcolor="white", style="filled",tooltip=" "]; +} diff --git a/docs/classEGS__Sobol-members.html b/docs/classEGS__Sobol-members.html index 848b83a4..49ff4ed3 100644 --- a/docs/classEGS__Sobol-members.html +++ b/docs/classEGS__Sobol-members.html @@ -3,7 +3,7 @@ - + EGS Brachy: Member List @@ -30,7 +30,7 @@ - + @@ -30,7 +30,7 @@ - + @@ -30,7 +30,7 @@ - + @@ -30,7 +30,7 @@ - + @@ -30,7 +30,7 @@ - + @@ -30,7 +30,7 @@ - + @@ -30,7 +30,7 @@ - + @@ -30,7 +30,7 @@ - + @@ -30,7 +30,7 @@ - + @@ -30,7 +30,7 @@ - + @@ -30,7 +30,7 @@ - + @@ -30,7 +30,7 @@ - + @@ -30,7 +30,7 @@ - + @@ -30,7 +30,7 @@ - + @@ -30,7 +30,7 @@ - + @@ -30,7 +30,7 @@ - + @@ -30,7 +30,7 @@ - + @@ -30,7 +30,7 @@ - + @@ -30,7 +30,7 @@ - + @@ -30,7 +30,7 @@ - + @@ -30,7 +30,7 @@ - + @@ -30,7 +30,7 @@ - + @@ -30,7 +30,7 @@ - + @@ -30,7 +30,7 @@ - + @@ -30,7 +30,7 @@ - + @@ -30,7 +30,7 @@ - + @@ -30,7 +30,7 @@ - + @@ -30,7 +30,7 @@ - + @@ -30,7 +30,7 @@ - + @@ -30,7 +30,7 @@ - + +
Go to the documentation of this file.
1import os
2
-
3def find_file_descriptions(dir_path, include_key=None):
+
+
3def find_file_descriptions(dir_path, include_key=None):
4
5 items = []
6
@@ -107,11 +113,12 @@
32 return "\n".join(items)
33
34
-
join
string join(const vector< string > &v, string delim)
Definition: ginfo.cpp:56
+
+
join
string join(const vector< string > &v, string delim)
Definition ginfo.cpp:56
-Generated by doxygen 1.9.5 +Generated by doxygen 1.9.8
diff --git a/docs/docd.svg b/docs/docd.svg new file mode 100644 index 00000000..ac18b275 --- /dev/null +++ b/docs/docd.svg @@ -0,0 +1,12 @@ + + + + + + + + + + + diff --git a/docs/doxygen.css b/docs/doxygen.css index 89dee6c4..009a9b55 100644 --- a/docs/doxygen.css +++ b/docs/doxygen.css @@ -1,4 +1,4 @@ -/* The standard CSS for doxygen 1.9.5*/ +/* The standard CSS for doxygen 1.9.8*/ html { /* page base colors */ @@ -39,7 +39,9 @@ html { --icon-background-color: #728DC1; --icon-foreground-color: white; ---icon-doc-image: url('doc.png'); +--icon-doc-image: url('doc.svg'); +--icon-folder-open-image: url('folderopen.svg'); +--icon-folder-closed-image: url('folderclosed.svg'); /* brief member declaration list */ --memdecl-background-color: #F9FAFC; @@ -100,6 +102,7 @@ html { --toc-background-color: #F4F6FA; --toc-border-color: #D8DFEE; --toc-header-color: #4665A2; +--toc-down-arrow-image: url("data:image/svg+xml;utf8,&%238595;"); /** search field */ --search-background-color: white; @@ -125,6 +128,7 @@ html { --code-preprocessor-color: #806020; --code-string-literal-color: #002080; --code-char-literal-color: #008080; +--code-xml-cdata-color: black; --code-vhdl-digit-color: #FF00FF; --code-vhdl-char-color: #000000; --code-vhdl-keyword-color: #700070; @@ -148,10 +152,15 @@ html { --tooltip-declaration-color: #006318; --tooltip-link-color: #4665A2; --tooltip-shadow: 1px 1px 7px gray; +--fold-line-color: #808080; +--fold-minus-image: url('minus.svg'); +--fold-plus-image: url('plus.svg'); +--fold-minus-image-relpath: url('../../minus.svg'); +--fold-plus-image-relpath: url('../../plus.svg'); /** font-family */ --font-family-normal: Roboto,sans-serif; ---font-family-monospace: monospace,fixed; +--font-family-monospace: 'JetBrains Mono',Consolas,Monaco,'Andale Mono','Ubuntu Mono',monospace,fixed; --font-family-nav: 'Lucida Grande',Geneva,Helvetica,Arial,sans-serif; --font-family-title: Tahoma,Arial,sans-serif; --font-family-toc: Verdana,'DejaVu Sans',Geneva,sans-serif; @@ -203,7 +212,9 @@ html { --icon-background-color: #334975; --icon-foreground-color: #C4CFE5; ---icon-doc-image: url('docd.png'); +--icon-doc-image: url('docd.svg'); +--icon-folder-open-image: url('folderopend.svg'); +--icon-folder-closed-image: url('folderclosedd.svg'); /* brief member declaration list */ --memdecl-background-color: #0B101A; @@ -264,6 +275,7 @@ html { --toc-background-color: #151E30; --toc-border-color: #202E4A; --toc-header-color: #A3B4D7; +--toc-down-arrow-image: url("data:image/svg+xml;utf8,&%238595;"); /** search field */ --search-background-color: black; @@ -289,9 +301,10 @@ html { --code-preprocessor-color: #65CABE; --code-string-literal-color: #7EC699; --code-char-literal-color: #00E0F0; +--code-xml-cdata-color: #C9D1D9; --code-vhdl-digit-color: #FF00FF; ---code-vhdl-char-color: #000000; ---code-vhdl-keyword-color: #700070; +--code-vhdl-char-color: #C0C0C0; +--code-vhdl-keyword-color: #CF53C9; --code-vhdl-logic-color: #FF0000; --code-link-color: #79C0FF; --code-external-link-color: #79C0FF; @@ -312,10 +325,15 @@ html { --tooltip-declaration-color: #20C348; --tooltip-link-color: #79C0FF; --tooltip-shadow: none; +--fold-line-color: #808080; +--fold-minus-image: url('minusd.svg'); +--fold-plus-image: url('plusd.svg'); +--fold-minus-image-relpath: url('../../minusd.svg'); +--fold-plus-image-relpath: url('../../plusd.svg'); /** font-family */ --font-family-normal: Roboto,sans-serif; ---font-family-monospace: monospace,fixed; +--font-family-monospace: 'JetBrains Mono',Consolas,Monaco,'Andale Mono','Ubuntu Mono',monospace,fixed; --font-family-nav: 'Lucida Grande',Geneva,Helvetica,Arial,sans-serif; --font-family-title: Tahoma,Arial,sans-serif; --font-family-toc: Verdana,'DejaVu Sans',Geneva,sans-serif; @@ -327,20 +345,6 @@ html { body { background-color: var(--page-background-color); color: var(--page-foreground-color); - scrollbar-color: var(--scrollbar-thumb-color) var(--scrollbar-background-color); -} - -::-webkit-scrollbar { - background-color: var(--scrollbar-background-color); - height: 10px; - width: 10px; -} -::-webkit-scrollbar-thumb { - background-color: var(--scrollbar-thumb-color); - border-radius: 8px; -} -::-webkit-scrollbar-corner { - background-color: var(--scrollbar-background-color); } body, table, div, p, dl { @@ -487,6 +491,12 @@ div.qindex{ color: var(--index-separator-color); } +#main-menu a:focus { + outline: auto; + z-index: 10; + position: relative; +} + dt.alphachar{ font-size: 180%; font-weight: bold; @@ -601,6 +611,16 @@ ul { overflow: visible; } +ul.multicol { + -moz-column-gap: 1em; + -webkit-column-gap: 1em; + column-gap: 1em; + -moz-column-count: 3; + -webkit-column-count: 3; + column-count: 3; + list-style-type: none; +} + #side-nav ul { overflow: visible; /* reset ul rule for scroll bar in GENERATE_TREEVIEW window */ } @@ -642,7 +662,7 @@ div.line { font-family: var(--font-family-monospace); font-size: 13px; min-height: 13px; - line-height: 1.0; + line-height: 1.2; text-wrap: unrestricted; white-space: -moz-pre-wrap; /* Moz */ white-space: -pre-wrap; /* Opera 4-6 */ @@ -675,6 +695,18 @@ div.line.glow { box-shadow: 0 0 10px var(--glow-color); } +span.fold { + margin-left: 5px; + margin-right: 1px; + margin-top: 0px; + margin-bottom: 0px; + padding: 0px; + display: inline-block; + width: 12px; + height: 12px; + background-repeat:no-repeat; + background-position:center; +} span.lineno { padding-right: 4px; @@ -812,6 +844,10 @@ span.charliteral { color: var(--code-char-literal-color); } +span.xmlcdata { + color: var(--code-xml-cdata-color); +} + span.vhdldigit { color: var(--code-vhdl-digit-color); } @@ -1226,8 +1262,7 @@ div.directory { width: 24px; height: 18px; margin-bottom: 4px; - background-image:url('folderopen.png'); - background-position: 0px -4px; + background-image:var(--icon-folder-open-image); background-repeat: repeat-y; vertical-align:top; display: inline-block; @@ -1237,8 +1272,7 @@ div.directory { width: 24px; height: 18px; margin-bottom: 4px; - background-image:url('folderclosed.png'); - background-position: 0px -4px; + background-image:var(--icon-folder-closed-image); background-repeat: repeat-y; vertical-align:top; display: inline-block; @@ -1657,7 +1691,7 @@ div.toc { } div.toc li { - background: url("bdwn.png") no-repeat scroll 0 5px transparent; + background: var(--toc-down-arrow-image) no-repeat scroll 0 5px transparent; font: 10px/1.2 var(--font-family-toc); margin-top: 5px; padding-left: 10px; @@ -1686,11 +1720,11 @@ div.toc li.level2 { } div.toc li.level3 { - margin-left: 30px; + margin-left: 15px; } div.toc li.level4 { - margin-left: 45px; + margin-left: 15px; } span.emoji { @@ -1971,3 +2005,41 @@ u { text-decoration: underline; } +details>summary { + list-style-type: none; +} + +details > summary::-webkit-details-marker { + display: none; +} + +details>summary::before { + content: "\25ba"; + padding-right:4px; + font-size: 80%; +} + +details[open]>summary::before { + content: "\25bc"; + padding-right:4px; + font-size: 80%; +} + +body { + scrollbar-color: var(--scrollbar-thumb-color) var(--scrollbar-background-color); +} + +::-webkit-scrollbar { + background-color: var(--scrollbar-background-color); + height: 12px; + width: 12px; +} +::-webkit-scrollbar-thumb { + border-radius: 6px; + box-shadow: inset 0 0 12px 12px var(--scrollbar-thumb-color); + border: solid 2px transparent; +} +::-webkit-scrollbar-corner { + background-color: var(--scrollbar-background-color); +} + diff --git a/docs/doxygen.svg b/docs/doxygen.svg index d42dad52..79a76354 100644 --- a/docs/doxygen.svg +++ b/docs/doxygen.svg @@ -1,4 +1,6 @@ + @@ -17,7 +19,7 @@ - + diff --git a/docs/dynsections.js b/docs/dynsections.js index 1f4cd14a..9b281563 100644 --- a/docs/dynsections.js +++ b/docs/dynsections.js @@ -120,6 +120,75 @@ function toggleInherit(id) $(img).attr('src',src.substring(0,src.length-10)+'open.png'); } } + +var opened=true; +// in case HTML_COLORSTYLE is LIGHT or DARK the vars will be replaced, so we write them out explicitly and use double quotes +var plusImg = [ "var(--fold-plus-image)", "var(--fold-plus-image-relpath)" ]; +var minusImg = [ "var(--fold-minus-image)", "var(--fold-minus-image-relpath)" ]; + +// toggle all folding blocks +function codefold_toggle_all(relPath) { + if (opened) { + $('#fold_all').css('background-image',plusImg[relPath]); + $('div[id^=foldopen]').hide(); + $('div[id^=foldclosed]').show(); + } else { + $('#fold_all').css('background-image',minusImg[relPath]); + $('div[id^=foldopen]').show(); + $('div[id^=foldclosed]').hide(); + } + opened=!opened; +} + +// toggle single folding block +function codefold_toggle(id) { + $('#foldopen'+id).toggle(); + $('#foldclosed'+id).toggle(); +} +function init_codefold(relPath) { + $('span[class=lineno]').css( + {'padding-right':'4px', + 'margin-right':'2px', + 'display':'inline-block', + 'width':'54px', + 'background':'linear-gradient(var(--fold-line-color),var(--fold-line-color)) no-repeat 46px/2px 100%' + }); + // add global toggle to first line + $('span[class=lineno]:first').append(''); + // add vertical lines to other rows + $('span[class=lineno]').not(':eq(0)').append(''); + // add toggle controls to lines with fold divs + $('div[class=foldopen]').each(function() { + // extract specific id to use + var id = $(this).attr('id').replace('foldopen',''); + // extract start and end foldable fragment attributes + var start = $(this).attr('data-start'); + var end = $(this).attr('data-end'); + // replace normal fold span with controls for the first line of a foldable fragment + $(this).find('span[class=fold]:first').replaceWith(''); + // append div for folded (closed) representation + $(this).after(''); + // extract the first line from the "open" section to represent closed content + var line = $(this).children().first().clone(); + // remove any glow that might still be active on the original line + $(line).removeClass('glow'); + if (start) { + // if line already ends with a start marker (e.g. trailing {), remove it + $(line).html($(line).html().replace(new RegExp('\\s*'+start+'\\s*$','g'),'')); + } + // replace minus with plus symbol + $(line).find('span[class=fold]').css('background-image',plusImg[relPath]); + // append ellipsis + $(line).append(' '+start+'…'+end); + // insert constructed line into closed div + $('#foldclosed'+id).html(line); + }); +} + /* @license-end */ $(document).ready(function() { $('.code,.codeRef').each(function() { diff --git a/docs/eb__iaeaphsp__source_8cpp.html b/docs/eb__iaeaphsp__source_8cpp.html index a9e41640..8668070f 100644 --- a/docs/eb__iaeaphsp__source_8cpp.html +++ b/docs/eb__iaeaphsp__source_8cpp.html @@ -3,9 +3,9 @@ - + -EGS Brachy: /Users/marc/dev/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/eb_iaeaphsp_source/eb_iaeaphsp_source.cpp File Reference +EGS Brachy: /Users/marc/Developer/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/eb_iaeaphsp_source/eb_iaeaphsp_source.cpp File Reference @@ -30,7 +30,7 @@ - + @@ -30,7 +30,7 @@ - + +
50IAEA_I32 EB_IAEASource::next_source_id = 0;
51const string EB_IAEASource::iaea_header_ext = ".IAEAheader";
52
+
53EB_IAEASource::EB_IAEASource(EGS_Input *input, EGS_ObjectFactory *f) :
54 EGS_BaseSource(input,f) {
55
@@ -178,8 +184,10 @@
102 description = ss.str();
103
104}
+
105
106
+
107EB_IAEASource::~EB_IAEASource() {
108 if (isValid()) {
109 IAEA_I32 result;
@@ -187,8 +195,10 @@
111 }
112
113}
+
114
115
+
116void EB_IAEASource::openPHSPFile() {
117
118 IAEA_I32 access = 1; // read only
@@ -203,7 +213,9 @@
127
128
129}
+
130
+
131void EB_IAEASource::initSourceParams() {
132
133 IAEA_Float ftmp;
@@ -229,7 +241,9 @@
153 Nfirst = 1;
154
155}
+
156
+
157IAEA_I64 EB_IAEASource::getNextParticle(EGS_RandomGenerator *rndm, int &q,
158 int &latch, EGS_Float &E, EGS_Float &wt, EGS_Vector &x, EGS_Vector &u) {
159
@@ -279,8 +293,10 @@
203
204 return count;
205}
+
206
207
+
208void EB_IAEASource::setSimulationChunk(IAEA_I64 nstart, IAEA_I64 nrun) {
209
210 if (nstart < 0 || nrun < 1 || nstart + nrun > Nparticle) {
@@ -303,21 +319,29 @@
227 }
228
229}
+
230
231
+
232EGS_Float EB_IAEASource::getEmax() const {
233 return Emax;
234};
+
235
+
236bool EB_IAEASource::isValid() const {
237 return is_valid;
238}
+
239
+
240EGS_Float EB_IAEASource::getFluence() const {
241 double aux = ((double) count)/((double) Nparticle);
242 return Nincident*aux;
243}
+
244
+
245bool EB_IAEASource::storeState(ostream &data) const {
246
247 data << endl;
@@ -354,7 +378,9 @@
278
279 return true;
280}
+
281
+
282bool EB_IAEASource::setState(istream &data) {
283
284
@@ -391,7 +417,9 @@
315 return res;
316
317};
+
318
+
319bool EB_IAEASource::addState(istream &data) {
320
321 IAEA_I64 tmp_Nread = Nread;
@@ -402,58 +430,63 @@
326
327 return res;
328};
+
329
+
330void EB_IAEASource::resetCounter() {
331 Nread = 0;
332 count = 0;
333}
+
334
335extern "C" {
336
+
337 EB_IAEA_SOURCE_EXPORT EGS_BaseSource *createSource(EGS_Input *input, EGS_ObjectFactory *f) {
338 return createSourceTemplate<EB_IAEASource>(input,f,"iaea phsp source");
339 }
+
340
341}
-
EB_IAEASource::next_source_id
static IAEA_I32 next_source_id
Definition: eb_iaeaphsp_source.h:157
-
EB_IAEASource::source_id
IAEA_I32 source_id
Definition: eb_iaeaphsp_source.h:135
-
EB_IAEASource::p_source_id
IAEA_I32 * p_source_id
Definition: eb_iaeaphsp_source.h:136
-
EB_IAEASource::iaea_header_ext
static const string iaea_header_ext
Definition: eb_iaeaphsp_source.h:159
-
EB_IAEASource::Emax
EGS_Float Emax
Maximum energy (obtained from the phsp file)
Definition: eb_iaeaphsp_source.h:138
-
EB_IAEASource::phsp_file_name
string phsp_file_name
The phase space file name.
Definition: eb_iaeaphsp_source.h:132
-
EB_IAEASource::i_parallel
IAEA_I32 i_parallel
Definition: eb_iaeaphsp_source.h:152
-
EB_IAEASource::Nfirst
IAEA_I64 Nfirst
first record this source can use
Definition: eb_iaeaphsp_source.h:146
-
EB_IAEASource::resetCounter
void resetCounter()
Definition: eb_iaeaphsp_source.cpp:330
-
EB_IAEASource::openPHSPFile
void openPHSPFile()
Definition: eb_iaeaphsp_source.cpp:116
-
EB_IAEASource::addState
bool addState(istream &data)
Definition: eb_iaeaphsp_source.cpp:319
-
EB_IAEASource::getFluence
EGS_Float getFluence() const
Definition: eb_iaeaphsp_source.cpp:240
-
EB_IAEASource::Nincident
EGS_Float Nincident
Number of incident particles that created the file.
Definition: eb_iaeaphsp_source.h:140
-
EB_IAEASource::Nlast
IAEA_I64 Nlast
Last record this source can use.
Definition: eb_iaeaphsp_source.h:147
-
EB_IAEASource::count
IAEA_I64 count
Particles delivered so far.
Definition: eb_iaeaphsp_source.h:149
-
EB_IAEASource::EB_IAEASource
EB_IAEASource(EGS_Input *, EGS_ObjectFactory *f=0)
Constructor.
Definition: eb_iaeaphsp_source.cpp:53
-
EB_IAEASource::Nparticle
IAEA_I64 Nparticle
Number of particles in the file.
Definition: eb_iaeaphsp_source.h:142
-
EB_IAEASource::Npos
IAEA_I64 Npos
Next record to be read.
Definition: eb_iaeaphsp_source.h:145
-
EB_IAEASource::storeState
bool storeState(ostream &data) const
Definition: eb_iaeaphsp_source.cpp:245
-
EB_IAEASource::~EB_IAEASource
~EB_IAEASource()
Definition: eb_iaeaphsp_source.cpp:107
-
EB_IAEASource::getEmax
EGS_Float getEmax() const
Definition: eb_iaeaphsp_source.cpp:232
-
EB_IAEASource::getNextParticle
EGS_I64 getNextParticle(EGS_RandomGenerator *rndm, int &q, int &latch, EGS_Float &E, EGS_Float &wt, EGS_Vector &x, EGS_Vector &u)
Definition: eb_iaeaphsp_source.cpp:157
-
EB_IAEASource::Nread
IAEA_I64 Nread
Number of particles read from file so far.
Definition: eb_iaeaphsp_source.h:148
-
EB_IAEASource::Nused
IAEA_I64 Nused
Number of particles used so far.
Definition: eb_iaeaphsp_source.h:144
-
EB_IAEASource::setSimulationChunk
void setSimulationChunk(EGS_I64 nstart, EGS_I64 nrun)
Definition: eb_iaeaphsp_source.cpp:208
-
EB_IAEASource::Emin
EGS_Float Emin
Minimum energy (obtained from the phsp file)
Definition: eb_iaeaphsp_source.h:139
-
EB_IAEASource::isValid
bool isValid() const
Definition: eb_iaeaphsp_source.cpp:236
-
EB_IAEASource::n_parallel
IAEA_I32 n_parallel
Definition: eb_iaeaphsp_source.h:151
-
EB_IAEASource::initSourceParams
void initSourceParams()
Definition: eb_iaeaphsp_source.cpp:131
-
EB_IAEASource::setState
bool setState(istream &data)
Definition: eb_iaeaphsp_source.cpp:282
-
EB_IAEASource::is_valid
bool is_valid
Definition: eb_iaeaphsp_source.h:131
-
createSource
EB_IAEA_SOURCE_EXPORT EGS_BaseSource * createSource(EGS_Input *input, EGS_ObjectFactory *f)
Definition: eb_iaeaphsp_source.cpp:337
+
EB_IAEASource::next_source_id
static IAEA_I32 next_source_id
Definition eb_iaeaphsp_source.h:157
+
EB_IAEASource::source_id
IAEA_I32 source_id
Definition eb_iaeaphsp_source.h:135
+
EB_IAEASource::p_source_id
IAEA_I32 * p_source_id
Definition eb_iaeaphsp_source.h:136
+
EB_IAEASource::iaea_header_ext
static const string iaea_header_ext
Definition eb_iaeaphsp_source.h:159
+
EB_IAEASource::Emax
EGS_Float Emax
Maximum energy (obtained from the phsp file)
Definition eb_iaeaphsp_source.h:138
+
EB_IAEASource::phsp_file_name
string phsp_file_name
The phase space file name.
Definition eb_iaeaphsp_source.h:132
+
EB_IAEASource::i_parallel
IAEA_I32 i_parallel
Definition eb_iaeaphsp_source.h:152
+
EB_IAEASource::Nfirst
IAEA_I64 Nfirst
first record this source can use
Definition eb_iaeaphsp_source.h:146
+
EB_IAEASource::resetCounter
void resetCounter()
Definition eb_iaeaphsp_source.cpp:330
+
EB_IAEASource::openPHSPFile
void openPHSPFile()
Definition eb_iaeaphsp_source.cpp:116
+
EB_IAEASource::addState
bool addState(istream &data)
Definition eb_iaeaphsp_source.cpp:319
+
EB_IAEASource::getFluence
EGS_Float getFluence() const
Definition eb_iaeaphsp_source.cpp:240
+
EB_IAEASource::Nincident
EGS_Float Nincident
Number of incident particles that created the file.
Definition eb_iaeaphsp_source.h:140
+
EB_IAEASource::Nlast
IAEA_I64 Nlast
Last record this source can use.
Definition eb_iaeaphsp_source.h:147
+
EB_IAEASource::count
IAEA_I64 count
Particles delivered so far.
Definition eb_iaeaphsp_source.h:149
+
EB_IAEASource::EB_IAEASource
EB_IAEASource(EGS_Input *, EGS_ObjectFactory *f=0)
Constructor.
Definition eb_iaeaphsp_source.cpp:53
+
EB_IAEASource::Nparticle
IAEA_I64 Nparticle
Number of particles in the file.
Definition eb_iaeaphsp_source.h:142
+
EB_IAEASource::Npos
IAEA_I64 Npos
Next record to be read.
Definition eb_iaeaphsp_source.h:145
+
EB_IAEASource::storeState
bool storeState(ostream &data) const
Definition eb_iaeaphsp_source.cpp:245
+
EB_IAEASource::~EB_IAEASource
~EB_IAEASource()
Definition eb_iaeaphsp_source.cpp:107
+
EB_IAEASource::getEmax
EGS_Float getEmax() const
Definition eb_iaeaphsp_source.cpp:232
+
EB_IAEASource::getNextParticle
EGS_I64 getNextParticle(EGS_RandomGenerator *rndm, int &q, int &latch, EGS_Float &E, EGS_Float &wt, EGS_Vector &x, EGS_Vector &u)
Definition eb_iaeaphsp_source.cpp:157
+
EB_IAEASource::Nread
IAEA_I64 Nread
Number of particles read from file so far.
Definition eb_iaeaphsp_source.h:148
+
EB_IAEASource::Nused
IAEA_I64 Nused
Number of particles used so far.
Definition eb_iaeaphsp_source.h:144
+
EB_IAEASource::setSimulationChunk
void setSimulationChunk(EGS_I64 nstart, EGS_I64 nrun)
Definition eb_iaeaphsp_source.cpp:208
+
EB_IAEASource::Emin
EGS_Float Emin
Minimum energy (obtained from the phsp file)
Definition eb_iaeaphsp_source.h:139
+
EB_IAEASource::isValid
bool isValid() const
Definition eb_iaeaphsp_source.cpp:236
+
EB_IAEASource::n_parallel
IAEA_I32 n_parallel
Definition eb_iaeaphsp_source.h:151
+
EB_IAEASource::initSourceParams
void initSourceParams()
Definition eb_iaeaphsp_source.cpp:131
+
EB_IAEASource::setState
bool setState(istream &data)
Definition eb_iaeaphsp_source.cpp:282
+
EB_IAEASource::is_valid
bool is_valid
Definition eb_iaeaphsp_source.h:131
+
createSource
EB_IAEA_SOURCE_EXPORT EGS_BaseSource * createSource(EGS_Input *input, EGS_ObjectFactory *f)
Definition eb_iaeaphsp_source.cpp:337
eb_iaeaphsp_source.h
a minimal IAEA phase space source for egs_brachy
-
EB_IAEA_SOURCE_EXPORT
#define EB_IAEA_SOURCE_EXPORT
Definition: eb_iaeaphsp_source.h:75
-
eb_tests.iaea_types.IAEA_I32
IAEA_I32
Definition: iaea_types.py:9
+
EB_IAEA_SOURCE_EXPORT
#define EB_IAEA_SOURCE_EXPORT
Definition eb_iaeaphsp_source.h:75
+
eb_tests.iaea_types.IAEA_I32
IAEA_I32
Definition iaea_types.py:9
-Generated by doxygen 1.9.5 +Generated by doxygen 1.9.8
diff --git a/docs/eb__iaeaphsp__source_8dox.html b/docs/eb__iaeaphsp__source_8dox.html index aad581ae..30e309e3 100644 --- a/docs/eb__iaeaphsp__source_8dox.html +++ b/docs/eb__iaeaphsp__source_8dox.html @@ -3,9 +3,9 @@ - + -EGS Brachy: /Users/marc/dev/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/eb_iaeaphsp_source/docs/eb_iaeaphsp_source.dox File Reference +EGS Brachy: /Users/marc/Developer/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/eb_iaeaphsp_source/docs/eb_iaeaphsp_source.dox File Reference @@ -30,7 +30,7 @@ - + @@ -30,7 +30,7 @@ - + @@ -30,7 +30,7 @@ - + +
69#else
70
71 #ifdef HAVE_VISIBILITY
-
72 #define EB_IAEA_SOURCE_EXPORT __attribute__ ((visibility ("default")))
-
73 #define EB_IAEA_SOURCE_LOCAL __attribute__ ((visibility ("hidden")))
+
72 #define EB_IAEA_SOURCE_EXPORT __attribute__ ((visibility ("default")))
+
73 #define EB_IAEA_SOURCE_LOCAL __attribute__ ((visibility ("hidden")))
74 #else
75 #define EB_IAEA_SOURCE_EXPORT
76 #define EB_IAEA_SOURCE_LOCAL
@@ -149,6 +154,7 @@
78
79#endif
80
+
101class EB_IAEA_SOURCE_EXPORT EB_IAEASource : public EGS_BaseSource {
102
103public:
@@ -207,34 +213,35 @@
160
161
162};
+
163
164#endif
-
EB_IAEASource
A phase space file source for egs_brachy.
Definition: eb_iaeaphsp_source.h:101
-
EB_IAEASource::next_source_id
static IAEA_I32 next_source_id
Definition: eb_iaeaphsp_source.h:157
-
EB_IAEASource::source_id
IAEA_I32 source_id
Definition: eb_iaeaphsp_source.h:135
-
EB_IAEASource::p_source_id
IAEA_I32 * p_source_id
Definition: eb_iaeaphsp_source.h:136
-
EB_IAEASource::iaea_header_ext
static const string iaea_header_ext
Definition: eb_iaeaphsp_source.h:159
-
EB_IAEASource::Emax
EGS_Float Emax
Maximum energy (obtained from the phsp file)
Definition: eb_iaeaphsp_source.h:138
-
EB_IAEASource::phsp_file_name
string phsp_file_name
The phase space file name.
Definition: eb_iaeaphsp_source.h:132
-
EB_IAEASource::i_parallel
IAEA_I32 i_parallel
Definition: eb_iaeaphsp_source.h:152
-
EB_IAEASource::Nfirst
IAEA_I64 Nfirst
first record this source can use
Definition: eb_iaeaphsp_source.h:146
-
EB_IAEASource::Nphoton
IAEA_I64 Nphoton
Number of photons in the file.
Definition: eb_iaeaphsp_source.h:143
-
EB_IAEASource::Nincident
EGS_Float Nincident
Number of incident particles that created the file.
Definition: eb_iaeaphsp_source.h:140
-
EB_IAEASource::Nlast
IAEA_I64 Nlast
Last record this source can use.
Definition: eb_iaeaphsp_source.h:147
-
EB_IAEASource::count
IAEA_I64 count
Particles delivered so far.
Definition: eb_iaeaphsp_source.h:149
-
EB_IAEASource::Nparticle
IAEA_I64 Nparticle
Number of particles in the file.
Definition: eb_iaeaphsp_source.h:142
-
EB_IAEASource::Npos
IAEA_I64 Npos
Next record to be read.
Definition: eb_iaeaphsp_source.h:145
-
EB_IAEASource::Nread
IAEA_I64 Nread
Number of particles read from file so far.
Definition: eb_iaeaphsp_source.h:148
-
EB_IAEASource::Nused
IAEA_I64 Nused
Number of particles used so far.
Definition: eb_iaeaphsp_source.h:144
-
EB_IAEASource::Emin
EGS_Float Emin
Minimum energy (obtained from the phsp file)
Definition: eb_iaeaphsp_source.h:139
-
EB_IAEASource::n_parallel
IAEA_I32 n_parallel
Definition: eb_iaeaphsp_source.h:151
-
EB_IAEASource::phsp_file
ifstream phsp_file
Phase space data stream.
Definition: eb_iaeaphsp_source.h:133
-
EB_IAEASource::is_valid
bool is_valid
Definition: eb_iaeaphsp_source.h:131
-
EB_IAEA_SOURCE_EXPORT
#define EB_IAEA_SOURCE_EXPORT
Definition: eb_iaeaphsp_source.h:75
+
EB_IAEASource
A phase space file source for egs_brachy.
Definition eb_iaeaphsp_source.h:101
+
EB_IAEASource::next_source_id
static IAEA_I32 next_source_id
Definition eb_iaeaphsp_source.h:157
+
EB_IAEASource::source_id
IAEA_I32 source_id
Definition eb_iaeaphsp_source.h:135
+
EB_IAEASource::p_source_id
IAEA_I32 * p_source_id
Definition eb_iaeaphsp_source.h:136
+
EB_IAEASource::iaea_header_ext
static const string iaea_header_ext
Definition eb_iaeaphsp_source.h:159
+
EB_IAEASource::Emax
EGS_Float Emax
Maximum energy (obtained from the phsp file)
Definition eb_iaeaphsp_source.h:138
+
EB_IAEASource::phsp_file_name
string phsp_file_name
The phase space file name.
Definition eb_iaeaphsp_source.h:132
+
EB_IAEASource::i_parallel
IAEA_I32 i_parallel
Definition eb_iaeaphsp_source.h:152
+
EB_IAEASource::Nfirst
IAEA_I64 Nfirst
first record this source can use
Definition eb_iaeaphsp_source.h:146
+
EB_IAEASource::Nphoton
IAEA_I64 Nphoton
Number of photons in the file.
Definition eb_iaeaphsp_source.h:143
+
EB_IAEASource::Nincident
EGS_Float Nincident
Number of incident particles that created the file.
Definition eb_iaeaphsp_source.h:140
+
EB_IAEASource::Nlast
IAEA_I64 Nlast
Last record this source can use.
Definition eb_iaeaphsp_source.h:147
+
EB_IAEASource::count
IAEA_I64 count
Particles delivered so far.
Definition eb_iaeaphsp_source.h:149
+
EB_IAEASource::Nparticle
IAEA_I64 Nparticle
Number of particles in the file.
Definition eb_iaeaphsp_source.h:142
+
EB_IAEASource::Npos
IAEA_I64 Npos
Next record to be read.
Definition eb_iaeaphsp_source.h:145
+
EB_IAEASource::Nread
IAEA_I64 Nread
Number of particles read from file so far.
Definition eb_iaeaphsp_source.h:148
+
EB_IAEASource::Nused
IAEA_I64 Nused
Number of particles used so far.
Definition eb_iaeaphsp_source.h:144
+
EB_IAEASource::Emin
EGS_Float Emin
Minimum energy (obtained from the phsp file)
Definition eb_iaeaphsp_source.h:139
+
EB_IAEASource::n_parallel
IAEA_I32 n_parallel
Definition eb_iaeaphsp_source.h:151
+
EB_IAEASource::phsp_file
ifstream phsp_file
Phase space data stream.
Definition eb_iaeaphsp_source.h:133
+
EB_IAEASource::is_valid
bool is_valid
Definition eb_iaeaphsp_source.h:131
+
EB_IAEA_SOURCE_EXPORT
#define EB_IAEA_SOURCE_EXPORT
Definition eb_iaeaphsp_source.h:75
-Generated by doxygen 1.9.5 +Generated by doxygen 1.9.8
diff --git a/docs/eb__volcor_8cpp.html b/docs/eb__volcor_8cpp.html index 0e4b1585..c8fd246d 100644 --- a/docs/eb__volcor_8cpp.html +++ b/docs/eb__volcor_8cpp.html @@ -3,9 +3,9 @@ - + -EGS Brachy: /Users/marc/dev/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/eb_volcor.cpp File Reference +EGS Brachy: /Users/marc/Developer/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/eb_volcor.cpp File Reference @@ -30,7 +30,7 @@ - + @@ -30,7 +30,7 @@ - + +
-
/Users/marc/dev/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/eb_volcor.cpp
+
/Users/marc/Developer/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/eb_volcor.cpp
Go to the documentation of this file.
1/*
@@ -116,12 +121,16 @@
47#include <fstream>
48#include "gzstream.h"
49
+
50namespace ebvolcor {
51
+
54bool isGZip(istream &vfile) {
55 return (vfile.get() == 0x1f && vfile.get() == 0x8b);
56}
+
57
+
77EGS_Float getShapeVolume(EGS_Input *shape_inp) {
78
79 if (!shape_inp) {
@@ -192,7 +201,9 @@
144 return -1;
145
146}
+
147
+
149void Options::setMode() {
150 vector<string> choices;
151 choices.push_back("none");
@@ -204,7 +215,9 @@
157 mode = (VolCorMode)input->getInput("correction type", choices, (int)NO_CORRECTION);
158 }
159}
+
160
+
162int Options::setBoundsShape() {
163
164 EGS_Input *shape_inp = input->takeInputItem("shape");
@@ -233,7 +246,9 @@
187 return 0;
188
189}
+
190
+
192void Options::setDensity() {
193
194 int err = input->getInput("density of random points (cm^-3)", density);
@@ -244,7 +259,9 @@
199
200 npoints = floor(max(1., density*bounds_volume));
201}
+
202
+
204void Options::setRNG() {
205
206 EGS_Input *rng_input = input->getInputItem("rng definition");
@@ -275,7 +292,9 @@
231 }
232
233}
+
234
+
236void Options::setCoveredThreshold() {
237
238 int err = input->getInput("total coverage threshold %", covered_threshold);
@@ -289,11 +308,15 @@
246 }
247
248}
+
249
+
250EGS_Vector Options::getRandomPoint() {
251 return bounds->getRandomPoint(rng);
252}
+
253
+
254void VolumeCorrector::setupOptions() {
255
256 EGS_Input *source_cor_inp = input->takeInputItem("source volume correction");
@@ -334,7 +357,9 @@
291 }
292
293}
+
294
+
295double VolumeCorrector::correctGeneralVolumes() {
296
297 HitCounterT hit_counter;
@@ -363,6 +388,7 @@
320 return 0;
321
322}
+
323// source specific MC volume calculation
324//
325// Works by generating random points within the sources boundary shape and
@@ -375,6 +401,7 @@
332// = V(reg) - V_b * n_points_in_source(reg)/n_total
333//
334// where V_b is volume of bounding shape
+
335double VolumeCorrector::correctPhantomVolumesForSources() {
336
337 EGS_Vector point;
@@ -417,7 +444,9 @@
374 return source_opts->bounds_volume*(double)n_in_source/(int)source_opts->npoints;
375
376}
+
377
+
378void VolumeCorrector::applyVolumeCorrections(Options *opts, HitCounterT hit_counter) {
379
380 bool zero_dose = opts->mode == ZERO_DOSE;
@@ -448,7 +477,9 @@
405 }
406
407}
+
408
+
409void readVolumes(istream &vfile, vector<RegVolume> &reg_volumes) {
410 size_t nrecords;
411 vfile >> nrecords;
@@ -460,7 +491,9 @@
417 reg_volumes.push_back(rvol);
418 }
419}
+
420
+
421int loadVolumes(string fname, vector<RegVolume> &reg_volumes) {
422 ifstream vfile(fname.c_str());
423 if (!vfile.is_open()) {
@@ -479,7 +512,9 @@
436 return 0;
437
438}
+
439
+
440map<string, int> VolumeCorrector::loadFileVolumeCorrections() {
441
442 map<string, int> nreg_read_for_phant;
@@ -512,64 +547,66 @@
469 }
470 return nreg_read_for_phant;
471}
+
472}
+
473
-
EGS_Sobol
EGS_RandomGenerator wrapper for Sobol library.
Definition: egs_sobol.h:71
-
GeomInfo::isSource
bool isSource(int ir)
Definition: ginfo.cpp:503
-
ebvolcor::Options
Volume correction initialization helper class.
Definition: eb_volcor.h:145
-
ebvolcor::Options::density
EGS_Float density
Definition: eb_volcor.h:202
- -
ebvolcor::Options::DEFAULT_RAND_POINT_DENSITY
static const unsigned long DEFAULT_RAND_POINT_DENSITY
Definition: eb_volcor.h:147
-
ebvolcor::Options::covered_threshold
EGS_Float covered_threshold
Definition: eb_volcor.h:205
-
ebvolcor::Options::bounds
EGS_BaseShape * bounds
Definition: eb_volcor.h:152
-
ebvolcor::Options::input
EGS_Input * input
Definition: eb_volcor.h:149
- -
ebvolcor::Options::setBoundsShape
int setBoundsShape()
create bounding shape from the shape input and calculate its volume
Definition: eb_volcor.cpp:162
- -
ebvolcor::Options::bounds_volume
EGS_Float bounds_volume
Definition: eb_volcor.h:201
-
ebvolcor::Options::setCoveredThreshold
void setCoveredThreshold()
Definition: eb_volcor.cpp:236
-
ebvolcor::Options::getRandomPoint
EGS_Vector getRandomPoint()
Definition: eb_volcor.cpp:250
-
ebvolcor::Options::mode
VolCorMode mode
Definition: eb_volcor.h:204
-
ebvolcor::Options::setMode
void setMode()
read mode from input
Definition: eb_volcor.cpp:149
-
ebvolcor::Options::npoints
EGS_Float npoints
Definition: eb_volcor.h:203
-
ebvolcor::Options::rng
EGS_RandomGenerator * rng
Definition: eb_volcor.h:156
- -
ebvolcor::VolumeCorrector::loadFileVolumeCorrections
map< string, int > loadFileVolumeCorrections()
Definition: eb_volcor.cpp:440
-
ebvolcor::VolumeCorrector::base_geom
EGS_BaseGeometry * base_geom
Definition: eb_volcor.h:318
-
ebvolcor::VolumeCorrector::transforms
vector< EGS_AffineTransform * > transforms
Definition: eb_volcor.h:321
-
ebvolcor::VolumeCorrector::applyVolumeCorrections
void applyVolumeCorrections(Options *options, HitCounterT hit_counter)
Definition: eb_volcor.cpp:378
- -
ebvolcor::VolumeCorrector::base_transform_inv
EGS_AffineTransform * base_transform_inv
Definition: eb_volcor.h:323
- -
ebvolcor::VolumeCorrector::correctPhantomVolumesForSources
double correctPhantomVolumesForSources()
Definition: eb_volcor.cpp:335
-
ebvolcor::VolumeCorrector::phantoms
vector< EB_Phantom * > phantoms
Definition: eb_volcor.h:317
-
ebvolcor::VolumeCorrector::base_transform
EGS_AffineTransform * base_transform
Definition: eb_volcor.h:322
- - -
ebvolcor::VolumeCorrector::phantom_files
map< string, string > phantom_files
Definition: eb_volcor.h:316
- -
gzstreambase::close
void close()
Definition: gzstream.C:154
- +
EGS_Sobol
EGS_RandomGenerator wrapper for Sobol library.
Definition egs_sobol.h:71
+
GeomInfo::isSource
bool isSource(int ir)
Definition ginfo.cpp:503
+
ebvolcor::Options
Volume correction initialization helper class.
Definition eb_volcor.h:145
+
ebvolcor::Options::density
EGS_Float density
Definition eb_volcor.h:202
+ +
ebvolcor::Options::DEFAULT_RAND_POINT_DENSITY
static const unsigned long DEFAULT_RAND_POINT_DENSITY
Definition eb_volcor.h:147
+
ebvolcor::Options::covered_threshold
EGS_Float covered_threshold
Definition eb_volcor.h:205
+
ebvolcor::Options::bounds
EGS_BaseShape * bounds
Definition eb_volcor.h:152
+
ebvolcor::Options::input
EGS_Input * input
Definition eb_volcor.h:149
+ +
ebvolcor::Options::setBoundsShape
int setBoundsShape()
create bounding shape from the shape input and calculate its volume
Definition eb_volcor.cpp:162
+ +
ebvolcor::Options::bounds_volume
EGS_Float bounds_volume
Definition eb_volcor.h:201
+
ebvolcor::Options::setCoveredThreshold
void setCoveredThreshold()
Definition eb_volcor.cpp:236
+
ebvolcor::Options::getRandomPoint
EGS_Vector getRandomPoint()
Definition eb_volcor.cpp:250
+
ebvolcor::Options::mode
VolCorMode mode
Definition eb_volcor.h:204
+
ebvolcor::Options::setMode
void setMode()
read mode from input
Definition eb_volcor.cpp:149
+
ebvolcor::Options::npoints
EGS_Float npoints
Definition eb_volcor.h:203
+
ebvolcor::Options::rng
EGS_RandomGenerator * rng
Definition eb_volcor.h:156
+ +
ebvolcor::VolumeCorrector::loadFileVolumeCorrections
map< string, int > loadFileVolumeCorrections()
Definition eb_volcor.cpp:440
+
ebvolcor::VolumeCorrector::base_geom
EGS_BaseGeometry * base_geom
Definition eb_volcor.h:318
+
ebvolcor::VolumeCorrector::transforms
vector< EGS_AffineTransform * > transforms
Definition eb_volcor.h:321
+
ebvolcor::VolumeCorrector::applyVolumeCorrections
void applyVolumeCorrections(Options *options, HitCounterT hit_counter)
Definition eb_volcor.cpp:378
+ +
ebvolcor::VolumeCorrector::base_transform_inv
EGS_AffineTransform * base_transform_inv
Definition eb_volcor.h:323
+ +
ebvolcor::VolumeCorrector::correctPhantomVolumesForSources
double correctPhantomVolumesForSources()
Definition eb_volcor.cpp:335
+
ebvolcor::VolumeCorrector::phantoms
vector< EB_Phantom * > phantoms
Definition eb_volcor.h:317
+
ebvolcor::VolumeCorrector::base_transform
EGS_AffineTransform * base_transform
Definition eb_volcor.h:322
+ + +
ebvolcor::VolumeCorrector::phantom_files
map< string, string > phantom_files
Definition eb_volcor.h:316
+ +
gzstreambase::close
void close()
Definition gzstream.C:154
+
eb_volcor.h
Volume correction routines for egs_brachy.
- -
ebvolcor::PhantRegT
pair< int, int > PhantRegT
PhantRegT is a pair of the form (PhantomNumber, PhantomRegion) e.g. a pair of (2, 12) would represent...
Definition: eb_volcor.h:86
-
ebvolcor::HitCounterT
std::map< PhantRegT, EGS_I64 > HitCounterT
HitCounterT is used for counting how many random points land in a given phantoms region.
Definition: eb_volcor.h:97
- -
ebvolcor::NO_CORRECTION
@ NO_CORRECTION
Definition: eb_volcor.h:78
-
ebvolcor::ZERO_DOSE
@ ZERO_DOSE
Definition: eb_volcor.h:78
-
ebvolcor::loadVolumes
int loadVolumes(string fname, vector< RegVolume > &reg_volumes)
Definition: eb_volcor.cpp:421
-
ebvolcor::readVolumes
void readVolumes(istream &vfile, vector< RegVolume > &reg_volumes)
Definition: eb_volcor.cpp:409
-
ebvolcor::getShapeVolume
EGS_Float getShapeVolume(EGS_Input *shape_inp)
get shape volume from a shape input item
Definition: eb_volcor.cpp:77
-
ebvolcor::isGZip
bool isGZip(istream &vfile)
Definition: eb_volcor.cpp:54
-
ebvolcor::RegVolume
RegVolumeT sruct with members (ir=RegionNumber, vol=Volume, unc=Unc)
Definition: eb_volcor.h:89
- - - + +
ebvolcor::PhantRegT
pair< int, int > PhantRegT
PhantRegT is a pair of the form (PhantomNumber, PhantomRegion) e.g. a pair of (2, 12) would represent...
Definition eb_volcor.h:86
+
ebvolcor::HitCounterT
std::map< PhantRegT, EGS_I64 > HitCounterT
HitCounterT is used for counting how many random points land in a given phantoms region.
Definition eb_volcor.h:97
+ +
ebvolcor::NO_CORRECTION
@ NO_CORRECTION
Definition eb_volcor.h:78
+
ebvolcor::ZERO_DOSE
@ ZERO_DOSE
Definition eb_volcor.h:78
+
ebvolcor::loadVolumes
int loadVolumes(string fname, vector< RegVolume > &reg_volumes)
Definition eb_volcor.cpp:421
+
ebvolcor::readVolumes
void readVolumes(istream &vfile, vector< RegVolume > &reg_volumes)
Definition eb_volcor.cpp:409
+
ebvolcor::getShapeVolume
EGS_Float getShapeVolume(EGS_Input *shape_inp)
get shape volume from a shape input item
Definition eb_volcor.cpp:77
+
ebvolcor::isGZip
bool isGZip(istream &vfile)
Definition eb_volcor.cpp:54
+
ebvolcor::RegVolume
RegVolumeT sruct with members (ir=RegionNumber, vol=Volume, unc=Unc)
Definition eb_volcor.h:89
+ + +
-Generated by doxygen 1.9.5 +Generated by doxygen 1.9.8
diff --git a/docs/eb__volcor_8h.html b/docs/eb__volcor_8h.html index 31d6d9ac..108dfbd4 100644 --- a/docs/eb__volcor_8h.html +++ b/docs/eb__volcor_8h.html @@ -3,9 +3,9 @@ - + -EGS Brachy: /Users/marc/dev/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/eb_volcor.h File Reference +EGS Brachy: /Users/marc/Developer/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/eb_volcor.h File Reference @@ -30,7 +30,7 @@
- + @@ -30,7 +30,7 @@ - + +
-
/Users/marc/dev/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/eb_volcor.h
+
/Users/marc/Developer/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/eb_volcor.h
Go to the documentation of this file.
1/*
@@ -137,15 +142,18 @@
82
86typedef pair<int, int> PhantRegT;
87
+
89struct RegVolume {
90 int ir;
91 EGS_Float vol;
92 EGS_Float unc;
93};
+
94
97typedef std::map<PhantRegT, EGS_I64> HitCounterT;
98
99
+
145class Options {
146
147 const static unsigned long DEFAULT_RAND_POINT_DENSITY = 100000000;
@@ -166,6 +174,7 @@
162 void setCoveredThreshold();
163
164public:
+
165 Options(EGS_Input *inp):
166
167 input(inp), bounds(NULL), sobolAllowed(false), rng(NULL) {
@@ -190,7 +199,9 @@
186 setCoveredThreshold();
187
188 }
+
189
+
190 ~Options() {
191 if (rng) {
192 delete rng;
@@ -199,6 +210,7 @@
195 delete bounds;
196 }
197 }
+
198
199 bool valid;
200
@@ -210,8 +222,10 @@
206
207 EGS_Vector getRandomPoint();
208};
+
209
210
+
212struct Results {
213
214 int success;
@@ -223,6 +237,7 @@
220 EGS_Float other_volume;
222 map<int, vector<int> > regions_corrected;
223
+
224 Results():
225 success(0),
226 status(""),
@@ -231,7 +246,9 @@
229 npoints(0),
230 bounds_volume(0),
231 other_volume(0) {};
+
232
+
233 Results(Options *opts):
234 success(0),
235 status(""),
@@ -241,7 +258,9 @@
239 npoints = opts->npoints;
240 bounds_volume = opts->bounds_volume;
241 }
+
242
+
243 void outputResults(string extra="") {
244
245 if (success == -1){
@@ -261,9 +280,12 @@
259 }
260
261 }
+
262
263};
+
264
+
265struct FileResults {
266
267 int success;
@@ -272,17 +294,22 @@
270 map<string, string> phantom_files;
271 map<string, int> nreg;
272
+
273 FileResults():
274 success(0),
275 status(""),
276 time(0) {};
+
277
+
278 FileResults(map<string, string> phant_files):
279 success(0),
280 status(""),
281 time(0),
282 phantom_files(phant_files) {};
+
283
+
284 void outputResults() {
285 if (success == -1){
286 egsFatal("File volume correction requested but failed: %s.\n", status.c_str());
@@ -301,10 +328,13 @@
299
300 }
301 }
+
302
303};
+
304
305
+
311class VolumeCorrector {
312
313 EGS_Input *input;
@@ -327,6 +357,7 @@
330 map<string, int> loadFileVolumeCorrections();
331
332public:
+
333 VolumeCorrector(EGS_Input *volcor_input,
334 vector<EB_Phantom *> phantoms, EGS_BaseGeometry *base_geom,
335 GeomInfo *geom_info, vector<EGS_AffineTransform *> transforms = vector<EGS_AffineTransform *>()):
@@ -346,7 +377,9 @@
349
350
351 };
+
352
+
353 ~VolumeCorrector() {
354 if (source_opts) {
355 delete source_opts;
@@ -359,7 +392,9 @@
362 delete base_transform_inv;
363 }
364 }
+
365
+
366 Results runSourceCorrection(EB_TimingTree &timer) {
367 timer.addTimer("VolumeCorrector::runSourceCorrection");
368 Results results(source_opts);
@@ -387,7 +422,9 @@
390
391 return results;
392 }
+
393
+
394 Results runGeneralCorrection(EB_TimingTree &timer) {
395 timer.addTimer("VolumeCorrector::runGeneralCorrection");
396 Results results(gen_opts);
@@ -415,7 +452,9 @@
418 timer.stopTimer();
419 return results;
420 }
+
421
+
422 FileResults runFileCorrection(EB_TimingTree &timer) {
423 timer.addTimer("VolumeCorrector::runFileCorrection");
424 vector<int> nreg_corrected;
@@ -439,97 +478,99 @@
442
443 return results;
444 };
+
445
446};
+
447
448}
449
450#endif
-
EB_TimingTree
Definition: timing.h:110
-
EB_TimingTree::stopTimer
void stopTimer()
Definition: timing.h:139
-
EB_TimingTree::addTimer
void addTimer(string name)
Definition: timing.h:132
-
GeomInfo
a container for organizing meta data about the geometries
Definition: ginfo.h:99
-
ebvolcor::Options
Volume correction initialization helper class.
Definition: eb_volcor.h:145
-
ebvolcor::Options::density
EGS_Float density
Definition: eb_volcor.h:202
- -
ebvolcor::Options::DEFAULT_RAND_POINT_DENSITY
static const unsigned long DEFAULT_RAND_POINT_DENSITY
Definition: eb_volcor.h:147
-
ebvolcor::Options::covered_threshold
EGS_Float covered_threshold
Definition: eb_volcor.h:205
-
ebvolcor::Options::bounds
EGS_BaseShape * bounds
Definition: eb_volcor.h:152
- -
ebvolcor::Options::input
EGS_Input * input
Definition: eb_volcor.h:149
- -
ebvolcor::Options::setBoundsShape
int setBoundsShape()
create bounding shape from the shape input and calculate its volume
Definition: eb_volcor.cpp:162
-
ebvolcor::Options::Options
Options(EGS_Input *inp)
Definition: eb_volcor.h:165
- -
ebvolcor::Options::bounds_volume
EGS_Float bounds_volume
Definition: eb_volcor.h:201
-
ebvolcor::Options::setCoveredThreshold
void setCoveredThreshold()
Definition: eb_volcor.cpp:236
-
ebvolcor::Options::getRandomPoint
EGS_Vector getRandomPoint()
Definition: eb_volcor.cpp:250
- -
ebvolcor::Options::mode
VolCorMode mode
Definition: eb_volcor.h:204
-
ebvolcor::Options::setMode
void setMode()
read mode from input
Definition: eb_volcor.cpp:149
-
ebvolcor::Options::npoints
EGS_Float npoints
Definition: eb_volcor.h:203
-
ebvolcor::Options::rng
EGS_RandomGenerator * rng
Definition: eb_volcor.h:156
-
ebvolcor::VolumeCorrector
An object for controlling the volume correction routine.
Definition: eb_volcor.h:311
- - -
ebvolcor::VolumeCorrector::loadFileVolumeCorrections
map< string, int > loadFileVolumeCorrections()
Definition: eb_volcor.cpp:440
-
ebvolcor::VolumeCorrector::runSourceCorrection
Results runSourceCorrection(EB_TimingTree &timer)
Definition: eb_volcor.h:366
-
ebvolcor::VolumeCorrector::base_geom
EGS_BaseGeometry * base_geom
Definition: eb_volcor.h:318
-
ebvolcor::VolumeCorrector::transforms
vector< EGS_AffineTransform * > transforms
Definition: eb_volcor.h:321
-
ebvolcor::VolumeCorrector::applyVolumeCorrections
void applyVolumeCorrections(Options *options, HitCounterT hit_counter)
Definition: eb_volcor.cpp:378
- -
ebvolcor::VolumeCorrector::base_transform_inv
EGS_AffineTransform * base_transform_inv
Definition: eb_volcor.h:323
-
ebvolcor::VolumeCorrector::runGeneralCorrection
Results runGeneralCorrection(EB_TimingTree &timer)
Definition: eb_volcor.h:394
- -
ebvolcor::VolumeCorrector::correctPhantomVolumesForSources
double correctPhantomVolumesForSources()
Definition: eb_volcor.cpp:335
-
ebvolcor::VolumeCorrector::VolumeCorrector
VolumeCorrector(EGS_Input *volcor_input, vector< EB_Phantom * > phantoms, EGS_BaseGeometry *base_geom, GeomInfo *geom_info, vector< EGS_AffineTransform * > transforms=vector< EGS_AffineTransform * >())
Definition: eb_volcor.h:333
-
ebvolcor::VolumeCorrector::phantoms
vector< EB_Phantom * > phantoms
Definition: eb_volcor.h:317
-
ebvolcor::VolumeCorrector::runFileCorrection
FileResults runFileCorrection(EB_TimingTree &timer)
Definition: eb_volcor.h:422
-
ebvolcor::VolumeCorrector::base_transform
EGS_AffineTransform * base_transform
Definition: eb_volcor.h:322
- - -
ebvolcor::VolumeCorrector::phantom_files
map< string, string > phantom_files
Definition: eb_volcor.h:316
- +
EB_TimingTree
Definition timing.h:110
+
EB_TimingTree::stopTimer
void stopTimer()
Definition timing.h:139
+
EB_TimingTree::addTimer
void addTimer(string name)
Definition timing.h:132
+
GeomInfo
a container for organizing meta data about the geometries
Definition ginfo.h:99
+
ebvolcor::Options
Volume correction initialization helper class.
Definition eb_volcor.h:145
+
ebvolcor::Options::density
EGS_Float density
Definition eb_volcor.h:202
+ +
ebvolcor::Options::DEFAULT_RAND_POINT_DENSITY
static const unsigned long DEFAULT_RAND_POINT_DENSITY
Definition eb_volcor.h:147
+
ebvolcor::Options::covered_threshold
EGS_Float covered_threshold
Definition eb_volcor.h:205
+
ebvolcor::Options::bounds
EGS_BaseShape * bounds
Definition eb_volcor.h:152
+ +
ebvolcor::Options::input
EGS_Input * input
Definition eb_volcor.h:149
+ +
ebvolcor::Options::setBoundsShape
int setBoundsShape()
create bounding shape from the shape input and calculate its volume
Definition eb_volcor.cpp:162
+
ebvolcor::Options::Options
Options(EGS_Input *inp)
Definition eb_volcor.h:165
+ +
ebvolcor::Options::bounds_volume
EGS_Float bounds_volume
Definition eb_volcor.h:201
+
ebvolcor::Options::setCoveredThreshold
void setCoveredThreshold()
Definition eb_volcor.cpp:236
+
ebvolcor::Options::getRandomPoint
EGS_Vector getRandomPoint()
Definition eb_volcor.cpp:250
+ +
ebvolcor::Options::mode
VolCorMode mode
Definition eb_volcor.h:204
+
ebvolcor::Options::setMode
void setMode()
read mode from input
Definition eb_volcor.cpp:149
+
ebvolcor::Options::npoints
EGS_Float npoints
Definition eb_volcor.h:203
+
ebvolcor::Options::rng
EGS_RandomGenerator * rng
Definition eb_volcor.h:156
+
ebvolcor::VolumeCorrector
An object for controlling the volume correction routine.
Definition eb_volcor.h:311
+ + +
ebvolcor::VolumeCorrector::loadFileVolumeCorrections
map< string, int > loadFileVolumeCorrections()
Definition eb_volcor.cpp:440
+
ebvolcor::VolumeCorrector::runSourceCorrection
Results runSourceCorrection(EB_TimingTree &timer)
Definition eb_volcor.h:366
+
ebvolcor::VolumeCorrector::base_geom
EGS_BaseGeometry * base_geom
Definition eb_volcor.h:318
+
ebvolcor::VolumeCorrector::transforms
vector< EGS_AffineTransform * > transforms
Definition eb_volcor.h:321
+
ebvolcor::VolumeCorrector::applyVolumeCorrections
void applyVolumeCorrections(Options *options, HitCounterT hit_counter)
Definition eb_volcor.cpp:378
+ +
ebvolcor::VolumeCorrector::base_transform_inv
EGS_AffineTransform * base_transform_inv
Definition eb_volcor.h:323
+
ebvolcor::VolumeCorrector::runGeneralCorrection
Results runGeneralCorrection(EB_TimingTree &timer)
Definition eb_volcor.h:394
+ +
ebvolcor::VolumeCorrector::correctPhantomVolumesForSources
double correctPhantomVolumesForSources()
Definition eb_volcor.cpp:335
+
ebvolcor::VolumeCorrector::VolumeCorrector
VolumeCorrector(EGS_Input *volcor_input, vector< EB_Phantom * > phantoms, EGS_BaseGeometry *base_geom, GeomInfo *geom_info, vector< EGS_AffineTransform * > transforms=vector< EGS_AffineTransform * >())
Definition eb_volcor.h:333
+
ebvolcor::VolumeCorrector::phantoms
vector< EB_Phantom * > phantoms
Definition eb_volcor.h:317
+
ebvolcor::VolumeCorrector::runFileCorrection
FileResults runFileCorrection(EB_TimingTree &timer)
Definition eb_volcor.h:422
+
ebvolcor::VolumeCorrector::base_transform
EGS_AffineTransform * base_transform
Definition eb_volcor.h:322
+ + +
ebvolcor::VolumeCorrector::phantom_files
map< string, string > phantom_files
Definition eb_volcor.h:316
+
ginfo.h
ginfo contains classes for organizing information about the geometries present in an egs_brachy simul...
- -
ebvolcor::PhantRegT
pair< int, int > PhantRegT
PhantRegT is a pair of the form (PhantomNumber, PhantomRegion) e.g. a pair of (2, 12) would represent...
Definition: eb_volcor.h:86
-
ebvolcor::HitCounterT
std::map< PhantRegT, EGS_I64 > HitCounterT
HitCounterT is used for counting how many random points land in a given phantoms region.
Definition: eb_volcor.h:97
- -
ebvolcor::NO_CORRECTION
@ NO_CORRECTION
Definition: eb_volcor.h:78
-
ebvolcor::CORRECT_VOLUME
@ CORRECT_VOLUME
Definition: eb_volcor.h:78
-
ebvolcor::ZERO_DOSE
@ ZERO_DOSE
Definition: eb_volcor.h:78
-
ebvolcor::getShapeVolume
EGS_Float getShapeVolume(EGS_Input *shape_inp)
get shape volume from a shape input item
Definition: eb_volcor.cpp:77
+ +
ebvolcor::PhantRegT
pair< int, int > PhantRegT
PhantRegT is a pair of the form (PhantomNumber, PhantomRegion) e.g. a pair of (2, 12) would represent...
Definition eb_volcor.h:86
+
ebvolcor::HitCounterT
std::map< PhantRegT, EGS_I64 > HitCounterT
HitCounterT is used for counting how many random points land in a given phantoms region.
Definition eb_volcor.h:97
+ +
ebvolcor::NO_CORRECTION
@ NO_CORRECTION
Definition eb_volcor.h:78
+
ebvolcor::CORRECT_VOLUME
@ CORRECT_VOLUME
Definition eb_volcor.h:78
+
ebvolcor::ZERO_DOSE
@ ZERO_DOSE
Definition eb_volcor.h:78
+
ebvolcor::getShapeVolume
EGS_Float getShapeVolume(EGS_Input *shape_inp)
get shape volume from a shape input item
Definition eb_volcor.cpp:77
phantom.h
Header file for phantom objects.
- - - -
ebvolcor::FileResults::phantom_files
map< string, string > phantom_files
Definition: eb_volcor.h:270
-
ebvolcor::FileResults::FileResults
FileResults(map< string, string > phant_files)
Definition: eb_volcor.h:278
-
ebvolcor::FileResults::nreg
map< string, int > nreg
Definition: eb_volcor.h:271
- - - -
ebvolcor::RegVolume
RegVolumeT sruct with members (ir=RegionNumber, vol=Volume, unc=Unc)
Definition: eb_volcor.h:89
- - - -
ebvolcor::Results
Struct used to collect and output results about a volume correction run.
Definition: eb_volcor.h:212
-
ebvolcor::Results::time
EGS_Float time
Definition: eb_volcor.h:216
- - -
ebvolcor::Results::Results
Results(Options *opts)
Definition: eb_volcor.h:233
-
ebvolcor::Results::other_volume
EGS_Float other_volume
Definition: eb_volcor.h:220
-
ebvolcor::Results::bounds_volume
EGS_Float bounds_volume
Definition: eb_volcor.h:219
-
ebvolcor::Results::outputResults
void outputResults(string extra="")
Definition: eb_volcor.h:243
- -
ebvolcor::Results::regions_corrected
map< int, vector< int > > regions_corrected
Definition: eb_volcor.h:222
- - + + + +
ebvolcor::FileResults::phantom_files
map< string, string > phantom_files
Definition eb_volcor.h:270
+
ebvolcor::FileResults::FileResults
FileResults(map< string, string > phant_files)
Definition eb_volcor.h:278
+
ebvolcor::FileResults::nreg
map< string, int > nreg
Definition eb_volcor.h:271
+ + + +
ebvolcor::RegVolume
RegVolumeT sruct with members (ir=RegionNumber, vol=Volume, unc=Unc)
Definition eb_volcor.h:89
+ + + +
ebvolcor::Results
Struct used to collect and output results about a volume correction run.
Definition eb_volcor.h:212
+ + + +
ebvolcor::Results::Results
Results(Options *opts)
Definition eb_volcor.h:233
+
ebvolcor::Results::other_volume
EGS_Float other_volume
Definition eb_volcor.h:220
+
ebvolcor::Results::bounds_volume
EGS_Float bounds_volume
Definition eb_volcor.h:219
+
ebvolcor::Results::outputResults
void outputResults(string extra="")
Definition eb_volcor.h:243
+ +
ebvolcor::Results::regions_corrected
map< int, vector< int > > regions_corrected
Definition eb_volcor.h:222
+ +
-Generated by doxygen 1.9.5 +Generated by doxygen 1.9.8
diff --git a/docs/egs__brachy_8cpp.html b/docs/egs__brachy_8cpp.html index f10fb877..e7569f69 100644 --- a/docs/egs__brachy_8cpp.html +++ b/docs/egs__brachy_8cpp.html @@ -3,9 +3,9 @@ - + -EGS Brachy: /Users/marc/dev/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/egs_brachy.cpp File Reference +EGS Brachy: /Users/marc/Developer/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/egs_brachy.cpp File Reference @@ -30,7 +30,7 @@
- + @@ -30,7 +30,7 @@ - + +
-
/Users/marc/dev/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/egs_brachy.cpp
+
/Users/marc/Developer/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/egs_brachy.cpp
Go to the documentation of this file.
1/*
@@ -116,2760 +121,3139 @@
46#include <string>
47#include <iomanip>
48#include <assert.h>
-
49#include "gzstream.h"
-
50#include "zlib.h"
-
51
-
52#include "egs_brachy.h"
-
53#include "egs_ausgab_object.h"
-
54#include "egs_rndm.h"
-
55#include "egs_run_control.h"
-
56
+
49#include <sys/stat.h>
+
50#include "gzstream.h"
+
51#include "zlib.h"
+
52
+
53#include "egs_brachy.h"
+
54#include "egs_ausgab_object.h"
+
55#include "egs_rndm.h"
+
56#include "egs_run_control.h"
57
-
58using namespace std;
-
59
-
60/* taken from egs_advance_application.cpp for outputData functions */
-
61#define egsGetRNGPointers F77_OBJ_(egs_get_rng_pointers,EGS_GET_RNG_POINTERS)
-
62extern __extc__ void egsGetRNGPointers(EGS_I32 *, EGS_I32 *);
-
63#define egsGetRNGArray F77_OBJ_(egs_get_rng_array,EGS_GET_RNG_ARRAY)
-
64extern __extc__ void egsGetRNGArray(EGS_Float *);
-
65#define egsSetRNGState F77_OBJ_(egs_set_rng_state,EGS_SET_RNG_STATE)
-
66extern __extc__ void egsSetRNGState(const EGS_I32 *, const EGS_Float *);
-
67#define egsGetSteps F77_OBJ_(egs_get_steps,EGS_GET_STEPS)
-
68extern __extc__ void egsGetSteps(double *, double *);
-
69#define egsSetSteps F77_OBJ_(egs_set_steps,EGS_SET_STEPS)
-
70extern __extc__ void egsSetSteps(const double *, const double *);
-
71#define egsOpenUnits F77_OBJ_(egs_open_units,EGS_OPEN_UNITS)
-
72extern __extc__ void egsOpenUnits(const EGS_I32 *);
-
73#define egsGetElectronData F77_OBJ_(egs_get_electron_data,EGS_GET_ELECTRON_DATA)
-
74extern __extc__ void egsGetElectronData(void (*func)(EGS_I32 *,EGS_Float *,
-
75 EGS_Float *,EGS_Float *,EGS_Float *),const EGS_I32 *,const EGS_I32 *);
-
76#define egsGetPhotonData F77_OBJ_(egs_get_photon_data,EGS_GET_PHOTON_DATA)
-
77extern __extc__ void egsGetPhotonData(void (*func)(EGS_I32 *,EGS_Float *,
-
78 EGS_Float *,EGS_Float *,EGS_Float *),const EGS_I32 *,const EGS_I32 *);
-
79/* end taken from egs_advance_application.cpp for outputData functions */
-
80
-
81extern "C" void F77_OBJ_(egs_scale_xcc,EGS_SCALE_XCC)(const int *,const EGS_Float *);
-
82extern "C" void F77_OBJ_(egs_scale_bc,EGS_SCALE_BC)(const int *,const EGS_Float *);
-
83extern "C" void F77_OBJ_(egs_bcse,EGS_BCSE)(const int *,const EGS_Float *);
-
84extern "C" void F77_OBJ_(egs_uniform_photons,EGS_UNIFORM_PHOTONS)(const int *,const EGS_Float *);
-
85
-
86void printParticleWithSpherical(EGS_Particle p) {
-
87 EGS_Float x,y,z, r, R, theta, phi;
-
88
-
89 x = p.x.x;
-
90 y = p.x.y;
-
91 z = p.x.z;
-
92
-
93 r = sqrt(x*x + y*y);
-
94 R = sqrt(x*x + y*y + z*z);
-
95 theta = acos(z/R)*180/M_PI;
-
96 phi = atan2(y, x)*180/M_PI;
-
97
-
98 PRINT_PARTICLE_WITH_DIR(p);
-
99 cout << " R = " << R << endl;
-
100 cout << " r = " << r << endl;
-
101 cout << " z = " << z << endl;
-
102 cout << " theta (deg) = " << theta << endl;
-
103 cout << " phi (deg) = " << phi << endl;
-
104
-
105}
-
106
+
58
+
59using namespace std;
+
60
+
61/* taken from egs_advance_application.cpp for outputData functions */
+
62#define egsGetRNGPointers F77_OBJ_(egs_get_rng_pointers,EGS_GET_RNG_POINTERS)
+
63extern __extc__ void egsGetRNGPointers(EGS_I32 *, EGS_I32 *);
+
64#define egsGetRNGArray F77_OBJ_(egs_get_rng_array,EGS_GET_RNG_ARRAY)
+
65extern __extc__ void egsGetRNGArray(EGS_Float *);
+
66#define egsSetRNGState F77_OBJ_(egs_set_rng_state,EGS_SET_RNG_STATE)
+
67extern __extc__ void egsSetRNGState(const EGS_I32 *, const EGS_Float *);
+
68#define egsGetSteps F77_OBJ_(egs_get_steps,EGS_GET_STEPS)
+
69extern __extc__ void egsGetSteps(double *, double *);
+
70#define egsSetSteps F77_OBJ_(egs_set_steps,EGS_SET_STEPS)
+
71extern __extc__ void egsSetSteps(const double *, const double *);
+
72#define egsOpenUnits F77_OBJ_(egs_open_units,EGS_OPEN_UNITS)
+
73extern __extc__ void egsOpenUnits(const EGS_I32 *);
+
74#define egsGetElectronData F77_OBJ_(egs_get_electron_data,EGS_GET_ELECTRON_DATA)
+
75extern __extc__ void egsGetElectronData(void (*func)(EGS_I32 *,EGS_Float *,
+
76 EGS_Float *,EGS_Float *,EGS_Float *),const EGS_I32 *,const EGS_I32 *);
+
77#define egsGetPhotonData F77_OBJ_(egs_get_photon_data,EGS_GET_PHOTON_DATA)
+
78extern __extc__ void egsGetPhotonData(void (*func)(EGS_I32 *,EGS_Float *,
+
79 EGS_Float *,EGS_Float *,EGS_Float *),const EGS_I32 *,const EGS_I32 *);
+
80/* end taken from egs_advance_application.cpp for outputData functions */
+
81
+
82extern "C" void F77_OBJ_(egs_scale_xcc,EGS_SCALE_XCC)(const int *,const EGS_Float *);
+
83extern "C" void F77_OBJ_(egs_scale_bc,EGS_SCALE_BC)(const int *,const EGS_Float *);
+
84extern "C" void F77_OBJ_(egs_bcse,EGS_BCSE)(const int *,const EGS_Float *);
+
85extern "C" void F77_OBJ_(egs_uniform_photons,EGS_UNIFORM_PHOTONS)(const int *,const EGS_Float *);
+
86
+
+
87void printParticleWithSpherical(EGS_Particle p) {
+
88 EGS_Float x,y,z, r, R, theta, phi;
+
89
+
90 x = p.x.x;
+
91 y = p.x.y;
+
92 z = p.x.z;
+
93
+
94 r = sqrt(x*x + y*y);
+
95 R = sqrt(x*x + y*y + z*z);
+
96 theta = acos(z/R)*180/M_PI;
+
97 phi = atan2(y, x)*180/M_PI;
+
98
+
99 PRINT_PARTICLE_WITH_DIR(p);
+
100 cout << " R = " << R << "\n";
+
101 cout << " r = " << r << "\n";
+
102 cout << " z = " << z << "\n";
+
103 cout << " theta (deg) = " << theta << "\n";
+
104 cout << " phi (deg) = " << phi << "\n";
+
105
+
106}
+
107
-
108string EB_Application::revision = "$Revision: 0.9.1 $";
-
109
-
110const EGS_Float EB_Application::DEFAULT_BCSE_FACTOR = 100;
-
111
+
108
+
109string EB_Application::revision = "$Revision: 0.9.1 $";
+
110
+
111const EGS_Float EB_Application::DEFAULT_BCSE_FACTOR = 100;
112
-
113void EB_Application::describeUserCode() const {
-
114 egsInformation(
-
115 "\n ***************************************************"
-
116 "\n * *"
-
117 "\n * egs_brachy *"
-
118 "\n * *"
-
119 "\n ***************************************************"
-
120 "\n\n");
-
121 egsInformation("This is EB_Application %s based on\n"
-
122 " EGS_AdvancedApplication %s\n\n",
-
123 egsSimplifyCVSKey(revision).c_str(),
-
124 egsSimplifyCVSKey(base_revision).c_str());
-
125}
-
126
-
127void EB_Application::describeSimulation() {
-
128
-
129 if (!geometry && !source) {
-
130 return;
-
131 }
-
132
-
133 egsInformation("\n\negs_brachy Run Mode Information\n%s\n\n",string(80,'=').c_str());
-
134 egsInformation("Run mode = %s\n", run_mode_name.c_str());
-
135 egsInformation("Single generator (may be overriden later) = %s\n", single_generator ? "yes" :"no");
-
136 if (gcr_phantom) {
-
137 egsInformation(
-
138 "getCurrentResult phantom/reg = %s %d",
-
139 gcr_phantom->geometry->getName().c_str(),
-
140 gcr_phantom_reg
-
141 );
-
142 }
-
143
-
144 egsInformation("\n\negs_brachy Geometry Information\n%s\n\n", string(80,'=').c_str());
-
145
-
146 ginfo.printInfo();
-
147
-
148 egsInformation("\n\negs_brachy Phantom Details\n%s\n\n", string(80,'=').c_str());
-
149 egsInformation(" | | | | Sph (Rmin, Rmax) | | \n");
-
150 egsInformation(" | | | Avg Vox Vol | RZ (Rmin, Rmax) | RZ (Zmin, Zmax) | \n");
-
151 egsInformation("Name | Type | Nreg | / cm^3 | XYZ (Xmin, Xmax) | XYZ (Ymin, Ymax) | XYZ (Zmin, Zmax)\n");
-
152 egsInformation("%s\n", string(145, '-').c_str());
-
153
-
154 for (size_t p=0; p < phantom_geoms.size(); p++) {
-
155
-
156 EB_Phantom *phant = phantom_geoms[p];
-
157 EGS_BaseGeometry *geom = phant->geometry;
-
158
-
159 string type = geom->getType();
-
160
-
161 if (type == "EGS_XYZGeometry") {
-
162 int nx, ny, nz;
-
163 nx = geom->getNRegDir(EB_Phantom::XDIR);
-
164 ny = geom->getNRegDir(EB_Phantom::YDIR);
-
165 nz = geom->getNRegDir(EB_Phantom::ZDIR);
-
166
-
167 EGS_Float xmin, xmax, ymin, ymax, zmin, zmax;
-
168 xmin = geom->getBound(EB_Phantom::XDIR, 0);
-
169 xmax = geom->getBound(EB_Phantom::XDIR, nx);
-
170 ymin = geom->getBound(EB_Phantom::YDIR, 0);
-
171 ymax = geom->getBound(EB_Phantom::YDIR, ny);
-
172 zmin = geom->getBound(EB_Phantom::ZDIR, 0);
-
173 zmax = geom->getBound(EB_Phantom::ZDIR, nz);
-
174
-
175 egsInformation(
-
176 "%-30s| %20s | %9d | %12.5G | (%8.3F, %8.3F) | (%8.3F, %8.3F) | (%8.3F, %8.3F)\n",
-
177 geom->getName().c_str(), type.c_str(), geom->regions(), phant->avgVoxelVol(),
-
178 xmin, xmax, ymin, ymax, zmin, zmax
-
179 );
-
180
-
181 } else if (type == "EGS_RZ") {
-
182 int nr, nz;
-
183 nr = geom->getNRegDir(EGS_RZGeometry::RDIR);
-
184 nz = geom->getNRegDir(EGS_RZGeometry::ZDIR);
-
185
-
186 EGS_Float rmin, rmax, zmin, zmax;
-
187 rmin = geom->getBound(EGS_RZGeometry::RDIR, 0);
-
188 rmax = geom->getBound(EGS_RZGeometry::RDIR, nr-1);
-
189 zmin = geom->getBound(EGS_RZGeometry::ZDIR, 0);
-
190 zmax = geom->getBound(EGS_RZGeometry::ZDIR, nz-1);
-
191
-
192 egsInformation(
-
193 "%-30s| %20s | %9d | %12.5G | (%8.3F, %8.3F) | (%8.3F, %8.3F) |\n",
-
194 geom->getName().c_str(), type.c_str(), geom->regions(), phant->avgVoxelVol(),
-
195 rmin, rmax, zmin, zmax
-
196 );
-
197 } else if (type == "EGS_cSphericalShell" || type == "EGS_cSpheres") {
-
198 type = (type == "EGS_cSphericalShell" ? "SphSh" : "Sph");
-
199
-
200 int nr = geom->getNRegDir(0);
-
201
-
202 EGS_Float rmin, rmax;
-
203 rmin = geom->getBound(EGS_cSpheres::RDIR, 0);
-
204 rmax = geom->getBound(EGS_cSpheres::RDIR, nr);
-
205
-
206 egsInformation(
-
207 "%-30s| %20s | %9d | %12.5G | (%8.3F, %8.3F) | | \n",
-
208 geom->getName().c_str(), type.c_str(), geom->regions(), phant->avgVoxelVol(),
-
209 rmin, rmax
-
210 );
-
211 } else {
-
212 egsInformation(
-
213 "%-30s| %20s | %9d | %12.5G | | | \n",
-
214 geom->getName().c_str(), type.c_str(), geom->regions(), phant->avgVoxelVol(),
-
215 -1, -1
-
216 );
-
217 }
-
218
-
219 if (type == "EGS_XYZGeometryT") {
-
220 egsWarning("\n***WARNING***\nPhantom of type transformed XYZ geometry used. The number of voxels in each direction and their bounds in the egslog, 3ddose, and egsphant files will be incorrect due to current limitations of the egs++ geometry library.\n***WARNING***\n");
-
221 }
-
222
-
223 }
-
224
-
225 egsInformation("\n\negs_brachy Volume correction details\n%s\n", string(80, '-').c_str());
-
226
-
227 egsInformation("\nSource specific volume correction details\n%s\n", string(80, '-').c_str());
-
228 source_vc_results.outputResults("Source");
-
229
-
230 egsInformation("\nExtra volume correction details\n%s\n", string(80, '-').c_str());
-
231 gen_vc_results.outputResults("Extra");
-
232
-
233 egsInformation("\nFile volume correction details\n%s\n", string(80, '-').c_str());
-
234 file_vc_results.outputResults();
-
235
-
236 egsInformation("\n\n");
-
237 if (geometry) {
-
238 geometry->printInfo();
-
239 }
-
240
-
241 if (source) {
-
242 egsInformation("\n\negs_brachy Source Information\n%s\n", string(80,'=').c_str());
-
243 egsInformation("%s\n\n", source->getSourceDescription());
-
244 egsInformation("Number of source locations = %d\n", source_transforms.size());
-
245 egsInformation("Single source generator = %s\n", (single_generator ? "yes" : "no"));
-
246 egsInformation("Source | Location (x cm, y cm, z cm) | Rotated | Weight\n%s\n", string(80,'-').c_str());
-
247 for (size_t tt =0; tt < source_transforms.size(); tt++) {
-
248 EGS_Vector trans = source_transforms[tt]->getTranslation();
-
249 egsInformation(
-
250 "%6d | ( % 7.3F, % 7.3F, % 7.3F) | %5s | % 7.2G\n",
-
251 tt+1, trans.x, trans.y, trans.z,
-
252 source_transforms[tt]->hasRotation() ? "true":"false",
-
253 source_weights[tt]
-
254 );
-
255 }
-
256 }
-
257
-
258 if (rndm) {
-
259 egsInformation("\n\n");
-
260 rndm->describeRNG();
-
261 }
-
262
-
263 if (a_objects_list.size() > 0) {
-
264 egsInformation("The following ausgab objects are included in the simulation\n");
-
265 egsInformation("===========================================================\n\n");
-
266 for (size_t j=0; j<a_objects_list.size(); ++j) {
-
267 egsInformation("%s",a_objects_list[j]->getObjectDescription());
-
268 }
-
269 egsInformation("\n\n");
-
270 }
-
271
-
272 printIncludedFiles();
-
273
-
274 if (final_job) {
-
275 helpInit(0,false);
-
276 }
-
277}
-
278
-
279bool containsInclude(string str) {
-
280 string::iterator end_pos = std::remove(str.begin(), str.end(), ' ');
-
281 str.erase(end_pos, str.end());
-
282 size_t found = str.find("includefile");
-
283 return found != string::npos;
-
284}
-
285
-
286void EB_Application::printIncludedFiles() {
-
287
+
113
+
+
114void EB_Application::describeUserCode() const {
+
115 egsInformation(
+
116 "\n ***************************************************"
+
117 "\n * *"
+
118 "\n * egs_brachy *"
+
119 "\n * *"
+
120 "\n ***************************************************"
+
121 "\n\n");
+
122 egsInformation("This is EB_Application %s based on\n"
+
123 " EGS_AdvancedApplication %s\n\n",
+
124 egsSimplifyCVSKey(revision).c_str(),
+
125 egsSimplifyCVSKey(base_revision).c_str());
+
126}
+
+
127
+
+
128void EB_Application::describeSimulation() {
+
129
+
130 if (!geometry && !source) {
+
131 return;
+
132 }
+
133
+
134 egsInformation("\n\negs_brachy Run Mode Information\n%s\n\n",string(80,'=').c_str());
+
135 egsInformation("Run mode = %s\n", run_mode_name.c_str());
+
136 egsInformation("Single generator (may be overriden later) = %s\n", single_generator ? "yes" :"no");
+
137 if (gcr_phantom) {
+
138 egsInformation(
+
139 "getCurrentResult phantom/reg = %s %d",
+
140 gcr_phantom->geometry->getName().c_str(),
+
141 gcr_phantom_reg
+
142 );
+
143 }
+
144
+
145 egsInformation("\n\negs_brachy Geometry Information\n%s\n\n", string(80,'=').c_str());
+
146
+
147 ginfo.printInfo();
+
148
+
149 egsInformation("\n\negs_brachy Phantom Details\n%s\n\n", string(80,'=').c_str());
+
150 egsInformation(" | | | | Sph (Rmin, Rmax) | | \n");
+
151 egsInformation(" | | | Avg Vox Vol | RZ (Rmin, Rmax) | RZ (Zmin, Zmax) | \n");
+
152 egsInformation("Name | Type | Nreg | / cm^3 | XYZ (Xmin, Xmax) | XYZ (Ymin, Ymax) | XYZ (Zmin, Zmax)\n");
+
153 egsInformation("%s\n", string(145, '-').c_str());
+
154
+
155 for (size_t p=0; p < phantom_geoms.size(); p++) {
+
156
+
157 EB_Phantom *phant = phantom_geoms[p];
+
158 EGS_BaseGeometry *geom = phant->geometry;
+
159
+
160 string type = geom->getType();
+
161
+
162 if (type == "EGS_XYZGeometry") {
+
163 int nx, ny, nz;
+
164 nx = geom->getNRegDir(EB_Phantom::XDIR);
+
165 ny = geom->getNRegDir(EB_Phantom::YDIR);
+
166 nz = geom->getNRegDir(EB_Phantom::ZDIR);
+
167
+
168 EGS_Float xmin, xmax, ymin, ymax, zmin, zmax;
+
169 xmin = geom->getBound(EB_Phantom::XDIR, 0);
+
170 xmax = geom->getBound(EB_Phantom::XDIR, nx);
+
171 ymin = geom->getBound(EB_Phantom::YDIR, 0);
+
172 ymax = geom->getBound(EB_Phantom::YDIR, ny);
+
173 zmin = geom->getBound(EB_Phantom::ZDIR, 0);
+
174 zmax = geom->getBound(EB_Phantom::ZDIR, nz);
+
175
+
176 egsInformation(
+
177 "%-30s| %20s | %9d | %12.5G | (%8.3F, %8.3F) | (%8.3F, %8.3F) | (%8.3F, %8.3F)\n",
+
178 geom->getName().c_str(), type.c_str(), geom->regions(), phant->avgVoxelVol(),
+
179 xmin, xmax, ymin, ymax, zmin, zmax
+
180 );
+
181
+
182 } else if (type == "EGS_RZ") {
+
183 int nr, nz;
+
184 nr = geom->getNRegDir(EGS_RZGeometry::RDIR);
+
185 nz = geom->getNRegDir(EGS_RZGeometry::ZDIR);
+
186
+
187 EGS_Float rmin, rmax, zmin, zmax;
+
188 rmin = geom->getBound(EGS_RZGeometry::RDIR, 0);
+
189 rmax = geom->getBound(EGS_RZGeometry::RDIR, nr-1);
+
190 zmin = geom->getBound(EGS_RZGeometry::ZDIR, 0);
+
191 zmax = geom->getBound(EGS_RZGeometry::ZDIR, nz-1);
+
192
+
193 egsInformation(
+
194 "%-30s| %20s | %9d | %12.5G | (%8.3F, %8.3F) | (%8.3F, %8.3F) |\n",
+
195 geom->getName().c_str(), type.c_str(), geom->regions(), phant->avgVoxelVol(),
+
196 rmin, rmax, zmin, zmax
+
197 );
+
198 } else if (type == "EGS_cSphericalShell" || type == "EGS_cSpheres") {
+
199 type = (type == "EGS_cSphericalShell" ? "SphSh" : "Sph");
+
200
+
201 int nr = geom->getNRegDir(0);
+
202
+
203 EGS_Float rmin, rmax;
+
204 rmin = geom->getBound(EGS_cSpheres::RDIR, 0);
+
205 rmax = geom->getBound(EGS_cSpheres::RDIR, nr);
+
206
+
207 egsInformation(
+
208 "%-30s| %20s | %9d | %12.5G | (%8.3F, %8.3F) | | \n",
+
209 geom->getName().c_str(), type.c_str(), geom->regions(), phant->avgVoxelVol(),
+
210 rmin, rmax
+
211 );
+
212 } else {
+
213 egsInformation(
+
214 "%-30s| %20s | %9d | %12.5G | | | \n",
+
215 geom->getName().c_str(), type.c_str(), geom->regions(), phant->avgVoxelVol(),
+
216 -1, -1
+
217 );
+
218 }
+
219
+
220 if (type == "EGS_XYZGeometryT") {
+
221 egsWarning("\n***WARNING***\nPhantom of type transformed XYZ geometry used. The number of voxels in each direction and their bounds in the egslog, 3ddose, and egsphant files will be incorrect due to current limitations of the egs++ geometry library.\n***WARNING***\n");
+
222 }
+
223
+
224 }
+
225
+
226 egsInformation("\n\negs_brachy Volume correction details\n%s\n", string(80, '-').c_str());
+
227
+
228 egsInformation("\nSource specific volume correction details\n%s\n", string(80, '-').c_str());
+
229 source_vc_results.outputResults("Source");
+
230
+
231 egsInformation("\nExtra volume correction details\n%s\n", string(80, '-').c_str());
+
232 gen_vc_results.outputResults("Extra");
+
233
+
234 egsInformation("\nFile volume correction details\n%s\n", string(80, '-').c_str());
+
235 file_vc_results.outputResults();
+
236
+
237 egsInformation("\n\n");
+
238 if (geometry) {
+
239 geometry->printInfo();
+
240 }
+
241
+
242 if (source) {
+
243 egsInformation("\n\negs_brachy Source Information\n%s\n", string(80,'=').c_str());
+
244 egsInformation("%s\n\n", source->getSourceDescription());
+
245 egsInformation("Number of source locations = %d\n", source_transforms.size());
+
246 egsInformation("Single source generator = %s\n", (single_generator ? "yes" : "no"));
+
247 egsInformation("Source | Location (x cm, y cm, z cm) | Rotated | Weight\n%s\n", string(80,'-').c_str());
+
248 for (size_t tt =0; tt < source_transforms.size(); tt++) {
+
249 EGS_Vector trans = source_transforms[tt]->getTranslation();
+
250 egsInformation(
+
251 "%6d | ( % 7.3F, % 7.3F, % 7.3F) | %5s | % 7.2G\n",
+
252 tt+1, trans.x, trans.y, trans.z,
+
253 source_transforms[tt]->hasRotation() ? "true":"false",
+
254 source_weights[tt]
+
255 );
+
256 }
+
257 }
+
258
+
259 if (rndm) {
+
260 egsInformation("\n\n");
+
261 rndm->describeRNG();
+
262 }
+
263
+
264 if (a_objects_list.size() > 0) {
+
265 egsInformation("The following ausgab objects are included in the simulation\n");
+
266 egsInformation("===========================================================\n\n");
+
267 for (size_t j=0; j<a_objects_list.size(); ++j) {
+
268 egsInformation("%s",a_objects_list[j]->getObjectDescription());
+
269 }
+
270 egsInformation("\n\n");
+
271 }
+
272
+
273 printIncludedFiles();
+
274
+
275 if (final_job) {
+
276 helpInit(0,false);
+
277 }
+
278}
+
+
279
+
+
280bool containsInclude(string str) {
+
281 string::iterator end_pos = std::remove(str.begin(), str.end(), ' ');
+
282 str.erase(end_pos, str.end());
+
283 size_t found = str.find("includefile");
+
284 return found != string::npos;
+
285}
+
+
286
+
+
287void EB_Application::printIncludedFiles() {
288
-
289 string fname = constructIOFileName(".egsinp", false);
-
290 egsInformation("\n\nIncluded Files\n%s\n", string(80,'=').c_str());
-
291 egsInformation("Input file:\n\t%s\n", fname.c_str());
-
292 egsInformation("The following files were included in this simulation:\n");
-
293 ifstream inf(fname.c_str());
-
294
-
295 string line;
-
296 while (inf) {
-
297 getline(inf, line);
-
298 if (containsInclude(line)) {
-
299 egsInformation("\t%s\n", muen::trim(line).c_str());
-
300 }
-
301 };
-
302
-
303}
-
304
+
289
+
290 string fname = constructIOFileName(".egsinp", false);
+
291 egsInformation("\n\nIncluded Files\n%s\n", string(80,'=').c_str());
+
292 egsInformation("Input file:\n\t%s\n", fname.c_str());
+
293 egsInformation("The following files were included in this simulation:\n");
+
294 ifstream inf(fname.c_str());
+
295
+
296 string line;
+
297 while (inf) {
+
298 getline(inf, line);
+
299 if (containsInclude(line)) {
+
300 egsInformation("\t%s\n", muen::trim(line).c_str());
+
301 }
+
302 };
+
303
+
304}
+
305
-
306int EB_Application::initGeometry() {
-
307 // override default initGeometry so we can manually create our own geometry
-
308 // which will allow us to track region numbers for each geometry object individually
-
309
-
310 timing_blocks.addTimer("egs_brachy::initGeometry");
-
311
-
312 EGS_Input *ginput = input->getInputItem("geometry definition");
-
313
-
314 if (!ginput) {
-
315 egsWarning("EB_Application::createGeometry: no geometry specification in this input\n");
-
316 egsFatal("Simulation stopped\n");
-
317 }
-
318
-
319 int err = ginfo.initializeFromInput(ginput);
-
320 if (err) {
-
321 egsWarning("EB_Application::createGeometry: incomplete or incorrect geometry specification\n");
-
322 delete ginput;
-
323 egsFatal("Simulation stopped\n");
-
324 }
-
325
-
326 err = EGS_AdvancedApplication::initGeometry();
-
327
-
328 if (err) {
-
329 egsWarning("Failed to create a geometry from input file\n");
-
330 delete ginput;
-
331 egsFatal("Simulation stopped\n");
-
332 }
-
333
-
334 geometry->ref();
-
335
-
336 ginfo.setGeometryIndexes(geometry);
-
337
+
306
+
+
307int EB_Application::initGeometry() {
+
308 // override default initGeometry so we can manually create our own geometry
+
309 // which will allow us to track region numbers for each geometry object individually
+
310
+
311 timing_blocks.addTimer("egs_brachy::initGeometry");
+
312
+
313 EGS_Input *ginput = input->getInputItem("geometry definition");
+
314
+
315 if (!ginput) {
+
316 egsWarning("EB_Application::createGeometry: no geometry specification in this input\n");
+
317 egsFatal("Simulation stopped\n");
+
318 }
+
319
+
320 int err = ginfo.initializeFromInput(ginput);
+
321 if (err) {
+
322 egsWarning("EB_Application::createGeometry: incomplete or incorrect geometry specification\n");
+
323 delete ginput;
+
324 egsFatal("Simulation stopped\n");
+
325 }
+
326
+
327 err = EGS_AdvancedApplication::initGeometry();
+
328
+
329 if (err) {
+
330 egsWarning("Failed to create a geometry from input file\n");
+
331 delete ginput;
+
332 egsFatal("Simulation stopped\n");
+
333 }
+
334
+
335 geometry->ref();
+
336
+
337 ginfo.setGeometryIndexes(geometry);
338
339
-
340 if (run_mode == RM_SUPERPOSITION) {
-
341 if (ginfo.source_envelope_name == "") {
-
342 egsFatal("Missing 'source envelope geometry' input required for superposition mode\n");
-
343 }
-
344
-
345 source_envelope_geom = EGS_BaseGeometry::getGeometry(ginfo.source_envelope_name);
-
346 if (!source_envelope_geom) {
-
347 egsFatal("source envelope geometry '%s' can not be found\n", ginfo.source_envelope_name.c_str());
-
348 }
-
349
-
350 if (source_envelope_geom->getType() != "EGS_ASwitchedEnvelope") {
-
351 egsFatal("You must use an %s source envelope geometry type for superposition mode\n", "EGS_ASwitchedEnvelope");
-
352 }
-
353 superpos_geom = static_cast<EGS_ASwitchedEnvelope *>(source_envelope_geom);
-
354 }else{
-
355 for (int gg=0; gg < ginfo.ngeom; gg++) {
-
356 GeomRegionInfo gr = ginfo.ordered_geom_data[gg];
-
357 if (gr.type == "EGS_ASwitchedEnvelope"){
-
358 egsFatal("EGS_ASwitchedEnvelope should not be used when not using 'run mode = superposition\n");
-
359 }
-
360 }
-
361 }
-
362
+
340
+
341 if (run_mode == RM_SUPERPOSITION) {
+
342 if (ginfo.source_envelope_name == "") {
+
343 egsFatal("Missing 'source envelope geometry' input required for superposition mode\n");
+
344 }
+
345
+
346 source_envelope_geom = EGS_BaseGeometry::getGeometry(ginfo.source_envelope_name);
+
347 if (!source_envelope_geom) {
+
348 egsFatal("source envelope geometry '%s' can not be found\n", ginfo.source_envelope_name.c_str());
+
349 }
+
350
+
351 if (source_envelope_geom->getType() != "EGS_ASwitchedEnvelope") {
+
352 egsFatal("You must use an %s source envelope geometry type for superposition mode\n", "EGS_ASwitchedEnvelope");
+
353 }
+
354 superpos_geom = static_cast<EGS_ASwitchedEnvelope *>(source_envelope_geom);
+
355 }else{
+
356 for (int gg=0; gg < ginfo.ngeom; gg++) {
+
357 GeomRegionInfo gr = ginfo.ordered_geom_data[gg];
+
358 if (gr.type == "EGS_ASwitchedEnvelope"){
+
359 egsFatal("EGS_ASwitchedEnvelope should not be used when not using 'run mode = superposition\n");
+
360 }
+
361 }
+
362 }
363
-
364 err = initSourceTransforms();
-
365 if (err) {
-
366 egsFatal("Failed to initiate source locations\n");
-
367 }
-
368
-
369 delete ginput;
-
370
-
371 err = createPhantoms();
-
372 if (err) {
-
373 egsWarning("Failed to create phantom objects\n");
-
374 egsFatal("Simulation stopped\n");
-
375 }
-
376
-
377 err = correctVolumes();
-
378
-
379 timing_blocks.stopTimer();
-
380 return 0;
-
381
-
382}
-
383
-
384vector<EGS_AffineTransform *> EB_Application::createTransforms(EGS_Input *input) {
-
385
-
386 vector<EGS_AffineTransform *> transforms;
-
387 if (input) {
-
388 EGS_Input *trans_inp;
-
389
-
390 while ((trans_inp = input->takeInputItem("transformation"))) {
-
391 EGS_AffineTransform *transform = EGS_AffineTransform::getTransformation(trans_inp);
-
392 if (!transform) {
-
393 egsWarning("Invalid transform input given\n");
-
394
-
395 }
-
396 transforms.push_back(transform);
-
397 delete trans_inp;
-
398
-
399 }
-
400 }
-
401
-
402 return transforms;
-
403
-
404}
-
405
-
406int EB_Application::initSourceTransforms() {
-
407
-
408 if (!input) {
-
409 return -1;
-
410 }
-
411
-
412 EGS_Input *source_inp = input->getInputItem("source definition");
-
413
-
414 if (!source_inp) {
-
415 return -1;
-
416 }
-
417
+
364
+
365 err = initSourceTransforms();
+
366 if (err) {
+
367 egsFatal("Failed to initiate source locations\n");
+
368 }
+
369
+
370 delete ginput;
+
371
+
372 err = createPhantoms();
+
373 if (err) {
+
374 egsWarning("Failed to create phantom objects\n");
+
375 egsFatal("Simulation stopped\n");
+
376 }
+
377
+
378 err = correctVolumes();
+
379
+
380 timing_blocks.stopTimer();
+
381 return 0;
+
382
+
383}
+
+
384
+
+
385vector<EGS_AffineTransform *> EB_Application::createTransforms(EGS_Input *input) {
+
386
+
387 vector<EGS_AffineTransform *> transforms;
+
388 if (input) {
+
389 EGS_Input *trans_inp;
+
390
+
391 while ((trans_inp = input->takeInputItem("transformation"))) {
+
392 EGS_AffineTransform *transform = EGS_AffineTransform::getTransformation(trans_inp);
+
393 if (!transform) {
+
394 egsWarning("Invalid transform input given\n");
+
395
+
396 }
+
397 transforms.push_back(transform);
+
398 delete trans_inp;
+
399
+
400 }
+
401 }
+
402
+
403 return transforms;
+
404
+
405}
+
+
406
+
+
407int EB_Application::initSourceTransforms() {
+
408
+
409 if (!input) {
+
410 return -1;
+
411 }
+
412
+
413 EGS_Input *source_inp = input->getInputItem("source definition");
+
414
+
415 if (!source_inp) {
+
416 return -1;
+
417 }
418
-
419 EGS_Input *source_loc_inp = source_inp->takeInputItem("transformations");
-
420
-
421 if (source_loc_inp) {
-
422 source_transforms = createTransforms(source_loc_inp);
-
423 delete source_loc_inp;
-
424 }
-
425
-
426 if (source_transforms.size() == 0) {
-
427 EGS_AffineTransform *unity_trans = new EGS_AffineTransform();
-
428 source_transforms.push_back(unity_trans);
-
429 egsWarning("EB_Application:: missing or invalid source `transformations` input item. Assuming single source at origin\n");
-
430 }
-
431 nsources = (int)source_transforms.size();
-
432 base_transform = source_transforms[0];
-
433 base_transform_inv = new EGS_AffineTransform(base_transform->inverse());
-
434
-
435 EGS_Input *source_overlap_inp = source_inp->takeInputItem("source overlap check");
-
436 if (source_overlap_inp){
-
437 int err = checkSourceOverlaps(source_overlap_inp);
-
438 if (err){
-
439 egsFatal("EB_Application:: checkSourceOverlaps detected an error.");
-
440 }
-
441 }
-
442
-
443 return 0;
-
444
-
445}
-
446
-
447int EB_Application::checkSourceOverlaps(EGS_Input *inp) {
-
448
-
449 timing_blocks.addTimer("egs_brachy::checkSourceOverlaps");
-
450
-
451 vector<string> yn_choices;
-
452 yn_choices.push_back("no");
-
453 yn_choices.push_back("yes");
-
454 bool check_source_overlap = (bool)inp->getInput("check source overlaps", yn_choices, 0);
-
455
-
456 if (!check_source_overlap || source_transforms.size() <= 1){
-
457 /* not requested or only 1 source so no need to check for overlap */
-
458 timing_blocks.stopTimer();
-
459 return 0;
-
460 }
-
461
-
462 vector<string> mode_choices;
-
463 mode_choices.push_back("warning");
-
464 mode_choices.push_back("fatal");
-
465
-
466 bool fatal = (bool)inp->getInput("warning mode", mode_choices, 1);
-
467
-
468 EGS_Input *shape_inp = inp->takeInputItem("shape");
-
469
-
470 EGS_BaseShape *bounds = EGS_BaseShape::createShape(shape_inp);
-
471
-
472 if (!shape_inp) {
-
473 egsWarning("egs_brachy::checkSourceOverlaps - no `shape` input found.\n");
-
474 return 1;
-
475 }
-
476
-
477 EGS_Float bounds_volume = ebvolcor::getShapeVolume(shape_inp);
-
478 if (bounds_volume < 0){
-
479 egsWarning("egs_brachy::checkSourceOverlaps - Unable to get shape volume.");
-
480 return 1;
-
481 }
-
482
-
483 vector<string> excluded;
-
484 inp->getInput("excluded geometries", excluded);
-
485
-
486 EGS_Float density;
-
487 int err = inp->getInput("density of random points (cm^-3)", density);
-
488 if (err) {
-
489 egsWarning("egs_brachy::checkSourceOverlaps - The volume correction 'density of random points (cm^-3)' input was not found. Using 1E6/cm^3\n");
-
490 density = 1E6;
-
491 }
-
492 EGS_I64 npoints = (EGS_I64)floor(max(1., density*bounds_volume));
-
493
+
419
+
420 EGS_Input *source_loc_inp = source_inp->takeInputItem("transformations");
+
421
+
422 if (source_loc_inp) {
+
423 source_transforms = createTransforms(source_loc_inp);
+
424 delete source_loc_inp;
+
425 }
+
426
+
427 if (source_transforms.size() == 0) {
+
428 EGS_AffineTransform *unity_trans = new EGS_AffineTransform();
+
429 source_transforms.push_back(unity_trans);
+
430 egsWarning("EB_Application:: missing or invalid source `transformations` input item. Assuming single source at origin\n");
+
431 }
+
432 nsources = (int)source_transforms.size();
+
433 base_transform = source_transforms[0];
+
434 base_transform_inv = new EGS_AffineTransform(base_transform->inverse());
+
435
+
436 EGS_Input *source_overlap_inp = source_inp->takeInputItem("source overlap check");
+
437 if (source_overlap_inp){
+
438 int err = checkSourceOverlaps(source_overlap_inp);
+
439 if (err){
+
440 egsFatal("EB_Application:: checkSourceOverlaps detected an error.");
+
441 }
+
442 }
+
443
+
444 return 0;
+
445
+
446}
+
+
447
+
+
448int EB_Application::checkSourceOverlaps(EGS_Input *inp) {
+
449
+
450 timing_blocks.addTimer("egs_brachy::checkSourceOverlaps");
+
451
+
452 vector<string> yn_choices;
+
453 yn_choices.push_back("no");
+
454 yn_choices.push_back("yes");
+
455 bool check_source_overlap = (bool)inp->getInput("check source overlaps", yn_choices, 0);
+
456
+
457 if (!check_source_overlap || source_transforms.size() <= 1){
+
458 /* not requested or only 1 source so no need to check for overlap */
+
459 timing_blocks.stopTimer();
+
460 return 0;
+
461 }
+
462
+
463 vector<string> mode_choices;
+
464 mode_choices.push_back("warning");
+
465 mode_choices.push_back("fatal");
+
466
+
467 bool fatal = (bool)inp->getInput("warning mode", mode_choices, 1);
+
468
+
469 EGS_Input *shape_inp = inp->takeInputItem("shape");
+
470
+
471 EGS_BaseShape *bounds = EGS_BaseShape::createShape(shape_inp);
+
472
+
473 if (!shape_inp) {
+
474 egsWarning("egs_brachy::checkSourceOverlaps - no `shape` input found.\n");
+
475 return 1;
+
476 }
+
477
+
478 EGS_Float bounds_volume = ebvolcor::getShapeVolume(shape_inp);
+
479 if (bounds_volume < 0){
+
480 egsWarning("egs_brachy::checkSourceOverlaps - Unable to get shape volume.");
+
481 return 1;
+
482 }
+
483
+
484 vector<string> excluded;
+
485 inp->getInput("excluded geometries", excluded);
+
486
+
487 EGS_Float density;
+
488 int err = inp->getInput("density of random points (cm^-3)", density);
+
489 if (err) {
+
490 egsWarning("egs_brachy::checkSourceOverlaps - The volume correction 'density of random points (cm^-3)' input was not found. Using 1E6/cm^3\n");
+
491 density = 1E6;
+
492 }
+
493 EGS_I64 npoints = (EGS_I64)floor(max(1., density*bounds_volume));
494
-
495 EGS_RandomGenerator *rng = EGS_RandomGenerator::defaultRNG();
-
496 EGS_Vector point;
-
497
-
498 /* find first source geometry defined */
-
499 EGS_BaseGeometry *base_source = 0;
-
500 string base_source_name;
-
501 for (int gg=0; gg < ginfo.ngeom; gg++) {
-
502 GeomRegionInfo gr = ginfo.ordered_geom_data[gg];
-
503 if (find(ginfo.source_names.begin(), ginfo.source_names.end(), gr.name) != ginfo.source_names.end()){
-
504 base_source = EGS_BaseGeometry::getGeometry(gr.name);
-
505 base_source_name = gr.name;
-
506 break;
-
507 }
-
508 }
-
509 if (!base_source){
-
510 egsFatal("egs_brachy::checkSourceOverlaps - did not find base source geometry");
-
511 }
-
512
-
513 /* now lets see if our base source is in an autoenvelope */
-
514 EGS_AffineTransform base_transform;
-
515 EGS_AffineTransform inv_base_transform;
-
516 for (int gg=0; gg < ginfo.ngeom; gg++) {
-
517 GeomRegionInfo gr = ginfo.ordered_geom_data[gg];
-
518 if (find(gr.children.begin(), gr.children.end(), base_source_name) != gr.children.end()){
-
519 /* base source is child of this geometry */
-
520 if (gr.type != "EGS_AEnvelope" && gr.type != "EGS_ASwitchedEnvelope"){
-
521 base_transform = *source_transforms[0];
-
522 inv_base_transform = base_transform.inverse();
-
523 }
-
524 break;
-
525 }
-
526 }
-
527
-
528 vector<int> overlaps;
-
529
-
530 for (EGS_I64 i=0; i < npoints; i++) {
-
531
-
532 /* Generate a point and check if its contained within base source. If
-
533 * it's not actually in a source, go back and generate a new point. */
-
534 point = bounds->getRandomPoint(rng);
-
535 base_transform.transform(point);
-
536 if (base_source->isWhere(point) < 0) {
-
537 continue;
-
538 }
-
539 inv_base_transform.transform(point);
-
540
-
541 for (size_t sa_idx = 0; sa_idx < source_transforms.size(); sa_idx++){
-
542
-
543 overlaps.clear();
-
544
-
545 EGS_Vector transformed(point);
-
546
-
547 // transform from point relative to origin to point
-
548 // relative to source A we are checking against other sources (B)
-
549 source_transforms[sa_idx]->transform(transformed);
-
550
-
551 for (size_t sb_idx = sa_idx + 1; sb_idx < source_transforms.size(); sb_idx++){
-
552
-
553 EGS_Vector inner_transformed(transformed);
-
554
-
555 // use current source we are checking transform to back relative to origin
-
556 source_transforms[sb_idx]->inverse().transform(inner_transformed);
-
557 base_transform.transform(inner_transformed);
-
558 if (base_source->isWhere(inner_transformed) >= 0) {
-
559 /* point falls within Source A & B so they must be overlapping */
-
560 overlaps.push_back(sa_idx);
-
561 overlaps.push_back(sb_idx);
-
562 goto overlap_found;
-
563 }
-
564 }
-
565 }
-
566 }
-
567
-
568overlap_found:
-
569
-
570 if (rng){
-
571 delete rng;
-
572 }
-
573 if (shape_inp){
-
574 delete shape_inp;
-
575 }
-
576 timing_blocks.stopTimer();
-
577
-
578 if (overlaps.size() > 1){
-
579 string msg = "Possible overlap of sources: ";
-
580 for (int i=0; i < overlaps.size(); i++){
-
581 msg += to_string(overlaps[i]);
-
582 if (i != overlaps.size() -1 ){
-
583 msg += ", ";
-
584 }
-
585 }
-
586 egsInformation((msg+"\n").c_str());
-
587 }
-
588
-
589 if (overlaps.size() > 1){
-
590 return fatal ? 1 : 0;
-
591 }
-
592
-
593 return 0;
-
594}
-
595
-
596int EB_Application::correctVolumes() {
-
597
+
495
+
496 EGS_RandomGenerator *rng = EGS_RandomGenerator::defaultRNG();
+
497 EGS_Vector point;
+
498
+
499 /* find first source geometry defined */
+
500 EGS_BaseGeometry *base_source = 0;
+
501 string base_source_name;
+
502 for (int gg=0; gg < ginfo.ngeom; gg++) {
+
503 GeomRegionInfo gr = ginfo.ordered_geom_data[gg];
+
504 if (find(ginfo.source_names.begin(), ginfo.source_names.end(), gr.name) != ginfo.source_names.end()){
+
505 base_source = EGS_BaseGeometry::getGeometry(gr.name);
+
506 base_source_name = gr.name;
+
507 break;
+
508 }
+
509 }
+
510 if (!base_source){
+
511 egsFatal("egs_brachy::checkSourceOverlaps - did not find base source geometry");
+
512 }
+
513
+
514 /* now lets see if our base source is in an autoenvelope */
+
515 EGS_AffineTransform base_transform;
+
516 EGS_AffineTransform inv_base_transform;
+
517 for (int gg=0; gg < ginfo.ngeom; gg++) {
+
518 GeomRegionInfo gr = ginfo.ordered_geom_data[gg];
+
519 if (find(gr.children.begin(), gr.children.end(), base_source_name) != gr.children.end()){
+
520 /* base source is child of this geometry */
+
521 if (gr.type != "EGS_AEnvelope" && gr.type != "EGS_ASwitchedEnvelope"){
+
522 base_transform = *source_transforms[0];
+
523 inv_base_transform = base_transform.inverse();
+
524 }
+
525 break;
+
526 }
+
527 }
+
528
+
529 vector<int> overlaps;
+
530
+
531 for (EGS_I64 i=0; i < npoints; i++) {
+
532
+
533 /* Generate a point and check if its contained within base source. If
+
534 * it's not actually in a source, go back and generate a new point. */
+
535 point = bounds->getRandomPoint(rng);
+
536 base_transform.transform(point);
+
537 if (base_source->isWhere(point) < 0) {
+
538 continue;
+
539 }
+
540 inv_base_transform.transform(point);
+
541
+
542 for (size_t sa_idx = 0; sa_idx < source_transforms.size(); sa_idx++){
+
543
+
544 overlaps.clear();
+
545
+
546 EGS_Vector transformed(point);
+
547
+
548 // transform from point relative to origin to point
+
549 // relative to source A we are checking against other sources (B)
+
550 source_transforms[sa_idx]->transform(transformed);
+
551
+
552 for (size_t sb_idx = sa_idx + 1; sb_idx < source_transforms.size(); sb_idx++){
+
553
+
554 EGS_Vector inner_transformed(transformed);
+
555
+
556 // use current source we are checking transform to back relative to origin
+
557 source_transforms[sb_idx]->inverse().transform(inner_transformed);
+
558 base_transform.transform(inner_transformed);
+
559 if (base_source->isWhere(inner_transformed) >= 0) {
+
560 /* point falls within Source A & B so they must be overlapping */
+
561 overlaps.push_back(sa_idx);
+
562 overlaps.push_back(sb_idx);
+
563 goto overlap_found;
+
564 }
+
565 }
+
566 }
+
567 }
+
568
+
569overlap_found:
+
570
+
571 if (rng){
+
572 delete rng;
+
573 }
+
574 if (shape_inp){
+
575 delete shape_inp;
+
576 }
+
577 timing_blocks.stopTimer();
+
578
+
579 if (overlaps.size() > 1){
+
580 string msg = "Possible overlap of sources: ";
+
581 for (int i=0; i < overlaps.size(); i++){
+
582 msg += to_string(overlaps[i]);
+
583 if (i != overlaps.size() -1 ){
+
584 msg += ", ";
+
585 }
+
586 }
+
587 egsInformation((msg+"\n").c_str());
+
588 }
+
589
+
590 if (overlaps.size() > 1){
+
591 return fatal ? 1 : 0;
+
592 }
+
593
+
594 return 0;
+
595}
+
+
596
+
+
597int EB_Application::correctVolumes() {
598
-
599 timing_blocks.addTimer("egs_brachy::correctVolumes");
-
600 EGS_Input *vol_cor_inp = input->takeInputItem("volume correction");
-
601 if (!vol_cor_inp) {
-
602 egsWarning("Input item `volume correction` was not found\n");
-
603 return 1;
-
604 }
-
605
-
606 if (run_mode == RM_SUPERPOSITION) {
-
607 for (int i=0; i < nsources; i++) {
-
608 superpos_geom->activateByIndex(i);
-
609 }
-
610 }
-
611 ebvolcor::VolumeCorrector vc(vol_cor_inp, phantom_geoms, geometry, &ginfo, source_transforms);
-
612
-
613 source_vc_results = vc.runSourceCorrection(timing_blocks);
-
614
-
615 gen_vc_results = vc.runGeneralCorrection(timing_blocks);
-
616
-
617 file_vc_results = vc.runFileCorrection(timing_blocks);
-
618
+
599
+
600 timing_blocks.addTimer("egs_brachy::correctVolumes");
+
601 EGS_Input *vol_cor_inp = input->takeInputItem("volume correction");
+
602 if (!vol_cor_inp) {
+
603 egsWarning("Input item `volume correction` was not found\n");
+
604 return 1;
+
605 }
+
606
+
607 if (run_mode == RM_SUPERPOSITION) {
+
608 for (int i=0; i < nsources; i++) {
+
609 superpos_geom->activateByIndex(i);
+
610 }
+
611 }
+
612 ebvolcor::VolumeCorrector vc(vol_cor_inp, phantom_geoms, geometry, &ginfo, source_transforms);
+
613
+
614 source_vc_results = vc.runSourceCorrection(timing_blocks);
+
615
+
616 gen_vc_results = vc.runGeneralCorrection(timing_blocks);
+
617
+
618 file_vc_results = vc.runFileCorrection(timing_blocks);
619
-
620 // automatic volumes now done, now get any manually specified volumes
-
621 EGS_Input *ij;
-
622 vector<string> user_vols;
-
623
-
624 while ((ij = vol_cor_inp->takeInputItem("phantom region volumes")) != 0) {
-
625
-
626 string phant_name;
-
627 ij->getInput("phantom name", phant_name);
-
628 EB_Phantom *phant = getPhantomByName(phant_name);
-
629 if (!phant) {
-
630 egsFatal("`phanton region volume` specified for phantom `%s` which does not exist.", phant_name.c_str());
-
631 }else{
-
632 user_vols.push_back(phant_name);
-
633 }
-
634
-
635 vector<int> phantom_regs;
-
636 ij->getInput("region numbers", phantom_regs);
-
637
-
638 vector<EGS_Float> phantom_vols;
-
639 ij->getInput("region volumes", phantom_vols);
-
640
-
641 if (phantom_regs.size() != phantom_vols.size()){
-
642 egsFatal(
-
643 "Mismatched number of inputs for `region numbers` and `region volumes` for phantom `%s`",
-
644 phant_name.c_str()
-
645 );
-
646 }else if (phantom_regs.size() == 0){
-
647 egsFatal(
-
648 "Missing `region numbers` or `region volumes` input for `phantom region volumes` block for phantom `%s`",
-
649 phant_name.c_str()
-
650 );
-
651 }
-
652
-
653 for (size_t r = 0; r < phantom_regs.size(); r++){
-
654 phant->setCorrectedVolume(phantom_regs[r], phantom_vols[r]);
-
655 }
-
656
+
620
+
621 // automatic volumes now done, now get any manually specified volumes
+
622 EGS_Input *ij;
+
623 vector<string> user_vols;
+
624
+
625 while ((ij = vol_cor_inp->takeInputItem("phantom region volumes")) != 0) {
+
626
+
627 string phant_name;
+
628 ij->getInput("phantom name", phant_name);
+
629 EB_Phantom *phant = getPhantomByName(phant_name);
+
630 if (!phant) {
+
631 egsFatal("`phanton region volume` specified for phantom `%s` which does not exist.", phant_name.c_str());
+
632 }else{
+
633 user_vols.push_back(phant_name);
+
634 }
+
635
+
636 vector<int> phantom_regs;
+
637 ij->getInput("region numbers", phantom_regs);
+
638
+
639 vector<EGS_Float> phantom_vols;
+
640 ij->getInput("region volumes", phantom_vols);
+
641
+
642 if (phantom_regs.size() != phantom_vols.size()){
+
643 egsFatal(
+
644 "Mismatched number of inputs for `region numbers` and `region volumes` for phantom `%s`",
+
645 phant_name.c_str()
+
646 );
+
647 }else if (phantom_regs.size() == 0){
+
648 egsFatal(
+
649 "Missing `region numbers` or `region volumes` input for `phantom region volumes` block for phantom `%s`",
+
650 phant_name.c_str()
+
651 );
+
652 }
+
653
+
654 for (size_t r = 0; r < phantom_regs.size(); r++){
+
655 phant->setCorrectedVolume(phantom_regs[r], phantom_vols[r]);
+
656 }
657
-
658 delete ij;
-
659 }
-
660
-
661 /* now we check to ensure that user has specified volumes for any phantoms
-
662 * which require it */
-
663 for (size_t p=0; p < phantom_geoms.size(); p++){
-
664 EB_Phantom *phant = phantom_geoms[p];
-
665 string name = phant->geometry->getName();
-
666 string type = phant->geometry->getType();
-
667 if (phant->needs_user_geoms && find(user_vols.begin(), user_vols.end(), name) == user_vols.end()){
-
668 egsFatal(
-
669 "Missing `phantom region volume` block for phantom `%s`."
-
670 "Phantoms of type `%s` can not calculate volumes automatically.",
-
671 name.c_str(),
-
672 type.c_str()
-
673 );
-
674 }
-
675 }
-
676
-
677 delete vol_cor_inp;
-
678
-
679 timing_blocks.stopTimer();
-
680
-
681 return 0;
-
682
-
683}
-
684
+
658
+
659 delete ij;
+
660 }
+
661
+
662 /* now we check to ensure that user has specified volumes for any phantoms
+
663 * which require it */
+
664 for (size_t p=0; p < phantom_geoms.size(); p++){
+
665 EB_Phantom *phant = phantom_geoms[p];
+
666 string name = phant->geometry->getName();
+
667 string type = phant->geometry->getType();
+
668 if (phant->needs_user_geoms && find(user_vols.begin(), user_vols.end(), name) == user_vols.end()){
+
669 egsFatal(
+
670 "Missing `phantom region volume` block for phantom `%s`."
+
671 "Phantoms of type `%s` can not calculate volumes automatically.",
+
672 name.c_str(),
+
673 type.c_str()
+
674 );
+
675 }
+
676 }
+
677
+
678 delete vol_cor_inp;
+
679
+
680 timing_blocks.stopTimer();
+
681
+
682 return 0;
+
683
+
684}
+
685
-
686// set up Phantom objects for any geometries that user has requested scoring for
-
687int EB_Application::createPhantoms() {
-
688
-
689 for (size_t idx=0; idx < ginfo.phantom_names.size(); idx++) {
-
690 string name = ginfo.phantom_names[idx];
-
691
-
692 EGS_BaseGeometry *phant_geom = EGS_BaseGeometry::getGeometry(name);
-
693 if (!phant_geom) {
-
694 egsInformation("\n\nUnable to find phantom geometry `%s`.\n\n This is a fatal error\n\n", name.c_str());
-
695 return 1;
-
696 }
-
697
+
686
+
687// set up Phantom objects for any geometries that user has requested scoring for
+
+
688int EB_Application::createPhantoms() {
+
689
+
690 for (size_t idx=0; idx < ginfo.phantom_names.size(); idx++) {
+
691 string name = ginfo.phantom_names[idx];
+
692
+
693 EGS_BaseGeometry *phant_geom = EGS_BaseGeometry::getGeometry(name);
+
694 if (!phant_geom) {
+
695 egsInformation("\n\nUnable to find phantom geometry `%s`.\n\n This is a fatal error\n\n", name.c_str());
+
696 return 1;
+
697 }
698
-
699 set<int> global_regions;
-
700
-
701 for (int reg=0; reg < ginfo.nreg_total; reg++) {
-
702 if (ginfo.phantomFromRegion(reg) == (int)idx) {
-
703 global_regions.insert(reg);
-
704 }
-
705 }
-
706
-
707 if (global_regions.size()==0) {
-
708 egsFatal(
-
709 "EB_Application::createPhantoms - No phantom regions detected for geometry '%s'.\n"
-
710 "Are you sure your phantom was included in the final simulation geometry?\n",
-
711 (phant_geom->getName()).c_str()
-
712 );
-
713 }
-
714 EB_Phantom *phantom = new EB_Phantom(this, phant_geom, global_regions, nsources, &pevent_pub);
-
715 phantom_geoms.push_back(phantom);
-
716
-
717 }
-
718
-
719 return 0;
-
720
-
721}
-
722
+
699
+
700 set<int> global_regions;
+
701
+
702 for (int reg=0; reg < ginfo.nreg_total; reg++) {
+
703 if (ginfo.phantomFromRegion(reg) == (int)idx) {
+
704 global_regions.insert(reg);
+
705 }
+
706 }
+
707
+
708 if (global_regions.size()==0) {
+
709 egsFatal(
+
710 "EB_Application::createPhantoms - No phantom regions detected for geometry '%s'.\n"
+
711 "Are you sure your phantom was included in the final simulation geometry?\n",
+
712 (phant_geom->getName()).c_str()
+
713 );
+
714 }
+
715 EB_Phantom *phantom = new EB_Phantom(this, phant_geom, global_regions, nsources, &pevent_pub);
+
716 phantom_geoms.push_back(phantom);
+
717
+
718 }
+
719
+
720 return 0;
+
721
+
722}
+
723
-
724int EB_Application::initSource() {
-
725
+
724
+
+
725int EB_Application::initSource() {
726
-
727 EGS_Input *source_inp = input->getInputItem("source definition");
-
728
-
729 if (!source_inp) {
-
730 return -1;
-
731 }
-
732
+
727
+
728 EGS_Input *source_inp = input->getInputItem("source definition");
+
729
+
730 if (!source_inp) {
+
731 return -1;
+
732 }
733
-
734 /* check if user has defined source weighting */
-
735 source_inp->getInput("source weights", source_weights);
-
736
-
737 // fill up source_weights so it always has length==nsources
-
738 while ((int)source_weights.size() < nsources) {
-
739 source_weights.push_back(1);
-
740 }
-
741
-
742 // normalize weights
-
743 double max_wt = *max_element(source_weights.begin(), source_weights.end());
-
744 vector<EGS_Float>::iterator it =source_weights.begin();
-
745 for (; it != source_weights.end(); ++it) {
-
746 *it /= max_wt;
-
747 }
-
748
-
749 int err = EGS_AdvancedApplication::initSource();
-
750 if (err) {
-
751 egsFatal("Failed to initialize source\n");
-
752 }
-
753
-
754 string stype = source->getObjectType();
-
755 is_phsp_source = stype == "EGS_PhspSource" || stype == "EB_IAEAPHSPSource";
-
756
-
757 if (is_phsp_source && !single_generator) {
-
758 single_generator = true;
-
759 egsInformation("Phase space being used. Overriding requested 'single generator = no' parameter. Setting to 'yes'\n");
-
760 }
-
761
+
734
+
735 /* check if user has defined source weighting */
+
736 source_inp->getInput("source weights", source_weights);
+
737
+
738 // fill up source_weights so it always has length==nsources
+
739 while ((int)source_weights.size() < nsources) {
+
740 source_weights.push_back(1);
+
741 }
+
742
+
743 // normalize weights
+
744 double max_wt = *max_element(source_weights.begin(), source_weights.end());
+
745 vector<EGS_Float>::iterator it =source_weights.begin();
+
746 for (; it != source_weights.end(); ++it) {
+
747 *it /= max_wt;
+
748 }
+
749
+
750 int err = EGS_AdvancedApplication::initSource();
+
751 if (err) {
+
752 egsFatal("Failed to initialize source\n");
+
753 }
+
754
+
755 string stype = source->getObjectType();
+
756 is_phsp_source = stype == "EGS_PhspSource" || stype == "EB_IAEAPHSPSource";
+
757
+
758 if (is_phsp_source && !single_generator) {
+
759 single_generator = true;
+
760 egsInformation("Phase space being used. Overriding requested 'single generator = no' parameter. Setting to 'yes'\n");
+
761 }
762
-
763 return err;
-
764
-
765}
-
766
-
767int EB_Application::initSimulation() {
-
768
-
769 timing_blocks.addTimer("egs_brachy::initSimulation");
-
770 initRunMode();
-
771
-
772 int res = EGS_AdvancedApplication::initSimulation();
-
773
-
774 if (run_mode == RM_VC_ONLY) {
-
775 output_3ddose_files = false;
-
776 describeSimulation();
-
777 finishSimulation();
-
778 timing_blocks.stopTimer();
-
779 return 1;
-
780 }
-
781
-
782 timing_blocks.stopTimer();
-
783 return res;
-
784
-
785}
-
786
-
787int EB_Application::initRunControl() {
-
788
-
789 vector<string> format_choices;
-
790 format_choices.push_back("text");
-
791 format_choices.push_back("gzip");
-
792 EGS_Input *run_control = input->getInputItem("run control");
-
793 int format = run_control->getInput("egsdat file format", format_choices, 0);
-
794 output_egsdat_format = format == 0 ? "text" : "gzip";
-
795
-
796 return EGS_AdvancedApplication::initRunControl();
-
797
-
798}
-
799
-
800int EB_Application::initRunMode() {
-
801 timing_blocks.addTimer("egs_brachy::initRunMode");
-
802
-
803 string run_mode_inp;
-
804 EGS_Input *rm = input->takeInputItem("run mode");
-
805 if (!rm) {
-
806 timing_blocks.stopTimer();
-
807 return 1;
+
763
+
764 return err;
+
765
+
766}
+
+
767
+
+
768int EB_Application::initSimulation() {
+
769
+
770 timing_blocks.addTimer("egs_brachy::initSimulation");
+
771 initRunMode();
+
772
+
773 int res = EGS_AdvancedApplication::initSimulation();
+
774
+
775 if (run_mode == RM_VC_ONLY) {
+
776 output_3ddose_files = false;
+
777 describeSimulation();
+
778 finishSimulation();
+
779 timing_blocks.stopTimer();
+
780 return 1;
+
781 }
+
782
+
783 timing_blocks.stopTimer();
+
784 return res;
+
785
+
786}
+
+
787
+
+
788int EB_Application::initRunControl() {
+
789
+
790 vector<string> format_choices;
+
791 format_choices.push_back("text");
+
792 format_choices.push_back("gzip");
+
793 EGS_Input *run_control = input->getInputItem("run control");
+
794 int format = run_control->getInput("egsdat file format", format_choices, 0);
+
795 output_egsdat_format = format == 0 ? "text" : "gzip";
+
796
+
797 if (run) {
+
798 delete run;
+
799 }
+
800 if (simple_run) {
+
801 run = new EGS_RunControl(this);
+
802 }
+
803 else if (uniform_run) {
+
804 run = new EB_UniformRunControl(this, output_egsdat_format);
+
805 }
+
806 else {
+
807 run = EGS_RunControl::getRunControlObject(this);
808 }
-
809
-
810 vector<string> choices;
-
811 choices.push_back("normal"); // RM_NORMAL
-
812 choices.push_back("superposition"); //RM_SUPERPOSITION
-
813 choices.push_back("volume correction only"); //RM_VC_ONLY
+
809 if (!run) {
+
810 return 1;
+
811 }
+
812 return 0;
+
813}
+
814
-
815 run_mode = (RunMode)rm->getInput("run mode", choices, (int)RM_NORMAL);
-
816 run_mode_name = choices[run_mode];
+
+
815int EB_Application::initRunMode() {
+
816 timing_blocks.addTimer("egs_brachy::initRunMode");
817
-
818
-
819 vector<string> yn_choices;
-
820 yn_choices.push_back("no");
-
821 yn_choices.push_back("yes");
-
822
-
823 single_generator = (bool)rm->getInput("single generator", yn_choices, 1);
+
818 string run_mode_inp;
+
819 EGS_Input *rm = input->takeInputItem("run mode");
+
820 if (!rm) {
+
821 timing_blocks.stopTimer();
+
822 return 1;
+
823 }
824
-
825 delete rm;
-
826
-
827 timing_blocks.stopTimer();
-
828
-
829 return 0;
-
830
-
831}
+
825 vector<string> choices;
+
826 choices.push_back("normal"); // RM_NORMAL
+
827 choices.push_back("superposition"); //RM_SUPERPOSITION
+
828 choices.push_back("volume correction only"); //RM_VC_ONLY
+
829
+
830 run_mode = (RunMode)rm->getInput("run mode", choices, (int)RM_NORMAL);
+
831 run_mode_name = choices[run_mode];
832
-
833int EB_Application::initCrossSections() {
-
834 timing_blocks.addTimer("egs_brachy::initCrossSections");
-
835 EGS_Input *transportp = input->getInputItem("MC transport parameter");
-
836 if (!transportp) {
-
837 transportp = input->getInputItem("transport parameter");
-
838 }
+
833
+
834 vector<string> yn_choices;
+
835 yn_choices.push_back("no");
+
836 yn_choices.push_back("yes");
+
837
+
838 single_generator = (bool)rm->getInput("single generator", yn_choices, 1);
839
-
840 if (!transportp) {
-
841 egsFatal("Missing `MC transport parameter` input item\n");
-
842 return 1;
-
843 }
-
844
-
845 int err = transportp->getInput("fluorescent photon cutoff", flu_cutoff);
-
846 if (err) {
-
847 flu_cutoff = 0.001;
-
848 }
-
849
-
850 int ret = EGS_AdvancedApplication::initCrossSections();
-
851
-
852 global_ecut = the_bounds->ecut;
-
853 global_pcut = the_bounds->pcut;
+
840 delete rm;
+
841
+
842 timing_blocks.stopTimer();
+
843
+
844 return 0;
+
845
+
846}
+
+
847
+
+
848int EB_Application::initCrossSections() {
+
849 timing_blocks.addTimer("egs_brachy::initCrossSections");
+
850 EGS_Input *transportp = input->getInputItem("MC transport parameter");
+
851 if (!transportp) {
+
852 transportp = input->getInputItem("transport parameter");
+
853 }
854
-
855 err = transportp->getInput("source ecut", source_ecut);
-
856 if (err) {
-
857 source_ecut = global_ecut;
+
855 if (!transportp) {
+
856 egsFatal("Missing `MC transport parameter` input item\n");
+
857 return 1;
858 }
859
-
860 err = transportp->getInput("source pcut", source_pcut);
+
860 int err = transportp->getInput("fluorescent photon cutoff", flu_cutoff);
861 if (err) {
-
862 source_pcut = global_pcut;
+
862 flu_cutoff = 0.001;
863 }
864
-
865 egsInformation("\negs_brachy transport parameter options:\n%s\n",string(80,'-').c_str());
-
866 egsInformation("Fluorescent photon cutoff %.3G\n", flu_cutoff);
-
867 egsInformation("Source PCUT %.3G\n", source_pcut);
-
868 egsInformation("Source ECUT %.3G\n", source_ecut);
+
865 int ret = EGS_AdvancedApplication::initCrossSections();
+
866
+
867 global_ecut = the_bounds->ecut;
+
868 global_pcut = the_bounds->pcut;
869
-
870 timing_blocks.stopTimer();
-
871 return ret;
-
872}
-
873
+
870 err = transportp->getInput("source ecut", source_ecut);
+
871 if (err) {
+
872 source_ecut = global_ecut;
+
873 }
874
-
875int EB_Application::initScoring() {
-
876
-
877 timing_blocks.addTimer("egs_brachy::initScoring");
-
878
-
879 EGS_Input *options = input->takeInputItem("scoring options");
-
880
-
881 if (options) {
-
882
-
883 initGCRScoring(options);
-
884 initAusgabCalls();
-
885 initTrackLengthScoring(options);
-
886 initEDepScoring(options);
-
887 initScatScoring(options);
-
888 initXCCScaling(options);
-
889 initDoseScaling(options);
-
890 initSpectrumScoring(options);
+
875 err = transportp->getInput("source pcut", source_pcut);
+
876 if (err) {
+
877 source_pcut = global_pcut;
+
878 }
+
879
+
880 egsInformation("\negs_brachy transport parameter options:\n%s\n",string(80,'-').c_str());
+
881 egsInformation("Fluorescent photon cutoff %.3G\n", flu_cutoff);
+
882 egsInformation("Source PCUT %.3G\n", source_pcut);
+
883 egsInformation("Source ECUT %.3G\n", source_ecut);
+
884
+
885 timing_blocks.stopTimer();
+
886 return ret;
+
887}
+
+
888
+
889
+
+
890int EB_Application::initScoring() {
891
-
892 escoring = new EnergyScoringStats(&pevent_pub);
+
892 timing_blocks.addTimer("egs_brachy::initScoring");
893
-
894 initPHSPScoring(options);
-
895 initOutputFiles(options);
-
896
+
894 EGS_Input *options = input->takeInputItem("scoring options");
+
895
+
896 if (options) {
897
-
898 delete options;
-
899 } else {
-
900 egsFatal("\n\nMissing input section 'scoring options'\n\n");
-
901 }
-
902
-
903 initVarianceReduction();
-
904
-
905 timing_blocks.stopTimer();
-
906 return 0;
-
907}
+
898 initGCRScoring(options);
+
899 initAusgabCalls();
+
900 initTrackLengthScoring(options);
+
901 initEDepScoring(options);
+
902 initScatScoring(options);
+
903 initXCCScaling(options);
+
904 initDoseScaling(options);
+
905 initSpectrumScoring(options);
+
906
+
907 escoring = new EnergyScoringStats(&pevent_pub);
908
-
909void EB_Application::initGCRScoring(EGS_Input *inp) {
-
910
-
911 gcr_phantom = 0;
-
912 gcr_phantom_reg = 0;
-
913
-
914 vector<string> gcr_inp;
-
915 int err = inp->getInput("current result phantom region", gcr_inp);
-
916 if (err || gcr_inp.size()==0) {
-
917 gcr_phantom = phantom_geoms[0];
-
918 gcr_phantom_reg = 0;
-
919 return;
-
920 }
-
921
-
922
-
923 // user requested a phantom, find it
-
924 if (gcr_inp.size() >= 1) {
-
925 for (size_t idx=0; idx < ginfo.phantom_names.size(); idx++) {
-
926 if (ginfo.phantom_names[idx] == gcr_inp[0]) {
-
927 gcr_phantom = phantom_geoms[idx];
-
928 }
-
929 }
-
930 }
-
931
-
932 // couldn't find requested phantom
-
933 if (!gcr_phantom) {
-
934 egsWarning(
-
935 "Did not find '%s' phantom for getCurrentResult. Using phantom %s\n",
-
936 gcr_inp[0].c_str(), ginfo.phantom_names[0].c_str()
-
937 );
-
938 gcr_phantom = phantom_geoms[0];
-
939 gcr_phantom_reg = 0;
-
940 return;
-
941 }
-
942
-
943 // user has also requested a region
-
944 if (gcr_inp.size() > 1) {
-
945 int ireg = atol(gcr_inp[1].c_str());
-
946 if (ireg > 0 && ireg < gcr_phantom->geometry->regions()) {
-
947 gcr_phantom_reg = ireg;
-
948 }
-
949 }
-
950
-
951}
-
952
-
953EB_Phantom* EB_Application::getPhantomByName(string name){
-
954 for (size_t idx=0; idx < ginfo.phantom_names.size(); idx++) {
-
955 if (ginfo.phantom_names[idx] == name) {
-
956 return phantom_geoms[idx];
-
957 }
-
958 }
-
959
-
960 return 0;
-
961}
-
962
-
963
-
964void EB_Application::initOutputFiles(EGS_Input *inp) {
+
909 initPHSPScoring(options);
+
910 initOutputFiles(options);
+
911
+
912
+
913 delete options;
+
914 } else {
+
915 egsFatal("\n\nMissing input section 'scoring options'\n\n");
+
916 }
+
917
+
918 initVarianceReduction();
+
919
+
920 timing_blocks.stopTimer();
+
921 return 0;
+
922}
+
+
923
+
+
924void EB_Application::initGCRScoring(EGS_Input *inp) {
+
925
+
926 gcr_phantom = 0;
+
927 gcr_phantom_reg = 0;
+
928
+
929 vector<string> gcr_inp;
+
930 int err = inp->getInput("current result phantom region", gcr_inp);
+
931 if (err || gcr_inp.size()==0) {
+
932 gcr_phantom = phantom_geoms[0];
+
933 gcr_phantom_reg = 0;
+
934 return;
+
935 }
+
936
+
937
+
938 // user requested a phantom, find it
+
939 if (gcr_inp.size() >= 1) {
+
940 for (size_t idx=0; idx < ginfo.phantom_names.size(); idx++) {
+
941 if (ginfo.phantom_names[idx] == gcr_inp[0]) {
+
942 gcr_phantom = phantom_geoms[idx];
+
943 }
+
944 }
+
945 }
+
946
+
947 // couldn't find requested phantom
+
948 if (!gcr_phantom) {
+
949 egsWarning(
+
950 "Did not find '%s' phantom for getCurrentResult. Using phantom %s\n",
+
951 gcr_inp[0].c_str(), ginfo.phantom_names[0].c_str()
+
952 );
+
953 gcr_phantom = phantom_geoms[0];
+
954 gcr_phantom_reg = 0;
+
955 return;
+
956 }
+
957
+
958 // user has also requested a region
+
959 if (gcr_inp.size() > 1) {
+
960 int ireg = atol(gcr_inp[1].c_str());
+
961 if (ireg > 0 && ireg < gcr_phantom->geometry->regions()) {
+
962 gcr_phantom_reg = ireg;
+
963 }
+
964 }
965
-
966 vector<string> yn_choices;
-
967 yn_choices.push_back("no");
-
968 yn_choices.push_back("yes");
-
969 output_egsphant = (bool)inp->getInput("output egsphant files", yn_choices, 0);
-
970 output_voxinfo = (bool)inp->getInput("output voxel info files", yn_choices, 0);
-
971 inp->getInput("output volume correction files for phantoms", output_volcor_phantoms);
-
972
-
973 vector<string> format_choices;
-
974 format_choices.push_back("text");
-
975 format_choices.push_back("gzip");
-
976
-
977 int format = inp->getInput("dose file format", format_choices, 0);
-
978 output_dose_format = format == 0 ? "text" : "gzip";
-
979
-
980 format = inp->getInput("egsphant file format", format_choices, 0);
-
981 output_egsphant_format = format == 0 ? "text" : "gzip";
-
982
-
983 format = inp->getInput("voxel info file format", format_choices, 0);
-
984 output_voxinfo_format = format == 0 ? "text" : "gzip";
-
985
-
986 format = inp->getInput("volume correction file format", format_choices, 0);
-
987 output_volcor_format = format == 0 ? "text" : "gzip";
-
988
-
989 inp->getInput("record initial particle positions", record_n_init);
-
990
-
991}
-
992
-
993void EB_Application::initPHSPScoring(EGS_Input *inp) {
+
966}
+
+
967
+
+
968EB_Phantom* EB_Application::getPhantomByName(string name){
+
969 for (size_t idx=0; idx < ginfo.phantom_names.size(); idx++) {
+
970 if (ginfo.phantom_names[idx] == name) {
+
971 return phantom_geoms[idx];
+
972 }
+
973 }
+
974
+
975 return 0;
+
976}
+
+
977
+
978
+
+
979void EB_Application::initOutputFiles(EGS_Input *inp) {
+
980
+
981 vector<string> yn_choices;
+
982 yn_choices.push_back("no");
+
983 yn_choices.push_back("yes");
+
984 output_egsphant = (bool)inp->getInput("output egsphant files", yn_choices, 0);
+
985 output_voxinfo = (bool)inp->getInput("output voxel info files", yn_choices, 0);
+
986 inp->getInput("output volume correction files for phantoms", output_volcor_phantoms);
+
987
+
988 vector<string> format_choices;
+
989 format_choices.push_back("text");
+
990 format_choices.push_back("gzip");
+
991
+
992 int format = inp->getInput("dose file format", format_choices, 0);
+
993 output_dose_format = format == 0 ? "text" : "gzip";
994
-
995 EGS_Input *phsp_inp = inp->takeInputItem("phsp scoring");
-
996
-
997 if (phsp_inp) {
-
998 phsp = new PHSPControl(phsp_inp, base_transform_inv, this, &pevent_pub);
-
999 }
+
995 format = inp->getInput("egsphant file format", format_choices, 0);
+
996 output_egsphant_format = format == 0 ? "text" : "gzip";
+
997
+
998 format = inp->getInput("voxel info file format", format_choices, 0);
+
999 output_voxinfo_format = format == 0 ? "text" : "gzip";
1000
-
1001}
-
1002
+
1001 format = inp->getInput("volume correction file format", format_choices, 0);
+
1002 output_volcor_format = format == 0 ? "text" : "gzip";
1003
-
1004int EB_Application::initVarianceReduction() {
+
1004 inp->getInput("record initial particle positions", record_n_init);
1005
-
1006 timing_blocks.addTimer("egs_brachy::initVarianceReduction");
+
1006}
+
1007
-
1008 egsInformation("\n\negs_brachy Variance Reduction Information\n%s\n\n",string(80,'=').c_str());
+
+
1008void EB_Application::initPHSPScoring(EGS_Input *inp) {
1009
-
1010 EGS_Input *vr = input->takeInputItem("variance reduction");
+
1010 EGS_Input *phsp_inp = inp->takeInputItem("phsp scoring");
1011
-
1012 /* Range rejection on by default in non source objects
-
1013 * and off in any source objects */
-
1014 global_i_do_rr = true;
-
1015 global_e_max_rr = 2.511;
-
1016
-
1017 source_i_do_rr = false;
-
1018 source_e_max_rr = 0.512;
-
1019
-
1020 the_egsvr->i_do_rr = (int)source_i_do_rr;
-
1021 the_egsvr->e_max_rr = source_e_max_rr;
+
1012 if (phsp_inp) {
+
1013 phsp = new PHSPControl(phsp_inp, base_transform_inv, this, &pevent_pub);
+
1014 }
+
1015
+
1016}
+
+
1017
+
1018
+
+
1019int EB_Application::initVarianceReduction() {
+
1020
+
1021 timing_blocks.addTimer("egs_brachy::initVarianceReduction");
1022
-
1023 if (!vr) {
-
1024 egsInformation("Global Range Rejection = %s\n", global_i_do_rr ? "Yes" : "No");
-
1025 egsInformation("Global Range Rejection Maximum Energy = %.3G MeV\n", global_e_max_rr);
-
1026 egsInformation("Source Range Rejection = %s\n", source_i_do_rr ? "Yes" : "No");
-
1027 egsInformation("Source Range Rejection Maximum Energy = %.3G MeV\n", source_e_max_rr);
-
1028 timing_blocks.stopTimer();
-
1029 return 1;
-
1030 }
+
1023 egsInformation("\n\negs_brachy Variance Reduction Information\n%s\n\n",string(80,'=').c_str());
+
1024
+
1025 EGS_Input *vr = input->takeInputItem("variance reduction");
+
1026
+
1027 /* Range rejection on by default in non source objects
+
1028 * and off in any source objects */
+
1029 global_i_do_rr = true;
+
1030 global_e_max_rr = 2.511;
1031
-
1032
-
1033 EGS_Input *ri = vr->takeInputItem("particle recycling");
-
1034 if (ri) {
-
1035
-
1036 egsInformation("Particle Recycling\n");
-
1037 recycle_opts = new RecycleOpts(ri);
-
1038 recycle_opts->printInfo();
-
1039 if (!single_generator) {
-
1040 single_generator = true;
-
1041 egsInformation(" Overriding requested 'single generator = no' parameter. Setting to 'yes'\n");
-
1042 }
-
1043 egsInformation("\n");
-
1044
-
1045 delete ri;
-
1046 }
+
1032 source_i_do_rr = false;
+
1033 source_e_max_rr = 0.512;
+
1034
+
1035 the_egsvr->i_do_rr = (int)source_i_do_rr;
+
1036 the_egsvr->e_max_rr = source_e_max_rr;
+
1037
+
1038 if (!vr) {
+
1039 egsInformation("Global Range Rejection = %s\n", global_i_do_rr ? "Yes" : "No");
+
1040 egsInformation("Global Range Rejection Maximum Energy = %.3G MeV\n", global_e_max_rr);
+
1041 egsInformation("Source Range Rejection = %s\n", source_i_do_rr ? "Yes" : "No");
+
1042 egsInformation("Source Range Rejection Maximum Energy = %.3G MeV\n", source_e_max_rr);
+
1043 timing_blocks.stopTimer();
+
1044 return 1;
+
1045 }
+
1046
1047
-
1048
-
1049 /* Range rejection */
-
1050 vector<string> yn_choices;
-
1051 yn_choices.push_back("no");
-
1052 yn_choices.push_back("yes");
-
1053
-
1054 string old_rr_setting;
-
1055 int err = vr->getInput("range rejection", old_rr_setting);
-
1056 if (!err) {
-
1057 egsFatal(
-
1058 "'range rejection' is not a valid setting for egs_brachy.\n"
-
1059 "Please use 'global range rejection' and 'source range rejection' settings instead.\n"
-
1060 );
-
1061 }
-
1062
-
1063 EGS_Float old_rr_max_e;
-
1064 err = vr->getInput("range rejection max energy", old_rr_max_e);
-
1065 if (!err) {
-
1066 egsFatal(
-
1067 "'range rejection max energy' is not a valid setting for egs_brachy.\n"
-
1068 "Please use 'global range rejection max energy' and 'source range rejection max energy' settings instead.\n"
-
1069 );
-
1070 }
-
1071
-
1072
-
1073 global_i_do_rr = vr->getInput("global range rejection", yn_choices, 1);
-
1074 egsInformation("Global Range Rejection = %s\n", global_i_do_rr ? "Yes" : "No");
-
1075 if (global_i_do_rr) {
-
1076 int err = vr->getInput("global range rejection max energy", global_e_max_rr);
-
1077 if (err) {
-
1078 global_e_max_rr = 2.511;
-
1079 }
-
1080 if (global_e_max_rr < 0.512) {
-
1081 egsFatal("Global Range Rejection max energy must be at least 0.512MeV\n");
-
1082 } else {
-
1083 egsInformation("Global Range Rejection Maximum Energy = %.3G MeV\n", global_e_max_rr);
-
1084 }
-
1085 }
-
1086
-
1087 source_i_do_rr = vr->getInput("source range rejection", yn_choices, 0);
-
1088 egsInformation("Source Range Rejection = %s\n", source_i_do_rr ? "Yes" : "No");
-
1089 if (source_i_do_rr) {
-
1090 int err = vr->getInput("source range rejection max energy", source_e_max_rr);
-
1091 if (err) {
-
1092 source_e_max_rr = 2.511;
-
1093 }
-
1094 if (source_e_max_rr < 0.512) {
-
1095 egsFatal("Source Range Rejection max energy must be at least 0.512MeV\n");
-
1096 } else {
-
1097 egsInformation("Source Range Rejection Maximum Energy = %.3G MeV\n", source_e_max_rr);
-
1098 }
-
1099 }
-
1100
-
1101 the_egsvr->i_do_rr = source_i_do_rr;
-
1102 the_egsvr->e_max_rr = source_e_max_rr;
-
1103
-
1104
-
1105 /* Brem Cross Section Enhancement*/
-
1106 err = initBCSE(vr);
-
1107 egsInformation("BCSE = %s\n", do_bcse ? "Yes" : "No");
-
1108 if (!err) {
-
1109 egsInformation(
-
1110 " Brem Cross Section Enhancement medium = %s (%d)\n",
-
1111 EGS_BaseGeometry::getMediumName(bcse_med_num), bcse_med_num
-
1112 );
-
1113 egsInformation(" Brem Cross Section Enhancement factor = %.3G\n", bcse_factor);
-
1114 }
-
1115
+
1048 EGS_Input *ri = vr->takeInputItem("particle recycling");
+
1049 if (ri) {
+
1050 if (score_scat) {
+
1051 egsFatal("Primary-scatter dose scoring is not available with recycling. Please turn off recycling or disable scatter dose scoring.\n");
+
1052 }
+
1053 egsInformation("Particle Recycling\n");
+
1054 recycle_opts = new RecycleOpts(ri);
+
1055 recycle_opts->printInfo();
+
1056 if (!single_generator) {
+
1057 single_generator = true;
+
1058 egsInformation(" Overriding requested 'single generator = no' parameter. Setting to 'yes'\n");
+
1059 }
+
1060 egsInformation("\n");
+
1061
+
1062 delete ri;
+
1063 }
+
1064
+
1065 /* Range rejection */
+
1066 vector<string> yn_choices;
+
1067 yn_choices.push_back("no");
+
1068 yn_choices.push_back("yes");
+
1069
+
1070 string old_rr_setting;
+
1071 int err = vr->getInput("range rejection", old_rr_setting);
+
1072 if (!err) {
+
1073 egsFatal(
+
1074 "'range rejection' is not a valid setting for egs_brachy.\n"
+
1075 "Please use 'global range rejection' and 'source range rejection' settings instead.\n"
+
1076 );
+
1077 }
+
1078
+
1079 EGS_Float old_rr_max_e;
+
1080 err = vr->getInput("range rejection max energy", old_rr_max_e);
+
1081 if (!err) {
+
1082 egsFatal(
+
1083 "'range rejection max energy' is not a valid setting for egs_brachy.\n"
+
1084 "Please use 'global range rejection max energy' and 'source range rejection max energy' settings instead.\n"
+
1085 );
+
1086 }
+
1087
+
1088
+
1089 global_i_do_rr = vr->getInput("global range rejection", yn_choices, 1);
+
1090 egsInformation("Global Range Rejection = %s\n", global_i_do_rr ? "Yes" : "No");
+
1091 if (global_i_do_rr) {
+
1092 int err = vr->getInput("global range rejection max energy", global_e_max_rr);
+
1093 if (err) {
+
1094 global_e_max_rr = 2.511;
+
1095 }
+
1096 if (global_e_max_rr < 0.512) {
+
1097 egsFatal("Global Range Rejection max energy must be at least 0.512MeV\n");
+
1098 } else {
+
1099 egsInformation("Global Range Rejection Maximum Energy = %.3G MeV\n", global_e_max_rr);
+
1100 }
+
1101 }
+
1102
+
1103 source_i_do_rr = vr->getInput("source range rejection", yn_choices, 0);
+
1104 egsInformation("Source Range Rejection = %s\n", source_i_do_rr ? "Yes" : "No");
+
1105 if (source_i_do_rr) {
+
1106 int err = vr->getInput("source range rejection max energy", source_e_max_rr);
+
1107 if (err) {
+
1108 source_e_max_rr = 2.511;
+
1109 }
+
1110 if (source_e_max_rr < 0.512) {
+
1111 egsFatal("Source Range Rejection max energy must be at least 0.512MeV\n");
+
1112 } else {
+
1113 egsInformation("Source Range Rejection Maximum Energy = %.3G MeV\n", source_e_max_rr);
+
1114 }
+
1115 }
1116
-
1117 /* Brem Splitting */
-
1118 err = vr->getInput("split brem photons", nbr_split);
-
1119 egsInformation("Brem Splitting = %s\n", nbr_split > 1? "Yes" : "No");
-
1120 if (!err && nbr_split > 1) {
-
1121 do_brem_split = true;
-
1122 egsInformation(" Splitting brem photons N times = %d\n", nbr_split);
-
1123 the_egsvr->nbr_split = nbr_split;
-
1124 }
-
1125
-
1126
-
1127 /* Charged Particle Russian Roulette*/
-
1128 err = initRussianRoulette(vr);
-
1129 egsInformation("Charged Particle Russian Roulette = %s\n", the_egsvr->i_play_RR ? "Yes" : "No");
-
1130 if (!err || the_egsvr->i_play_RR) {
+
1117 the_egsvr->i_do_rr = source_i_do_rr;
+
1118 the_egsvr->e_max_rr = source_e_max_rr;
+
1119
+
1120
+
1121 /* Brem Cross Section Enhancement*/
+
1122 err = initBCSE(vr);
+
1123 egsInformation("BCSE = %s\n", do_bcse ? "Yes" : "No");
+
1124 if (!err) {
+
1125 egsInformation(
+
1126 " Brem Cross Section Enhancement medium = %s (%d)\n",
+
1127 EGS_BaseGeometry::getMediumName(bcse_med_num), bcse_med_num
+
1128 );
+
1129 egsInformation(" Brem Cross Section Enhancement factor = %.3G\n", bcse_factor);
+
1130 }
1131
-
1132 if (bcse_factor > 1) {
-
1133 the_egsvr->prob_RR = 1./(nbr_split*bcse_factor);
-
1134 egsInformation(
-
1135 " Survival probability (1/nbrsplt*bcse) = 1/(%d*%.3G) (%.3G%%)\n",
-
1136 nbr_split, bcse_factor, the_egsvr->prob_RR*100
-
1137 );
-
1138 } else {
-
1139 the_egsvr->prob_RR = 1./nbr_split;
-
1140 egsInformation(
-
1141 " Survival probability (1/nbrsplt) = 1/%d (%.3G%%)\n",
-
1142 nbr_split, the_egsvr->prob_RR*100
-
1143 );
-
1144 }
-
1145 }
-
1146
+
1132
+
1133 /* Brem Splitting */
+
1134 err = vr->getInput("split brem photons", nbr_split);
+
1135 egsInformation("Brem Splitting = %s\n", nbr_split > 1? "Yes" : "No");
+
1136 if (!err && nbr_split > 1) {
+
1137 do_brem_split = true;
+
1138 egsInformation(" Splitting brem photons N times = %d\n", nbr_split);
+
1139 the_egsvr->nbr_split = nbr_split;
+
1140 }
+
1141
+
1142
+
1143 /* Charged Particle Russian Roulette*/
+
1144 err = initRussianRoulette(vr);
+
1145 egsInformation("Charged Particle Russian Roulette = %s\n", the_egsvr->i_play_RR ? "Yes" : "No");
+
1146 if (!err || the_egsvr->i_play_RR) {
1147
-
1148 delete vr;
-
1149 timing_blocks.stopTimer();
-
1150 return 0;
-
1151
-
1152}
-
1153
-
1154int EB_Application::initRussianRoulette(EGS_Input *scoring_options) {
-
1155
-
1156 vector<string> yn_choices;
-
1157 yn_choices.push_back("no");
-
1158 yn_choices.push_back("yes");
-
1159
-
1160 int play_rr = scoring_options->getInput("russian roulette", yn_choices, 0);
-
1161 if (play_rr == 0) {
-
1162 return 1;
-
1163 }
-
1164
-
1165 the_egsvr->i_play_RR = 1;
-
1166
-
1167 AusgabCall rr_calls[] = {
-
1168 BeforeBrems, AfterBrems,
-
1169 BeforeAnnihFlight, AfterAnnihFlight,
-
1170 BeforeAnnihRest, AfterAnnihRest,
-
1171 FluorescentEvent
-
1172 };
-
1173
-
1174 int ncalls = sizeof(rr_calls)/sizeof(rr_calls[0]);
-
1175 enableAusgabCalls(ncalls, rr_calls);
-
1176
-
1177 return 0;
-
1178}
-
1179
-
1180int EB_Application::initBCSE(EGS_Input *inp) {
-
1181
-
1182 vector<string> bcse_inp;
-
1183 int err = inp->getInput("bcse medium", bcse_inp);
-
1184 if (err || bcse_inp.size()==0) {
-
1185 return 1;
-
1186 }
-
1187
-
1188 bcse_med_num = EGS_BaseGeometry::getMediumIndex(bcse_inp[0]);
-
1189 if (bcse_med_num < 0) {
-
1190 egsWarning("Requested an unknown medium `%s` for BCSE\n",bcse_inp[0].c_str());
-
1191 return 1;
-
1192 }
-
1193
-
1194
-
1195 if (bcse_inp.size() == 1) {
-
1196 bcse_factor = DEFAULT_BCSE_FACTOR;
-
1197 } else {
-
1198 bcse_factor = atof(bcse_inp[1].c_str());
-
1199 }
-
1200
-
1201 do_bcse = bcse_factor > 1;
-
1202 if (!do_bcse) {
-
1203 return 1;
-
1204 }
-
1205
-
1206 the_egsvr->i_play_RR = 1;
-
1207
-
1208 AusgabCall bcse_calls[] = {BeforeBrems, AfterBrems, FluorescentEvent};
-
1209 enableAusgabCalls(3, bcse_calls);
+
1148 if (bcse_factor > 1) {
+
1149 the_egsvr->prob_RR = 1./(nbr_split*bcse_factor);
+
1150 egsInformation(
+
1151 " Survival probability (1/nbrsplt*bcse) = 1/(%d*%.3G) (%.3G%%)\n",
+
1152 nbr_split, bcse_factor, the_egsvr->prob_RR*100
+
1153 );
+
1154 } else {
+
1155 the_egsvr->prob_RR = 1./nbr_split;
+
1156 egsInformation(
+
1157 " Survival probability (1/nbrsplt) = 1/%d (%.3G%%)\n",
+
1158 nbr_split, the_egsvr->prob_RR*100
+
1159 );
+
1160 }
+
1161 }
+
1162
+
1163
+
1164 delete vr;
+
1165 timing_blocks.stopTimer();
+
1166 return 0;
+
1167
+
1168}
+
+
1169
+
+
1170int EB_Application::initRussianRoulette(EGS_Input *scoring_options) {
+
1171
+
1172 vector<string> yn_choices;
+
1173 yn_choices.push_back("no");
+
1174 yn_choices.push_back("yes");
+
1175
+
1176 int play_rr = scoring_options->getInput("russian roulette", yn_choices, 0);
+
1177 if (play_rr == 0) {
+
1178 return 1;
+
1179 }
+
1180
+
1181 the_egsvr->i_play_RR = 1;
+
1182
+
1183 AusgabCall rr_calls[] = {
+
1184 BeforeBrems, AfterBrems,
+
1185 BeforeAnnihFlight, AfterAnnihFlight,
+
1186 BeforeAnnihRest, AfterAnnihRest,
+
1187 FluorescentEvent
+
1188 };
+
1189
+
1190 int ncalls = sizeof(rr_calls)/sizeof(rr_calls[0]);
+
1191 enableAusgabCalls(ncalls, rr_calls);
+
1192
+
1193 return 0;
+
1194}
+
+
1195
+
+
1196int EB_Application::initBCSE(EGS_Input *inp) {
+
1197
+
1198 vector<string> bcse_inp;
+
1199 int err = inp->getInput("bcse medium", bcse_inp);
+
1200 if (err || bcse_inp.size()==0) {
+
1201 return 1;
+
1202 }
+
1203
+
1204 bcse_med_num = EGS_BaseGeometry::getMediumIndex(bcse_inp[0]);
+
1205 if (bcse_med_num < 0) {
+
1206 egsWarning("Requested an unknown medium `%s` for BCSE\n",bcse_inp[0].c_str());
+
1207 return 1;
+
1208 }
+
1209
1210
-
1211 int egs_med_num = bcse_med_num+1;
-
1212 F77_OBJ_(egs_bcse, EGS_BCSE)(&egs_med_num, &bcse_factor);
-
1213
-
1214 return 0;
-
1215}
+
1211 if (bcse_inp.size() == 1) {
+
1212 bcse_factor = DEFAULT_BCSE_FACTOR;
+
1213 } else {
+
1214 bcse_factor = atof(bcse_inp[1].c_str());
+
1215 }
1216
-
1217void EB_Application::initSpectrumScoring(EGS_Input *scoring_input) {
-
1218
-
1219 bool header_printed = false;
-
1220
-
1221 while (EGS_Input *spec_inp=scoring_input->takeInputItem("spectrum scoring")) {
-
1222
-
1223 if (!header_printed) {
-
1224 egsInformation("\n\negs_brachy Spectrum Scoring Information\n%s\n\n",string(80,'=').c_str());
-
1225 header_printed = true;
-
1226 }
-
1227
-
1228 BaseSpectrumScorer *scorer = BaseSpectrumScorer::getSpectrumScorer(spec_inp, source, &ginfo, &pevent_pub);
+
1217 do_bcse = bcse_factor > 1;
+
1218 if (!do_bcse) {
+
1219 return 1;
+
1220 }
+
1221
+
1222 the_egsvr->i_play_RR = 1;
+
1223
+
1224 AusgabCall bcse_calls[] = {BeforeBrems, AfterBrems, FluorescentEvent};
+
1225 enableAusgabCalls(3, bcse_calls);
+
1226
+
1227 int egs_med_num = bcse_med_num+1;
+
1228 F77_OBJ_(egs_bcse, EGS_BCSE)(&egs_med_num, &bcse_factor);
1229
-
1230 if (scorer) {
-
1231 spectrum_scorers.push_back(scorer);
-
1232 egsInformation("Added scorer with title: %s\n", scorer->getInfo().c_str());
-
1233 }
-
1234 delete spec_inp;
-
1235 }
-
1236}
-
1237
-
1238void EB_Application::clearAusgabCalls() {
-
1239 for (size_t call=BeforeTransport; call <= UnknownCall; call++) {
-
1240 setAusgabCall((AusgabCall)call, false);
-
1241 }
-
1242
-
1243}
-
1244
-
1245void EB_Application::initAusgabCalls() {
-
1246
-
1247
-
1248 clearAusgabCalls();
-
1249
-
1250 AusgabCall always_call[] = {BeforeTransport, AfterTransport, FluorescentEvent};
-
1251 enableAusgabCalls(3, always_call);
-
1252
-
1253}
-
1254
-
1255
-
1256
-
1257void EB_Application::initTrackLengthScoring(EGS_Input *scoring_options) {
+
1230 return 0;
+
1231}
+
+
1232
+
+
1233void EB_Application::initSpectrumScoring(EGS_Input *scoring_input) {
+
1234
+
1235 bool header_printed = false;
+
1236
+
1237 while (EGS_Input *spec_inp=scoring_input->takeInputItem("spectrum scoring")) {
+
1238
+
1239 if (!header_printed) {
+
1240 egsInformation("\n\negs_brachy Spectrum Scoring Information\n%s\n\n",string(80,'=').c_str());
+
1241 header_printed = true;
+
1242 }
+
1243
+
1244 BaseSpectrumScorer *scorer = BaseSpectrumScorer::getSpectrumScorer(spec_inp, source, &ginfo, &pevent_pub);
+
1245
+
1246 if (scorer) {
+
1247 spectrum_scorers.push_back(scorer);
+
1248 egsInformation("Added scorer with title: %s\n", scorer->getInfo().c_str());
+
1249 }
+
1250 delete spec_inp;
+
1251 }
+
1252}
+
+
1253
+
+
1254void EB_Application::clearAusgabCalls() {
+
1255 for (size_t call=BeforeTransport; call <= UnknownCall; call++) {
+
1256 setAusgabCall((AusgabCall)call, false);
+
1257 }
1258
-
1259 vector<string> choices;
-
1260 choices.push_back("no");
-
1261 choices.push_back("yes");
+
1259}
+
+
1260
+
+
1261void EB_Application::initAusgabCalls() {
1262
-
1263 score_tlen = scoring_options->getInput("score tracklength dose", choices, 1);
-
1264
-
1265 if (score_tlen) {
-
1266 for (size_t p=0; p < phantom_geoms.size(); p++) {
-
1267 phantom_geoms[p]->enableTLenScoring();
-
1268 }
-
1269 initMuenData(scoring_options);
-
1270 }
+
1263
+
1264 clearAusgabCalls();
+
1265
+
1266 AusgabCall always_call[] = {BeforeTransport, AfterTransport, FluorescentEvent};
+
1267 enableAusgabCalls(3, always_call);
+
1268
+
1269}
+
+
1270
1271
-
1272}
-
1273
-
1274map<string, string> getMuenForMedia(EGS_Input *scoring_options) {
-
1275
-
1276 map<string, string> muen_for_med;
-
1277
-
1278 vector<string> muen_meds;
-
1279 scoring_options->getInput("muen for media", muen_meds);
+
1272
+
+
1273void EB_Application::initTrackLengthScoring(EGS_Input *scoring_options) {
+
1274
+
1275 vector<string> choices;
+
1276 choices.push_back("no");
+
1277 choices.push_back("yes");
+
1278
+
1279 score_tlen = scoring_options->getInput("score tracklength dose", choices, 1);
1280
-
1281 for (size_t i=0; i < muen_meds.size(); i++) {
-
1282 string med_name = muen_meds[i];
-
1283 muen_for_med[med_name] = med_name;
-
1284 };
-
1285
-
1286 EGS_Input *muen_inp;
-
1287 while ((muen_inp = scoring_options->takeInputItem("muen for medium"))) {
-
1288 string scoring, transport;
-
1289 int err = muen_inp->getInput("transport medium", transport);
-
1290 if (err) {
-
1291 egsFatal("Missing 'transport medium' key in 'muen for medium' block\n");
-
1292 delete muen_inp;
-
1293 }
-
1294 err = muen_inp->getInput("scoring medium", scoring);
-
1295 if (err) {
-
1296 egsFatal("Missing 'scoring medium' key in 'muen for medium' block\n");
-
1297 delete muen_inp;
-
1298 }
-
1299
-
1300 muen_for_med[transport] = scoring;
+
1281 if (score_tlen) {
+
1282 for (size_t p=0; p < phantom_geoms.size(); p++) {
+
1283 phantom_geoms[p]->enableTLenScoring();
+
1284 }
+
1285 initMuenData(scoring_options);
+
1286 }
+
1287
+
1288}
+
+
1289
+
+
1290map<string, string> getMuenForMedia(EGS_Input *scoring_options) {
+
1291
+
1292 map<string, string> muen_for_med;
+
1293
+
1294 vector<string> muen_meds;
+
1295 scoring_options->getInput("muen for media", muen_meds);
+
1296
+
1297 for (size_t i=0; i < muen_meds.size(); i++) {
+
1298 string med_name = muen_meds[i];
+
1299 muen_for_med[med_name] = med_name;
+
1300 };
1301
-
1302 delete muen_inp;
-
1303 }
-
1304
-
1305 return muen_for_med;
-
1306
-
1307}
-
1308
-
1309void EB_Application::initMuenData(EGS_Input *scoring_options) {
-
1310
-
1311 egsInformation("\n\negs_brachy Muen Data Information\n%s\n\n",string(80,'=').c_str());
-
1312
-
1313 string muen_file;
-
1314 bool missing_muen = scoring_options->getInput("muen file", muen_file) != 0;
-
1315 if (missing_muen) {
-
1316 egsFatal("\n\nMissing input scoring options: muen file\n\n This is a fatal error\n\n");
-
1317 }
-
1318
-
1319 // transport med name -> scoring med name
-
1320 media_muen_names = getMuenForMedia(scoring_options);
-
1321
-
1322 if (media_muen_names.size()==0) {
-
1323 egsWarning(
-
1324 "EB_Application:: missing or invalid 'muen for media' input item or 'muen substitution' block(s).\n"
-
1325 " No muen data has been read.\n"
-
1326 );
-
1327 }
+
1302 EGS_Input *muen_inp;
+
1303 while ((muen_inp = scoring_options->takeInputItem("muen for medium"))) {
+
1304 string scoring, transport;
+
1305 int err = muen_inp->getInput("transport medium", transport);
+
1306 if (err) {
+
1307 egsFatal("Missing 'transport medium' key in 'muen for medium' block\n");
+
1308 delete muen_inp;
+
1309 }
+
1310 err = muen_inp->getInput("scoring medium", scoring);
+
1311 if (err) {
+
1312 egsFatal("Missing 'scoring medium' key in 'muen for medium' block\n");
+
1313 delete muen_inp;
+
1314 }
+
1315
+
1316 muen_for_med[transport] = scoring;
+
1317
+
1318 delete muen_inp;
+
1319 }
+
1320
+
1321 return muen_for_med;
+
1322
+
1323}
+
+
1324
+
+
1325void EB_Application::initMuenData(EGS_Input *scoring_options) {
+
1326
+
1327 egsInformation("\n\negs_brachy Muen Data Information\n%s\n\n",string(80,'=').c_str());
1328
-
1329 // read muen data file and set media_muen for all media requested
-
1330 muen::MuenDataParser dp;
-
1331 int err = dp.setMuenFile(muen_file);
-
1332 if (err) {
-
1333 egsFatal("Failed to read muen data from %s\n",muen_file.c_str());
-
1334 }
-
1335
-
1336 egsInformation("Read muen data from %s\n", muen_file.c_str());
+
1329 string muen_file;
+
1330 bool missing_muen = scoring_options->getInput("muen file", muen_file) != 0;
+
1331 if (missing_muen) {
+
1332 egsFatal("\n\nMissing input scoring options: muen file\n\n This is a fatal error\n\n");
+
1333 }
+
1334
+
1335 // transport med name -> scoring med name
+
1336 media_muen_names = getMuenForMedia(scoring_options);
1337
-
1338 map<string, string>::iterator mit = media_muen_names.begin();
-
1339 for (; mit != media_muen_names.end(); mit++) {
-
1340
-
1341 string transport_med = mit->first;
-
1342 string scoring_med = mit->second;
-
1343 EGS_Interpolator *tmp_muen = dp.getMuenInterpolator(scoring_med);
-
1344 if (!tmp_muen) {
-
1345 egsFatal("EB_Application::Failed to get muen interpolator for %s\n", scoring_med.c_str());
-
1346 }
-
1347
-
1348 int med_idx = EGS_BaseGeometry::getMediumIndex(transport_med);
-
1349 if (med_idx < 0) {
-
1350 egsFatal(
-
1351 "EB_Application:: You requested scoring medium %s for transport medium %s but %s"
-
1352 " is not present in the geometry\n", scoring_med.c_str(), transport_med.c_str(), transport_med.c_str()
-
1353 );
-
1354 }
-
1355
-
1356 media_muen[med_idx] = tmp_muen;
-
1357 egsInformation(
-
1358 "Set medium %d (%s) to use muen data: %s\n",
-
1359 med_idx, transport_med.c_str(), scoring_med.c_str()
-
1360 );
-
1361 }
-
1362
+
1338 if (media_muen_names.size()==0) {
+
1339 egsWarning(
+
1340 "EB_Application:: missing or invalid 'muen for media' input item or 'muen substitution' block(s).\n"
+
1341 " No muen data has been read.\n"
+
1342 );
+
1343 }
+
1344
+
1345 // read muen data file and set media_muen for all media requested
+
1346 muen::MuenDataParser dp;
+
1347 int err = dp.setMuenFile(muen_file);
+
1348 if (err) {
+
1349 egsFatal("Failed to read muen data from %s\n",muen_file.c_str());
+
1350 }
+
1351
+
1352 egsInformation("Read muen data from %s\n", muen_file.c_str());
+
1353
+
1354 map<string, string>::iterator mit = media_muen_names.begin();
+
1355 for (; mit != media_muen_names.end(); mit++) {
+
1356
+
1357 string transport_med = mit->first;
+
1358 string scoring_med = mit->second;
+
1359 EGS_Interpolator *tmp_muen = dp.getMuenInterpolator(scoring_med);
+
1360 if (!tmp_muen) {
+
1361 egsFatal("EB_Application::Failed to get muen interpolator for %s\n", scoring_med.c_str());
+
1362 }
1363
-
1364}
-
1365
-
1366void EB_Application::enableAusgabCalls(int ncalls, AusgabCall calls[]) {
-
1367 for (int i= 0; i < ncalls; i++) {
-
1368 setAusgabCall(calls[i], true);
-
1369 }
-
1370
-
1371}
-
1372
-
1373void EB_Application::initEDepScoring(EGS_Input *scoring_options) {
-
1374 // Set up energy deposition scoring if requested by user
-
1375
-
1376 vector<string> choices;
-
1377 choices.push_back("no");
-
1378 choices.push_back("yes");
+
1364 int med_idx = EGS_BaseGeometry::getMediumIndex(transport_med);
+
1365 if (med_idx < 0) {
+
1366 egsFatal(
+
1367 "EB_Application:: You requested scoring medium %s for transport medium %s but %s"
+
1368 " is not present in the geometry\n", scoring_med.c_str(), transport_med.c_str(), transport_med.c_str()
+
1369 );
+
1370 }
+
1371
+
1372 media_muen[med_idx] = tmp_muen;
+
1373 egsInformation(
+
1374 "Set medium %d (%s) to use muen data: %s\n",
+
1375 med_idx, transport_med.c_str(), scoring_med.c_str()
+
1376 );
+
1377 }
+
1378
1379
-
1380 score_edep = scoring_options->getInput("score energy deposition", choices, 0);
+
1380}
+
1381
-
1382 if (score_edep) {
-
1383 for (size_t p=0; p < phantom_geoms.size(); p++) {
-
1384 phantom_geoms[p]->enableInteractionScoring();
-
1385 }
+
+
1382void EB_Application::enableAusgabCalls(int ncalls, AusgabCall calls[]) {
+
1383 for (int i= 0; i < ncalls; i++) {
+
1384 setAusgabCall(calls[i], true);
+
1385 }
1386
-
1387 AusgabCall edep_calls[] = {ExtraEnergy, UserDiscard, PegsCut, EgsCut};
-
1388 enableAusgabCalls(4, edep_calls);
-
1389 }
-
1390}
+
1387}
+
+
1388
+
+
1389void EB_Application::initEDepScoring(EGS_Input *scoring_options) {
+
1390 // Set up energy deposition scoring if requested by user
1391
-
1392void EB_Application::initScatScoring(EGS_Input *scoring_options) {
-
1393 // Set up energy deposition scoring if requested by user
-
1394
-
1395 vector<string> choices;
-
1396 choices.push_back("no");
-
1397 choices.push_back("yes");
-
1398
-
1399 score_scat = scoring_options->getInput("score scatter dose", choices, 0);
-
1400 if (score_scat && !score_tlen) {
-
1401 egsFatal("Tracklength scoring must be enabled to score scatter dose\n");
-
1402 }
-
1403
-
1404 if (score_scat) {
-
1405
-
1406 for (size_t p=0; p < phantom_geoms.size(); p++) {
-
1407 phantom_geoms[p]->enableScatterScoring();
-
1408 }
-
1409
-
1410 AusgabCall photon_scat_calls[] = {
-
1411 AfterAnnihFlight, AfterAnnihRest,
-
1412 AfterPair, AfterCompton, AfterPhoto, AfterRayleigh,
-
1413 FluorescentEvent
-
1414 };
-
1415
-
1416 int ncalls = sizeof(photon_scat_calls)/sizeof(photon_scat_calls[0]);
-
1417 enableAusgabCalls(ncalls, photon_scat_calls);
+
1392 vector<string> choices;
+
1393 choices.push_back("no");
+
1394 choices.push_back("yes");
+
1395
+
1396 score_edep = scoring_options->getInput("score energy deposition", choices, 0);
+
1397
+
1398 if (score_edep) {
+
1399 for (size_t p=0; p < phantom_geoms.size(); p++) {
+
1400 phantom_geoms[p]->enableInteractionScoring();
+
1401 }
+
1402
+
1403 AusgabCall edep_calls[] = {ExtraEnergy, UserDiscard, PegsCut, EgsCut};
+
1404 enableAusgabCalls(4, edep_calls);
+
1405 }
+
1406}
+
+
1407
+
+
1408void EB_Application::initScatScoring(EGS_Input *scoring_options) {
+
1409 // Set up energy deposition scoring if requested by user
+
1410
+
1411 vector<string> choices;
+
1412 choices.push_back("no");
+
1413 choices.push_back("yes");
+
1414
+
1415 score_scat = scoring_options->getInput("score scatter dose", choices, 0);
+
1416 if (score_scat && !score_tlen) {
+
1417 egsFatal("\nPrimary-scatter dose scoring requires tracklength scoring. Please enable tracklength scoring or disable scatter dose scoring.\n");
1418 }
-
1419}
-
1420
-
1421void EB_Application::initDoseScaling(EGS_Input *scoring_options) {
-
1422
-
1423 EGS_Float scale = 1.;
-
1424
-
1425 int err = scoring_options->getInput("dose scaling factor", scale);
-
1426
-
1427 if (!err && scale > 0) {
-
1428 for (size_t p=0; p < phantom_geoms.size(); p++) {
-
1429 phantom_geoms[p]->setDoseScale(scale);
-
1430 }
-
1431 }
-
1432}
+
1419
+
1420 if (score_scat && (source_transforms.size() > 1)) {
+
1421 egsFatal("\nPrimary-scatter dose scoring is only available in simulations with a single source. Please simulate a single source or disable scatter dose scoring.\n");
+
1422 }
+
1423
+
1424 if (score_scat && is_phsp_source) {
+
1425 egsFatal("\nPrimary-scatter dose scoring is not available with phase-space sources. Please do not use a phase-space source or disable scatter dose scoring.\n");
+
1426 }
+
1427
+
1428 if (score_scat) {
+
1429
+
1430 for (size_t p=0; p < phantom_geoms.size(); p++) {
+
1431 phantom_geoms[p]->enableScatterScoring();
+
1432 }
1433
-
1434void EB_Application::initXCCScaling(EGS_Input *scoring_options) {
-
1435
-
1436 EGS_Input *scale;
-
1437
-
1438 while ((scale = scoring_options->takeInputItem("scale xcc"))) {
-
1439 vector<string> tmp;
-
1440 int err = scale->getInput("scale xcc",tmp);
-
1441 //egsInformation("Found 'scale xcc', err=%d tmp.size()=%d\n",err,tmp.size());
-
1442 if (!err && tmp.size() == 2) {
-
1443 int imed = EGS_BaseGeometry::getMediumIndex(tmp[0]) + 1;
-
1444 if (imed > 0) {
-
1445 EGS_Float fac = atof(tmp[1].c_str());
-
1446 egsInformation("\n ***** Scaling xcc of medium %d with %G\n",imed,fac);
-
1447 F77_OBJ_(egs_scale_xcc,EGS_SCALE_XCC)(&imed,&fac);
-
1448 }
-
1449 }
-
1450 delete scale;
-
1451 }
-
1452
-
1453 while ((scale = scoring_options->takeInputItem("scale bc"))) {
-
1454 vector<string> tmp;
-
1455 int err = scale->getInput("scale bc",tmp);
-
1456 //egsInformation("Found 'scale xcc', err=%d tmp.size()=%d\n",err,tmp.size());
-
1457 if (!err && tmp.size() == 2) {
-
1458 int imed = EGS_BaseGeometry::getMediumIndex(tmp[0]) + 1;
-
1459 if (imed > 0) {
-
1460 EGS_Float fac = atof(tmp[1].c_str());
-
1461 egsInformation("\n ***** Scaling bc of medium %d with %G\n",imed,fac);
-
1462 F77_OBJ_(egs_scale_bc,EGS_SCALE_BC)(&imed,&fac);
-
1463 }
-
1464 }
-
1465 delete scale;
-
1466 }
-
1467}
-
1468
-
1469
-
1470void EB_Application::copyParticleToSourceLoc(EGS_Particle *p, int source, bool kill_orig, bool rotate,
-
1471 EGS_Float new_wt) {
-
1472
-
1473 // copy current location of particle
-
1474 EGS_Vector new_loc(p->x);
-
1475 EGS_Vector new_dir(p->u);
+
1434 AusgabCall photon_scat_calls[] = {
+
1435 AfterAnnihFlight, AfterAnnihRest,
+
1436 AfterPair, AfterCompton, AfterPhoto, AfterRayleigh,
+
1437 FluorescentEvent
+
1438 };
+
1439
+
1440 int ncalls = sizeof(photon_scat_calls)/sizeof(photon_scat_calls[0]);
+
1441 enableAusgabCalls(ncalls, photon_scat_calls);
+
1442 }
+
1443}
+
+
1444
+
+
1445void EB_Application::initDoseScaling(EGS_Input *scoring_options) {
+
1446
+
1447 EGS_Float scale = 1.;
+
1448
+
1449 int err = scoring_options->getInput("dose scaling factor", scale);
+
1450
+
1451 if (!err && scale > 0) {
+
1452 for (size_t p=0; p < phantom_geoms.size(); p++) {
+
1453 phantom_geoms[p]->setDoseScale(scale);
+
1454 }
+
1455 }
+
1456}
+
+
1457
+
+
1458void EB_Application::initXCCScaling(EGS_Input *scoring_options) {
+
1459
+
1460 EGS_Input *scale;
+
1461
+
1462 while ((scale = scoring_options->takeInputItem("scale xcc"))) {
+
1463 vector<string> tmp;
+
1464 int err = scale->getInput("scale xcc",tmp);
+
1465 //egsInformation("Found 'scale xcc', err=%d tmp.size()=%d\n",err,tmp.size());
+
1466 if (!err && tmp.size() == 2) {
+
1467 int imed = EGS_BaseGeometry::getMediumIndex(tmp[0]) + 1;
+
1468 if (imed > 0) {
+
1469 EGS_Float fac = atof(tmp[1].c_str());
+
1470 egsInformation("\n ***** Scaling xcc of medium %d with %G\n",imed,fac);
+
1471 F77_OBJ_(egs_scale_xcc,EGS_SCALE_XCC)(&imed,&fac);
+
1472 }
+
1473 }
+
1474 delete scale;
+
1475 }
1476
-
1477 // first move back to non transformed location
-
1478 base_transform_inv->transform(new_loc);
-
1479 base_transform_inv->rotate(new_dir);
-
1480
-
1481 if (rotate) {
-
1482 double angle = 2*M_PI*rndm->getUniform();
-
1483 EGS_RotationMatrix rot = EGS_RotationMatrix::rotZ(angle);
-
1484 new_loc *= rot;
-
1485 new_dir *= rot;
-
1486 }
-
1487
-
1488 // now transform particle to position of requested source
-
1489 source_transforms[source]->transform(new_loc);
-
1490 source_transforms[source]->rotate(new_dir);
-
1491
-
1492 // where is new particle
-
1493 int new_reg = geometry->isWhere(new_loc);
-
1494 int new_med = geometry->medium(new_reg);
-
1495
-
1496 // add a new particle to top of stack
-
1497
-
1498 int cur_np = the_stack->np;
-
1499 int new_np = the_stack->np+1;
-
1500 int np_idx = new_np-1;
-
1501
-
1502 the_stack->ir[np_idx] = new_reg + 2;
-
1503 the_stack->latch[np_idx] = p->latch;
-
1504 the_stack->E[np_idx] = p->E;
-
1505 the_stack->wt[np_idx] = new_wt;;
-
1506 the_stack->iq[np_idx] = p->q;
-
1507 the_stack->x[np_idx] = new_loc.x;
-
1508 the_stack->y[np_idx] = new_loc.y;
-
1509 the_stack->z[np_idx] = new_loc.z;
-
1510 the_stack->u[np_idx] = new_dir.x;
-
1511 the_stack->v[np_idx] = new_dir.y;
-
1512 the_stack->w[np_idx] = new_dir.z;
-
1513 the_stack->dnear[np_idx] = 0; // set to 0 because this move happens at boundary
-
1514
-
1515 the_stack->np += 1;
-
1516 the_stack->npold = cur_np;
-
1517
-
1518 the_epcont->irnew = new_reg+2;
-
1519 the_useful->medium_new = new_med+1;
-
1520
-
1521 enterNewRegion();
-
1522
-
1523 if (kill_orig) {
-
1524 the_stack->wt[np_idx-1] = 0;
-
1525 p->wt = 0;
-
1526 }
-
1527}
-
1528
-
1529void EB_Application::startNewParticle() {
-
1530
-
1531 EGS_AdvancedApplication::startNewParticle();
-
1532
-
1533 int ireg = the_stack->ir[the_stack->np-1] - 2;
-
1534 if (ginfo.isSource(ireg)) {
-
1535 the_bounds->ecut = source_ecut;
-
1536 the_bounds->pcut = source_pcut;
-
1537 } else {
-
1538 the_bounds->ecut = global_ecut;
-
1539 the_bounds->pcut = global_pcut;
-
1540 }
+
1477 while ((scale = scoring_options->takeInputItem("scale bc"))) {
+
1478 vector<string> tmp;
+
1479 int err = scale->getInput("scale bc",tmp);
+
1480 //egsInformation("Found 'scale xcc', err=%d tmp.size()=%d\n",err,tmp.size());
+
1481 if (!err && tmp.size() == 2) {
+
1482 int imed = EGS_BaseGeometry::getMediumIndex(tmp[0]) + 1;
+
1483 if (imed > 0) {
+
1484 EGS_Float fac = atof(tmp[1].c_str());
+
1485 egsInformation("\n ***** Scaling bc of medium %d with %G\n",imed,fac);
+
1486 F77_OBJ_(egs_scale_bc,EGS_SCALE_BC)(&imed,&fac);
+
1487 }
+
1488 }
+
1489 delete scale;
+
1490 }
+
1491}
+
+
1492
+
1493
+
+
1494void EB_Application::copyParticleToSourceLoc(EGS_Particle *p, int source, bool kill_orig, bool rotate,
+
1495 EGS_Float new_wt) {
+
1496
+
1497 // copy current location of particle
+
1498 EGS_Vector new_loc(p->x);
+
1499 EGS_Vector new_dir(p->u);
+
1500
+
1501 // first move back to non transformed location
+
1502 base_transform_inv->transform(new_loc);
+
1503 base_transform_inv->rotate(new_dir);
+
1504
+
1505 if (rotate) {
+
1506 double angle = 2*M_PI*rndm->getUniform();
+
1507 EGS_RotationMatrix rot = EGS_RotationMatrix::rotZ(angle);
+
1508 new_loc *= rot;
+
1509 new_dir *= rot;
+
1510 }
+
1511
+
1512 // now transform particle to position of requested source
+
1513 source_transforms[source]->transform(new_loc);
+
1514 source_transforms[source]->rotate(new_dir);
+
1515
+
1516 // where is new particle
+
1517 int new_reg = geometry->isWhere(new_loc);
+
1518 int new_med = geometry->medium(new_reg);
+
1519
+
1520 // add a new particle to top of stack
+
1521
+
1522 int cur_np = the_stack->np;
+
1523 int new_np = the_stack->np+1;
+
1524 int np_idx = new_np-1;
+
1525
+
1526 the_stack->ir[np_idx] = new_reg + 2;
+
1527 the_stack->latch[np_idx] = p->latch;
+
1528 the_stack->E[np_idx] = p->E;
+
1529 the_stack->wt[np_idx] = new_wt;;
+
1530 the_stack->iq[np_idx] = p->q;
+
1531 the_stack->x[np_idx] = new_loc.x;
+
1532 the_stack->y[np_idx] = new_loc.y;
+
1533 the_stack->z[np_idx] = new_loc.z;
+
1534 the_stack->u[np_idx] = new_dir.x;
+
1535 the_stack->v[np_idx] = new_dir.y;
+
1536 the_stack->w[np_idx] = new_dir.z;
+
1537 the_stack->dnear[np_idx] = 0; // set to 0 because this move happens at boundary
+
1538
+
1539 the_stack->np += 1;
+
1540 the_stack->npold = cur_np;
1541
-
1542}
-
1543
-
1544void EB_Application::enterNewRegion() {
-
1545
-
1546 EGS_AdvancedApplication::enterNewRegion();
-
1547
-
1548 int ireg = the_epcont->irnew-2;
-
1549 if (ginfo.isSource(ireg)) {
-
1550 the_bounds->ecut_new = source_ecut;
-
1551 the_bounds->pcut_new = source_pcut;
-
1552 the_egsvr->i_do_rr = source_i_do_rr;
-
1553 the_egsvr->e_max_rr = source_e_max_rr;
-
1554 } else {
-
1555 the_bounds->ecut_new = global_ecut;
-
1556 the_bounds->pcut_new = global_pcut;
-
1557 the_egsvr->i_do_rr = global_i_do_rr;
-
1558 the_egsvr->e_max_rr = global_e_max_rr;
-
1559 }
-
1560
-
1561}
-
1562
-
1563void EB_Application::discardTopParticle(int idisc) {
-
1564
-
1565 top_p.wt = 0;
-
1566 the_stack->wt[the_stack->np-1] = 0;
-
1567 the_epcont->idisc = idisc;
-
1568
-
1569}
-
1570
-
1571void EB_Application::addRecycledParticlesToStack(EGS_Particle *p, bool new_hist) {
-
1572
-
1573 if (!recycle_opts) {
-
1574 return;
-
1575 }
-
1576
-
1577 EGS_Float wt = p->wt/source_weights[active_source];
-
1578
-
1579 for (int recycle_idx=0; recycle_idx < recycle_opts->nrecycle; recycle_idx++) {
-
1580
-
1581 int start_loc, stop_loc;
-
1582
-
1583 if (run_mode == RM_SUPERPOSITION) {
-
1584 start_loc = active_source;
-
1585 stop_loc = start_loc + 1;
-
1586 } else {
-
1587 start_loc = 0;
-
1588 stop_loc = nsources;
-
1589 }
-
1590
-
1591 for (int source_loc = start_loc; source_loc < stop_loc; source_loc++) {
-
1592 // we only want to kill the original particle if this is not
-
1593 // new history from phsp
-
1594 bool kill = source_loc == start_loc && recycle_idx == 0 && !new_hist;
-
1595 EGS_Float new_wt = wt*source_weights[source_loc];
-
1596 copyParticleToSourceLoc(p, source_loc, kill, recycle_opts->rotate, new_wt);
-
1597 }
-
1598 }
-
1599
+
1542 the_epcont->irnew = new_reg+2;
+
1543 the_useful->medium_new = new_med+1;
+
1544
+
1545 enterNewRegion();
+
1546
+
1547 if (kill_orig) {
+
1548 the_stack->wt[np_idx-1] = 0;
+
1549 p->wt = 0;
+
1550 }
+
1551}
+
+
1552
+
+
1553void EB_Application::startNewParticle() {
+
1554
+
1555 EGS_AdvancedApplication::startNewParticle();
+
1556
+
1557 int ireg = the_stack->ir[the_stack->np-1] - 2;
+
1558 if (ginfo.isSource(ireg)) {
+
1559 the_bounds->ecut = source_ecut;
+
1560 the_bounds->pcut = source_pcut;
+
1561 } else {
+
1562 the_bounds->ecut = global_ecut;
+
1563 the_bounds->pcut = global_pcut;
+
1564 }
+
1565
+
1566}
+
+
1567
+
+
1568void EB_Application::enterNewRegion() {
+
1569
+
1570 EGS_AdvancedApplication::enterNewRegion();
+
1571
+
1572 int ireg = the_epcont->irnew-2;
+
1573 if (ginfo.isSource(ireg)) {
+
1574 the_bounds->ecut_new = source_ecut;
+
1575 the_bounds->pcut_new = source_pcut;
+
1576 the_egsvr->i_do_rr = source_i_do_rr;
+
1577 the_egsvr->e_max_rr = source_e_max_rr;
+
1578 } else {
+
1579 the_bounds->ecut_new = global_ecut;
+
1580 the_bounds->pcut_new = global_pcut;
+
1581 the_egsvr->i_do_rr = global_i_do_rr;
+
1582 the_egsvr->e_max_rr = global_e_max_rr;
+
1583 }
+
1584
+
1585}
+
+
1586
+
+
1587void EB_Application::discardTopParticle(int idisc) {
+
1588
+
1589 top_p.wt = 0;
+
1590 the_stack->wt[the_stack->np-1] = 0;
+
1591 the_epcont->idisc = idisc;
+
1592
+
1593}
+
+
1594
+
+
1595void EB_Application::addRecycledParticlesToStack(EGS_Particle *p, bool new_hist) {
+
1596
+
1597 if (!recycle_opts) {
+
1598 return;
+
1599 }
1600
-
1601}
+
1601 EGS_Float wt = p->wt/source_weights[active_source];
1602
-
1603bool EB_Application::isStuck() {
+
1603 for (int recycle_idx=0; recycle_idx < recycle_opts->nrecycle; recycle_idx++) {
1604
-
1605 /* if particle number has changed, reset the stuck particle counter so that
-
1606 * particles generated from splitting don't trigger same position error */
-
1607 bool same_particle = the_stack->npold == the_stack->np;
-
1608 if (!same_particle){
-
1609 steps_at_same_loc = 0;
-
1610 return false;
-
1611 }
-
1612
-
1613 cur_R = top_p.x.length2();
-
1614 bool in_same_pos = fabs(cur_R - last_R) < SAME_POSITION_TOLERANCE;
-
1615 if (in_same_pos) {
-
1616 steps_at_same_loc++;
-
1617 }
-
1618 last_R = cur_R;
-
1619
-
1620 if (steps_at_same_loc > NUM_STUCK_STEPS) {
-
1621 //PRINT_PARTICLE(top_p);
-
1622 egsWarning("Particle hasn't moved in %d steps. Discarding particle\n", NUM_STUCK_STEPS);
-
1623 printParticleWithSpherical(top_p);
-
1624 n_stuck++;
-
1625 discardTopParticle();
+
1605 int start_loc, stop_loc;
+
1606
+
1607 if (run_mode == RM_SUPERPOSITION) {
+
1608 start_loc = active_source;
+
1609 stop_loc = start_loc + 1;
+
1610 } else {
+
1611 start_loc = 0;
+
1612 stop_loc = nsources;
+
1613 }
+
1614
+
1615 for (int source_loc = start_loc; source_loc < stop_loc; source_loc++) {
+
1616 // we only want to kill the original particle if this is not
+
1617 // new history from phsp
+
1618 bool kill = source_loc == start_loc && recycle_idx == 0 && !new_hist;
+
1619 EGS_Float new_wt = wt*source_weights[source_loc];
+
1620 copyParticleToSourceLoc(p, source_loc, kill, recycle_opts->rotate, new_wt);
+
1621 }
+
1622 }
+
1623
+
1624
+
1625}
+
1626
-
1627 return true;
-
1628 }
-
1629 return false;
-
1630
-
1631}
-
1632
-
1633int EB_Application::ausgab(int iarg) {
-
1634
-
1635 bool is_photon = top_p.q == 0;
-
1636 bool is_before_transport = iarg == BeforeTransport;
-
1637 bool is_after_transport = iarg == AfterTransport;
-
1638
-
1639 if (is_after_transport && isStuck()) {
-
1640 the_stack->latch[the_stack->np - 1] = top_p.latch;
-
1641 return 1;
-
1642 }
+
+
1627bool EB_Application::isStuck() {
+
1628
+
1629 /* if particle number has changed, reset the stuck particle counter so that
+
1630 * particles generated from splitting don't trigger same position error */
+
1631 bool same_particle = the_stack->npold == the_stack->np;
+
1632 if (!same_particle){
+
1633 steps_at_same_loc = 0;
+
1634 return false;
+
1635 }
+
1636
+
1637 cur_R = top_p.x.length2();
+
1638 bool in_same_pos = fabs(cur_R - last_R) < SAME_POSITION_TOLERANCE;
+
1639 if (in_same_pos) {
+
1640 steps_at_same_loc++;
+
1641 }
+
1642 last_R = cur_R;
1643
-
1644 int global_ir = top_p.ir;
-
1645 int irnew = the_epcont->irnew-2;
-
1646 int irold = the_epcont->irold-2;
-
1647
-
1648 bool in_phantom = ginfo.isPhantom(global_ir);
-
1649 bool in_source = ginfo.isSource(global_ir);
+
1644 if (steps_at_same_loc > NUM_STUCK_STEPS) {
+
1645 //PRINT_PARTICLE(top_p);
+
1646 egsWarning("Particle hasn't moved in %d steps. Discarding particle\n", NUM_STUCK_STEPS);
+
1647 printParticleWithSpherical(top_p);
+
1648 n_stuck++;
+
1649 discardTopParticle();
1650
-
1651 bool is_extra_scoring_reg = false;
-
1652 string local_geom_name = "";
-
1653 int local_geom_ir = -1;
-
1654 int extra_reg_dose_index = -1;
-
1655
-
1656 if (extra_scoring_reg.size() > 0 && global_ir >= 0){
-
1657
-
1658 // local geom object info
-
1659 GeomRegT local = ginfo.globalToLocal(global_ir);
-
1660 local_geom_ir = local.second;
-
1661 local_geom_name = local.first->getName();
+
1651 return true;
+
1652 }
+
1653 return false;
+
1654
+
1655}
+
+
1656
+
+
1657int EB_Application::ausgab(int iarg) {
+
1658
+
1659 bool is_photon = top_p.q == 0;
+
1660 bool is_before_transport = iarg == BeforeTransport;
+
1661 bool is_after_transport = iarg == AfterTransport;
1662
-
1663 // check if the current geometry has extra scoring regions
-
1664 map<string, vector<int> >::iterator i = extra_scoring_reg.find(local_geom_name);
-
1665 if (i != extra_scoring_reg.end()){
-
1666 vector<int>::iterator it = find(i->second.begin(), i->second.end(), local_geom_ir);
-
1667 if (it != i->second.end()){
-
1668 is_extra_scoring_reg = true;
-
1669 extra_reg_dose_index = distance(i->second.begin(), it);
-
1670 }
-
1671 }
-
1672 }
-
1673
-
1674 /* track number of steps */
-
1675 if (is_before_transport) {
-
1676 if (in_source) {
-
1677 steps_in_sources[top_p.q]++;
-
1678 } else if (in_phantom) {
-
1679 steps_in_phantoms[top_p.q]++;
-
1680 } else {
-
1681 steps_in_other[top_p.q]++;
-
1682 }
-
1683 }
-
1684
-
1685 /* Fluorescent photon cutoff */
-
1686 bool discard_fluorescent = iarg == FluorescentEvent && top_p.E <= flu_cutoff;
-
1687 if (discard_fluorescent) {
-
1688 discardTopParticle();
-
1689 the_stack->latch[the_stack->np - 1] = top_p.latch;
-
1690 return 0;
-
1691 }
-
1692
-
1693 /* track scattering with latch bits if required */
-
1694 if (score_scat && (iarg > AfterTransport) && !in_source) {
-
1695 latch_control.addScatter(&top_p);
-
1696 for (int ip=the_stack->npold-1; ip < the_stack->np; ip++) {
-
1697 latch_control.addScatter(the_stack->latch[ip]);
-
1698 }
-
1699 }
-
1700
-
1701 bool next_is_source = ginfo.isSource(irnew);
-
1702 bool last_was_source = ginfo.isSource(irold);
-
1703
-
1704 /* note a particle leaving source could be a particle that has re-entered a
-
1705 * source. escaping_source will only be true on first time leaving source*/
-
1706 bool leaving_source = is_before_transport && in_source && !next_is_source;
-
1707 bool escaping_source = leaving_source && !latch_control.hasEscaped(&top_p);
+
1663 if (is_after_transport && isStuck()) {
+
1664 the_stack->latch[the_stack->np - 1] = top_p.latch;
+
1665 return 1;
+
1666 }
+
1667
+
1668 int global_ir = top_p.ir;
+
1669 int irnew = the_epcont->irnew-2;
+
1670 int irold = the_epcont->irold-2;
+
1671
+
1672 bool in_phantom = ginfo.isPhantom(global_ir);
+
1673 bool in_source = ginfo.isSource(global_ir);
+
1674
+
1675 bool is_extra_scoring_reg = false;
+
1676 string local_geom_name = "";
+
1677 int local_geom_ir = -1;
+
1678 int extra_reg_dose_index = -1;
+
1679
+
1680 if (extra_scoring_reg.size() > 0 && global_ir >= 0){
+
1681
+
1682 // local geom object info
+
1683 GeomRegT local = ginfo.globalToLocal(global_ir);
+
1684 local_geom_ir = local.second;
+
1685 local_geom_name = local.first->getName();
+
1686
+
1687 // check if the current geometry has extra scoring regions
+
1688 map<string, vector<int> >::iterator i = extra_scoring_reg.find(local_geom_name);
+
1689 if (i != extra_scoring_reg.end()){
+
1690 vector<int>::iterator it = find(i->second.begin(), i->second.end(), local_geom_ir);
+
1691 if (it != i->second.end()){
+
1692 is_extra_scoring_reg = true;
+
1693 extra_reg_dose_index = distance(i->second.begin(), it);
+
1694 }
+
1695 }
+
1696 }
+
1697
+
1698 /* track number of steps */
+
1699 if (is_before_transport) {
+
1700 if (in_source) {
+
1701 steps_in_sources[top_p.q]++;
+
1702 } else if (in_phantom) {
+
1703 steps_in_phantoms[top_p.q]++;
+
1704 } else {
+
1705 steps_in_other[top_p.q]++;
+
1706 }
+
1707 }
1708
-
1709 /* same as leaving/escaping but for after transport rather than before*/
-
1710 bool left_source = is_after_transport && !in_source && last_was_source;
-
1711 bool escaped_source = left_source && !latch_control.hasEscaped(&top_p);
-
1712
-
1713 bool escaping_geom = is_before_transport && irnew < 0;
-
1714 bool escaped_geom = global_ir < 0;
-
1715
+
1709 /* Fluorescent photon cutoff */
+
1710 bool discard_fluorescent = iarg == FluorescentEvent && top_p.E <= flu_cutoff;
+
1711 if (discard_fluorescent) {
+
1712 discardTopParticle();
+
1713 the_stack->latch[the_stack->np - 1] = top_p.latch;
+
1714 return 0;
+
1715 }
1716
-
1717 /* these notifications may be used by subscribers like spectrum
-
1718 * scoring objects, latch control etc */
-
1719 EBSendMessage send_messages[] = {
-
1720 EBSendMessage(is_before_transport, PARTICLE_TAKING_STEP),
-
1721 EBSendMessage(is_after_transport, PARTICLE_TOOK_STEP),
-
1722 EBSendMessage(escaping_source, PARTICLE_ESCAPING_SOURCE),
-
1723 EBSendMessage(escaped_source, PARTICLE_ESCAPED_SOURCE),
-
1724 EBSendMessage(escaping_geom, PARTICLE_ESCAPING_GEOM),
-
1725 EBSendMessage(escaped_geom, PARTICLE_ESCAPED_GEOM)
-
1726 };
-
1727 int nmesg = sizeof(send_messages)/sizeof(send_messages[0]);
-
1728 for (int m=0; m < nmesg; m++) {
-
1729 if (send_messages[m].first) {
-
1730 pevent_pub.notify(send_messages[m].second, &top_p);
-
1731 }
-
1732 }
-
1733
-
1734 /* copy the top_p.latch bit to the stack before returning from ausgab.
-
1735 * Since top_p.latch gets reset every step */
-
1736 the_stack->latch[the_stack->np - 1] = top_p.latch;
-
1737
-
1738 if (escaped_geom) {
-
1739 return 0;
-
1740 }
-
1741
-
1742 /* move particles to new locations if single generator or recycling */
-
1743 if (escaped_source && is_after_transport) {
-
1744
-
1745 EGS_Float wt = top_p.wt;
-
1746
-
1747 if (run_mode == RM_SUPERPOSITION) {
-
1748 superpos_geom->setActiveByIndex(active_source);
-
1749 }
-
1750
-
1751 if (recycle_opts) {
-
1752 addRecycledParticlesToStack(&top_p);
-
1753 } else if (single_generator && active_source > 0) {
-
1754 copyParticleToSourceLoc(&top_p, active_source, true, false, wt);
+
1717 /* track scattering with latch bits if required */
+
1718 if (score_scat && (iarg > AfterTransport) && !in_source) {
+
1719 latch_control.addScatter(&top_p);
+
1720 for (int ip=the_stack->npold-1; ip < the_stack->np; ip++) {
+
1721 latch_control.addScatter(the_stack->latch[ip]);
+
1722 }
+
1723 }
+
1724
+
1725 bool next_is_source = ginfo.isSource(irnew);
+
1726 bool last_was_source = ginfo.isSource(irold);
+
1727
+
1728 /* note a particle leaving source could be a particle that has re-entered a
+
1729 * source. escaping_source will only be true on first time leaving source*/
+
1730 bool leaving_source = is_before_transport && in_source && !next_is_source;
+
1731 bool escaping_source = leaving_source && !latch_control.hasEscaped(&top_p);
+
1732
+
1733 /* same as leaving/escaping but for after transport rather than before*/
+
1734 bool left_source = is_after_transport && !in_source && last_was_source;
+
1735 bool escaped_source = left_source && !latch_control.hasEscaped(&top_p);
+
1736
+
1737 bool escaping_geom = is_before_transport && irnew < 0;
+
1738 bool escaped_geom = global_ir < 0;
+
1739
+
1740
+
1741 /* these notifications may be used by subscribers like spectrum
+
1742 * scoring objects, latch control etc */
+
1743 EBSendMessage send_messages[] = {
+
1744 EBSendMessage(is_before_transport, PARTICLE_TAKING_STEP),
+
1745 EBSendMessage(is_after_transport, PARTICLE_TOOK_STEP),
+
1746 EBSendMessage(escaping_source, PARTICLE_ESCAPING_SOURCE),
+
1747 EBSendMessage(escaped_source, PARTICLE_ESCAPED_SOURCE),
+
1748 EBSendMessage(escaping_geom, PARTICLE_ESCAPING_GEOM),
+
1749 EBSendMessage(escaped_geom, PARTICLE_ESCAPED_GEOM)
+
1750 };
+
1751 int nmesg = sizeof(send_messages)/sizeof(send_messages[0]);
+
1752 for (int m=0; m < nmesg; m++) {
+
1753 if (send_messages[m].first) {
+
1754 pevent_pub.notify(send_messages[m].second, &top_p);
1755 }
-
1756
-
1757 return 0;
-
1758
-
1759 }
-
1760
-
1761 /* handle bcse and splitting */
-
1762 doPhotonSplitting(iarg);
-
1763
-
1764
-
1765 /* And finally below here we handle dose scoring */
-
1766 bool in_vaccuum = the_useful->medium <= 0;
-
1767 bool score_tracklength = score_tlen && is_photon && is_before_transport;
-
1768 bool score_interaction = score_edep && iarg <= ExtraEnergy;
-
1769 bool dose_scoring_not_needed = !is_extra_scoring_reg && (!in_phantom || in_vaccuum || !(score_tracklength || score_interaction));
+
1756 }
+
1757
+
1758 /* copy the top_p.latch bit to the stack before returning from ausgab.
+
1759 * Since top_p.latch gets reset every step */
+
1760 the_stack->latch[the_stack->np - 1] = top_p.latch;
+
1761
+
1762 if (escaped_geom) {
+
1763 return 0;
+
1764 }
+
1765
+
1766 /* move particles to new locations if single generator or recycling */
+
1767 if (escaped_source && is_after_transport) {
+
1768
+
1769 EGS_Float wt = top_p.wt;
1770
-
1771 if (dose_scoring_not_needed) {
-
1772 return 0;
-
1773 }
+
1771 if (run_mode == RM_SUPERPOSITION) {
+
1772 superpos_geom->setActiveByIndex(active_source);
+
1773 }
1774
-
1775
-
1776 // which phantom/region are we in
-
1777 int phant_idx = ginfo.phantomFromRegion(global_ir);
-
1778 int phant_ir = ginfo.globalToLocalReg(global_ir);
-
1779
-
1780 EB_Phantom *phant = phantom_geoms[phant_idx];
-
1781
-
1782 bool needs_vol_cor = run_mode == RM_SUPERPOSITION && superpos_geom->hasInactiveGeom(global_ir);
-
1783
+
1775 if (recycle_opts) {
+
1776 addRecycledParticlesToStack(&top_p);
+
1777 } else if (single_generator && active_source > 0) {
+
1778 copyParticleToSourceLoc(&top_p, active_source, true, false, wt);
+
1779 }
+
1780
+
1781 return 0;
+
1782
+
1783 }
1784
-
1785 if (score_tracklength) {
-
1786
-
1787 EGS_Interpolator *interp = media_muen[the_useful->medium-1];
-
1788 EGS_Float muen_val = interp ? interp->interpolateFast(the_epcont->gle) : 0;
-
1789 EGS_Float tracklength_edep = the_epcont->tvstep*top_p.E*muen_val*top_p.wt;
-
1790
-
1791 EGS_Float vol;
-
1792
-
1793 if (in_phantom){
-
1794 if (needs_vol_cor) {
-
1795 vol = phant->getUncorrectedVolume(phant_ir);
-
1796 } else {
-
1797 vol = phant->getCorrectedVolume(phant_ir);
-
1798 }
+
1785 /* handle bcse and splitting */
+
1786 doPhotonSplitting(iarg);
+
1787
+
1788
+
1789 /* And finally below here we handle dose scoring */
+
1790 bool in_vaccuum = the_useful->medium <= 0;
+
1791 bool score_tracklength = score_tlen && is_photon && is_before_transport;
+
1792 bool score_interaction = score_edep && iarg <= ExtraEnergy;
+
1793 bool dose_scoring_not_needed = !is_extra_scoring_reg && (!in_phantom || in_vaccuum || !(score_tracklength || score_interaction));
+
1794
+
1795 if (dose_scoring_not_needed) {
+
1796 return 0;
+
1797 }
+
1798
1799
-
1800 if (vol > 0) {
-
1801 phant->scoreTlen(phant_ir, tracklength_edep / vol, &top_p);
-
1802 }
-
1803 }
-
1804
-
1805 if (is_extra_scoring_reg){
-
1806 vol = extra_scoring_vols[local_geom_name][extra_reg_dose_index];
-
1807 extra_scoring_doses[local_geom_name]->score(extra_reg_dose_index, tracklength_edep / vol);
-
1808 }
-
1809 }
+
1800 // which phantom/region are we in
+
1801 int phant_idx = ginfo.phantomFromRegion(global_ir);
+
1802 int phant_ir = ginfo.globalToLocalReg(global_ir);
+
1803
+
1804 EB_Phantom *phant = phantom_geoms[phant_idx];
+
1805
+
1806 bool needs_vol_cor = run_mode == RM_SUPERPOSITION && superpos_geom->hasInactiveGeom(global_ir);
+
1807
+
1808
+
1809 if (score_tracklength) {
1810
-
1811 if (score_interaction) {
-
1812
-
1813 EGS_Float mass;
+
1811 EGS_Interpolator *interp = media_muen[the_useful->medium-1];
+
1812 EGS_Float muen_val = interp ? interp->interpolateFast(the_epcont->gle) : 0;
+
1813 EGS_Float tracklength_edep = the_epcont->tvstep*top_p.E*muen_val*top_p.wt;
1814
-
1815 EGS_Float edep = getEdep()*top_p.wt;
+
1815 EGS_Float vol;
1816
1817 if (in_phantom){
-
1818
-
1819 if(needs_vol_cor) {
-
1820 mass = phant->getUncorrectedMass(phant_ir);
-
1821 } else {
-
1822 mass = phant->getRealMass(phant_ir);
-
1823 }
-
1824
-
1825 if (mass > 0) {
-
1826 phant->scoreEdep(phant_ir, edep / mass);
-
1827 }
-
1828 }
-
1829
-
1830 if (is_extra_scoring_reg){
-
1831 mass = extra_scoring_mass[local_geom_name][extra_reg_dose_index];
-
1832 extra_scoring_doses[local_geom_name]->score(extra_reg_dose_index, edep / mass);
-
1833 }
-
1834 }
-
1835
-
1836 return 0;
-
1837}
+
1818 if (needs_vol_cor) {
+
1819 vol = phant->getUncorrectedVolume(phant_ir);
+
1820 } else {
+
1821 vol = phant->getCorrectedVolume(phant_ir);
+
1822 }
+
1823
+
1824 if (vol > 0) {
+
1825 phant->scoreTlen(phant_ir, tracklength_edep / vol, &top_p);
+
1826 }
+
1827 }
+
1828
+
1829 if (is_extra_scoring_reg){
+
1830 vol = extra_scoring_vols[local_geom_name][extra_reg_dose_index];
+
1831 extra_scoring_doses[local_geom_name]->score(extra_reg_dose_index, tracklength_edep / vol);
+
1832 }
+
1833 }
+
1834
+
1835 if (score_interaction) {
+
1836
+
1837 EGS_Float mass;
1838
-
1839void EB_Application::doPhotonSplitting(int iarg) {
+
1839 EGS_Float edep = getEdep()*top_p.wt;
1840
-
1841 bool is_phat = fabs(top_p.wt - 1.) < EB_EPSILON;
+
1841 if (in_phantom){
1842
-
1843 if (do_bcse) {
-
1844
-
1845 bool in_bcse_med = the_useful->medium - 1 == bcse_med_num;
-
1846
-
1847 if (iarg == BeforeBrems) {
-
1848 the_egsvr->nbr_split = do_brem_split ? nbr_split : 1;
-
1849 if (!in_bcse_med) {
-
1850 /* standard UBS for brem photons OUTSIDE MED_BCSE */
-
1851 the_egsvr->nbr_split *= (int)bcse_factor;
-
1852 }
-
1853 } else if (iarg == AfterBrems) {
-
1854 if (in_bcse_med) {
-
1855 /* Just came back from a brem event in MED_BCSE, reduce photon weight
-
1856 and play Russian Roulette to whether or not reduce electron energy */
-
1857 for (int ip=the_stack->npold; ip < the_stack->np; ip++) {
-
1858 the_stack->wt[ip] /= bcse_factor;
-
1859 }
-
1860 EGS_Float rnd = rndm->getUniform();
-
1861 if (rnd > 1./bcse_factor) {
-
1862 the_stack->E[the_stack->npold-1] += top_p.E;
-
1863 }
-
1864 } else {
-
1865 /* Turn off UBS after splitting that one fat brem photons outside MED_BCSE */
-
1866 the_egsvr->nbr_split = 1;
-
1867 }
+
1843 if(needs_vol_cor) {
+
1844 mass = phant->getUncorrectedMass(phant_ir);
+
1845 } else {
+
1846 mass = phant->getRealMass(phant_ir);
+
1847 }
+
1848
+
1849 if (mass > 0) {
+
1850 phant->scoreEdep(phant_ir, edep / mass);
+
1851 }
+
1852 }
+
1853
+
1854 if (is_extra_scoring_reg){
+
1855 mass = extra_scoring_mass[local_geom_name][extra_reg_dose_index];
+
1856 extra_scoring_doses[local_geom_name]->score(extra_reg_dose_index, edep / mass);
+
1857 }
+
1858 }
+
1859
+
1860 return 0;
+
1861}
+
+
1862
+
+
1863void EB_Application::doPhotonSplitting(int iarg) {
+
1864
+
1865 bool is_phat = fabs(top_p.wt - 1.) < EB_EPSILON;
+
1866
+
1867 if (do_bcse) {
1868
-
1869 } else if (iarg == FluorescentEvent && is_phat) {
+
1869 bool in_bcse_med = the_useful->medium - 1 == bcse_med_num;
1870
-
1871 /* Uniformly splits fat relaxation photons that are descendents of either:
-
1872 1. eii in MED_BCSE (usually MED_BCSE is the target) or, 2.
-
1873 back-scattered fat electrons that escaped target and interacted
-
1874 elsewhere (eii and photo) This is done using UNIFORM_PHOTONS */
-
1875
-
1876 int nsplit = do_brem_split ? (int)(bcse_factor*nbr_split) : (int)(bcse_factor);
-
1877 the_stack->npold = the_stack->np;
-
1878 F77_OBJ_(egs_uniform_photons, EGS_UNIFORM_PHOTONS)(&nsplit, &top_p.E);
-
1879
-
1880 }
-
1881
-
1882 } else if (do_brem_split && iarg == FluorescentEvent && is_phat) {
-
1883
-
1884 /* a fluorescent photon has just been put on the stack - split it */
-
1885 the_stack->npold = the_stack->np;
-
1886 F77_OBJ_(egs_uniform_photons, EGS_UNIFORM_PHOTONS)(&nbr_split, &top_p.E);
-
1887 }
-
1888
-
1889}
-
1890
-
1891void EB_Application::calcEffectiveHistories() {
+
1871 if (iarg == BeforeBrems) {
+
1872 the_egsvr->nbr_split = do_brem_split ? nbr_split : 1;
+
1873 if (!in_bcse_med) {
+
1874 /* standard UBS for brem photons OUTSIDE MED_BCSE */
+
1875 the_egsvr->nbr_split *= (int)bcse_factor;
+
1876 }
+
1877 } else if (iarg == AfterBrems) {
+
1878 if (in_bcse_med) {
+
1879 /* Just came back from a brem event in MED_BCSE, reduce photon weight
+
1880 and play Russian Roulette to whether or not reduce electron energy */
+
1881 for (int ip=the_stack->npold; ip < the_stack->np; ip++) {
+
1882 the_stack->wt[ip] /= bcse_factor;
+
1883 }
+
1884 EGS_Float rnd = rndm->getUniform();
+
1885 if (rnd > 1./bcse_factor) {
+
1886 the_stack->E[the_stack->npold-1] += top_p.E;
+
1887 }
+
1888 } else {
+
1889 /* Turn off UBS after splitting that one fat brem photons outside MED_BCSE */
+
1890 the_egsvr->nbr_split = 1;
+
1891 }
1892
-
1893 if (is_phsp_source) {
-
1894 effective_histories = source->getFluence();
-
1895 } else {
-
1896 effective_histories = last_case;
-
1897 }
-
1898
-
1899 if (recycle_opts) {
-
1900 if (run_mode == RM_SUPERPOSITION) {
-
1901 // only recycle at 1 source location in superposition mode
-
1902 effective_histories *= recycle_opts->nrecycle;
-
1903 } else {
-
1904 effective_histories *= recycle_opts->nrecycle*nsources;
-
1905 }
-
1906 }
-
1907}
-
1908
-
1909
-
1910void EB_Application::outputResults() {
-
1911 timing_blocks.addTimer("egs_brachy::outputResults");
+
1893 } else if (iarg == FluorescentEvent && is_phat) {
+
1894
+
1895 /* Uniformly splits fat relaxation photons that are descendents of either:
+
1896 1. eii in MED_BCSE (usually MED_BCSE is the target) or, 2.
+
1897 back-scattered fat electrons that escaped target and interacted
+
1898 elsewhere (eii and photo) This is done using UNIFORM_PHOTONS */
+
1899
+
1900 int nsplit = do_brem_split ? (int)(bcse_factor*nbr_split) : (int)(bcse_factor);
+
1901 the_stack->npold = the_stack->np;
+
1902 F77_OBJ_(egs_uniform_photons, EGS_UNIFORM_PHOTONS)(&nsplit, &top_p.E);
+
1903
+
1904 }
+
1905
+
1906 } else if (do_brem_split && iarg == FluorescentEvent && is_phat) {
+
1907
+
1908 /* a fluorescent photon has just been put on the stack - split it */
+
1909 the_stack->npold = the_stack->np;
+
1910 F77_OBJ_(egs_uniform_photons, EGS_UNIFORM_PHOTONS)(&nbr_split, &top_p.E);
+
1911 }
1912
-
1913 calcEffectiveHistories();
+
1913}
+
1914
-
1915 string sep(80, '=');
-
1916 egsInformation(
-
1917 "\n\nResults for egs_brachy run\n%s\n",
-
1918 string(80, '-').c_str()
-
1919 );
-
1920
-
1921
-
1922 egsInformation("\n\nHistory Information\n%s\n",sep.c_str());
-
1923 egsInformation("Last case = %llu\n", last_case);
-
1924 egsInformation("current case = %llu\n", current_case);
-
1925 egsInformation("run->getNcase() = %llu\n", run->getNcase());
-
1926 egsInformation("source->getFluence() = %f\n", source->getFluence());
-
1927 if (recycle_opts) {
-
1928 egsInformation("Particles recycled = %d\n", recycle_opts->nrecycle);
-
1929 }
-
1930 egsInformation("Effective histories = %.5G\n", effective_histories);
-
1931
+
+
1915void EB_Application::calcEffectiveHistories() {
+
1916
+
1917 if (is_phsp_source) {
+
1918 effective_histories = source->getFluence();
+
1919 } else {
+
1920 effective_histories = last_case;
+
1921 }
+
1922
+
1923 if (recycle_opts) {
+
1924 if (run_mode == RM_SUPERPOSITION) {
+
1925 // only recycle at 1 source location in superposition mode
+
1926 effective_histories *= recycle_opts->nrecycle;
+
1927 } else {
+
1928 effective_histories *= recycle_opts->nrecycle*nsources;
+
1929 }
+
1930 }
+
1931}
+
1932
-
1933 egsInformation("\n\nGeometry Errors\n%s\n", sep.c_str());
-
1934 egsInformation("Number of geometry errors (/max allowed) = %d / %d\n", run->geomErrorCount, run->geomErrorMax);
-
1935 egsInformation("Number of 'stuck' particles discarded = %llu\n", n_stuck);
+
1933
+
+
1934void EB_Application::outputResults() {
+
1935 timing_blocks.addTimer("egs_brachy::outputResults");
1936
-
1937
-
1938 // tell scoring objects how many histories were actually run
-
1939 // (needed for parallel run normalization)
-
1940 EGS_I64 hist_norm = run->getNdone();
-
1941 pevent_pub.notify(NEW_HISTORY, &hist_norm);
-
1942
-
1943 if (!single_generator) {
-
1944 egsInformation(
-
1945 "Warning: Stats about energy escaping source may not be accurate when "
-
1946 "not using a single source generator\n"
-
1947 );
-
1948 }
-
1949
-
1950 if (phsp) {
-
1951 phsp->finish(current_case);
-
1952 phsp->outputResults();
-
1953 phsp->destroySource();
-
1954 }
+
1937 calcEffectiveHistories();
+
1938
+
1939 string sep(80, '=');
+
1940 egsInformation(
+
1941 "\n\nResults for egs_brachy run\n%s\n",
+
1942 string(80, '-').c_str()
+
1943 );
+
1944
+
1945
+
1946 egsInformation("\n\nHistory Information\n%s\n",sep.c_str());
+
1947 egsInformation("Last case = %llu\n", last_case);
+
1948 egsInformation("current case = %llu\n", current_case);
+
1949 egsInformation("run->getNcase() = %llu\n", run->getNcase());
+
1950 egsInformation("source->getFluence() = %f\n", source->getFluence());
+
1951 if (recycle_opts) {
+
1952 egsInformation("Particles recycled = %d\n", recycle_opts->nrecycle);
+
1953 }
+
1954 egsInformation("Effective histories = %.5G\n", effective_histories);
1955
-
1956 if (escoring) {
-
1957 escoring->outputResults();
-
1958 }
-
1959
-
1960 if (spectrum_scorers.size() > 0) {
-
1961 egsInformation("\nSpectrum scoring results\n%s\n",sep.c_str());
-
1962 string root = constructIOFileName("", true);
-
1963 vector<BaseSpectrumScorer *>::iterator it = spectrum_scorers.begin();
-
1964 for (; it != spectrum_scorers.end(); it++) {
-
1965 (*it)->setEffectiveHistories(effective_histories);
-
1966 (*it)->outputResults(root);
-
1967 }
-
1968 }
-
1969
-
1970 if (record_n_init > 0) {
-
1971
-
1972 string fname = constructIOFileName("", true)+".pinit";
-
1973 ofstream out;
-
1974 out.open(fname.c_str());
-
1975 out << std::fixed << std::showpoint << std::setprecision(6);
-
1976 for (vector<EGS_Vector>::iterator it = p_init_locs.begin(); it != p_init_locs.end(); ++it) {
-
1977 out << (*it).x << "\t" << (*it).y << "\t" << (*it).z << endl;
-
1978 }
-
1979 out.close();
-
1980 egsInformation("\nInitial Particle Positions\n%s\n",sep.c_str());
-
1981 egsInformation("%d Initial particle positions written to .pinit file\n", p_init_locs.size());
+
1956
+
1957 egsInformation("\n\nGeometry Errors\n%s\n", sep.c_str());
+
1958 egsInformation("Number of geometry errors (/max allowed) = %d / %d\n", run->geomErrorCount, run->geomErrorMax);
+
1959 egsInformation("Number of 'stuck' particles discarded = %llu\n", n_stuck);
+
1960
+
1961
+
1962 // tell scoring objects how many histories were actually run
+
1963 // (needed for parallel run normalization)
+
1964 EGS_I64 hist_norm = run->getNdone();
+
1965 pevent_pub.notify(NEW_HISTORY, &hist_norm);
+
1966
+
1967 if (!single_generator) {
+
1968 egsInformation(
+
1969 "Warning: Stats about energy escaping source may not be accurate when "
+
1970 "not using a single source generator\n"
+
1971 );
+
1972 }
+
1973
+
1974 if (phsp) {
+
1975 phsp->finish(current_case);
+
1976 phsp->outputResults();
+
1977 phsp->destroySource();
+
1978 }
+
1979
+
1980 if (escoring) {
+
1981 escoring->outputResults();
1982 }
1983
-
1984 timing_blocks.addTimer("egs_brachy::outputPhantomResults");
-
1985 for (vector<EB_Phantom *>::iterator p = phantom_geoms.begin(); p != phantom_geoms.end(); p++) {
-
1986 (*p)->setEffectiveHistories(effective_histories);
-
1987 bool output_vc = find(output_volcor_phantoms.begin(), output_volcor_phantoms.end(),
-
1988 (*p)->geometry->getName()) != output_volcor_phantoms.end();
-
1989 string dd_format = output_3ddose_files ? output_dose_format : "";
-
1990 string vc_format = output_vc ? output_volcor_format : "";
-
1991 string ep_format = output_egsphant ? output_egsphant_format : "";
-
1992 string vi_format = output_voxinfo ? output_voxinfo_format : "";
-
1993 (*p)->outputResults(20, dd_format, ep_format, vi_format, vc_format);
-
1994 }
+
1984 if (spectrum_scorers.size() > 0) {
+
1985 egsInformation("\nSpectrum scoring results\n%s\n",sep.c_str());
+
1986 string root = constructIOFileName("", true);
+
1987 vector<BaseSpectrumScorer *>::iterator it = spectrum_scorers.begin();
+
1988 for (; it != spectrum_scorers.end(); it++) {
+
1989 (*it)->setEffectiveHistories(effective_histories);
+
1990 (*it)->outputResults(root);
+
1991 }
+
1992 }
+
1993
+
1994 if (record_n_init > 0) {
1995
-
1996 timing_blocks.stopTimer();
-
1997
-
1998 egsInformation("\nStep Counts\n%s\n", sep.c_str());
-
1999 EGS_Float total_steps = 0;
-
2000
-
2001 for (int i=-1; i < 2; i++) {
-
2002 total_steps += steps_in_sources[i];
-
2003 total_steps += steps_in_phantoms[i];
-
2004 total_steps += steps_in_other[i];
-
2005 }
-
2006
-
2007 egsInformation("Total particle steps : %20llu\n", (EGS_I64)total_steps);
-
2008 for (int i=-1; i < 2; i++) {
-
2009 if (steps_in_sources[i] > 0) {
-
2010 egsInformation("q=%2d Steps taken in sources : %20llu (%.2f%%)\n", i, steps_in_sources[i],
-
2011 100*steps_in_sources[i]/total_steps);
-
2012 }
-
2013 if (steps_in_phantoms[i] > 0) {
-
2014 egsInformation("q=%2d Steps taken in phantoms : %20llu (%.2f%%)\n", i, steps_in_phantoms[i],
-
2015 100*steps_in_phantoms[i]/total_steps);
-
2016 }
-
2017 if (steps_in_other[i] > 0) {
-
2018 egsInformation("q=%2d Steps taken in other objects : %20llu (%.2f%%)\n", i, steps_in_other[i],
-
2019 100*steps_in_other[i]/total_steps);
-
2020 }
-
2021 }
-
2022
-
2023 timing_blocks.stopTimer();
-
2024 timing_blocks.outputInfo();
-
2025
-
2026
-
2027}
-
2028
-
2029
-
2030void EB_Application::getCurrentResult(double &sum, double &sum2, double &norm, double &count) {
-
2031
-
2032 count = current_case;
-
2033 calcEffectiveHistories();
-
2034 gcr_phantom->setEffectiveHistories(effective_histories);
-
2035 gcr_phantom->getCurrentScore(gcr_phantom_reg, sum, sum2);
-
2036 norm=gcr_phantom->getTlenNorm(gcr_phantom_reg);
-
2037
-
2038}
-
2039
-
2040int EB_Application::runSimulation() {
-
2041 timing_blocks.addTimer("egs_brachy::runSimulation");
-
2042 int result = EGS_Application::runSimulation();
-
2043 timing_blocks.stopTimer();
-
2044 return result;
-
2045}
+
1996 string fname = constructIOFileName("", true)+".pinit";
+
1997 ofstream out;
+
1998 out.open(fname.c_str());
+
1999 out << std::fixed << std::showpoint << std::setprecision(6);
+
2000 for (vector<EGS_Vector>::iterator it = p_init_locs.begin(); it != p_init_locs.end(); ++it) {
+
2001 out << (*it).x << "\t" << (*it).y << "\t" << (*it).z << "\n";
+
2002 }
+
2003 out.close();
+
2004 egsInformation("\nInitial Particle Positions\n%s\n",sep.c_str());
+
2005 egsInformation("%d Initial particle positions written to .pinit file\n", p_init_locs.size());
+
2006 }
+
2007
+
2008 timing_blocks.addTimer("egs_brachy::outputPhantomResults");
+
2009 for (vector<EB_Phantom *>::iterator p = phantom_geoms.begin(); p != phantom_geoms.end(); p++) {
+
2010 (*p)->setEffectiveHistories(effective_histories);
+
2011 bool output_vc = find(output_volcor_phantoms.begin(), output_volcor_phantoms.end(),
+
2012 (*p)->geometry->getName()) != output_volcor_phantoms.end();
+
2013 string dd_format = output_3ddose_files ? output_dose_format : "";
+
2014 string vc_format = output_vc ? output_volcor_format : "";
+
2015 string ep_format = output_egsphant ? output_egsphant_format : "";
+
2016 string vi_format = output_voxinfo ? output_voxinfo_format : "";
+
2017 (*p)->outputResults(20, dd_format, ep_format, vi_format, vc_format);
+
2018 }
+
2019
+
2020 timing_blocks.stopTimer();
+
2021
+
2022 egsInformation("\nStep Counts\n%s\n", sep.c_str());
+
2023 EGS_Float total_steps = 0;
+
2024
+
2025 for (int i=-1; i < 2; i++) {
+
2026 total_steps += steps_in_sources[i];
+
2027 total_steps += steps_in_phantoms[i];
+
2028 total_steps += steps_in_other[i];
+
2029 }
+
2030
+
2031 egsInformation("Total particle steps : %20llu\n", (EGS_I64)total_steps);
+
2032 for (int i=-1; i < 2; i++) {
+
2033 if (steps_in_sources[i] > 0) {
+
2034 egsInformation("q=%2d Steps taken in sources : %20llu (%.2f%%)\n", i, steps_in_sources[i],
+
2035 100*steps_in_sources[i]/total_steps);
+
2036 }
+
2037 if (steps_in_phantoms[i] > 0) {
+
2038 egsInformation("q=%2d Steps taken in phantoms : %20llu (%.2f%%)\n", i, steps_in_phantoms[i],
+
2039 100*steps_in_phantoms[i]/total_steps);
+
2040 }
+
2041 if (steps_in_other[i] > 0) {
+
2042 egsInformation("q=%2d Steps taken in other objects : %20llu (%.2f%%)\n", i, steps_in_other[i],
+
2043 100*steps_in_other[i]/total_steps);
+
2044 }
+
2045 }
2046
-
2047/* \brief initialize a particle from source and then transform to next source */
-
2048int EB_Application::simulateSingleShower() {
+
2047 timing_blocks.stopTimer();
+
2048 timing_blocks.outputInfo();
2049
-
2050 last_case = current_case;
-
2051
-
2052 current_case = source->getNextParticle(rndm, p.q, p.latch, p.E, p.wt, p.x, p.u);
+
2050
+
2051}
+
+
2052
2053
-
2054 int initial_source;
-
2055 if ((is_phsp_source && !recycle_opts) || !single_generator) {
-
2056 initial_source = active_source;
-
2057 } else {
-
2058 initial_source = 0;
-
2059 }
-
2060
-
2061 p.wt *= source_weights[active_source];
-
2062
-
2063 if (run_mode == RM_SUPERPOSITION) {
-
2064 superpos_geom->setActiveByIndex(initial_source);
-
2065 }
-
2066
-
2067 // transform particle to position of next source
-
2068 source_transforms[initial_source]->transform(p.x);
-
2069 source_transforms[initial_source]->rotate(p.u);
+
+
2054void EB_Application::getCurrentResult(double &sum, double &sum2, double &norm, double &count) {
+
2055
+
2056 count = current_case;
+
2057 calcEffectiveHistories();
+
2058 gcr_phantom->setEffectiveHistories(effective_histories);
+
2059 gcr_phantom->getCurrentScore(gcr_phantom_reg, sum, sum2);
+
2060 norm=gcr_phantom->getTlenNorm(gcr_phantom_reg);
+
2061
+
2062}
+
+
2063
+
+
2064int EB_Application::runSimulation() {
+
2065 timing_blocks.addTimer("egs_brachy::runSimulation");
+
2066 int result = EGS_Application::runSimulation();
+
2067 timing_blocks.stopTimer();
+
2068 return result;
+
2069}
+
2070
-
2071 p.ir = geometry->isWhere(p.x);
-
2072
-
2073 if (p.ir < 0) {
-
2074 egsWarning("EB_Application::simulateSingleShower() - particle initiated at (x, y, z) = (%.2g, %.2g, %.2g)\n", p.x.x, p.x.y, p.x.z);
-
2075 egsFatal("EB_Application::simulateSingleShower() - Particle initiated outside "
-
2076 "the geometry! Please check your source locations.\n");
-
2077 }
-
2078
-
2079 if (is_phsp_source) {
-
2080 // we assume phase space particles are outside the source
-
2081 pevent_pub.notify(PARTICLE_ESCAPED_SOURCE, &p);
-
2082
-
2083 // set up stack with particles if recyling and phsp source
-
2084 if (recycle_opts) {
-
2085 addRecycledParticlesToStack(&p, true);
-
2086 }
-
2087 } else if (!ginfo.isSource(p.ir)) {
-
2088
-
2089 GeomRegT r = ginfo.globalToLocal(p.ir);
+
2071/* \brief initialize a particle from source and then transform to next source */
+
+
2072int EB_Application::simulateSingleShower() {
+
2073
+
2074 last_case = current_case;
+
2075
+
2076 current_case = source->getNextParticle(rndm, p.q, p.latch, p.E, p.wt, p.x, p.u);
+
2077
+
2078 int initial_source;
+
2079 if ((is_phsp_source && !recycle_opts) || !single_generator) {
+
2080 initial_source = active_source;
+
2081 } else {
+
2082 initial_source = 0;
+
2083 }
+
2084
+
2085 p.wt *= source_weights[active_source];
+
2086
+
2087 if (run_mode == RM_SUPERPOSITION) {
+
2088 superpos_geom->setActiveByIndex(initial_source);
+
2089 }
2090
-
2091 printParticleWithSpherical(p);
-
2092 egsFatal(
-
2093 "Particle started in region %d (%s reg %d) which is outside a source geometry. Please check your geometry\n",
-
2094 p.ir,
-
2095 r.first->getName().c_str(),
-
2096 r.second
-
2097 );
-
2098
-
2099 }
-
2100
-
2101 if (record_n_init > 0 && (int)p_init_locs.size() < record_n_init) {
-
2102 p_init_locs.push_back(p.x);
-
2103 }
-
2104
-
2105 cur_R = p.x.length2();
-
2106 last_R = cur_R;
-
2107 steps_at_same_loc = 0;
-
2108
-
2109 int err = startNewShower();
-
2110 if (err) {
-
2111 return err;
-
2112 }
-
2113
-
2114 // shower() just resets the stack before calling egsShower() but when using
-
2115 // a phsp source with recycling, we've already set up stack so go straight
-
2116 // to egsShower() in that case;
-
2117 if (is_phsp_source && recycle_opts) {
-
2118 err = 0;
-
2119 egsShower();
-
2120 } else {
-
2121 err = shower();
-
2122 }
-
2123
-
2124 active_source++;
-
2125 if (active_source == nsources) {
-
2126 active_source =0;
+
2091 // transform particle to position of next source
+
2092 source_transforms[initial_source]->transform(p.x);
+
2093 source_transforms[initial_source]->rotate(p.u);
+
2094
+
2095 p.ir = geometry->isWhere(p.x);
+
2096
+
2097 if (p.ir < 0) {
+
2098 egsWarning("EB_Application::simulateSingleShower() - particle initiated at (x, y, z) = (%.2g, %.2g, %.2g)\n", p.x.x, p.x.y, p.x.z);
+
2099 egsFatal("EB_Application::simulateSingleShower() - Particle initiated outside "
+
2100 "the geometry! Please check your source locations.\n");
+
2101 }
+
2102
+
2103 if (is_phsp_source) {
+
2104 // we assume phase space particles are outside the source
+
2105 pevent_pub.notify(PARTICLE_ESCAPED_SOURCE, &p);
+
2106
+
2107 // set up stack with particles if recyling and phsp source
+
2108 if (recycle_opts) {
+
2109 addRecycledParticlesToStack(&p, true);
+
2110 }
+
2111 } else if (!ginfo.isSource(p.ir)) {
+
2112
+
2113 GeomRegT r = ginfo.globalToLocal(p.ir);
+
2114
+
2115 printParticleWithSpherical(p);
+
2116 egsFatal(
+
2117 "Particle started in region %d (%s reg %d) which is outside a source geometry. Please check your geometry\n",
+
2118 p.ir,
+
2119 r.first->getName().c_str(),
+
2120 r.second
+
2121 );
+
2122
+
2123 }
+
2124
+
2125 if (record_n_init > 0 && (int)p_init_locs.size() < record_n_init) {
+
2126 p_init_locs.push_back(p.x);
2127 }
2128
-
2129 return err || finishShower();
-
2130}
-
2131
+
2129 cur_R = p.x.length2();
+
2130 last_R = cur_R;
+
2131 steps_at_same_loc = 0;
2132
-
2133int EB_Application::startNewShower() {
-
2134
-
2135
-
2136 // notify subscribers a valid particle has been initialized
-
2137 pevent_pub.notify(PARTICLE_INITIALIZED, &p);
-
2138
-
2139 // sets current case in ausgab objects
-
2140 int err = EGS_Application::startNewShower();
-
2141
-
2142 if (err) {
-
2143 return err;
-
2144 }
-
2145
-
2146 // now set current case in all phantom objects
-
2147 if (current_case != last_case) {
-
2148
-
2149 pevent_pub.notify(NEW_HISTORY, &current_case);
-
2150
-
2151 last_case = current_case;
-
2152 }
-
2153
-
2154 return 0;
-
2155}
+
2133 int err = startNewShower();
+
2134 if (err) {
+
2135 return err;
+
2136 }
+
2137
+
2138 // shower() just resets the stack before calling egsShower() but when using
+
2139 // a phsp source with recycling, we've already set up stack so go straight
+
2140 // to egsShower() in that case;
+
2141 if (is_phsp_source && recycle_opts) {
+
2142 err = 0;
+
2143 egsShower();
+
2144 } else {
+
2145 err = shower();
+
2146 }
+
2147
+
2148 active_source++;
+
2149 if (active_source == nsources) {
+
2150 active_source =0;
+
2151 }
+
2152
+
2153 return err || finishShower();
+
2154}
+
+
2155
2156
-
2157
-
2158/* start of stop/restart functionality ****************************************/
-
2159int EB_Application::egsApplicationOutputData(ostream *out) {
-
2160 /* adapted from egs_application.cpp::outputData */
-
2161 if (!run->storeState(*out)) {
-
2162 return 2;
-
2163 }
-
2164 if (!egsStoreI64(*out,current_case)) {
-
2165 return 3;
-
2166 }
-
2167 (*out) << endl;
-
2168 if (!rndm->storeState(*out)) {
-
2169 return 4;
-
2170 }
-
2171 if (!source->storeState(*out)) {
-
2172 return 5;
-
2173 }
-
2174 for (size_t j=0; j<a_objects_list.size(); ++j) {
-
2175 if (!a_objects_list[j]->storeState(*out)) {
-
2176 return 6;
-
2177 }
-
2178 }
-
2179
-
2180 return 0;
-
2181}
-
2182
-
2183int EB_Application::egsAdvApplicationOutputData(ostream *out) {
-
2184 /* adapted from egs_advanced_application.cpp::outputData */
-
2185 EGS_I32 np, ip;
-
2186 egsGetRNGPointers(&np,&ip);
-
2187 if (np < 1) {
-
2188 return 11;
-
2189 }
-
2190 if (np > 10000000) {
-
2191 egsWarning("EGS_AdvancedApplication::outputData(): egsGetRNGPointers"
-
2192 " returns a huge number? (%d)\n",np);
-
2193 return 12;
+
+
2157int EB_Application::startNewShower() {
+
2158
+
2159
+
2160 // notify subscribers a valid particle has been initialized
+
2161 pevent_pub.notify(PARTICLE_INITIALIZED, &p);
+
2162
+
2163 // sets current case in ausgab objects
+
2164 int err = EGS_Application::startNewShower();
+
2165
+
2166 if (err) {
+
2167 return err;
+
2168 }
+
2169
+
2170 // now set current case in all phantom objects
+
2171 if (current_case != last_case) {
+
2172
+
2173 pevent_pub.notify(NEW_HISTORY, &current_case);
+
2174
+
2175 last_case = current_case;
+
2176 }
+
2177
+
2178 return 0;
+
2179}
+
+
2180
+
2181
+
2182/* start of stop/restart functionality ****************************************/
+
+
2183int EB_Application::egsApplicationOutputData(ostream *out) {
+
2184 /* adapted from egs_application.cpp::outputData */
+
2185 if (!run->storeState(*out)) {
+
2186 return 2;
+
2187 }
+
2188 if (!egsStoreI64(*out,current_case)) {
+
2189 return 3;
+
2190 }
+
2191 (*out) << "\n";
+
2192 if (!rndm->storeState(*out)) {
+
2193 return 4;
2194 }
-
2195 EGS_Float *array = new EGS_Float [np];
-
2196 egsGetRNGArray(array);
-
2197 (*out) << " " << np << " " << ip << endl;
-
2198 for (int j=0; j<np; j++) {
-
2199 (*out) << array[j] << " ";
-
2200 }
-
2201 (*out) << endl;
-
2202 double ch_steps, all_steps;
-
2203 egsGetSteps(&ch_steps,&all_steps);
-
2204 (*out) << ch_steps << " " << all_steps << endl;
-
2205 delete [] array;
-
2206 return out->good() ? 0 : 13;
-
2207
-
2208}
-
2209
-
2210int EB_Application::egsBrachyOutputData(ostream *out) {
-
2211
-
2212 int err;
-
2213
-
2214 (*out) << std::setprecision(9);
-
2215
-
2216 if (escoring) {
-
2217 err= escoring->outputData(out);
-
2218 if (err) {
-
2219 return err;
-
2220 }
-
2221 }
-
2222
-
2223 vector<BaseSpectrumScorer *>::iterator spec_it = spectrum_scorers.begin();
-
2224 for (; spec_it != spectrum_scorers.end(); ++spec_it) {
-
2225 err = (*spec_it)->outputData(out);
-
2226 if (err) {
-
2227 return err;
-
2228 }
-
2229 }
-
2230
-
2231 vector<EB_Phantom *>::iterator phant_it = phantom_geoms.begin();
-
2232 for (; phant_it != phantom_geoms.end(); phant_it++) {
-
2233 err = (*phant_it)->outputData(out);
-
2234 if (err) {
-
2235 return err;
-
2236 }
-
2237 }
-
2238
-
2239 return 0;
-
2240
-
2241}
-
2242
-
2243int EB_Application::outputDataHelper(ostream *out) {
-
2244
-
2245 int err = egsApplicationOutputData(out);
-
2246 if (err) {
-
2247 return err;
-
2248 }
-
2249 err = egsAdvApplicationOutputData(out);
-
2250 if (err) {
-
2251 return err;
-
2252 }
-
2253
-
2254 return egsBrachyOutputData(out);
-
2255}
-
2256
-
2257int EB_Application::outputData() {
-
2258
-
2259 timing_blocks.addTimer("egs_brachy::outputData");
+
2195 if (!source->storeState(*out)) {
+
2196 return 5;
+
2197 }
+
2198 for (size_t j=0; j<a_objects_list.size(); ++j) {
+
2199 if (!a_objects_list[j]->storeState(*out)) {
+
2200 return 6;
+
2201 }
+
2202 }
+
2203
+
2204 return 0;
+
2205}
+
+
2206
+
+
2207int EB_Application::egsAdvApplicationOutputData(ostream *out) {
+
2208 /* adapted from egs_advanced_application.cpp::outputData */
+
2209 EGS_I32 np, ip;
+
2210 egsGetRNGPointers(&np,&ip);
+
2211 if (np < 1) {
+
2212 return 11;
+
2213 }
+
2214 if (np > 10000000) {
+
2215 egsWarning("EGS_AdvancedApplication::outputData(): egsGetRNGPointers"
+
2216 " returns a huge number? (%d)\n",np);
+
2217 return 12;
+
2218 }
+
2219 EGS_Float *array = new EGS_Float [np];
+
2220 egsGetRNGArray(array);
+
2221 (*out) << " " << np << " " << ip << "\n";
+
2222 for (int j=0; j<np; j++) {
+
2223 (*out) << array[j] << " ";
+
2224 }
+
2225 (*out) << "\n";
+
2226 double ch_steps, all_steps;
+
2227 egsGetSteps(&ch_steps,&all_steps);
+
2228 (*out) << ch_steps << " " << all_steps << "\n";
+
2229 delete [] array;
+
2230 return out->good() ? 0 : 13;
+
2231
+
2232}
+
+
2233
+
+
2234int EB_Application::egsBrachyOutputData(ostream *out) {
+
2235
+
2236 int err;
+
2237
+
2238 (*out) << std::setprecision(9);
+
2239
+
2240 for (int i=-1; i < 2; i++) {
+
2241 (*out) << steps_in_sources[i] << " ";
+
2242 (*out) << steps_in_phantoms[i] << " ";
+
2243 (*out) << steps_in_other[i] << "\n";
+
2244 }
+
2245
+
2246 if (escoring) {
+
2247 err= escoring->outputData(out);
+
2248 if (err) {
+
2249 return err;
+
2250 }
+
2251 }
+
2252
+
2253 vector<BaseSpectrumScorer *>::iterator spec_it = spectrum_scorers.begin();
+
2254 for (; spec_it != spectrum_scorers.end(); ++spec_it) {
+
2255 err = (*spec_it)->outputData(out);
+
2256 if (err) {
+
2257 return err;
+
2258 }
+
2259 }
2260
-
2261 bool use_gz = output_egsdat_format == "gzip";
-
2262 string extension(".egsdat");
-
2263 extension += (use_gz ? ".gz" : "");
-
2264 string ofile = constructIOFileName(extension.c_str(), true);
-
2265
-
2266 int err;
-
2267 if (use_gz) {
-
2268 if (gz_data_out) {
-
2269 delete gz_data_out;
-
2270 }
-
2271 gz_data_out = new ogzstream(ofile.c_str());
+
2261 vector<EB_Phantom *>::iterator phant_it = phantom_geoms.begin();
+
2262 for (; phant_it != phantom_geoms.end(); phant_it++) {
+
2263 err = (*phant_it)->outputData(out);
+
2264 if (err) {
+
2265 return err;
+
2266 }
+
2267 }
+
2268
+
2269 return 0;
+
2270
+
2271}
+
2272
-
2273 if (!(gz_data_out)) {
-
2274 egsWarning("EGS_Application::outputData: failed to open %s for writing\n",ofile.c_str());
-
2275 timing_blocks.stopTimer();
-
2276 return 1;
-
2277 }
-
2278 err = outputDataHelper(gz_data_out);
-
2279 gz_data_out->close();
-
2280 } else {
-
2281
-
2282 if (data_out) {
-
2283 delete data_out;
-
2284 }
-
2285 data_out = new ofstream(ofile.c_str());
-
2286 if (!(*data_out)) {
-
2287 egsWarning("EGS_Application::outputData: failed to open %s for writing\n",ofile.c_str());
-
2288 timing_blocks.stopTimer();
-
2289 return 1;
-
2290 }
-
2291 err = outputDataHelper(data_out);
-
2292 }
-
2293
-
2294 timing_blocks.stopTimer();
-
2295 return err;
-
2296
-
2297}
-
2298
-
2299int EB_Application::egsApplicationReadData(istream *in) {
-
2300 /* adapted from egs_application.cpp::readData */
-
2301 if (!run->setState(*in)) {
-
2302 return 2;
-
2303 }
-
2304 if (!egsGetI64(*in,current_case)) {
-
2305 return 3;
-
2306 }
-
2307 last_case = current_case;
-
2308 if (!rndm->setState(*in)) {
-
2309 return 4;
-
2310 }
-
2311 if (!source->setState(*in)) {
-
2312 return 5;
-
2313 }
-
2314 for (int j=0; j<a_objects_list.size(); ++j) {
-
2315 if (!a_objects_list[j]->setState(*in)) {
-
2316 return 6;
-
2317 }
-
2318 }
-
2319 return 0;
-
2320}
-
2321
-
2322int EB_Application::egsAdvApplicationReadData(istream *in) {
-
2323 /* adapted from egs_advanced_application.cpp::readData */
-
2324 int np, ip;
-
2325 (*in) >> np >> ip;
-
2326 if (np < 1) {
-
2327 return 11;
-
2328 }
-
2329 if (np > 10000000) {
-
2330 egsWarning("EB_Application::egsAdvApplicationReadData(): got huge size "
-
2331 "for the mortran random array? (%d)\n",np);
-
2332 return 12;
+
+
2273int EB_Application::outputDataHelper(ostream *out) {
+
2274
+
2275 int err = egsApplicationOutputData(out);
+
2276 if (err) {
+
2277 return err;
+
2278 }
+
2279 err = egsAdvApplicationOutputData(out);
+
2280 if (err) {
+
2281 return err;
+
2282 }
+
2283
+
2284 return egsBrachyOutputData(out);
+
2285}
+
+
2286
+
+
2287int EB_Application::outputData() {
+
2288
+
2289 timing_blocks.addTimer("egs_brachy::outputData");
+
2290
+
2291 bool use_gz = output_egsdat_format == "gzip";
+
2292 string extension(".egsdat");
+
2293 extension += (use_gz ? ".gz" : "");
+
2294 string ofile = constructIOFileName(extension.c_str(), true);
+
2295
+
2296 int err;
+
2297 if (use_gz) {
+
2298 if (gz_data_out) {
+
2299 delete gz_data_out;
+
2300 }
+
2301 gz_data_out = new ogzstream(ofile.c_str());
+
2302
+
2303 if (!(gz_data_out)) {
+
2304 egsWarning("EGS_Application::outputData: failed to open %s for writing\n",ofile.c_str());
+
2305 timing_blocks.stopTimer();
+
2306 return 1;
+
2307 }
+
2308 err = outputDataHelper(gz_data_out);
+
2309 gz_data_out->close();
+
2310 } else {
+
2311
+
2312 if (data_out) {
+
2313 delete data_out;
+
2314 }
+
2315 data_out = new ofstream(ofile.c_str());
+
2316 if (!(*data_out)) {
+
2317 egsWarning("EGS_Application::outputData: failed to open %s for writing\n",ofile.c_str());
+
2318 timing_blocks.stopTimer();
+
2319 return 1;
+
2320 }
+
2321 err = outputDataHelper(data_out);
+
2322 }
+
2323
+
2324 timing_blocks.stopTimer();
+
2325 return err;
+
2326
+
2327}
+
+
2328
+
+
2329int EB_Application::egsApplicationReadData(istream *in) {
+
2330 /* adapted from egs_application.cpp::readData */
+
2331 if (!run->setState(*in)) {
+
2332 return 2;
2333 }
-
2334 EGS_Float *array = new EGS_Float [np];
-
2335 for (int j=0; j<np; j++) {
-
2336 (*in) >> array[j];
-
2337 }
-
2338 if (!in->good()) {
-
2339 return 13;
+
2334 if (!egsGetI64(*in,current_case)) {
+
2335 return 3;
+
2336 }
+
2337 last_case = current_case;
+
2338 if (!rndm->setState(*in)) {
+
2339 return 4;
2340 }
-
2341 egsSetRNGState(&ip,array);
-
2342 delete [] array;
-
2343 double ch_steps, all_steps;
-
2344 (*in) >> ch_steps >> all_steps;
-
2345 egsSetSteps(&ch_steps,&all_steps);
-
2346 return in->good() ? 0 : 13;
-
2347
-
2348}
-
2349
-
2350int EB_Application::egsBrachyReadData(istream *in) {
-
2351 int err;
-
2352
-
2353 if (escoring) {
-
2354 err= escoring->readData(in);
-
2355 if (err) {
-
2356 return err;
-
2357 }
+
2341 if (!source->setState(*in)) {
+
2342 return 5;
+
2343 }
+
2344 for (int j=0; j<a_objects_list.size(); ++j) {
+
2345 if (!a_objects_list[j]->setState(*in)) {
+
2346 return 6;
+
2347 }
+
2348 }
+
2349 return 0;
+
2350}
+
+
2351
+
+
2352int EB_Application::egsAdvApplicationReadData(istream *in) {
+
2353 /* adapted from egs_advanced_application.cpp::readData */
+
2354 int np, ip;
+
2355 (*in) >> np >> ip;
+
2356 if (np < 1) {
+
2357 return 11;
2358 }
-
2359
-
2360 vector<BaseSpectrumScorer *>::iterator spec_it = spectrum_scorers.begin();
-
2361 for (; spec_it != spectrum_scorers.end(); ++spec_it) {
-
2362 err = (*spec_it)->readData(in);
-
2363 if (err) {
-
2364 return err;
-
2365 }
-
2366 }
-
2367
-
2368 vector<EB_Phantom *>::iterator phant_it = phantom_geoms.begin();
-
2369 for (; phant_it != phantom_geoms.end(); phant_it++) {
-
2370 err = (*phant_it)->readData(in);
-
2371 if (err) {
-
2372 return err;
-
2373 }
-
2374 }
-
2375 return 0;
-
2376
-
2377}
-
2378
-
2379int EB_Application::readDataHelper(istream *in) {
-
2380
-
2381 int err = egsApplicationReadData(in);
-
2382 if (err) {
-
2383 return err;
-
2384 }
-
2385 err = egsAdvApplicationReadData(in);
-
2386 if (err) {
-
2387 return err;
-
2388 }
-
2389
-
2390 return egsBrachyReadData(in);
-
2391}
-
2392
-
2393/* start of stop/restart functionality ****************************************/
-
2394int EB_Application::readData() {
+
2359 if (np > 10000000) {
+
2360 egsWarning("EB_Application::egsAdvApplicationReadData(): got huge size "
+
2361 "for the mortran random array? (%d)\n",np);
+
2362 return 12;
+
2363 }
+
2364 EGS_Float *array = new EGS_Float [np];
+
2365 for (int j=0; j<np; j++) {
+
2366 (*in) >> array[j];
+
2367 }
+
2368 if (!in->good()) {
+
2369 return 13;
+
2370 }
+
2371 egsSetRNGState(&ip,array);
+
2372 delete [] array;
+
2373 double ch_steps, all_steps;
+
2374 (*in) >> ch_steps >> all_steps;
+
2375 egsSetSteps(&ch_steps,&all_steps);
+
2376 return in->good() ? 0 : 13;
+
2377
+
2378}
+
+
2379
+
+
2380int EB_Application::egsBrachyReadData(istream *in) {
+
2381 int err;
+
2382
+
2383 for (int i=-1; i < 2; i++) {
+
2384 (*in) >> steps_in_sources[i];
+
2385 (*in) >> steps_in_phantoms[i];
+
2386 (*in) >> steps_in_other[i];
+
2387 }
+
2388
+
2389 if (escoring) {
+
2390 err= escoring->readData(in);
+
2391 if (err) {
+
2392 return err;
+
2393 }
+
2394 }
2395
-
2396 timing_blocks.addTimer("egs_brachy::readData");
-
2397
-
2398 bool use_gz = output_egsdat_format == "gzip";
-
2399 string extension(".egsdat");
-
2400 extension += (use_gz ? ".gz" : "");
-
2401 string ifile = constructIOFileName(extension.c_str(), false);
-
2402
-
2403 int err;
-
2404 if (use_gz) {
-
2405 if (gz_data_in) {
-
2406 delete gz_data_in;
-
2407 }
-
2408 gz_data_in = new igzstream(ifile.c_str());
-
2409
-
2410 if (!(gz_data_in)) {
-
2411 egsWarning("EGS_Application::readData: failed to open %s for reading\n", ifile.c_str());
-
2412 timing_blocks.stopTimer();
-
2413 return 1;
-
2414 }
-
2415 err = readDataHelper(gz_data_in);
-
2416 } else {
-
2417
-
2418 if (data_in) {
-
2419 delete data_in;
-
2420 }
-
2421 data_in = new ifstream(ifile.c_str());
-
2422 if (!(*data_in)) {
-
2423 egsWarning("EGS_Application::readData: failed to open %s for writing\n",ifile.c_str());
-
2424 timing_blocks.stopTimer();
-
2425 return 1;
-
2426 }
-
2427 err = readDataHelper(data_in);
-
2428 }
-
2429
-
2430 timing_blocks.stopTimer();
-
2431 return err;
-
2432
-
2433}
-
2434
-
2435
-
2436int EB_Application::combineResults() {
-
2437 /* Adapted from egs_application.cpp::combineResults */
-
2438 egsInformation(
-
2439 "\n Suming the following .egsdat files:\n"
-
2440 "=======================================================================\n");
-
2441 char buf[512];
-
2442 resetCounter();
-
2443 EGS_Float last_cpu = 0;
-
2444 EGS_I64 last_ncase = 0;
-
2445 int ndat = 0;
-
2446 bool ok = true;
-
2447 for (int j=1; j<500; j++) {
-
2448
-
2449 bool use_gz = output_egsdat_format == "gzip";
-
2450 string name("%s_w%d.egsdat");
-
2451 name += (use_gz ? ".gz" : "");
-
2452
-
2453 sprintf(buf, name.c_str(), output_file.c_str(), j);
-
2454 string dfile = egsJoinPath(app_dir,buf);
-
2455 istream *data;
-
2456 ifstream in;
-
2457 igzstream gzin;
-
2458 bool opened = false;
-
2459 if (use_gz) {
-
2460 gzin.open(dfile.c_str());
-
2461 opened = gzin.rdbuf()->is_open();
-
2462 data = &gzin;
-
2463 } else {
-
2464 in.open(dfile.c_str());
-
2465 opened = in.is_open();
-
2466 data = &in;
-
2467 }
+
2396 vector<BaseSpectrumScorer *>::iterator spec_it = spectrum_scorers.begin();
+
2397 for (; spec_it != spectrum_scorers.end(); ++spec_it) {
+
2398 err = (*spec_it)->readData(in);
+
2399 if (err) {
+
2400 return err;
+
2401 }
+
2402 }
+
2403
+
2404 vector<EB_Phantom *>::iterator phant_it = phantom_geoms.begin();
+
2405 for (; phant_it != phantom_geoms.end(); phant_it++) {
+
2406 err = (*phant_it)->readData(in);
+
2407 if (err) {
+
2408 return err;
+
2409 }
+
2410 }
+
2411 return 0;
+
2412
+
2413}
+
+
2414
+
+
2415int EB_Application::readDataHelper(istream *in) {
+
2416
+
2417 int err = egsApplicationReadData(in);
+
2418 if (err) {
+
2419 return err;
+
2420 }
+
2421 err = egsAdvApplicationReadData(in);
+
2422 if (err) {
+
2423 return err;
+
2424 }
+
2425
+
2426 return egsBrachyReadData(in);
+
2427}
+
+
2428
+
2429/* start of stop/restart functionality ****************************************/
+
+
2430int EB_Application::readData() {
+
2431
+
2432 timing_blocks.addTimer("egs_brachy::readData");
+
2433
+
2434 bool use_gz = output_egsdat_format == "gzip";
+
2435 string extension(".egsdat");
+
2436 extension += (use_gz ? ".gz" : "");
+
2437 string ifile = constructIOFileName(extension.c_str(), false);
+
2438
+
2439 int err;
+
2440 if (use_gz) {
+
2441 if (gz_data_in) {
+
2442 delete gz_data_in;
+
2443 }
+
2444 gz_data_in = new igzstream(ifile.c_str());
+
2445
+
2446 if (!(gz_data_in)) {
+
2447 egsWarning("EGS_Application::readData: failed to open %s for reading\n", ifile.c_str());
+
2448 timing_blocks.stopTimer();
+
2449 return 1;
+
2450 }
+
2451 err = readDataHelper(gz_data_in);
+
2452 } else {
+
2453
+
2454 if (data_in) {
+
2455 delete data_in;
+
2456 }
+
2457 data_in = new ifstream(ifile.c_str());
+
2458 if (!(*data_in)) {
+
2459 egsWarning("EGS_Application::readData: failed to open %s for writing\n",ifile.c_str());
+
2460 timing_blocks.stopTimer();
+
2461 return 1;
+
2462 }
+
2463 err = readDataHelper(data_in);
+
2464 }
+
2465
+
2466 timing_blocks.stopTimer();
+
2467 return err;
2468
-
2469 if (opened) {
-
2470 int err = addState(*data);
-
2471 ++ndat;
-
2472 if (!err) {
-
2473 EGS_I64 ncase = run->getNdone();
-
2474 EGS_Float cpu = run->getCPUTime();
-
2475 egsInformation("%2d %-30s ncase=%-14lld cpu=%-11.2f\n",
-
2476 ndat,buf,ncase-last_ncase,cpu-last_cpu);
-
2477 last_ncase = ncase;
-
2478 last_cpu = cpu;
-
2479 } else {
-
2480 ok = false;
-
2481 egsWarning("%2d %-30s error %d\n",ndat,buf,err);
-
2482 }
-
2483 }
-
2484 }
-
2485 if (ndat > 0) {
-
2486 egsInformation(
-
2487 "=======================================================================\n");
-
2488 egsInformation("%40s%-14lld cpu=%-11.2f\n\n","Total ncase=",last_ncase,
-
2489 last_cpu);
-
2490 }
-
2491 if (ndat > 0) {
-
2492 return ok ? 0 : -1;
-
2493 } else {
-
2494 return 1;
-
2495 }
-
2496}
-
2497
-
2498void EB_Application::resetCounter() {
-
2499 // Reset everything in the base class
-
2500 EGS_AdvancedApplication::resetCounter();
-
2501 // Reset our own data to zero.
-
2502
-
2503 if (escoring) {
-
2504 escoring->resetCounter();
-
2505 }
-
2506
-
2507 vector<BaseSpectrumScorer *>::iterator spec_it = spectrum_scorers.begin();
-
2508 for (; spec_it != spectrum_scorers.end(); ++spec_it) {
-
2509 (*spec_it)->resetCounter();
-
2510 }
-
2511
-
2512 vector<EB_Phantom *>::iterator phant_it = phantom_geoms.begin();
-
2513 for (; phant_it != phantom_geoms.end(); phant_it++) {
-
2514 (*phant_it)->resetCounter();
-
2515 }
-
2516
-
2517}
-
2518
-
2519int EB_Application::addState(istream &data) {
-
2520 // Call first the base class addState() function to read and add
-
2521 // all data related to source, RNG, CPU time, etc.
-
2522 int err = EGS_AdvancedApplication::addState(data);
-
2523 if (err) {
-
2524 return err;
-
2525 }
-
2526
-
2527 if (escoring) {
-
2528 err = escoring->addState(data);
-
2529 if (err) {
-
2530 return err;
-
2531 }
-
2532 }
+
2469}
+
+
2470
+
2471
+
+
2472int EB_Application::combineResults() {
+
2473 /* Adapted from egs_application.cpp::combineResults */
+
2474 egsInformation(
+
2475 "\n Suming the following .egsdat files:\n"
+
2476 "=======================================================================\n");
+
2477 char buf[512];
+
2478 resetCounter();
+
2479 EGS_Float last_cpu = 0;
+
2480 EGS_I64 last_ncase = 0;
+
2481 int ndat = 0;
+
2482 bool ok = true;
+
2483 for (int j=1; j<500; j++) {
+
2484
+
2485 bool use_gz = output_egsdat_format == "gzip";
+
2486 string name("%s_w%d.egsdat");
+
2487 name += (use_gz ? ".gz" : "");
+
2488
+
2489 sprintf(buf, name.c_str(), output_file.c_str(), j);
+
2490 string dfile = egsJoinPath(app_dir,buf);
+
2491 istream *data;
+
2492 ifstream in;
+
2493 igzstream gzin;
+
2494 bool opened = false;
+
2495 if (use_gz) {
+
2496 gzin.open(dfile.c_str());
+
2497 opened = gzin.rdbuf()->is_open();
+
2498 data = &gzin;
+
2499 } else {
+
2500 in.open(dfile.c_str());
+
2501 opened = in.is_open();
+
2502 data = &in;
+
2503 }
+
2504
+
2505 if (opened) {
+
2506 int err = addState(*data);
+
2507 ++ndat;
+
2508 if (!err) {
+
2509 EGS_I64 ncase = run->getNdone();
+
2510 EGS_Float cpu = run->getCPUTime();
+
2511 egsInformation("%2d %-30s ncase=%-14lld cpu=%-11.2f\n",
+
2512 ndat,buf,ncase-last_ncase,cpu-last_cpu);
+
2513 last_ncase = ncase;
+
2514 last_cpu = cpu;
+
2515 } else {
+
2516 ok = false;
+
2517 egsWarning("%2d %-30s error %d\n",ndat,buf,err);
+
2518 }
+
2519 }
+
2520 }
+
2521 if (ndat > 0) {
+
2522 egsInformation(
+
2523 "=======================================================================\n");
+
2524 egsInformation("%40s%-14lld cpu=%-11.2f\n\n","Total ncase=",last_ncase,
+
2525 last_cpu);
+
2526 }
+
2527 if (ndat > 0) {
+
2528 return ok ? 0 : -1;
+
2529 } else {
+
2530 return 1;
+
2531 }
+
2532}
+
2533
-
2534 vector<BaseSpectrumScorer *>::iterator spec_it = spectrum_scorers.begin();
-
2535 for (; spec_it != spectrum_scorers.end(); ++spec_it) {
-
2536 err = (*spec_it)->addState(data);
-
2537 if (err) {
-
2538 return err;
-
2539 }
-
2540 }
-
2541
-
2542 vector<EB_Phantom *>::iterator phant_it = phantom_geoms.begin();
-
2543 for (; phant_it != phantom_geoms.end(); phant_it++) {
-
2544 err = (*phant_it)->addState(data);
-
2545 if (err) {
-
2546 return err;
-
2547 }
-
2548 }
-
2549
-
2550 return 0;
-
2551
-
2552}
-
2553/* end of stop/restart functionality ****************************************/
-
2554
-
2555#ifdef BUILD_APP_LIB
-
2556APP_LIB(EB_Application);
-
2557#else
-
2558APP_MAIN(EB_Application);
-
2559#endif
-
BaseSpectrumScorer
abstract base class for scoring spectrum information
Definition: spec_scoring.h:260
-
BaseSpectrumScorer::getSpectrumScorer
static BaseSpectrumScorer * getSpectrumScorer(EGS_Input *inp, EGS_BaseSource *source, GeomInfo *ginfo, Publisher *publisher)
factory method for creating one of the derived spectrum scoring classes
Definition: spec_scoring.cpp:85
-
BaseSpectrumScorer::getInfo
virtual string getInfo() const
Definition: spec_scoring.h:376
-
EB_Application
The main egs_brachy application class. See the Main Page for full documentation.
Definition: egs_brachy.h:90
-
EB_Application::spectrum_scorers
vector< BaseSpectrumScorer * > spectrum_scorers
Definition: egs_brachy.h:103
-
EB_Application::extra_scoring_mass
map< string, vector< EGS_Float > > extra_scoring_mass
Definition: egs_brachy.h:181
-
EB_Application::initRunControl
int initRunControl()
egs_brachy specific run control initialization
Definition: egs_brachy.cpp:787
-
EB_Application::initPHSPScoring
void initPHSPScoring(EGS_Input *)
set up phsp scoring
Definition: egs_brachy.cpp:993
-
EB_Application::checkSourceOverlaps
int checkSourceOverlaps(EGS_Input *)
Definition: egs_brachy.cpp:447
-
EB_Application::escoring
EnergyScoringStats * escoring
Energy related scoring/stats.
Definition: egs_brachy.h:102
-
EB_Application::initSource
int initSource()
Definition: egs_brachy.cpp:724
-
EB_Application::initSimulation
int initSimulation()
set the run mode and then call EGS_AdvancedApplication::initSimulation
Definition: egs_brachy.cpp:767
-
EB_Application::initEDepScoring
void initEDepScoring(EGS_Input *)
energy deposition scoring initialization
Definition: egs_brachy.cpp:1373
-
EB_Application::copyParticleToSourceLoc
void copyParticleToSourceLoc(EGS_Particle *p, int source, bool kill_orig, bool rotate, EGS_Float new_wt)
Definition: egs_brachy.cpp:1470
-
EB_Application::doPhotonSplitting
void doPhotonSplitting(int)
Definition: egs_brachy.cpp:1839
-
EB_Application::outputData
int outputData()
Output intermediate results. The egs_brachy version outputs the standard egs++ data along with egs_br...
Definition: egs_brachy.cpp:2257
-
EB_Application::source_transforms
vector< EGS_AffineTransform * > source_transforms
transforms to locations of all sources
Definition: egs_brachy.h:146
-
EB_Application::extra_scoring_reg
map< string, vector< int > > extra_scoring_reg
Definition: egs_brachy.h:179
-
EB_Application::initDoseScaling
void initDoseScaling(EGS_Input *)
Initialize dose scaling factor if requested.
Definition: egs_brachy.cpp:1421
-
EB_Application::steps_in_phantoms
map< int, EGS_I64 > steps_in_phantoms
Definition: egs_brachy.h:194
-
EB_Application::initSourceTransforms
int initSourceTransforms()
read in the location of all particle sources
Definition: egs_brachy.cpp:406
-
EB_Application::n_stuck
EGS_I64 n_stuck
Definition: egs_brachy.h:139
-
EB_Application::outputDataHelper
int outputDataHelper(ostream *)
helper function for outputData
Definition: egs_brachy.cpp:2243
-
EB_Application::timing_blocks
EB_TimingTree timing_blocks
Track CPU times of various functions.
Definition: egs_brachy.h:191
-
EB_Application::initRussianRoulette
int initRussianRoulette(EGS_Input *)
Initialize Russian roulette variance reduction if requested.
Definition: egs_brachy.cpp:1154
-
EB_Application::steps_at_same_loc
int steps_at_same_loc
Definition: egs_brachy.h:138
-
EB_Application::extra_scoring_doses
map< string, EGS_ScoringArray * > extra_scoring_doses
Definition: egs_brachy.h:182
-
EB_Application::output_volcor_format
string output_volcor_format
text or gzip
Definition: egs_brachy.h:130
-
EB_Application::createPhantoms
int createPhantoms()
set up Phantom objects for any geometries that user has requested scoring for
Definition: egs_brachy.cpp:687
-
EB_Application::pevent_pub
Publisher pevent_pub
Particle event publisher.
Definition: egs_brachy.h:189
-
EB_Application::do_brem_split
bool do_brem_split
Definition: egs_brachy.h:154
-
EB_Application::startNewParticle
virtual void startNewParticle()
Set source ecut/pcut if different from global ecut/pcut.
Definition: egs_brachy.cpp:1529
-
EB_Application::describeUserCode
void describeUserCode() const
Print information about the egs_brachy user code.
Definition: egs_brachy.cpp:113
-
EB_Application::initRunMode
int initRunMode()
Get run mode from the input file.
Definition: egs_brachy.cpp:800
-
EB_Application::describeSimulation
void describeSimulation()
Describe the simulation.
Definition: egs_brachy.cpp:127
-
EB_Application::enableAusgabCalls
void enableAusgabCalls(int ncalls, AusgabCall calls[])
enable an array of ausgab calls
Definition: egs_brachy.cpp:1366
-
EB_Application::initAusgabCalls
void initAusgabCalls()
setup any required ausgab calls
Definition: egs_brachy.cpp:1245
-
EB_Application::initMuenData
void initMuenData(EGS_Input *)
load muen data for requested media
Definition: egs_brachy.cpp:1309
-
EB_Application::output_egsdat_format
string output_egsdat_format
text or gzip
Definition: egs_brachy.h:119
-
EB_Application::run_mode_name
string run_mode_name
Definition: egs_brachy.h:100
-
EB_Application::output_volcor_phantoms
vector< string > output_volcor_phantoms
vector of phantom names to output volume correctino files for
Definition: egs_brachy.h:129
-
EB_Application::output_voxinfo_format
string output_voxinfo_format
text or gzip
Definition: egs_brachy.h:127
-
EB_Application::gz_data_in
igzstream * gz_data_in
GZip file for outputing egsdat.
Definition: egs_brachy.h:198
-
EB_Application::last_R
EGS_Float last_R
Definition: egs_brachy.h:136
-
EB_Application::global_e_max_rr
EGS_Float global_e_max_rr
max range rejection energy globally
Definition: egs_brachy.h:169
-
EB_Application::egsAdvApplicationOutputData
int egsAdvApplicationOutputData(ostream *)
helper function for outputData
Definition: egs_brachy.cpp:2183
-
EB_Application::discardTopParticle
void discardTopParticle(int idisc=1)
Definition: egs_brachy.cpp:1563
-
EB_Application::gcr_phantom_reg
int gcr_phantom_reg
region of phantom to use for getCurrentResult (default to 0)
Definition: egs_brachy.h:177
-
EB_Application::effective_histories
EGS_Float effective_histories
Definition: egs_brachy.h:369
-
EB_Application::initBCSE
int initBCSE(EGS_Input *)
Initialize BCSE variance reduction if requested.
Definition: egs_brachy.cpp:1180
-
EB_Application::source_i_do_rr
bool source_i_do_rr
enable range rejection in sources
Definition: egs_brachy.h:171
-
EB_Application::output_egsphant
bool output_egsphant
true if user requests egsphant ouput
Definition: egs_brachy.h:123
-
EB_Application::latch_control
Latch latch_control
Definition: egs_brachy.h:371
-
EB_Application::printIncludedFiles
void printIncludedFiles()
Definition: egs_brachy.cpp:286
-
EB_Application::global_i_do_rr
bool global_i_do_rr
enable range rejection outside of sources
Definition: egs_brachy.h:168
-
EB_Application::source_pcut
EGS_Float source_pcut
pcut for source objects
Definition: egs_brachy.h:164
-
EB_Application::bcse_factor
EGS_Float bcse_factor
Definition: egs_brachy.h:159
-
EB_Application::egsBrachyReadData
int egsBrachyReadData(istream *)
helper function for outputData
Definition: egs_brachy.cpp:2350
-
EB_Application::isStuck
bool isStuck()
Definition: egs_brachy.cpp:1603
-
EB_Application::initTrackLengthScoring
void initTrackLengthScoring(EGS_Input *)
track length scoring initialization
Definition: egs_brachy.cpp:1257
-
EB_Application::revision
static string revision
the usercode revision number
Definition: egs_brachy.h:200
-
EB_Application::active_source
int active_source
Definition: egs_brachy.h:111
-
EB_Application::global_pcut
EGS_Float global_pcut
pcut for source objects
Definition: egs_brachy.h:166
-
EB_Application::getCurrentResult
void getCurrentResult(double &sum, double &sum2, double &norm, double &count)
Reports the current results for this batch of the simulation.
Definition: egs_brachy.cpp:2030
-
EB_Application::correctVolumes
int correctVolumes()
run the volume correction routines
Definition: egs_brachy.cpp:596
-
EB_Application::bcse_med_num
int bcse_med_num
Definition: egs_brachy.h:158
-
EB_Application::output_3ddose_files
bool output_3ddose_files
false if run mode is 'volume correction only'
Definition: egs_brachy.h:121
-
EB_Application::initSpectrumScoring
void initSpectrumScoring(EGS_Input *)
Initialize all spectrum scoring objects.
Definition: egs_brachy.cpp:1217
-
EB_Application::gcr_phantom
EB_Phantom * gcr_phantom
phantom object to use in getCurrentResult (defaults to 1st phantom)
Definition: egs_brachy.h:176
-
EB_Application::getPhantomByName
EB_Phantom * getPhantomByName(string name)
takes a phantom geometry name and returns the EB_Phantom object
Definition: egs_brachy.cpp:953
-
EB_Application::addRecycledParticlesToStack
void addRecycledParticlesToStack(EGS_Particle *p, bool new_hist=false)
Definition: egs_brachy.cpp:1571
-
EB_Application::DEFAULT_BCSE_FACTOR
static const EGS_Float DEFAULT_BCSE_FACTOR
Definition: egs_brachy.h:160
-
EB_Application::media_muen_names
map< string, string > media_muen_names
Definition: egs_brachy.h:151
-
EB_Application::readDataHelper
int readDataHelper(istream *)
helper function for outputData
Definition: egs_brachy.cpp:2379
-
EB_Application::initScatScoring
void initScatScoring(EGS_Input *)
energy deposition scoring initialization
Definition: egs_brachy.cpp:1392
-
EB_Application::superpos_geom
EGS_ASwitchedEnvelope * superpos_geom
an ASwitchedEnv cast of simulation geometry.
Definition: egs_brachy.h:142
-
EB_Application::output_dose_format
string output_dose_format
text or gzip
Definition: egs_brachy.h:122
-
EB_Application::source_weights
vector< EGS_Float > source_weights
Definition: egs_brachy.h:110
-
EB_Application::startNewShower
int startNewShower()
Definition: egs_brachy.cpp:2133
-
EB_Application::createTransforms
vector< EGS_AffineTransform * > createTransforms(EGS_Input *input)
Definition: egs_brachy.cpp:384
-
EB_Application::enterNewRegion
virtual void enterNewRegion()
Definition: egs_brachy.cpp:1544
-
EB_Application::extra_scoring_vols
map< string, vector< EGS_Float > > extra_scoring_vols
Definition: egs_brachy.h:180
-
EB_Application::resetCounter
void resetCounter()
Reset the application to a 'pristine' state. Adapted from egs_application.cpp to allow combining in t...
Definition: egs_brachy.cpp:2498
-
EB_Application::combineResults
int combineResults()
Definition: egs_brachy.cpp:2436
-
EB_Application::base_transform
EGS_AffineTransform * base_transform
same as source_transforms[0]
Definition: egs_brachy.h:147
-
EB_Application::source_envelope_geom
EGS_BaseGeometry * source_envelope_geom
geometry that the sources are embedded in
Definition: egs_brachy.h:141
-
EB_Application::phantom_geoms
vector< EB_Phantom * > phantom_geoms
pointers to all of the phantom objects
Definition: egs_brachy.h:144
-
EB_Application::outputResults
void outputResults()
Definition: egs_brachy.cpp:1910
-
EB_Application::calcEffectiveHistories
void calcEffectiveHistories()
Definition: egs_brachy.cpp:1891
-
EB_Application::score_scat
bool score_scat
true when scatter scoring is enabled
Definition: egs_brachy.h:117
-
EB_Application::output_egsphant_format
string output_egsphant_format
text or gzip
Definition: egs_brachy.h:124
-
EB_Application::egsBrachyOutputData
int egsBrachyOutputData(ostream *)
helper function for outputData
Definition: egs_brachy.cpp:2210
-
EB_Application::gz_data_out
ogzstream * gz_data_out
GZip file for outputing egsdat.
Definition: egs_brachy.h:197
-
EB_Application::initCrossSections
int initCrossSections()
Definition: egs_brachy.cpp:833
-
EB_Application::nbr_split
int nbr_split
Number of times to split bremstrahlung phtons.
Definition: egs_brachy.h:155
-
EB_Application::media_muen
map< int, EGS_Interpolator * > media_muen
Map from medium index to muen interpolator for that medium.
Definition: egs_brachy.h:150
-
EB_Application::gen_vc_results
ebvolcor::Results gen_vc_results
results from general volume correction
Definition: egs_brachy.h:186
-
EB_Application::base_transform_inv
EGS_AffineTransform * base_transform_inv
same as source_transforms[0].inverse()
Definition: egs_brachy.h:148
-
EB_Application::steps_in_sources
map< int, EGS_I64 > steps_in_sources
Definition: egs_brachy.h:193
-
EB_Application::output_voxinfo
bool output_voxinfo
true if user requests voxel info file
Definition: egs_brachy.h:126
-
EB_Application::steps_in_other
map< int, EGS_I64 > steps_in_other
Definition: egs_brachy.h:195
-
EB_Application::phsp
PHSPControl * phsp
Definition: egs_brachy.h:113
-
EB_Application::ausgab
int ausgab(int iarg)
user scoring of dose, spectra etc
Definition: egs_brachy.cpp:1633
-
EB_Application::readData
int readData()
Read data required for restarting simulations.
Definition: egs_brachy.cpp:2394
-
EB_Application::egsApplicationReadData
int egsApplicationReadData(istream *)
helper function for outputData
Definition: egs_brachy.cpp:2299
-
EB_Application::nsources
int nsources
total number of particle sources in current simulation
Definition: egs_brachy.h:367
-
EB_Application::flu_cutoff
EGS_Float flu_cutoff
fluorescent photon cutoff energy
Definition: egs_brachy.h:162
-
EB_Application::cur_R
EGS_Float cur_R
Definition: egs_brachy.h:137
-
EB_Application::RunMode
RunMode
Definition: egs_brachy.h:92
-
EB_Application::RM_VC_ONLY
@ RM_VC_ONLY
Run volume correction routines then quit.
Definition: egs_brachy.h:95
-
EB_Application::RM_SUPERPOSITION
@ RM_SUPERPOSITION
Superposition mode for intersource effects.
Definition: egs_brachy.h:94
-
EB_Application::RM_NORMAL
@ RM_NORMAL
Standard running mode.
Definition: egs_brachy.h:93
-
EB_Application::egsAdvApplicationReadData
int egsAdvApplicationReadData(istream *)
helper function for outputData
Definition: egs_brachy.cpp:2322
-
EB_Application::do_bcse
bool do_bcse
Definition: egs_brachy.h:157
-
EB_Application::egsApplicationOutputData
int egsApplicationOutputData(ostream *)
helper function for outputData
Definition: egs_brachy.cpp:2159
-
EB_Application::ginfo
GeomInfo ginfo
meta data about the geometries
Definition: egs_brachy.h:174
-
EB_Application::clearAusgabCalls
void clearAusgabCalls()
disable all ausgab calls
Definition: egs_brachy.cpp:1238
-
EB_Application::source_vc_results
ebvolcor::Results source_vc_results
results from source volume correctio box phantom
Definition: egs_brachy.h:185
-
EB_Application::is_phsp_source
bool is_phsp_source
Definition: egs_brachy.h:108
-
EB_Application::initXCCScaling
void initXCCScaling(EGS_Input *)
Initialize cross section scaling if requested.
Definition: egs_brachy.cpp:1434
-
EB_Application::simulateSingleShower
int simulateSingleShower()
Definition: egs_brachy.cpp:2048
-
EB_Application::source_ecut
EGS_Float source_ecut
ecut for source objects
Definition: egs_brachy.h:163
-
EB_Application::score_edep
bool score_edep
true when energy deposition is enabled
Definition: egs_brachy.h:116
-
EB_Application::initGCRScoring
void initGCRScoring(EGS_Input *)
setup which phantom/region will be used for getCurrentResult
Definition: egs_brachy.cpp:909
-
EB_Application::source_e_max_rr
EGS_Float source_e_max_rr
max range rejection energy for source objects
Definition: egs_brachy.h:172
-
EB_Application::initScoring
int initScoring()
initialze all scoring and variance reduction parameters
Definition: egs_brachy.cpp:875
-
EB_Application::addState
int addState(istream &data)
Add data from a parallel job. Add standard egs++ data as well as egs_brachy specific scoring informat...
Definition: egs_brachy.cpp:2519
-
EB_Application::global_ecut
EGS_Float global_ecut
ecut for source objects
Definition: egs_brachy.h:165
-
EB_Application::initGeometry
int initGeometry()
override default initGeometry so we can manually create our own geometry.
Definition: egs_brachy.cpp:306
-
EB_Application::initOutputFiles
void initOutputFiles(EGS_Input *)
set up whether to output extra info files
Definition: egs_brachy.cpp:964
-
EB_Application::initVarianceReduction
int initVarianceReduction()
initialze all variance reduction parameters
Definition: egs_brachy.cpp:1004
-
EB_Application::p_init_locs
vector< EGS_Vector > p_init_locs
Definition: egs_brachy.h:133
-
EB_Application::score_tlen
bool score_tlen
true when tracklength estimator is enabled
Definition: egs_brachy.h:115
-
EB_Application::run_mode
RunMode run_mode
Which run mode are we using (RM_NORMAL, RM_SUPERPOSITION or RM_VC_ONLY *‍/.
Definition: egs_brachy.h:99
-
EB_Application::recycle_opts
RecycleOpts * recycle_opts
Definition: egs_brachy.h:106
-
EB_Application::single_generator
bool single_generator
Definition: egs_brachy.h:107
-
EB_Application::record_n_init
int record_n_init
if > 0 write initial pos of record_n_init particles to {input_file}.pinit
Definition: egs_brachy.h:132
-
EB_Application::file_vc_results
ebvolcor::FileResults file_vc_results
results from precomputed volume correction
Definition: egs_brachy.h:187
-
EB_Application::runSimulation
virtual int runSimulation()
Definition: egs_brachy.cpp:2040
-
EB_Phantom
A class to represent a single phantom for scoring dose in egs_brachy.
Definition: phantom.h:71
-
EB_Phantom::YDIR
@ YDIR
YDIR=1 y dir for rectilinear, r dir for cylindrical.
Definition: phantom.h:137
-
EB_Phantom::XDIR
@ XDIR
XDIR=0 x dir for rectilinear, r dir for spherical, z dir for cylindrical.
Definition: phantom.h:136
-
EB_Phantom::ZDIR
@ ZDIR
ZDIR=2 z dir for rectilinear.
Definition: phantom.h:138
-
EB_Phantom::scoreTlen
void scoreTlen(int ir, EGS_Float dose, EGS_Particle *p)
add tracklength dose to region ir
Definition: phantom.cpp:133
-
EB_Phantom::getUncorrectedVolume
EGS_Float getUncorrectedVolume(int ireg)
get corrected volume for a given region
Definition: phantom.cpp:302
-
EB_Phantom::geometry
EGS_BaseGeometry * geometry
the phantom geometry object
Definition: phantom.h:284
-
EB_Phantom::getCurrentScore
void getCurrentScore(int ireg, double &sum, double &sum2)
get current tlen score for region
Definition: phantom.cpp:332
-
EB_Phantom::getTlenNorm
double getTlenNorm(int ireg)
Definition: phantom.cpp:344
-
EB_Phantom::setEffectiveHistories
void setEffectiveHistories(EGS_Float current_case)
set number of effective histories for normalizing scoring arrays
Definition: phantom.cpp:253
-
EB_Phantom::needs_user_geoms
bool needs_user_geoms
this phantom requires user specified geometries
Definition: phantom.h:296
-
EB_Phantom::scoreEdep
void scoreEdep(int ir, EGS_Float dose)
add energy deposition dose to region ir
Definition: phantom.cpp:155
-
EB_Phantom::getRealMass
EGS_Float getRealMass(int ireg)
return (corrected) real mass for region
Definition: phantom.cpp:291
-
EB_Phantom::setCorrectedVolume
void setCorrectedVolume(int ir, double fraction, double unc=0)
Allow user to tell phantom what the actual volume of a region is.
Definition: phantom.cpp:202
-
EB_Phantom::getCorrectedVolume
EGS_Float getCorrectedVolume(int ireg)
get uncorrected volume for a given region
Definition: phantom.cpp:314
-
EB_Phantom::getUncorrectedMass
EGS_Float getUncorrectedMass(int ireg)
return uncorrected for region
Definition: phantom.cpp:298
-
EB_Phantom::avgVoxelVol
EGS_Float avgVoxelVol()
return average voxel volume
Definition: phantom.cpp:855
-
EB_TimingTree::stopTimer
void stopTimer()
Definition: timing.h:139
-
EB_TimingTree::outputInfo
void outputInfo()
Definition: timing.h:159
-
EB_TimingTree::addTimer
void addTimer(string name)
Definition: timing.h:132
-
EnergyScoringStats
a class to use for scoring information about total energy initialzed, escaping sources etc
Definition: spec_scoring.h:57
- -
EnergyScoringStats::readData
int readData(istream *ifile)
Definition: spec_scoring.h:192
-
EnergyScoringStats::outputData
int outputData(ostream *ofile)
Definition: spec_scoring.h:185
-
EnergyScoringStats::addState
int addState(istream &data)
Definition: spec_scoring.h:205
-
EnergyScoringStats::outputResults
void outputResults()
write results to console
Definition: spec_scoring.h:165
-
GeomInfo::source_envelope_name
string source_envelope_name
Definition: ginfo.h:131
-
GeomInfo::ordered_geom_data
vector< GeomRegionInfo > ordered_geom_data
Definition: ginfo.h:149
-
GeomInfo::isSource
bool isSource(int ir)
Definition: ginfo.cpp:503
-
GeomInfo::phantomFromRegion
int phantomFromRegion(int ir)
return the phantom index for this region number or -1 if region is not in a phantom
Definition: ginfo.cpp:508
-
GeomInfo::initializeFromInput
int initializeFromInput(EGS_Input *input)
Initialize the GeomInfo structure (ginfo) This function reads the geometry input block,...
Definition: ginfo.cpp:85
-
GeomInfo::ngeom
int ngeom
total number of geometries created
Definition: ginfo.h:138
-
GeomInfo::isPhantom
bool isPhantom(int ir)
Definition: ginfo.cpp:498
-
GeomInfo::setGeometryIndexes
void setGeometryIndexes(EGS_BaseGeometry *sim_geom)
Setup all arrays required to decide which geometry/phantom a region is in and whether or not we are s...
Definition: ginfo.cpp:441
-
GeomInfo::printInfo
void printInfo()
Definition: ginfo.cpp:513
-
GeomInfo::globalToLocal
GeomRegT globalToLocal(int ir)
convert global region number to (EGS_BaseGeometry, local_reg_num) pair
Definition: ginfo.cpp:479
-
GeomInfo::nreg_total
int nreg_total
total number of regions in the simulation geometry
Definition: ginfo.h:139
-
GeomInfo::globalToLocalReg
int globalToLocalReg(int ir)
convert global region number to local_reg_num
Definition: ginfo.cpp:487
-
GeomInfo::source_names
vector< string > source_names
Definition: ginfo.h:134
-
GeomInfo::phantom_names
vector< string > phantom_names
Definition: ginfo.h:132
-
Latch::hasEscaped
static bool hasEscaped(EGS_Particle *p)
True if particle is currently in a source.
Definition: latch.cpp:134
-
Latch::addScatter
static void addScatter(EGS_Particle *p)
Definition: latch.cpp:80
- -
PHSPControl::outputResults
void outputResults()
output file name and number of particles written
Definition: phsp.cpp:199
-
PHSPControl::finish
void finish(EGS_I64 n_orig_particles)
set final number of particles written and destroy source
Definition: phsp.cpp:193
-
PHSPControl::destroySource
void destroySource()
destroy the source
Definition: phsp.cpp:221
-
Publisher::notify
void notify(EB_Message message, void *what=0, Subscriber *s=0)
Definition: pubsub.cpp:46
- -
RecycleOpts::nrecycle
int nrecycle
Definition: recycle.h:71
-
RecycleOpts::rotate
bool rotate
Definition: recycle.h:72
-
RecycleOpts::printInfo
void printInfo()
Definition: recycle.cpp:68
-
ebvolcor::VolumeCorrector
An object for controlling the volume correction routine.
Definition: eb_volcor.h:311
-
ebvolcor::VolumeCorrector::runSourceCorrection
Results runSourceCorrection(EB_TimingTree &timer)
Definition: eb_volcor.h:366
-
ebvolcor::VolumeCorrector::runGeneralCorrection
Results runGeneralCorrection(EB_TimingTree &timer)
Definition: eb_volcor.h:394
-
ebvolcor::VolumeCorrector::runFileCorrection
FileResults runFileCorrection(EB_TimingTree &timer)
Definition: eb_volcor.h:422
-
gzstreambase::close
void close()
Definition: gzstream.C:154
-
gzstreambuf::is_open
int is_open()
Definition: gzstream.h:64
- -
igzstream::open
void open(const char *name, int open_mode=std::ios::in)
Definition: gzstream.h:108
-
igzstream::rdbuf
gzstreambuf * rdbuf()
Definition: gzstream.h:105
-
muen::MuenDataParser
class for parsing muen data from a file.
Definition: muen.h:131
-
muen::MuenDataParser::setMuenFile
int setMuenFile(string filename)
Definition: muen.h:207
-
muen::MuenDataParser::getMuenInterpolator
EGS_Interpolator * getMuenInterpolator(string med_name)
Create a new EGS_Interpolator of muen data for the requested medium and return pointer to it....
Definition: muen.h:228
- -
egsOpenUnits
#define egsOpenUnits
Definition: egs_brachy.cpp:71
-
egsGetRNGArray
#define egsGetRNGArray
Definition: egs_brachy.cpp:63
-
egsGetSteps
#define egsGetSteps
Definition: egs_brachy.cpp:67
+
+
2534void EB_Application::resetCounter() {
+
2535 // Reset everything in the base class
+
2536 EGS_AdvancedApplication::resetCounter();
+
2537 // Reset our own data to zero.
+
2538
+
2539 for (int i=-1; i < 2; i++) {
+
2540 steps_in_sources[i] = 0;
+
2541 steps_in_phantoms[i] = 0;
+
2542 steps_in_other[i] = 0;
+
2543 }
+
2544
+
2545 if (escoring) {
+
2546 escoring->resetCounter();
+
2547 }
+
2548
+
2549 vector<BaseSpectrumScorer *>::iterator spec_it = spectrum_scorers.begin();
+
2550 for (; spec_it != spectrum_scorers.end(); ++spec_it) {
+
2551 (*spec_it)->resetCounter();
+
2552 }
+
2553
+
2554 vector<EB_Phantom *>::iterator phant_it = phantom_geoms.begin();
+
2555 for (; phant_it != phantom_geoms.end(); phant_it++) {
+
2556 (*phant_it)->resetCounter();
+
2557 }
+
2558
+
2559}
+
+
2560
+
+
2561int EB_Application::addState(istream &data) {
+
2562 // Call first the base class addState() function to read and add
+
2563 // all data related to source, RNG, CPU time, etc.
+
2564 int err = EGS_AdvancedApplication::addState(data);
+
2565 if (err) {
+
2566 return err;
+
2567 }
+
2568
+
2569 for (int i=-1; i < 2; i++) {
+
2570 EGS_I64 steps_in_sources_tmp;
+
2571 EGS_I64 steps_in_phantoms_tmp;
+
2572 EGS_I64 steps_in_other_tmp;
+
2573
+
2574 data >> steps_in_sources_tmp;
+
2575 data >> steps_in_phantoms_tmp;
+
2576 data >> steps_in_other_tmp;
+
2577
+
2578 steps_in_sources[i] += steps_in_sources_tmp;
+
2579 steps_in_phantoms[i] += steps_in_phantoms_tmp;
+
2580 steps_in_other[i] += steps_in_other_tmp;
+
2581 }
+
2582
+
2583 if (escoring) {
+
2584 err = escoring->addState(data);
+
2585 if (err) {
+
2586 return err;
+
2587 }
+
2588 }
+
2589
+
2590 vector<BaseSpectrumScorer *>::iterator spec_it = spectrum_scorers.begin();
+
2591 for (; spec_it != spectrum_scorers.end(); ++spec_it) {
+
2592 err = (*spec_it)->addState(data);
+
2593 if (err) {
+
2594 return err;
+
2595 }
+
2596 }
+
2597
+
2598 vector<EB_Phantom *>::iterator phant_it = phantom_geoms.begin();
+
2599 for (; phant_it != phantom_geoms.end(); phant_it++) {
+
2600 err = (*phant_it)->addState(data);
+
2601 if (err) {
+
2602 return err;
+
2603 }
+
2604 }
+
2605
+
2606 return 0;
+
2607
+
2608}
+
+
2609/* end of stop/restart functionality ****************************************/
+
2610
+
+
2611bool fileExists(const string &name) {
+
2612 struct stat buffer;
+
2613 return (stat(name.c_str(), &buffer) == 0);
+
2614}
+
+
2615
+
+
2616int EB_Application::howManyJobsDone() {
+
2617
+
2618 char buf[512];
+
2619 int n_of_egsdat = 0;
+
2620
+
2621 bool use_gz = output_egsdat_format == "gzip";
+
2622 string name("%s_w%d.egsdat");
+
2623 name += (use_gz ? ".gz" : "");
+
2624
+
2625 for (int i = first_parallel; i < first_parallel + n_parallel; i++) {
+
2626 sprintf(buf,name.c_str(),final_output_file.c_str(),i);
+
2627 string dfile = egsJoinPath(app_dir,buf);
+
2628 if (fileExists(dfile)) {
+
2629 n_of_egsdat++;
+
2630 }
+
2631 }
+
2632
+
2633 return n_of_egsdat;
+
2634}
+
+
2635
+
+
2636EB_UniformRunControl::EB_UniformRunControl(EB_Application *a, string egsdat_format) :
+
2637 EGS_RunControl(a), app(a), output_egsdat_format(egsdat_format), milliseconds(1000), check_intervals(5),
+
2638 njob(0), npar(app->getNparallel()), ipar(app->getIparallel()), ifirst(app->getFirstParallel()),
+
2639 check_egsdat(true), watcher_job(false) {
+
2640
+
2641 rco_type = uniform;
+
2642
+
2643 if (input) {
+
2644
+
2645 /*Change waiting time to check for parallel run completion*/
+
2646 int dummy;
+
2647 int err = input->getInput("interval wait time", dummy);
+
2648 if (!err) {
+
2649 milliseconds = dummy;
+
2650 }
+
2651
+
2652 /*Change how many times to check for parallel run completion*/
+
2653 err = input->getInput("number of intervals", dummy);
+
2654 if (!err) {
+
2655 check_intervals = dummy;
+
2656 }
+
2657
+
2658 /* Define watcher jobs to check for parallel run completion*/
+
2659 vector<int> w_jobs;
+
2660 err = input->getInput("watcher jobs", w_jobs);
+
2661 if (!err) {
+
2662 for (int i = 0; i < w_jobs.size(); i++) {
+
2663 if (ipar == w_jobs[i]) {
+
2664 watcher_job = true;
+
2665 break;
+
2666 }
+
2667 }
+
2668 }
+
2669 else { // use defaults
+
2670 /* last job is watcher job */
+
2671 if (ipar == ifirst + npar - 1) {
+
2672 watcher_job = true;
+
2673 }
+
2674 else {
+
2675 watcher_job = false;
+
2676 }
+
2677 }
+
2678
+
2679 /* Request checking parallel run completion */
+
2680 vector<string> check_options;
+
2681 check_options.push_back("yes");
+
2682 check_options.push_back("no");
+
2683 int ichk = input->getInput("check jobs completed",check_options,0);
+
2684 if (ichk != 0) {
+
2685 check_egsdat = false; // true by default
+
2686 }
+
2687
+
2688 }
+
2689 else { // use defaults if no RCO input found
+
2690 /* last job is watcher job */
+
2691 if (ipar == ifirst + npar - 1) {
+
2692 watcher_job = true;
+
2693 }
+
2694 }
+
2695}
+
+
2696
+
+
2697int EB_UniformRunControl::startSimulation() {
+
2698
+
2699
+
2700 /* Check run completion based on *egsdat files requires erasing
+
2701 existing files from previous runs.
+
2702 */
+
2703 bool use_gz = output_egsdat_format == "gzip";
+
2704 string name("%s_w%d.egsdat");
+
2705 name += (use_gz ? ".gz" : "");
+
2706
+
2707 if (check_egsdat) {
+
2708 char buf[512];
+
2709 sprintf(buf,name.c_str(),app->getFinalOutputFile().c_str(), ipar);
+
2710 string datFile = egsJoinPath(app->getAppDir(),buf);
+
2711 if (remove(datFile.c_str()) == 0) {
+
2712 egsWarning("EB_UniformRunControl: %s deleted\n",
+
2713 datFile.c_str());
+
2714 }
+
2715 }
+
2716
+
2717 return EGS_RunControl::startSimulation();
+
2718}
+
+
2719
+
+
2720void EB_UniformRunControl::describeRCO() {
+
2721
+
2722 EGS_RunControl::describeRCO();
+
2723
+
2724 if (watcher_job) {
+
2725 if (check_egsdat) {
+
2726 egsInformation(
+
2727 " Watcher job: remains running after completion checking\n"
+
2728 " for other jobs finishing every %d s for %d s!\n",
+
2729 milliseconds/1000, check_intervals*milliseconds/1000);
+
2730 }
+
2731 else {
+
2732 egsInformation(
+
2733 " Option to check for finishing jobs is OFF!\n\n");
+
2734 }
+
2735 }
+
2736
+
2737}
+
+
2738
+
+
2739void rco_sleep(const int &mscnds) {
+
2740#ifdef WIN32
+
2741 Sleep(mscnds);
+
2742#else
+
2743 usleep(mscnds * 1000);
+
2744#endif
+
2745}
+
+
2746
+
+
2747int EB_UniformRunControl::finishSimulation() {
+
2748 int err = EGS_RunControl::finishSimulation();
+
2749 if (err < 0) {
+
2750 return err;
+
2751 }
+
2752 /* Check and wait for all jobs to finish */
+
2753 if (watcher_job) {
+
2754 int interval = 0, njobs_done = 0, njobs_done_old= 0;
+
2755 while (interval < check_intervals) {
+
2756 rco_sleep(milliseconds);
+
2757 if (check_egsdat) {
+
2758 njobs_done = app->howManyJobsDone();
+
2759 //egsInformation("\n-> Finished %d jobs...\n",njobs_done);
+
2760 if (njobs_done == npar - 1) {
+
2761 watcher_job=false;//don't enter this after all jobs done!
+
2762 break;
+
2763 }
+
2764 // Only combine if new jobs finished
+
2765 if (njobs_done_old < njobs_done) {
+
2766 egsInformation("=> Combining %d jobs ...\n",njobs_done);
+
2767 app->combinePartialResults();
+
2768 }
+
2769 njobs_done_old = njobs_done;
+
2770 }
+
2771 interval++;
+
2772 }
+
2773 return 1;
+
2774 }
+
2775 /*I am not a watcher job, do not combine results yet!*/
+
2776 return 0;
+
2777}
+
+
2778
+
2779#ifdef BUILD_APP_LIB
+
2780APP_LIB(EB_Application);
+
2781#else
+
2782APP_MAIN(EB_Application);
+
2783#endif
+
BaseSpectrumScorer
abstract base class for scoring spectrum information
Definition spec_scoring.h:260
+
BaseSpectrumScorer::getSpectrumScorer
static BaseSpectrumScorer * getSpectrumScorer(EGS_Input *inp, EGS_BaseSource *source, GeomInfo *ginfo, Publisher *publisher)
factory method for creating one of the derived spectrum scoring classes
Definition spec_scoring.cpp:85
+
BaseSpectrumScorer::getInfo
virtual string getInfo() const
Definition spec_scoring.h:376
+
EB_Application
The main egs_brachy application class. See the Main Page for full documentation.
Definition egs_brachy.h:91
+
EB_Application::spectrum_scorers
vector< BaseSpectrumScorer * > spectrum_scorers
Definition egs_brachy.h:104
+
EB_Application::extra_scoring_mass
map< string, vector< EGS_Float > > extra_scoring_mass
Definition egs_brachy.h:182
+
EB_Application::initRunControl
int initRunControl()
egs_brachy specific run control initialization
Definition egs_brachy.cpp:788
+
EB_Application::initPHSPScoring
void initPHSPScoring(EGS_Input *)
set up phsp scoring
Definition egs_brachy.cpp:1008
+
EB_Application::checkSourceOverlaps
int checkSourceOverlaps(EGS_Input *)
Definition egs_brachy.cpp:448
+
EB_Application::escoring
EnergyScoringStats * escoring
Energy related scoring/stats.
Definition egs_brachy.h:103
+
EB_Application::initSource
int initSource()
Definition egs_brachy.cpp:725
+
EB_Application::initSimulation
int initSimulation()
set the run mode and then call EGS_AdvancedApplication::initSimulation
Definition egs_brachy.cpp:768
+
EB_Application::initEDepScoring
void initEDepScoring(EGS_Input *)
energy deposition scoring initialization
Definition egs_brachy.cpp:1389
+
EB_Application::copyParticleToSourceLoc
void copyParticleToSourceLoc(EGS_Particle *p, int source, bool kill_orig, bool rotate, EGS_Float new_wt)
Definition egs_brachy.cpp:1494
+
EB_Application::doPhotonSplitting
void doPhotonSplitting(int)
Definition egs_brachy.cpp:1863
+
EB_Application::outputData
int outputData()
Output intermediate results. The egs_brachy version outputs the standard egs++ data along with egs_br...
Definition egs_brachy.cpp:2287
+
EB_Application::source_transforms
vector< EGS_AffineTransform * > source_transforms
transforms to locations of all sources
Definition egs_brachy.h:147
+
EB_Application::extra_scoring_reg
map< string, vector< int > > extra_scoring_reg
Definition egs_brachy.h:180
+
EB_Application::initDoseScaling
void initDoseScaling(EGS_Input *)
Initialize dose scaling factor if requested.
Definition egs_brachy.cpp:1445
+
EB_Application::steps_in_phantoms
map< int, EGS_I64 > steps_in_phantoms
Definition egs_brachy.h:195
+
EB_Application::initSourceTransforms
int initSourceTransforms()
read in the location of all particle sources
Definition egs_brachy.cpp:407
+
EB_Application::n_stuck
EGS_I64 n_stuck
Definition egs_brachy.h:140
+
EB_Application::outputDataHelper
int outputDataHelper(ostream *)
helper function for outputData
Definition egs_brachy.cpp:2273
+
EB_Application::timing_blocks
EB_TimingTree timing_blocks
Track CPU times of various functions.
Definition egs_brachy.h:192
+
EB_Application::initRussianRoulette
int initRussianRoulette(EGS_Input *)
Initialize Russian roulette variance reduction if requested.
Definition egs_brachy.cpp:1170
+
EB_Application::steps_at_same_loc
int steps_at_same_loc
Definition egs_brachy.h:139
+
EB_Application::extra_scoring_doses
map< string, EGS_ScoringArray * > extra_scoring_doses
Definition egs_brachy.h:183
+
EB_Application::output_volcor_format
string output_volcor_format
text or gzip
Definition egs_brachy.h:131
+
EB_Application::createPhantoms
int createPhantoms()
set up Phantom objects for any geometries that user has requested scoring for
Definition egs_brachy.cpp:688
+
EB_Application::pevent_pub
Publisher pevent_pub
Particle event publisher.
Definition egs_brachy.h:190
+
EB_Application::do_brem_split
bool do_brem_split
Definition egs_brachy.h:155
+
EB_Application::startNewParticle
virtual void startNewParticle()
Set source ecut/pcut if different from global ecut/pcut.
Definition egs_brachy.cpp:1553
+
EB_Application::describeUserCode
void describeUserCode() const
Print information about the egs_brachy user code.
Definition egs_brachy.cpp:114
+
EB_Application::initRunMode
int initRunMode()
Get run mode from the input file.
Definition egs_brachy.cpp:815
+
EB_Application::describeSimulation
void describeSimulation()
Describe the simulation.
Definition egs_brachy.cpp:128
+
EB_Application::enableAusgabCalls
void enableAusgabCalls(int ncalls, AusgabCall calls[])
enable an array of ausgab calls
Definition egs_brachy.cpp:1382
+
EB_Application::initAusgabCalls
void initAusgabCalls()
setup any required ausgab calls
Definition egs_brachy.cpp:1261
+
EB_Application::initMuenData
void initMuenData(EGS_Input *)
load muen data for requested media
Definition egs_brachy.cpp:1325
+
EB_Application::output_egsdat_format
string output_egsdat_format
text or gzip
Definition egs_brachy.h:120
+
EB_Application::run_mode_name
string run_mode_name
Definition egs_brachy.h:101
+
EB_Application::output_volcor_phantoms
vector< string > output_volcor_phantoms
vector of phantom names to output volume correctino files for
Definition egs_brachy.h:130
+
EB_Application::output_voxinfo_format
string output_voxinfo_format
text or gzip
Definition egs_brachy.h:128
+
EB_Application::howManyJobsDone
int howManyJobsDone()
Definition egs_brachy.cpp:2616
+
EB_Application::gz_data_in
igzstream * gz_data_in
GZip file for outputing egsdat.
Definition egs_brachy.h:199
+
EB_Application::last_R
EGS_Float last_R
Definition egs_brachy.h:137
+
EB_Application::global_e_max_rr
EGS_Float global_e_max_rr
max range rejection energy globally
Definition egs_brachy.h:170
+
EB_Application::egsAdvApplicationOutputData
int egsAdvApplicationOutputData(ostream *)
helper function for outputData
Definition egs_brachy.cpp:2207
+
EB_Application::discardTopParticle
void discardTopParticle(int idisc=1)
Definition egs_brachy.cpp:1587
+
EB_Application::gcr_phantom_reg
int gcr_phantom_reg
region of phantom to use for getCurrentResult (default to 0)
Definition egs_brachy.h:178
+
EB_Application::effective_histories
EGS_Float effective_histories
Definition egs_brachy.h:370
+
EB_Application::initBCSE
int initBCSE(EGS_Input *)
Initialize BCSE variance reduction if requested.
Definition egs_brachy.cpp:1196
+
EB_Application::source_i_do_rr
bool source_i_do_rr
enable range rejection in sources
Definition egs_brachy.h:172
+
EB_Application::output_egsphant
bool output_egsphant
true if user requests egsphant ouput
Definition egs_brachy.h:124
+
EB_Application::latch_control
Latch latch_control
Definition egs_brachy.h:372
+
EB_Application::printIncludedFiles
void printIncludedFiles()
Definition egs_brachy.cpp:287
+
EB_Application::global_i_do_rr
bool global_i_do_rr
enable range rejection outside of sources
Definition egs_brachy.h:169
+
EB_Application::source_pcut
EGS_Float source_pcut
pcut for source objects
Definition egs_brachy.h:165
+
EB_Application::bcse_factor
EGS_Float bcse_factor
Definition egs_brachy.h:160
+
EB_Application::egsBrachyReadData
int egsBrachyReadData(istream *)
helper function for outputData
Definition egs_brachy.cpp:2380
+
EB_Application::isStuck
bool isStuck()
Definition egs_brachy.cpp:1627
+
EB_Application::initTrackLengthScoring
void initTrackLengthScoring(EGS_Input *)
track length scoring initialization
Definition egs_brachy.cpp:1273
+
EB_Application::revision
static string revision
the usercode revision number
Definition egs_brachy.h:201
+
EB_Application::active_source
int active_source
Definition egs_brachy.h:112
+
EB_Application::global_pcut
EGS_Float global_pcut
pcut for source objects
Definition egs_brachy.h:167
+
EB_Application::getCurrentResult
void getCurrentResult(double &sum, double &sum2, double &norm, double &count)
Reports the current results for this batch of the simulation.
Definition egs_brachy.cpp:2054
+
EB_Application::correctVolumes
int correctVolumes()
run the volume correction routines
Definition egs_brachy.cpp:597
+
EB_Application::bcse_med_num
int bcse_med_num
Definition egs_brachy.h:159
+
EB_Application::output_3ddose_files
bool output_3ddose_files
false if run mode is 'volume correction only'
Definition egs_brachy.h:122
+
EB_Application::initSpectrumScoring
void initSpectrumScoring(EGS_Input *)
Initialize all spectrum scoring objects.
Definition egs_brachy.cpp:1233
+
EB_Application::gcr_phantom
EB_Phantom * gcr_phantom
phantom object to use in getCurrentResult (defaults to 1st phantom)
Definition egs_brachy.h:177
+
EB_Application::getPhantomByName
EB_Phantom * getPhantomByName(string name)
takes a phantom geometry name and returns the EB_Phantom object
Definition egs_brachy.cpp:968
+
EB_Application::addRecycledParticlesToStack
void addRecycledParticlesToStack(EGS_Particle *p, bool new_hist=false)
Definition egs_brachy.cpp:1595
+
EB_Application::DEFAULT_BCSE_FACTOR
static const EGS_Float DEFAULT_BCSE_FACTOR
Definition egs_brachy.h:161
+
EB_Application::media_muen_names
map< string, string > media_muen_names
Definition egs_brachy.h:152
+
EB_Application::readDataHelper
int readDataHelper(istream *)
helper function for outputData
Definition egs_brachy.cpp:2415
+
EB_Application::initScatScoring
void initScatScoring(EGS_Input *)
energy deposition scoring initialization
Definition egs_brachy.cpp:1408
+
EB_Application::superpos_geom
EGS_ASwitchedEnvelope * superpos_geom
an ASwitchedEnv cast of simulation geometry.
Definition egs_brachy.h:143
+
EB_Application::output_dose_format
string output_dose_format
text or gzip
Definition egs_brachy.h:123
+
EB_Application::source_weights
vector< EGS_Float > source_weights
Definition egs_brachy.h:111
+
EB_Application::startNewShower
int startNewShower()
Definition egs_brachy.cpp:2157
+
EB_Application::createTransforms
vector< EGS_AffineTransform * > createTransforms(EGS_Input *input)
Definition egs_brachy.cpp:385
+
EB_Application::enterNewRegion
virtual void enterNewRegion()
Definition egs_brachy.cpp:1568
+
EB_Application::extra_scoring_vols
map< string, vector< EGS_Float > > extra_scoring_vols
Definition egs_brachy.h:181
+
EB_Application::resetCounter
void resetCounter()
Reset the application to a 'pristine' state. Adapted from egs_application.cpp to allow combining in t...
Definition egs_brachy.cpp:2534
+
EB_Application::combineResults
int combineResults()
Definition egs_brachy.cpp:2472
+
EB_Application::base_transform
EGS_AffineTransform * base_transform
same as source_transforms[0]
Definition egs_brachy.h:148
+
EB_Application::source_envelope_geom
EGS_BaseGeometry * source_envelope_geom
geometry that the sources are embedded in
Definition egs_brachy.h:142
+
EB_Application::phantom_geoms
vector< EB_Phantom * > phantom_geoms
pointers to all of the phantom objects
Definition egs_brachy.h:145
+
EB_Application::outputResults
void outputResults()
Definition egs_brachy.cpp:1934
+
EB_Application::calcEffectiveHistories
void calcEffectiveHistories()
Definition egs_brachy.cpp:1915
+
EB_Application::score_scat
bool score_scat
true when scatter scoring is enabled
Definition egs_brachy.h:118
+
EB_Application::output_egsphant_format
string output_egsphant_format
text or gzip
Definition egs_brachy.h:125
+
EB_Application::egsBrachyOutputData
int egsBrachyOutputData(ostream *)
helper function for outputData
Definition egs_brachy.cpp:2234
+
EB_Application::gz_data_out
ogzstream * gz_data_out
GZip file for outputing egsdat.
Definition egs_brachy.h:198
+
EB_Application::initCrossSections
int initCrossSections()
Definition egs_brachy.cpp:848
+
EB_Application::nbr_split
int nbr_split
Number of times to split bremstrahlung phtons.
Definition egs_brachy.h:156
+
EB_Application::media_muen
map< int, EGS_Interpolator * > media_muen
Map from medium index to muen interpolator for that medium.
Definition egs_brachy.h:151
+
EB_Application::gen_vc_results
ebvolcor::Results gen_vc_results
results from general volume correction
Definition egs_brachy.h:187
+
EB_Application::base_transform_inv
EGS_AffineTransform * base_transform_inv
same as source_transforms[0].inverse()
Definition egs_brachy.h:149
+
EB_Application::steps_in_sources
map< int, EGS_I64 > steps_in_sources
Definition egs_brachy.h:194
+
EB_Application::output_voxinfo
bool output_voxinfo
true if user requests voxel info file
Definition egs_brachy.h:127
+
EB_Application::steps_in_other
map< int, EGS_I64 > steps_in_other
Definition egs_brachy.h:196
+
EB_Application::phsp
PHSPControl * phsp
Definition egs_brachy.h:114
+
EB_Application::ausgab
int ausgab(int iarg)
user scoring of dose, spectra etc
Definition egs_brachy.cpp:1657
+
EB_Application::readData
int readData()
Read data required for restarting simulations.
Definition egs_brachy.cpp:2430
+
EB_Application::egsApplicationReadData
int egsApplicationReadData(istream *)
helper function for outputData
Definition egs_brachy.cpp:2329
+
EB_Application::nsources
int nsources
total number of particle sources in current simulation
Definition egs_brachy.h:368
+
EB_Application::flu_cutoff
EGS_Float flu_cutoff
fluorescent photon cutoff energy
Definition egs_brachy.h:163
+
EB_Application::cur_R
EGS_Float cur_R
Definition egs_brachy.h:138
+
EB_Application::RunMode
RunMode
Definition egs_brachy.h:93
+
EB_Application::RM_VC_ONLY
@ RM_VC_ONLY
Run volume correction routines then quit.
Definition egs_brachy.h:96
+
EB_Application::RM_SUPERPOSITION
@ RM_SUPERPOSITION
Superposition mode for intersource effects.
Definition egs_brachy.h:95
+
EB_Application::RM_NORMAL
@ RM_NORMAL
Standard running mode.
Definition egs_brachy.h:94
+
EB_Application::egsAdvApplicationReadData
int egsAdvApplicationReadData(istream *)
helper function for outputData
Definition egs_brachy.cpp:2352
+
EB_Application::do_bcse
bool do_bcse
Definition egs_brachy.h:158
+
EB_Application::egsApplicationOutputData
int egsApplicationOutputData(ostream *)
helper function for outputData
Definition egs_brachy.cpp:2183
+
EB_Application::ginfo
GeomInfo ginfo
meta data about the geometries
Definition egs_brachy.h:175
+
EB_Application::clearAusgabCalls
void clearAusgabCalls()
disable all ausgab calls
Definition egs_brachy.cpp:1254
+
EB_Application::source_vc_results
ebvolcor::Results source_vc_results
results from source volume correctio box phantom
Definition egs_brachy.h:186
+
EB_Application::is_phsp_source
bool is_phsp_source
Definition egs_brachy.h:109
+
EB_Application::initXCCScaling
void initXCCScaling(EGS_Input *)
Initialize cross section scaling if requested.
Definition egs_brachy.cpp:1458
+
EB_Application::simulateSingleShower
int simulateSingleShower()
Definition egs_brachy.cpp:2072
+
EB_Application::source_ecut
EGS_Float source_ecut
ecut for source objects
Definition egs_brachy.h:164
+
EB_Application::score_edep
bool score_edep
true when energy deposition is enabled
Definition egs_brachy.h:117
+
EB_Application::initGCRScoring
void initGCRScoring(EGS_Input *)
setup which phantom/region will be used for getCurrentResult
Definition egs_brachy.cpp:924
+
EB_Application::source_e_max_rr
EGS_Float source_e_max_rr
max range rejection energy for source objects
Definition egs_brachy.h:173
+
EB_Application::initScoring
int initScoring()
initialze all scoring and variance reduction parameters
Definition egs_brachy.cpp:890
+
EB_Application::addState
int addState(istream &data)
Add data from a parallel job. Add standard egs++ data as well as egs_brachy specific scoring informat...
Definition egs_brachy.cpp:2561
+
EB_Application::global_ecut
EGS_Float global_ecut
ecut for source objects
Definition egs_brachy.h:166
+
EB_Application::initGeometry
int initGeometry()
override default initGeometry so we can manually create our own geometry.
Definition egs_brachy.cpp:307
+
EB_Application::initOutputFiles
void initOutputFiles(EGS_Input *)
set up whether to output extra info files
Definition egs_brachy.cpp:979
+
EB_Application::initVarianceReduction
int initVarianceReduction()
initialze all variance reduction parameters
Definition egs_brachy.cpp:1019
+
EB_Application::p_init_locs
vector< EGS_Vector > p_init_locs
Definition egs_brachy.h:134
+
EB_Application::score_tlen
bool score_tlen
true when tracklength estimator is enabled
Definition egs_brachy.h:116
+
EB_Application::run_mode
RunMode run_mode
Which run mode are we using (RM_NORMAL, RM_SUPERPOSITION or RM_VC_ONLY *‍/.
Definition egs_brachy.h:100
+
EB_Application::recycle_opts
RecycleOpts * recycle_opts
Definition egs_brachy.h:107
+
EB_Application::single_generator
bool single_generator
Definition egs_brachy.h:108
+
EB_Application::record_n_init
int record_n_init
if > 0 write initial pos of record_n_init particles to {input_file}.pinit
Definition egs_brachy.h:133
+
EB_Application::file_vc_results
ebvolcor::FileResults file_vc_results
results from precomputed volume correction
Definition egs_brachy.h:188
+
EB_Application::runSimulation
virtual int runSimulation()
Definition egs_brachy.cpp:2064
+
EB_Phantom
A class to represent a single phantom for scoring dose in egs_brachy.
Definition phantom.h:71
+
EB_Phantom::YDIR
@ YDIR
YDIR=1 y dir for rectilinear, r dir for cylindrical.
Definition phantom.h:137
+
EB_Phantom::XDIR
@ XDIR
XDIR=0 x dir for rectilinear, r dir for spherical, z dir for cylindrical.
Definition phantom.h:136
+
EB_Phantom::ZDIR
@ ZDIR
ZDIR=2 z dir for rectilinear.
Definition phantom.h:138
+
EB_Phantom::scoreTlen
void scoreTlen(int ir, EGS_Float dose, EGS_Particle *p)
add tracklength dose to region ir
Definition phantom.cpp:133
+
EB_Phantom::getUncorrectedVolume
EGS_Float getUncorrectedVolume(int ireg)
get corrected volume for a given region
Definition phantom.cpp:302
+
EB_Phantom::geometry
EGS_BaseGeometry * geometry
the phantom geometry object
Definition phantom.h:284
+
EB_Phantom::getCurrentScore
void getCurrentScore(int ireg, double &sum, double &sum2)
get current tlen score for region
Definition phantom.cpp:332
+
EB_Phantom::getTlenNorm
double getTlenNorm(int ireg)
Definition phantom.cpp:344
+
EB_Phantom::setEffectiveHistories
void setEffectiveHistories(EGS_Float current_case)
set number of effective histories for normalizing scoring arrays
Definition phantom.cpp:253
+
EB_Phantom::needs_user_geoms
bool needs_user_geoms
this phantom requires user specified geometries
Definition phantom.h:296
+
EB_Phantom::scoreEdep
void scoreEdep(int ir, EGS_Float dose)
add energy deposition dose to region ir
Definition phantom.cpp:155
+
EB_Phantom::getRealMass
EGS_Float getRealMass(int ireg)
return (corrected) real mass for region
Definition phantom.cpp:291
+
EB_Phantom::setCorrectedVolume
void setCorrectedVolume(int ir, double fraction, double unc=0)
Allow user to tell phantom what the actual volume of a region is.
Definition phantom.cpp:202
+
EB_Phantom::getCorrectedVolume
EGS_Float getCorrectedVolume(int ireg)
get uncorrected volume for a given region
Definition phantom.cpp:314
+
EB_Phantom::getUncorrectedMass
EGS_Float getUncorrectedMass(int ireg)
return uncorrected for region
Definition phantom.cpp:298
+
EB_Phantom::avgVoxelVol
EGS_Float avgVoxelVol()
return average voxel volume
Definition phantom.cpp:855
+
EB_TimingTree::stopTimer
void stopTimer()
Definition timing.h:139
+
EB_TimingTree::outputInfo
void outputInfo()
Definition timing.h:159
+
EB_TimingTree::addTimer
void addTimer(string name)
Definition timing.h:132
+
EB_UniformRunControl
Definition egs_brachy.h:520
+
EB_UniformRunControl::startSimulation
int startSimulation()
Definition egs_brachy.cpp:2697
+
EB_UniformRunControl::ipar
int ipar
Definition egs_brachy.h:555
+
EB_UniformRunControl::ifirst
int ifirst
Definition egs_brachy.h:556
+
EB_UniformRunControl::check_intervals
int check_intervals
Definition egs_brachy.h:550
+
EB_UniformRunControl::npar
int npar
Definition egs_brachy.h:554
+
EB_UniformRunControl::check_egsdat
bool check_egsdat
Definition egs_brachy.h:557
+
EB_UniformRunControl::EB_UniformRunControl
EB_UniformRunControl(EB_Application *app, string egsdat_format)
Definition egs_brachy.cpp:2636
+
EB_UniformRunControl::app
EB_Application * app
Definition egs_brachy.h:543
+
EB_UniformRunControl::milliseconds
int milliseconds
Definition egs_brachy.h:547
+
EB_UniformRunControl::describeRCO
void describeRCO()
Definition egs_brachy.cpp:2720
+
EB_UniformRunControl::output_egsdat_format
string output_egsdat_format
text or gzip
Definition egs_brachy.h:545
+
EB_UniformRunControl::finishSimulation
int finishSimulation()
Uses 'watcher' jobs to determine if the simulation has finished.
Definition egs_brachy.cpp:2747
+
EB_UniformRunControl::watcher_job
bool watcher_job
Definition egs_brachy.h:558
+
EnergyScoringStats
a class to use for scoring information about total energy initialzed, escaping sources etc
Definition spec_scoring.h:57
+ +
EnergyScoringStats::readData
int readData(istream *ifile)
Definition spec_scoring.h:192
+
EnergyScoringStats::outputData
int outputData(ostream *ofile)
Definition spec_scoring.h:185
+
EnergyScoringStats::addState
int addState(istream &data)
Definition spec_scoring.h:205
+
EnergyScoringStats::outputResults
void outputResults()
write results to console
Definition spec_scoring.h:165
+
GeomInfo::source_envelope_name
string source_envelope_name
Definition ginfo.h:131
+
GeomInfo::ordered_geom_data
vector< GeomRegionInfo > ordered_geom_data
Definition ginfo.h:149
+
GeomInfo::isSource
bool isSource(int ir)
Definition ginfo.cpp:503
+
GeomInfo::phantomFromRegion
int phantomFromRegion(int ir)
return the phantom index for this region number or -1 if region is not in a phantom
Definition ginfo.cpp:508
+
GeomInfo::initializeFromInput
int initializeFromInput(EGS_Input *input)
Initialize the GeomInfo structure (ginfo) This function reads the geometry input block,...
Definition ginfo.cpp:85
+
GeomInfo::ngeom
int ngeom
total number of geometries created
Definition ginfo.h:138
+
GeomInfo::isPhantom
bool isPhantom(int ir)
Definition ginfo.cpp:498
+
GeomInfo::setGeometryIndexes
void setGeometryIndexes(EGS_BaseGeometry *sim_geom)
Setup all arrays required to decide which geometry/phantom a region is in and whether or not we are s...
Definition ginfo.cpp:441
+
GeomInfo::printInfo
void printInfo()
Definition ginfo.cpp:513
+
GeomInfo::globalToLocal
GeomRegT globalToLocal(int ir)
convert global region number to (EGS_BaseGeometry, local_reg_num) pair
Definition ginfo.cpp:479
+
GeomInfo::nreg_total
int nreg_total
total number of regions in the simulation geometry
Definition ginfo.h:139
+
GeomInfo::globalToLocalReg
int globalToLocalReg(int ir)
convert global region number to local_reg_num
Definition ginfo.cpp:487
+
GeomInfo::source_names
vector< string > source_names
Definition ginfo.h:134
+
GeomInfo::phantom_names
vector< string > phantom_names
Definition ginfo.h:132
+
Latch::hasEscaped
static bool hasEscaped(EGS_Particle *p)
True if particle is currently in a source.
Definition latch.cpp:134
+
Latch::addScatter
static void addScatter(EGS_Particle *p)
Definition latch.cpp:80
+ +
PHSPControl::outputResults
void outputResults()
output file name and number of particles written
Definition phsp.cpp:199
+
PHSPControl::finish
void finish(EGS_I64 n_orig_particles)
set final number of particles written and destroy source
Definition phsp.cpp:193
+
PHSPControl::destroySource
void destroySource()
destroy the source
Definition phsp.cpp:221
+
Publisher::notify
void notify(EB_Message message, void *what=0, Subscriber *s=0)
Definition pubsub.cpp:46
+ +
RecycleOpts::nrecycle
int nrecycle
Definition recycle.h:71
+
RecycleOpts::rotate
bool rotate
Definition recycle.h:72
+
RecycleOpts::printInfo
void printInfo()
Definition recycle.cpp:68
+
ebvolcor::VolumeCorrector
An object for controlling the volume correction routine.
Definition eb_volcor.h:311
+
ebvolcor::VolumeCorrector::runSourceCorrection
Results runSourceCorrection(EB_TimingTree &timer)
Definition eb_volcor.h:366
+
ebvolcor::VolumeCorrector::runGeneralCorrection
Results runGeneralCorrection(EB_TimingTree &timer)
Definition eb_volcor.h:394
+
ebvolcor::VolumeCorrector::runFileCorrection
FileResults runFileCorrection(EB_TimingTree &timer)
Definition eb_volcor.h:422
+
gzstreambase::close
void close()
Definition gzstream.C:154
+
gzstreambuf::is_open
int is_open()
Definition gzstream.h:64
+ +
igzstream::open
void open(const char *name, int open_mode=std::ios::in)
Definition gzstream.h:108
+
igzstream::rdbuf
gzstreambuf * rdbuf()
Definition gzstream.h:105
+
muen::MuenDataParser
class for parsing muen data from a file.
Definition muen.h:131
+
muen::MuenDataParser::setMuenFile
int setMuenFile(string filename)
Definition muen.h:207
+
muen::MuenDataParser::getMuenInterpolator
EGS_Interpolator * getMuenInterpolator(string med_name)
Create a new EGS_Interpolator of muen data for the requested medium and return pointer to it....
Definition muen.h:228
+ +
egsOpenUnits
#define egsOpenUnits
Definition egs_brachy.cpp:72
+
egsGetRNGArray
#define egsGetRNGArray
Definition egs_brachy.cpp:64
+
egsGetSteps
#define egsGetSteps
Definition egs_brachy.cpp:68
F77_OBJ_
void F77_OBJ_(egs_scale_xcc, EGS_SCALE_XCC)(const int *
-
egsGetPhotonData
#define egsGetPhotonData
Definition: egs_brachy.cpp:76
-
getMuenForMedia
map< string, string > getMuenForMedia(EGS_Input *scoring_options)
Definition: egs_brachy.cpp:1274
-
egsSetRNGState
#define egsSetRNGState
Definition: egs_brachy.cpp:65
-
containsInclude
bool containsInclude(string str)
Definition: egs_brachy.cpp:279
-
egsGetRNGPointers
#define egsGetRNGPointers
Definition: egs_brachy.cpp:61
-
printParticleWithSpherical
void const EGS_Float *void const EGS_Float *void const EGS_Float *void const EGS_Float *void printParticleWithSpherical(EGS_Particle p)
Definition: egs_brachy.cpp:86
-
egsSetSteps
#define egsSetSteps
Definition: egs_brachy.cpp:69
+
egsGetPhotonData
#define egsGetPhotonData
Definition egs_brachy.cpp:77
+
getMuenForMedia
map< string, string > getMuenForMedia(EGS_Input *scoring_options)
Definition egs_brachy.cpp:1290
+
rco_sleep
void rco_sleep(const int &mscnds)
Definition egs_brachy.cpp:2739
+
fileExists
bool fileExists(const string &name)
Definition egs_brachy.cpp:2611
+
egsSetRNGState
#define egsSetRNGState
Definition egs_brachy.cpp:66
+
containsInclude
bool containsInclude(string str)
Definition egs_brachy.cpp:280
+
egsGetRNGPointers
#define egsGetRNGPointers
Definition egs_brachy.cpp:62
+
printParticleWithSpherical
void const EGS_Float *void const EGS_Float *void const EGS_Float *void const EGS_Float *void printParticleWithSpherical(EGS_Particle p)
Definition egs_brachy.cpp:87
+
egsSetSteps
#define egsSetSteps
Definition egs_brachy.cpp:70
APP_MAIN
APP_MAIN(EB_Application)
-
egsGetElectronData
#define egsGetElectronData
Definition: egs_brachy.cpp:73
+
egsGetElectronData
#define egsGetElectronData
Definition egs_brachy.cpp:74
egs_brachy.h
the main egs_brachy application header file
-
PRINT_PARTICLE_WITH_DIR
#define PRINT_PARTICLE_WITH_DIR(P)
Definition: egs_brachy.h:81
-
EB_EPSILON
#define EB_EPSILON
Definition: egs_brachy.h:84
-
NUM_STUCK_STEPS
#define NUM_STUCK_STEPS
Definition: egs_brachy.h:82
-
SAME_POSITION_TOLERANCE
#define SAME_POSITION_TOLERANCE
Definition: egs_brachy.h:83
-
GeomRegT
pair< EGS_BaseGeometry *, int > GeomRegT
pair of geometry and local region number
Definition: ginfo.h:79
+
PRINT_PARTICLE_WITH_DIR
#define PRINT_PARTICLE_WITH_DIR(P)
Definition egs_brachy.h:82
+
EB_EPSILON
#define EB_EPSILON
Definition egs_brachy.h:85
+
NUM_STUCK_STEPS
#define NUM_STUCK_STEPS
Definition egs_brachy.h:83
+
SAME_POSITION_TOLERANCE
#define SAME_POSITION_TOLERANCE
Definition egs_brachy.h:84
+
GeomRegT
pair< EGS_BaseGeometry *, int > GeomRegT
pair of geometry and local region number
Definition ginfo.h:79
-
ebvolcor::getShapeVolume
EGS_Float getShapeVolume(EGS_Input *shape_inp)
get shape volume from a shape input item
Definition: eb_volcor.cpp:77
-
EBSendMessage
pair< bool, EB_Message > EBSendMessage
Definition: pubsub.h:69
-
PARTICLE_ESCAPING_SOURCE
@ PARTICLE_ESCAPING_SOURCE
Definition: pubsub.h:60
-
NEW_HISTORY
@ NEW_HISTORY
Definition: pubsub.h:56
-
PARTICLE_ESCAPED_SOURCE
@ PARTICLE_ESCAPED_SOURCE
Definition: pubsub.h:61
-
PARTICLE_TAKING_STEP
@ PARTICLE_TAKING_STEP
Definition: pubsub.h:58
-
PARTICLE_ESCAPED_GEOM
@ PARTICLE_ESCAPED_GEOM
Definition: pubsub.h:63
-
PARTICLE_TOOK_STEP
@ PARTICLE_TOOK_STEP
Definition: pubsub.h:59
-
PARTICLE_INITIALIZED
@ PARTICLE_INITIALIZED
Definition: pubsub.h:57
-
PARTICLE_ESCAPING_GEOM
@ PARTICLE_ESCAPING_GEOM
Definition: pubsub.h:62
-
GeomRegionInfo
a struct to contain elementary information aboud a geometry
Definition: ginfo.h:83
-
GeomRegionInfo::children
vector< string > children
Definition: ginfo.h:87
-
GeomRegionInfo::type
string type
Definition: ginfo.h:86
-
GeomRegionInfo::name
string name
Definition: ginfo.h:85
- -
ebvolcor::Results::outputResults
void outputResults(string extra="")
Definition: eb_volcor.h:243
+
ebvolcor::getShapeVolume
EGS_Float getShapeVolume(EGS_Input *shape_inp)
get shape volume from a shape input item
Definition eb_volcor.cpp:77
+
EBSendMessage
pair< bool, EB_Message > EBSendMessage
Definition pubsub.h:69
+
PARTICLE_ESCAPING_SOURCE
@ PARTICLE_ESCAPING_SOURCE
Definition pubsub.h:60
+
NEW_HISTORY
@ NEW_HISTORY
Definition pubsub.h:56
+
PARTICLE_ESCAPED_SOURCE
@ PARTICLE_ESCAPED_SOURCE
Definition pubsub.h:61
+
PARTICLE_TAKING_STEP
@ PARTICLE_TAKING_STEP
Definition pubsub.h:58
+
PARTICLE_ESCAPED_GEOM
@ PARTICLE_ESCAPED_GEOM
Definition pubsub.h:63
+
PARTICLE_TOOK_STEP
@ PARTICLE_TOOK_STEP
Definition pubsub.h:59
+
PARTICLE_INITIALIZED
@ PARTICLE_INITIALIZED
Definition pubsub.h:57
+
PARTICLE_ESCAPING_GEOM
@ PARTICLE_ESCAPING_GEOM
Definition pubsub.h:62
+
GeomRegionInfo
a struct to contain elementary information aboud a geometry
Definition ginfo.h:83
+
GeomRegionInfo::children
vector< string > children
Definition ginfo.h:87
+
GeomRegionInfo::type
string type
Definition ginfo.h:86
+
GeomRegionInfo::name
string name
Definition ginfo.h:85
+ +
ebvolcor::Results::outputResults
void outputResults(string extra="")
Definition eb_volcor.h:243
-Generated by doxygen 1.9.5 +Generated by doxygen 1.9.8
diff --git a/docs/egs__brachy_8dox.html b/docs/egs__brachy_8dox.html index e78da349..5f379d06 100644 --- a/docs/egs__brachy_8dox.html +++ b/docs/egs__brachy_8dox.html @@ -3,7 +3,7 @@ - + EGS Brachy: egs_brachy.dox File Reference @@ -30,7 +30,7 @@
- + @@ -30,7 +30,7 @@ - + @@ -30,7 +30,7 @@ - + +
-
/Users/marc/dev/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/egs_brachy.h
+
/Users/marc/Developer/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/egs_brachy.h
Go to the documentation of this file.
1/*
@@ -128,485 +133,549 @@
58#include "egs_interpolator.h"
59#include "egs_alias_table.h"
60#include "egs_rndm.h"
-
61#include "egs_scoring.h"
-
62#include "egs_transformations.h"
-
63#include "egs_autoenvelope/egs_autoenvelope.h" // required for Superposition mode
-
64#include "egs_rz/egs_rz.h"
-
65#include "egs_spheres/egs_spheres.h"
-
66
-
67// local dependencies
-
68#include "pubsub.h"
-
69#include "ginfo.h"
-
70#include "muen.h"
-
71#include "phantom.h"
-
72#include "eb_volcor.h"
-
73#include "spec_scoring.h"
-
74#include "recycle.h"
-
75#include "latch.h"
-
76#include "phsp.h"
-
77#include "timing.h"
-
78
+
61#include "egs_run_control.h"
+
62#include "egs_scoring.h"
+
63#include "egs_transformations.h"
+
64#include "egs_autoenvelope/egs_autoenvelope.h" // required for Superposition mode
+
65#include "egs_rz/egs_rz.h"
+
66#include "egs_spheres/egs_spheres.h"
+
67
+
68// local dependencies
+
69#include "pubsub.h"
+
70#include "ginfo.h"
+
71#include "muen.h"
+
72#include "phantom.h"
+
73#include "eb_volcor.h"
+
74#include "spec_scoring.h"
+
75#include "recycle.h"
+
76#include "latch.h"
+
77#include "phsp.h"
+
78#include "timing.h"
79
-
80#define PRINT_PARTICLE(P) cout << "\nParticle in reg "<<P.ir << " at "<<P.x.x << " "<<P.x.y<<" "<<P.x.z << " wt "<<P.wt<< " E "<<P.E << " q "<<P.q << " latch "<<P.latch<<endl;
-
81#define PRINT_PARTICLE_WITH_DIR(P) cout << "\nParticle in reg "<<P.ir << " at "<<P.x.x << " "<<P.x.y<<" "<<P.x.z << " dir "<<P.u.x << " "<<P.u.y<<" "<<P.u.z << " wt "<<P.wt<< " E "<<P.E << " q "<<P.q << " latch "<<P.latch<<endl;
-
82#define NUM_STUCK_STEPS 1000
-
83#define SAME_POSITION_TOLERANCE 1E-10
-
84#define EB_EPSILON 1E-10
-
85
+
80
+
81#define PRINT_PARTICLE(P) cout << "\nParticle in reg "<<P.ir << " at "<<P.x.x << " "<<P.x.y<<" "<<P.x.z << " wt "<<P.wt<< " E "<<P.E << " q "<<P.q << " latch "<<P.latch<<"\n";
+
82#define PRINT_PARTICLE_WITH_DIR(P) cout << "\nParticle in reg "<<P.ir << " at "<<P.x.x << " "<<P.x.y<<" "<<P.x.z << " dir "<<P.u.x << " "<<P.u.y<<" "<<P.u.z << " wt "<<P.wt<< " E "<<P.E << " q "<<P.q << " latch "<<P.latch<<"\n";
+
83#define NUM_STUCK_STEPS 1000
+
84#define SAME_POSITION_TOLERANCE 1E-10
+
85#define EB_EPSILON 1E-10
86
-
87
-
90class APP_EXPORT EB_Application : public EGS_AdvancedApplication {
-
91
-
92 enum RunMode {
-
93 RM_NORMAL,
-
94 RM_SUPERPOSITION,
-
95 RM_VC_ONLY
-
96 };
-
97
+
87class EB_UniformRunControl;
+
88
+
+
91class APP_EXPORT EB_Application : public EGS_AdvancedApplication {
+
92
+
+
93 enum RunMode {
+
94 RM_NORMAL,
+
95 RM_SUPERPOSITION,
+
96 RM_VC_ONLY
+
97 };
+
98
-
99 RunMode run_mode;
-
100 string run_mode_name;
-
101
-
102 EnergyScoringStats *escoring;
-
103 vector<BaseSpectrumScorer *> spectrum_scorers;
-
104 //SpectrumScoringControl *spec_scoring;
-
105
-
106 RecycleOpts *recycle_opts;
-
107 bool single_generator;
-
108 bool is_phsp_source;
-
109
-
110 vector<EGS_Float> source_weights;
-
111 int active_source;
-
112
-
113 PHSPControl *phsp;
-
114
-
115 bool score_tlen;
-
116 bool score_edep;
-
117 bool score_scat;
-
118
-
119 string output_egsdat_format;
-
120
-
121 bool output_3ddose_files;
-
122 string output_dose_format;
-
123 bool output_egsphant;
-
124 string output_egsphant_format;
-
125
-
126 bool output_voxinfo;
-
127 string output_voxinfo_format;
-
128
-
129 vector<string> output_volcor_phantoms;
-
130 string output_volcor_format;
-
131
-
132 int record_n_init;
-
133 vector<EGS_Vector> p_init_locs;
-
134
-
135 EGS_Vector last_position;
-
136 EGS_Float last_R;
-
137 EGS_Float cur_R;
-
138 int steps_at_same_loc;
-
139 EGS_I64 n_stuck;
-
140
-
141 EGS_BaseGeometry *source_envelope_geom;
-
142 EGS_ASwitchedEnvelope *superpos_geom;
-
143
-
144 vector<EB_Phantom *> phantom_geoms;
-
145
-
146 vector<EGS_AffineTransform *> source_transforms;
-
147 EGS_AffineTransform *base_transform;
-
148 EGS_AffineTransform *base_transform_inv;
-
149
-
150 map<int, EGS_Interpolator *> media_muen;
-
151 map<string, string> media_muen_names;
-
152
+
99
+
100 RunMode run_mode;
+
101 string run_mode_name;
+
102
+
103 EnergyScoringStats *escoring;
+
104 vector<BaseSpectrumScorer *> spectrum_scorers;
+
105 //SpectrumScoringControl *spec_scoring;
+
106
+
107 RecycleOpts *recycle_opts;
+
108 bool single_generator;
+
109 bool is_phsp_source;
+
110
+
111 vector<EGS_Float> source_weights;
+
112 int active_source;
+
113
+
114 PHSPControl *phsp;
+
115
+
116 bool score_tlen;
+
117 bool score_edep;
+
118 bool score_scat;
+
119
+
120 string output_egsdat_format;
+
121
+
122 bool output_3ddose_files;
+
123 string output_dose_format;
+
124 bool output_egsphant;
+
125 string output_egsphant_format;
+
126
+
127 bool output_voxinfo;
+
128 string output_voxinfo_format;
+
129
+
130 vector<string> output_volcor_phantoms;
+
131 string output_volcor_format;
+
132
+
133 int record_n_init;
+
134 vector<EGS_Vector> p_init_locs;
+
135
+
136 EGS_Vector last_position;
+
137 EGS_Float last_R;
+
138 EGS_Float cur_R;
+
139 int steps_at_same_loc;
+
140 EGS_I64 n_stuck;
+
141
+
142 EGS_BaseGeometry *source_envelope_geom;
+
143 EGS_ASwitchedEnvelope *superpos_geom;
+
144
+
145 vector<EB_Phantom *> phantom_geoms;
+
146
+
147 vector<EGS_AffineTransform *> source_transforms;
+
148 EGS_AffineTransform *base_transform;
+
149 EGS_AffineTransform *base_transform_inv;
+
150
+
151 map<int, EGS_Interpolator *> media_muen;
+
152 map<string, string> media_muen_names;
153
-
154 bool do_brem_split;
-
155 int nbr_split;
-
156
-
157 bool do_bcse;
-
158 int bcse_med_num;
-
159 EGS_Float bcse_factor;
-
160 static const EGS_Float DEFAULT_BCSE_FACTOR;
-
161
-
162 EGS_Float flu_cutoff;
-
163 EGS_Float source_ecut;
-
164 EGS_Float source_pcut;
-
165 EGS_Float global_ecut;
-
166 EGS_Float global_pcut;
-
167
-
168 bool global_i_do_rr;
-
169 EGS_Float global_e_max_rr;
-
170
-
171 bool source_i_do_rr;
-
172 EGS_Float source_e_max_rr;
-
173
-
174 GeomInfo ginfo;
-
175
-
176 EB_Phantom *gcr_phantom;
-
177 int gcr_phantom_reg;
-
178
-
179 map<string, vector<int> > extra_scoring_reg;
-
180 map<string, vector<EGS_Float> > extra_scoring_vols;
-
181 map<string, vector<EGS_Float> > extra_scoring_mass;
-
182 map<string, EGS_ScoringArray* > extra_scoring_doses;
-
183 map<string, EGS_ScoringArray* > extra_scoring_doses_edep;
-
184
-
185 ebvolcor::Results source_vc_results;
-
186 ebvolcor::Results gen_vc_results;
-
187 ebvolcor::FileResults file_vc_results;
-
188
-
189 Publisher pevent_pub;
-
190
-
191 EB_TimingTree timing_blocks;
-
192
-
193 map<int, EGS_I64> steps_in_sources;
-
194 map<int, EGS_I64> steps_in_phantoms;
-
195 map<int, EGS_I64> steps_in_other;
-
196
-
197 ogzstream *gz_data_out;
-
198 igzstream *gz_data_in;
-
199
-
200 static string revision;
-
201
+
154
+
155 bool do_brem_split;
+
156 int nbr_split;
+
157
+
158 bool do_bcse;
+
159 int bcse_med_num;
+
160 EGS_Float bcse_factor;
+
161 static const EGS_Float DEFAULT_BCSE_FACTOR;
+
162
+
163 EGS_Float flu_cutoff;
+
164 EGS_Float source_ecut;
+
165 EGS_Float source_pcut;
+
166 EGS_Float global_ecut;
+
167 EGS_Float global_pcut;
+
168
+
169 bool global_i_do_rr;
+
170 EGS_Float global_e_max_rr;
+
171
+
172 bool source_i_do_rr;
+
173 EGS_Float source_e_max_rr;
+
174
+
175 GeomInfo ginfo;
+
176
+
177 EB_Phantom *gcr_phantom;
+
178 int gcr_phantom_reg;
+
179
+
180 map<string, vector<int> > extra_scoring_reg;
+
181 map<string, vector<EGS_Float> > extra_scoring_vols;
+
182 map<string, vector<EGS_Float> > extra_scoring_mass;
+
183 map<string, EGS_ScoringArray* > extra_scoring_doses;
+
184 map<string, EGS_ScoringArray* > extra_scoring_doses_edep;
+
185
+
186 ebvolcor::Results source_vc_results;
+
187 ebvolcor::Results gen_vc_results;
+
188 ebvolcor::FileResults file_vc_results;
+
189
+
190 Publisher pevent_pub;
+
191
+
192 EB_TimingTree timing_blocks;
+
193
+
194 map<int, EGS_I64> steps_in_sources;
+
195 map<int, EGS_I64> steps_in_phantoms;
+
196 map<int, EGS_I64> steps_in_other;
+
197
+
198 ogzstream *gz_data_out;
+
199 igzstream *gz_data_in;
+
200
+
201 static string revision;
202
-
205 int createPhantoms();
-
206
+
203
+
206 int createPhantoms();
207
-
209 int correctVolumes();
-
210
-
211 /* \brief check sources for overlap using a simple MC routine */
-
212 int checkSourceOverlaps(EGS_Input *);
-
213
-
215 void initTrackLengthScoring(EGS_Input *);
-
216
-
218 void initMuenData(EGS_Input *);
-
219
-
221 void initOutputFiles(EGS_Input *);
-
222
-
224 void initPHSPScoring(EGS_Input *);
-
225
-
227 void initEDepScoring(EGS_Input *);
-
228
-
230 void initScatScoring(EGS_Input *);
-
231
-
233 void clearAusgabCalls();
-
234
-
236 void enableAusgabCalls(int ncalls, AusgabCall calls[]);
-
237
+
208
+
210 int correctVolumes();
+
211
+
212 /* \brief check sources for overlap using a simple MC routine */
+
213 int checkSourceOverlaps(EGS_Input *);
+
214
+
216 void initTrackLengthScoring(EGS_Input *);
+
217
+
219 void initMuenData(EGS_Input *);
+
220
+
222 void initOutputFiles(EGS_Input *);
+
223
+
225 void initPHSPScoring(EGS_Input *);
+
226
+
228 void initEDepScoring(EGS_Input *);
+
229
+
231 void initScatScoring(EGS_Input *);
+
232
+
234 void clearAusgabCalls();
+
235
+
237 void enableAusgabCalls(int ncalls, AusgabCall calls[]);
238
-
240 void initGCRScoring(EGS_Input *);
-
241
-
246 void initAusgabCalls();
-
247
-
249 void initDoseScaling(EGS_Input *);
-
250
-
252 void initXCCScaling(EGS_Input *);
-
253
-
255 void initSpectrumScoring(EGS_Input *);
-
256
-
257 int initCrossSections();
-
258
-
259 void discardTopParticle(int idisc=1);
-
260
-
261 void calcEffectiveHistories();
-
262
-
263 bool isStuck();
-
264
-
265public:
-
266
+
239
+
241 void initGCRScoring(EGS_Input *);
+
242
+
247 void initAusgabCalls();
+
248
+
250 void initDoseScaling(EGS_Input *);
+
251
+
253 void initXCCScaling(EGS_Input *);
+
254
+
256 void initSpectrumScoring(EGS_Input *);
+
257
+
258 int initCrossSections();
+
259
+
260 void discardTopParticle(int idisc=1);
+
261
+
262 void calcEffectiveHistories();
+
263
+
264 bool isStuck();
+
265
+
266public:
267
-
269 EB_Application(int argc, char **argv) :
-
270 EGS_AdvancedApplication(argc,argv),
-
271 run_mode(RM_NORMAL),
-
272 escoring(),
-
273 recycle_opts(0),
-
274 active_source(0),
-
275 phsp(0),
-
276 score_edep(0),
-
277 score_scat(0),
-
278 output_3ddose_files(true),
-
279 record_n_init(0),
-
280 n_stuck(0),
-
281 superpos_geom(0),
-
282 phantom_geoms(),
-
283 do_brem_split(false),
-
284 nbr_split(1),
-
285 do_bcse(false),
-
286 bcse_factor(1),
-
287 flu_cutoff(0),
-
288 ginfo(),
-
289 gcr_phantom(0), gcr_phantom_reg(0),
-
290 gz_data_out(0),
-
291 gz_data_in(0),
-
292 nsources(0),
-
293 effective_histories(0) {
-
294
-
295 for (int i=-1; i < 2; i++) {
-
296 steps_in_sources[i] = 0;
-
297 steps_in_phantoms[i] = 0;
-
298 steps_in_other[i] = 0;
-
299 }
-
300
-
301 pevent_pub.subscribe(&latch_control, PARTICLE_ESCAPING_SOURCE);
-
302 pevent_pub.subscribe(&latch_control, PARTICLE_ESCAPED_SOURCE);
-
303 }
-
304
-
306 ~EB_Application() {
-
307
-
308 for (vector<EB_Phantom>::size_type pp=0; pp < phantom_geoms.size(); pp++) {
-
309 delete phantom_geoms[pp];
-
310 }
-
311 phantom_geoms.clear();
-
312
-
313 map<int, EGS_Interpolator *>::iterator mit = media_muen.begin();
-
314 for (; mit != media_muen.end(); mit++) {
-
315 delete mit->second;
-
316 }
-
317 media_muen.clear();
-
318
+
268
+
+
270 EB_Application(int argc, char **argv) :
+
271 EGS_AdvancedApplication(argc,argv),
+
272 run_mode(RM_NORMAL),
+
273 escoring(),
+
274 recycle_opts(0),
+
275 active_source(0),
+
276 phsp(0),
+
277 score_edep(0),
+
278 score_scat(0),
+
279 output_3ddose_files(true),
+
280 record_n_init(0),
+
281 n_stuck(0),
+
282 superpos_geom(0),
+
283 phantom_geoms(),
+
284 do_brem_split(false),
+
285 nbr_split(1),
+
286 do_bcse(false),
+
287 bcse_factor(1),
+
288 flu_cutoff(0),
+
289 ginfo(),
+
290 gcr_phantom(0), gcr_phantom_reg(0),
+
291 gz_data_out(0),
+
292 gz_data_in(0),
+
293 nsources(0),
+
294 effective_histories(0) {
+
295
+
296 for (int i=-1; i < 2; i++) {
+
297 steps_in_sources[i] = 0;
+
298 steps_in_phantoms[i] = 0;
+
299 steps_in_other[i] = 0;
+
300 }
+
301
+
302 pevent_pub.subscribe(&latch_control, PARTICLE_ESCAPING_SOURCE);
+
303 pevent_pub.subscribe(&latch_control, PARTICLE_ESCAPED_SOURCE);
+
304 }
+
+
305
+
+
307 ~EB_Application() {
+
308
+
309 for (vector<EB_Phantom>::size_type pp=0; pp < phantom_geoms.size(); pp++) {
+
310 delete phantom_geoms[pp];
+
311 }
+
312 phantom_geoms.clear();
+
313
+
314 map<int, EGS_Interpolator *>::iterator mit = media_muen.begin();
+
315 for (; mit != media_muen.end(); mit++) {
+
316 delete mit->second;
+
317 }
+
318 media_muen.clear();
319
-
320 for (vector<EGS_AffineTransform *>::size_type st=0; st < source_transforms.size(); st++) {
-
321 delete source_transforms[st];
-
322 }
-
323 source_transforms.clear();
-
324
-
325 for (map<string, EGS_ScoringArray* >::iterator sa=extra_scoring_doses.begin(); sa != extra_scoring_doses.end(); sa++) {
-
326 delete sa->second;
-
327 }
-
328 extra_scoring_doses.clear();
-
329
-
330 for (map<string, EGS_ScoringArray* >::iterator sa=extra_scoring_doses_edep.begin(); sa != extra_scoring_doses_edep.end(); sa++) {
-
331 delete sa->second;
-
332 }
-
333 extra_scoring_doses_edep.clear();
-
334
-
335 if (phsp) {
-
336 delete phsp;
-
337 }
-
338
-
339 if (escoring) {
-
340 delete escoring;
-
341 }
-
342
-
343 vector<BaseSpectrumScorer *>::iterator it = spectrum_scorers.begin();
-
344 for (; it != spectrum_scorers.end(); it++) {
-
345 delete *it;
-
346 }
-
347 spectrum_scorers.clear();
-
348
-
349 if (recycle_opts) {
-
350 delete recycle_opts;
-
351 }
-
352
-
353 if (base_transform_inv) {
-
354 delete base_transform_inv;
-
355 }
-
356
-
357 if (gz_data_in) {
-
358 delete gz_data_in;
-
359 }
-
360
-
361 if (gz_data_out) {
-
362 delete gz_data_out;
-
363 }
-
364
-
365 };
-
366
-
367 int nsources;
-
368
-
369 EGS_Float effective_histories;
-
370
-
371 Latch latch_control;
-
372
-
374 void describeUserCode() const;
-
375
-
380 void describeSimulation();
-
381
-
382 void printIncludedFiles();
-
383
-
385 int initSimulation();
-
386
-
388 int initRunControl();
-
389
-
391 int initRunMode();
-
392
-
394 int initScoring();
-
395
-
397 int initVarianceReduction();
-
398
-
400 int initRussianRoulette(EGS_Input *);
-
401
-
403 int initBCSE(EGS_Input *);
-
404
-
406 int ausgab(int iarg);
-
407
-
414 int outputData();
-
415
-
417 int outputDataHelper(ostream *);
-
418
-
420 int egsApplicationOutputData(ostream *);
-
421
-
423 int egsAdvApplicationOutputData(ostream *);
-
424
-
426 int egsBrachyOutputData(ostream *);
-
427
-
431 int readData();
-
432
-
434 int readDataHelper(istream *);
-
435
-
437 int egsApplicationReadData(istream *);
-
438
-
440 int egsAdvApplicationReadData(istream *);
-
441
-
443 int egsBrachyReadData(istream *);
-
444
-
445 int combineResults();
-
446
-
451 void resetCounter();
-
452
-
457 int addState(istream &data);
-
458
+
320
+
321 for (vector<EGS_AffineTransform *>::size_type st=0; st < source_transforms.size(); st++) {
+
322 delete source_transforms[st];
+
323 }
+
324 source_transforms.clear();
+
325
+
326 for (map<string, EGS_ScoringArray* >::iterator sa=extra_scoring_doses.begin(); sa != extra_scoring_doses.end(); sa++) {
+
327 delete sa->second;
+
328 }
+
329 extra_scoring_doses.clear();
+
330
+
331 for (map<string, EGS_ScoringArray* >::iterator sa=extra_scoring_doses_edep.begin(); sa != extra_scoring_doses_edep.end(); sa++) {
+
332 delete sa->second;
+
333 }
+
334 extra_scoring_doses_edep.clear();
+
335
+
336 if (phsp) {
+
337 delete phsp;
+
338 }
+
339
+
340 if (escoring) {
+
341 delete escoring;
+
342 }
+
343
+
344 vector<BaseSpectrumScorer *>::iterator it = spectrum_scorers.begin();
+
345 for (; it != spectrum_scorers.end(); it++) {
+
346 delete *it;
+
347 }
+
348 spectrum_scorers.clear();
+
349
+
350 if (recycle_opts) {
+
351 delete recycle_opts;
+
352 }
+
353
+
354 if (base_transform_inv) {
+
355 delete base_transform_inv;
+
356 }
+
357
+
358 if (gz_data_in) {
+
359 delete gz_data_in;
+
360 }
+
361
+
362 if (gz_data_out) {
+
363 delete gz_data_out;
+
364 }
+
365
+
366 };
+
+
367
+
368 int nsources;
+
369
+
370 EGS_Float effective_histories;
+
371
+
372 Latch latch_control;
+
373
+
375 void describeUserCode() const;
+
376
+
381 void describeSimulation();
+
382
+
383 void printIncludedFiles();
+
384
+
386 int initSimulation();
+
387
+
389 int initRunControl();
+
390
+
392 int initRunMode();
+
393
+
395 int initScoring();
+
396
+
398 int initVarianceReduction();
+
399
+
401 int initRussianRoulette(EGS_Input *);
+
402
+
404 int initBCSE(EGS_Input *);
+
405
+
407 int ausgab(int iarg);
+
408
+
415 int outputData();
+
416
+
418 int outputDataHelper(ostream *);
+
419
+
421 int egsApplicationOutputData(ostream *);
+
422
+
424 int egsAdvApplicationOutputData(ostream *);
+
425
+
427 int egsBrachyOutputData(ostream *);
+
428
+
432 int readData();
+
433
+
435 int readDataHelper(istream *);
+
436
+
438 int egsApplicationReadData(istream *);
+
439
+
441 int egsAdvApplicationReadData(istream *);
+
442
+
444 int egsBrachyReadData(istream *);
+
445
+
446 int combineResults();
+
447
+
452 void resetCounter();
+
453
+
458 int addState(istream &data);
459
-
460 /* \brief output any results to console */
-
461 void outputResults();
-
462
+
460
+
461 /* \brief output any results to console */
+
462 void outputResults();
463
-
465 void getCurrentResult(double &sum, double &sum2, double &norm,
-
466 double &count);
-
467
-
469 EB_Phantom* getPhantomByName(string name);
-
470
-
472 virtual void startNewParticle();
-
473 virtual void enterNewRegion();
-
474
-
475 virtual int runSimulation();
-
476
-
477 string getOutputVolcorFormat() {
-
478 return output_volcor_format;
-
479 }
-
480
-
481protected:
-
482
-
483 void addRecycledParticlesToStack(EGS_Particle *p, bool new_hist=false);
-
484 void copyParticleToSourceLoc(EGS_Particle *p, int source, bool kill_orig, bool rotate, EGS_Float new_wt);
+
464
+
466 void getCurrentResult(double &sum, double &sum2, double &norm,
+
467 double &count);
+
468
+
470 EB_Phantom* getPhantomByName(string name);
+
471
+
473 virtual void startNewParticle();
+
474 virtual void enterNewRegion();
+
475
+
476 virtual int runSimulation();
+
477
+
+
478 string getOutputVolcorFormat() {
+
479 return output_volcor_format;
+
480 }
+
+
481
+
482 int howManyJobsDone();
+
483
+
484protected:
485
-
486 void doPhotonSplitting(int);
-
487
+
486 void addRecycledParticlesToStack(EGS_Particle *p, bool new_hist=false);
+
487 void copyParticleToSourceLoc(EGS_Particle *p, int source, bool kill_orig, bool rotate, EGS_Float new_wt);
488
-
489 /* \brief initialize a single shower history.
-
490 *
-
491 * Particle is initiated from source and then transformed to location
-
492 * of next source */
-
493 int simulateSingleShower();
-
494 int startNewShower();
-
495
-
500 int initGeometry();
-
501
-
502
-
503 /* \brief override default initSource to allow us to get source position weighting */
-
504 int initSource();
+
489 void doPhotonSplitting(int);
+
490
+
491
+
492 /* \brief initialize a single shower history.
+
493 *
+
494 * Particle is initiated from source and then transformed to location
+
495 * of next source */
+
496 int simulateSingleShower();
+
497 int startNewShower();
+
498
+
503 int initGeometry();
+
504
505
-
506
-
508 int initSourceTransforms();
+
506 /* \brief override default initSource to allow us to get source position weighting */
+
507 int initSource();
+
508
509
-
510 /* \brief take an input containging multiple `transformation` input blocks
-
511 * and return a vector of pointers to the generated transforms.
-
512 */
-
513 vector<EGS_AffineTransform *> createTransforms(EGS_Input *input);
-
514
-
515};
-
516#endif
-
EB_Application
The main egs_brachy application class. See the Main Page for full documentation.
Definition: egs_brachy.h:90
-
EB_Application::spectrum_scorers
vector< BaseSpectrumScorer * > spectrum_scorers
Definition: egs_brachy.h:103
-
EB_Application::extra_scoring_mass
map< string, vector< EGS_Float > > extra_scoring_mass
Definition: egs_brachy.h:181
-
EB_Application::escoring
EnergyScoringStats * escoring
Energy related scoring/stats.
Definition: egs_brachy.h:102
-
EB_Application::source_transforms
vector< EGS_AffineTransform * > source_transforms
transforms to locations of all sources
Definition: egs_brachy.h:146
-
EB_Application::extra_scoring_reg
map< string, vector< int > > extra_scoring_reg
Definition: egs_brachy.h:179
-
EB_Application::steps_in_phantoms
map< int, EGS_I64 > steps_in_phantoms
Definition: egs_brachy.h:194
-
EB_Application::n_stuck
EGS_I64 n_stuck
Definition: egs_brachy.h:139
-
EB_Application::timing_blocks
EB_TimingTree timing_blocks
Track CPU times of various functions.
Definition: egs_brachy.h:191
-
EB_Application::steps_at_same_loc
int steps_at_same_loc
Definition: egs_brachy.h:138
-
EB_Application::extra_scoring_doses
map< string, EGS_ScoringArray * > extra_scoring_doses
Definition: egs_brachy.h:182
-
EB_Application::output_volcor_format
string output_volcor_format
text or gzip
Definition: egs_brachy.h:130
-
EB_Application::pevent_pub
Publisher pevent_pub
Particle event publisher.
Definition: egs_brachy.h:189
-
EB_Application::do_brem_split
bool do_brem_split
Definition: egs_brachy.h:154
-
EB_Application::output_egsdat_format
string output_egsdat_format
text or gzip
Definition: egs_brachy.h:119
-
EB_Application::run_mode_name
string run_mode_name
Definition: egs_brachy.h:100
-
EB_Application::output_volcor_phantoms
vector< string > output_volcor_phantoms
vector of phantom names to output volume correctino files for
Definition: egs_brachy.h:129
-
EB_Application::output_voxinfo_format
string output_voxinfo_format
text or gzip
Definition: egs_brachy.h:127
-
EB_Application::gz_data_in
igzstream * gz_data_in
GZip file for outputing egsdat.
Definition: egs_brachy.h:198
-
EB_Application::last_R
EGS_Float last_R
Definition: egs_brachy.h:136
-
EB_Application::global_e_max_rr
EGS_Float global_e_max_rr
max range rejection energy globally
Definition: egs_brachy.h:169
-
EB_Application::EB_Application
EB_Application(int argc, char **argv)
egs_brachy constructor
Definition: egs_brachy.h:269
-
EB_Application::gcr_phantom_reg
int gcr_phantom_reg
region of phantom to use for getCurrentResult (default to 0)
Definition: egs_brachy.h:177
-
EB_Application::effective_histories
EGS_Float effective_histories
Definition: egs_brachy.h:369
-
EB_Application::source_i_do_rr
bool source_i_do_rr
enable range rejection in sources
Definition: egs_brachy.h:171
-
EB_Application::output_egsphant
bool output_egsphant
true if user requests egsphant ouput
Definition: egs_brachy.h:123
-
EB_Application::latch_control
Latch latch_control
Definition: egs_brachy.h:371
-
EB_Application::global_i_do_rr
bool global_i_do_rr
enable range rejection outside of sources
Definition: egs_brachy.h:168
-
EB_Application::source_pcut
EGS_Float source_pcut
pcut for source objects
Definition: egs_brachy.h:164
-
EB_Application::bcse_factor
EGS_Float bcse_factor
Definition: egs_brachy.h:159
-
EB_Application::revision
static string revision
the usercode revision number
Definition: egs_brachy.h:200
-
EB_Application::active_source
int active_source
Definition: egs_brachy.h:111
-
EB_Application::global_pcut
EGS_Float global_pcut
pcut for source objects
Definition: egs_brachy.h:166
-
EB_Application::bcse_med_num
int bcse_med_num
Definition: egs_brachy.h:158
-
EB_Application::output_3ddose_files
bool output_3ddose_files
false if run mode is 'volume correction only'
Definition: egs_brachy.h:121
-
EB_Application::extra_scoring_doses_edep
map< string, EGS_ScoringArray * > extra_scoring_doses_edep
Definition: egs_brachy.h:183
-
EB_Application::gcr_phantom
EB_Phantom * gcr_phantom
phantom object to use in getCurrentResult (defaults to 1st phantom)
Definition: egs_brachy.h:176
-
EB_Application::DEFAULT_BCSE_FACTOR
static const EGS_Float DEFAULT_BCSE_FACTOR
Definition: egs_brachy.h:160
-
EB_Application::media_muen_names
map< string, string > media_muen_names
Definition: egs_brachy.h:151
-
EB_Application::~EB_Application
~EB_Application()
egs_brachy destructor
Definition: egs_brachy.h:306
-
EB_Application::superpos_geom
EGS_ASwitchedEnvelope * superpos_geom
an ASwitchedEnv cast of simulation geometry.
Definition: egs_brachy.h:142
-
EB_Application::output_dose_format
string output_dose_format
text or gzip
Definition: egs_brachy.h:122
-
EB_Application::source_weights
vector< EGS_Float > source_weights
Definition: egs_brachy.h:110
-
EB_Application::extra_scoring_vols
map< string, vector< EGS_Float > > extra_scoring_vols
Definition: egs_brachy.h:180
-
EB_Application::base_transform
EGS_AffineTransform * base_transform
same as source_transforms[0]
Definition: egs_brachy.h:147
-
EB_Application::source_envelope_geom
EGS_BaseGeometry * source_envelope_geom
geometry that the sources are embedded in
Definition: egs_brachy.h:141
-
EB_Application::phantom_geoms
vector< EB_Phantom * > phantom_geoms
pointers to all of the phantom objects
Definition: egs_brachy.h:144
-
EB_Application::score_scat
bool score_scat
true when scatter scoring is enabled
Definition: egs_brachy.h:117
-
EB_Application::output_egsphant_format
string output_egsphant_format
text or gzip
Definition: egs_brachy.h:124
-
EB_Application::gz_data_out
ogzstream * gz_data_out
GZip file for outputing egsdat.
Definition: egs_brachy.h:197
-
EB_Application::nbr_split
int nbr_split
Number of times to split bremstrahlung phtons.
Definition: egs_brachy.h:155
-
EB_Application::media_muen
map< int, EGS_Interpolator * > media_muen
Map from medium index to muen interpolator for that medium.
Definition: egs_brachy.h:150
-
EB_Application::gen_vc_results
ebvolcor::Results gen_vc_results
results from general volume correction
Definition: egs_brachy.h:186
-
EB_Application::base_transform_inv
EGS_AffineTransform * base_transform_inv
same as source_transforms[0].inverse()
Definition: egs_brachy.h:148
-
EB_Application::steps_in_sources
map< int, EGS_I64 > steps_in_sources
Definition: egs_brachy.h:193
-
EB_Application::output_voxinfo
bool output_voxinfo
true if user requests voxel info file
Definition: egs_brachy.h:126
-
EB_Application::steps_in_other
map< int, EGS_I64 > steps_in_other
Definition: egs_brachy.h:195
-
EB_Application::last_position
EGS_Vector last_position
Definition: egs_brachy.h:135
-
EB_Application::phsp
PHSPControl * phsp
Definition: egs_brachy.h:113
-
EB_Application::nsources
int nsources
total number of particle sources in current simulation
Definition: egs_brachy.h:367
-
EB_Application::flu_cutoff
EGS_Float flu_cutoff
fluorescent photon cutoff energy
Definition: egs_brachy.h:162
-
EB_Application::cur_R
EGS_Float cur_R
Definition: egs_brachy.h:137
-
EB_Application::RunMode
RunMode
Definition: egs_brachy.h:92
-
EB_Application::RM_SUPERPOSITION
@ RM_SUPERPOSITION
Superposition mode for intersource effects.
Definition: egs_brachy.h:94
-
EB_Application::RM_NORMAL
@ RM_NORMAL
Standard running mode.
Definition: egs_brachy.h:93
-
EB_Application::do_bcse
bool do_bcse
Definition: egs_brachy.h:157
-
EB_Application::ginfo
GeomInfo ginfo
meta data about the geometries
Definition: egs_brachy.h:174
-
EB_Application::source_vc_results
ebvolcor::Results source_vc_results
results from source volume correctio box phantom
Definition: egs_brachy.h:185
-
EB_Application::is_phsp_source
bool is_phsp_source
Definition: egs_brachy.h:108
-
EB_Application::source_ecut
EGS_Float source_ecut
ecut for source objects
Definition: egs_brachy.h:163
-
EB_Application::score_edep
bool score_edep
true when energy deposition is enabled
Definition: egs_brachy.h:116
-
EB_Application::source_e_max_rr
EGS_Float source_e_max_rr
max range rejection energy for source objects
Definition: egs_brachy.h:172
-
EB_Application::global_ecut
EGS_Float global_ecut
ecut for source objects
Definition: egs_brachy.h:165
-
EB_Application::p_init_locs
vector< EGS_Vector > p_init_locs
Definition: egs_brachy.h:133
-
EB_Application::score_tlen
bool score_tlen
true when tracklength estimator is enabled
Definition: egs_brachy.h:115
-
EB_Application::getOutputVolcorFormat
string getOutputVolcorFormat()
Definition: egs_brachy.h:477
-
EB_Application::run_mode
RunMode run_mode
Which run mode are we using (RM_NORMAL, RM_SUPERPOSITION or RM_VC_ONLY *‍/.
Definition: egs_brachy.h:99
-
EB_Application::recycle_opts
RecycleOpts * recycle_opts
Definition: egs_brachy.h:106
-
EB_Application::single_generator
bool single_generator
Definition: egs_brachy.h:107
-
EB_Application::record_n_init
int record_n_init
if > 0 write initial pos of record_n_init particles to {input_file}.pinit
Definition: egs_brachy.h:132
-
EB_Application::file_vc_results
ebvolcor::FileResults file_vc_results
results from precomputed volume correction
Definition: egs_brachy.h:187
-
EB_Phantom
A class to represent a single phantom for scoring dose in egs_brachy.
Definition: phantom.h:71
-
EB_TimingTree
Definition: timing.h:110
-
EnergyScoringStats
a class to use for scoring information about total energy initialzed, escaping sources etc
Definition: spec_scoring.h:57
-
GeomInfo
a container for organizing meta data about the geometries
Definition: ginfo.h:99
-
Latch
A class for handling latch bits relevant to egs_brachy. The Latch class listens for particle events a...
Definition: latch.h:51
- - -
Publisher::subscribe
void subscribe(Subscriber *s, EB_Message message)
Definition: pubsub.h:83
- - - +
511 int initSourceTransforms();
+
512
+
513 /* \brief take an input containging multiple `transformation` input blocks
+
514 * and return a vector of pointers to the generated transforms.
+
515 */
+
516 vector<EGS_AffineTransform *> createTransforms(EGS_Input *input);
+
517
+
518};
+
+
519
+
+
520class EB_UniformRunControl : public EGS_RunControl {
+
521
+
522public:
+
523
+
524 EB_UniformRunControl(EB_Application *app, string egsdat_format);
+
525 ~EB_UniformRunControl() {};
+
526
+
527 void describeRCO();
+
528
+
529 int startSimulation();
+
530
+
539 int finishSimulation();
+
540
+
541protected:
+
542
+
543 EB_Application *app;
+
544
+
545 string output_egsdat_format;
+
546
+
547 int milliseconds; // time interval for checking
+
548 // if all jobs finished (default 1000 ms)
+
549
+
550 int check_intervals;// Number of intervals to check
+
551 // if all jobs done (default 5)
+
552
+
553 int njob;
+
554 int npar;
+
555 int ipar;
+
556 int ifirst;
+
557 bool check_egsdat;// If true, and a 'watcher' job, produce intermediate results
+
558 bool watcher_job; // If true, job is a 'watcher'
+
559};
+
+
560
+
561#endif
+
EB_Application
The main egs_brachy application class. See the Main Page for full documentation.
Definition egs_brachy.h:91
+
EB_Application::spectrum_scorers
vector< BaseSpectrumScorer * > spectrum_scorers
Definition egs_brachy.h:104
+
EB_Application::extra_scoring_mass
map< string, vector< EGS_Float > > extra_scoring_mass
Definition egs_brachy.h:182
+
EB_Application::escoring
EnergyScoringStats * escoring
Energy related scoring/stats.
Definition egs_brachy.h:103
+
EB_Application::source_transforms
vector< EGS_AffineTransform * > source_transforms
transforms to locations of all sources
Definition egs_brachy.h:147
+
EB_Application::extra_scoring_reg
map< string, vector< int > > extra_scoring_reg
Definition egs_brachy.h:180
+
EB_Application::steps_in_phantoms
map< int, EGS_I64 > steps_in_phantoms
Definition egs_brachy.h:195
+
EB_Application::n_stuck
EGS_I64 n_stuck
Definition egs_brachy.h:140
+
EB_Application::timing_blocks
EB_TimingTree timing_blocks
Track CPU times of various functions.
Definition egs_brachy.h:192
+
EB_Application::steps_at_same_loc
int steps_at_same_loc
Definition egs_brachy.h:139
+
EB_Application::extra_scoring_doses
map< string, EGS_ScoringArray * > extra_scoring_doses
Definition egs_brachy.h:183
+
EB_Application::output_volcor_format
string output_volcor_format
text or gzip
Definition egs_brachy.h:131
+
EB_Application::pevent_pub
Publisher pevent_pub
Particle event publisher.
Definition egs_brachy.h:190
+
EB_Application::do_brem_split
bool do_brem_split
Definition egs_brachy.h:155
+
EB_Application::output_egsdat_format
string output_egsdat_format
text or gzip
Definition egs_brachy.h:120
+
EB_Application::run_mode_name
string run_mode_name
Definition egs_brachy.h:101
+
EB_Application::output_volcor_phantoms
vector< string > output_volcor_phantoms
vector of phantom names to output volume correctino files for
Definition egs_brachy.h:130
+
EB_Application::output_voxinfo_format
string output_voxinfo_format
text or gzip
Definition egs_brachy.h:128
+
EB_Application::gz_data_in
igzstream * gz_data_in
GZip file for outputing egsdat.
Definition egs_brachy.h:199
+
EB_Application::last_R
EGS_Float last_R
Definition egs_brachy.h:137
+
EB_Application::global_e_max_rr
EGS_Float global_e_max_rr
max range rejection energy globally
Definition egs_brachy.h:170
+
EB_Application::EB_Application
EB_Application(int argc, char **argv)
egs_brachy constructor
Definition egs_brachy.h:270
+
EB_Application::gcr_phantom_reg
int gcr_phantom_reg
region of phantom to use for getCurrentResult (default to 0)
Definition egs_brachy.h:178
+
EB_Application::effective_histories
EGS_Float effective_histories
Definition egs_brachy.h:370
+
EB_Application::source_i_do_rr
bool source_i_do_rr
enable range rejection in sources
Definition egs_brachy.h:172
+
EB_Application::output_egsphant
bool output_egsphant
true if user requests egsphant ouput
Definition egs_brachy.h:124
+
EB_Application::latch_control
Latch latch_control
Definition egs_brachy.h:372
+
EB_Application::global_i_do_rr
bool global_i_do_rr
enable range rejection outside of sources
Definition egs_brachy.h:169
+
EB_Application::source_pcut
EGS_Float source_pcut
pcut for source objects
Definition egs_brachy.h:165
+
EB_Application::bcse_factor
EGS_Float bcse_factor
Definition egs_brachy.h:160
+
EB_Application::revision
static string revision
the usercode revision number
Definition egs_brachy.h:201
+
EB_Application::active_source
int active_source
Definition egs_brachy.h:112
+
EB_Application::global_pcut
EGS_Float global_pcut
pcut for source objects
Definition egs_brachy.h:167
+
EB_Application::bcse_med_num
int bcse_med_num
Definition egs_brachy.h:159
+
EB_Application::output_3ddose_files
bool output_3ddose_files
false if run mode is 'volume correction only'
Definition egs_brachy.h:122
+
EB_Application::extra_scoring_doses_edep
map< string, EGS_ScoringArray * > extra_scoring_doses_edep
Definition egs_brachy.h:184
+
EB_Application::gcr_phantom
EB_Phantom * gcr_phantom
phantom object to use in getCurrentResult (defaults to 1st phantom)
Definition egs_brachy.h:177
+
EB_Application::DEFAULT_BCSE_FACTOR
static const EGS_Float DEFAULT_BCSE_FACTOR
Definition egs_brachy.h:161
+
EB_Application::media_muen_names
map< string, string > media_muen_names
Definition egs_brachy.h:152
+
EB_Application::~EB_Application
~EB_Application()
egs_brachy destructor
Definition egs_brachy.h:307
+
EB_Application::superpos_geom
EGS_ASwitchedEnvelope * superpos_geom
an ASwitchedEnv cast of simulation geometry.
Definition egs_brachy.h:143
+
EB_Application::output_dose_format
string output_dose_format
text or gzip
Definition egs_brachy.h:123
+
EB_Application::source_weights
vector< EGS_Float > source_weights
Definition egs_brachy.h:111
+
EB_Application::extra_scoring_vols
map< string, vector< EGS_Float > > extra_scoring_vols
Definition egs_brachy.h:181
+
EB_Application::base_transform
EGS_AffineTransform * base_transform
same as source_transforms[0]
Definition egs_brachy.h:148
+
EB_Application::source_envelope_geom
EGS_BaseGeometry * source_envelope_geom
geometry that the sources are embedded in
Definition egs_brachy.h:142
+
EB_Application::phantom_geoms
vector< EB_Phantom * > phantom_geoms
pointers to all of the phantom objects
Definition egs_brachy.h:145
+
EB_Application::score_scat
bool score_scat
true when scatter scoring is enabled
Definition egs_brachy.h:118
+
EB_Application::output_egsphant_format
string output_egsphant_format
text or gzip
Definition egs_brachy.h:125
+
EB_Application::gz_data_out
ogzstream * gz_data_out
GZip file for outputing egsdat.
Definition egs_brachy.h:198
+
EB_Application::nbr_split
int nbr_split
Number of times to split bremstrahlung phtons.
Definition egs_brachy.h:156
+
EB_Application::media_muen
map< int, EGS_Interpolator * > media_muen
Map from medium index to muen interpolator for that medium.
Definition egs_brachy.h:151
+
EB_Application::gen_vc_results
ebvolcor::Results gen_vc_results
results from general volume correction
Definition egs_brachy.h:187
+
EB_Application::base_transform_inv
EGS_AffineTransform * base_transform_inv
same as source_transforms[0].inverse()
Definition egs_brachy.h:149
+
EB_Application::steps_in_sources
map< int, EGS_I64 > steps_in_sources
Definition egs_brachy.h:194
+
EB_Application::output_voxinfo
bool output_voxinfo
true if user requests voxel info file
Definition egs_brachy.h:127
+
EB_Application::steps_in_other
map< int, EGS_I64 > steps_in_other
Definition egs_brachy.h:196
+
EB_Application::last_position
EGS_Vector last_position
Definition egs_brachy.h:136
+
EB_Application::phsp
PHSPControl * phsp
Definition egs_brachy.h:114
+
EB_Application::nsources
int nsources
total number of particle sources in current simulation
Definition egs_brachy.h:368
+
EB_Application::flu_cutoff
EGS_Float flu_cutoff
fluorescent photon cutoff energy
Definition egs_brachy.h:163
+
EB_Application::cur_R
EGS_Float cur_R
Definition egs_brachy.h:138
+
EB_Application::RunMode
RunMode
Definition egs_brachy.h:93
+
EB_Application::RM_SUPERPOSITION
@ RM_SUPERPOSITION
Superposition mode for intersource effects.
Definition egs_brachy.h:95
+
EB_Application::RM_NORMAL
@ RM_NORMAL
Standard running mode.
Definition egs_brachy.h:94
+
EB_Application::do_bcse
bool do_bcse
Definition egs_brachy.h:158
+
EB_Application::ginfo
GeomInfo ginfo
meta data about the geometries
Definition egs_brachy.h:175
+
EB_Application::source_vc_results
ebvolcor::Results source_vc_results
results from source volume correctio box phantom
Definition egs_brachy.h:186
+
EB_Application::is_phsp_source
bool is_phsp_source
Definition egs_brachy.h:109
+
EB_Application::source_ecut
EGS_Float source_ecut
ecut for source objects
Definition egs_brachy.h:164
+
EB_Application::score_edep
bool score_edep
true when energy deposition is enabled
Definition egs_brachy.h:117
+
EB_Application::source_e_max_rr
EGS_Float source_e_max_rr
max range rejection energy for source objects
Definition egs_brachy.h:173
+
EB_Application::global_ecut
EGS_Float global_ecut
ecut for source objects
Definition egs_brachy.h:166
+
EB_Application::p_init_locs
vector< EGS_Vector > p_init_locs
Definition egs_brachy.h:134
+
EB_Application::score_tlen
bool score_tlen
true when tracklength estimator is enabled
Definition egs_brachy.h:116
+
EB_Application::getOutputVolcorFormat
string getOutputVolcorFormat()
Definition egs_brachy.h:478
+
EB_Application::run_mode
RunMode run_mode
Which run mode are we using (RM_NORMAL, RM_SUPERPOSITION or RM_VC_ONLY *‍/.
Definition egs_brachy.h:100
+
EB_Application::recycle_opts
RecycleOpts * recycle_opts
Definition egs_brachy.h:107
+
EB_Application::single_generator
bool single_generator
Definition egs_brachy.h:108
+
EB_Application::record_n_init
int record_n_init
if > 0 write initial pos of record_n_init particles to {input_file}.pinit
Definition egs_brachy.h:133
+
EB_Application::file_vc_results
ebvolcor::FileResults file_vc_results
results from precomputed volume correction
Definition egs_brachy.h:188
+
EB_Phantom
A class to represent a single phantom for scoring dose in egs_brachy.
Definition phantom.h:71
+
EB_TimingTree
Definition timing.h:110
+
EB_UniformRunControl
Definition egs_brachy.h:520
+
EB_UniformRunControl::startSimulation
int startSimulation()
Definition egs_brachy.cpp:2697
+
EB_UniformRunControl::ipar
int ipar
Definition egs_brachy.h:555
+
EB_UniformRunControl::ifirst
int ifirst
Definition egs_brachy.h:556
+
EB_UniformRunControl::check_intervals
int check_intervals
Definition egs_brachy.h:550
+
EB_UniformRunControl::npar
int npar
Definition egs_brachy.h:554
+
EB_UniformRunControl::check_egsdat
bool check_egsdat
Definition egs_brachy.h:557
+
EB_UniformRunControl::app
EB_Application * app
Definition egs_brachy.h:543
+
EB_UniformRunControl::milliseconds
int milliseconds
Definition egs_brachy.h:547
+
EB_UniformRunControl::describeRCO
void describeRCO()
Definition egs_brachy.cpp:2720
+
EB_UniformRunControl::output_egsdat_format
string output_egsdat_format
text or gzip
Definition egs_brachy.h:545
+
EB_UniformRunControl::finishSimulation
int finishSimulation()
Uses 'watcher' jobs to determine if the simulation has finished.
Definition egs_brachy.cpp:2747
+
EB_UniformRunControl::njob
int njob
Definition egs_brachy.h:553
+
EB_UniformRunControl::~EB_UniformRunControl
~EB_UniformRunControl()
Definition egs_brachy.h:525
+
EB_UniformRunControl::watcher_job
bool watcher_job
Definition egs_brachy.h:558
+
EnergyScoringStats
a class to use for scoring information about total energy initialzed, escaping sources etc
Definition spec_scoring.h:57
+
GeomInfo
a container for organizing meta data about the geometries
Definition ginfo.h:99
+
Latch
A class for handling latch bits relevant to egs_brachy. The Latch class listens for particle events a...
Definition latch.h:51
+ + +
Publisher::subscribe
void subscribe(Subscriber *s, EB_Message message)
Definition pubsub.h:83
+ + +
eb_volcor.h
Volume correction routines for egs_brachy.
ginfo.h
ginfo contains classes for organizing information about the geometries present in an egs_brachy simul...
latch.h
handle particles latch bits for egs_brachy
@@ -614,17 +683,17 @@
phantom.h
Header file for phantom objects.
phsp.h
Definition of the PHSPControl object.
pubsub.h
A simple pub/sub module to allow various egs_brachy classes to subscribe to particle events.
-
PARTICLE_ESCAPING_SOURCE
@ PARTICLE_ESCAPING_SOURCE
Definition: pubsub.h:60
-
PARTICLE_ESCAPED_SOURCE
@ PARTICLE_ESCAPED_SOURCE
Definition: pubsub.h:61
+
PARTICLE_ESCAPING_SOURCE
@ PARTICLE_ESCAPING_SOURCE
Definition pubsub.h:60
+
PARTICLE_ESCAPED_SOURCE
@ PARTICLE_ESCAPED_SOURCE
Definition pubsub.h:61
recycle.h
class definitions for recycling
spec_scoring.h
Definition of spectrum scoring classes.
- -
ebvolcor::Results
Struct used to collect and output results about a volume correction run.
Definition: eb_volcor.h:212
+ +
ebvolcor::Results
Struct used to collect and output results about a volume correction run.
Definition eb_volcor.h:212
-Generated by doxygen 1.9.5 +Generated by doxygen 1.9.8
diff --git a/docs/egs__brachy_8md.html b/docs/egs__brachy_8md.html index 92beb3b4..24c3e458 100644 --- a/docs/egs__brachy_8md.html +++ b/docs/egs__brachy_8md.html @@ -3,7 +3,7 @@ - + EGS Brachy: egs_brachy.md File Reference @@ -30,7 +30,7 @@
- + @@ -30,7 +30,7 @@ - + @@ -30,7 +30,7 @@ - + +
-
/Users/marc/dev/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/egs_sobol.cpp
+
/Users/marc/Developer/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/egs_sobol.cpp
Go to the documentation of this file.
1/*
@@ -106,6 +111,7 @@
31
38#include "egs_sobol.h"
39
+
40void EGS_Sobol::saveState() {
41 if (copy) {
42 copy->setState(this);
@@ -115,19 +121,25 @@
46 }
47 copy->copy = 0;
48}
+
49
+
50void EGS_Sobol::resetState() {
51 if (copy) {
52 setState(copy);
53 }
54}
+
55
+
56EGS_RandomGenerator *EGS_Sobol::getCopy() {
57 EGS_Sobol *c = new EGS_Sobol(dim, init_seed);
58 c->setState(dim, cur_seed);
59 return c;
60}
+
61
+
62void EGS_Sobol::setState(EGS_RandomGenerator *r) {
63
64 EGS_Sobol *r1 = dynamic_cast<EGS_Sobol *>(r);
@@ -139,7 +151,9 @@
70 dim = r1->dim;
71 np = dim;
72}
+
73
+
74bool EGS_Sobol::storePrivateState(ostream &data) {
75
76 if (!egsStoreI64(data, count)) {
@@ -150,11 +164,13 @@
81 return false;
82 }
83
-
84 data << dim << endl;
+
84 data << dim << "\n";
85
86 return data.good();
87}
+
88
+
89bool EGS_Sobol::setPrivateState(istream &data) {
90
91 if (!egsGetI64(data, count)) {
@@ -172,8 +188,10 @@
103
104 return data.good();
105}
+
106
107
+
108void EGS_Sobol::describeRNG() const {
109 egsInformation("Random number generator:\n"
110 "============================================\n");
@@ -183,7 +201,9 @@
114 egsInformation(" current seed = %lld\n", cur_seed);
115 egsInformation(" numbers used so far = %lld\n", count);
116}
+
117
+
118void EGS_Sobol::setState(int dimension, EGS_I64 seed) {
119
120 cur_seed = seed;
@@ -195,32 +215,35 @@
126 dim = dimension;
127 }
128}
+
129
+
130void EGS_Sobol::fillArray(int n, EGS_Float *array) {
131 // note cur_seed gets updated each call to i8_sobol
132 sobol::i8_sobol(dim, &cur_seed, array);
133 count += dim; // we generate dim number every call
134}
+
135
-
EGS_Sobol
EGS_RandomGenerator wrapper for Sobol library.
Definition: egs_sobol.h:71
-
EGS_Sobol::saveState
void saveState()
Definition: egs_sobol.cpp:40
-
EGS_Sobol::dim
int dim
Definition: egs_sobol.h:155
-
EGS_Sobol::setPrivateState
bool setPrivateState(istream &data)
Definition: egs_sobol.cpp:89
-
EGS_Sobol::describeRNG
void describeRNG() const
Output information about this RNG using egsInformation()
Definition: egs_sobol.cpp:108
-
EGS_Sobol::fillArray
void fillArray(int n, EGS_Float *array)
Fill the array pointed to by array with random numbers.
Definition: egs_sobol.cpp:130
-
EGS_Sobol::getCopy
EGS_RandomGenerator * getCopy()
Definition: egs_sobol.cpp:56
-
EGS_Sobol::setState
void setState(EGS_RandomGenerator *r)
Definition: egs_sobol.cpp:62
-
EGS_Sobol::cur_seed
EGS_I64 cur_seed
initial seed for random number generator
Definition: egs_sobol.h:157
-
EGS_Sobol::resetState
void resetState()
Definition: egs_sobol.cpp:50
-
EGS_Sobol::copy
EGS_Sobol * copy
current seed being used for random number generator (required to reinitialize
Definition: egs_sobol.h:159
-
EGS_Sobol::storePrivateState
bool storePrivateState(ostream &data)
Definition: egs_sobol.cpp:74
-
EGS_Sobol::init_seed
EGS_I64 init_seed
Definition: egs_sobol.h:156
+
EGS_Sobol
EGS_RandomGenerator wrapper for Sobol library.
Definition egs_sobol.h:71
+
EGS_Sobol::saveState
void saveState()
Definition egs_sobol.cpp:40
+
EGS_Sobol::dim
int dim
Definition egs_sobol.h:155
+
EGS_Sobol::setPrivateState
bool setPrivateState(istream &data)
Definition egs_sobol.cpp:89
+
EGS_Sobol::describeRNG
void describeRNG() const
Output information about this RNG using egsInformation()
Definition egs_sobol.cpp:108
+
EGS_Sobol::fillArray
void fillArray(int n, EGS_Float *array)
Fill the array pointed to by array with random numbers.
Definition egs_sobol.cpp:130
+
EGS_Sobol::getCopy
EGS_RandomGenerator * getCopy()
Definition egs_sobol.cpp:56
+
EGS_Sobol::setState
void setState(EGS_RandomGenerator *r)
Definition egs_sobol.cpp:62
+
EGS_Sobol::cur_seed
EGS_I64 cur_seed
initial seed for random number generator
Definition egs_sobol.h:157
+
EGS_Sobol::resetState
void resetState()
Definition egs_sobol.cpp:50
+
EGS_Sobol::copy
EGS_Sobol * copy
current seed being used for random number generator (required to reinitialize
Definition egs_sobol.h:159
+
EGS_Sobol::storePrivateState
bool storePrivateState(ostream &data)
Definition egs_sobol.cpp:74
+
EGS_Sobol::init_seed
EGS_I64 init_seed
Definition egs_sobol.h:156
egs_sobol.h
Header file for EGS_Sobol (EGS_RandomGenerator wrapper for Sobol QRNG)
-
sobol::i8_sobol
void i8_sobol(int dim_num, long long int *seed, double quasi[])
Definition: sobol.cpp:14163
+
sobol::i8_sobol
void i8_sobol(int dim_num, long long int *seed, double quasi[])
Definition sobol.cpp:14163
-Generated by doxygen 1.9.5 +Generated by doxygen 1.9.8
diff --git a/docs/egs__sobol_8h.html b/docs/egs__sobol_8h.html index 13c77094..8f1acd0c 100644 --- a/docs/egs__sobol_8h.html +++ b/docs/egs__sobol_8h.html @@ -3,9 +3,9 @@ - + -EGS Brachy: /Users/marc/dev/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/egs_sobol.h File Reference +EGS Brachy: /Users/marc/Developer/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/egs_sobol.h File Reference @@ -30,7 +30,7 @@
- + @@ -30,7 +30,7 @@ - + +
-
/Users/marc/dev/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/egs_sobol.h
+
/Users/marc/Developer/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/egs_sobol.h
Go to the documentation of this file.
1/*
@@ -119,8 +124,8 @@
50#else
51
52 #ifdef HAVE_VISIBILITY
-
53 #define EGS_SOBOL_EXPORT __attribute__ ((visibility ("default")))
-
54 #define EGS_SOBOL_LOCAL __attribute__ ((visibility ("hidden")))
+
53 #define EGS_SOBOL_EXPORT __attribute__ ((visibility ("default")))
+
54 #define EGS_SOBOL_LOCAL __attribute__ ((visibility ("hidden")))
55 #else
56 #define EGS_SOBOL_EXPORT
57 #define EGS_SOBOL_LOCAL
@@ -135,10 +140,12 @@
66#include "egs_functions.h"
67
68
+
71class EGS_SOBOL_LOCAL EGS_Sobol : public EGS_RandomGenerator {
72
73public:
74
+
75 EGS_Sobol(EGS_Input *inp): copy(0) {
76
77 int dimension;
@@ -157,7 +164,9 @@
90
91 setState(dimension, init_seed);
92 };
+
93
+
94 EGS_Sobol(int dimension=3, EGS_I64 iseed=-1) :
95 EGS_RandomGenerator(dimension), copy(0) {
96
@@ -171,19 +180,24 @@
104
105 setState(dimension, iseed);
106 };
+
107
+
108 EGS_Sobol(const EGS_Sobol &r): copy(0) {
109 np = r.dim;
110 init_seed = r.init_seed;
111 setState(r.dim, r.init_seed);
112 };
+
113
+
114 ~EGS_Sobol() {
115 /*if (copy){
116 delete copy;
117 }
118 */
119 };
+
120
123 void fillArray(int n, EGS_Float *array);
124
@@ -197,9 +211,11 @@
133
134 void resetState();
135
+
136 int rngSize() const {
137 return baseSize() + sizeof(int) + 2*sizeof(EGS_I64);
138 };
+
139
140protected:
141
@@ -217,24 +233,25 @@
157 cur_seed;
159 EGS_Sobol *copy;
160};
+
161#endif
-
EGS_Sobol
EGS_RandomGenerator wrapper for Sobol library.
Definition: egs_sobol.h:71
-
EGS_Sobol::~EGS_Sobol
~EGS_Sobol()
Definition: egs_sobol.h:114
-
EGS_Sobol::EGS_Sobol
EGS_Sobol(EGS_Input *inp)
Definition: egs_sobol.h:75
-
EGS_Sobol::dim
int dim
Definition: egs_sobol.h:155
-
EGS_Sobol::EGS_Sobol
EGS_Sobol(const EGS_Sobol &r)
Definition: egs_sobol.h:108
-
EGS_Sobol::rngSize
int rngSize() const
Definition: egs_sobol.h:136
-
EGS_Sobol::cur_seed
EGS_I64 cur_seed
initial seed for random number generator
Definition: egs_sobol.h:157
-
EGS_Sobol::copy
EGS_Sobol * copy
current seed being used for random number generator (required to reinitialize
Definition: egs_sobol.h:159
-
EGS_Sobol::EGS_Sobol
EGS_Sobol(int dimension=3, EGS_I64 iseed=-1)
Definition: egs_sobol.h:94
-
EGS_Sobol::init_seed
EGS_I64 init_seed
Definition: egs_sobol.h:156
-
EGS_SOBOL_LOCAL
#define EGS_SOBOL_LOCAL
Definition: egs_sobol.h:57
-
sobol::tau_sobol
int tau_sobol(int dim_num)
Definition: sobol.cpp:28474
+
EGS_Sobol
EGS_RandomGenerator wrapper for Sobol library.
Definition egs_sobol.h:71
+
EGS_Sobol::~EGS_Sobol
~EGS_Sobol()
Definition egs_sobol.h:114
+
EGS_Sobol::EGS_Sobol
EGS_Sobol(EGS_Input *inp)
Definition egs_sobol.h:75
+
EGS_Sobol::dim
int dim
Definition egs_sobol.h:155
+
EGS_Sobol::EGS_Sobol
EGS_Sobol(const EGS_Sobol &r)
Definition egs_sobol.h:108
+
EGS_Sobol::rngSize
int rngSize() const
Definition egs_sobol.h:136
+
EGS_Sobol::cur_seed
EGS_I64 cur_seed
initial seed for random number generator
Definition egs_sobol.h:157
+
EGS_Sobol::copy
EGS_Sobol * copy
current seed being used for random number generator (required to reinitialize
Definition egs_sobol.h:159
+
EGS_Sobol::EGS_Sobol
EGS_Sobol(int dimension=3, EGS_I64 iseed=-1)
Definition egs_sobol.h:94
+
EGS_Sobol::init_seed
EGS_I64 init_seed
Definition egs_sobol.h:156
+
EGS_SOBOL_LOCAL
#define EGS_SOBOL_LOCAL
Definition egs_sobol.h:57
+
sobol::tau_sobol
int tau_sobol(int dim_num)
Definition sobol.cpp:28474
sobol.h
Sobol library functions from http://people.sc.fsu.edu/~jburkardt/cpp_src/sobol/sobol....
-Generated by doxygen 1.9.5 +Generated by doxygen 1.9.8
diff --git a/docs/eye__plaques_2README_8md.html b/docs/eye__plaques_2README_8md.html index 17cb16b0..4eea8745 100644 --- a/docs/eye__plaques_2README_8md.html +++ b/docs/eye__plaques_2README_8md.html @@ -3,9 +3,9 @@ - + -EGS Brachy: /Users/marc/dev/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/lib/geometry/eye_plaques/README.md File Reference +EGS Brachy: /Users/marc/Developer/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/lib/geometry/eye_plaques/README.md File Reference @@ -30,7 +30,7 @@
- + @@ -30,7 +30,7 @@ - + @@ -30,7 +30,7 @@ - + +
-Generated by doxygen 1.9.5 +Generated by doxygen 1.9.8
diff --git a/docs/flu__cutoff_2test_8py.html b/docs/flu__cutoff_2test_8py.html index 71ab8f2b..7b64dc10 100644 --- a/docs/flu__cutoff_2test_8py.html +++ b/docs/flu__cutoff_2test_8py.html @@ -3,9 +3,9 @@ - + -EGS Brachy: /Users/marc/dev/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/eb_tests/flu_cutoff/test.py File Reference +EGS Brachy: /Users/marc/Developer/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/eb_tests/flu_cutoff/test.py File Reference @@ -30,7 +30,7 @@ - + @@ -30,7 +30,7 @@ - + +
Go to the documentation of this file.
1"""
2
3A test for ensuring that the fluorescent photon cutoff works. A monoenergetic
-
4source of 0.015keV is placed within a thin Ti sphere and photon counts are
-
5scored on the outer surface of the sphere. Normally there would be a
-
6fluorescent peak at ~4.5keV so when the `fluorescent photon cutoff` setting is
-
7set to 0.005 MeV that peak should not be present.
-
8
-
9Two energy bins from 0-10keV and 10-20keV are used. If fluorescent photon cutoff
-
10feature is working correctly 100% of photons should be in the 10-20keV range.
-
11
+
4source of 0.015keV is placed within a thin Ti sphere and photon counts are
+
5scored on the outer surface of the sphere. Normally there would be a
+
6fluorescent peak at ~4.5keV so when the `fluorescent photon cutoff` setting is
+
7set to 0.005 MeV that peak should not be present.
+
8
+
9Two energy bins from 0-10keV and 10-20keV are used. If fluorescent photon cutoff
+
10feature is working correctly 100% of photons should be in the 10-20keV range.
+
11
12"""
-
13
-
14import math
-
15import re
-
16
-
17from eb_tests.utils import read_csv_spectrum, values_close
-
18
-
19EGSINP = "flu_cutoff.egsinp"
-
20TIME_LIMIT_S_PER_MHZ = 2/2993. # s / MHz
-
21
-
22
-
23def compare_results(egslst, inp_name):
-
24
-
25 energies, counts, uncs = read_csv_spectrum(inp_name+".surfcount.csv")
+
13
+
14import math
+
15import re
+
16
+
17from eb_tests.utils import read_csv_spectrum, values_close
+
18
+
19EGSINP = "flu_cutoff.egsinp"
+
20TIME_LIMIT_S_PER_MHZ = 2/2993. # s / MHz
+
21
+
22
+
+
23def compare_results(egslst, inp_name):
+
24
+
25 energies, counts, uncs = read_csv_spectrum(inp_name+".surfcount.csv")
26
27 lower, upper = counts
28 if not (lower == 0 and upper == 100):
29 return False, "Photon Count < 10keV = %f" %(lower), "Expected 0"
30
31 return True, "", ""
+
+
eb_tests.utils
Definition utils.py:1
-Generated by doxygen 1.9.5 +Generated by doxygen 1.9.8
diff --git a/docs/folderclosed.svg b/docs/folderclosed.svg new file mode 100644 index 00000000..b04bed2e --- /dev/null +++ b/docs/folderclosed.svg @@ -0,0 +1,11 @@ + + + + + + + + + + diff --git a/docs/folderclosedd.svg b/docs/folderclosedd.svg new file mode 100644 index 00000000..52f0166a --- /dev/null +++ b/docs/folderclosedd.svg @@ -0,0 +1,11 @@ + + + + + + + + + + diff --git a/docs/folderopen.svg b/docs/folderopen.svg new file mode 100644 index 00000000..f6896dd2 --- /dev/null +++ b/docs/folderopen.svg @@ -0,0 +1,17 @@ + + + + + + + + + + diff --git a/docs/folderopend.svg b/docs/folderopend.svg new file mode 100644 index 00000000..2d1f06e7 --- /dev/null +++ b/docs/folderopend.svg @@ -0,0 +1,12 @@ + + + + + + + + + + + diff --git a/docs/functions.html b/docs/functions.html index b5c6802a..8842fa90 100644 --- a/docs/functions.html +++ b/docs/functions.html @@ -3,7 +3,7 @@ - + EGS Brachy: Class Members @@ -30,7 +30,7 @@ - + + + + + + + + +
+
+ + + + + + +
+
EGS Brachy +
+
An egs++ user code for rapid brachytherapy calculations
+
+
+ + + + + + + +
+ +
+
+ + +
+
+
+
+
+
Loading...
+
Searching...
+
No Matches
+
+
+
+
+ +
+
Here is a list of all variables with links to the classes they belong to:
+ +

- w -

+
+ +
+Generated by doxygen 1.9.8 +
+ + diff --git a/docs/functions_w.html b/docs/functions_w.html index 83371d5c..799af395 100644 --- a/docs/functions_w.html +++ b/docs/functions_w.html @@ -3,7 +3,7 @@ - + EGS Brachy: Class Members @@ -30,7 +30,7 @@ - + +
14]
15
16
-
17def gen_docs():
+
+
17def gen_docs():
18 for module, outfile in modules:
19 module.gen_docs(outfile)
20
21
+
22if __name__ == "__main__":
23 gen_docs()
24
-
gen_docs
Definition: gen_docs.py:1
-
gen_docs.gen_docs
def gen_docs()
Definition: gen_docs.py:17
+
gen_docs
Definition gen_docs.py:1
+
gen_docs.gen_docs
gen_docs()
Definition gen_docs.py:17
-Generated by doxygen 1.9.5 +Generated by doxygen 1.9.8
diff --git a/docs/gen__geom_8py.html b/docs/gen__geom_8py.html index bb1438d0..66694e36 100644 --- a/docs/gen__geom_8py.html +++ b/docs/gen__geom_8py.html @@ -3,7 +3,7 @@ - + EGS Brachy: gen_geom.py File Reference @@ -30,7 +30,7 @@ - + +
7abs_root = os.path.abspath(root)
8geom = os.path.join(abs_root, "geometry")
9
-
10def get_readme(dir_path):
+
+
10def get_readme(dir_path):
11
12 """Look in directory dir_path for a file called README.md and return
13 it's contents if available"""
-
14
-
15 try:
+
14
+
15 try:
16 readme = open(os.path.join(dir_path, "README.md")).read()
17 return "\n%s\n" % readme
18 except IOError:
19 return ""
20
21
-
22def get_filetype_links(dir_path, extension):
+
+
+
22def get_filetype_links(dir_path, extension):
23 relpath = os.path.relpath(dir_path)
24 files = [os.path.join(relpath, g) for g in os.listdir(dir_path) if g.endswith(extension)]
25 links = ["[%s](%s)" % (os.path.split(f)[1], f) for f in files]
26 return links
27
28
-
29def get_images(dir_path):
+
+
+
29def get_images(dir_path):
30 relpath = os.path.relpath(dir_path)
31 files = [os.path.join(relpath, g) for g in os.listdir(dir_path) if g.lower().endswith(".png")]
32 files = [f.replace('../lib', '../egs_brachy/lib') for f in files]
@@ -109,7 +119,9 @@
34 return images
35
36
-
37def gen_geom_docs(droot, title, is_sources=False):
+
+
+
37def gen_geom_docs(droot, title, is_sources=False):
38
39 types = [os.path.join(droot, t) for t in os.listdir(droot) if os.path.isdir(os.path.join(droot, t))]
40
@@ -132,16 +144,16 @@
57 docs.append("\subsubsection %s %s" % (subsection, subname))
58
59
-
60 geom_links = get_filetype_links(d, ".geom")
-
61 shape_links = get_filetype_links(d, ".shape")
+
60 geom_links = get_filetype_links(d, ".geom")
+
61 shape_links = get_filetype_links(d, ".shape")
62 docs.append("<dl>")
-
63 docs.append("<dt>Description</dt><dd>%s</dd>" % (get_readme(d) or "<em>No description available</em>"))
+
63 docs.append("<dt>Description</dt><dd>%s</dd>" % (get_readme(d) or "<em>No description available</em>"))
64 if geom_links:
65 docs.append("<dt>Geometry Files</dt><dd>%s</dt>" % ','.join(geom_links))
66 if shape_links:
67 docs.append("<dt>Shape Files</dt><dd>%s</dt>" % ', '.join(shape_links))
68
-
69 images = get_images(d)
+
69 images = get_images(d)
70 docs.append("<dt>Images</dt><dd>%s</dd>" % ('\n'.join(images) or "<em>No images available</em>"))
71
72 docs.append("</dl>")
@@ -149,9 +161,11 @@
74 return "\n".join(docs)
75
76
-
77def gen_docs(fname):
+
+
+
77def gen_docs(fname):
78 params = {}
-
79 params["sources"] = gen_geom_docs(os.path.join(geom, "sources"), "Sources")
+
79 params["sources"] = gen_geom_docs(os.path.join(geom, "sources"), "Sources")
80 params["eye_plaques"] = find_file_descriptions(os.path.join(geom, "eye_plaques"), "start geometry")
81 params["transforms"] = find_file_descriptions(os.path.join(geom, "transformations"), "start transformation")
82 params["phantoms"] = find_file_descriptions(os.path.join(geom, "phantoms"), "start geometry")
@@ -206,21 +220,22 @@
131
132 open(fname, "w").write(docs)
133
+
134if __name__ == "__main__":
-
135 outfile = "geom.md"
+
135 outfile = "geom.md"
136 gen_docs(outfile)
137
138
-
join
string join(const vector< string > &v, string delim)
Definition: ginfo.cpp:56
-
gen_docs
Definition: gen_docs.py:1
-
gen_geom.get_images
def get_images(dir_path)
Definition: gen_geom.py:29
-
gen_geom.get_readme
def get_readme(dir_path)
Definition: gen_geom.py:10
-
gen_geom.get_filetype_links
def get_filetype_links(dir_path, extension)
Definition: gen_geom.py:22
-
gen_geom.gen_geom_docs
def gen_geom_docs(droot, title, is_sources=False)
Definition: gen_geom.py:37
+
join
string join(const vector< string > &v, string delim)
Definition ginfo.cpp:56
+
gen_docs
Definition gen_docs.py:1
+
gen_geom.gen_geom_docs
gen_geom_docs(droot, title, is_sources=False)
Definition gen_geom.py:37
+
gen_geom.get_readme
get_readme(dir_path)
Definition gen_geom.py:10
+
gen_geom.get_images
get_images(dir_path)
Definition gen_geom.py:29
+
gen_geom.get_filetype_links
get_filetype_links(dir_path, extension)
Definition gen_geom.py:22
-Generated by doxygen 1.9.5 +Generated by doxygen 1.9.8
diff --git a/docs/gen__media_8py.html b/docs/gen__media_8py.html index d08ec7bf..3365a2c3 100644 --- a/docs/gen__media_8py.html +++ b/docs/gen__media_8py.html @@ -3,7 +3,7 @@ - + EGS Brachy: gen_media.py File Reference @@ -30,7 +30,7 @@ - + +
5media_file = os.path.join(abs_root, "media", "material.dat")
6muen_dir = os.path.join(abs_root, "muen")
7
-
8def get_pegsless_materials():
+
+
8def get_pegsless_materials():
9
10 data = open(media_file, "r")
11
@@ -105,7 +111,9 @@
30 return "<dl>%s</dl>" % "\n".join(sorted(media))
31
32
-
33def get_muen():
+
+
+
33def get_muen():
34
35 files = []
36 doc = ""
@@ -136,11 +144,13 @@
61
62
63
-
64def gen_docs(fname):
+
+
+
64def gen_docs(fname):
65
66 params = {
-
67 "materials": get_pegsless_materials(),
-
68 "muen": get_muen()
+
67 "materials": get_pegsless_materials(),
+
68 "muen": get_muen()
69 }
70
71 docs = """@anchor egs_brachy_media_lib
@@ -170,17 +180,18 @@
95
96 open(fname, "w").write(docs)
97
+
98if __name__ == "__main__":
-
99 outfile = "media.md"
+
99 outfile = "media.md"
100 gen_docs(outfile)
-
join
string join(const vector< string > &v, string delim)
Definition: ginfo.cpp:56
-
gen_docs
Definition: gen_docs.py:1
-
gen_media.get_muen
def get_muen()
Definition: gen_media.py:33
-
gen_media.get_pegsless_materials
def get_pegsless_materials()
Definition: gen_media.py:8
+
join
string join(const vector< string > &v, string delim)
Definition ginfo.cpp:56
+
gen_docs
Definition gen_docs.py:1
+
gen_media.get_muen
get_muen()
Definition gen_media.py:33
+
gen_media.get_pegsless_materials
get_pegsless_materials()
Definition gen_media.py:8
-Generated by doxygen 1.9.5 +Generated by doxygen 1.9.8
diff --git a/docs/gen__specs_8py.html b/docs/gen__specs_8py.html index dc674ad0..540bd401 100644 --- a/docs/gen__specs_8py.html +++ b/docs/gen__specs_8py.html @@ -3,7 +3,7 @@ - + EGS Brachy: gen_specs.py File Reference @@ -30,7 +30,7 @@ - + +
5specs = os.path.join(abs_root, "spectra")
6
7
-
8def get_spectra():
+
+
8def get_spectra():
9 items = []
10
11 for root, dirs, files in os.walk(specs):
@@ -98,7 +104,9 @@
23 return "\n".join(items)
24
25
-
26def gen_docs(fname):
+
+
+
26def gen_docs(fname):
27
28 docs = """@anchor egs_brachy_spectra_lib
29
@@ -112,23 +120,24 @@
37
38%s
39
-
40""" % (get_spectra())
+
40""" % (get_spectra())
41
42
43 open(fname, "w").write(docs)
44
+
45if __name__ == "__main__":
-
46 outfile = "spectra.md"
+
46 outfile = "spectra.md"
47 gen_docs(outfile)
48
49
-
join
string join(const vector< string > &v, string delim)
Definition: ginfo.cpp:56
-
gen_docs
Definition: gen_docs.py:1
-
gen_specs.get_spectra
def get_spectra()
Definition: gen_specs.py:8
+
join
string join(const vector< string > &v, string delim)
Definition ginfo.cpp:56
+
gen_docs
Definition gen_docs.py:1
+
gen_specs.get_spectra
get_spectra()
Definition gen_specs.py:8
-Generated by doxygen 1.9.5 +Generated by doxygen 1.9.8
diff --git a/docs/gen__tests_8py.html b/docs/gen__tests_8py.html index e6397038..55bc9d4a 100644 --- a/docs/gen__tests_8py.html +++ b/docs/gen__tests_8py.html @@ -3,7 +3,7 @@ - + EGS Brachy: gen_tests.py File Reference @@ -30,7 +30,7 @@ - + +
8
9globber = os.path.join(root_tests, "*", "test.py")
10
-
11def get_tests():
+
+
11def get_tests():
12 items = []
13
14
@@ -102,7 +108,9 @@
27 return "\n".join(items)
28
29
-
30def gen_docs(fname):
+
+
+
30def gen_docs(fname):
31
32 docs = """@anchor egs_brachy_test_suite
33
@@ -113,22 +121,23 @@
38
39%s
40
-
41""" % (get_tests())
+
41""" % (get_tests())
42
43
44 open(fname, "w").write(docs)
45
+
46if __name__ == "__main__":
-
47 outfile = "tests.md"
+
47 outfile = "tests.md"
48 gen_docs(outfile)
49
-
join
string join(const vector< string > &v, string delim)
Definition: ginfo.cpp:56
-
gen_docs
Definition: gen_docs.py:1
-
gen_tests.get_tests
def get_tests()
Definition: gen_tests.py:11
+
join
string join(const vector< string > &v, string delim)
Definition ginfo.cpp:56
+
gen_docs
Definition gen_docs.py:1
+
gen_tests.get_tests
get_tests()
Definition gen_tests.py:11
-Generated by doxygen 1.9.5 +Generated by doxygen 1.9.8
diff --git a/docs/gen__transport_8py.html b/docs/gen__transport_8py.html index bf6aaf50..3adfc154 100644 --- a/docs/gen__transport_8py.html +++ b/docs/gen__transport_8py.html @@ -3,7 +3,7 @@ - + EGS Brachy: gen_transport.py File Reference @@ -30,7 +30,7 @@ - + +
6transport = os.path.join(abs_root, "transport")
7
8
-
9def gen_docs(fname):
+
+
9def gen_docs(fname):
10
11 docs = """@anchor egs_brachy_transport_lib
12
@@ -97,16 +103,17 @@
22
23 open(fname, "w").write(docs)
24
+
25if __name__ == "__main__":
-
26 outfile = "transport.md"
+
26 outfile = "transport.md"
27 gen_docs(outfile)
28
29
-
gen_docs
Definition: gen_docs.py:1
+
gen_docs
Definition gen_docs.py:1
-Generated by doxygen 1.9.5 +Generated by doxygen 1.9.8
diff --git a/docs/geom_8md.html b/docs/geom_8md.html index 22bc1490..b300f926 100644 --- a/docs/geom_8md.html +++ b/docs/geom_8md.html @@ -3,7 +3,7 @@ - + EGS Brachy: geom.md File Reference @@ -30,7 +30,7 @@ - + @@ -30,7 +30,7 @@ - + @@ -30,7 +30,7 @@ - + +
-
/Users/marc/dev/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/ginfo.cpp
+
/Users/marc/Developer/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/ginfo.cpp
Go to the documentation of this file.
1/*
@@ -119,11 +124,14 @@
48typedef pair <string, vector<int> > CDGeomRegType;
49
50// comarison function for sorting CD 'set geometry' region definitions
+
51bool pairCompare(const CDGeomRegType &firstElem, const CDGeomRegType &secondElem) {
52 return firstElem.second[0] < secondElem.second[0];
53}
+
54
55// simple string join routine
+
56string join(const vector<string> &v, string delim) {
57
58 string s="";
@@ -136,23 +144,27 @@
65 }
66 return s;
67}
+
68
69
70// build up our geometry tree based from composite geometries
+
71Node GeomInfo::build_tree(string root, vector<Node> &children) {
72
73 for (size_t i =0; i < gmap[root].children.size(); i++) {
-
74 string child = gmap[root].children[i];
+
74 string child = gmap[root].children[i];
75 vector<Node> empty;
76 children.push_back(build_tree(child, empty));
77 }
78
79 return Node(root, children);
80}
+
81
82// parse the input geometry definition and figures out which geometries are inscribed in others
83// and then builds up a tree of nodes that can be used for figuring out the egs++ region
84// numbers assigned to each geometry
+
85int GeomInfo::initializeFromInput(EGS_Input *input) {
86
87 int err = input->getInput("simulation geometry", sim_geom_name);
@@ -213,11 +225,13 @@
142 return 0;
143
144}
+
145
146
147/* counts the number of transformation blocks for an auto envelope geometry
148 * and hence counts the number of inscribed geometries in an envelope
149 */
+
150size_t countAutoEnvelopeInscribed(EGS_Input *input) {
151
152 EGS_Input *inscribedInp = input->getInputItem("inscribed geometry");
@@ -247,17 +261,21 @@
176
177 return count;
178}
+
179
180
181// return base geometrty name for egs_genvelope or egs_autoenvelope geometry
+
182string getGeomBaseName(EGS_Input *input) {
183 string base;
184 input->getInput("base geometry", base);
185 return base;
186}
+
187
188
189// return a vector of all the names of the inscribed geometries in an EGS_AutoEnvelope input
+
190vector<string> getAutoEnvelopeChildren(EGS_Input *input) {
191
192 vector<string> children;
@@ -278,18 +296,22 @@
207
208 return children;
209}
+
210
211
212// return a vector of all the names of the inscribedd geometries in an egs_genvelope input
+
213vector<string> getGEnvelopeChildren(EGS_Input *input) {
214 vector<string> children;
215 input->getInput("inscribed geometries", children);
216 children.insert(children.begin(), getGeomBaseName(input));
217 return children;
218}
+
219
220
221// return a vector of all the names of the inscribed geometries in an egs_cdgeometry input
+
222vector<string> getCDChildren(EGS_Input *input) {
223 vector<string> children;
224 string name;
@@ -346,9 +368,11 @@
275
276 return children;
277}
+
278
279
280// return a vector of all the names of the inscribedd geometries in an egs_genvelope input
+
281vector<string> getNDChildren(EGS_Input *input) {
282
283 vector<string> children;
@@ -363,29 +387,36 @@
292 input->getInput("dimensions", children);
293 return children;
294}
+
295
296
297// return a vector of all the names of the inscribedd geometries in an egs_genvelope input
+
298vector<string> getUnionChildren(EGS_Input *input) {
299 vector<string> children;
300 input->getInput("geometries", children);
301 return children;
302}
+
303
304
305// return a vector of all the names of the inscribedd geometries in an egs_genvelope input
+
306vector<string> getGStackChildren(EGS_Input *input) {
307 vector<string> children;
308 input->getInput("geometries", children);
309 return children;
310}
+
311
312// return a vector of all the names of the inscribedd geometries in an egs_gtransformed input
+
313vector<string> getGTransformedChildren(EGS_Input *input) {
314 vector<string> children;
315 input->getInput("my geometry", children);
316 return children;
317}
+
318
319
320
@@ -400,6 +431,7 @@
329 * egs_gtransformed
330 *
331 * */
+
332vector<string> GeomInfo::getChildren(string name, EGS_Input *input) {
333
334 string library;
@@ -428,9 +460,11 @@
357
358 return children;
359}
+
360
361
362// return the index of the geometry name in the the given input vector or -1 if not found
+
363int findGeomInVec(EGS_BaseGeometry *geom, vector<string> geoms) {
364 for (size_t p=0; p < geoms.size(); p++) {
365 if (geoms[p] == geom->getName()) {
@@ -440,9 +474,11 @@
369
370 return -1;
371}
+
372
373
374// return the maximum number of regions for the input geometry names
+
375int maxNRegOfGeoms(vector<string> gnames, int start) {
376 int max = 0;
377 for (size_t i = start; i < gnames.size(); i++) {
@@ -451,9 +487,11 @@
380 }
381 return max;
382}
+
383
384
385// return the number of regions in the subdivision at index idx of a composite geometry
+
386int nregForSubDiv(GeomRegionInfo gri, int idx) {
387
388 EGS_BaseGeometry *geom = EGS_BaseGeometry::getGeometry(gri.name);
@@ -482,9 +520,11 @@
411
412 return geom->regions();
413}
+
414
415
416// traverse tree and set geometry start/end regions for a given geometry
+
417void GeomInfo::getGeomRegs(Node root, vector<GeomRegionInfo> &ordered, int start) {
418
419 EGS_BaseGeometry *g = EGS_BaseGeometry::getGeometry(root.name);
@@ -502,6 +542,7 @@
431 }
432
433}
+
434
435
436// set up all arrays required to decide which geometry/phantom a region
@@ -509,6 +550,7 @@
438// To do this we loop through all geometries, decide whether it is a phantom
439// or not, then loop through each region in the geometry and set the local
440// region number phantom index etc
+
441void GeomInfo::setGeometryIndexes(EGS_BaseGeometry *geom) {
442
443 getGeomRegs(*geom_tree, ordered_geom_data, 0);
@@ -545,42 +587,56 @@
474 }
475 }
476}
+
477
478
+
479GeomRegT GeomInfo::globalToLocal(int ir) {
480 if (ir < 0) {
481 return GeomRegT(0,0);
482 }
483 return GeomRegT(global_ir_to_geom[ir], global_ir_to_local_ir[ir]);
484}
+
485
486
+
487int GeomInfo::globalToLocalReg(int ir) {
488 return ir >= 0 && ir < nreg_total ? global_ir_to_local_ir[ir] : -1;
489}
+
490
491
+
492int GeomInfo::localToGlobal(GeomRegT local) {
493 GeomRegionInfo gri = geom_to_regioninfo[local.first];
494 return gri.start + local.second;
495}
+
496
497
+
498bool GeomInfo::isPhantom(int ir) {
499 return ir >= 0 && ir < nreg_total && global_ir_to_phant[ir] >= 0;
500}
+
501
502
+
503bool GeomInfo::isSource(int ir) {
504 return ir >= 0 && ir < nreg_total && global_ir_to_source[ir] >= 0;
505}
+
506
507
+
508int GeomInfo::phantomFromRegion(int ir) {
509 return ir >= 0 && ir < nreg_total ? global_ir_to_phant[ir] : -1;
510}
+
511
512
+
513void GeomInfo::printInfo() {
514
515 egsInformation("Total number of geometries = %d\n", ngeom);
@@ -598,61 +654,63 @@
527 }
528 egsInformation("%s\n",string(80, '-').c_str());
529}
-
GeomInfo::geom_to_regioninfo
map< EGS_BaseGeometry *, GeomRegionInfo > geom_to_regioninfo
Definition: ginfo.h:151
-
GeomInfo::getGeomRegs
void getGeomRegs(Node, vector< GeomRegionInfo > &, int)
Definition: ginfo.cpp:417
-
GeomInfo::source_envelope_name
string source_envelope_name
Definition: ginfo.h:131
-
GeomInfo::global_ir_to_local_ir
vector< int > global_ir_to_local_ir
pointer for the geometry it belongs to
Definition: ginfo.h:111
-
GeomInfo::gmap
GeomRegionInfoMapT gmap
Definition: ginfo.h:118
-
GeomInfo::ordered_geom_data
vector< GeomRegionInfo > ordered_geom_data
Definition: ginfo.h:149
-
GeomInfo::global_ir_to_geom
vector< EGS_BaseGeometry * > global_ir_to_geom
the source geometry index or -1 if not a source
Definition: ginfo.h:108
-
GeomInfo::isSource
bool isSource(int ir)
Definition: ginfo.cpp:503
-
GeomInfo::phantomFromRegion
int phantomFromRegion(int ir)
return the phantom index for this region number or -1 if region is not in a phantom
Definition: ginfo.cpp:508
-
GeomInfo::localToGlobal
int localToGlobal(GeomRegT)
Definition: ginfo.cpp:492
-
GeomInfo::initializeFromInput
int initializeFromInput(EGS_Input *input)
Initialize the GeomInfo structure (ginfo) This function reads the geometry input block,...
Definition: ginfo.cpp:85
-
GeomInfo::build_tree
Node build_tree(string root, vector< Node > &children)
Definition: ginfo.cpp:71
-
GeomInfo::global_ir_to_source
vector< int > global_ir_to_source
the phantoms geometry index or -1 if not a phant
Definition: ginfo.h:104
-
GeomInfo::sim_geom_name
string sim_geom_name
Definition: ginfo.h:130
-
GeomInfo::ngeom
int ngeom
total number of geometries created
Definition: ginfo.h:138
-
GeomInfo::isPhantom
bool isPhantom(int ir)
Definition: ginfo.cpp:498
-
GeomInfo::setGeometryIndexes
void setGeometryIndexes(EGS_BaseGeometry *sim_geom)
Setup all arrays required to decide which geometry/phantom a region is in and whether or not we are s...
Definition: ginfo.cpp:441
-
GeomInfo::global_ir_to_phant
vector< int > global_ir_to_phant
array of size nreg mapping global region number to
Definition: ginfo.h:101
-
GeomInfo::printInfo
void printInfo()
Definition: ginfo.cpp:513
-
GeomInfo::globalToLocal
GeomRegT globalToLocal(int ir)
convert global region number to (EGS_BaseGeometry, local_reg_num) pair
Definition: ginfo.cpp:479
-
GeomInfo::nreg_total
int nreg_total
total number of regions in the simulation geometry
Definition: ginfo.h:139
-
GeomInfo::geom_tree
Node * geom_tree
Definition: ginfo.h:136
-
GeomInfo::globalToLocalReg
int globalToLocalReg(int ir)
convert global region number to local_reg_num
Definition: ginfo.cpp:487
-
GeomInfo::getChildren
vector< string > getChildren(string name, EGS_Input *inp)
Definition: ginfo.cpp:332
-
GeomInfo::source_names
vector< string > source_names
Definition: ginfo.h:134
-
GeomInfo::phantom_names
vector< string > phantom_names
Definition: ginfo.h:132
-
Node
Definition: ginfo.h:58
-
getUnionChildren
vector< string > getUnionChildren(EGS_Input *input)
Definition: ginfo.cpp:298
-
getAutoEnvelopeChildren
vector< string > getAutoEnvelopeChildren(EGS_Input *input)
Definition: ginfo.cpp:190
-
getGEnvelopeChildren
vector< string > getGEnvelopeChildren(EGS_Input *input)
Definition: ginfo.cpp:213
-
getGTransformedChildren
vector< string > getGTransformedChildren(EGS_Input *input)
Definition: ginfo.cpp:313
-
join
string join(const vector< string > &v, string delim)
Definition: ginfo.cpp:56
-
CDGeomRegType
pair< string, vector< int > > CDGeomRegType
Definition: ginfo.cpp:48
-
nregForSubDiv
int nregForSubDiv(GeomRegionInfo gri, int idx)
Definition: ginfo.cpp:386
-
maxNRegOfGeoms
int maxNRegOfGeoms(vector< string > gnames, int start)
Definition: ginfo.cpp:375
-
pairCompare
bool pairCompare(const CDGeomRegType &firstElem, const CDGeomRegType &secondElem)
Definition: ginfo.cpp:51
-
getCDChildren
vector< string > getCDChildren(EGS_Input *input)
Definition: ginfo.cpp:222
-
getNDChildren
vector< string > getNDChildren(EGS_Input *input)
Definition: ginfo.cpp:281
-
getGeomBaseName
string getGeomBaseName(EGS_Input *input)
Definition: ginfo.cpp:182
-
findGeomInVec
int findGeomInVec(EGS_BaseGeometry *geom, vector< string > geoms)
Definition: ginfo.cpp:363
-
getGStackChildren
vector< string > getGStackChildren(EGS_Input *input)
Definition: ginfo.cpp:306
-
countAutoEnvelopeInscribed
size_t countAutoEnvelopeInscribed(EGS_Input *input)
Definition: ginfo.cpp:150
+
+
GeomInfo::geom_to_regioninfo
map< EGS_BaseGeometry *, GeomRegionInfo > geom_to_regioninfo
Definition ginfo.h:151
+
GeomInfo::getGeomRegs
void getGeomRegs(Node, vector< GeomRegionInfo > &, int)
Definition ginfo.cpp:417
+
GeomInfo::source_envelope_name
string source_envelope_name
Definition ginfo.h:131
+
GeomInfo::global_ir_to_local_ir
vector< int > global_ir_to_local_ir
pointer for the geometry it belongs to
Definition ginfo.h:111
+
GeomInfo::gmap
GeomRegionInfoMapT gmap
Definition ginfo.h:118
+
GeomInfo::ordered_geom_data
vector< GeomRegionInfo > ordered_geom_data
Definition ginfo.h:149
+
GeomInfo::global_ir_to_geom
vector< EGS_BaseGeometry * > global_ir_to_geom
the source geometry index or -1 if not a source
Definition ginfo.h:108
+
GeomInfo::isSource
bool isSource(int ir)
Definition ginfo.cpp:503
+
GeomInfo::phantomFromRegion
int phantomFromRegion(int ir)
return the phantom index for this region number or -1 if region is not in a phantom
Definition ginfo.cpp:508
+
GeomInfo::localToGlobal
int localToGlobal(GeomRegT)
Definition ginfo.cpp:492
+
GeomInfo::initializeFromInput
int initializeFromInput(EGS_Input *input)
Initialize the GeomInfo structure (ginfo) This function reads the geometry input block,...
Definition ginfo.cpp:85
+
GeomInfo::build_tree
Node build_tree(string root, vector< Node > &children)
Definition ginfo.cpp:71
+
GeomInfo::global_ir_to_source
vector< int > global_ir_to_source
the phantoms geometry index or -1 if not a phant
Definition ginfo.h:104
+
GeomInfo::sim_geom_name
string sim_geom_name
Definition ginfo.h:130
+
GeomInfo::ngeom
int ngeom
total number of geometries created
Definition ginfo.h:138
+
GeomInfo::isPhantom
bool isPhantom(int ir)
Definition ginfo.cpp:498
+
GeomInfo::setGeometryIndexes
void setGeometryIndexes(EGS_BaseGeometry *sim_geom)
Setup all arrays required to decide which geometry/phantom a region is in and whether or not we are s...
Definition ginfo.cpp:441
+
GeomInfo::global_ir_to_phant
vector< int > global_ir_to_phant
array of size nreg mapping global region number to
Definition ginfo.h:101
+
GeomInfo::printInfo
void printInfo()
Definition ginfo.cpp:513
+
GeomInfo::globalToLocal
GeomRegT globalToLocal(int ir)
convert global region number to (EGS_BaseGeometry, local_reg_num) pair
Definition ginfo.cpp:479
+
GeomInfo::nreg_total
int nreg_total
total number of regions in the simulation geometry
Definition ginfo.h:139
+
GeomInfo::geom_tree
Node * geom_tree
Definition ginfo.h:136
+
GeomInfo::globalToLocalReg
int globalToLocalReg(int ir)
convert global region number to local_reg_num
Definition ginfo.cpp:487
+
GeomInfo::getChildren
vector< string > getChildren(string name, EGS_Input *inp)
Definition ginfo.cpp:332
+
GeomInfo::source_names
vector< string > source_names
Definition ginfo.h:134
+
GeomInfo::phantom_names
vector< string > phantom_names
Definition ginfo.h:132
+
Node
Definition ginfo.h:58
+
Node::children
vector< Node > children
Definition ginfo.h:61
+
getUnionChildren
vector< string > getUnionChildren(EGS_Input *input)
Definition ginfo.cpp:298
+
getAutoEnvelopeChildren
vector< string > getAutoEnvelopeChildren(EGS_Input *input)
Definition ginfo.cpp:190
+
getGEnvelopeChildren
vector< string > getGEnvelopeChildren(EGS_Input *input)
Definition ginfo.cpp:213
+
getGTransformedChildren
vector< string > getGTransformedChildren(EGS_Input *input)
Definition ginfo.cpp:313
+
join
string join(const vector< string > &v, string delim)
Definition ginfo.cpp:56
+
CDGeomRegType
pair< string, vector< int > > CDGeomRegType
Definition ginfo.cpp:48
+
nregForSubDiv
int nregForSubDiv(GeomRegionInfo gri, int idx)
Definition ginfo.cpp:386
+
maxNRegOfGeoms
int maxNRegOfGeoms(vector< string > gnames, int start)
Definition ginfo.cpp:375
+
pairCompare
bool pairCompare(const CDGeomRegType &firstElem, const CDGeomRegType &secondElem)
Definition ginfo.cpp:51
+
getCDChildren
vector< string > getCDChildren(EGS_Input *input)
Definition ginfo.cpp:222
+
getNDChildren
vector< string > getNDChildren(EGS_Input *input)
Definition ginfo.cpp:281
+
getGeomBaseName
string getGeomBaseName(EGS_Input *input)
Definition ginfo.cpp:182
+
findGeomInVec
int findGeomInVec(EGS_BaseGeometry *geom, vector< string > geoms)
Definition ginfo.cpp:363
+
getGStackChildren
vector< string > getGStackChildren(EGS_Input *input)
Definition ginfo.cpp:306
+
countAutoEnvelopeInscribed
size_t countAutoEnvelopeInscribed(EGS_Input *input)
Definition ginfo.cpp:150
ginfo.h
ginfo contains classes for organizing information about the geometries present in an egs_brachy simul...
-
GeomRegT
pair< EGS_BaseGeometry *, int > GeomRegT
pair of geometry and local region number
Definition: ginfo.h:79
-
GeomRegionInfo
a struct to contain elementary information aboud a geometry
Definition: ginfo.h:83
- -
GeomRegionInfo::nreg
int nreg
Definition: ginfo.h:88
-
GeomRegionInfo::start
int start
Definition: ginfo.h:89
-
GeomRegionInfo::children
vector< string > children
Definition: ginfo.h:87
-
GeomRegionInfo::type
string type
Definition: ginfo.h:86
-
GeomRegionInfo::name
string name
Definition: ginfo.h:85
+
GeomRegT
pair< EGS_BaseGeometry *, int > GeomRegT
pair of geometry and local region number
Definition ginfo.h:79
+
GeomRegionInfo
a struct to contain elementary information aboud a geometry
Definition ginfo.h:83
+ + + +
GeomRegionInfo::children
vector< string > children
Definition ginfo.h:87
+
GeomRegionInfo::type
string type
Definition ginfo.h:86
+
GeomRegionInfo::name
string name
Definition ginfo.h:85
-Generated by doxygen 1.9.5 +Generated by doxygen 1.9.8
diff --git a/docs/ginfo_8h.html b/docs/ginfo_8h.html index 6cee99df..395535ed 100644 --- a/docs/ginfo_8h.html +++ b/docs/ginfo_8h.html @@ -3,9 +3,9 @@ - + -EGS Brachy: /Users/marc/dev/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/ginfo.h File Reference +EGS Brachy: /Users/marc/Developer/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/ginfo.h File Reference @@ -30,7 +30,7 @@
- + @@ -30,7 +30,7 @@ - + +
-
/Users/marc/dev/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/ginfo.h
+
/Users/marc/Developer/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/ginfo.h
Go to the documentation of this file.
1/*
@@ -125,11 +130,13 @@
55
56
57// Tree node used for organizing/sorting geometries and their children
+
58class Node {
59public:
60 string name;
61 vector<Node> children;
62
+
63 Node(string n, vector<Node> children) {
64 name = n;
65 for (size_t i=0; i < children.size(); i++) {
@@ -137,17 +144,22 @@
67 }
68
69 };
+
70
+
71 void addNode(Node node) {
72 children.push_back(node);
73 }
+
74
75};
+
76
77
79typedef pair<EGS_BaseGeometry *, int> GeomRegT;
80
81
+
83struct GeomRegionInfo {
84
85 string name;
@@ -157,10 +169,12 @@
89 int start;
90 int end;
92};
+
93
95typedef map<string, GeomRegionInfo> GeomRegionInfoMapT;
96
97
+
99class GeomInfo {
100
101 vector<int> global_ir_to_phant;
@@ -194,11 +208,13 @@
140
141
142 GeomInfo() {};
+
143 ~GeomInfo() {
144 if (geom_tree) {
145 delete geom_tree;
146 }
147 }
+
148
149 vector<GeomRegionInfo> ordered_geom_data;
151 map<EGS_BaseGeometry *, GeomRegionInfo> geom_to_regioninfo;
@@ -229,58 +245,59 @@
195 void printInfo();
196
197};
+
198
199#endif
-
GeomInfo
a container for organizing meta data about the geometries
Definition: ginfo.h:99
-
GeomInfo::geom_to_regioninfo
map< EGS_BaseGeometry *, GeomRegionInfo > geom_to_regioninfo
Definition: ginfo.h:151
-
GeomInfo::getGeomRegs
void getGeomRegs(Node, vector< GeomRegionInfo > &, int)
Definition: ginfo.cpp:417
-
GeomInfo::source_envelope_name
string source_envelope_name
Definition: ginfo.h:131
-
GeomInfo::global_ir_to_local_ir
vector< int > global_ir_to_local_ir
pointer for the geometry it belongs to
Definition: ginfo.h:111
-
GeomInfo::gmap
GeomRegionInfoMapT gmap
Definition: ginfo.h:118
-
GeomInfo::ordered_geom_data
vector< GeomRegionInfo > ordered_geom_data
Definition: ginfo.h:149
+
GeomInfo
a container for organizing meta data about the geometries
Definition ginfo.h:99
+
GeomInfo::geom_to_regioninfo
map< EGS_BaseGeometry *, GeomRegionInfo > geom_to_regioninfo
Definition ginfo.h:151
+
GeomInfo::getGeomRegs
void getGeomRegs(Node, vector< GeomRegionInfo > &, int)
Definition ginfo.cpp:417
+
GeomInfo::source_envelope_name
string source_envelope_name
Definition ginfo.h:131
+
GeomInfo::global_ir_to_local_ir
vector< int > global_ir_to_local_ir
pointer for the geometry it belongs to
Definition ginfo.h:111
+
GeomInfo::gmap
GeomRegionInfoMapT gmap
Definition ginfo.h:118
+
GeomInfo::ordered_geom_data
vector< GeomRegionInfo > ordered_geom_data
Definition ginfo.h:149
GeomInfo::setGeomMap
void setGeomMap()
-
GeomInfo::global_ir_to_geom
vector< EGS_BaseGeometry * > global_ir_to_geom
the source geometry index or -1 if not a source
Definition: ginfo.h:108
-
GeomInfo::phantom_geoms
vector< EB_Phantom * > phantom_geoms
pointers to all of the phantom objects
Definition: ginfo.h:153
-
GeomInfo::isSource
bool isSource(int ir)
Definition: ginfo.cpp:503
-
GeomInfo::phantomFromRegion
int phantomFromRegion(int ir)
return the phantom index for this region number or -1 if region is not in a phantom
Definition: ginfo.cpp:508
-
GeomInfo::localToGlobal
int localToGlobal(GeomRegT)
Definition: ginfo.cpp:492
-
GeomInfo::GeomInfo
GeomInfo()
Definition: ginfo.h:142
-
GeomInfo::initializeFromInput
int initializeFromInput(EGS_Input *input)
Initialize the GeomInfo structure (ginfo) This function reads the geometry input block,...
Definition: ginfo.cpp:85
-
GeomInfo::build_tree
Node build_tree(string root, vector< Node > &children)
Definition: ginfo.cpp:71
-
GeomInfo::global_ir_to_source
vector< int > global_ir_to_source
the phantoms geometry index or -1 if not a phant
Definition: ginfo.h:104
-
GeomInfo::sim_geom_name
string sim_geom_name
Definition: ginfo.h:130
-
GeomInfo::~GeomInfo
~GeomInfo()
Definition: ginfo.h:143
-
GeomInfo::ngeom
int ngeom
total number of geometries created
Definition: ginfo.h:138
-
GeomInfo::isPhantom
bool isPhantom(int ir)
Definition: ginfo.cpp:498
-
GeomInfo::setGeometryIndexes
void setGeometryIndexes(EGS_BaseGeometry *sim_geom)
Setup all arrays required to decide which geometry/phantom a region is in and whether or not we are s...
Definition: ginfo.cpp:441
-
GeomInfo::global_ir_to_phant
vector< int > global_ir_to_phant
array of size nreg mapping global region number to
Definition: ginfo.h:101
-
GeomInfo::printInfo
void printInfo()
Definition: ginfo.cpp:513
-
GeomInfo::globalToLocal
GeomRegT globalToLocal(int ir)
convert global region number to (EGS_BaseGeometry, local_reg_num) pair
Definition: ginfo.cpp:479
-
GeomInfo::nreg_total
int nreg_total
total number of regions in the simulation geometry
Definition: ginfo.h:139
-
GeomInfo::geom_tree
Node * geom_tree
Definition: ginfo.h:136
-
GeomInfo::globalToLocalReg
int globalToLocalReg(int ir)
convert global region number to local_reg_num
Definition: ginfo.cpp:487
-
GeomInfo::getChildren
vector< string > getChildren(string name, EGS_Input *inp)
Definition: ginfo.cpp:332
-
GeomInfo::source_names
vector< string > source_names
Definition: ginfo.h:134
-
GeomInfo::phantom_names
vector< string > phantom_names
Definition: ginfo.h:132
-
Node
Definition: ginfo.h:58
-
Node::addNode
void addNode(Node node)
Definition: ginfo.h:71
-
Node::name
string name
Definition: ginfo.h:60
-
Node::children
vector< Node > children
Definition: ginfo.h:61
-
Node::Node
Node(string n, vector< Node > children)
Definition: ginfo.h:63
-
GeomRegionInfoMapT
map< string, GeomRegionInfo > GeomRegionInfoMapT
a mapping from geometry name to information about that geometry
Definition: ginfo.h:95
-
GeomRegT
pair< EGS_BaseGeometry *, int > GeomRegT
pair of geometry and local region number
Definition: ginfo.h:79
+
GeomInfo::global_ir_to_geom
vector< EGS_BaseGeometry * > global_ir_to_geom
the source geometry index or -1 if not a source
Definition ginfo.h:108
+
GeomInfo::phantom_geoms
vector< EB_Phantom * > phantom_geoms
pointers to all of the phantom objects
Definition ginfo.h:153
+
GeomInfo::isSource
bool isSource(int ir)
Definition ginfo.cpp:503
+
GeomInfo::phantomFromRegion
int phantomFromRegion(int ir)
return the phantom index for this region number or -1 if region is not in a phantom
Definition ginfo.cpp:508
+
GeomInfo::localToGlobal
int localToGlobal(GeomRegT)
Definition ginfo.cpp:492
+
GeomInfo::GeomInfo
GeomInfo()
Definition ginfo.h:142
+
GeomInfo::initializeFromInput
int initializeFromInput(EGS_Input *input)
Initialize the GeomInfo structure (ginfo) This function reads the geometry input block,...
Definition ginfo.cpp:85
+
GeomInfo::build_tree
Node build_tree(string root, vector< Node > &children)
Definition ginfo.cpp:71
+
GeomInfo::global_ir_to_source
vector< int > global_ir_to_source
the phantoms geometry index or -1 if not a phant
Definition ginfo.h:104
+
GeomInfo::sim_geom_name
string sim_geom_name
Definition ginfo.h:130
+
GeomInfo::~GeomInfo
~GeomInfo()
Definition ginfo.h:143
+
GeomInfo::ngeom
int ngeom
total number of geometries created
Definition ginfo.h:138
+
GeomInfo::isPhantom
bool isPhantom(int ir)
Definition ginfo.cpp:498
+
GeomInfo::setGeometryIndexes
void setGeometryIndexes(EGS_BaseGeometry *sim_geom)
Setup all arrays required to decide which geometry/phantom a region is in and whether or not we are s...
Definition ginfo.cpp:441
+
GeomInfo::global_ir_to_phant
vector< int > global_ir_to_phant
array of size nreg mapping global region number to
Definition ginfo.h:101
+
GeomInfo::printInfo
void printInfo()
Definition ginfo.cpp:513
+
GeomInfo::globalToLocal
GeomRegT globalToLocal(int ir)
convert global region number to (EGS_BaseGeometry, local_reg_num) pair
Definition ginfo.cpp:479
+
GeomInfo::nreg_total
int nreg_total
total number of regions in the simulation geometry
Definition ginfo.h:139
+
GeomInfo::geom_tree
Node * geom_tree
Definition ginfo.h:136
+
GeomInfo::globalToLocalReg
int globalToLocalReg(int ir)
convert global region number to local_reg_num
Definition ginfo.cpp:487
+
GeomInfo::getChildren
vector< string > getChildren(string name, EGS_Input *inp)
Definition ginfo.cpp:332
+
GeomInfo::source_names
vector< string > source_names
Definition ginfo.h:134
+
GeomInfo::phantom_names
vector< string > phantom_names
Definition ginfo.h:132
+
Node
Definition ginfo.h:58
+
Node::addNode
void addNode(Node node)
Definition ginfo.h:71
+
Node::name
string name
Definition ginfo.h:60
+
Node::children
vector< Node > children
Definition ginfo.h:61
+
Node::Node
Node(string n, vector< Node > children)
Definition ginfo.h:63
+
GeomRegionInfoMapT
map< string, GeomRegionInfo > GeomRegionInfoMapT
a mapping from geometry name to information about that geometry
Definition ginfo.h:95
+
GeomRegT
pair< EGS_BaseGeometry *, int > GeomRegT
pair of geometry and local region number
Definition ginfo.h:79
phantom.h
Header file for phantom objects.
-
GeomRegionInfo
a struct to contain elementary information aboud a geometry
Definition: ginfo.h:83
- -
GeomRegionInfo::nreg
int nreg
Definition: ginfo.h:88
-
GeomRegionInfo::start
int start
Definition: ginfo.h:89
-
GeomRegionInfo::children
vector< string > children
Definition: ginfo.h:87
-
GeomRegionInfo::type
string type
Definition: ginfo.h:86
-
GeomRegionInfo::name
string name
Definition: ginfo.h:85
+
GeomRegionInfo
a struct to contain elementary information aboud a geometry
Definition ginfo.h:83
+ + + +
GeomRegionInfo::children
vector< string > children
Definition ginfo.h:87
+
GeomRegionInfo::type
string type
Definition ginfo.h:86
+
GeomRegionInfo::name
string name
Definition ginfo.h:85
-Generated by doxygen 1.9.5 +Generated by doxygen 1.9.8
diff --git a/docs/globals.html b/docs/globals.html index 18784a02..5bbab46b 100644 --- a/docs/globals.html +++ b/docs/globals.html @@ -3,7 +3,7 @@ - + EGS Brachy: File Members @@ -30,7 +30,7 @@
- + @@ -30,7 +30,7 @@ - + @@ -30,7 +30,7 @@ - + +
42// class gzstreambuf:
43// --------------------------------------
44
+
45gzstreambuf* gzstreambuf::open( const char* name, int open_mode) {
46 if ( is_open())
47 return (gzstreambuf*)0;
@@ -143,7 +149,9 @@
64 opened = 1;
65 return this;
66}
+
67
+
68gzstreambuf * gzstreambuf::close() {
69 if ( is_open()) {
70 sync();
@@ -153,7 +161,9 @@
74 }
75 return (gzstreambuf*)0;
76}
+
77
+
78int gzstreambuf::underflow() { // used for input buffer only
79 if ( gptr() && ( gptr() < egptr()))
80 return * reinterpret_cast<unsigned char *>( gptr());
@@ -178,7 +188,9 @@
99 // return next character
100 return * reinterpret_cast<unsigned char *>( gptr());
101}
+
102
+
103int gzstreambuf::flush_buffer() {
104 // Separate the writing of the buffer from overflow() and
105 // sync() operation.
@@ -188,7 +200,9 @@
109 pbump( -w);
110 return w;
111}
+
112
+
113int gzstreambuf::overflow( int c) { // used for output buffer only
114 if ( ! ( mode & std::ios::out) || ! opened)
115 return EOF;
@@ -200,7 +214,9 @@
121 return EOF;
122 return c;
123}
+
124
+
125int gzstreambuf::sync() {
126 // Changed to use flush_buffer() instead of overflow( EOF)
127 // which caused improper behavior with std::endl and flush(),
@@ -211,30 +227,39 @@
132 }
133 return 0;
134}
+
135
136// --------------------------------------
137// class gzstreambase:
138// --------------------------------------
139
+
140gzstreambase::gzstreambase( const char* name, int mode) {
141 init( &buf);
142 open( name, mode);
143}
+
144
+
145gzstreambase::~gzstreambase() {
146 buf.close();
147}
+
148
+
149void gzstreambase::open( const char* name, int open_mode) {
150 if ( ! buf.open( name, open_mode))
151 clear( rdstate() | std::ios::badbit);
152}
+
153
+
154void gzstreambase::close() {
155 if ( buf.is_open())
156 if ( ! buf.close())
157 clear( rdstate() | std::ios::badbit);
158}
+
159
160#ifdef GZSTREAM_NAMESPACE
161} // namespace GZSTREAM_NAMESPACE
@@ -242,22 +267,22 @@
163
164// ============================================================================
165// EOF //
-
gzstreambase::~gzstreambase
~gzstreambase()
Definition: gzstream.C:145
-
gzstreambase::open
void open(const char *name, int open_mode)
Definition: gzstream.C:149
-
gzstreambase::close
void close()
Definition: gzstream.C:154
-
gzstreambase::gzstreambase
gzstreambase()
Definition: gzstream.h:82
-
gzstreambuf
Definition: gzstream.h:45
-
gzstreambuf::sync
virtual int sync()
Definition: gzstream.C:125
-
gzstreambuf::flush_buffer
int flush_buffer()
Definition: gzstream.C:103
-
gzstreambuf::underflow
virtual int underflow()
Definition: gzstream.C:78
-
gzstreambuf::close
gzstreambuf * close()
Definition: gzstream.C:68
-
gzstreambuf::overflow
virtual int overflow(int c=EOF)
Definition: gzstream.C:113
-
gzstreambuf::open
gzstreambuf * open(const char *name, int open_mode)
Definition: gzstream.C:45
+
gzstreambase::~gzstreambase
~gzstreambase()
Definition gzstream.C:145
+
gzstreambase::open
void open(const char *name, int open_mode)
Definition gzstream.C:149
+
gzstreambase::close
void close()
Definition gzstream.C:154
+
gzstreambase::gzstreambase
gzstreambase()
Definition gzstream.h:82
+
gzstreambuf
Definition gzstream.h:45
+
gzstreambuf::sync
virtual int sync()
Definition gzstream.C:125
+
gzstreambuf::flush_buffer
int flush_buffer()
Definition gzstream.C:103
+
gzstreambuf::underflow
virtual int underflow()
Definition gzstream.C:78
+
gzstreambuf::close
gzstreambuf * close()
Definition gzstream.C:68
+
gzstreambuf::overflow
virtual int overflow(int c=EOF)
Definition gzstream.C:113
+
gzstreambuf::open
gzstreambuf * open(const char *name, int open_mode)
Definition gzstream.C:45
gzstream.h
-Generated by doxygen 1.9.5 +Generated by doxygen 1.9.8
diff --git a/docs/gzstream_8h.html b/docs/gzstream_8h.html index a03e5e35..4183284a 100644 --- a/docs/gzstream_8h.html +++ b/docs/gzstream_8h.html @@ -3,9 +3,9 @@ - + -EGS Brachy: /Users/marc/dev/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/gzstream/gzstream.h File Reference +EGS Brachy: /Users/marc/Developer/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/gzstream/gzstream.h File Reference @@ -30,7 +30,7 @@ - + @@ -30,7 +30,7 @@ - + +
42// Internal classes to implement gzstream. See below for user classes.
43// ----------------------------------------------------------------------------
44
+
45class gzstreambuf : public std::streambuf {
46private:
47 static const int bufferSize = 47+256; // size of data buff
@@ -133,6 +139,7 @@
54
55 int flush_buffer();
56public:
+
57 gzstreambuf() : opened(0) {
58 setp(buffer, buffer + (bufferSize-1));
59 setg(buffer + 4, // beginning of putback area
@@ -140,35 +147,47 @@
61 buffer + 4); // end position
62 // ASSERT: both input & output capabilities will not be used together
63 }
+
+
64 int is_open() {
65 return opened;
66 }
+
67 gzstreambuf *open(const char *name, int open_mode);
68 gzstreambuf *close();
+
69 ~gzstreambuf() {
70 close();
71 }
+
72
73 virtual int overflow(int c = EOF);
74 virtual int underflow();
75 virtual int sync();
76};
+
77
+
78class gzstreambase : virtual public std::ios {
79protected:
80 gzstreambuf buf;
81public:
+
82 gzstreambase() {
83 init(&buf);
84 }
+
85 gzstreambase(const char *name, int open_mode);
86 ~gzstreambase();
87 void open(const char *name, int open_mode);
88 void close();
+
89 gzstreambuf *rdbuf() {
90 return &buf;
91 }
+
92};
+
93
94// ----------------------------------------------------------------------------
95// User classes. Use igzstream and ogzstream analogously to ifstream and
@@ -176,31 +195,47 @@
97// function interface of the zlib. Files are compatible with gzip compression.
98// ----------------------------------------------------------------------------
99
+
100class igzstream : public gzstreambase, public std::istream {
101public:
102 igzstream() : std::istream(&buf) {}
+
103 igzstream(const char *name, int open_mode = std::ios::in)
104 : gzstreambase(name, open_mode), std::istream(&buf) {}
+
+
105 gzstreambuf *rdbuf() {
106 return gzstreambase::rdbuf();
107 }
+
+
108 void open(const char *name, int open_mode = std::ios::in) {
109 gzstreambase::open(name, open_mode);
110 }
+
111};
+
112
+
113class ogzstream : public gzstreambase, public std::ostream {
114public:
115 ogzstream() : std::ostream(&buf) {}
+
116 ogzstream(const char *name, int mode = std::ios::out)
117 : gzstreambase(name, mode), std::ostream(&buf) {}
+
+
118 gzstreambuf *rdbuf() {
119 return gzstreambase::rdbuf();
120 }
+
+
121 void open(const char *name, int open_mode = std::ios::out) {
122 gzstreambase::open(name, open_mode);
123 }
+
124};
+
125
126#ifdef GZSTREAM_NAMESPACE
127} // namespace GZSTREAM_NAMESPACE
@@ -210,32 +245,32 @@
131// ============================================================================
132// EOF //
133
-
gzstreambase
Definition: gzstream.h:78
-
gzstreambase::buf
gzstreambuf buf
Definition: gzstream.h:80
-
gzstreambase::rdbuf
gzstreambuf * rdbuf()
Definition: gzstream.h:89
-
gzstreambase::open
void open(const char *name, int open_mode)
Definition: gzstream.C:149
-
gzstreambase::gzstreambase
gzstreambase()
Definition: gzstream.h:82
-
gzstreambuf
Definition: gzstream.h:45
-
gzstreambuf::opened
char opened
Definition: gzstream.h:52
-
gzstreambuf::~gzstreambuf
~gzstreambuf()
Definition: gzstream.h:69
-
gzstreambuf::is_open
int is_open()
Definition: gzstream.h:64
-
gzstreambuf::file
gzFile file
Definition: gzstream.h:50
-
gzstreambuf::mode
int mode
Definition: gzstream.h:53
-
gzstreambuf::gzstreambuf
gzstreambuf()
Definition: gzstream.h:57
-
igzstream
Definition: gzstream.h:100
-
igzstream::igzstream
igzstream(const char *name, int open_mode=std::ios::in)
Definition: gzstream.h:103
-
igzstream::open
void open(const char *name, int open_mode=std::ios::in)
Definition: gzstream.h:108
-
igzstream::igzstream
igzstream()
Definition: gzstream.h:102
-
igzstream::rdbuf
gzstreambuf * rdbuf()
Definition: gzstream.h:105
-
ogzstream
Definition: gzstream.h:113
-
ogzstream::ogzstream
ogzstream()
Definition: gzstream.h:115
-
ogzstream::rdbuf
gzstreambuf * rdbuf()
Definition: gzstream.h:118
-
ogzstream::ogzstream
ogzstream(const char *name, int mode=std::ios::out)
Definition: gzstream.h:116
-
ogzstream::open
void open(const char *name, int open_mode=std::ios::out)
Definition: gzstream.h:121
+
gzstreambase
Definition gzstream.h:78
+
gzstreambase::buf
gzstreambuf buf
Definition gzstream.h:80
+
gzstreambase::rdbuf
gzstreambuf * rdbuf()
Definition gzstream.h:89
+
gzstreambase::open
void open(const char *name, int open_mode)
Definition gzstream.C:149
+
gzstreambase::gzstreambase
gzstreambase()
Definition gzstream.h:82
+
gzstreambuf
Definition gzstream.h:45
+
gzstreambuf::opened
char opened
Definition gzstream.h:52
+
gzstreambuf::~gzstreambuf
~gzstreambuf()
Definition gzstream.h:69
+
gzstreambuf::is_open
int is_open()
Definition gzstream.h:64
+
gzstreambuf::file
gzFile file
Definition gzstream.h:50
+
gzstreambuf::mode
int mode
Definition gzstream.h:53
+
gzstreambuf::gzstreambuf
gzstreambuf()
Definition gzstream.h:57
+
igzstream
Definition gzstream.h:100
+
igzstream::igzstream
igzstream(const char *name, int open_mode=std::ios::in)
Definition gzstream.h:103
+
igzstream::open
void open(const char *name, int open_mode=std::ios::in)
Definition gzstream.h:108
+
igzstream::igzstream
igzstream()
Definition gzstream.h:102
+
igzstream::rdbuf
gzstreambuf * rdbuf()
Definition gzstream.h:105
+
ogzstream
Definition gzstream.h:113
+
ogzstream::ogzstream
ogzstream()
Definition gzstream.h:115
+
ogzstream::rdbuf
gzstreambuf * rdbuf()
Definition gzstream.h:118
+
ogzstream::ogzstream
ogzstream(const char *name, int mode=std::ios::out)
Definition gzstream.h:116
+
ogzstream::open
void open(const char *name, int open_mode=std::ios::out)
Definition gzstream.h:121
-Generated by doxygen 1.9.5 +Generated by doxygen 1.9.8
diff --git a/docs/hierarchy.html b/docs/hierarchy.html index ecd7d890..a8bb229f 100644 --- a/docs/hierarchy.html +++ b/docs/hierarchy.html @@ -3,7 +3,7 @@ - + EGS Brachy: Class Hierarchy @@ -30,7 +30,7 @@ - + @@ -30,7 +30,7 @@ - + @@ -30,7 +30,7 @@ - + +
22iaeadll = ctypes.CDLL(IAEA_DLL)
23
24
+
25class IAEAPhaseSpace(object):
26
-
27 header_ext = '.IAEAheader'
-
28 phsp_ext = '.IAEAphsp'
+
27 header_ext = '.IAEAheader'
+
28 phsp_ext = '.IAEAphsp'
29
30 #--------------------------------------------------------------------------
-
31 def __init__(self,path,mode='r'):
+
+
31 def __init__(self,path,mode='r'):
32 """Set up access to an IAEA phase space file
33
34 Arguments:
35 path -- The path to the iaea phase space file
36
37 Keyword arguments:
-
38 mode -- 'r' for read, 'w' for read/write or 'a' for 'append' (default 'r')
-
39
-
40 """
-
41 self._set_path(path)
-
42 self._source_id = iaea_types.IAEA_I32(-1)
-
43
-
44 try:
+
38 mode -- 'r' for read, 'w' for read/write or 'a' for 'append' (default 'r')
+
39
+
40 """
+
41 self._set_path(path)
+
42 self._source_id = iaea_types.IAEA_I32(-1)
+
43
+
44 try:
45 self.access = iaea_types.iaea_file_modes[mode]
46 except:
47 err_msg = 'Invalid file mode specified: %s' % mode
48 raise iaea_errors.IAEAPhaseSpaceSetupError(err_msg)
49
-
50 self._create_source()
+
50 self._create_source()
+
51 #--------------------------------------------------------------------------
-
52 def _create_source(self):
+
+
52 def _create_source(self):
53 result = iaea_types.IAEA_I32(0)
54 iaeadll.iaea_new_source(byref(self._source_id), self.path.encode(), byref(self.access),
55 byref(result), ctypes.c_int(len(self.path.encode())))
@@ -136,19 +145,21 @@
57 print( result)
58 if 0 > result.value > iaea_types.max_sources:
59 raise iaea_errors.IAEAPhaseSpaceError(result.value)
+
60 #--------------------------------------------------------------------------
-
61 def num_particles(self,particle_type = 'all'):
+
+
61 def num_particles(self,particle_type = 'all'):
62 """Return max number of particles of type particle_type
63
64 Keyword arguments:
-
65 particle_type -- type or category of particle to check (default 'all')
-
66
-
67 """
-
68
-
69 num_particles = 0
-
70 np = iaea_types.IAEA_I64(0)
-
71
-
72 try:
+
65 particle_type -- type or category of particle to check (default 'all')
+
66
+
67 """
+
68
+
69 num_particles = 0
+
70 np = iaea_types.IAEA_I64(0)
+
71
+
72 try:
73 ptypes = tuple(iaea_types.particle_types[particle_type])
74 except TypeError:
75 ptypes = (iaea_types.particle_types[particle_type],)
@@ -163,28 +174,32 @@
84 raise iaea_errors.IAEAPhaseSpaceError(message=message)
85
86 return num_particles
+
87 #--------------------------------------------------------------------------
-
88 def num_orig_particles(self):
+
+
88 def num_orig_particles(self):
89 """Return max number of particles of type particle_type
90
91 Keyword arguments:
-
92 particle_type -- type or category of particle to check (default 'all')
-
93
-
94 """
-
95
-
96 num_particles = 0
-
97 np = iaea_types.IAEA_I64(0)
-
98
-
99 iaeadll.iaea_get_total_original_particles(byref(self._source_id), byref(np))
-
100 num_particles = np.value
-
101
-
102 if num_particles < 0:
+
92 particle_type -- type or category of particle to check (default 'all')
+
93
+
94 """
+
95
+
96 num_particles = 0
+
97 np = iaea_types.IAEA_I64(0)
+
98
+
99 iaeadll.iaea_get_total_original_particles(byref(self._source_id), byref(np))
+
100 num_particles = np.value
+
101
+
102 if num_particles < 0:
103 message = "Unable to read number of particles of type: %s" % particle_type
104 raise iaea_errors.IAEAPhaseSpaceError(message=message)
105
106 return num_particles
+
107 #----------------------------------------------------------------------
-
108 def maximum_energy(self):
+
+
108 def maximum_energy(self):
109 """Return maximum energy in this source in (MeV)"""
110
111 emax = iaea_types.IAEA_Float()
@@ -193,33 +208,39 @@
114 raise iaea_errors.IAEAPhaseSpaceError(message="Source not initialized")
115
116 return emax.value
+
117 #--------------------------------------------------------------------------
118 @property
-
119 def source_id(self):
+
+
119 def source_id(self):
120 return self._source_id.value
+
121 #--------------------------------------------------------------------------
-
122 def _set_path(self,path):
+
+
122 def _set_path(self,path):
123 self.path = os.path.realpath(path)
-
124 self.path = self.path.replace(self.header_ext,"").replace(self.phsp_ext, "")
-
eb_tests.iaea.IAEAPhaseSpace
Definition: iaea.py:25
-
eb_tests.iaea.IAEAPhaseSpace.num_orig_particles
def num_orig_particles(self)
Definition: iaea.py:88
-
eb_tests.iaea.IAEAPhaseSpace.__init__
def __init__(self, path, mode='r')
Definition: iaea.py:31
-
eb_tests.iaea.IAEAPhaseSpace.num_particles
def num_particles(self, particle_type='all')
Definition: iaea.py:61
-
eb_tests.iaea.IAEAPhaseSpace.maximum_energy
def maximum_energy(self)
Definition: iaea.py:108
-
eb_tests.iaea.IAEAPhaseSpace.path
path
Definition: iaea.py:123
-
eb_tests.iaea.IAEAPhaseSpace.phsp_ext
string phsp_ext
Definition: iaea.py:28
-
eb_tests.iaea.IAEAPhaseSpace._set_path
def _set_path(self, path)
Definition: iaea.py:122
-
eb_tests.iaea.IAEAPhaseSpace._source_id
_source_id
Definition: iaea.py:42
-
eb_tests.iaea.IAEAPhaseSpace._create_source
def _create_source(self)
Definition: iaea.py:52
-
eb_tests.iaea.IAEAPhaseSpace.header_ext
string header_ext
Definition: iaea.py:27
-
eb_tests.iaea.IAEAPhaseSpace.source_id
def source_id(self)
Definition: iaea.py:119
-
eb_tests.iaea.IAEAPhaseSpace.access
access
Definition: iaea.py:45
-
eb_tests.iaea_errors.IAEAPhaseSpaceError
Definition: iaea_errors.py:28
-
eb_tests.iaea_errors.IAEAPhaseSpaceSetupError
Definition: iaea_errors.py:25
+
124 self.path = self.path.replace(self.header_ext,"").replace(self.phsp_ext, "")
+
+
+
eb_tests.iaea.IAEAPhaseSpace
Definition iaea.py:25
+
eb_tests.iaea.IAEAPhaseSpace.num_orig_particles
num_orig_particles(self)
Definition iaea.py:88
+
eb_tests.iaea.IAEAPhaseSpace.num_particles
num_particles(self, particle_type='all')
Definition iaea.py:61
+
eb_tests.iaea.IAEAPhaseSpace.maximum_energy
maximum_energy(self)
Definition iaea.py:108
+
eb_tests.iaea.IAEAPhaseSpace.__init__
__init__(self, path, mode='r')
Definition iaea.py:31
+
eb_tests.iaea.IAEAPhaseSpace._create_source
_create_source(self)
Definition iaea.py:52
+
eb_tests.iaea.IAEAPhaseSpace._set_path
_set_path(self, path)
Definition iaea.py:122
+
eb_tests.iaea.IAEAPhaseSpace.path
path
Definition iaea.py:123
+
eb_tests.iaea.IAEAPhaseSpace.phsp_ext
str phsp_ext
Definition iaea.py:28
+
eb_tests.iaea.IAEAPhaseSpace._source_id
_source_id
Definition iaea.py:42
+
eb_tests.iaea.IAEAPhaseSpace.header_ext
str header_ext
Definition iaea.py:27
+
eb_tests.iaea.IAEAPhaseSpace.source_id
source_id(self)
Definition iaea.py:119
+
eb_tests.iaea.IAEAPhaseSpace.access
access
Definition iaea.py:45
+
eb_tests.iaea_errors.IAEAPhaseSpaceError
Definition iaea_errors.py:28
+
eb_tests.iaea_errors.IAEAPhaseSpaceSetupError
Definition iaea_errors.py:25
-Generated by doxygen 1.9.5 +Generated by doxygen 1.9.8
diff --git a/docs/iaea__errors_8py.html b/docs/iaea__errors_8py.html index d92a5da4..a491ef6b 100644 --- a/docs/iaea__errors_8py.html +++ b/docs/iaea__errors_8py.html @@ -3,9 +3,9 @@ - + -EGS Brachy: /Users/marc/dev/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/eb_tests/iaea_errors.py File Reference +EGS Brachy: /Users/marc/Developer/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/eb_tests/iaea_errors.py File Reference @@ -30,7 +30,7 @@ - + @@ -30,7 +30,7 @@ - + +
iaea_errors.py
-Go to the documentation of this file.
1error_messages = {}
+Go to the documentation of this file.
1error_messages = {}
2
3
4new_source_errors = (
@@ -101,11 +106,15 @@
22
23error_messages.update(new_source_errors)
24
+
25class IAEAPhaseSpaceSetupError(Exception):
26 pass
27
+
+
28class IAEAPhaseSpaceError(Exception):
-
29 def __init__(self,err_id=None,message=""):
+
+
29 def __init__(self,err_id=None,message=""):
30 if err_id is not None:
31 try:
32 self.message = error_messages[err_id]
@@ -113,14 +122,16 @@
34 self.message = "Unknown IAEAPhsp Error %s" % str(err_id)
35 else:
36 self.message = message
-
eb_tests.iaea_errors.IAEAPhaseSpaceError
Definition: iaea_errors.py:28
-
eb_tests.iaea_errors.IAEAPhaseSpaceError.__init__
def __init__(self, err_id=None, message="")
Definition: iaea_errors.py:29
-
eb_tests.iaea_errors.IAEAPhaseSpaceError.message
message
Definition: iaea_errors.py:32
-
eb_tests.iaea_errors.IAEAPhaseSpaceSetupError
Definition: iaea_errors.py:25
+
+
+
eb_tests.iaea_errors.IAEAPhaseSpaceError
Definition iaea_errors.py:28
+
eb_tests.iaea_errors.IAEAPhaseSpaceError.__init__
__init__(self, err_id=None, message="")
Definition iaea_errors.py:29
+
eb_tests.iaea_errors.IAEAPhaseSpaceError.message
message
Definition iaea_errors.py:32
+
eb_tests.iaea_errors.IAEAPhaseSpaceSetupError
Definition iaea_errors.py:25
-Generated by doxygen 1.9.5 +Generated by doxygen 1.9.8
diff --git a/docs/iaea__types_8py.html b/docs/iaea__types_8py.html index 70645e97..47007023 100644 --- a/docs/iaea__types_8py.html +++ b/docs/iaea__types_8py.html @@ -3,9 +3,9 @@ - + -EGS Brachy: /Users/marc/dev/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/eb_tests/iaea_types.py File Reference +EGS Brachy: /Users/marc/Developer/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/eb_tests/iaea_types.py File Reference @@ -30,7 +30,7 @@
- + @@ -30,7 +30,7 @@ - + +
11IAEA_I64 = ctypes.c_longlong
12PIAEA_I64 = ctypes.POINTER(IAEA_I64)
13
-
14iaea_file_modes = {
+
14iaea_file_modes = {
15 'r': IAEA_I32(1),
16 'w': IAEA_I32(2),
17 'a': IAEA_I32(3)
@@ -103,7 +108,7 @@
24neutrons = 4
25protons = 5
26
-
27particle_types = {
+
27particle_types = {
28 'all' : all_particles,
29 'photon' : photons,
30 'electron': electrons,
@@ -116,11 +121,11 @@
37
38
39max_sources = 30
-
eb_tests.iaea_types.IAEA_I32
IAEA_I32
Definition: iaea_types.py:9
+
eb_tests.iaea_types.IAEA_I32
IAEA_I32
Definition iaea_types.py:9
-Generated by doxygen 1.9.5 +Generated by doxygen 1.9.8
diff --git a/docs/index.html b/docs/index.html index 475ff9fb..574a7732 100644 --- a/docs/index.html +++ b/docs/index.html @@ -3,7 +3,7 @@ - + EGS Brachy: EGS Brachy @@ -30,7 +30,7 @@ - + @@ -30,7 +30,7 @@ - + @@ -30,7 +30,7 @@ - + +
-
/Users/marc/dev/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/latch.cpp
+
/Users/marc/Developer/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/latch.cpp
Go to the documentation of this file.
1/*
@@ -113,30 +118,43 @@
38
44#include "latch.h"
45
+
46void Latch::setFlag(Flag flag, EGS_Particle *p) {
47 setFlag(flag, p->latch);
48}
+
49
+
50void Latch::setFlag(Flag flag, int &latch) {
51 latch |= (1 << flag);
52}
+
53
+
54void Latch::unsetFlag(Flag flag, EGS_Particle *p) {
55 unsetFlag(flag, p->latch);
56}
+
57
+
58void Latch::unsetFlag(Flag flag, int &latch) {
59 latch &= ~(1 << flag);
60}
+
61
+
62bool Latch::checkFlag(Flag flag, EGS_Particle *p) {
63 return checkFlag(flag, p->latch);
64}
+
65
+
66bool Latch::checkFlag(Flag flag, int latch) {
67 return latch & (1 << flag);
68}
+
69
+
70void Latch::update(EB_Message message, void *particle) {
71
72 if (message == PARTICLE_ESCAPED_SOURCE) {
@@ -146,19 +164,27 @@
76 }
77
78}
+
79
+
80void Latch::addScatter(EGS_Particle *p) {
81 addScatter(p->latch);
82}
+
83
+
84void Latch::setPrimary(EGS_Particle *p) {
85 setPrimary(p->latch);
86}
+
87
+
88void Latch::setPrimary(int &latch) {
89 setFlag(PRIM_PARTICLE, latch);
90}
+
91
+
92void Latch::addScatter(int &latch) {
93 if (checkFlag(PRIM_PARTICLE, latch)) {
94 unsetFlag(PRIM_PARTICLE, latch);
@@ -170,63 +196,78 @@
100 setFlag(SSCAT_PARTICLE, latch);
101 }
102}
+
103
104
+
105bool Latch::isPrimary(int latch) {
106 return checkFlag(PRIM_PARTICLE, latch);
107}
+
108
+
109bool Latch::isPrimary(EGS_Particle *p) {
110 return isPrimary(p->latch);
111}
+
112
+
113bool Latch::isSingleScat(int latch) {
114 return checkFlag(SSCAT_PARTICLE, latch) && !checkFlag(MSCAT_PARTICLE, latch);
115}
+
116
+
117bool Latch::isSingleScat(EGS_Particle *p) {
118 return isSingleScat(p->latch);
119}
+
120
+
121bool Latch::isMultScat(int latch) {
122 return checkFlag(MSCAT_PARTICLE, latch);
123}
+
124
+
125bool Latch::isMultScat(EGS_Particle *p) {
126 return isMultScat(p->latch);
127}
+
128
129/*bool Latch::inSource(EGS_Particle *p){
130 return checkFlag(IN_SOURCE, p);
131}
132*/
133
+
134bool Latch::hasEscaped(EGS_Particle *p) {
135 return checkFlag(ESCAPED_SOURCE, p);
136}
+
137
-
Latch::hasEscaped
static bool hasEscaped(EGS_Particle *p)
True if particle is currently in a source.
Definition: latch.cpp:134
-
Latch::setPrimary
static void setPrimary(int &latch)
Definition: latch.cpp:88
-
Latch::isMultScat
static bool isMultScat(int latch)
Definition: latch.cpp:121
-
Latch::checkFlag
static bool checkFlag(Flag flag, EGS_Particle *p)
Check whether flag is set on particle p.
Definition: latch.cpp:62
-
Latch::addScatter
static void addScatter(EGS_Particle *p)
Definition: latch.cpp:80
-
Latch::Flag
Flag
Definition: latch.h:53
-
Latch::PRIM_PARTICLE
@ PRIM_PARTICLE
Definition: latch.h:60
-
Latch::MSCAT_PARTICLE
@ MSCAT_PARTICLE
Definition: latch.h:62
-
Latch::SSCAT_PARTICLE
@ SSCAT_PARTICLE
Definition: latch.h:61
-
Latch::ESCAPED_SOURCE
@ ESCAPED_SOURCE
Definition: latch.h:56
-
Latch::isPrimary
static bool isPrimary(int latch)
Definition: latch.cpp:105
-
Latch::isSingleScat
static bool isSingleScat(int latch)
Definition: latch.cpp:113
-
Latch::unsetFlag
static void unsetFlag(Flag flag, EGS_Particle *p)
Unset flag on input particle p.
Definition: latch.cpp:54
-
Latch::update
void update(EB_Message message, void *particle)
listen to events and delegate to appropriate handler
Definition: latch.cpp:70
-
Latch::setFlag
static void setFlag(Flag flag, EGS_Particle *p)
Set flag on input particle p.
Definition: latch.cpp:46
+
Latch::hasEscaped
static bool hasEscaped(EGS_Particle *p)
True if particle is currently in a source.
Definition latch.cpp:134
+
Latch::setPrimary
static void setPrimary(int &latch)
Definition latch.cpp:88
+
Latch::isMultScat
static bool isMultScat(int latch)
Definition latch.cpp:121
+
Latch::checkFlag
static bool checkFlag(Flag flag, EGS_Particle *p)
Check whether flag is set on particle p.
Definition latch.cpp:62
+
Latch::addScatter
static void addScatter(EGS_Particle *p)
Definition latch.cpp:80
+
Latch::Flag
Flag
Definition latch.h:53
+
Latch::PRIM_PARTICLE
@ PRIM_PARTICLE
Definition latch.h:60
+
Latch::MSCAT_PARTICLE
@ MSCAT_PARTICLE
Definition latch.h:62
+
Latch::SSCAT_PARTICLE
@ SSCAT_PARTICLE
Definition latch.h:61
+
Latch::ESCAPED_SOURCE
@ ESCAPED_SOURCE
Definition latch.h:56
+
Latch::isPrimary
static bool isPrimary(int latch)
Definition latch.cpp:105
+
Latch::isSingleScat
static bool isSingleScat(int latch)
Definition latch.cpp:113
+
Latch::unsetFlag
static void unsetFlag(Flag flag, EGS_Particle *p)
Unset flag on input particle p.
Definition latch.cpp:54
+
Latch::update
void update(EB_Message message, void *particle)
listen to events and delegate to appropriate handler
Definition latch.cpp:70
+
Latch::setFlag
static void setFlag(Flag flag, EGS_Particle *p)
Set flag on input particle p.
Definition latch.cpp:46
latch.h
handle particles latch bits for egs_brachy
-
EB_Message
EB_Message
Definition: pubsub.h:54
-
PARTICLE_ESCAPED_SOURCE
@ PARTICLE_ESCAPED_SOURCE
Definition: pubsub.h:61
+
EB_Message
EB_Message
Definition pubsub.h:54
+
PARTICLE_ESCAPED_SOURCE
@ PARTICLE_ESCAPED_SOURCE
Definition pubsub.h:61
-Generated by doxygen 1.9.5 +Generated by doxygen 1.9.8
diff --git a/docs/latch_8h.html b/docs/latch_8h.html index 199cde6d..726952ae 100644 --- a/docs/latch_8h.html +++ b/docs/latch_8h.html @@ -3,9 +3,9 @@ - + -EGS Brachy: /Users/marc/dev/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/latch.h File Reference +EGS Brachy: /Users/marc/Developer/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/latch.h File Reference @@ -30,7 +30,7 @@
- + @@ -30,7 +30,7 @@ - + +
-
/Users/marc/dev/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/latch.h
+
/Users/marc/Developer/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/latch.h
Go to the documentation of this file.
1/*
@@ -116,8 +121,10 @@
45#include "egs_advanced_application.h"
46#include "pubsub.h"
47
+
51class Latch : public Subscriber {
52
+
53 enum Flag {
54 IN_SOURCE,
56 ESCAPED_SOURCE,
@@ -126,6 +133,7 @@
62 MSCAT_PARTICLE
63
64 };
+
65
66
67
@@ -175,32 +183,33 @@
120 static bool isMultScat(EGS_Particle *p);
121
122};
+
123
124#endif
-
Latch
A class for handling latch bits relevant to egs_brachy. The Latch class listens for particle events a...
Definition: latch.h:51
-
Latch::hasEscaped
static bool hasEscaped(EGS_Particle *p)
True if particle is currently in a source.
Definition: latch.cpp:134
-
Latch::setPrimary
static void setPrimary(int &latch)
Definition: latch.cpp:88
-
Latch::isMultScat
static bool isMultScat(int latch)
Definition: latch.cpp:121
-
Latch::checkFlag
static bool checkFlag(Flag flag, EGS_Particle *p)
Check whether flag is set on particle p.
Definition: latch.cpp:62
-
Latch::addScatter
static void addScatter(EGS_Particle *p)
Definition: latch.cpp:80
-
Latch::Flag
Flag
Definition: latch.h:53
-
Latch::IN_SOURCE
@ IN_SOURCE
Definition: latch.h:54
-
Latch::PRIM_PARTICLE
@ PRIM_PARTICLE
Definition: latch.h:60
-
Latch::MSCAT_PARTICLE
@ MSCAT_PARTICLE
Definition: latch.h:62
-
Latch::SSCAT_PARTICLE
@ SSCAT_PARTICLE
Definition: latch.h:61
-
Latch::ESCAPED_SOURCE
@ ESCAPED_SOURCE
Definition: latch.h:56
-
Latch::isPrimary
static bool isPrimary(int latch)
Definition: latch.cpp:105
-
Latch::isSingleScat
static bool isSingleScat(int latch)
Definition: latch.cpp:113
-
Latch::unsetFlag
static void unsetFlag(Flag flag, EGS_Particle *p)
Unset flag on input particle p.
Definition: latch.cpp:54
-
Latch::update
void update(EB_Message message, void *particle)
listen to events and delegate to appropriate handler
Definition: latch.cpp:70
-
Latch::setFlag
static void setFlag(Flag flag, EGS_Particle *p)
Set flag on input particle p.
Definition: latch.cpp:46
- +
Latch
A class for handling latch bits relevant to egs_brachy. The Latch class listens for particle events a...
Definition latch.h:51
+
Latch::hasEscaped
static bool hasEscaped(EGS_Particle *p)
True if particle is currently in a source.
Definition latch.cpp:134
+
Latch::setPrimary
static void setPrimary(int &latch)
Definition latch.cpp:88
+
Latch::isMultScat
static bool isMultScat(int latch)
Definition latch.cpp:121
+
Latch::checkFlag
static bool checkFlag(Flag flag, EGS_Particle *p)
Check whether flag is set on particle p.
Definition latch.cpp:62
+
Latch::addScatter
static void addScatter(EGS_Particle *p)
Definition latch.cpp:80
+
Latch::Flag
Flag
Definition latch.h:53
+
Latch::IN_SOURCE
@ IN_SOURCE
Definition latch.h:54
+
Latch::PRIM_PARTICLE
@ PRIM_PARTICLE
Definition latch.h:60
+
Latch::MSCAT_PARTICLE
@ MSCAT_PARTICLE
Definition latch.h:62
+
Latch::SSCAT_PARTICLE
@ SSCAT_PARTICLE
Definition latch.h:61
+
Latch::ESCAPED_SOURCE
@ ESCAPED_SOURCE
Definition latch.h:56
+
Latch::isPrimary
static bool isPrimary(int latch)
Definition latch.cpp:105
+
Latch::isSingleScat
static bool isSingleScat(int latch)
Definition latch.cpp:113
+
Latch::unsetFlag
static void unsetFlag(Flag flag, EGS_Particle *p)
Unset flag on input particle p.
Definition latch.cpp:54
+
Latch::update
void update(EB_Message message, void *particle)
listen to events and delegate to appropriate handler
Definition latch.cpp:70
+
Latch::setFlag
static void setFlag(Flag flag, EGS_Particle *p)
Set flag on input particle p.
Definition latch.cpp:46
+
pubsub.h
A simple pub/sub module to allow various egs_brachy classes to subscribe to particle events.
-
EB_Message
EB_Message
Definition: pubsub.h:54
+
EB_Message
EB_Message
Definition pubsub.h:54
-Generated by doxygen 1.9.5 +Generated by doxygen 1.9.8
diff --git a/docs/md__2Users_2marc_2Developer_2EGSnrc_2HEN__HOUSE_2user__codes_2egs__brachy_2egs__brachy_2lib_2geometry_2eye__plaques_2README.html b/docs/md__2Users_2marc_2Developer_2EGSnrc_2HEN__HOUSE_2user__codes_2egs__brachy_2egs__brachy_2lib_2geometry_2eye__plaques_2README.html new file mode 100644 index 00000000..77179cfb --- /dev/null +++ b/docs/md__2Users_2marc_2Developer_2EGSnrc_2HEN__HOUSE_2user__codes_2egs__brachy_2egs__brachy_2lib_2geometry_2eye__plaques_2README.html @@ -0,0 +1,91 @@ + + + + + + + +EGS Brachy: CLRP egs++ eye plaque models vesrion 2 (CLRP_EPv2) + + + + + + + + + +
+
+ + + + + + +
+
EGS Brachy +
+
An egs++ user code for rapid brachytherapy calculations
+
+
+ + + + + + + + +
+
+ + +
+
+
+
+
+
Loading...
+
Searching...
+
No Matches
+
+
+
+
+ +
+
+
CLRP egs++ eye plaque models vesrion 2 (CLRP_EPv2)
+
+
+

CLRP Eye Plaque Database version 2 (CLRP_EPv2) of egs_brachy models for photon-emitting sources

+

This repository contains geometry model files for 8 COMS, 5 BEBIG, and 4 Representative models for Pd-103, I-125, and Cs-131 seeds described and validated in the CLRP_EPv2 database. The models are to be used with the open-source Monte Carlo code egs_brachy which is an EGSnrc application available at https://github.com/clrp-code/egs_brachy. The CLRP-TG43v2 database is hosted at a Carleton University website: https://physics.carleton.ca/clrp/eye_plaque_v2 with DOI http://doi.org/10.22215/clrp/EPv2.

+

If you use geometry models from this site, please cite:

+
H Safigholi, Z Parsons, S G Deering, and R M Thomson,
+ Update of the CLRP eye plaque brachytherapy database for photon-emitting sources, Medical Physics,48(2021) 3373-3383, https://doi.org/10.1002/mp.14844
+

and
+ 

M Chamberland, R E P Taylor, D W O Rogers and R M Thomson
+egs_brachy: a versatile and fast Monte Carlo code for brachytherapy, Phys Med Biol 61(2016) 8214 - 8231  
+
+
+ +
+Generated by doxygen 1.9.8 +
+ + diff --git a/docs/md__2Users_2marc_2Developer_2EGSnrc_2HEN__HOUSE_2user__codes_2egs__brachy_2egs__brachy_2lib_2geometry_2sources_2README.html b/docs/md__2Users_2marc_2Developer_2EGSnrc_2HEN__HOUSE_2user__codes_2egs__brachy_2egs__brachy_2lib_2geometry_2sources_2README.html new file mode 100644 index 00000000..046e9a17 --- /dev/null +++ b/docs/md__2Users_2marc_2Developer_2EGSnrc_2HEN__HOUSE_2user__codes_2egs__brachy_2egs__brachy_2lib_2geometry_2sources_2README.html @@ -0,0 +1,90 @@ + + + + + + + +EGS Brachy: CLRP egs++ brachytherapy source models + + + + + + + + + +
+
+ + + + + + +
+
EGS Brachy +
+
An egs++ user code for rapid brachytherapy calculations
+
+
+ + + + + + + + +
+
+ + +
+
+
+
+
+
Loading...
+
Searching...
+
No Matches
+
+
+
+
+ +
+
+
CLRP egs++ brachytherapy source models
+
+
+

CLRP TG43v2 low-energy seeds

+

This repository contains geometry model files for 40 low-energy brachytherapy seeds described and benchmarked in the CLRP TG-43 dosimetry parameter database. The models are to be used with the open source Monte Carlo code egs_brachy which is an EGSnrc application available at https://github.com/clrp-code/egs_brachy.

+

The CLRP-TG43v2 database is hosted at a Carleton University website (https://physics.carleton.ca/clrp/egs_brachy/seed_database_v2) with DOI doi.org/10.22215/clrp/tg43v2

+

If you use geometry models from this site, please cite:

+

• Habib Safigholi, Marc J.P. Chamberland, Randle E.P. Taylor, Christian H. Allen, Martin P. Martinov, D. W. O. Rogers and Rowan M. Thomson, Update of the CLRP TG-43 parameter database for low-energy brachytherapy sources, Med. Phys. 47 (2020), 4656-4669

+

and

+

• M Chamberland, R E P Taylor, D W O Rogers and R M Thomson, egs_brachy: a versatile and fast Monte Carlo code for brachytherapy Phys Med Biol 61 (2016), 8214-8231

+
+
+ +
+Generated by doxygen 1.9.8 +
+ + diff --git a/docs/md_geom.html b/docs/md_geom.html index 3e5fa83b..fe4a53d0 100644 --- a/docs/md_geom.html +++ b/docs/md_geom.html @@ -3,7 +3,7 @@ - + EGS Brachy: geom @@ -30,7 +30,7 @@
- + @@ -30,7 +30,7 @@ - + @@ -30,7 +30,7 @@ - + +
-
/Users/marc/dev/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/muen.h
+
/Users/marc/Developer/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/muen.h
Go to the documentation of this file.
1/*
@@ -129,11 +134,13 @@
59#ifndef MUENDATA_
60#define MUENDATA_
61
+
62namespace muen {
63
64using namespace std;
65
66
+
68std::vector<std::string> &split(const std::string &s, char delim, std::vector<std::string> &elems) {
69 std::stringstream ss(s);
70 std::string item;
@@ -142,21 +149,24 @@
73 }
74 return elems;
75}
+
76
77
+
79std::vector<std::string> split(const std::string &s, char delim) {
80 std::vector<std::string> elems;
81 split(s, delim, elems);
82 return elems;
83}
+
84
86static inline std::string &ltrim(std::string &s) {
-
87 s.erase(s.begin(), std::find_if(s.begin(), s.end(), std::not1(std::ptr_fun<int, int>(std::isspace))));
+
87 s.erase(s.begin(), std::find_if(s.begin(), s.end(), [](unsigned char ch) {return !std::isspace(ch);}));
88 return s;
89}
90
92static inline std::string &rtrim(std::string &s) {
-
93 s.erase(std::find_if(s.rbegin(), s.rend(), std::not1(std::ptr_fun<int, int>(std::isspace))).base(), s.end());
+
93 s.erase(std::find_if(s.rbegin(), s.rend(), [](unsigned char ch) {return !std::isspace(ch);}).base(), s.end());
94 return s;
95}
96
@@ -169,10 +179,12 @@
105
107typedef map<string, vector<MuenAtET> > MuenMapT;
108
+
131class MuenDataParser {
132
133 MuenMapT med_data;
135 static const int NSKIP = 3;
+
141 MuenMapT splitFileByMed(ifstream &in) {
142
143 MuenMapT med_lines;
@@ -221,6 +233,7 @@
186 return med_lines;
187
188 }
+
189
190
191public:
@@ -228,6 +241,7 @@
193 static const string MUEN_START;
205 MuenDataParser() {};
206
+
207 int setMuenFile(string filename) {
208
209 ifstream muen_data(filename.c_str());
@@ -241,7 +255,9 @@
217 return 0;
218
219 };
+
220
+
228 EGS_Interpolator *getMuenInterpolator(string med_name) {
229
230 size_t ndat = med_data[med_name].size();
@@ -262,30 +278,33 @@
245 return muen;
246
247 }
+
248};
+
249
250
251const string MuenDataParser::MUEN_START = "Muen values for medium MEDIUM =";
252
253}
+
254
255#endif
-
muen::MuenDataParser
class for parsing muen data from a file.
Definition: muen.h:131
-
muen::MuenDataParser::setMuenFile
int setMuenFile(string filename)
Definition: muen.h:207
-
muen::MuenDataParser::splitFileByMed
MuenMapT splitFileByMed(ifstream &in)
does the actual parsing of data from the muen file
Definition: muen.h:141
-
muen::MuenDataParser::NSKIP
static const int NSKIP
Definition: muen.h:135
-
muen::MuenDataParser::getMuenInterpolator
EGS_Interpolator * getMuenInterpolator(string med_name)
Create a new EGS_Interpolator of muen data for the requested medium and return pointer to it....
Definition: muen.h:228
-
muen::MuenDataParser::MUEN_START
static const string MUEN_START
Definition: muen.h:193
-
muen::MuenDataParser::MuenDataParser
MuenDataParser()
construct class by parsing the data file. Note the actual EGS_Interpolator classes are only created w...
Definition: muen.h:205
-
muen::MuenDataParser::med_data
MuenMapT med_data
Definition: muen.h:133
-
muen
Definition: muen.h:62
-
muen::split
std::vector< std::string > & split(const std::string &s, char delim, std::vector< std::string > &elems)
Split a string on input delimeter.
Definition: muen.h:68
-
muen::MuenMapT
map< string, vector< MuenAtET > > MuenMapT
Map from medium name to vector of (e, muen(e)) data for that medium.
Definition: muen.h:107
-
muen::MuenAtET
pair< double, double > MuenAtET
pair of form (energy, muen(energy))
Definition: muen.h:104
+
muen::MuenDataParser
class for parsing muen data from a file.
Definition muen.h:131
+
muen::MuenDataParser::setMuenFile
int setMuenFile(string filename)
Definition muen.h:207
+
muen::MuenDataParser::splitFileByMed
MuenMapT splitFileByMed(ifstream &in)
does the actual parsing of data from the muen file
Definition muen.h:141
+
muen::MuenDataParser::NSKIP
static const int NSKIP
Definition muen.h:135
+
muen::MuenDataParser::getMuenInterpolator
EGS_Interpolator * getMuenInterpolator(string med_name)
Create a new EGS_Interpolator of muen data for the requested medium and return pointer to it....
Definition muen.h:228
+
muen::MuenDataParser::MUEN_START
static const string MUEN_START
Definition muen.h:193
+
muen::MuenDataParser::MuenDataParser
MuenDataParser()
construct class by parsing the data file. Note the actual EGS_Interpolator classes are only created w...
Definition muen.h:205
+
muen::MuenDataParser::med_data
MuenMapT med_data
Definition muen.h:133
+
muen
Definition muen.h:62
+
muen::split
std::vector< std::string > & split(const std::string &s, char delim, std::vector< std::string > &elems)
Split a string on input delimeter.
Definition muen.h:68
+
muen::MuenMapT
map< string, vector< MuenAtET > > MuenMapT
Map from medium name to vector of (e, muen(e)) data for that medium.
Definition muen.h:107
+
muen::MuenAtET
pair< double, double > MuenAtET
pair of form (energy, muen(energy))
Definition muen.h:104
-Generated by doxygen 1.9.5 +Generated by doxygen 1.9.8
diff --git a/docs/namespacedoc__utils.html b/docs/namespacedoc__utils.html index 9b6c718d..34da7f1e 100644 --- a/docs/namespacedoc__utils.html +++ b/docs/namespacedoc__utils.html @@ -3,7 +3,7 @@ - + EGS Brachy: doc_utils Namespace Reference @@ -30,7 +30,7 @@
- + @@ -30,7 +30,7 @@ - + @@ -30,7 +30,7 @@ - + +
-
/Users/marc/dev/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/phantom.cpp
+
/Users/marc/Developer/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/phantom.cpp
Go to the documentation of this file.
1/*
@@ -124,6 +129,7 @@
54
55/* Used internally for keeping track of results for regions, allowing us
56 * to sort by dose etc */
+
57struct RegionResult {
58
59 int reg;
@@ -137,20 +143,26 @@
67 double edep_err;
68
69};
+
70
71
72/* comparison function useful for sorting vectors of RegionResults */
+
73bool tlenRegTopResultCompare(const RegionResult &firstElem, const RegionResult &secondElem) {
74 return firstElem.tlen > secondElem.tlen;
75}
+
76
+
77bool edepRegTopResultCompare(const RegionResult &firstElem, const RegionResult &secondElem) {
78 return firstElem.edep > secondElem.edep;
79}
+
80
81
82
83/* utility function for replacing spaces with underscores in a string */
+
84string space2underscore(std::string text) {
85 for (std::string::iterator it = text.begin(); it != text.end(); ++it) {
86 if (*it == ' ') {
@@ -159,6 +171,7 @@
89 }
90 return text;
91}
+
92
93/* geometries that support getting regional volume/mass can be used as phantoms
94 * without specifying their volumes. Other geometry type need to have their
@@ -171,6 +184,7 @@
101const string EB_Phantom::threeddose_geom_types[] = {"EGS_cSpheres", "EGS_cSphericalShell", "EGS_XYZGeometry", "EGS_XYZGeometryT", "EGS_RZ"};
102
103/* initializer for phantom class */
+
104EB_Phantom::EB_Phantom(EGS_Application *parent, EGS_BaseGeometry *geom, set<int> global_regions, int nsource,
105 Publisher *pub) :
106 app(parent), tlen_score(0), edep_score(0),
@@ -190,7 +204,9 @@
120 publisher->subscribe(this, NEW_HISTORY);
121
122}
+
123
+
124void EB_Phantom::update(EB_Message message, void *data) {
125 if (message == NEW_HISTORY) {
126 setHistory(*((EGS_I64 *)data));
@@ -199,7 +215,9 @@
129 total_radiant_e += p->E*p->wt;
130 }
131}
+
132
+
133void EB_Phantom::scoreTlen(int ir, EGS_Float dose, EGS_Particle *p) {
134 if (ir < 0 || ir >= geometry->regions()) {
135 egsFatal("bad %d \n", ir);
@@ -220,17 +238,23 @@
150 }
151 }
152}
+
153
+
155void EB_Phantom::scoreEdep(int ir, EGS_Float dose) {
156 if (edep_score) {
157 edep_score->score(ir, dose);
158 }
159}
+
160
+
162void EB_Phantom::setDoseScale(EGS_Float scale) {
163 dose_scale = scale;
164}
+
165
+
166bool EB_Phantom::needsUserVolumes(const string &geom_type) {
167 // Check if the input geometry is one that egs_brachy can handle
168
@@ -244,7 +268,9 @@
176
177 return true;
178}
+
179
+
180bool EB_Phantom::canWrite3ddose(const string &geom_type) {
181 // Check if the input geometry is one that egs_brachy can handle
182
@@ -258,7 +284,9 @@
190
191 return false;
192}
+
193
+
194vector<int> EB_Phantom::getRegionsWithCorrections() {
195 vector<int> regs;
196 for (std::map<int, double>::iterator it=corrected_volumes.begin(); it != corrected_volumes.end(); ++it) {
@@ -266,27 +294,35 @@
198 }
199 return regs;
200}
+
201
+
202void EB_Phantom::setCorrectedVolume(int ir, double corrected_vol, double unc) {
203 corrected_volumes[ir] = corrected_vol;
204 volume_uncertainty[ir] = unc;
205}
+
206
207/* turn on interaction scoring */
+
208void EB_Phantom::enableTLenScoring() {
209 if (!tlen_score) {
210 tlen_score = new EGS_ScoringArray(geometry->regions());
211 }
212}
+
213
214/* turn on interaction scoring */
+
215void EB_Phantom::enableInteractionScoring() {
216 if (!edep_score) {
217 edep_score = new EGS_ScoringArray(geometry->regions());
218 }
219}
+
220
221/* turn on interaction scoring */
+
222void EB_Phantom::enableScatterScoring() {
223 if (!prim_score) {
224 prim_score = new EGS_ScoringArray(geometry->regions());
@@ -296,9 +332,11 @@
228 publisher->subscribe(this, PARTICLE_ESCAPING_SOURCE);
229 }
230}
+
231
232/* needs to be called at start of every history for every phantom for
233 * proper scoring of statistics */
+
234void EB_Phantom::setHistory(EGS_I64 current_case) {
235
236 cur_history = current_case;
@@ -317,13 +355,17 @@
249 mscat_score->setHistory(current_case);
250 }
251}
+
252
+
253void EB_Phantom::setEffectiveHistories(EGS_Float neff) {
254
255 effective_histories = neff;
256}
+
257
258/* call to tell phantom to output its results */
+
259void EB_Phantom::outputResults(int top_n, string output_3ddose, string output_egsphant, string output_voxinfo,
260 string output_volcor) {
261
@@ -350,23 +392,31 @@
282 }
283
284}
+
+
285EGS_Float EB_Phantom::getRealRho(int ireg) {
286 int med = geometry->medium(ireg);
287 return geometry->getRelativeRho(ireg)*the_media->rho[med];
288}
+
289
290
+
291EGS_Float EB_Phantom::getRealMass(int ireg) {
292 if (needs_user_geoms && !hasVolCor(ireg)) {
293 return -1;
294 }
295 return getCorrectedVolume(ireg)*getRealRho(ireg);
296}
+
297
+
298EGS_Float EB_Phantom::getUncorrectedMass(int ireg) {
299 return needs_user_geoms ? -1 : getUncorrectedVolume(ireg)*getRealRho(ireg);
300}
+
301
+
302EGS_Float EB_Phantom::getUncorrectedVolume(int ireg) {
303 if (needs_user_geoms) {
304 return -1;
@@ -374,11 +424,15 @@
306 EGS_Float volume = geometry->getVolume(ireg);
307 return volume;
308}
+
309
+
310bool EB_Phantom::hasVolCor(int ireg){
311 return corrected_volumes.find(ireg) != corrected_volumes.end();
312}
+
313
+
314EGS_Float EB_Phantom::getCorrectedVolume(int ireg) {
315 bool has_correction = hasVolCor(ireg);
316
@@ -387,7 +441,9 @@
319 }
320 return has_correction ? corrected_volumes[ireg] : getUncorrectedVolume(ireg);
321}
+
322
+
323EGS_Float EB_Phantom::getVolumeUncertainty(int ireg) {
324 bool has_correction = hasVolCor(ireg);
325
@@ -396,7 +452,9 @@
328 }
329 return has_correction ? volume_uncertainty[ireg] : 0;
330}
+
331
+
332void EB_Phantom::getCurrentScore(int ireg, double &sum, double &sum2) {
333 if (tlen_score) {
334 tlen_score->currentScore(ireg, sum, sum2);
@@ -408,12 +466,16 @@
340 }
341
342}
+
343
+
344double EB_Phantom::getTlenNorm(int ireg) {
345 double eff_hist_norm = (double)effective_histories/cur_history;
346 return 1.60217662E-10*nsources*dose_scale/eff_hist_norm;
347}
+
348
+
349void EB_Phantom::getResult(EGS_ScoringArray *score, int ireg, string type, EGS_Float &r, EGS_Float &dr) {
350
351 score->currentResult(ireg, r, dr);
@@ -438,10 +500,12 @@
370
371
372}
+
373
374// Note: this could be made more memory efficient by using an ordered set;
375// For every iteration, insert new region result and then if the
376// set has more than TOP_N results, reduce the size to TOP_N
+
377vector<RegionResult> EB_Phantom::getRegionResults() {
378
379 int nreg = geometry->regions();
@@ -471,8 +535,10 @@
403 return region_results;
404
405}
+
406
407/* output statistics about dose arrays */
+
408void EB_Phantom::outputDoseStats(EGS_ScoringArray *score, string type) {
409
410 int nreg = score->regions();
@@ -630,8 +696,10 @@
562 n_gt_20 ? 100.*avg_tot_gt_20_err / n_gt_20 : 0);
563
564}
+
565
566/* output Top N doses for tracklength and interaction scoring */
+
567void EB_Phantom::outputTopDoses(int top_n, vector<RegionResult> region_results) {
568
569 top_n = min(top_n, geometry->regions());
@@ -700,7 +768,9 @@
632 }
633
634}
+
635
+
636void EB_Phantom::getScoringArrays(vector<EGS_ScoringArray *> &scores, vector<string> &types,
637 vector<string> &descriptions) {
638
@@ -732,7 +802,9 @@
664 }
665
666}
+
667
+
668void EB_Phantom::getEGSdatScoringArrays(vector<EGS_ScoringArray *> &scores) {
669
670 if (tlen_score) {
@@ -750,9 +822,11 @@
682 }
683
684}
+
685
686
687/* create 3ddose file and write bounds/doses to it */
+
688void EB_Phantom::output3ddoseResults(string format) {
689
690 vector<EGS_ScoringArray *> scores;
@@ -795,11 +869,13 @@
727 }
728
729}
+
730
731
732/* write the boundaries section for a 3dose files. This will work for arbitrary EGS_BaseGeometry
733 * classes, but will of course only be accurate for geometries which have implemented getNRegDir
734 * and getBound. */
+
735void EB_Phantom::output3DBounds(ostream &out) {
736
737 int nx = max(1, geometry->getNRegDir(XDIR));
@@ -822,7 +898,9 @@
754 }
755 }
756}
+
757
+
758void EB_Phantom::output3DDoses(ostream &out, EGS_ScoringArray *score, string type) {
759
760
@@ -841,24 +919,26 @@
773 }
774
775 }
-
776 out << endl;
+
776 out << "\n";
777 }
778
779}
+
780
+
781void EB_Phantom::writeEGSPhant(ostream &out) {
782
783 int nmed = EGS_BaseGeometry::nMedia();
784
-
785 out << nmed << endl;
+
785 out << nmed << "\n";
786 for (int i=0; i < nmed; i++) {
-
787 out << EGS_BaseGeometry::getMediumName(i) << endl;
+
787 out << EGS_BaseGeometry::getMediumName(i) << "\n";
788 }
789
790 for (int i=0; i < nmed; i++) {
791 out << the_etcontrol->estepe << "\t";
792 }
-
793 out << endl;
+
793 out << "\n";
794
795 output3DBounds(out);
796
@@ -880,14 +960,16 @@
812 out << getRealRho(ireg) << "\t";
813 }
814 }
-
815 out << endl;
+
815 out << "\n";
816 }
-
817 out << endl;
+
817 out << "\n";
818 }
819 }
820
821}
+
822
+
823string EB_Phantom::medIndex(int medium){
824
825 string medIdx = "123456789ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz";
@@ -897,7 +979,9 @@
829
830 return string(1, medIdx[medium]);
831}
+
832
+
833void EB_Phantom::outputEGSPhant(string format) {
834
835 egsInformation("\nEGSPhant Output File for %s\n%s\n", geometry->getName().c_str(), string(80,'=').c_str());
@@ -919,7 +1003,9 @@
851 out.close();
852 }
853}
+
854
+
855EGS_Float EB_Phantom::avgVoxelVol() {
856
857 EGS_Float total = 0;
@@ -929,7 +1015,9 @@
861 }
862 return nreg > 0 ? total / nreg : 0;
863}
+
864
+
865void EB_Phantom::writeVoxelInfo(ostream &out) {
866
867 out << std::setprecision(6) << std::scientific;
@@ -940,7 +1028,7 @@
872 if (edep_score){
873 header += ", Dose (interaction) / Gy/hist, Total Dose Unc (interaction), Dose Unc (interaction)";
874 }
-
875 out << header << endl;
+
875 out << header << "\n";
876
877 for (int i=0; i < geometry->regions(); i++) {
878 EGS_Float r=0, dr=0, r_edep, dr_edep, dv;
@@ -958,10 +1046,12 @@
890 if (edep_score){
891 out << ", " << r_edep << ", " << sqrt(dr_edep*dr_edep + dv*dv) << ", " << dr_edep;
892 }
-
893 out <<endl;
+
893 out << "\n";
894 }
895}
+
896
+
897void EB_Phantom::outputVoxelInfo(string format) {
898
899 egsInformation("\nVoxel Info File Output File for %s\n%s\n", geometry->getName().c_str(), string(80,'=').c_str());
@@ -986,19 +1076,23 @@
918 out.close();
919 }
920}
+
921
+
922void EB_Phantom::writeVolumeCorrection(ostream &out) {
923 size_t nrecords = corrected_volumes.size();
924
-
925 out << nrecords << endl;
+
925 out << nrecords << "\n";
926
927 for (int i=0; i < geometry->regions(); i++) {
928 if (hasVolCor(i)) {
-
929 out << i << " " << getCorrectedVolume(i) << " " << volume_uncertainty[i] << endl;
+
929 out << i << " " << getCorrectedVolume(i) << " " << volume_uncertainty[i] << "\n";
930 }
931 }
932}
+
933
+
934void EB_Phantom::outputVolumeCorrection(string format) {
935
936 egsInformation("\nVolume Correction Output File for %s\n%s\n", geometry->getName().c_str(), string(80,'=').c_str());
@@ -1022,10 +1116,12 @@
954 out.close();
955 }
956}
+
957
+
958int EB_Phantom::outputData(ostream *ofile) {
959
-
960 (*ofile) << total_radiant_e << endl;
+
960 (*ofile) << total_radiant_e << "\n";
961
962 vector<EGS_ScoringArray *> scores;
963 getEGSdatScoringArrays(scores);
@@ -1041,7 +1137,9 @@
973 return 0;
974
975}
+
976
+
977int EB_Phantom::readData(istream *ifile) {
978
979
@@ -1060,7 +1158,9 @@
992 return 0;
993
994}
+
995
+
996int EB_Phantom::addState(istream &data) {
997
998 EGS_Float total_radiant_e_tmp;
@@ -1086,7 +1186,9 @@
1018 return 0;
1019
1020}
+
1021
+
1022void EB_Phantom::resetCounter() {
1023 total_radiant_e = 0;
1024
@@ -1100,105 +1202,106 @@
1032
1033
1034}
-
EB_Phantom::YDIR
@ YDIR
YDIR=1 y dir for rectilinear, r dir for cylindrical.
Definition: phantom.h:137
-
EB_Phantom::XDIR
@ XDIR
XDIR=0 x dir for rectilinear, r dir for spherical, z dir for cylindrical.
Definition: phantom.h:136
-
EB_Phantom::ZDIR
@ ZDIR
ZDIR=2 z dir for rectilinear.
Definition: phantom.h:138
-
EB_Phantom::getResult
void getResult(EGS_ScoringArray *, int ireg, string type, EGS_Float &r, EGS_Float &dr)
get result for region from scoring array and normalize based on the type requested.
Definition: phantom.cpp:349
-
EB_Phantom::outputEGSPhant
void outputEGSPhant(string)
initialize and write an egsphant file for this phantom
Definition: phantom.cpp:833
-
EB_Phantom::scoreTlen
void scoreTlen(int ir, EGS_Float dose, EGS_Particle *p)
add tracklength dose to region ir
Definition: phantom.cpp:133
-
EB_Phantom::hasVolCor
bool hasVolCor(int ireg)
Definition: phantom.cpp:310
-
EB_Phantom::output3ddoseResults
void output3ddoseResults(string)
write the phantom boundaries, doses and uncertainties to 3ddose file
Definition: phantom.cpp:688
-
EB_Phantom::outputVoxelInfo
void outputVoxelInfo(string format)
write voxel volumes, mass, desnity etc
Definition: phantom.cpp:897
-
EB_Phantom::volume_uncertainty
std::map< int, double > volume_uncertainty
Definition: phantom.h:96
-
EB_Phantom::global_reg_stop
int global_reg_stop
ending global region index for this phantom
Definition: phantom.h:294
-
EB_Phantom::update
void update(EB_Message message, void *data)
Definition: phantom.cpp:124
-
EB_Phantom::can_write_3ddose
bool can_write_3ddose
this phantom can output 3ddose files
Definition: phantom.h:297
-
EB_Phantom::getUncorrectedVolume
EGS_Float getUncorrectedVolume(int ireg)
get corrected volume for a given region
Definition: phantom.cpp:302
-
EB_Phantom::geometry
EGS_BaseGeometry * geometry
the phantom geometry object
Definition: phantom.h:284
-
EB_Phantom::getCurrentScore
void getCurrentScore(int ireg, double &sum, double &sum2)
get current tlen score for region
Definition: phantom.cpp:332
-
EB_Phantom::output3DDoses
void output3DDoses(ostream &out, EGS_ScoringArray *score, string type)
write input scoring array to 3ddose file
Definition: phantom.cpp:758
-
EB_Phantom::getRegionsWithCorrections
vector< int > getRegionsWithCorrections()
return a vector of all regions which were corrected
Definition: phantom.cpp:194
-
EB_Phantom::getTlenNorm
double getTlenNorm(int ireg)
Definition: phantom.cpp:344
-
EB_Phantom::global_reg_start
int global_reg_start
starting global region index for this phantom
Definition: phantom.h:293
-
EB_Phantom::effective_histories
EGS_Float effective_histories
Definition: phantom.h:91
-
EB_Phantom::outputTopDoses
void outputTopDoses(int top_n, vector< RegionResult > region_results)
write the top_n doses to console
Definition: phantom.cpp:567
-
EB_Phantom::getRealRho
EGS_Float getRealRho(int ireg)
return actual density for region
Definition: phantom.cpp:285
-
EB_Phantom::resetCounter
void resetCounter()
Definition: phantom.cpp:1022
-
EB_Phantom::writeVolumeCorrection
void writeVolumeCorrection(ostream &)
write voxel volumes to file
Definition: phantom.cpp:922
-
EB_Phantom::setEffectiveHistories
void setEffectiveHistories(EGS_Float current_case)
set number of effective histories for normalizing scoring arrays
Definition: phantom.cpp:253
-
EB_Phantom::enableScatterScoring
void enableScatterScoring()
enableInteractionScoring must be called before simulation begins if you want to score dose with inter...
Definition: phantom.cpp:222
-
EB_Phantom::setHistory
void setHistory(EGS_I64 current_case)
set current history on scoring arrays for proper statistics
Definition: phantom.cpp:234
-
EB_Phantom::needs_user_geoms
bool needs_user_geoms
this phantom requires user specified geometries
Definition: phantom.h:296
-
EB_Phantom::EB_Phantom
EB_Phantom(EGS_Application *, EGS_BaseGeometry *, set< int > global_regions, int nsource, Publisher *publisher)
EB_Phantom constructor.
Definition: phantom.cpp:104
-
EB_Phantom::threeddose_geom_types
static const string threeddose_geom_types[]
Definition: phantom.h:76
-
EB_Phantom::readData
int readData(istream *ifile)
Definition: phantom.cpp:977
-
EB_Phantom::scoreEdep
void scoreEdep(int ir, EGS_Float dose)
add energy deposition dose to region ir
Definition: phantom.cpp:155
-
EB_Phantom::getRealMass
EGS_Float getRealMass(int ireg)
return (corrected) real mass for region
Definition: phantom.cpp:291
-
EB_Phantom::autovol_phantom_geom_types
static const string autovol_phantom_geom_types[]
Definition: phantom.h:75
-
EB_Phantom::app
EGS_Application * app
Parent application instance. Required for constructing filenames.
Definition: phantom.h:78
-
EB_Phantom::sscat_score
EGS_ScoringArray * sscat_score
Tracklenth scored dose from single scattered particles.
Definition: phantom.h:82
-
EB_Phantom::getRegionResults
vector< RegionResult > getRegionResults()
create a vector of RegionResult structs which can then be sorted by dose value. used for output routi...
Definition: phantom.cpp:377
-
EB_Phantom::total_radiant_e
EGS_Float total_radiant_e
Definition: phantom.h:89
-
EB_Phantom::setCorrectedVolume
void setCorrectedVolume(int ir, double fraction, double unc=0)
Allow user to tell phantom what the actual volume of a region is.
Definition: phantom.cpp:202
-
EB_Phantom::getScoringArrays
void getScoringArrays(vector< EGS_ScoringArray * > &scores, vector< string > &types, vector< string > &descriptions)
get all active scoring arrays, their types and descriptions
Definition: phantom.cpp:636
-
EB_Phantom::medIndex
string medIndex(int medium)
get medium index 1-9A-Z
Definition: phantom.cpp:823
-
EB_Phantom::mscat_score
EGS_ScoringArray * mscat_score
Tracklenth scored dose from multiple scattered particles.
Definition: phantom.h:84
-
EB_Phantom::canWrite3ddose
static bool canWrite3ddose(const string &geom_type)
function for checking whether a given geometry type can output 3ddose files
Definition: phantom.cpp:180
-
EB_Phantom::outputResults
void outputResults(int top_n=20, string output_3ddose="text", string output_egsphant="text", string output_voxinfo="text", string output_volcor="text")
tell phantom to output its results.
Definition: phantom.cpp:259
-
EB_Phantom::addState
int addState(istream &ifile)
Definition: phantom.cpp:996
-
EB_Phantom::prim_score
EGS_ScoringArray * prim_score
Tracklenth scored dose from primary particles.
Definition: phantom.h:81
-
EB_Phantom::writeEGSPhant
void writeEGSPhant(ostream &)
write actual egsphant data to file for this phantom
Definition: phantom.cpp:781
-
EB_Phantom::getEGSdatScoringArrays
void getEGSdatScoringArrays(vector< EGS_ScoringArray * > &scores)
get all active scoring arrays for writing to egsdat file
Definition: phantom.cpp:668
-
EB_Phantom::enableTLenScoring
void enableTLenScoring()
enableTLenScoring must be called before simulation begins if you want to score dose with tracklength ...
Definition: phantom.cpp:208
-
EB_Phantom::outputDoseStats
void outputDoseStats(EGS_ScoringArray *score, string type)
write some stats about dose arrays
Definition: phantom.cpp:408
-
EB_Phantom::publisher
Publisher * publisher
Definition: phantom.h:93
-
EB_Phantom::cur_history
EGS_I64 cur_history
Definition: phantom.h:90
-
EB_Phantom::tlen_score
EGS_ScoringArray * tlen_score
Tracklength dose scoring array.
Definition: phantom.h:79
-
EB_Phantom::corrected_volumes
std::map< int, double > corrected_volumes
Corrected volume in a given region.
Definition: phantom.h:95
-
EB_Phantom::outputVolumeCorrection
void outputVolumeCorrection(string format)
intialize and output write voxel volumes to file
Definition: phantom.cpp:934
-
EB_Phantom::dose_scale
EGS_Float dose_scale
Definition: phantom.h:87
-
EB_Phantom::output3DBounds
void output3DBounds(ostream &out)
write the phantom bounds to 3ddose file
Definition: phantom.cpp:735
-
EB_Phantom::getCorrectedVolume
EGS_Float getCorrectedVolume(int ireg)
get uncorrected volume for a given region
Definition: phantom.cpp:314
-
EB_Phantom::setDoseScale
void setDoseScale(EGS_Float)
set dose scaling factor for output
Definition: phantom.cpp:162
-
EB_Phantom::needsUserVolumes
static bool needsUserVolumes(const string &geom_type)
function for checking whether a given geometry type requires user specified volumes
Definition: phantom.cpp:166
-
EB_Phantom::writeVoxelInfo
void writeVoxelInfo(ostream &)
write voxel info file
Definition: phantom.cpp:865
-
EB_Phantom::outputData
int outputData(ostream *ofile)
Definition: phantom.cpp:958
-
EB_Phantom::global_regions
set< int > global_regions
the set of all global regions contained in this phantom
Definition: phantom.h:291
-
EB_Phantom::getUncorrectedMass
EGS_Float getUncorrectedMass(int ireg)
return uncorrected for region
Definition: phantom.cpp:298
-
EB_Phantom::nsources
int nsources
Definition: phantom.h:86
-
EB_Phantom::getVolumeUncertainty
EGS_Float getVolumeUncertainty(int ireg)
get volume unc
Definition: phantom.cpp:323
-
EB_Phantom::enableInteractionScoring
void enableInteractionScoring()
enableInteractionScoring must be called before simulation begins if you want to score dose with inter...
Definition: phantom.cpp:215
-
EB_Phantom::avgVoxelVol
EGS_Float avgVoxelVol()
return average voxel volume
Definition: phantom.cpp:855
-
EB_Phantom::edep_score
EGS_ScoringArray * edep_score
Interaction scored dose scoring array.
Definition: phantom.h:80
-
Latch::isMultScat
static bool isMultScat(int latch)
Definition: latch.cpp:121
-
Latch::isPrimary
static bool isPrimary(int latch)
Definition: latch.cpp:105
-
Latch::isSingleScat
static bool isSingleScat(int latch)
Definition: latch.cpp:113
- -
Publisher::subscribe
void subscribe(Subscriber *s, EB_Message message)
Definition: pubsub.h:83
-
gzstreambase::close
void close()
Definition: gzstream.C:154
- -
ogzstream::open
void open(const char *name, int open_mode=std::ios::out)
Definition: gzstream.h:121
+
+
EB_Phantom::YDIR
@ YDIR
YDIR=1 y dir for rectilinear, r dir for cylindrical.
Definition phantom.h:137
+
EB_Phantom::XDIR
@ XDIR
XDIR=0 x dir for rectilinear, r dir for spherical, z dir for cylindrical.
Definition phantom.h:136
+
EB_Phantom::ZDIR
@ ZDIR
ZDIR=2 z dir for rectilinear.
Definition phantom.h:138
+
EB_Phantom::getResult
void getResult(EGS_ScoringArray *, int ireg, string type, EGS_Float &r, EGS_Float &dr)
get result for region from scoring array and normalize based on the type requested.
Definition phantom.cpp:349
+
EB_Phantom::outputEGSPhant
void outputEGSPhant(string)
initialize and write an egsphant file for this phantom
Definition phantom.cpp:833
+
EB_Phantom::scoreTlen
void scoreTlen(int ir, EGS_Float dose, EGS_Particle *p)
add tracklength dose to region ir
Definition phantom.cpp:133
+
EB_Phantom::hasVolCor
bool hasVolCor(int ireg)
Definition phantom.cpp:310
+
EB_Phantom::output3ddoseResults
void output3ddoseResults(string)
write the phantom boundaries, doses and uncertainties to 3ddose file
Definition phantom.cpp:688
+
EB_Phantom::outputVoxelInfo
void outputVoxelInfo(string format)
write voxel volumes, mass, desnity etc
Definition phantom.cpp:897
+
EB_Phantom::volume_uncertainty
std::map< int, double > volume_uncertainty
Definition phantom.h:96
+
EB_Phantom::global_reg_stop
int global_reg_stop
ending global region index for this phantom
Definition phantom.h:294
+
EB_Phantom::update
void update(EB_Message message, void *data)
Definition phantom.cpp:124
+
EB_Phantom::can_write_3ddose
bool can_write_3ddose
this phantom can output 3ddose files
Definition phantom.h:297
+
EB_Phantom::getUncorrectedVolume
EGS_Float getUncorrectedVolume(int ireg)
get corrected volume for a given region
Definition phantom.cpp:302
+
EB_Phantom::geometry
EGS_BaseGeometry * geometry
the phantom geometry object
Definition phantom.h:284
+
EB_Phantom::getCurrentScore
void getCurrentScore(int ireg, double &sum, double &sum2)
get current tlen score for region
Definition phantom.cpp:332
+
EB_Phantom::output3DDoses
void output3DDoses(ostream &out, EGS_ScoringArray *score, string type)
write input scoring array to 3ddose file
Definition phantom.cpp:758
+
EB_Phantom::getRegionsWithCorrections
vector< int > getRegionsWithCorrections()
return a vector of all regions which were corrected
Definition phantom.cpp:194
+
EB_Phantom::getTlenNorm
double getTlenNorm(int ireg)
Definition phantom.cpp:344
+
EB_Phantom::global_reg_start
int global_reg_start
starting global region index for this phantom
Definition phantom.h:293
+
EB_Phantom::effective_histories
EGS_Float effective_histories
Definition phantom.h:91
+
EB_Phantom::outputTopDoses
void outputTopDoses(int top_n, vector< RegionResult > region_results)
write the top_n doses to console
Definition phantom.cpp:567
+
EB_Phantom::getRealRho
EGS_Float getRealRho(int ireg)
return actual density for region
Definition phantom.cpp:285
+
EB_Phantom::resetCounter
void resetCounter()
Definition phantom.cpp:1022
+
EB_Phantom::writeVolumeCorrection
void writeVolumeCorrection(ostream &)
write voxel volumes to file
Definition phantom.cpp:922
+
EB_Phantom::setEffectiveHistories
void setEffectiveHistories(EGS_Float current_case)
set number of effective histories for normalizing scoring arrays
Definition phantom.cpp:253
+
EB_Phantom::enableScatterScoring
void enableScatterScoring()
enableInteractionScoring must be called before simulation begins if you want to score dose with inter...
Definition phantom.cpp:222
+
EB_Phantom::setHistory
void setHistory(EGS_I64 current_case)
set current history on scoring arrays for proper statistics
Definition phantom.cpp:234
+
EB_Phantom::needs_user_geoms
bool needs_user_geoms
this phantom requires user specified geometries
Definition phantom.h:296
+
EB_Phantom::EB_Phantom
EB_Phantom(EGS_Application *, EGS_BaseGeometry *, set< int > global_regions, int nsource, Publisher *publisher)
EB_Phantom constructor.
Definition phantom.cpp:104
+
EB_Phantom::threeddose_geom_types
static const string threeddose_geom_types[]
Definition phantom.h:101
+
EB_Phantom::readData
int readData(istream *ifile)
Definition phantom.cpp:977
+
EB_Phantom::scoreEdep
void scoreEdep(int ir, EGS_Float dose)
add energy deposition dose to region ir
Definition phantom.cpp:155
+
EB_Phantom::getRealMass
EGS_Float getRealMass(int ireg)
return (corrected) real mass for region
Definition phantom.cpp:291
+
EB_Phantom::autovol_phantom_geom_types
static const string autovol_phantom_geom_types[]
Definition phantom.h:97
+
EB_Phantom::app
EGS_Application * app
Parent application instance. Required for constructing filenames.
Definition phantom.h:78
+
EB_Phantom::sscat_score
EGS_ScoringArray * sscat_score
Tracklenth scored dose from single scattered particles.
Definition phantom.h:82
+
EB_Phantom::getRegionResults
vector< RegionResult > getRegionResults()
create a vector of RegionResult structs which can then be sorted by dose value. used for output routi...
Definition phantom.cpp:377
+
EB_Phantom::total_radiant_e
EGS_Float total_radiant_e
Definition phantom.h:89
+
EB_Phantom::setCorrectedVolume
void setCorrectedVolume(int ir, double fraction, double unc=0)
Allow user to tell phantom what the actual volume of a region is.
Definition phantom.cpp:202
+
EB_Phantom::getScoringArrays
void getScoringArrays(vector< EGS_ScoringArray * > &scores, vector< string > &types, vector< string > &descriptions)
get all active scoring arrays, their types and descriptions
Definition phantom.cpp:636
+
EB_Phantom::medIndex
string medIndex(int medium)
get medium index 1-9A-Z
Definition phantom.cpp:823
+
EB_Phantom::mscat_score
EGS_ScoringArray * mscat_score
Tracklenth scored dose from multiple scattered particles.
Definition phantom.h:84
+
EB_Phantom::canWrite3ddose
static bool canWrite3ddose(const string &geom_type)
function for checking whether a given geometry type can output 3ddose files
Definition phantom.cpp:180
+
EB_Phantom::outputResults
void outputResults(int top_n=20, string output_3ddose="text", string output_egsphant="text", string output_voxinfo="text", string output_volcor="text")
tell phantom to output its results.
Definition phantom.cpp:259
+
EB_Phantom::addState
int addState(istream &ifile)
Definition phantom.cpp:996
+
EB_Phantom::prim_score
EGS_ScoringArray * prim_score
Tracklenth scored dose from primary particles.
Definition phantom.h:81
+
EB_Phantom::writeEGSPhant
void writeEGSPhant(ostream &)
write actual egsphant data to file for this phantom
Definition phantom.cpp:781
+
EB_Phantom::getEGSdatScoringArrays
void getEGSdatScoringArrays(vector< EGS_ScoringArray * > &scores)
get all active scoring arrays for writing to egsdat file
Definition phantom.cpp:668
+
EB_Phantom::enableTLenScoring
void enableTLenScoring()
enableTLenScoring must be called before simulation begins if you want to score dose with tracklength ...
Definition phantom.cpp:208
+
EB_Phantom::outputDoseStats
void outputDoseStats(EGS_ScoringArray *score, string type)
write some stats about dose arrays
Definition phantom.cpp:408
+
EB_Phantom::publisher
Publisher * publisher
Definition phantom.h:93
+
EB_Phantom::cur_history
EGS_I64 cur_history
Definition phantom.h:90
+
EB_Phantom::tlen_score
EGS_ScoringArray * tlen_score
Tracklength dose scoring array.
Definition phantom.h:79
+
EB_Phantom::corrected_volumes
std::map< int, double > corrected_volumes
Corrected volume in a given region.
Definition phantom.h:95
+
EB_Phantom::outputVolumeCorrection
void outputVolumeCorrection(string format)
intialize and output write voxel volumes to file
Definition phantom.cpp:934
+
EB_Phantom::dose_scale
EGS_Float dose_scale
Definition phantom.h:87
+
EB_Phantom::output3DBounds
void output3DBounds(ostream &out)
write the phantom bounds to 3ddose file
Definition phantom.cpp:735
+
EB_Phantom::getCorrectedVolume
EGS_Float getCorrectedVolume(int ireg)
get uncorrected volume for a given region
Definition phantom.cpp:314
+
EB_Phantom::setDoseScale
void setDoseScale(EGS_Float)
set dose scaling factor for output
Definition phantom.cpp:162
+
EB_Phantom::needsUserVolumes
static bool needsUserVolumes(const string &geom_type)
function for checking whether a given geometry type requires user specified volumes
Definition phantom.cpp:166
+
EB_Phantom::writeVoxelInfo
void writeVoxelInfo(ostream &)
write voxel info file
Definition phantom.cpp:865
+
EB_Phantom::outputData
int outputData(ostream *ofile)
Definition phantom.cpp:958
+
EB_Phantom::global_regions
set< int > global_regions
the set of all global regions contained in this phantom
Definition phantom.h:291
+
EB_Phantom::getUncorrectedMass
EGS_Float getUncorrectedMass(int ireg)
return uncorrected for region
Definition phantom.cpp:298
+
EB_Phantom::nsources
int nsources
Definition phantom.h:86
+
EB_Phantom::getVolumeUncertainty
EGS_Float getVolumeUncertainty(int ireg)
get volume unc
Definition phantom.cpp:323
+
EB_Phantom::enableInteractionScoring
void enableInteractionScoring()
enableInteractionScoring must be called before simulation begins if you want to score dose with inter...
Definition phantom.cpp:215
+
EB_Phantom::avgVoxelVol
EGS_Float avgVoxelVol()
return average voxel volume
Definition phantom.cpp:855
+
EB_Phantom::edep_score
EGS_ScoringArray * edep_score
Interaction scored dose scoring array.
Definition phantom.h:80
+
Latch::isMultScat
static bool isMultScat(int latch)
Definition latch.cpp:121
+
Latch::isPrimary
static bool isPrimary(int latch)
Definition latch.cpp:105
+
Latch::isSingleScat
static bool isSingleScat(int latch)
Definition latch.cpp:113
+ +
Publisher::subscribe
void subscribe(Subscriber *s, EB_Message message)
Definition pubsub.h:83
+
gzstreambase::close
void close()
Definition gzstream.C:154
+ +
ogzstream::open
void open(const char *name, int open_mode=std::ios::out)
Definition gzstream.h:121
latch.h
handle particles latch bits for egs_brachy
-
space2underscore
string space2underscore(std::string text)
Definition: phantom.cpp:84
-
tlenRegTopResultCompare
bool tlenRegTopResultCompare(const RegionResult &firstElem, const RegionResult &secondElem)
Definition: phantom.cpp:73
-
edepRegTopResultCompare
bool edepRegTopResultCompare(const RegionResult &firstElem, const RegionResult &secondElem)
Definition: phantom.cpp:77
+
space2underscore
string space2underscore(std::string text)
Definition phantom.cpp:84
+
tlenRegTopResultCompare
bool tlenRegTopResultCompare(const RegionResult &firstElem, const RegionResult &secondElem)
Definition phantom.cpp:73
+
edepRegTopResultCompare
bool edepRegTopResultCompare(const RegionResult &firstElem, const RegionResult &secondElem)
Definition phantom.cpp:77
phantom.h
Header file for phantom objects.
-
EB_Message
EB_Message
Definition: pubsub.h:54
-
PARTICLE_ESCAPING_SOURCE
@ PARTICLE_ESCAPING_SOURCE
Definition: pubsub.h:60
-
NEW_HISTORY
@ NEW_HISTORY
Definition: pubsub.h:56
- - -
RegionResult::tlen
double tlen
Definition: phantom.cpp:63
-
RegionResult::volume_unc
double volume_unc
Definition: phantom.cpp:61
-
RegionResult::volume
double volume
Definition: phantom.cpp:60
-
RegionResult::edep_err
double edep_err
Definition: phantom.cpp:67
-
RegionResult::tlen_err
double tlen_err
Definition: phantom.cpp:64
-
RegionResult::edep
double edep
Definition: phantom.cpp:66
+
EB_Message
EB_Message
Definition pubsub.h:54
+
PARTICLE_ESCAPING_SOURCE
@ PARTICLE_ESCAPING_SOURCE
Definition pubsub.h:60
+
NEW_HISTORY
@ NEW_HISTORY
Definition pubsub.h:56
+ + +
RegionResult::tlen
double tlen
Definition phantom.cpp:63
+
RegionResult::volume_unc
double volume_unc
Definition phantom.cpp:61
+
RegionResult::volume
double volume
Definition phantom.cpp:60
+
RegionResult::edep_err
double edep_err
Definition phantom.cpp:67
+
RegionResult::tlen_err
double tlen_err
Definition phantom.cpp:64
+
RegionResult::edep
double edep
Definition phantom.cpp:66
-Generated by doxygen 1.9.5 +Generated by doxygen 1.9.8
diff --git a/docs/phantom_8h.html b/docs/phantom_8h.html index 98e341a6..94c9eb30 100644 --- a/docs/phantom_8h.html +++ b/docs/phantom_8h.html @@ -3,9 +3,9 @@ - + -EGS Brachy: /Users/marc/dev/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/phantom.h File Reference +EGS Brachy: /Users/marc/Developer/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/phantom.h File Reference @@ -30,7 +30,7 @@
- + @@ -30,7 +30,7 @@ - + +
-
/Users/marc/dev/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/phantom.h
+
/Users/marc/Developer/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/phantom.h
Go to the documentation of this file.
1/*
@@ -123,12 +128,13 @@
53
56struct RegionResult;
57
+
71class EB_Phantom : public Subscriber {
72
73private:
74
-
75 const static string autovol_phantom_geom_types[];
-
76 const static string threeddose_geom_types[];
+
75 const static string autovol_phantom_geom_types[];
+
76 const static string threeddose_geom_types[];
77
78 EGS_Application *app;
79 EGS_ScoringArray *tlen_score;
@@ -149,7 +155,7 @@
94
95 std::map<int, double> corrected_volumes;
96 std::map<int, double> volume_uncertainty;
-
97
+
97
99 void outputDoseStats(EGS_ScoringArray *score, string type);
100
102 void outputTopDoses(int top_n, vector<RegionResult> region_results);
@@ -175,14 +181,17 @@
132
133public:
134
+
140
142 EB_Phantom(EGS_Application *, EGS_BaseGeometry *, set<int> global_regions, int nsource, Publisher *publisher);
143
+
145 ~EB_Phantom() {
146
147 if (tlen_score) {
@@ -202,6 +211,7 @@
161 }
162
163 };
+
164
167 static bool needsUserVolumes(const string &geom_type);
168
@@ -256,10 +266,13 @@
245 void outputResults(int top_n=20, string output_3ddose="text", string output_egsphant="text",
246 string output_voxinfo="text", string output_volcor="text");
247
+
249 bool globalRegIsInPhant(int global_reg) {
250 return (global_reg_start <= global_reg) && (global_reg <= global_reg_stop);
251 }
+
252
+
254 int globalToLocal(int global_reg) {
255 if ((global_reg_start <= global_reg) && (global_reg <= global_reg_stop)) {
256 return global_reg - global_reg_start;
@@ -267,6 +280,7 @@
258
259 return -1;
260 }
+
261
262
263
@@ -295,91 +309,92 @@
297 bool can_write_3ddose;
298
299};
+
300
301#endif
-
EB_Phantom
A class to represent a single phantom for scoring dose in egs_brachy.
Definition: phantom.h:71
-
EB_Phantom::GeomDirections
GeomDirections
Definition: phantom.h:135
-
EB_Phantom::YDIR
@ YDIR
YDIR=1 y dir for rectilinear, r dir for cylindrical.
Definition: phantom.h:137
-
EB_Phantom::XDIR
@ XDIR
XDIR=0 x dir for rectilinear, r dir for spherical, z dir for cylindrical.
Definition: phantom.h:136
-
EB_Phantom::ZDIR
@ ZDIR
ZDIR=2 z dir for rectilinear.
Definition: phantom.h:138
-
EB_Phantom::getResult
void getResult(EGS_ScoringArray *, int ireg, string type, EGS_Float &r, EGS_Float &dr)
get result for region from scoring array and normalize based on the type requested.
Definition: phantom.cpp:349
-
EB_Phantom::outputEGSPhant
void outputEGSPhant(string)
initialize and write an egsphant file for this phantom
Definition: phantom.cpp:833
-
EB_Phantom::scoreTlen
void scoreTlen(int ir, EGS_Float dose, EGS_Particle *p)
add tracklength dose to region ir
Definition: phantom.cpp:133
-
EB_Phantom::hasVolCor
bool hasVolCor(int ireg)
Definition: phantom.cpp:310
-
EB_Phantom::output3ddoseResults
void output3ddoseResults(string)
write the phantom boundaries, doses and uncertainties to 3ddose file
Definition: phantom.cpp:688
-
EB_Phantom::outputVoxelInfo
void outputVoxelInfo(string format)
write voxel volumes, mass, desnity etc
Definition: phantom.cpp:897
-
EB_Phantom::volume_uncertainty
std::map< int, double > volume_uncertainty
Definition: phantom.h:96
-
EB_Phantom::global_reg_stop
int global_reg_stop
ending global region index for this phantom
Definition: phantom.h:294
-
EB_Phantom::~EB_Phantom
~EB_Phantom()
EB_Phantom destructor.
Definition: phantom.h:145
-
EB_Phantom::update
void update(EB_Message message, void *data)
Definition: phantom.cpp:124
-
EB_Phantom::can_write_3ddose
bool can_write_3ddose
this phantom can output 3ddose files
Definition: phantom.h:297
-
EB_Phantom::getUncorrectedVolume
EGS_Float getUncorrectedVolume(int ireg)
get corrected volume for a given region
Definition: phantom.cpp:302
-
EB_Phantom::geometry
EGS_BaseGeometry * geometry
the phantom geometry object
Definition: phantom.h:284
-
EB_Phantom::getCurrentScore
void getCurrentScore(int ireg, double &sum, double &sum2)
get current tlen score for region
Definition: phantom.cpp:332
-
EB_Phantom::output3DDoses
void output3DDoses(ostream &out, EGS_ScoringArray *score, string type)
write input scoring array to 3ddose file
Definition: phantom.cpp:758
-
EB_Phantom::getRegionsWithCorrections
vector< int > getRegionsWithCorrections()
return a vector of all regions which were corrected
Definition: phantom.cpp:194
-
EB_Phantom::globalRegIsInPhant
bool globalRegIsInPhant(int global_reg)
check whether a global region falls within this phantom
Definition: phantom.h:249
-
EB_Phantom::getTlenNorm
double getTlenNorm(int ireg)
Definition: phantom.cpp:344
-
EB_Phantom::global_reg_start
int global_reg_start
starting global region index for this phantom
Definition: phantom.h:293
-
EB_Phantom::effective_histories
EGS_Float effective_histories
Definition: phantom.h:91
-
EB_Phantom::outputTopDoses
void outputTopDoses(int top_n, vector< RegionResult > region_results)
write the top_n doses to console
Definition: phantom.cpp:567
-
EB_Phantom::getRealRho
EGS_Float getRealRho(int ireg)
return actual density for region
Definition: phantom.cpp:285
-
EB_Phantom::resetCounter
void resetCounter()
Definition: phantom.cpp:1022
-
EB_Phantom::writeVolumeCorrection
void writeVolumeCorrection(ostream &)
write voxel volumes to file
Definition: phantom.cpp:922
-
EB_Phantom::setEffectiveHistories
void setEffectiveHistories(EGS_Float current_case)
set number of effective histories for normalizing scoring arrays
Definition: phantom.cpp:253
-
EB_Phantom::enableScatterScoring
void enableScatterScoring()
enableInteractionScoring must be called before simulation begins if you want to score dose with inter...
Definition: phantom.cpp:222
-
EB_Phantom::setHistory
void setHistory(EGS_I64 current_case)
set current history on scoring arrays for proper statistics
Definition: phantom.cpp:234
-
EB_Phantom::needs_user_geoms
bool needs_user_geoms
this phantom requires user specified geometries
Definition: phantom.h:296
-
EB_Phantom::threeddose_geom_types
static const string threeddose_geom_types[]
Definition: phantom.h:76
-
EB_Phantom::readData
int readData(istream *ifile)
Definition: phantom.cpp:977
-
EB_Phantom::scoreEdep
void scoreEdep(int ir, EGS_Float dose)
add energy deposition dose to region ir
Definition: phantom.cpp:155
-
EB_Phantom::getRealMass
EGS_Float getRealMass(int ireg)
return (corrected) real mass for region
Definition: phantom.cpp:291
-
EB_Phantom::autovol_phantom_geom_types
static const string autovol_phantom_geom_types[]
Definition: phantom.h:75
-
EB_Phantom::app
EGS_Application * app
Parent application instance. Required for constructing filenames.
Definition: phantom.h:78
-
EB_Phantom::sscat_score
EGS_ScoringArray * sscat_score
Tracklenth scored dose from single scattered particles.
Definition: phantom.h:82
-
EB_Phantom::getRegionResults
vector< RegionResult > getRegionResults()
create a vector of RegionResult structs which can then be sorted by dose value. used for output routi...
Definition: phantom.cpp:377
-
EB_Phantom::total_radiant_e
EGS_Float total_radiant_e
Definition: phantom.h:89
-
EB_Phantom::setCorrectedVolume
void setCorrectedVolume(int ir, double fraction, double unc=0)
Allow user to tell phantom what the actual volume of a region is.
Definition: phantom.cpp:202
-
EB_Phantom::getScoringArrays
void getScoringArrays(vector< EGS_ScoringArray * > &scores, vector< string > &types, vector< string > &descriptions)
get all active scoring arrays, their types and descriptions
Definition: phantom.cpp:636
-
EB_Phantom::medIndex
string medIndex(int medium)
get medium index 1-9A-Z
Definition: phantom.cpp:823
-
EB_Phantom::globalToLocal
int globalToLocal(int global_reg)
convert global region to local phantom region
Definition: phantom.h:254
-
EB_Phantom::mscat_score
EGS_ScoringArray * mscat_score
Tracklenth scored dose from multiple scattered particles.
Definition: phantom.h:84
-
EB_Phantom::canWrite3ddose
static bool canWrite3ddose(const string &geom_type)
function for checking whether a given geometry type can output 3ddose files
Definition: phantom.cpp:180
-
EB_Phantom::outputResults
void outputResults(int top_n=20, string output_3ddose="text", string output_egsphant="text", string output_voxinfo="text", string output_volcor="text")
tell phantom to output its results.
Definition: phantom.cpp:259
-
EB_Phantom::addState
int addState(istream &ifile)
Definition: phantom.cpp:996
-
EB_Phantom::prim_score
EGS_ScoringArray * prim_score
Tracklenth scored dose from primary particles.
Definition: phantom.h:81
-
EB_Phantom::writeEGSPhant
void writeEGSPhant(ostream &)
write actual egsphant data to file for this phantom
Definition: phantom.cpp:781
-
EB_Phantom::getEGSdatScoringArrays
void getEGSdatScoringArrays(vector< EGS_ScoringArray * > &scores)
get all active scoring arrays for writing to egsdat file
Definition: phantom.cpp:668
-
EB_Phantom::enableTLenScoring
void enableTLenScoring()
enableTLenScoring must be called before simulation begins if you want to score dose with tracklength ...
Definition: phantom.cpp:208
-
EB_Phantom::outputDoseStats
void outputDoseStats(EGS_ScoringArray *score, string type)
write some stats about dose arrays
Definition: phantom.cpp:408
-
EB_Phantom::publisher
Publisher * publisher
Definition: phantom.h:93
-
EB_Phantom::cur_history
EGS_I64 cur_history
Definition: phantom.h:90
-
EB_Phantom::tlen_score
EGS_ScoringArray * tlen_score
Tracklength dose scoring array.
Definition: phantom.h:79
-
EB_Phantom::corrected_volumes
std::map< int, double > corrected_volumes
Corrected volume in a given region.
Definition: phantom.h:95
-
EB_Phantom::outputVolumeCorrection
void outputVolumeCorrection(string format)
intialize and output write voxel volumes to file
Definition: phantom.cpp:934
-
EB_Phantom::dose_scale
EGS_Float dose_scale
Definition: phantom.h:87
-
EB_Phantom::output3DBounds
void output3DBounds(ostream &out)
write the phantom bounds to 3ddose file
Definition: phantom.cpp:735
-
EB_Phantom::getCorrectedVolume
EGS_Float getCorrectedVolume(int ireg)
get uncorrected volume for a given region
Definition: phantom.cpp:314
-
EB_Phantom::setDoseScale
void setDoseScale(EGS_Float)
set dose scaling factor for output
Definition: phantom.cpp:162
-
EB_Phantom::needsUserVolumes
static bool needsUserVolumes(const string &geom_type)
function for checking whether a given geometry type requires user specified volumes
Definition: phantom.cpp:166
-
EB_Phantom::writeVoxelInfo
void writeVoxelInfo(ostream &)
write voxel info file
Definition: phantom.cpp:865
-
EB_Phantom::outputData
int outputData(ostream *ofile)
Definition: phantom.cpp:958
-
EB_Phantom::global_regions
set< int > global_regions
the set of all global regions contained in this phantom
Definition: phantom.h:291
-
EB_Phantom::getUncorrectedMass
EGS_Float getUncorrectedMass(int ireg)
return uncorrected for region
Definition: phantom.cpp:298
-
EB_Phantom::nsources
int nsources
Definition: phantom.h:86
-
EB_Phantom::getVolumeUncertainty
EGS_Float getVolumeUncertainty(int ireg)
get volume unc
Definition: phantom.cpp:323
-
EB_Phantom::enableInteractionScoring
void enableInteractionScoring()
enableInteractionScoring must be called before simulation begins if you want to score dose with inter...
Definition: phantom.cpp:215
-
EB_Phantom::avgVoxelVol
EGS_Float avgVoxelVol()
return average voxel volume
Definition: phantom.cpp:855
-
EB_Phantom::edep_score
EGS_ScoringArray * edep_score
Interaction scored dose scoring array.
Definition: phantom.h:80
- - +
EB_Phantom
A class to represent a single phantom for scoring dose in egs_brachy.
Definition phantom.h:71
+
EB_Phantom::GeomDirections
GeomDirections
Definition phantom.h:135
+
EB_Phantom::YDIR
@ YDIR
YDIR=1 y dir for rectilinear, r dir for cylindrical.
Definition phantom.h:137
+
EB_Phantom::XDIR
@ XDIR
XDIR=0 x dir for rectilinear, r dir for spherical, z dir for cylindrical.
Definition phantom.h:136
+
EB_Phantom::ZDIR
@ ZDIR
ZDIR=2 z dir for rectilinear.
Definition phantom.h:138
+
EB_Phantom::getResult
void getResult(EGS_ScoringArray *, int ireg, string type, EGS_Float &r, EGS_Float &dr)
get result for region from scoring array and normalize based on the type requested.
Definition phantom.cpp:349
+
EB_Phantom::outputEGSPhant
void outputEGSPhant(string)
initialize and write an egsphant file for this phantom
Definition phantom.cpp:833
+
EB_Phantom::scoreTlen
void scoreTlen(int ir, EGS_Float dose, EGS_Particle *p)
add tracklength dose to region ir
Definition phantom.cpp:133
+
EB_Phantom::hasVolCor
bool hasVolCor(int ireg)
Definition phantom.cpp:310
+
EB_Phantom::output3ddoseResults
void output3ddoseResults(string)
write the phantom boundaries, doses and uncertainties to 3ddose file
Definition phantom.cpp:688
+
EB_Phantom::outputVoxelInfo
void outputVoxelInfo(string format)
write voxel volumes, mass, desnity etc
Definition phantom.cpp:897
+
EB_Phantom::volume_uncertainty
std::map< int, double > volume_uncertainty
Definition phantom.h:96
+
EB_Phantom::global_reg_stop
int global_reg_stop
ending global region index for this phantom
Definition phantom.h:294
+
EB_Phantom::~EB_Phantom
~EB_Phantom()
EB_Phantom destructor.
Definition phantom.h:145
+
EB_Phantom::update
void update(EB_Message message, void *data)
Definition phantom.cpp:124
+
EB_Phantom::can_write_3ddose
bool can_write_3ddose
this phantom can output 3ddose files
Definition phantom.h:297
+
EB_Phantom::getUncorrectedVolume
EGS_Float getUncorrectedVolume(int ireg)
get corrected volume for a given region
Definition phantom.cpp:302
+
EB_Phantom::geometry
EGS_BaseGeometry * geometry
the phantom geometry object
Definition phantom.h:284
+
EB_Phantom::getCurrentScore
void getCurrentScore(int ireg, double &sum, double &sum2)
get current tlen score for region
Definition phantom.cpp:332
+
EB_Phantom::output3DDoses
void output3DDoses(ostream &out, EGS_ScoringArray *score, string type)
write input scoring array to 3ddose file
Definition phantom.cpp:758
+
EB_Phantom::getRegionsWithCorrections
vector< int > getRegionsWithCorrections()
return a vector of all regions which were corrected
Definition phantom.cpp:194
+
EB_Phantom::globalRegIsInPhant
bool globalRegIsInPhant(int global_reg)
check whether a global region falls within this phantom
Definition phantom.h:249
+
EB_Phantom::getTlenNorm
double getTlenNorm(int ireg)
Definition phantom.cpp:344
+
EB_Phantom::global_reg_start
int global_reg_start
starting global region index for this phantom
Definition phantom.h:293
+
EB_Phantom::effective_histories
EGS_Float effective_histories
Definition phantom.h:91
+
EB_Phantom::outputTopDoses
void outputTopDoses(int top_n, vector< RegionResult > region_results)
write the top_n doses to console
Definition phantom.cpp:567
+
EB_Phantom::getRealRho
EGS_Float getRealRho(int ireg)
return actual density for region
Definition phantom.cpp:285
+
EB_Phantom::resetCounter
void resetCounter()
Definition phantom.cpp:1022
+
EB_Phantom::writeVolumeCorrection
void writeVolumeCorrection(ostream &)
write voxel volumes to file
Definition phantom.cpp:922
+
EB_Phantom::setEffectiveHistories
void setEffectiveHistories(EGS_Float current_case)
set number of effective histories for normalizing scoring arrays
Definition phantom.cpp:253
+
EB_Phantom::enableScatterScoring
void enableScatterScoring()
enableInteractionScoring must be called before simulation begins if you want to score dose with inter...
Definition phantom.cpp:222
+
EB_Phantom::setHistory
void setHistory(EGS_I64 current_case)
set current history on scoring arrays for proper statistics
Definition phantom.cpp:234
+
EB_Phantom::needs_user_geoms
bool needs_user_geoms
this phantom requires user specified geometries
Definition phantom.h:296
+
EB_Phantom::threeddose_geom_types
static const string threeddose_geom_types[]
Definition phantom.h:101
+
EB_Phantom::readData
int readData(istream *ifile)
Definition phantom.cpp:977
+
EB_Phantom::scoreEdep
void scoreEdep(int ir, EGS_Float dose)
add energy deposition dose to region ir
Definition phantom.cpp:155
+
EB_Phantom::getRealMass
EGS_Float getRealMass(int ireg)
return (corrected) real mass for region
Definition phantom.cpp:291
+
EB_Phantom::autovol_phantom_geom_types
static const string autovol_phantom_geom_types[]
Definition phantom.h:97
+
EB_Phantom::app
EGS_Application * app
Parent application instance. Required for constructing filenames.
Definition phantom.h:78
+
EB_Phantom::sscat_score
EGS_ScoringArray * sscat_score
Tracklenth scored dose from single scattered particles.
Definition phantom.h:82
+
EB_Phantom::getRegionResults
vector< RegionResult > getRegionResults()
create a vector of RegionResult structs which can then be sorted by dose value. used for output routi...
Definition phantom.cpp:377
+
EB_Phantom::total_radiant_e
EGS_Float total_radiant_e
Definition phantom.h:89
+
EB_Phantom::setCorrectedVolume
void setCorrectedVolume(int ir, double fraction, double unc=0)
Allow user to tell phantom what the actual volume of a region is.
Definition phantom.cpp:202
+
EB_Phantom::getScoringArrays
void getScoringArrays(vector< EGS_ScoringArray * > &scores, vector< string > &types, vector< string > &descriptions)
get all active scoring arrays, their types and descriptions
Definition phantom.cpp:636
+
EB_Phantom::medIndex
string medIndex(int medium)
get medium index 1-9A-Z
Definition phantom.cpp:823
+
EB_Phantom::globalToLocal
int globalToLocal(int global_reg)
convert global region to local phantom region
Definition phantom.h:254
+
EB_Phantom::mscat_score
EGS_ScoringArray * mscat_score
Tracklenth scored dose from multiple scattered particles.
Definition phantom.h:84
+
EB_Phantom::canWrite3ddose
static bool canWrite3ddose(const string &geom_type)
function for checking whether a given geometry type can output 3ddose files
Definition phantom.cpp:180
+
EB_Phantom::outputResults
void outputResults(int top_n=20, string output_3ddose="text", string output_egsphant="text", string output_voxinfo="text", string output_volcor="text")
tell phantom to output its results.
Definition phantom.cpp:259
+
EB_Phantom::addState
int addState(istream &ifile)
Definition phantom.cpp:996
+
EB_Phantom::prim_score
EGS_ScoringArray * prim_score
Tracklenth scored dose from primary particles.
Definition phantom.h:81
+
EB_Phantom::writeEGSPhant
void writeEGSPhant(ostream &)
write actual egsphant data to file for this phantom
Definition phantom.cpp:781
+
EB_Phantom::getEGSdatScoringArrays
void getEGSdatScoringArrays(vector< EGS_ScoringArray * > &scores)
get all active scoring arrays for writing to egsdat file
Definition phantom.cpp:668
+
EB_Phantom::enableTLenScoring
void enableTLenScoring()
enableTLenScoring must be called before simulation begins if you want to score dose with tracklength ...
Definition phantom.cpp:208
+
EB_Phantom::outputDoseStats
void outputDoseStats(EGS_ScoringArray *score, string type)
write some stats about dose arrays
Definition phantom.cpp:408
+
EB_Phantom::publisher
Publisher * publisher
Definition phantom.h:93
+
EB_Phantom::cur_history
EGS_I64 cur_history
Definition phantom.h:90
+
EB_Phantom::tlen_score
EGS_ScoringArray * tlen_score
Tracklength dose scoring array.
Definition phantom.h:79
+
EB_Phantom::corrected_volumes
std::map< int, double > corrected_volumes
Corrected volume in a given region.
Definition phantom.h:95
+
EB_Phantom::outputVolumeCorrection
void outputVolumeCorrection(string format)
intialize and output write voxel volumes to file
Definition phantom.cpp:934
+
EB_Phantom::dose_scale
EGS_Float dose_scale
Definition phantom.h:87
+
EB_Phantom::output3DBounds
void output3DBounds(ostream &out)
write the phantom bounds to 3ddose file
Definition phantom.cpp:735
+
EB_Phantom::getCorrectedVolume
EGS_Float getCorrectedVolume(int ireg)
get uncorrected volume for a given region
Definition phantom.cpp:314
+
EB_Phantom::setDoseScale
void setDoseScale(EGS_Float)
set dose scaling factor for output
Definition phantom.cpp:162
+
EB_Phantom::needsUserVolumes
static bool needsUserVolumes(const string &geom_type)
function for checking whether a given geometry type requires user specified volumes
Definition phantom.cpp:166
+
EB_Phantom::writeVoxelInfo
void writeVoxelInfo(ostream &)
write voxel info file
Definition phantom.cpp:865
+
EB_Phantom::outputData
int outputData(ostream *ofile)
Definition phantom.cpp:958
+
EB_Phantom::global_regions
set< int > global_regions
the set of all global regions contained in this phantom
Definition phantom.h:291
+
EB_Phantom::getUncorrectedMass
EGS_Float getUncorrectedMass(int ireg)
return uncorrected for region
Definition phantom.cpp:298
+
EB_Phantom::nsources
int nsources
Definition phantom.h:86
+
EB_Phantom::getVolumeUncertainty
EGS_Float getVolumeUncertainty(int ireg)
get volume unc
Definition phantom.cpp:323
+
EB_Phantom::enableInteractionScoring
void enableInteractionScoring()
enableInteractionScoring must be called before simulation begins if you want to score dose with inter...
Definition phantom.cpp:215
+
EB_Phantom::avgVoxelVol
EGS_Float avgVoxelVol()
return average voxel volume
Definition phantom.cpp:855
+
EB_Phantom::edep_score
EGS_ScoringArray * edep_score
Interaction scored dose scoring array.
Definition phantom.h:80
+ +
pubsub.h
A simple pub/sub module to allow various egs_brachy classes to subscribe to particle events.
-
EB_Message
EB_Message
Definition: pubsub.h:54
- +
EB_Message
EB_Message
Definition pubsub.h:54
+
-Generated by doxygen 1.9.5 +Generated by doxygen 1.9.8
diff --git a/docs/phsp_8cpp.html b/docs/phsp_8cpp.html index 1cb311c5..9c46850e 100644 --- a/docs/phsp_8cpp.html +++ b/docs/phsp_8cpp.html @@ -3,9 +3,9 @@ - + -EGS Brachy: /Users/marc/dev/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/phsp.cpp File Reference +EGS Brachy: /Users/marc/Developer/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/phsp.cpp File Reference @@ -30,7 +30,7 @@
- + @@ -30,7 +30,7 @@ - + +
-
/Users/marc/dev/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/phsp.cpp
+
/Users/marc/Developer/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/phsp.cpp
Go to the documentation of this file.
1/*
@@ -117,14 +122,17 @@
47#include "egs_interface2.h"
48#include "iaea_header.h"
49
+
51bool dirExists(string path) {
52
53 struct stat info;
54 int res = stat(path.c_str(), &info);
55 return res == 0 && (info.st_mode & S_IFDIR);
56}
+
57
58
+
59PHSPControl::PHSPControl(EGS_Input *inp, EGS_AffineTransform *trans, EGS_AdvancedApplication *app, Publisher *pub):
60 num_written(0), transform(trans), boundary_step(1E-4) {
61
@@ -167,8 +175,10 @@
98
99 pub->subscribe(this, PARTICLE_ESCAPED_SOURCE);
100}
+
101
102
+
103short PHSPControl::getIAEAParticleType(const EGS_Particle *p) {
104
105 if (p->q == 0) {
@@ -182,7 +192,9 @@
113 egsFatal("PHSPControl::Tried to write unknown particle type\n");
114 return -1;
115}
+
116
+
117void PHSPControl::writeParticle(EGS_Particle *p) {
118
119
@@ -227,8 +239,10 @@
158 }
159
160}
+
161
162
+
163void PHSPControl::initSource() {
164
165 char *hname = new char[fname.size()+1];
@@ -249,22 +263,28 @@
180 delete[] hname;
181
182}
+
183
184
+
185void PHSPControl::update(EB_Message message, void *particle) {
186 if (message == PARTICLE_ESCAPED_SOURCE) {
187 EGS_Particle *p = static_cast<EGS_Particle *>(particle);
188 writeParticle(p);
189 }
190}
+
191
192
+
193void PHSPControl::finish(EGS_I64 n_orig_particles) {
194 IAEA_I64 n_orig = n_orig_particles;
195 iaea_set_total_original_particles(&id, &n_orig);
196}
+
197
198
+
199void PHSPControl::outputResults() {
200
201 string sep(80, '=');
@@ -286,43 +306,46 @@
217 }
218
219}
+
220
+
221void PHSPControl::destroySource() {
222 IAEA_I32 result;
223 iaea_destroy_source(&id, &result);
224}
+
225
-
PHSPControl::kill_after_scoring
bool kill_after_scoring
Set wt = 0 for particle after scoring if true.
Definition: phsp.h:82
-
PHSPControl::initSource
void initSource()
create/open new source and set extra numbers
Definition: phsp.cpp:163
-
PHSPControl::APPEND
@ APPEND
IAEA Append mode.
Definition: phsp.h:56
-
PHSPControl::WRITE
@ WRITE
IAEA Write mode.
Definition: phsp.h:55
-
PHSPControl::transform
EGS_AffineTransform * transform
Definition: phsp.h:75
-
PHSPControl::outputResults
void outputResults()
output file name and number of particles written
Definition: phsp.cpp:199
-
PHSPControl::finish
void finish(EGS_I64 n_orig_particles)
set final number of particles written and destroy source
Definition: phsp.cpp:193
-
PHSPControl::update
void update(EB_Message message, void *particle)
receive PARTICLE_ESCAPED_SOURCE message
Definition: phsp.cpp:185
-
PHSPControl::writeParticle
void writeParticle(EGS_Particle *p)
write a single particle to the phsp
Definition: phsp.cpp:117
-
PHSPControl::mode
IAEA_I32 mode
Access mode.
Definition: phsp.h:68
-
PHSPControl::print_header
bool print_header
User has requested the phsp header gets printed after run.
Definition: phsp.h:84
-
PHSPControl::getIAEAParticleType
short getIAEAParticleType(const EGS_Particle *p)
convert a particle to its IAEA Particle type
Definition: phsp.cpp:103
-
PHSPControl::ALL_TYPES
@ ALL_TYPES
Definition: phsp.h:60
-
PHSPControl::PHOTON
@ PHOTON
Definition: phsp.h:61
-
PHSPControl::ELECTRON
@ ELECTRON
Definition: phsp.h:62
-
PHSPControl::POSITRON
@ POSITRON
Definition: phsp.h:63
-
PHSPControl::destroySource
void destroySource()
destroy the source
Definition: phsp.cpp:221
-
PHSPControl::fname
string fname
root name of phsp header
Definition: phsp.h:69
-
PHSPControl::num_written
IAEA_I64 num_written
Number of particles written to phsp file.
Definition: phsp.h:72
-
PHSPControl::boundary_step
EGS_Float boundary_step
Definition: phsp.h:78
-
PHSPControl::PHSPControl
PHSPControl(EGS_Input *inp, EGS_AffineTransform *trans, EGS_AdvancedApplication *app, Publisher *pub)
PHSP Control constructor.
Definition: phsp.cpp:59
- -
Publisher::subscribe
void subscribe(Subscriber *s, EB_Message message)
Definition: pubsub.h:83
-
dirExists
bool dirExists(string path)
return true if input path is an existing directory
Definition: phsp.cpp:51
+
PHSPControl::kill_after_scoring
bool kill_after_scoring
Set wt = 0 for particle after scoring if true.
Definition phsp.h:82
+
PHSPControl::initSource
void initSource()
create/open new source and set extra numbers
Definition phsp.cpp:163
+
PHSPControl::APPEND
@ APPEND
IAEA Append mode.
Definition phsp.h:56
+
PHSPControl::WRITE
@ WRITE
IAEA Write mode.
Definition phsp.h:55
+
PHSPControl::transform
EGS_AffineTransform * transform
Definition phsp.h:75
+
PHSPControl::outputResults
void outputResults()
output file name and number of particles written
Definition phsp.cpp:199
+
PHSPControl::finish
void finish(EGS_I64 n_orig_particles)
set final number of particles written and destroy source
Definition phsp.cpp:193
+
PHSPControl::update
void update(EB_Message message, void *particle)
receive PARTICLE_ESCAPED_SOURCE message
Definition phsp.cpp:185
+
PHSPControl::writeParticle
void writeParticle(EGS_Particle *p)
write a single particle to the phsp
Definition phsp.cpp:117
+
PHSPControl::mode
IAEA_I32 mode
Access mode.
Definition phsp.h:68
+
PHSPControl::print_header
bool print_header
User has requested the phsp header gets printed after run.
Definition phsp.h:84
+
PHSPControl::getIAEAParticleType
short getIAEAParticleType(const EGS_Particle *p)
convert a particle to its IAEA Particle type
Definition phsp.cpp:103
+
PHSPControl::ALL_TYPES
@ ALL_TYPES
Definition phsp.h:60
+
PHSPControl::PHOTON
@ PHOTON
Definition phsp.h:61
+
PHSPControl::ELECTRON
@ ELECTRON
Definition phsp.h:62
+
PHSPControl::POSITRON
@ POSITRON
Definition phsp.h:63
+
PHSPControl::destroySource
void destroySource()
destroy the source
Definition phsp.cpp:221
+
PHSPControl::fname
string fname
root name of phsp header
Definition phsp.h:69
+
PHSPControl::num_written
IAEA_I64 num_written
Number of particles written to phsp file.
Definition phsp.h:72
+
PHSPControl::boundary_step
EGS_Float boundary_step
Definition phsp.h:78
+
PHSPControl::PHSPControl
PHSPControl(EGS_Input *inp, EGS_AffineTransform *trans, EGS_AdvancedApplication *app, Publisher *pub)
PHSP Control constructor.
Definition phsp.cpp:59
+ +
Publisher::subscribe
void subscribe(Subscriber *s, EB_Message message)
Definition pubsub.h:83
+
dirExists
bool dirExists(string path)
return true if input path is an existing directory
Definition phsp.cpp:51
phsp.h
Definition of the PHSPControl object.
-
EB_Message
EB_Message
Definition: pubsub.h:54
-
PARTICLE_ESCAPED_SOURCE
@ PARTICLE_ESCAPED_SOURCE
Definition: pubsub.h:61
+
EB_Message
EB_Message
Definition pubsub.h:54
+
PARTICLE_ESCAPED_SOURCE
@ PARTICLE_ESCAPED_SOURCE
Definition pubsub.h:61
-Generated by doxygen 1.9.5 +Generated by doxygen 1.9.8
diff --git a/docs/phsp_8h.html b/docs/phsp_8h.html index b0ecbe96..f907ba6e 100644 --- a/docs/phsp_8h.html +++ b/docs/phsp_8h.html @@ -3,9 +3,9 @@ - + -EGS Brachy: /Users/marc/dev/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/phsp.h File Reference +EGS Brachy: /Users/marc/Developer/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/phsp.h File Reference @@ -30,7 +30,7 @@
- + @@ -30,7 +30,7 @@ - + +
-
/Users/marc/dev/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/phsp.h
+
/Users/marc/Developer/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/phsp.h
Go to the documentation of this file.
1/*
@@ -118,14 +123,18 @@
48#include "pubsub.h"
49#include "iaea_phsp.h"
50
+
51class PHSPControl : public Subscriber {
52
+
53 enum ACCESS {
54 READ = 1,
55 WRITE = 2,
56 APPEND = 3
57 };
+
58
+
59 enum PARTICLE_TYPE {
60 ALL_TYPES = -1,
61 PHOTON = 1,
@@ -134,6 +143,7 @@
64 NEUTRON = 4,
65 PROTON = 5
66 };
+
67
68 IAEA_I32 mode;
69 string fname;
@@ -171,42 +181,43 @@
114 void update(EB_Message message, void *particle);
115
116};
+
117
- -
PHSPControl::kill_after_scoring
bool kill_after_scoring
Set wt = 0 for particle after scoring if true.
Definition: phsp.h:82
-
PHSPControl::initSource
void initSource()
create/open new source and set extra numbers
Definition: phsp.cpp:163
- -
PHSPControl::READ
@ READ
IAEA Read mode.
Definition: phsp.h:54
-
PHSPControl::APPEND
@ APPEND
IAEA Append mode.
Definition: phsp.h:56
-
PHSPControl::WRITE
@ WRITE
IAEA Write mode.
Definition: phsp.h:55
-
PHSPControl::transform
EGS_AffineTransform * transform
Definition: phsp.h:75
-
PHSPControl::outputResults
void outputResults()
output file name and number of particles written
Definition: phsp.cpp:199
-
PHSPControl::finish
void finish(EGS_I64 n_orig_particles)
set final number of particles written and destroy source
Definition: phsp.cpp:193
-
PHSPControl::update
void update(EB_Message message, void *particle)
receive PARTICLE_ESCAPED_SOURCE message
Definition: phsp.cpp:185
-
PHSPControl::writeParticle
void writeParticle(EGS_Particle *p)
write a single particle to the phsp
Definition: phsp.cpp:117
-
PHSPControl::mode
IAEA_I32 mode
Access mode.
Definition: phsp.h:68
-
PHSPControl::id
IAEA_I32 id
IAEA Source ID (just set to 1 currently)
Definition: phsp.h:70
-
PHSPControl::print_header
bool print_header
User has requested the phsp header gets printed after run.
Definition: phsp.h:84
-
PHSPControl::getIAEAParticleType
short getIAEAParticleType(const EGS_Particle *p)
convert a particle to its IAEA Particle type
Definition: phsp.cpp:103
-
PHSPControl::PARTICLE_TYPE
PARTICLE_TYPE
Definition: phsp.h:59
-
PHSPControl::PROTON
@ PROTON
Definition: phsp.h:65
-
PHSPControl::ALL_TYPES
@ ALL_TYPES
Definition: phsp.h:60
-
PHSPControl::PHOTON
@ PHOTON
Definition: phsp.h:61
-
PHSPControl::NEUTRON
@ NEUTRON
Definition: phsp.h:64
-
PHSPControl::ELECTRON
@ ELECTRON
Definition: phsp.h:62
-
PHSPControl::POSITRON
@ POSITRON
Definition: phsp.h:63
-
PHSPControl::destroySource
void destroySource()
destroy the source
Definition: phsp.cpp:221
-
PHSPControl::fname
string fname
root name of phsp header
Definition: phsp.h:69
-
PHSPControl::num_written
IAEA_I64 num_written
Number of particles written to phsp file.
Definition: phsp.h:72
-
PHSPControl::boundary_step
EGS_Float boundary_step
Definition: phsp.h:78
- - + +
PHSPControl::kill_after_scoring
bool kill_after_scoring
Set wt = 0 for particle after scoring if true.
Definition phsp.h:82
+
PHSPControl::initSource
void initSource()
create/open new source and set extra numbers
Definition phsp.cpp:163
+ +
PHSPControl::READ
@ READ
IAEA Read mode.
Definition phsp.h:54
+
PHSPControl::APPEND
@ APPEND
IAEA Append mode.
Definition phsp.h:56
+
PHSPControl::WRITE
@ WRITE
IAEA Write mode.
Definition phsp.h:55
+
PHSPControl::transform
EGS_AffineTransform * transform
Definition phsp.h:75
+
PHSPControl::outputResults
void outputResults()
output file name and number of particles written
Definition phsp.cpp:199
+
PHSPControl::finish
void finish(EGS_I64 n_orig_particles)
set final number of particles written and destroy source
Definition phsp.cpp:193
+
PHSPControl::update
void update(EB_Message message, void *particle)
receive PARTICLE_ESCAPED_SOURCE message
Definition phsp.cpp:185
+
PHSPControl::writeParticle
void writeParticle(EGS_Particle *p)
write a single particle to the phsp
Definition phsp.cpp:117
+
PHSPControl::mode
IAEA_I32 mode
Access mode.
Definition phsp.h:68
+
PHSPControl::id
IAEA_I32 id
IAEA Source ID (just set to 1 currently)
Definition phsp.h:70
+
PHSPControl::print_header
bool print_header
User has requested the phsp header gets printed after run.
Definition phsp.h:84
+
PHSPControl::getIAEAParticleType
short getIAEAParticleType(const EGS_Particle *p)
convert a particle to its IAEA Particle type
Definition phsp.cpp:103
+
PHSPControl::PARTICLE_TYPE
PARTICLE_TYPE
Definition phsp.h:59
+
PHSPControl::PROTON
@ PROTON
Definition phsp.h:65
+
PHSPControl::ALL_TYPES
@ ALL_TYPES
Definition phsp.h:60
+
PHSPControl::PHOTON
@ PHOTON
Definition phsp.h:61
+
PHSPControl::NEUTRON
@ NEUTRON
Definition phsp.h:64
+
PHSPControl::ELECTRON
@ ELECTRON
Definition phsp.h:62
+
PHSPControl::POSITRON
@ POSITRON
Definition phsp.h:63
+
PHSPControl::destroySource
void destroySource()
destroy the source
Definition phsp.cpp:221
+
PHSPControl::fname
string fname
root name of phsp header
Definition phsp.h:69
+
PHSPControl::num_written
IAEA_I64 num_written
Number of particles written to phsp file.
Definition phsp.h:72
+
PHSPControl::boundary_step
EGS_Float boundary_step
Definition phsp.h:78
+ +
pubsub.h
A simple pub/sub module to allow various egs_brachy classes to subscribe to particle events.
-
EB_Message
EB_Message
Definition: pubsub.h:54
+
EB_Message
EB_Message
Definition pubsub.h:54
-Generated by doxygen 1.9.5 +Generated by doxygen 1.9.8
diff --git a/docs/phsp__run_2____init_____8py.html b/docs/phsp__run_2____init_____8py.html index 01f012f4..21a331ac 100644 --- a/docs/phsp__run_2____init_____8py.html +++ b/docs/phsp__run_2____init_____8py.html @@ -3,9 +3,9 @@ - + -EGS Brachy: /Users/marc/dev/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/eb_tests/phsp_run/__init__.py File Reference +EGS Brachy: /Users/marc/Developer/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/eb_tests/phsp_run/__init__.py File Reference @@ -30,7 +30,7 @@
- + @@ -30,7 +30,7 @@ - + +
-Generated by doxygen 1.9.5 +Generated by doxygen 1.9.8
diff --git a/docs/phsp__run_2test_8py.html b/docs/phsp__run_2test_8py.html index a0099a90..62d6183c 100644 --- a/docs/phsp__run_2test_8py.html +++ b/docs/phsp__run_2test_8py.html @@ -3,9 +3,9 @@ - + -EGS Brachy: /Users/marc/dev/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/eb_tests/phsp_run/test.py File Reference +EGS Brachy: /Users/marc/Developer/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/eb_tests/phsp_run/test.py File Reference @@ -30,7 +30,7 @@ - + @@ -30,7 +30,7 @@ - + +
12from eb_tests.utils import (compare_3ddose_files, doses_approx_equal,
13 extract_all_doses, read3ddose)
14
-
15EGSINP = "phsp_run.egsinp"
+
15EGSINP = "phsp_run.egsinp"
16TIME_LIMIT_S_PER_MHZ = 80/2993. # s / MHz
17
18
-
19def compare_results(egslst, inp_name):
+
+
19def compare_results(egslst, inp_name):
20
21 gold_standard = os.path.join(os.path.dirname(os.path.abspath(__file__)), "phsp_run_compare.phantom.3ddose")
22 run_doses = inp_name+".phantom.3ddose"
@@ -106,11 +112,12 @@
27 actual_doses = read3ddose(run_doses)
28
29 return doses_close, actual_doses, gs_doses
-
eb_tests.utils
Definition: utils.py:1
+
+
eb_tests.utils
Definition utils.py:1
-Generated by doxygen 1.9.5 +Generated by doxygen 1.9.8
diff --git a/docs/phsp__scoring_2____init_____8py.html b/docs/phsp__scoring_2____init_____8py.html index eb591630..f81672dc 100644 --- a/docs/phsp__scoring_2____init_____8py.html +++ b/docs/phsp__scoring_2____init_____8py.html @@ -3,9 +3,9 @@ - + -EGS Brachy: /Users/marc/dev/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/eb_tests/phsp_scoring/__init__.py File Reference +EGS Brachy: /Users/marc/Developer/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/eb_tests/phsp_scoring/__init__.py File Reference @@ -30,7 +30,7 @@ - + @@ -30,7 +30,7 @@ - + +
-Generated by doxygen 1.9.5 +Generated by doxygen 1.9.8
diff --git a/docs/phsp__scoring_2test_8py.html b/docs/phsp__scoring_2test_8py.html index 757a5543..39f1e777 100644 --- a/docs/phsp__scoring_2test_8py.html +++ b/docs/phsp__scoring_2test_8py.html @@ -3,9 +3,9 @@ - + -EGS Brachy: /Users/marc/dev/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/eb_tests/phsp_scoring/test.py File Reference +EGS Brachy: /Users/marc/Developer/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/eb_tests/phsp_scoring/test.py File Reference @@ -30,7 +30,7 @@ - + @@ -30,7 +30,7 @@ - + +
10from eb_tests.iaea import IAEAPhaseSpace
11from eb_tests.utils import read_csv_spectrum, values_close
12
-
13EGSINP = "phsp_score.egsinp"
+
13EGSINP = "phsp_score.egsinp"
14TIME_LIMIT_S_PER_MHZ = 10/2993. # s / MHz
15
16SOURCE_WEIGHTS = (1., 9.)
@@ -97,7 +102,7 @@
18NHIST= 1000
19RM = 0.511
20
-
21EXPECTED = {
+
21EXPECTED = {
22 'num_e': NHIST*SOURCE_WEIGHTS[0]/sum(SOURCE_WEIGHTS),
23 'num_p': NHIST*SOURCE_WEIGHTS[1]/sum(SOURCE_WEIGHTS),
24 'max_energy': 0.05,
@@ -105,7 +110,8 @@
26}
27
28
-
29def compare_results(egslst, inp_name):
+
+
29def compare_results(egslst, inp_name):
30
31 iaea_path = "%s.phsp%s" %(inp_name, IAEAPhaseSpace.phsp_ext)
32 phsp = IAEAPhaseSpace(iaea_path)
@@ -128,14 +134,15 @@
49
50 all_correct = num_e_close and num_p_close and max_e_close and num_orig_equal
51 return all_correct, actual, EXPECTED
-
eb_tests.iaea.IAEAPhaseSpace
Definition: iaea.py:25
-
eb_tests.iaea_types
Definition: iaea_types.py:1
-
eb_tests.iaea
Definition: iaea.py:1
-
eb_tests.utils
Definition: utils.py:1
+
+
eb_tests.iaea.IAEAPhaseSpace
Definition iaea.py:25
+
eb_tests.iaea_types
Definition iaea_types.py:1
+
eb_tests.iaea
Definition iaea.py:1
+
eb_tests.utils
Definition utils.py:1
-Generated by doxygen 1.9.5 +Generated by doxygen 1.9.8
diff --git a/docs/plus.svg b/docs/plus.svg new file mode 100644 index 00000000..07520165 --- /dev/null +++ b/docs/plus.svg @@ -0,0 +1,9 @@ + + + + + + + + + diff --git a/docs/plusd.svg b/docs/plusd.svg new file mode 100644 index 00000000..0c65bfe9 --- /dev/null +++ b/docs/plusd.svg @@ -0,0 +1,9 @@ + + + + + + + + + diff --git a/docs/pubsub_8cpp.html b/docs/pubsub_8cpp.html index 41765858..21363e0f 100644 --- a/docs/pubsub_8cpp.html +++ b/docs/pubsub_8cpp.html @@ -3,9 +3,9 @@ - + -EGS Brachy: /Users/marc/dev/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/pubsub.cpp File Reference +EGS Brachy: /Users/marc/Developer/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/pubsub.cpp File Reference @@ -30,7 +30,7 @@ - + @@ -30,7 +30,7 @@ - + +
-
/Users/marc/dev/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/pubsub.cpp
+
/Users/marc/Developer/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/pubsub.cpp
Go to the documentation of this file.
1/*
@@ -118,6 +123,7 @@
43 */
44#include "pubsub.h"
45
+
46void Publisher::notify(EB_Message message, void *what, Subscriber *s) {
47 if (notifyEnabled) {
48 list<Subscriber *>::iterator p;
@@ -129,16 +135,17 @@
54 }
55 notifyEnabled = true;
56}
-
Publisher::subscribers
map< EB_Message, list< Subscriber * > > subscribers
Definition: pubsub.h:97
-
Publisher::notifyEnabled
bool notifyEnabled
Definition: pubsub.h:98
-
Publisher::notify
void notify(EB_Message message, void *what=0, Subscriber *s=0)
Definition: pubsub.cpp:46
- +
+
Publisher::subscribers
map< EB_Message, list< Subscriber * > > subscribers
Definition pubsub.h:97
+
Publisher::notifyEnabled
bool notifyEnabled
Definition pubsub.h:98
+
Publisher::notify
void notify(EB_Message message, void *what=0, Subscriber *s=0)
Definition pubsub.cpp:46
+
pubsub.h
A simple pub/sub module to allow various egs_brachy classes to subscribe to particle events.
-
EB_Message
EB_Message
Definition: pubsub.h:54
+
EB_Message
EB_Message
Definition pubsub.h:54
-Generated by doxygen 1.9.5 +Generated by doxygen 1.9.8
diff --git a/docs/pubsub_8h.html b/docs/pubsub_8h.html index 11912d6a..586973b6 100644 --- a/docs/pubsub_8h.html +++ b/docs/pubsub_8h.html @@ -3,9 +3,9 @@ - + -EGS Brachy: /Users/marc/dev/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/pubsub.h File Reference +EGS Brachy: /Users/marc/Developer/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/pubsub.h File Reference @@ -30,7 +30,7 @@
- + @@ -30,7 +30,7 @@ - + +
-
/Users/marc/dev/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/pubsub.h
+
/Users/marc/Developer/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/pubsub.h
Go to the documentation of this file.
1/*
@@ -119,6 +124,7 @@
51using namespace std;
52class Publisher;
53
+
54enum EB_Message {
55
56 NEW_HISTORY,
@@ -133,68 +139,83 @@
65 NON_SOURCE_PHOTON_SCATTER_EVENT // scatter occuring outside source
66
67};
+
68
69typedef pair<bool, EB_Message> EBSendMessage;
70
+
71class Subscriber {
72public:
73 virtual ~Subscriber() {}
74 virtual void update(EB_Message message, void *what = 0) = 0;
75};
+
76
+
77class Publisher {
78public:
+
79 Publisher() {
80 notifyEnabled = true;
81 }
+
82 virtual ~Publisher() { }
+
83 void subscribe(Subscriber *s, EB_Message message) {
84 subscribers[message].push_back(s);
85 }
+
+
86 void unsubscribe(Subscriber *s, EB_Message message) {
87 subscribers[message].remove(s);
88 }
+
89 void notify(EB_Message message, void *what = 0, Subscriber *s = 0);
+
90 void setNotifyEnabled(bool flag) {
91 notifyEnabled = flag;
92 }
+
+
93 bool getNotifyEnabled() const {
94 return notifyEnabled;
95 }
+
96private:
97 map<EB_Message, list<Subscriber *> > subscribers;
98 bool notifyEnabled;
99};
+
100#endif
- -
Publisher::setNotifyEnabled
void setNotifyEnabled(bool flag)
Definition: pubsub.h:90
-
Publisher::subscribe
void subscribe(Subscriber *s, EB_Message message)
Definition: pubsub.h:83
-
Publisher::subscribers
map< EB_Message, list< Subscriber * > > subscribers
Definition: pubsub.h:97
-
Publisher::Publisher
Publisher()
Definition: pubsub.h:79
-
Publisher::unsubscribe
void unsubscribe(Subscriber *s, EB_Message message)
Definition: pubsub.h:86
-
Publisher::getNotifyEnabled
bool getNotifyEnabled() const
Definition: pubsub.h:93
-
Publisher::~Publisher
virtual ~Publisher()
Definition: pubsub.h:82
-
Publisher::notifyEnabled
bool notifyEnabled
Definition: pubsub.h:98
-
Publisher::notify
void notify(EB_Message message, void *what=0, Subscriber *s=0)
Definition: pubsub.cpp:46
- -
Subscriber::~Subscriber
virtual ~Subscriber()
Definition: pubsub.h:73
+ +
Publisher::setNotifyEnabled
void setNotifyEnabled(bool flag)
Definition pubsub.h:90
+
Publisher::subscribe
void subscribe(Subscriber *s, EB_Message message)
Definition pubsub.h:83
+
Publisher::subscribers
map< EB_Message, list< Subscriber * > > subscribers
Definition pubsub.h:97
+
Publisher::Publisher
Publisher()
Definition pubsub.h:79
+
Publisher::unsubscribe
void unsubscribe(Subscriber *s, EB_Message message)
Definition pubsub.h:86
+
Publisher::getNotifyEnabled
bool getNotifyEnabled() const
Definition pubsub.h:93
+
Publisher::~Publisher
virtual ~Publisher()
Definition pubsub.h:82
+
Publisher::notifyEnabled
bool notifyEnabled
Definition pubsub.h:98
+
Publisher::notify
void notify(EB_Message message, void *what=0, Subscriber *s=0)
Definition pubsub.cpp:46
+ +
Subscriber::~Subscriber
virtual ~Subscriber()
Definition pubsub.h:73
Subscriber::update
virtual void update(EB_Message message, void *what=0)=0
-
EBSendMessage
pair< bool, EB_Message > EBSendMessage
Definition: pubsub.h:69
-
EB_Message
EB_Message
Definition: pubsub.h:54
-
PARTICLE_ESCAPING_SOURCE
@ PARTICLE_ESCAPING_SOURCE
Definition: pubsub.h:60
-
NEW_HISTORY
@ NEW_HISTORY
Definition: pubsub.h:56
-
PARTICLE_ESCAPED_SOURCE
@ PARTICLE_ESCAPED_SOURCE
Definition: pubsub.h:61
-
PARTICLE_TAKING_STEP
@ PARTICLE_TAKING_STEP
Definition: pubsub.h:58
-
NON_SOURCE_PHOTON_SCATTER_EVENT
@ NON_SOURCE_PHOTON_SCATTER_EVENT
Definition: pubsub.h:65
-
PARTICLE_ESCAPED_GEOM
@ PARTICLE_ESCAPED_GEOM
Definition: pubsub.h:63
-
PHOTON_SCATTER_EVENT
@ PHOTON_SCATTER_EVENT
Definition: pubsub.h:64
-
PARTICLE_TOOK_STEP
@ PARTICLE_TOOK_STEP
Definition: pubsub.h:59
-
PARTICLE_INITIALIZED
@ PARTICLE_INITIALIZED
Definition: pubsub.h:57
-
PARTICLE_ESCAPING_GEOM
@ PARTICLE_ESCAPING_GEOM
Definition: pubsub.h:62
+
EBSendMessage
pair< bool, EB_Message > EBSendMessage
Definition pubsub.h:69
+
EB_Message
EB_Message
Definition pubsub.h:54
+
PARTICLE_ESCAPING_SOURCE
@ PARTICLE_ESCAPING_SOURCE
Definition pubsub.h:60
+
NEW_HISTORY
@ NEW_HISTORY
Definition pubsub.h:56
+
PARTICLE_ESCAPED_SOURCE
@ PARTICLE_ESCAPED_SOURCE
Definition pubsub.h:61
+
PARTICLE_TAKING_STEP
@ PARTICLE_TAKING_STEP
Definition pubsub.h:58
+
NON_SOURCE_PHOTON_SCATTER_EVENT
@ NON_SOURCE_PHOTON_SCATTER_EVENT
Definition pubsub.h:65
+
PARTICLE_ESCAPED_GEOM
@ PARTICLE_ESCAPED_GEOM
Definition pubsub.h:63
+
PHOTON_SCATTER_EVENT
@ PHOTON_SCATTER_EVENT
Definition pubsub.h:64
+
PARTICLE_TOOK_STEP
@ PARTICLE_TOOK_STEP
Definition pubsub.h:59
+
PARTICLE_INITIALIZED
@ PARTICLE_INITIALIZED
Definition pubsub.h:57
+
PARTICLE_ESCAPING_GEOM
@ PARTICLE_ESCAPING_GEOM
Definition pubsub.h:62
-Generated by doxygen 1.9.5 +Generated by doxygen 1.9.8
diff --git a/docs/recycle_8cpp.html b/docs/recycle_8cpp.html index 77a6b41f..7747ebef 100644 --- a/docs/recycle_8cpp.html +++ b/docs/recycle_8cpp.html @@ -3,9 +3,9 @@ - + -EGS Brachy: /Users/marc/dev/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/recycle.cpp File Reference +EGS Brachy: /Users/marc/Developer/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/recycle.cpp File Reference @@ -30,7 +30,7 @@
- + @@ -30,7 +30,7 @@ - + +
-
/Users/marc/dev/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/recycle.cpp
+
/Users/marc/Developer/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/recycle.cpp
Go to the documentation of this file.
1/*
@@ -113,6 +118,7 @@
38
43#include "recycle.h"
44
+
45RecycleOpts::RecycleOpts(EGS_Input *inp) {
46
47 if (!inp) {
@@ -135,23 +141,26 @@
64
65
66}
+
67
+
68void RecycleOpts::printInfo() {
69
70 egsInformation(" Number of times to recycle particles = %d\n", nrecycle);
71 egsInformation(" Rotate recycled particles = %s\n", rotate ? "yes" : "no");
72
73}
+
74
-
RecycleOpts::nrecycle
int nrecycle
Definition: recycle.h:71
-
RecycleOpts::rotate
bool rotate
Definition: recycle.h:72
-
RecycleOpts::printInfo
void printInfo()
Definition: recycle.cpp:68
-
RecycleOpts::RecycleOpts
RecycleOpts(EGS_Input *inp)
Definition: recycle.cpp:45
+
RecycleOpts::nrecycle
int nrecycle
Definition recycle.h:71
+
RecycleOpts::rotate
bool rotate
Definition recycle.h:72
+
RecycleOpts::printInfo
void printInfo()
Definition recycle.cpp:68
+
RecycleOpts::RecycleOpts
RecycleOpts(EGS_Input *inp)
Definition recycle.cpp:45
recycle.h
class definitions for recycling
-Generated by doxygen 1.9.5 +Generated by doxygen 1.9.8
diff --git a/docs/recycle_8h.html b/docs/recycle_8h.html index 7353becf..db8d057f 100644 --- a/docs/recycle_8h.html +++ b/docs/recycle_8h.html @@ -3,9 +3,9 @@ - + -EGS Brachy: /Users/marc/dev/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/recycle.h File Reference +EGS Brachy: /Users/marc/Developer/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/recycle.h File Reference @@ -30,7 +30,7 @@
- + @@ -30,7 +30,7 @@ - + +
-
/Users/marc/dev/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/recycle.h
+
/Users/marc/Developer/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/recycle.h
Go to the documentation of this file.
1/*
@@ -132,6 +137,7 @@
61#include "latch.h"
62
63
+
64class RecycleOpts {
65
66
@@ -145,19 +151,20 @@
74 void printInfo();
75
76};
+
77
78#endif
- -
RecycleOpts::nrecycle
int nrecycle
Definition: recycle.h:71
-
RecycleOpts::rotate
bool rotate
Definition: recycle.h:72
-
RecycleOpts::printInfo
void printInfo()
Definition: recycle.cpp:68
+ +
RecycleOpts::nrecycle
int nrecycle
Definition recycle.h:71
+
RecycleOpts::rotate
bool rotate
Definition recycle.h:72
+
RecycleOpts::printInfo
void printInfo()
Definition recycle.cpp:68
ginfo.h
ginfo contains classes for organizing information about the geometries present in an egs_brachy simul...
latch.h
handle particles latch bits for egs_brachy
pubsub.h
A simple pub/sub module to allow various egs_brachy classes to subscribe to particle events.
-Generated by doxygen 1.9.5 +Generated by doxygen 1.9.8
diff --git a/docs/recycling_2____init_____8py.html b/docs/recycling_2____init_____8py.html index ecdcf5da..5f9c2683 100644 --- a/docs/recycling_2____init_____8py.html +++ b/docs/recycling_2____init_____8py.html @@ -3,9 +3,9 @@ - + -EGS Brachy: /Users/marc/dev/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/eb_tests/recycling/__init__.py File Reference +EGS Brachy: /Users/marc/Developer/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/eb_tests/recycling/__init__.py File Reference @@ -30,7 +30,7 @@
- + @@ -30,7 +30,7 @@ - + +
-Generated by doxygen 1.9.5 +Generated by doxygen 1.9.8
diff --git a/docs/recycling_2test_8py.html b/docs/recycling_2test_8py.html index f934293d..c5cec307 100644 --- a/docs/recycling_2test_8py.html +++ b/docs/recycling_2test_8py.html @@ -3,9 +3,9 @@ - + -EGS Brachy: /Users/marc/dev/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/eb_tests/recycling/test.py File Reference +EGS Brachy: /Users/marc/Developer/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/eb_tests/recycling/test.py File Reference @@ -30,7 +30,7 @@ - + @@ -30,7 +30,7 @@ - + +
12from eb_tests.utils import (compare_3ddose_files, doses_approx_equal,
13 extract_all_doses, read3ddose)
14
-
15EGSINP = "recycling.egsinp"
+
15EGSINP = "recycling.egsinp"
16TIME_LIMIT_S_PER_MHZ = 16/2993. # s / MHz
17
18
-
19def compare_results(egslst, inp_name):
+
+
19def compare_results(egslst, inp_name):
20
21 gold_standard = os.path.join(os.path.dirname(os.path.abspath(__file__)), "gold_standard.3ddose")
22 run_doses = inp_name+".phantom.3ddose"
@@ -103,11 +109,12 @@
24 doses_close = compare_3ddose_files(gold_standard, run_doses, max_percent_diff=0.01)
25
26 return doses_close, read3ddose(run_doses), read3ddose(gold_standard)
-
eb_tests.utils
Definition: utils.py:1
+
+
eb_tests.utils
Definition utils.py:1
-Generated by doxygen 1.9.5 +Generated by doxygen 1.9.8
diff --git a/docs/run__tests_8py.html b/docs/run__tests_8py.html index 8235647a..74295432 100644 --- a/docs/run__tests_8py.html +++ b/docs/run__tests_8py.html @@ -3,9 +3,9 @@ - + -EGS Brachy: /Users/marc/dev/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/run_tests.py File Reference +EGS Brachy: /Users/marc/Developer/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/run_tests.py File Reference @@ -30,7 +30,7 @@ - + @@ -30,7 +30,7 @@ - + +
-
/Users/marc/dev/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/run_tests.py
+
/Users/marc/Developer/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/run_tests.py
Go to the documentation of this file.
1import glob
@@ -86,42 +91,42 @@
11 VERBOSE = True
12 sys.argv.remove("-v")
13
-
14timing_hard_fail = "--timing-hard-fail" in sys.argv
+
14timing_hard_fail = "--timing-hard-fail" in sys.argv
15
16EGS_HOME = os.environ["EGS_HOME"]
17EGS_BRACHY = os.path.join(EGS_HOME, "egs_brachy")
18
-
19USER_CODE = "egs_brachy"
-
20TEST_EGSINP_FILE = "eb_test_run"
+
19USER_CODE = "egs_brachy"
+
20TEST_EGSINP_FILE = "eb_test_run"
21TEST_EGSINP_PATH_ROOT = os.path.join(EGS_BRACHY, TEST_EGSINP_FILE)
-
22TEST_EGSINP_PATH = TEST_EGSINP_PATH_ROOT + ".egsinp"
+
22TEST_EGSINP_PATH = TEST_EGSINP_PATH_ROOT + ".egsinp"
23
24
-
25PASS_FMT = "%(pass_fail)s - %(test)s - ran in %(actual_time).3G s/MHz (%(real_time).3G s)"
+
25PASS_FMT = "%(pass_fail)s - %(test)s - ran in %(actual_time).3G s/MHz (%(real_time).3G s)"
26
-
27TIMING_WARN_FMT = """%(pass_fail)s - %(test)s
+
27TIMING_WARN_FMT = """%(pass_fail)s - %(test)s
28 Timing: %(timing_pass_fail)s
29 Limit: %(time_limit).3G s/MHz
30 Actual : %(actual_time).3G s/MHz
31 Results: %(results_pass_fail)s
32"""
-
33
-
34FAIL_FMT = """%(pass_fail)s - %(test)s
-
35 Timing: %(timing_pass_fail)s
-
36 Limit: %(time_limit).3G s/MHz
-
37 Actual : %(actual_time).3G s/MHz
-
38 Results: %(results_pass_fail)s
-
39 Expected: %(expected_results)s
-
40 Actual : %(actual_results)s
+
33
+
34FAIL_FMT = """%(pass_fail)s - %(test)s
+
35 Timing: %(timing_pass_fail)s
+
36 Limit: %(time_limit).3G s/MHz
+
37 Actual : %(actual_time).3G s/MHz
+
38 Results: %(results_pass_fail)s
+
39 Expected: %(expected_results)s
+
40 Actual : %(actual_results)s
41"""
-
42
-
43cpu_speed_cmd = """grep -i "cpu mhz" /proc/cpuinfo | tail -1 | awk -F ":" '{print $2}'"""
-
44
-
45try:
-
46
-
47 try:
+
42
+
43cpu_speed_cmd = """grep -i "cpu mhz" /proc/cpuinfo | tail -1 | awk -F ":" '{print $2}'"""
+
44
+
45try:
+
46
+
47 try:
48 CPU_MHZ = float(os.environ["CPU_MHZ"])
-
49 source = "CPU_MHZ env variable"
+
49 source = "CPU_MHZ env variable"
50 except (ValueError, KeyError):
51 #stdin, stdout, stderr = os.popen3(cpu_speed_cmd)
52
@@ -142,7 +147,8 @@
67TIMING_MARGIN = 1.05
68
69
-
70def dyn_import(name):
+
+
70def dyn_import(name):
71 mod = __import__(name)
72 components = name.split('.')
73 for comp in components[1:]:
@@ -150,21 +156,27 @@
75 return mod
76
77
-
78def create_egsinp(test_module):
+
+
+
78def create_egsinp(test_module):
79 egsinp = test_module.EGSINP
80 path_components = test_module.__name__.split(".") + [egsinp]
81 src = os.path.join(*path_components)
82 shutil.copy(src, TEST_EGSINP_PATH)
83
84
-
85def find_cpu_time(egslst):
+
+
+
85def find_cpu_time(egslst):
86 try:
87 return float(re.findall("Finished simulation.*?CPU time:(.*?)s.*", egslst, re.S)[0])
88 except:
89 return None
90
91
-
92def run_simulation():
+
+
+
92def run_simulation():
93
94 command = "%s -i %s" % (USER_CODE, TEST_EGSINP_FILE)
95 p = Popen(command, shell=True,
@@ -175,12 +187,14 @@
100 if not isinstance(egslst, str):
101 egslst = egslst.decode("utf-8")
102 errors = errors.decode("utf-8")
-
103 cpu_time = find_cpu_time(egslst) or -1
+
103 cpu_time = find_cpu_time(egslst) or -1
104
105 return egslst, errors, cpu_time/CPU_MHZ
106
107
-
108def cleanup():
+
+
+
108def cleanup():
109 to_clean = glob.glob(TEST_EGSINP_PATH_ROOT+".*")
110 for f in to_clean:
111 # sanity check to make sure we're not deleting anything outside of this directory
@@ -193,7 +207,9 @@
118 print("{} was not deleted because of a permission error.".format(os.path.basename(f)))
119
120
-
121def find_tests():
+
+
+
121def find_tests():
122 if len(sys.argv) > 1:
123 tests = glob.glob(os.path.join(os.path.normpath(sys.argv[1]), "__init__.py"))
124 else:
@@ -202,21 +218,23 @@
127 return [x.replace(os.path.join(os.path.sep, "__init__.py"), "").replace(os.path.sep, ".") for x in tests]
128
129
-
130def run_all_tests():
+
+
+
130def run_all_tests():
131
132 pass_count = 0
133 warn_count = 0
-
134 all_tests = find_tests()
+
134 all_tests = find_tests()
135 for t in all_tests:
136
137 print(("Running test '%s'..." % (t,)))
-
138 test_module = dyn_import(t)
-
139 create_egsinp(test_module)
+
138 test_module = dyn_import(t)
+
139 create_egsinp(test_module)
140
141 time_limit = test_module.TIME_LIMIT_S_PER_MHZ
142
143 try:
-
144 egslst, errors, actual_time = run_simulation()
+
144 egslst, errors, actual_time = run_simulation()
145 if VERBOSE:
146 print(egslst)
147 print(errors)
@@ -256,24 +274,25 @@
181 "results_pass_fail": ["FAIL", "PASS"][results_pass],
182 }))
183
-
184 cleanup()
+
184 cleanup()
185
186 print(("="*80))
187 print(("Tests finished %d/%d passed with %d warnings" % (pass_count, len(all_tests), warn_count)))
188
+
189if __name__ == "__main__":
-
190 run_all_tests()
-
run_tests.find_tests
def find_tests()
Definition: run_tests.py:121
-
run_tests.run_simulation
def run_simulation()
Definition: run_tests.py:92
-
run_tests.dyn_import
def dyn_import(name)
Definition: run_tests.py:70
-
run_tests.cleanup
def cleanup()
Definition: run_tests.py:108
-
run_tests.run_all_tests
def run_all_tests()
Definition: run_tests.py:130
-
run_tests.create_egsinp
def create_egsinp(test_module)
Definition: run_tests.py:78
-
run_tests.find_cpu_time
def find_cpu_time(egslst)
Definition: run_tests.py:85
+
190 run_all_tests()
+
run_tests.dyn_import
dyn_import(name)
Definition run_tests.py:70
+
run_tests.find_cpu_time
find_cpu_time(egslst)
Definition run_tests.py:85
+
run_tests.create_egsinp
create_egsinp(test_module)
Definition run_tests.py:78
+
run_tests.run_all_tests
run_all_tests()
Definition run_tests.py:130
+
run_tests.run_simulation
run_simulation()
Definition run_tests.py:92
+
run_tests.find_tests
find_tests()
Definition run_tests.py:121
+
run_tests.cleanup
cleanup()
Definition run_tests.py:108
-Generated by doxygen 1.9.5 +Generated by doxygen 1.9.8
diff --git a/docs/scatter_2____init_____8py.html b/docs/scatter_2____init_____8py.html index 65dbb9df..865d9137 100644 --- a/docs/scatter_2____init_____8py.html +++ b/docs/scatter_2____init_____8py.html @@ -3,9 +3,9 @@ - + -EGS Brachy: /Users/marc/dev/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/eb_tests/scatter/__init__.py File Reference +EGS Brachy: /Users/marc/Developer/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/eb_tests/scatter/__init__.py File Reference @@ -30,7 +30,7 @@
- + @@ -30,7 +30,7 @@ - + +
-Generated by doxygen 1.9.5 +Generated by doxygen 1.9.8
diff --git a/docs/scatter_2test_8py.html b/docs/scatter_2test_8py.html index 1584b7b8..7c61f8d9 100644 --- a/docs/scatter_2test_8py.html +++ b/docs/scatter_2test_8py.html @@ -3,9 +3,9 @@ - + -EGS Brachy: /Users/marc/dev/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/eb_tests/scatter/test.py File Reference +EGS Brachy: /Users/marc/Developer/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/eb_tests/scatter/test.py File Reference @@ -30,7 +30,7 @@ - + @@ -30,7 +30,7 @@ - + +
12from eb_tests.utils import (doses_approx_equal, extract_all_doses, read3ddose,
13 values_close)
14
-
15EGSINP = "scatter.egsinp"
+
15EGSINP = "scatter.egsinp"
16TIME_LIMIT_S_PER_MHZ = 65/2993. # s / MHz
17NCOMPARE = 10 # only compare 10 highest doses
18
19
-
20def get_n_highest_doses(doses, uncs, n=NCOMPARE):
+
+
20def get_n_highest_doses(doses, uncs, n=NCOMPARE):
21 return list(zip(*sorted(zip(doses, uncs))))[-NCOMPARE:]
22
23
-
24def compare_results(egslst, inp_name):
+
+
+
24def compare_results(egslst, inp_name):
25 base_gold = os.path.join(os.path.dirname(os.path.abspath(__file__)), "gold%s.3ddose")
26 base_eb = inp_name+".phantom%s.3ddose"
27 extensions = ["",".to",".pr",".ss", ".ms"]
@@ -109,8 +117,8 @@
30 eb = [read3ddose(base_eb % e) for e in extensions]
31
32 for kind, actual, expected in zip(extensions, eb, gold):
-
33 act_doses, act_unc = get_n_highest_doses(actual['doses'], actual['uncs'])
-
34 act_doses, act_unc = get_n_highest_doses(expected['doses'], expected['uncs'])
+
33 act_doses, act_unc = get_n_highest_doses(actual['doses'], actual['uncs'])
+
34 act_doses, act_unc = get_n_highest_doses(expected['doses'], expected['uncs'])
35 exp_doses, exp_unc = list(zip(*sorted(zip(expected['doses'], expected['uncs']))))[:NCOMPARE]
36
37
@@ -122,12 +130,13 @@
43
44
45 return True, [], []
-
eb_tests.scatter.test.get_n_highest_doses
def get_n_highest_doses(doses, uncs, n=NCOMPARE)
Definition: test.py:20
-
eb_tests.utils
Definition: utils.py:1
+
+
eb_tests.scatter.test.get_n_highest_doses
get_n_highest_doses(doses, uncs, n=NCOMPARE)
Definition test.py:20
+
eb_tests.utils
Definition utils.py:1
-Generated by doxygen 1.9.5 +Generated by doxygen 1.9.8
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this.OnSearchSelectHide = function() { - this.hideTimeout = setTimeout(this.name +".CloseSelectionWindow()", + this.hideTimeout = setTimeout(this.CloseSelectionWindow.bind(this), this.closeSelectionTimeout); } @@ -195,6 +195,7 @@ function SearchBox(name, resultsPath, extension) } else if (e.keyCode==27) // Escape out of the search field { + e.stopPropagation(); this.DOMSearchField().blur(); this.DOMPopupSearchResultsWindow().style.display = 'none'; this.DOMSearchClose().style.display = 'none'; @@ -211,7 +212,7 @@ function SearchBox(name, resultsPath, extension) if (searchValue != "") // non-empty search { // set timer for search update - this.keyTimeout = setTimeout(this.name + '.Search()', + this.keyTimeout = setTimeout(this.Search.bind(this), this.keyTimeoutLength); } else // empty search field @@ -289,6 +290,7 @@ function SearchBox(name, resultsPath, extension) } else if (e.keyCode==13 || e.keyCode==27) { + e.stopPropagation(); this.OnSelectItem(this.searchIndex); this.CloseSelectionWindow(); this.DOMSearchField().focus(); @@ -356,7 +358,11 @@ function SearchBox(name, resultsPath, extension) document.getElementById("NoMatches").style.display="none"; } - searchResults.Search(searchValue); + if (idx!=-1) { + searchResults.Search(searchValue); + } else { // no file with search results => force empty search results + searchResults.Search('===='); + } if (domPopupSearchResultsWindow.style.display!='block') { @@ -666,6 +672,7 @@ function SearchResults(name) } else if (this.lastKey==27) // Escape { + e.stopPropagation(); searchBox.CloseResultsWindow(); document.getElementById("MSearchField").focus(); } @@ -709,6 +716,7 @@ function SearchResults(name) } else if (this.lastKey==27) // Escape { + e.stopPropagation(); searchBox.CloseResultsWindow(); document.getElementById("MSearchField").focus(); } @@ -802,6 +810,7 @@ function createResults(resultsPath) function init_search() { var results = document.getElementById("MSearchSelectWindow"); + results.tabIndex=0; for (var key in indexSectionLabels) { var link = document.createElement('a'); @@ -812,5 +821,20 @@ function init_search() results.appendChild(link); } searchBox.OnSelectItem(0); + + var input = document.getElementById("MSearchSelect"); + var searchSelectWindow = document.getElementById("MSearchSelectWindow"); + input.tabIndex=0; + input.addEventListener("keydown", function(event) { + if (event.keyCode==13 || event.keyCode==40) { + event.preventDefault(); + if (searchSelectWindow.style.display == 'block') { + searchBox.CloseSelectionWindow(); + } else { + searchBox.OnSearchSelectShow(); + searchBox.DOMSearchSelectWindow().focus(); + } + } + }); } /* @license-end */ diff --git a/docs/search/searchdata.js b/docs/search/searchdata.js index 517d6f36..fd9500f4 100644 --- a/docs/search/searchdata.js +++ b/docs/search/searchdata.js @@ -1,16 +1,16 @@ var indexSectionsWithContent = { - 0: "_abcdefghijklmnoprstuvwxyz~", + 0: "01234568_abcdefghijklmnoprstuvwxyz~", 1: 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b/docs/seeds__in__xyz_2____init_____8py.html @@ -3,9 +3,9 @@ - + -EGS Brachy: /Users/marc/dev/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/eb_tests/seeds_in_xyz/__init__.py File Reference +EGS Brachy: /Users/marc/Developer/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/eb_tests/seeds_in_xyz/__init__.py File Reference @@ -30,7 +30,7 @@ - + @@ -30,7 +30,7 @@ - + +
-Generated by doxygen 1.9.5 +Generated by doxygen 1.9.8
diff --git a/docs/seeds__in__xyz_2test_8py.html b/docs/seeds__in__xyz_2test_8py.html index 4fb62197..501ae3f7 100644 --- a/docs/seeds__in__xyz_2test_8py.html +++ b/docs/seeds__in__xyz_2test_8py.html @@ -3,9 +3,9 @@ - + -EGS Brachy: /Users/marc/dev/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/eb_tests/seeds_in_xyz/test.py File Reference +EGS Brachy: /Users/marc/Developer/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/eb_tests/seeds_in_xyz/test.py File Reference @@ -30,7 +30,7 @@ - + @@ -30,7 +30,7 @@ - + +
16from eb_tests.utils import (compare_3ddose_files, doses_approx_equal,
17 extract_all_doses, read3ddose)
18
-
19EGSINP = "seeds_in_xyz.egsinp"
+
19EGSINP = "seeds_in_xyz.egsinp"
20TIME_LIMIT_S_PER_MHZ = 25/2993. # s / MHz
21
22
-
23def compare_results(egslst, inp_name):
+
+
23def compare_results(egslst, inp_name):
24
25 gold_standard = os.path.join(os.path.dirname(os.path.abspath(__file__)), "gold_standard.3ddose")
26 run_doses = inp_name+".phantom.3ddose"
@@ -107,11 +113,12 @@
28 doses_close = compare_3ddose_files(gold_standard, run_doses, max_percent_diff=0.01)
29
30 return doses_close, read3ddose(run_doses), read3ddose(gold_standard)
-
eb_tests.utils
Definition: utils.py:1
+
+
eb_tests.utils
Definition utils.py:1
-Generated by doxygen 1.9.5 +Generated by doxygen 1.9.8
diff --git a/docs/seeds__in__xyz__genvelope_2____init_____8py.html b/docs/seeds__in__xyz__genvelope_2____init_____8py.html index 3b6a30ec..c557db62 100644 --- a/docs/seeds__in__xyz__genvelope_2____init_____8py.html +++ b/docs/seeds__in__xyz__genvelope_2____init_____8py.html @@ -3,9 +3,9 @@ - + -EGS Brachy: /Users/marc/dev/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/eb_tests/seeds_in_xyz_genvelope/__init__.py File Reference +EGS Brachy: /Users/marc/Developer/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/eb_tests/seeds_in_xyz_genvelope/__init__.py File Reference @@ -30,7 +30,7 @@ - + @@ -30,7 +30,7 @@ - + +
-Generated by doxygen 1.9.5 +Generated by doxygen 1.9.8
diff --git a/docs/seeds__in__xyz__genvelope_2test_8py.html b/docs/seeds__in__xyz__genvelope_2test_8py.html index 113be634..99549649 100644 --- a/docs/seeds__in__xyz__genvelope_2test_8py.html +++ b/docs/seeds__in__xyz__genvelope_2test_8py.html @@ -3,9 +3,9 @@ - + -EGS Brachy: /Users/marc/dev/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/eb_tests/seeds_in_xyz_genvelope/test.py File Reference +EGS Brachy: /Users/marc/Developer/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/eb_tests/seeds_in_xyz_genvelope/test.py File Reference @@ -30,7 +30,7 @@ - + @@ -30,7 +30,7 @@ - + +
12from eb_tests.utils import (compare_3ddose_files, doses_approx_equal,
13 extract_all_doses, read3ddose)
14
-
15EGSINP = "seeds_in_xyz_genvelope.egsinp"
+
15EGSINP = "seeds_in_xyz_genvelope.egsinp"
16TIME_LIMIT_S_PER_MHZ = 25/2993. # s / MHz
17
18
-
19def compare_results(egslst, inp_name):
+
+
19def compare_results(egslst, inp_name):
20
21 gold_standard = os.path.join(os.path.dirname(os.path.abspath(__file__)), "gold_standard.3ddose")
22 run_doses = inp_name+".phantom.3ddose"
@@ -103,11 +109,12 @@
24 doses_close = compare_3ddose_files(gold_standard, run_doses, max_percent_diff=0.01)
25
26 return doses_close, read3ddose(run_doses), read3ddose(gold_standard)
-
eb_tests.utils
Definition: utils.py:1
+
+
eb_tests.utils
Definition utils.py:1
-Generated by doxygen 1.9.5 +Generated by doxygen 1.9.8
diff --git a/docs/simple__dose__sph_2____init_____8py.html b/docs/simple__dose__sph_2____init_____8py.html index 54faef36..2faeb73e 100644 --- a/docs/simple__dose__sph_2____init_____8py.html +++ b/docs/simple__dose__sph_2____init_____8py.html @@ -3,9 +3,9 @@ - + -EGS Brachy: /Users/marc/dev/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/eb_tests/simple_dose_sph/__init__.py File Reference +EGS Brachy: /Users/marc/Developer/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/eb_tests/simple_dose_sph/__init__.py File Reference @@ -30,7 +30,7 @@ - + @@ -30,7 +30,7 @@ - + +
-Generated by doxygen 1.9.5 +Generated by doxygen 1.9.8
diff --git a/docs/simple__dose__sph_2test_8py.html b/docs/simple__dose__sph_2test_8py.html index 49d0e44e..9fc95637 100644 --- a/docs/simple__dose__sph_2test_8py.html +++ b/docs/simple__dose__sph_2test_8py.html @@ -3,9 +3,9 @@ - + -EGS Brachy: /Users/marc/dev/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/eb_tests/simple_dose_sph/test.py File Reference +EGS Brachy: /Users/marc/Developer/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/eb_tests/simple_dose_sph/test.py File Reference @@ -30,7 +30,7 @@ - + @@ -30,7 +30,7 @@ - + +
11
12from eb_tests.utils import doses_approx_equal, extract_all_doses
13
-
14EGSINP = "simple_dose_sph.egsinp"
+
14EGSINP = "simple_dose_sph.egsinp"
15TIME_LIMIT_S_PER_MHZ = 22/2993. # s / MHz
16
17# expected doses taken from initial run of simple_dose_sph.egsinp
18# when egs_brachy believed to be in a good state.
19# regions 1-5 (reg 0 excluded because of source overlap)
-
20expected_doses = {
+
20expected_doses = {
21 "tlen": [
22 (5.219E-12, 0.0004),
23 (1.117E-12, 0.0002),
@@ -111,7 +116,8 @@
32
33
34
-
35def compare_results(egslst, inp_name):
+
+
35def compare_results(egslst, inp_name):
36
37 actual = {
38 "tlen": [],
@@ -143,11 +149,12 @@
64 all_close = False
65
66 return all_close, actual, expected_doses
-
eb_tests.utils
Definition: utils.py:1
+
+
eb_tests.utils
Definition utils.py:1
-Generated by doxygen 1.9.5 +Generated by doxygen 1.9.8
diff --git a/docs/single__generator_2____init_____8py.html b/docs/single__generator_2____init_____8py.html index 585daa6d..3c33822e 100644 --- a/docs/single__generator_2____init_____8py.html +++ b/docs/single__generator_2____init_____8py.html @@ -3,9 +3,9 @@ - + -EGS Brachy: /Users/marc/dev/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/eb_tests/single_generator/__init__.py File Reference +EGS Brachy: /Users/marc/Developer/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/eb_tests/single_generator/__init__.py File Reference @@ -30,7 +30,7 @@ - + @@ -30,7 +30,7 @@ - + +
-Generated by doxygen 1.9.5 +Generated by doxygen 1.9.8
diff --git a/docs/single__generator_2test_8py.html b/docs/single__generator_2test_8py.html index 7c49f87d..7edfa2fa 100644 --- a/docs/single__generator_2test_8py.html +++ b/docs/single__generator_2test_8py.html @@ -3,9 +3,9 @@ - + -EGS Brachy: /Users/marc/dev/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/eb_tests/single_generator/test.py File Reference +EGS Brachy: /Users/marc/Developer/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/eb_tests/single_generator/test.py File Reference @@ -30,7 +30,7 @@ - + @@ -30,7 +30,7 @@ - + +
14from eb_tests.utils import (compare_3ddose_files, doses_approx_equal,
15 extract_all_doses, read3ddose)
16
-
17EGSINP = "single_generator.egsinp"
+
17EGSINP = "single_generator.egsinp"
18TIME_LIMIT_S_PER_MHZ = 25/2993. # s / MHz
19
20
-
21def compare_results(egslst, inp_name):
+
+
21def compare_results(egslst, inp_name):
22
23 gold_standard = os.path.join(os.path.dirname(os.path.abspath(__file__)), "gold_standard.3ddose")
24 run_doses = inp_name+".phantom.3ddose"
@@ -105,11 +111,12 @@
26 doses_close = compare_3ddose_files(gold_standard, run_doses, max_percent_diff=0.01)
27
28 return doses_close, read3ddose(run_doses), read3ddose(gold_standard)
-
eb_tests.utils
Definition: utils.py:1
+
+
eb_tests.utils
Definition utils.py:1
-Generated by doxygen 1.9.5 +Generated by doxygen 1.9.8
diff --git a/docs/sobol_8cpp.html b/docs/sobol_8cpp.html index f4e73f31..f2e5ee2a 100644 --- a/docs/sobol_8cpp.html +++ b/docs/sobol_8cpp.html @@ -3,9 +3,9 @@ - + -EGS Brachy: /Users/marc/dev/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/sobol.cpp File Reference +EGS Brachy: /Users/marc/Developer/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/sobol.cpp File Reference @@ -30,7 +30,7 @@ - + @@ -30,7 +30,7 @@ - + +
-
/Users/marc/dev/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/sobol.cpp
+
/Users/marc/Developer/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/sobol.cpp
Go to the documentation of this file.
1
@@ -90,7 +95,9 @@
21
22
23//****************************************************************************80
+
24namespace sobol {
+
25int i4_bit_hi1(int n)
26
27//****************************************************************************80
@@ -157,8 +164,10 @@
88
89 return bit;
90}
+
91//****************************************************************************80
92
+
93int i4_bit_lo0(int n)
94
95//****************************************************************************80
@@ -232,8 +241,10 @@
163
164 return bit;
165}
+
166//****************************************************************************80
167
+
168int i4_max(int i1, int i2)
169
170//****************************************************************************80
@@ -269,8 +280,10 @@
200 }
201
202}
+
203//****************************************************************************80
204
+
205int i4_min(int i1, int i2)
206
207//****************************************************************************80
@@ -306,8 +319,10 @@
237 }
238
239}
+
240//****************************************************************************80
241
+
242void i4_sobol(int dim_num, int *seed, float quasi[ ])
243
244//****************************************************************************80
@@ -13941,8 +13956,10 @@
13872# undef DIM_MAX2
13873# undef LOG_MAX
13874}
+
13875//****************************************************************************80
13876
+
13877float *i4_sobol_generate(int m, int n, int skip)
13878
13879//****************************************************************************80
@@ -13988,8 +14005,10 @@
13919
13920 return r;
13921}
+
13922//****************************************************************************80
13923
+
13924int i4_uniform(int a, int b, int *seed)
13925
13926//****************************************************************************80
@@ -14084,8 +14103,10 @@
14015
14016 return value;
14017}
+
14018//****************************************************************************80
14019
+
14020int i8_bit_hi1(long long int n)
14021
14022//****************************************************************************80
@@ -14152,8 +14173,10 @@
14083
14084 return bit;
14085}
+
14086//****************************************************************************80
14087
+
14088int i8_bit_lo0(long long int n)
14089
14090//****************************************************************************80
@@ -14227,8 +14250,10 @@
14158
14159 return bit;
14160}
+
14161//****************************************************************************80
14162
+
14163void i8_sobol(int dim_num, long long int *seed, double quasi[ ])
14164
14165//****************************************************************************80
@@ -14334,7 +14359,7 @@
14265 long long int j;
14266 long long int j2;
14267 long long int k;
-
14268 long long int l;
+
14268 long long int l = 0;
14269 static long long int lastq[DIM_MAX2];
14270 long long int m;
14271 static long long int maxcol;
@@ -27872,8 +27897,10 @@
27803# undef DIM_MAX2
27804# undef LOG_MAX
27805}
+
27806//****************************************************************************80
27807
+
27808double *i8_sobol_generate(int m, int n, int skip)
27809
27810//****************************************************************************80
@@ -27919,8 +27946,10 @@
27850
27851 return r;
27852}
+
27853//****************************************************************************80
27854
+
27855long long int i8_max(long long int i1, long long int i2)
27856
27857//****************************************************************************80
@@ -27956,8 +27985,10 @@
27887 }
27888
27889}
+
27890//****************************************************************************80
27891
+
27892long long int i8_min(long long int i1, long long int i2)
27893
27894//****************************************************************************80
@@ -27993,8 +28024,10 @@
27924 }
27925
27926}
+
27927//****************************************************************************80
27928
+
27929long long int i8_uniform(long long int a, long long int b, int *seed)
27930
27931//****************************************************************************80
@@ -28089,8 +28122,10 @@
28020
28021 return value;
28022}
+
28023//****************************************************************************80
28024
+
28025float r4_abs(float x)
28026
28027//****************************************************************************80
@@ -28128,8 +28163,10 @@
28059 }
28060 return value;
28061}
+
28062//****************************************************************************80
28063
+
28064int r4_nint(float x)
28065
28066//****************************************************************************80
@@ -28181,8 +28218,10 @@
28112
28113 return value;
28114}
+
28115//****************************************************************************80
28116
+
28117float r4_uniform_01(int *seed)
28118
28119//****************************************************************************80
@@ -28280,8 +28319,10 @@
28211
28212 return r;
28213}
+
28214//****************************************************************************80
28215
+
28216double r8_abs(double x)
28217
28218//****************************************************************************80
@@ -28319,8 +28360,10 @@
28250 }
28251 return value;
28252}
+
28253//****************************************************************************80
28254
+
28255int r8_nint(double x)
28256
28257//****************************************************************************80
@@ -28372,8 +28415,10 @@
28303
28304 return value;
28305}
+
28306//****************************************************************************80
28307
+
28308double r8_uniform_01(int *seed)
28309
28310//****************************************************************************80
@@ -28471,8 +28516,10 @@
28402
28403 return r;
28404}
+
28405//****************************************************************************80
28406
+
28407void r8mat_write(string output_filename, int m, int n, double table[])
28408
28409//****************************************************************************80
@@ -28538,8 +28585,10 @@
28469
28470 return;
28471}
+
28472//****************************************************************************80
28473
+
28474int tau_sobol(int dim_num)
28475
28476//****************************************************************************80
@@ -28636,32 +28685,34 @@
28567
28568# undef DIM_MAX
28569}
+
28570}
+
28571//****************************************************************************80
28572
-
sobol
Definition: sobol.cpp:24
-
sobol::i8_uniform
long long int i8_uniform(long long int a, long long int b, int *seed)
Definition: sobol.cpp:27929
-
sobol::r8_uniform_01
double r8_uniform_01(int *seed)
Definition: sobol.cpp:28308
-
sobol::i4_min
int i4_min(int i1, int i2)
Definition: sobol.cpp:205
-
sobol::i4_uniform
int i4_uniform(int a, int b, int *seed)
Definition: sobol.cpp:13924
-
sobol::i8_sobol
void i8_sobol(int dim_num, long long int *seed, double quasi[])
Definition: sobol.cpp:14163
-
sobol::i4_bit_hi1
int i4_bit_hi1(int n)
Definition: sobol.cpp:25
-
sobol::r4_uniform_01
float r4_uniform_01(int *seed)
Definition: sobol.cpp:28117
-
sobol::i4_max
int i4_max(int i1, int i2)
Definition: sobol.cpp:168
-
sobol::i4_sobol
void i4_sobol(int dim_num, int *seed, float quasi[])
Definition: sobol.cpp:242
-
sobol::i4_bit_lo0
int i4_bit_lo0(int n)
Definition: sobol.cpp:93
-
sobol::r4_abs
float r4_abs(float x)
Definition: sobol.cpp:28025
-
sobol::r8mat_write
void r8mat_write(string output_filename, int m, int n, double table[])
Definition: sobol.cpp:28407
-
sobol::r4_nint
int r4_nint(float x)
Definition: sobol.cpp:28064
-
sobol::r8_nint
int r8_nint(double x)
Definition: sobol.cpp:28255
-
sobol::i8_bit_lo0
int i8_bit_lo0(long long int n)
Definition: sobol.cpp:14088
-
sobol::i8_max
long long int i8_max(long long int i1, long long int i2)
Definition: sobol.cpp:27855
-
sobol::i8_bit_hi1
int i8_bit_hi1(long long int n)
Definition: sobol.cpp:14020
-
sobol::i8_sobol_generate
double * i8_sobol_generate(int m, int n, int skip)
Definition: sobol.cpp:27808
-
sobol::tau_sobol
int tau_sobol(int dim_num)
Definition: sobol.cpp:28474
-
sobol::i4_sobol_generate
float * i4_sobol_generate(int m, int n, int skip)
Definition: sobol.cpp:13877
-
sobol::i8_min
long long int i8_min(long long int i1, long long int i2)
Definition: sobol.cpp:27892
-
sobol::r8_abs
double r8_abs(double x)
Definition: sobol.cpp:28216
+ +
sobol::i8_uniform
long long int i8_uniform(long long int a, long long int b, int *seed)
Definition sobol.cpp:27929
+
sobol::r8_uniform_01
double r8_uniform_01(int *seed)
Definition sobol.cpp:28308
+
sobol::i4_min
int i4_min(int i1, int i2)
Definition sobol.cpp:205
+
sobol::i4_uniform
int i4_uniform(int a, int b, int *seed)
Definition sobol.cpp:13924
+
sobol::i8_sobol
void i8_sobol(int dim_num, long long int *seed, double quasi[])
Definition sobol.cpp:14163
+
sobol::i4_bit_hi1
int i4_bit_hi1(int n)
Definition sobol.cpp:25
+
sobol::r4_uniform_01
float r4_uniform_01(int *seed)
Definition sobol.cpp:28117
+
sobol::i4_max
int i4_max(int i1, int i2)
Definition sobol.cpp:168
+
sobol::i4_sobol
void i4_sobol(int dim_num, int *seed, float quasi[])
Definition sobol.cpp:242
+
sobol::i4_bit_lo0
int i4_bit_lo0(int n)
Definition sobol.cpp:93
+
sobol::r4_abs
float r4_abs(float x)
Definition sobol.cpp:28025
+
sobol::r8mat_write
void r8mat_write(string output_filename, int m, int n, double table[])
Definition sobol.cpp:28407
+
sobol::r4_nint
int r4_nint(float x)
Definition sobol.cpp:28064
+
sobol::r8_nint
int r8_nint(double x)
Definition sobol.cpp:28255
+
sobol::i8_bit_lo0
int i8_bit_lo0(long long int n)
Definition sobol.cpp:14088
+
sobol::i8_max
long long int i8_max(long long int i1, long long int i2)
Definition sobol.cpp:27855
+
sobol::i8_bit_hi1
int i8_bit_hi1(long long int n)
Definition sobol.cpp:14020
+
sobol::i8_sobol_generate
double * i8_sobol_generate(int m, int n, int skip)
Definition sobol.cpp:27808
+
sobol::tau_sobol
int tau_sobol(int dim_num)
Definition sobol.cpp:28474
+
sobol::i4_sobol_generate
float * i4_sobol_generate(int m, int n, int skip)
Definition sobol.cpp:13877
+
sobol::i8_min
long long int i8_min(long long int i1, long long int i2)
Definition sobol.cpp:27892
+
sobol::r8_abs
double r8_abs(double x)
Definition sobol.cpp:28216
DIM_MAX2
#define DIM_MAX2
DIM_MAX
#define DIM_MAX
LOG_MAX
#define LOG_MAX
@@ -28669,7 +28720,7 @@
-Generated by doxygen 1.9.5 +Generated by doxygen 1.9.8
diff --git a/docs/sobol_8h.html b/docs/sobol_8h.html index 1987c605..d78cd4da 100644 --- a/docs/sobol_8h.html +++ b/docs/sobol_8h.html @@ -3,9 +3,9 @@ - + -EGS Brachy: /Users/marc/dev/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/sobol.h File Reference +EGS Brachy: /Users/marc/Developer/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/sobol.h File Reference @@ -30,7 +30,7 @@
- + @@ -30,7 +30,7 @@ - + +
-
/Users/marc/dev/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/sobol.h
+
/Users/marc/Developer/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/sobol.h
Go to the documentation of this file.
1
@@ -89,8 +94,8 @@
20#else
21
22 #ifdef HAVE_VISIBILITY
-
23 #define AE_SOBOL_EXPORT __attribute__ ((visibility ("default")))
-
24 #define AE_SOBOL_LOCAL __attribute__ ((visibility ("hidden")))
+
23 #define AE_SOBOL_EXPORT __attribute__ ((visibility ("default")))
+
24 #define AE_SOBOL_LOCAL __attribute__ ((visibility ("hidden")))
25 #else
26 #define AE_SOBOL_EXPORT
27 #define AE_SOBOL_LOCAL
@@ -137,33 +142,33 @@
68
69
70#endif
-
sobol
Definition: sobol.cpp:24
-
sobol::i8_uniform
long long int i8_uniform(long long int a, long long int b, int *seed)
Definition: sobol.cpp:27929
-
sobol::r8_uniform_01
double r8_uniform_01(int *seed)
Definition: sobol.cpp:28308
-
sobol::i4_min
int i4_min(int i1, int i2)
Definition: sobol.cpp:205
-
sobol::i4_uniform
int i4_uniform(int a, int b, int *seed)
Definition: sobol.cpp:13924
-
sobol::i8_sobol
void i8_sobol(int dim_num, long long int *seed, double quasi[])
Definition: sobol.cpp:14163
-
sobol::i4_bit_hi1
int i4_bit_hi1(int n)
Definition: sobol.cpp:25
-
sobol::r4_uniform_01
float r4_uniform_01(int *seed)
Definition: sobol.cpp:28117
-
sobol::i4_max
int i4_max(int i1, int i2)
Definition: sobol.cpp:168
-
sobol::i4_sobol
void i4_sobol(int dim_num, int *seed, float quasi[])
Definition: sobol.cpp:242
-
sobol::i4_bit_lo0
int i4_bit_lo0(int n)
Definition: sobol.cpp:93
-
sobol::r4_abs
float r4_abs(float x)
Definition: sobol.cpp:28025
-
sobol::r8mat_write
void r8mat_write(string output_filename, int m, int n, double table[])
Definition: sobol.cpp:28407
-
sobol::r4_nint
int r4_nint(float x)
Definition: sobol.cpp:28064
-
sobol::r8_nint
int r8_nint(double x)
Definition: sobol.cpp:28255
-
sobol::i8_bit_lo0
int i8_bit_lo0(long long int n)
Definition: sobol.cpp:14088
-
sobol::i8_max
long long int i8_max(long long int i1, long long int i2)
Definition: sobol.cpp:27855
-
sobol::i8_bit_hi1
int i8_bit_hi1(long long int n)
Definition: sobol.cpp:14020
-
sobol::i8_sobol_generate
double * i8_sobol_generate(int m, int n, int skip)
Definition: sobol.cpp:27808
-
sobol::tau_sobol
int tau_sobol(int dim_num)
Definition: sobol.cpp:28474
-
sobol::i4_sobol_generate
float * i4_sobol_generate(int m, int n, int skip)
Definition: sobol.cpp:13877
-
sobol::i8_min
long long int i8_min(long long int i1, long long int i2)
Definition: sobol.cpp:27892
-
sobol::r8_abs
double r8_abs(double x)
Definition: sobol.cpp:28216
+ +
sobol::i8_uniform
long long int i8_uniform(long long int a, long long int b, int *seed)
Definition sobol.cpp:27929
+
sobol::r8_uniform_01
double r8_uniform_01(int *seed)
Definition sobol.cpp:28308
+
sobol::i4_min
int i4_min(int i1, int i2)
Definition sobol.cpp:205
+
sobol::i4_uniform
int i4_uniform(int a, int b, int *seed)
Definition sobol.cpp:13924
+
sobol::i8_sobol
void i8_sobol(int dim_num, long long int *seed, double quasi[])
Definition sobol.cpp:14163
+
sobol::i4_bit_hi1
int i4_bit_hi1(int n)
Definition sobol.cpp:25
+
sobol::r4_uniform_01
float r4_uniform_01(int *seed)
Definition sobol.cpp:28117
+
sobol::i4_max
int i4_max(int i1, int i2)
Definition sobol.cpp:168
+
sobol::i4_sobol
void i4_sobol(int dim_num, int *seed, float quasi[])
Definition sobol.cpp:242
+
sobol::i4_bit_lo0
int i4_bit_lo0(int n)
Definition sobol.cpp:93
+
sobol::r4_abs
float r4_abs(float x)
Definition sobol.cpp:28025
+
sobol::r8mat_write
void r8mat_write(string output_filename, int m, int n, double table[])
Definition sobol.cpp:28407
+
sobol::r4_nint
int r4_nint(float x)
Definition sobol.cpp:28064
+
sobol::r8_nint
int r8_nint(double x)
Definition sobol.cpp:28255
+
sobol::i8_bit_lo0
int i8_bit_lo0(long long int n)
Definition sobol.cpp:14088
+
sobol::i8_max
long long int i8_max(long long int i1, long long int i2)
Definition sobol.cpp:27855
+
sobol::i8_bit_hi1
int i8_bit_hi1(long long int n)
Definition sobol.cpp:14020
+
sobol::i8_sobol_generate
double * i8_sobol_generate(int m, int n, int skip)
Definition sobol.cpp:27808
+
sobol::tau_sobol
int tau_sobol(int dim_num)
Definition sobol.cpp:28474
+
sobol::i4_sobol_generate
float * i4_sobol_generate(int m, int n, int skip)
Definition sobol.cpp:13877
+
sobol::i8_min
long long int i8_min(long long int i1, long long int i2)
Definition sobol.cpp:27892
+
sobol::r8_abs
double r8_abs(double x)
Definition sobol.cpp:28216
-Generated by doxygen 1.9.5 +Generated by doxygen 1.9.8
diff --git a/docs/source__energies_2____init_____8py.html b/docs/source__energies_2____init_____8py.html index f789cda4..e2e400f7 100644 --- a/docs/source__energies_2____init_____8py.html +++ b/docs/source__energies_2____init_____8py.html @@ -3,9 +3,9 @@ - + -EGS Brachy: /Users/marc/dev/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/eb_tests/source_energies/__init__.py File Reference +EGS Brachy: /Users/marc/Developer/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/eb_tests/source_energies/__init__.py File Reference @@ -30,7 +30,7 @@
- + @@ -30,7 +30,7 @@ - + +
-Generated by doxygen 1.9.5 +Generated by doxygen 1.9.8
diff --git a/docs/source__energies_2test_8py.html b/docs/source__energies_2test_8py.html index 0cfef6a0..be848157 100644 --- a/docs/source__energies_2test_8py.html +++ b/docs/source__energies_2test_8py.html @@ -3,9 +3,9 @@ - + -EGS Brachy: /Users/marc/dev/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/eb_tests/source_energies/test.py File Reference +EGS Brachy: /Users/marc/Developer/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/eb_tests/source_energies/test.py File Reference @@ -30,7 +30,7 @@ - + @@ -30,7 +30,7 @@ - + +
11
12from eb_tests.utils import values_close
13
-
14EGSINP = "source_energies.egsinp"
+
14EGSINP = "source_energies.egsinp"
15TIME_LIMIT_S_PER_MHZ = 2/2993. # s / MHz
16
-
17expected_results = {
+
17expected_results = {
18 'initialized': 1135.1,
19 'escaping_source': 898.8,
20 'escaping_geom': 702.01,
21}
22
23
-
24def compare_results(egslst, inp_name):
+
+
24def compare_results(egslst, inp_name):
25
26
27 actual_results = {
@@ -117,11 +123,12 @@
38
39
40 return all_good, actual_results, expected_results
-
eb_tests.utils
Definition: utils.py:1
+
+
eb_tests.utils
Definition utils.py:1
-Generated by doxygen 1.9.5 +Generated by doxygen 1.9.8
diff --git a/docs/sources_2README_8md.html b/docs/sources_2README_8md.html index 64ff4465..8a9ab0b5 100644 --- a/docs/sources_2README_8md.html +++ b/docs/sources_2README_8md.html @@ -3,9 +3,9 @@ - + -EGS Brachy: /Users/marc/dev/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/lib/geometry/sources/README.md File Reference +EGS Brachy: /Users/marc/Developer/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/lib/geometry/sources/README.md File Reference @@ -30,7 +30,7 @@ - + @@ -30,7 +30,7 @@ - + @@ -30,7 +30,7 @@ - + +
-Generated by doxygen 1.9.5 +Generated by doxygen 1.9.8
diff --git a/docs/spec__absolute_2test_8py.html b/docs/spec__absolute_2test_8py.html index 048c3264..26bd7784 100644 --- a/docs/spec__absolute_2test_8py.html +++ b/docs/spec__absolute_2test_8py.html @@ -3,9 +3,9 @@ - + -EGS Brachy: /Users/marc/dev/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/eb_tests/spec_absolute/test.py File Reference +EGS Brachy: /Users/marc/Developer/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/eb_tests/spec_absolute/test.py File Reference @@ -30,7 +30,7 @@ - + @@ -30,7 +30,7 @@ - + +
12
13from eb_tests.utils import read_csv_spectrum, values_close
14
-
15EGSINP = "spec_absolute.egsinp"
+
15EGSINP = "spec_absolute.egsinp"
16TIME_LIMIT_S_PER_MHZ = 6/2993. # s / MHz
17
18EMIN, EMAX = 0.015, 0.025
19
-
20def expected(e):
+
+
20def expected(e):
21 if EMIN <= e <= EMAX:
22 return 1./(EMAX-EMIN)
23 return 0
24
-
25def compare_results(egslst, inp_name):
+
+
+
25def compare_results(egslst, inp_name):
26
27 energies, counts, uncs = read_csv_spectrum(inp_name+".surfcount.csv")
28
29 for e, c in zip(energies, counts):
-
30 exp = expected(e)
+
30 exp = expected(e)
31 if not values_close(c, exp, 0.005):
32 return False, "Count at %f=%f" %(e, c), "Expected %f" % exp
33
34 return True, [], []
-
eb_tests.spec_absolute.test.expected
def expected(e)
Definition: test.py:20
-
eb_tests.utils
Definition: utils.py:1
+
+
eb_tests.spec_absolute.test.expected
expected(e)
Definition test.py:20
+
eb_tests.utils
Definition utils.py:1
-Generated by doxygen 1.9.5 +Generated by doxygen 1.9.8
diff --git a/docs/spec__eflu_2____init_____8py.html b/docs/spec__eflu_2____init_____8py.html index 688cfa74..6c89df2d 100644 --- a/docs/spec__eflu_2____init_____8py.html +++ b/docs/spec__eflu_2____init_____8py.html @@ -3,9 +3,9 @@ - + -EGS Brachy: /Users/marc/dev/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/eb_tests/spec_eflu/__init__.py File Reference +EGS Brachy: /Users/marc/Developer/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/eb_tests/spec_eflu/__init__.py File Reference @@ -30,7 +30,7 @@ - + @@ -30,7 +30,7 @@ - + +
-Generated by doxygen 1.9.5 +Generated by doxygen 1.9.8
diff --git a/docs/spec__eflu_2test_8py.html b/docs/spec__eflu_2test_8py.html index e0820380..77017b54 100644 --- a/docs/spec__eflu_2test_8py.html +++ b/docs/spec__eflu_2test_8py.html @@ -3,9 +3,9 @@ - + -EGS Brachy: /Users/marc/dev/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/eb_tests/spec_eflu/test.py File Reference +EGS Brachy: /Users/marc/Developer/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/eb_tests/spec_eflu/test.py File Reference @@ -30,7 +30,7 @@ - + @@ -30,7 +30,7 @@ - + +
12
13from eb_tests.utils import read_csv_spectrum, values_close
14
-
15EGSINP = "spec_eflu.egsinp"
+
15EGSINP = "spec_eflu.egsinp"
16TIME_LIMIT_S_PER_MHZ = 6/2993. # s / MHz
17
18EMIN, EMAX = 0.015, 0.025
@@ -106,27 +111,31 @@
27SCORED_IN_BIN = NHIST/N_BINS_IN_RANGE
28SCORED_IN_BIN_PER_MEV = SCORED_IN_BIN / BIN_WIDTH
29
-
30def expected(e):
+
+
30def expected(e):
31 if EMIN <= e <= EMAX:
32 return e*SCORED_IN_BIN_PER_MEV / TOTAL_E
33 return 0
34
-
35def compare_results(egslst, inp_name):
+
+
+
35def compare_results(egslst, inp_name):
36
37 energies, counts, uncs = read_csv_spectrum(inp_name+".ewsurf.csv")
38
39 for e, c in zip(energies, counts):
-
40 exp = expected(e)
+
40 exp = expected(e)
41 if (exp > 0 and not values_close(c, exp, 0.005)) or (exp == 0 and c > 0.0001):
42 return False, "Fluence at E = %f MeV was %f" %(e, c), "Expected %f" % exp
43
44 return True, [], []
-
eb_tests.spec_eflu.test.expected
def expected(e)
Definition: test.py:30
-
eb_tests.utils
Definition: utils.py:1
+
+
eb_tests.spec_eflu.test.expected
expected(e)
Definition test.py:30
+
eb_tests.utils
Definition utils.py:1
-Generated by doxygen 1.9.5 +Generated by doxygen 1.9.8
diff --git a/docs/spec__scoring_8cpp.html b/docs/spec__scoring_8cpp.html index c579a9d3..474268a1 100644 --- a/docs/spec__scoring_8cpp.html +++ b/docs/spec__scoring_8cpp.html @@ -3,9 +3,9 @@ - + -EGS Brachy: /Users/marc/dev/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/spec_scoring.cpp File Reference +EGS Brachy: /Users/marc/Developer/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/spec_scoring.cpp File Reference @@ -30,7 +30,7 @@ - + @@ -30,7 +30,7 @@ - + +
-
/Users/marc/dev/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/spec_scoring.cpp
+
/Users/marc/Developer/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/spec_scoring.cpp
Go to the documentation of this file.
1/*
@@ -115,6 +120,7 @@
44#include <fstream>
45#include <stdarg.h> // For va_start, etc.
46
+
47std::string string_format(const std::string fmt, ...) {
48 int size = ((int)fmt.size()) * 2 + 50; // Use a rubric appropriate for your code
49 std::string str;
@@ -136,7 +142,9 @@
65 }
66 return str;
67}
+
68
+
69string getFileNameFromPath(const string &s) {
70
71 char sep = '/';
@@ -152,7 +160,9 @@
81
82 return ("");
83}
+
84
+
85BaseSpectrumScorer *BaseSpectrumScorer::getSpectrumScorer(EGS_Input *inp, EGS_BaseSource *source, GeomInfo *ginfo,
86 Publisher *publisher) {
87
@@ -182,7 +192,9 @@
111 return scorer;
112
113}
+
114
+
115BaseSpectrumScorer::BaseSpectrumScorer(EGS_Input *input, EGS_BaseSource *src, GeomInfo *ginfo, Publisher *publisher) {
116
117 valid = true;
@@ -254,32 +266,44 @@
183
184 publisher->subscribe(this, NEW_HISTORY);
185}
+
186
187
+
188BaseSpectrumScorer::~BaseSpectrumScorer() {
189 if (bins) {
190 delete bins;
191 }
192}
+
193
+
194void BaseSpectrumScorer::setEffectiveHistories(EGS_Float effh) {
195 eff_history = (EGS_I64)effh;
196}
+
197
+
198int BaseSpectrumScorer::getBin(EGS_Float E) const {
199 return min(nbins-1, (int)((E - e_min)/bin_width));
200}
+
201
202
+
203EGS_Float BaseSpectrumScorer::getBinWidth() const {
204 return bin_width;
205}
+
206
+
207double BaseSpectrumScorer::getParticleEnergy(const EGS_Particle *p) const {
208 double rest_mass = p->q == 0 ? 0 : the_useful->prm;
209 return (p->E - rest_mass);
210}
+
211
+
212int BaseSpectrumScorer::outputResults(string rootname) {
213
214 string fname;
@@ -307,7 +331,9 @@
236
237 return 0;
238}
+
239
+
240string BaseSpectrumScorer::outputCSV(string rootname) {
241 ofstream out;
242 string fname = getFileName(rootname)+".csv";
@@ -323,18 +349,20 @@
252 out.close();
253 return fname;
254}
+
255
+
256string BaseSpectrumScorer::outputEGSnrc(string rootname) {
257
258 ofstream out;
259 string fname = getFileName(rootname)+".spectrum";
260 out.open(fname.c_str());
-
261 out << "egs_brachy scored spectrum"<< endl;
+
261 out << "egs_brachy scored spectrum"<< "\n";
262
263
264 if (egsnrc_mode == 0 || egsnrc_mode == 1) {
265 // egsnrc modes
-
266 out << nbins <<","<<e_min<<","<< egsnrc_mode << endl;
+
266 out << nbins <<","<<e_min<<","<< egsnrc_mode << "\n";
267
268 double top, prob, r, dr;
269 for (int i=0; i < nbins; i++) {
@@ -376,7 +404,9 @@
305
306 return fname;
307}
+
308
+
309string BaseSpectrumScorer::outputXMGR(string rootname) {
310
311 ofstream out;
@@ -433,7 +463,9 @@
362 out.close();
363 return fname;
364}
+
365
+
366void BaseSpectrumScorer::update(EB_Message message, void *data) {
367
368 if (message == NEW_HISTORY) {
@@ -444,15 +476,19 @@
373 }
374
375}
+
376
+
377void BaseSpectrumScorer::getResult(int i, EGS_Float &r, EGS_Float &dr) {
378 bins->currentResult(i, r, dr);
379}
+
380
+
381int BaseSpectrumScorer::outputData(ostream *ofile) {
382
-
383 (*ofile) << cur_history << " " << eff_history << endl;
-
384 (*ofile) << total_scored << endl;
+
383 (*ofile) << cur_history << " " << eff_history << "\n";
+
384 (*ofile) << total_scored << "\n";
385 bool ok = bins->storeState(*ofile);
386 if (!ok) {
387 return 1;
@@ -461,7 +497,9 @@
390 return 0;
391
392}
+
393
+
394int BaseSpectrumScorer::readData(istream *ifile) {
395
396 (*ifile) >> cur_history >> eff_history;
@@ -474,7 +512,9 @@
403 return 0;
404
405}
+
406
+
407void BaseSpectrumScorer::resetCounter() {
408
409 cur_history = 0;
@@ -483,7 +523,9 @@
412 bins->reset();
413
414}
+
415
+
416int BaseSpectrumScorer::addState(istream &data) {
417
418 EGS_I64 cur_history_tmp, eff_history_tmp;
@@ -504,11 +546,13 @@
433
434 return 0;
435}
+
436
437
438/*********************************************************************************
439 * Surface Count Spectrum */
440
+
441void SurfaceCountSpectrum::score(EB_Message message, void *data) {
442
443 if (message == PARTICLE_ESCAPING_SOURCE) {
@@ -523,7 +567,9 @@
452 }
453
454}
+
455
+
456void SurfaceCountSpectrum::getResult(int i, EGS_Float &r, EGS_Float &dr) {
457
458 bins->currentResult(i, r, dr);
@@ -532,18 +578,22 @@
461 dr /= norm;
462
463}
+
464
+
465void SurfaceCountSpectrum::outputTotal() {
466
467
468 egsInformation("Scoring metric : absolute photon counts on surface of source\n") ;
469 egsInformation("Total counts : %.5G \n", total_scored);
470}
+
471
472
473/*********************************************************************************
474 * Energy weighted surface spectrum */
475
+
476void EnergyWeightedSurfaceSpectrum::score(EB_Message message, void *data) {
477
478 if (message == PARTICLE_ESCAPING_SOURCE) {
@@ -558,7 +608,9 @@
487 }
488
489}
+
490
+
491void EnergyWeightedSurfaceSpectrum::getResult(int i, EGS_Float &r, EGS_Float &dr) {
492
493 bins->currentResult(i, r, dr);
@@ -567,19 +619,23 @@
496 dr /= norm;
497
498}
+
499
+
500void EnergyWeightedSurfaceSpectrum::outputTotal() {
501
502 egsInformation("Scoring metric : Energy weighted spectrum on surface of source\n") ;
503 egsInformation("Total Radiant E : %.5G MeV\n", total_scored);
504
505}
+
506
507/*********************************************************************************
508 * Fluence spectrum in Voxel */
509
510/* Note: this only works if there are no other geometries overlapping
511 * the scoring region! */
+
512void FluenceSpectrumInVoxel::score(EB_Message message, void *data) {
513
514 if (message == PARTICLE_TAKING_STEP) {
@@ -597,7 +653,9 @@
526 }
527
528}
+
529
+
530void FluenceSpectrumInVoxel::getResult(int i, EGS_Float &r, EGS_Float &dr) {
531
532 double eff_history_norm = eff_history / cur_history;
@@ -607,7 +665,9 @@
536 dr /= norm;
537
538}
+
539
+
540void FluenceSpectrumInVoxel::outputTotal() {
541
542 egsInformation("Scoring metric : Fluence in region\n") ;
@@ -617,12 +677,14 @@
546 egsInformation("Total E fluence : %.5G MeV/cm^2\n", total_scored);
547
548}
+
549
550/*********************************************************************************
551 * Energy fluence spectrum in Voxel */
552
553/* Note: this only works if there are no other geometries overlapping
554 * the scoring region! */
+
555void EnergyFluenceSpectrumInVoxel::score(EB_Message message, void *data) {
556
557 if (message == PARTICLE_TAKING_STEP) {
@@ -640,7 +702,9 @@
569 }
570
571}
+
572
+
573void EnergyFluenceSpectrumInVoxel::getResult(int i, EGS_Float &r, EGS_Float &dr) {
574
575 double eff_history_norm = eff_history / cur_history;
@@ -650,7 +714,9 @@
579 dr /= norm;
580
581}
+
582
+
583void EnergyFluenceSpectrumInVoxel::outputTotal() {
584
585 egsInformation("Scoring metric : Energy fluence in region\n") ;
@@ -660,86 +726,87 @@
589 egsInformation("Total E fluence : %.5G MeV/cm^2\n", total_scored);
590
591}
-
BaseSpectrumScorer
abstract base class for scoring spectrum information
Definition: spec_scoring.h:260
-
BaseSpectrumScorer::getSubTitle
virtual string getSubTitle() const
Definition: spec_scoring.h:296
- -
BaseSpectrumScorer::source
EGS_BaseSource * source
Definition: spec_scoring.h:273
- -
BaseSpectrumScorer::bins
EGS_ScoringArray * bins
spectrum scoring array
Definition: spec_scoring.h:345
-
BaseSpectrumScorer::readData
int readData(istream *ifile)
Definition: spec_scoring.cpp:394
- -
BaseSpectrumScorer::getParticleName
string getParticleName() const
Return name of particle we are scoring.
Definition: spec_scoring.h:321
-
BaseSpectrumScorer::getBinWidth
EGS_Float getBinWidth() const
Definition: spec_scoring.cpp:203
-
BaseSpectrumScorer::setEffectiveHistories
void setEffectiveHistories(EGS_Float effective_histories)
Definition: spec_scoring.cpp:194
-
BaseSpectrumScorer::outputCSV
string outputCSV(string filename)
output results to csv file
Definition: spec_scoring.cpp:240
-
BaseSpectrumScorer::addState
int addState(istream &data)
Definition: spec_scoring.cpp:416
- - -
BaseSpectrumScorer::nbins
int nbins
number of bins to score spectrum in
Definition: spec_scoring.h:344
-
BaseSpectrumScorer::getResult
virtual void getResult(int bin, EGS_Float &r, EGS_Float &dr)
set r & dr to result/uncertainty for given bin. Normalization can be done in this routine
Definition: spec_scoring.cpp:377
-
BaseSpectrumScorer::outputXMGR
string outputXMGR(string filename)
output results to xmgrace file
Definition: spec_scoring.cpp:309
-
BaseSpectrumScorer::getSpectrumScorer
static BaseSpectrumScorer * getSpectrumScorer(EGS_Input *inp, EGS_BaseSource *source, GeomInfo *ginfo, Publisher *publisher)
factory method for creating one of the derived spectrum scoring classes
Definition: spec_scoring.cpp:85
- -
BaseSpectrumScorer::isValid
bool isValid() const
Definition: spec_scoring.h:381
- +
+
BaseSpectrumScorer
abstract base class for scoring spectrum information
Definition spec_scoring.h:260
+
BaseSpectrumScorer::getSubTitle
virtual string getSubTitle() const
Definition spec_scoring.h:296
+ +
BaseSpectrumScorer::source
EGS_BaseSource * source
Definition spec_scoring.h:273
+ +
BaseSpectrumScorer::bins
EGS_ScoringArray * bins
spectrum scoring array
Definition spec_scoring.h:345
+
BaseSpectrumScorer::readData
int readData(istream *ifile)
Definition spec_scoring.cpp:394
+ +
BaseSpectrumScorer::getParticleName
string getParticleName() const
Return name of particle we are scoring.
Definition spec_scoring.h:321
+
BaseSpectrumScorer::getBinWidth
EGS_Float getBinWidth() const
Definition spec_scoring.cpp:203
+
BaseSpectrumScorer::setEffectiveHistories
void setEffectiveHistories(EGS_Float effective_histories)
Definition spec_scoring.cpp:194
+
BaseSpectrumScorer::outputCSV
string outputCSV(string filename)
output results to csv file
Definition spec_scoring.cpp:240
+
BaseSpectrumScorer::addState
int addState(istream &data)
Definition spec_scoring.cpp:416
+ + +
BaseSpectrumScorer::nbins
int nbins
number of bins to score spectrum in
Definition spec_scoring.h:344
+
BaseSpectrumScorer::getResult
virtual void getResult(int bin, EGS_Float &r, EGS_Float &dr)
set r & dr to result/uncertainty for given bin. Normalization can be done in this routine
Definition spec_scoring.cpp:377
+
BaseSpectrumScorer::outputXMGR
string outputXMGR(string filename)
output results to xmgrace file
Definition spec_scoring.cpp:309
+
BaseSpectrumScorer::getSpectrumScorer
static BaseSpectrumScorer * getSpectrumScorer(EGS_Input *inp, EGS_BaseSource *source, GeomInfo *ginfo, Publisher *publisher)
factory method for creating one of the derived spectrum scoring classes
Definition spec_scoring.cpp:85
+ +
BaseSpectrumScorer::isValid
bool isValid() const
Definition spec_scoring.h:381
+
BaseSpectrumScorer::score
virtual void score(EB_Message message, void *data=0)=0
-
BaseSpectrumScorer::getTitle
virtual string getTitle() const
Definition: spec_scoring.h:292
-
BaseSpectrumScorer::getBin
int getBin(EGS_Float E) const
get index of bin that that E falls in
Definition: spec_scoring.cpp:198
-
BaseSpectrumScorer::update
virtual void update(EB_Message message, void *data=0)
Receives messages from application. This method handles NEW_HISTORY messages but delegates all other ...
Definition: spec_scoring.cpp:366
-
BaseSpectrumScorer::outputTotal
virtual void outputTotal()
Definition: spec_scoring.h:334
-
BaseSpectrumScorer::BaseSpectrumScorer
BaseSpectrumScorer(EGS_Input *input, EGS_BaseSource *src, GeomInfo *ginfo, Publisher *publisher)
Definition: spec_scoring.cpp:115
-
BaseSpectrumScorer::outputData
int outputData(ostream *ofile)
Definition: spec_scoring.cpp:381
-
BaseSpectrumScorer::getFileName
string getFileName(string root) const
Definition: spec_scoring.h:308
-
BaseSpectrumScorer::~BaseSpectrumScorer
virtual ~BaseSpectrumScorer()
Definition: spec_scoring.cpp:188
-
BaseSpectrumScorer::DEFAULT_NBINS
static const int DEFAULT_NBINS
Definition: spec_scoring.h:341
-
BaseSpectrumScorer::getXAxisLabel
virtual string getXAxisLabel() const
Definition: spec_scoring.h:304
- -
BaseSpectrumScorer::e_max
EGS_Float e_max
maximum spectrum energy to score
Definition: spec_scoring.h:347
-
BaseSpectrumScorer::getYAxisLabel
virtual string getYAxisLabel() const
Definition: spec_scoring.h:300
-
BaseSpectrumScorer::getParticleEnergy
double getParticleEnergy(const EGS_Particle *p) const
Definition: spec_scoring.cpp:207
- -
BaseSpectrumScorer::outputEGSnrc
string outputEGSnrc(string filename)
output results to EGSnrc tabulated spectrum format
Definition: spec_scoring.cpp:256
-
BaseSpectrumScorer::e_min
EGS_Float e_min
minimum spectrum energy to score
Definition: spec_scoring.h:346
-
BaseSpectrumScorer::total_scored
EGS_Float total_scored
Definition: spec_scoring.h:271
-
BaseSpectrumScorer::outputResults
int outputResults(string root_name)
, write the scored spectrum to file with filename. Returns 0 on success, all other values indicate a ...
Definition: spec_scoring.cpp:212
-
EnergyFluenceSpectrumInVoxel
A class for scoring the energy fluence of particles enter a voxel of the scoring phantom geometry.
Definition: spec_scoring.h:636
- - -
EnergyFluenceSpectrumInVoxel::geometry
EGS_BaseGeometry * geometry
Definition: spec_scoring.h:638
- -
EnergyFluenceSpectrumInVoxel::score
virtual void score(EB_Message message, void *data=0)
Definition: spec_scoring.cpp:555
- -
EnergyFluenceSpectrumInVoxel::getResult
void getResult(int bin, EGS_Float &r, EGS_Float &dr)
set r & dr to result/uncertainty for given bin. Normalization can be done in this routine
Definition: spec_scoring.cpp:573
-
EnergyWeightedSurfaceSpectrum
A class for scoring the energy weighted spectrum (normalized to total radiant energy) of particles on...
Definition: spec_scoring.h:473
-
EnergyWeightedSurfaceSpectrum::getResult
void getResult(int bin, EGS_Float &r, EGS_Float &dr)
set r & dr to result/uncertainty for given bin. Normalization can be done in this routine
Definition: spec_scoring.cpp:491
-
EnergyWeightedSurfaceSpectrum::score
virtual void score(EB_Message message, void *data=0)
Definition: spec_scoring.cpp:476
- -
FluenceSpectrumInVoxel
A class for scoring the fluence of particles enter a voxel of the scoring phantom geometry.
Definition: spec_scoring.h:530
-
FluenceSpectrumInVoxel::score
virtual void score(EB_Message message, void *data=0)
Definition: spec_scoring.cpp:512
- - - -
FluenceSpectrumInVoxel::getResult
void getResult(int bin, EGS_Float &r, EGS_Float &dr)
set r & dr to result/uncertainty for given bin. Normalization can be done in this routine
Definition: spec_scoring.cpp:530
-
FluenceSpectrumInVoxel::geometry
EGS_BaseGeometry * geometry
Definition: spec_scoring.h:532
- -
GeomInfo
a container for organizing meta data about the geometries
Definition: ginfo.h:99
- -
Publisher::subscribe
void subscribe(Subscriber *s, EB_Message message)
Definition: pubsub.h:83
-
SurfaceCountSpectrum
A class for scoring a histogram of the number of particles escaping a source geometry.
Definition: spec_scoring.h:414
-
SurfaceCountSpectrum::getResult
void getResult(int bin, EGS_Float &r, EGS_Float &dr)
set r & dr to result/uncertainty for given bin. Normalization can be done in this routine
Definition: spec_scoring.cpp:456
- -
SurfaceCountSpectrum::score
virtual void score(EB_Message message, void *data=0)
Definition: spec_scoring.cpp:441
-
EB_Message
EB_Message
Definition: pubsub.h:54
-
PARTICLE_ESCAPING_SOURCE
@ PARTICLE_ESCAPING_SOURCE
Definition: pubsub.h:60
-
NEW_HISTORY
@ NEW_HISTORY
Definition: pubsub.h:56
-
PARTICLE_TAKING_STEP
@ PARTICLE_TAKING_STEP
Definition: pubsub.h:58
-
string_format
std::string string_format(const std::string fmt,...)
Definition: spec_scoring.cpp:47
-
getFileNameFromPath
string getFileNameFromPath(const string &s)
Definition: spec_scoring.cpp:69
+
BaseSpectrumScorer::getTitle
virtual string getTitle() const
Definition spec_scoring.h:292
+
BaseSpectrumScorer::getBin
int getBin(EGS_Float E) const
get index of bin that that E falls in
Definition spec_scoring.cpp:198
+
BaseSpectrumScorer::update
virtual void update(EB_Message message, void *data=0)
Receives messages from application. This method handles NEW_HISTORY messages but delegates all other ...
Definition spec_scoring.cpp:366
+
BaseSpectrumScorer::outputTotal
virtual void outputTotal()
Definition spec_scoring.h:334
+
BaseSpectrumScorer::BaseSpectrumScorer
BaseSpectrumScorer(EGS_Input *input, EGS_BaseSource *src, GeomInfo *ginfo, Publisher *publisher)
Definition spec_scoring.cpp:115
+
BaseSpectrumScorer::outputData
int outputData(ostream *ofile)
Definition spec_scoring.cpp:381
+
BaseSpectrumScorer::getFileName
string getFileName(string root) const
Definition spec_scoring.h:308
+
BaseSpectrumScorer::~BaseSpectrumScorer
virtual ~BaseSpectrumScorer()
Definition spec_scoring.cpp:188
+
BaseSpectrumScorer::DEFAULT_NBINS
static const int DEFAULT_NBINS
Definition spec_scoring.h:341
+
BaseSpectrumScorer::getXAxisLabel
virtual string getXAxisLabel() const
Definition spec_scoring.h:304
+ +
BaseSpectrumScorer::e_max
EGS_Float e_max
maximum spectrum energy to score
Definition spec_scoring.h:347
+
BaseSpectrumScorer::getYAxisLabel
virtual string getYAxisLabel() const
Definition spec_scoring.h:300
+
BaseSpectrumScorer::getParticleEnergy
double getParticleEnergy(const EGS_Particle *p) const
Definition spec_scoring.cpp:207
+ +
BaseSpectrumScorer::outputEGSnrc
string outputEGSnrc(string filename)
output results to EGSnrc tabulated spectrum format
Definition spec_scoring.cpp:256
+
BaseSpectrumScorer::e_min
EGS_Float e_min
minimum spectrum energy to score
Definition spec_scoring.h:346
+ +
BaseSpectrumScorer::outputResults
int outputResults(string root_name)
, write the scored spectrum to file with filename. Returns 0 on success, all other values indicate a ...
Definition spec_scoring.cpp:212
+
EnergyFluenceSpectrumInVoxel
A class for scoring the energy fluence of particles enter a voxel of the scoring phantom geometry.
Definition spec_scoring.h:636
+ + +
EnergyFluenceSpectrumInVoxel::geometry
EGS_BaseGeometry * geometry
Definition spec_scoring.h:638
+ +
EnergyFluenceSpectrumInVoxel::score
virtual void score(EB_Message message, void *data=0)
Definition spec_scoring.cpp:555
+ +
EnergyFluenceSpectrumInVoxel::getResult
void getResult(int bin, EGS_Float &r, EGS_Float &dr)
set r & dr to result/uncertainty for given bin. Normalization can be done in this routine
Definition spec_scoring.cpp:573
+
EnergyWeightedSurfaceSpectrum
A class for scoring the energy weighted spectrum (normalized to total radiant energy) of particles on...
Definition spec_scoring.h:473
+
EnergyWeightedSurfaceSpectrum::getResult
void getResult(int bin, EGS_Float &r, EGS_Float &dr)
set r & dr to result/uncertainty for given bin. Normalization can be done in this routine
Definition spec_scoring.cpp:491
+
EnergyWeightedSurfaceSpectrum::score
virtual void score(EB_Message message, void *data=0)
Definition spec_scoring.cpp:476
+ +
FluenceSpectrumInVoxel
A class for scoring the fluence of particles enter a voxel of the scoring phantom geometry.
Definition spec_scoring.h:530
+
FluenceSpectrumInVoxel::score
virtual void score(EB_Message message, void *data=0)
Definition spec_scoring.cpp:512
+ + + +
FluenceSpectrumInVoxel::getResult
void getResult(int bin, EGS_Float &r, EGS_Float &dr)
set r & dr to result/uncertainty for given bin. Normalization can be done in this routine
Definition spec_scoring.cpp:530
+
FluenceSpectrumInVoxel::geometry
EGS_BaseGeometry * geometry
Definition spec_scoring.h:532
+ +
GeomInfo
a container for organizing meta data about the geometries
Definition ginfo.h:99
+ +
Publisher::subscribe
void subscribe(Subscriber *s, EB_Message message)
Definition pubsub.h:83
+
SurfaceCountSpectrum
A class for scoring a histogram of the number of particles escaping a source geometry.
Definition spec_scoring.h:414
+
SurfaceCountSpectrum::getResult
void getResult(int bin, EGS_Float &r, EGS_Float &dr)
set r & dr to result/uncertainty for given bin. Normalization can be done in this routine
Definition spec_scoring.cpp:456
+ +
SurfaceCountSpectrum::score
virtual void score(EB_Message message, void *data=0)
Definition spec_scoring.cpp:441
+
EB_Message
EB_Message
Definition pubsub.h:54
+
PARTICLE_ESCAPING_SOURCE
@ PARTICLE_ESCAPING_SOURCE
Definition pubsub.h:60
+
NEW_HISTORY
@ NEW_HISTORY
Definition pubsub.h:56
+
PARTICLE_TAKING_STEP
@ PARTICLE_TAKING_STEP
Definition pubsub.h:58
+
string_format
std::string string_format(const std::string fmt,...)
Definition spec_scoring.cpp:47
+
getFileNameFromPath
string getFileNameFromPath(const string &s)
Definition spec_scoring.cpp:69
spec_scoring.h
Definition of spectrum scoring classes.
-Generated by doxygen 1.9.5 +Generated by doxygen 1.9.8
diff --git a/docs/spec__scoring_8h.html b/docs/spec__scoring_8h.html index 5e2e2e9b..573adee8 100644 --- a/docs/spec__scoring_8h.html +++ b/docs/spec__scoring_8h.html @@ -3,9 +3,9 @@ - + -EGS Brachy: /Users/marc/dev/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/spec_scoring.h File Reference +EGS Brachy: /Users/marc/Developer/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/spec_scoring.h File Reference @@ -30,7 +30,7 @@
- + @@ -30,7 +30,7 @@ - + +
-
/Users/marc/dev/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/spec_scoring.h
+
/Users/marc/Developer/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/spec_scoring.h
Go to the documentation of this file.
1/*
@@ -121,11 +126,13 @@
51#include "pubsub.h"
52
53
+
57class EnergyScoringStats : public Subscriber {
58
59 EGS_Float total_energy_initialized;
60 EGS_Float energy_escaping_sources;
64 EGS_Float energy_escaping_geom;
+
66 EGS_Float getParticleEnergy(const EGS_Particle *p, bool subtractRM=true) {
67 EGS_Float rest_mass = 0;
68 if (subtractRM && p->q != 0){
@@ -133,24 +140,32 @@
70 }
71 return (p->E - rest_mass)*p->wt;
72 }
+
73
+
75 void scoreParticleInitialized(EGS_Particle *p) {
76 /* When particle is first initialized by getNextParticle it does not
77 * include rest mass so we tell getParticleEnergy not to subtract the
78 * rest mass here. */
79 total_energy_initialized += getParticleEnergy(p, false);
80 }
+
81
+
86
+
88 void scoreParticleEscapingGeom(EGS_Particle *p) {
89 energy_escaping_geom += getParticleEnergy(p);
90 }
+
91
92public:
93
+
94 EnergyScoringStats(Publisher *publisher) :
95 total_energy_initialized(0),
96 energy_escaping_sources(0),
@@ -161,19 +176,25 @@
101 publisher->subscribe(this, PARTICLE_ESCAPING_GEOM);
102
103 };
+
104
105
+
107 void scoreEnergyInitialized(EGS_Float E) {
108 total_energy_initialized += E;
109 }
+
+
112 EGS_Float escapingSourcesRatio() {
113 if (total_energy_initialized > 0) {
114 return energy_escaping_sources/total_energy_initialized;
115 }
116 return 0;
117 };
+
118
119
+
122 EGS_Float escapingGeomRatio() {
123 if (total_energy_initialized > 0) {
124 return energy_escaping_geom/total_energy_initialized;
@@ -181,20 +202,28 @@
126
127 return 0;
128 }
+
129
+
131 EGS_Float totalEnergyInitialized() {
132 return total_energy_initialized;
133 }
+
134
+
136 EGS_Float energyEscapingSources() {
137 return energy_escaping_sources;
138 }
+
139
+
141 EGS_Float energyEscapingGeom() {
142 return energy_escaping_geom;
143 }
+
144
145
+
147 void update(EB_Message message, void *particle) {
148
149 if (message == PARTICLE_INITIALIZED) {
@@ -210,8 +239,10 @@
159 }
160
161 }
+
162
163
+
165 void outputResults() {
166
167 string sep(80, '=');
@@ -231,27 +262,35 @@
181 );
182
183 }
+
184
+
185 int outputData(ostream *ofile) {
186 (*ofile) << total_energy_initialized << " ";
187 (*ofile) << energy_escaping_sources << " ";
188 (*ofile) << energy_escaping_geom << "\n";
189 return 0;
190 };
+
191
+
192 int readData(istream *ifile) {
193 (*ifile) >> total_energy_initialized;
194 (*ifile) >> energy_escaping_sources;
195 (*ifile) >> energy_escaping_geom;
196 return 0;
197 }
+
198
+
204
+
205 int addState(istream &data) {
206 EGS_Float total_energy_initialized_tmp;
207 EGS_Float energy_escaping_sources_tmp;
@@ -267,10 +306,13 @@
217
218 return 0;
219 };
+
220
221};
+
222
223
+
260class BaseSpectrumScorer : public Subscriber {
261
262protected:
@@ -295,32 +337,45 @@
288
290 int getBin(EGS_Float E) const;
291
+
292 virtual string getTitle() const {
293 return "EGS_Brachy: spectrum";
294 }
+
295
+
296 virtual string getSubTitle() const {
297 return "";
298 }
+
299
+
300 virtual string getYAxisLabel() const {
301 return "";
302 }
+
303
+
304 virtual string getXAxisLabel() const {
305 return "E / MeV";
306 }
+
307
+
308 string getFileName(string root) const {
309 return root + "." + getFileExtension();
310 }
+
311
+
312 virtual string getFileExtension() const {
313 return "spec";
314 };
+
315
318 virtual void getResult(int bin, EGS_Float &r, EGS_Float &dr);
319
+
321 string getParticleName() const {
322
323 if (particle_type == 0) {
@@ -333,10 +388,13 @@
330
331 return "";
332 }
+
333
+
334 virtual void outputTotal() {
335 egsInformation("Total quantity scored: %.3g\n", total_scored);
336 };
+
337
338
339public:
@@ -367,13 +425,17 @@
371
374 int outputResults(string root_name);
375
+
376 virtual string getInfo() const {
377 return getTitle();
378 }
+
379
+
381 bool isValid() const {
382 return valid;
383 }
+
384
385
386 int outputData(ostream *ofile);
@@ -386,80 +448,106 @@
393
394
395};
+
396
+
414class SurfaceCountSpectrum : public BaseSpectrumScorer {
415
416
417 void getResult(int bin, EGS_Float &r, EGS_Float &dr);
418
+
419 string getTitle() const {
420 return "EGS_Brachy: " + getParticleName() + " counts on surface of source";
421 }
+
422
+
423 string getSubTitle() const {
424 return "";
425 }
+
426
+
427 string getYAxisLabel() const {
428 return "counts / total counts / MeV\\S-1";
429 }
+
430
431 void outputTotal();
432
+
433 string getFileExtension() const {
434 return fextension != "" ? fextension : "surfcount";
435 }
+
436
437public:
438
439
+
440 SurfaceCountSpectrum(EGS_Input *input, EGS_BaseSource *src, GeomInfo *ginfo, Publisher *publisher):
441 BaseSpectrumScorer(input, src, ginfo, publisher) {
442
443 publisher->subscribe(this, PARTICLE_ESCAPING_SOURCE);
444 };
+
445
446 virtual void score(EB_Message message, void *data=0);
447
448
449};
+
450
451
+
473class EnergyWeightedSurfaceSpectrum : public BaseSpectrumScorer {
474
475 void getResult(int bin, EGS_Float &r, EGS_Float &dr);
476
+
477 string getTitle() const {
478 return "EGS_Brachy: energy weighted surface " + getParticleName() + " spectrum";
479 }
+
480
+
481 string getSubTitle() const {
482 return "";
483 }
+
484
+
485 string getYAxisLabel() const {
486 return "(dR/dE)/R / MeV\\S-1";
487 }
+
488
489 void outputTotal();
490
+
491 string getFileExtension() const {
492 return fextension != "" ? fextension : "ewsurf";
493 }
+
494
495public:
496
+
497 EnergyWeightedSurfaceSpectrum(EGS_Input *input, EGS_BaseSource *src, GeomInfo *ginfo, Publisher *publisher):
498 BaseSpectrumScorer(input, src, ginfo, publisher) {
499
500 publisher->subscribe(this, PARTICLE_ESCAPING_SOURCE);
501 };
+
502
503 virtual void score(EB_Message message, void *data=0);
504
505
506};
+
507
+
530class FluenceSpectrumInVoxel : public BaseSpectrumScorer {
531
532 EGS_BaseGeometry *geometry;
@@ -470,26 +558,33 @@
537
538 void getResult(int bin, EGS_Float &r, EGS_Float &dr);
539
+
540 string getTitle() const {
541 stringstream ss;
542 ss << "EGS_Brachy: " << getParticleName() << " fluence spectrum in region ";
543 ss << local_scoring_region << " of '"<<geometry->getName()<<"'";
544 return ss.str();
545 }
+
546
+
547 string getYAxisLabel() const {
548 return "fluence / MeV / cm\\S2";
549 }
+
550
551 void outputTotal();
552
+
553 string getFileExtension() const {
554 return fextension != "" ? fextension : "voxelflu";
555 }
+
556
557public:
558
559
+
560 FluenceSpectrumInVoxel(EGS_Input *input, EGS_BaseSource *src, GeomInfo *ginfo, Publisher *publisher):
561 BaseSpectrumScorer(input, src, ginfo, publisher) {
562
@@ -535,15 +630,18 @@
602 publisher->subscribe(this, PARTICLE_TAKING_STEP);
603
604 };
+
605
606
607 virtual void score(EB_Message message, void *data=0);
608
609
610};
+
611
612
613
+
636class EnergyFluenceSpectrumInVoxel : public BaseSpectrumScorer {
637
638 EGS_BaseGeometry *geometry;
@@ -554,26 +652,33 @@
643
644 void getResult(int bin, EGS_Float &r, EGS_Float &dr);
645
+
646 string getTitle() const {
647 stringstream ss;
648 ss << "EGS_Brachy: " << getParticleName() << " energy fluence spectrum in region ";
649 ss << local_scoring_region << " of '"<<geometry->getName()<<"'";
650 return ss.str();
651 }
+
652
+
653 string getYAxisLabel() const {
654 return "fluence / MeV / cm\\S2";
655 }
+
656
657 void outputTotal();
658
+
659 string getFileExtension() const {
660 return fextension != "" ? fextension : "voxelflu";
661 }
+
662
663public:
664
665
+
666 EnergyFluenceSpectrumInVoxel(EGS_Input *input, EGS_BaseSource *src, GeomInfo *ginfo, Publisher *publisher):
667 BaseSpectrumScorer(input, src, ginfo, publisher) {
668
@@ -619,135 +724,137 @@
708 publisher->subscribe(this, PARTICLE_TAKING_STEP);
709
710 };
+
711
712
713 virtual void score(EB_Message message, void *data=0);
714
715
716};
-
BaseSpectrumScorer
abstract base class for scoring spectrum information
Definition: spec_scoring.h:260
-
BaseSpectrumScorer::getSubTitle
virtual string getSubTitle() const
Definition: spec_scoring.h:296
- -
BaseSpectrumScorer::source
EGS_BaseSource * source
Definition: spec_scoring.h:273
- -
BaseSpectrumScorer::bins
EGS_ScoringArray * bins
spectrum scoring array
Definition: spec_scoring.h:345
-
BaseSpectrumScorer::readData
int readData(istream *ifile)
Definition: spec_scoring.cpp:394
- -
BaseSpectrumScorer::getParticleName
string getParticleName() const
Return name of particle we are scoring.
Definition: spec_scoring.h:321
-
BaseSpectrumScorer::getBinWidth
EGS_Float getBinWidth() const
Definition: spec_scoring.cpp:203
-
BaseSpectrumScorer::setEffectiveHistories
void setEffectiveHistories(EGS_Float effective_histories)
Definition: spec_scoring.cpp:194
-
BaseSpectrumScorer::outputCSV
string outputCSV(string filename)
output results to csv file
Definition: spec_scoring.cpp:240
-
BaseSpectrumScorer::addState
int addState(istream &data)
Definition: spec_scoring.cpp:416
- - -
BaseSpectrumScorer::nbins
int nbins
number of bins to score spectrum in
Definition: spec_scoring.h:344
-
BaseSpectrumScorer::getResult
virtual void getResult(int bin, EGS_Float &r, EGS_Float &dr)
set r & dr to result/uncertainty for given bin. Normalization can be done in this routine
Definition: spec_scoring.cpp:377
-
BaseSpectrumScorer::outputXMGR
string outputXMGR(string filename)
output results to xmgrace file
Definition: spec_scoring.cpp:309
-
BaseSpectrumScorer::getSpectrumScorer
static BaseSpectrumScorer * getSpectrumScorer(EGS_Input *inp, EGS_BaseSource *source, GeomInfo *ginfo, Publisher *publisher)
factory method for creating one of the derived spectrum scoring classes
Definition: spec_scoring.cpp:85
- -
BaseSpectrumScorer::isValid
bool isValid() const
Definition: spec_scoring.h:381
- +
+
BaseSpectrumScorer
abstract base class for scoring spectrum information
Definition spec_scoring.h:260
+
BaseSpectrumScorer::getSubTitle
virtual string getSubTitle() const
Definition spec_scoring.h:296
+ +
BaseSpectrumScorer::source
EGS_BaseSource * source
Definition spec_scoring.h:273
+ +
BaseSpectrumScorer::bins
EGS_ScoringArray * bins
spectrum scoring array
Definition spec_scoring.h:345
+
BaseSpectrumScorer::readData
int readData(istream *ifile)
Definition spec_scoring.cpp:394
+ +
BaseSpectrumScorer::getParticleName
string getParticleName() const
Return name of particle we are scoring.
Definition spec_scoring.h:321
+
BaseSpectrumScorer::getBinWidth
EGS_Float getBinWidth() const
Definition spec_scoring.cpp:203
+
BaseSpectrumScorer::setEffectiveHistories
void setEffectiveHistories(EGS_Float effective_histories)
Definition spec_scoring.cpp:194
+
BaseSpectrumScorer::outputCSV
string outputCSV(string filename)
output results to csv file
Definition spec_scoring.cpp:240
+
BaseSpectrumScorer::addState
int addState(istream &data)
Definition spec_scoring.cpp:416
+ + +
BaseSpectrumScorer::nbins
int nbins
number of bins to score spectrum in
Definition spec_scoring.h:344
+
BaseSpectrumScorer::getResult
virtual void getResult(int bin, EGS_Float &r, EGS_Float &dr)
set r & dr to result/uncertainty for given bin. Normalization can be done in this routine
Definition spec_scoring.cpp:377
+
BaseSpectrumScorer::outputXMGR
string outputXMGR(string filename)
output results to xmgrace file
Definition spec_scoring.cpp:309
+
BaseSpectrumScorer::getSpectrumScorer
static BaseSpectrumScorer * getSpectrumScorer(EGS_Input *inp, EGS_BaseSource *source, GeomInfo *ginfo, Publisher *publisher)
factory method for creating one of the derived spectrum scoring classes
Definition spec_scoring.cpp:85
+ +
BaseSpectrumScorer::isValid
bool isValid() const
Definition spec_scoring.h:381
+
BaseSpectrumScorer::score
virtual void score(EB_Message message, void *data=0)=0
-
BaseSpectrumScorer::getTitle
virtual string getTitle() const
Definition: spec_scoring.h:292
-
BaseSpectrumScorer::getBin
int getBin(EGS_Float E) const
get index of bin that that E falls in
Definition: spec_scoring.cpp:198
-
BaseSpectrumScorer::getInfo
virtual string getInfo() const
Definition: spec_scoring.h:376
-
BaseSpectrumScorer::update
virtual void update(EB_Message message, void *data=0)
Receives messages from application. This method handles NEW_HISTORY messages but delegates all other ...
Definition: spec_scoring.cpp:366
-
BaseSpectrumScorer::outputTotal
virtual void outputTotal()
Definition: spec_scoring.h:334
-
BaseSpectrumScorer::outputData
int outputData(ostream *ofile)
Definition: spec_scoring.cpp:381
-
BaseSpectrumScorer::getFileName
string getFileName(string root) const
Definition: spec_scoring.h:308
-
BaseSpectrumScorer::~BaseSpectrumScorer
virtual ~BaseSpectrumScorer()
Definition: spec_scoring.cpp:188
-
BaseSpectrumScorer::DEFAULT_NBINS
static const int DEFAULT_NBINS
Definition: spec_scoring.h:341
-
BaseSpectrumScorer::getXAxisLabel
virtual string getXAxisLabel() const
Definition: spec_scoring.h:304
- -
BaseSpectrumScorer::e_max
EGS_Float e_max
maximum spectrum energy to score
Definition: spec_scoring.h:347
-
BaseSpectrumScorer::getYAxisLabel
virtual string getYAxisLabel() const
Definition: spec_scoring.h:300
-
BaseSpectrumScorer::getFileExtension
virtual string getFileExtension() const
Definition: spec_scoring.h:312
-
BaseSpectrumScorer::getParticleEnergy
double getParticleEnergy(const EGS_Particle *p) const
Definition: spec_scoring.cpp:207
- -
BaseSpectrumScorer::outputEGSnrc
string outputEGSnrc(string filename)
output results to EGSnrc tabulated spectrum format
Definition: spec_scoring.cpp:256
-
BaseSpectrumScorer::e_min
EGS_Float e_min
minimum spectrum energy to score
Definition: spec_scoring.h:346
-
BaseSpectrumScorer::total_scored
EGS_Float total_scored
Definition: spec_scoring.h:271
-
BaseSpectrumScorer::outputResults
int outputResults(string root_name)
, write the scored spectrum to file with filename. Returns 0 on success, all other values indicate a ...
Definition: spec_scoring.cpp:212
-
EnergyFluenceSpectrumInVoxel
A class for scoring the energy fluence of particles enter a voxel of the scoring phantom geometry.
Definition: spec_scoring.h:636
- - - - -
EnergyFluenceSpectrumInVoxel::geometry
EGS_BaseGeometry * geometry
Definition: spec_scoring.h:638
-
EnergyFluenceSpectrumInVoxel::getFileExtension
string getFileExtension() const
Definition: spec_scoring.h:659
- -
EnergyFluenceSpectrumInVoxel::EnergyFluenceSpectrumInVoxel
EnergyFluenceSpectrumInVoxel(EGS_Input *input, EGS_BaseSource *src, GeomInfo *ginfo, Publisher *publisher)
Definition: spec_scoring.h:666
-
EnergyFluenceSpectrumInVoxel::score
virtual void score(EB_Message message, void *data=0)
Definition: spec_scoring.cpp:555
- -
EnergyFluenceSpectrumInVoxel::getResult
void getResult(int bin, EGS_Float &r, EGS_Float &dr)
set r & dr to result/uncertainty for given bin. Normalization can be done in this routine
Definition: spec_scoring.cpp:573
-
EnergyScoringStats
a class to use for scoring information about total energy initialzed, escaping sources etc
Definition: spec_scoring.h:57
-
EnergyScoringStats::scoreParticleEscapingGeom
void scoreParticleEscapingGeom(EGS_Particle *p)
add energy from a escaping simulation geometry to the total
Definition: spec_scoring.h:88
-
EnergyScoringStats::energyEscapingGeom
EGS_Float energyEscapingGeom()
returns the total energy of particles escaping simulation geometry
Definition: spec_scoring.h:141
-
EnergyScoringStats::energyEscapingSources
EGS_Float energyEscapingSources()
returns the total paticle energy escaping source geometry
Definition: spec_scoring.h:136
-
EnergyScoringStats::EnergyScoringStats
EnergyScoringStats(Publisher *publisher)
Definition: spec_scoring.h:94
-
EnergyScoringStats::escapingGeomRatio
EGS_Float escapingGeomRatio()
return the ratio of energy escaping the simulation geometry to total energy initialized
Definition: spec_scoring.h:122
- -
EnergyScoringStats::scoreEnergyInitialized
void scoreEnergyInitialized(EGS_Float E)
Needed for loading data from egsdat file.
Definition: spec_scoring.h:107
-
EnergyScoringStats::getParticleEnergy
EGS_Float getParticleEnergy(const EGS_Particle *p, bool subtractRM=true)
Definition: spec_scoring.h:66
-
EnergyScoringStats::total_energy_initialized
EGS_Float total_energy_initialized
total energy of particles initialized so far
Definition: spec_scoring.h:59
-
EnergyScoringStats::update
void update(EB_Message message, void *particle)
delegate messages to appropriate scoring functions
Definition: spec_scoring.h:147
-
EnergyScoringStats::scoreParticleEscapingSource
void scoreParticleEscapingSource(EGS_Particle *p)
add energy from a particle escaping a source to the total
Definition: spec_scoring.h:83
-
EnergyScoringStats::readData
int readData(istream *ifile)
Definition: spec_scoring.h:192
-
EnergyScoringStats::scoreParticleInitialized
void scoreParticleInitialized(EGS_Particle *p)
add energy from initial particle to total
Definition: spec_scoring.h:75
-
EnergyScoringStats::outputData
int outputData(ostream *ofile)
Definition: spec_scoring.h:185
-
EnergyScoringStats::totalEnergyInitialized
EGS_Float totalEnergyInitialized()
returns the total energy initialized
Definition: spec_scoring.h:131
-
EnergyScoringStats::energy_escaping_geom
EGS_Float energy_escaping_geom
total energy of particles escaping the simulation geometry
Definition: spec_scoring.h:64
-
EnergyScoringStats::energy_escaping_sources
EGS_Float energy_escaping_sources
total energy of particles escaping the source geometry note: doesn't currently exclude particles reen...
Definition: spec_scoring.h:60
-
EnergyScoringStats::addState
int addState(istream &data)
Definition: spec_scoring.h:205
-
EnergyScoringStats::escapingSourcesRatio
EGS_Float escapingSourcesRatio()
return the ratio of energy escaping the source to total energy initialized
Definition: spec_scoring.h:112
-
EnergyScoringStats::outputResults
void outputResults()
write results to console
Definition: spec_scoring.h:165
-
EnergyWeightedSurfaceSpectrum
A class for scoring the energy weighted spectrum (normalized to total radiant energy) of particles on...
Definition: spec_scoring.h:473
- -
EnergyWeightedSurfaceSpectrum::EnergyWeightedSurfaceSpectrum
EnergyWeightedSurfaceSpectrum(EGS_Input *input, EGS_BaseSource *src, GeomInfo *ginfo, Publisher *publisher)
Definition: spec_scoring.h:497
-
EnergyWeightedSurfaceSpectrum::getResult
void getResult(int bin, EGS_Float &r, EGS_Float &dr)
set r & dr to result/uncertainty for given bin. Normalization can be done in this routine
Definition: spec_scoring.cpp:491
-
EnergyWeightedSurfaceSpectrum::score
virtual void score(EB_Message message, void *data=0)
Definition: spec_scoring.cpp:476
- - - - -
FluenceSpectrumInVoxel
A class for scoring the fluence of particles enter a voxel of the scoring phantom geometry.
Definition: spec_scoring.h:530
-
FluenceSpectrumInVoxel::score
virtual void score(EB_Message message, void *data=0)
Definition: spec_scoring.cpp:512
-
FluenceSpectrumInVoxel::getFileExtension
string getFileExtension() const
Definition: spec_scoring.h:553
-
FluenceSpectrumInVoxel::getYAxisLabel
string getYAxisLabel() const
Definition: spec_scoring.h:547
-
FluenceSpectrumInVoxel::FluenceSpectrumInVoxel
FluenceSpectrumInVoxel(EGS_Input *input, EGS_BaseSource *src, GeomInfo *ginfo, Publisher *publisher)
Definition: spec_scoring.h:560
- -
FluenceSpectrumInVoxel::getTitle
string getTitle() const
Definition: spec_scoring.h:540
- - -
FluenceSpectrumInVoxel::getResult
void getResult(int bin, EGS_Float &r, EGS_Float &dr)
set r & dr to result/uncertainty for given bin. Normalization can be done in this routine
Definition: spec_scoring.cpp:530
-
FluenceSpectrumInVoxel::geometry
EGS_BaseGeometry * geometry
Definition: spec_scoring.h:532
- -
GeomInfo
a container for organizing meta data about the geometries
Definition: ginfo.h:99
-
GeomInfo::localToGlobal
int localToGlobal(GeomRegT)
Definition: ginfo.cpp:492
- -
Publisher::subscribe
void subscribe(Subscriber *s, EB_Message message)
Definition: pubsub.h:83
- -
SurfaceCountSpectrum
A class for scoring a histogram of the number of particles escaping a source geometry.
Definition: spec_scoring.h:414
-
SurfaceCountSpectrum::getResult
void getResult(int bin, EGS_Float &r, EGS_Float &dr)
set r & dr to result/uncertainty for given bin. Normalization can be done in this routine
Definition: spec_scoring.cpp:456
-
SurfaceCountSpectrum::SurfaceCountSpectrum
SurfaceCountSpectrum(EGS_Input *input, EGS_BaseSource *src, GeomInfo *ginfo, Publisher *publisher)
Definition: spec_scoring.h:440
-
SurfaceCountSpectrum::getFileExtension
string getFileExtension() const
Definition: spec_scoring.h:433
-
SurfaceCountSpectrum::getYAxisLabel
string getYAxisLabel() const
Definition: spec_scoring.h:427
-
SurfaceCountSpectrum::getTitle
string getTitle() const
Definition: spec_scoring.h:419
- -
SurfaceCountSpectrum::score
virtual void score(EB_Message message, void *data=0)
Definition: spec_scoring.cpp:441
-
SurfaceCountSpectrum::getSubTitle
string getSubTitle() const
Definition: spec_scoring.h:423
+
BaseSpectrumScorer::getTitle
virtual string getTitle() const
Definition spec_scoring.h:292
+
BaseSpectrumScorer::getBin
int getBin(EGS_Float E) const
get index of bin that that E falls in
Definition spec_scoring.cpp:198
+
BaseSpectrumScorer::getInfo
virtual string getInfo() const
Definition spec_scoring.h:376
+
BaseSpectrumScorer::update
virtual void update(EB_Message message, void *data=0)
Receives messages from application. This method handles NEW_HISTORY messages but delegates all other ...
Definition spec_scoring.cpp:366
+
BaseSpectrumScorer::outputTotal
virtual void outputTotal()
Definition spec_scoring.h:334
+
BaseSpectrumScorer::outputData
int outputData(ostream *ofile)
Definition spec_scoring.cpp:381
+
BaseSpectrumScorer::getFileName
string getFileName(string root) const
Definition spec_scoring.h:308
+
BaseSpectrumScorer::~BaseSpectrumScorer
virtual ~BaseSpectrumScorer()
Definition spec_scoring.cpp:188
+
BaseSpectrumScorer::DEFAULT_NBINS
static const int DEFAULT_NBINS
Definition spec_scoring.h:341
+
BaseSpectrumScorer::getXAxisLabel
virtual string getXAxisLabel() const
Definition spec_scoring.h:304
+ +
BaseSpectrumScorer::e_max
EGS_Float e_max
maximum spectrum energy to score
Definition spec_scoring.h:347
+
BaseSpectrumScorer::getYAxisLabel
virtual string getYAxisLabel() const
Definition spec_scoring.h:300
+
BaseSpectrumScorer::getFileExtension
virtual string getFileExtension() const
Definition spec_scoring.h:312
+
BaseSpectrumScorer::getParticleEnergy
double getParticleEnergy(const EGS_Particle *p) const
Definition spec_scoring.cpp:207
+ +
BaseSpectrumScorer::outputEGSnrc
string outputEGSnrc(string filename)
output results to EGSnrc tabulated spectrum format
Definition spec_scoring.cpp:256
+
BaseSpectrumScorer::e_min
EGS_Float e_min
minimum spectrum energy to score
Definition spec_scoring.h:346
+ +
BaseSpectrumScorer::outputResults
int outputResults(string root_name)
, write the scored spectrum to file with filename. Returns 0 on success, all other values indicate a ...
Definition spec_scoring.cpp:212
+
EnergyFluenceSpectrumInVoxel
A class for scoring the energy fluence of particles enter a voxel of the scoring phantom geometry.
Definition spec_scoring.h:636
+ + + + +
EnergyFluenceSpectrumInVoxel::geometry
EGS_BaseGeometry * geometry
Definition spec_scoring.h:638
+ + +
EnergyFluenceSpectrumInVoxel::EnergyFluenceSpectrumInVoxel
EnergyFluenceSpectrumInVoxel(EGS_Input *input, EGS_BaseSource *src, GeomInfo *ginfo, Publisher *publisher)
Definition spec_scoring.h:666
+
EnergyFluenceSpectrumInVoxel::score
virtual void score(EB_Message message, void *data=0)
Definition spec_scoring.cpp:555
+ +
EnergyFluenceSpectrumInVoxel::getResult
void getResult(int bin, EGS_Float &r, EGS_Float &dr)
set r & dr to result/uncertainty for given bin. Normalization can be done in this routine
Definition spec_scoring.cpp:573
+
EnergyScoringStats
a class to use for scoring information about total energy initialzed, escaping sources etc
Definition spec_scoring.h:57
+
EnergyScoringStats::scoreParticleEscapingGeom
void scoreParticleEscapingGeom(EGS_Particle *p)
add energy from a escaping simulation geometry to the total
Definition spec_scoring.h:88
+
EnergyScoringStats::energyEscapingGeom
EGS_Float energyEscapingGeom()
returns the total energy of particles escaping simulation geometry
Definition spec_scoring.h:141
+
EnergyScoringStats::energyEscapingSources
EGS_Float energyEscapingSources()
returns the total paticle energy escaping source geometry
Definition spec_scoring.h:136
+
EnergyScoringStats::EnergyScoringStats
EnergyScoringStats(Publisher *publisher)
Definition spec_scoring.h:94
+
EnergyScoringStats::escapingGeomRatio
EGS_Float escapingGeomRatio()
return the ratio of energy escaping the simulation geometry to total energy initialized
Definition spec_scoring.h:122
+ +
EnergyScoringStats::scoreEnergyInitialized
void scoreEnergyInitialized(EGS_Float E)
Needed for loading data from egsdat file.
Definition spec_scoring.h:107
+
EnergyScoringStats::getParticleEnergy
EGS_Float getParticleEnergy(const EGS_Particle *p, bool subtractRM=true)
Definition spec_scoring.h:66
+
EnergyScoringStats::total_energy_initialized
EGS_Float total_energy_initialized
total energy of particles initialized so far
Definition spec_scoring.h:59
+
EnergyScoringStats::update
void update(EB_Message message, void *particle)
delegate messages to appropriate scoring functions
Definition spec_scoring.h:147
+
EnergyScoringStats::scoreParticleEscapingSource
void scoreParticleEscapingSource(EGS_Particle *p)
add energy from a particle escaping a source to the total
Definition spec_scoring.h:83
+
EnergyScoringStats::readData
int readData(istream *ifile)
Definition spec_scoring.h:192
+
EnergyScoringStats::scoreParticleInitialized
void scoreParticleInitialized(EGS_Particle *p)
add energy from initial particle to total
Definition spec_scoring.h:75
+
EnergyScoringStats::outputData
int outputData(ostream *ofile)
Definition spec_scoring.h:185
+
EnergyScoringStats::totalEnergyInitialized
EGS_Float totalEnergyInitialized()
returns the total energy initialized
Definition spec_scoring.h:131
+
EnergyScoringStats::energy_escaping_geom
EGS_Float energy_escaping_geom
total energy of particles escaping the simulation geometry
Definition spec_scoring.h:64
+
EnergyScoringStats::energy_escaping_sources
EGS_Float energy_escaping_sources
total energy of particles escaping the source geometry note: doesn't currently exclude particles reen...
Definition spec_scoring.h:60
+
EnergyScoringStats::addState
int addState(istream &data)
Definition spec_scoring.h:205
+
EnergyScoringStats::escapingSourcesRatio
EGS_Float escapingSourcesRatio()
return the ratio of energy escaping the source to total energy initialized
Definition spec_scoring.h:112
+
EnergyScoringStats::outputResults
void outputResults()
write results to console
Definition spec_scoring.h:165
+
EnergyWeightedSurfaceSpectrum
A class for scoring the energy weighted spectrum (normalized to total radiant energy) of particles on...
Definition spec_scoring.h:473
+ +
EnergyWeightedSurfaceSpectrum::EnergyWeightedSurfaceSpectrum
EnergyWeightedSurfaceSpectrum(EGS_Input *input, EGS_BaseSource *src, GeomInfo *ginfo, Publisher *publisher)
Definition spec_scoring.h:497
+
EnergyWeightedSurfaceSpectrum::getResult
void getResult(int bin, EGS_Float &r, EGS_Float &dr)
set r & dr to result/uncertainty for given bin. Normalization can be done in this routine
Definition spec_scoring.cpp:491
+
EnergyWeightedSurfaceSpectrum::score
virtual void score(EB_Message message, void *data=0)
Definition spec_scoring.cpp:476
+ + + + +
FluenceSpectrumInVoxel
A class for scoring the fluence of particles enter a voxel of the scoring phantom geometry.
Definition spec_scoring.h:530
+
FluenceSpectrumInVoxel::score
virtual void score(EB_Message message, void *data=0)
Definition spec_scoring.cpp:512
+
FluenceSpectrumInVoxel::getFileExtension
string getFileExtension() const
Definition spec_scoring.h:553
+
FluenceSpectrumInVoxel::getYAxisLabel
string getYAxisLabel() const
Definition spec_scoring.h:547
+
FluenceSpectrumInVoxel::FluenceSpectrumInVoxel
FluenceSpectrumInVoxel(EGS_Input *input, EGS_BaseSource *src, GeomInfo *ginfo, Publisher *publisher)
Definition spec_scoring.h:560
+ +
FluenceSpectrumInVoxel::getTitle
string getTitle() const
Definition spec_scoring.h:540
+ + +
FluenceSpectrumInVoxel::getResult
void getResult(int bin, EGS_Float &r, EGS_Float &dr)
set r & dr to result/uncertainty for given bin. Normalization can be done in this routine
Definition spec_scoring.cpp:530
+
FluenceSpectrumInVoxel::geometry
EGS_BaseGeometry * geometry
Definition spec_scoring.h:532
+ +
GeomInfo
a container for organizing meta data about the geometries
Definition ginfo.h:99
+
GeomInfo::localToGlobal
int localToGlobal(GeomRegT)
Definition ginfo.cpp:492
+ +
Publisher::subscribe
void subscribe(Subscriber *s, EB_Message message)
Definition pubsub.h:83
+ +
SurfaceCountSpectrum
A class for scoring a histogram of the number of particles escaping a source geometry.
Definition spec_scoring.h:414
+
SurfaceCountSpectrum::getResult
void getResult(int bin, EGS_Float &r, EGS_Float &dr)
set r & dr to result/uncertainty for given bin. Normalization can be done in this routine
Definition spec_scoring.cpp:456
+
SurfaceCountSpectrum::SurfaceCountSpectrum
SurfaceCountSpectrum(EGS_Input *input, EGS_BaseSource *src, GeomInfo *ginfo, Publisher *publisher)
Definition spec_scoring.h:440
+
SurfaceCountSpectrum::getFileExtension
string getFileExtension() const
Definition spec_scoring.h:433
+
SurfaceCountSpectrum::getYAxisLabel
string getYAxisLabel() const
Definition spec_scoring.h:427
+
SurfaceCountSpectrum::getTitle
string getTitle() const
Definition spec_scoring.h:419
+ +
SurfaceCountSpectrum::score
virtual void score(EB_Message message, void *data=0)
Definition spec_scoring.cpp:441
+
SurfaceCountSpectrum::getSubTitle
string getSubTitle() const
Definition spec_scoring.h:423
ginfo.h
ginfo contains classes for organizing information about the geometries present in an egs_brachy simul...
-
GeomRegT
pair< EGS_BaseGeometry *, int > GeomRegT
pair of geometry and local region number
Definition: ginfo.h:79
+
GeomRegT
pair< EGS_BaseGeometry *, int > GeomRegT
pair of geometry and local region number
Definition ginfo.h:79
pubsub.h
A simple pub/sub module to allow various egs_brachy classes to subscribe to particle events.
-
EB_Message
EB_Message
Definition: pubsub.h:54
-
PARTICLE_ESCAPING_SOURCE
@ PARTICLE_ESCAPING_SOURCE
Definition: pubsub.h:60
-
PARTICLE_TAKING_STEP
@ PARTICLE_TAKING_STEP
Definition: pubsub.h:58
-
PARTICLE_INITIALIZED
@ PARTICLE_INITIALIZED
Definition: pubsub.h:57
-
PARTICLE_ESCAPING_GEOM
@ PARTICLE_ESCAPING_GEOM
Definition: pubsub.h:62
+
EB_Message
EB_Message
Definition pubsub.h:54
+
PARTICLE_ESCAPING_SOURCE
@ PARTICLE_ESCAPING_SOURCE
Definition pubsub.h:60
+
PARTICLE_TAKING_STEP
@ PARTICLE_TAKING_STEP
Definition pubsub.h:58
+
PARTICLE_INITIALIZED
@ PARTICLE_INITIALIZED
Definition pubsub.h:57
+
PARTICLE_ESCAPING_GEOM
@ PARTICLE_ESCAPING_GEOM
Definition pubsub.h:62
-Generated by doxygen 1.9.5 +Generated by doxygen 1.9.8
diff --git a/docs/spec__vox_2____init_____8py.html b/docs/spec__vox_2____init_____8py.html index f2dbd61b..fcf4eb02 100644 --- a/docs/spec__vox_2____init_____8py.html +++ b/docs/spec__vox_2____init_____8py.html @@ -3,9 +3,9 @@ - + -EGS Brachy: /Users/marc/dev/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/eb_tests/spec_vox/__init__.py File Reference +EGS Brachy: /Users/marc/Developer/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/eb_tests/spec_vox/__init__.py File Reference @@ -30,7 +30,7 @@
- + @@ -30,7 +30,7 @@ - + +
-Generated by doxygen 1.9.5 +Generated by doxygen 1.9.8
diff --git a/docs/spec__vox_2test_8py.html b/docs/spec__vox_2test_8py.html index f8de4245..0bfe38fc 100644 --- a/docs/spec__vox_2test_8py.html +++ b/docs/spec__vox_2test_8py.html @@ -3,9 +3,9 @@ - + -EGS Brachy: /Users/marc/dev/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/eb_tests/spec_vox/test.py File Reference +EGS Brachy: /Users/marc/Developer/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/eb_tests/spec_vox/test.py File Reference @@ -30,7 +30,7 @@ - + @@ -30,7 +30,7 @@ - + +
11
12from eb_tests.utils import read_csv_spectrum, values_close
13
-
14EGSINP = "spec_vox.egsinp"
+
14EGSINP = "spec_vox.egsinp"
15TIME_LIMIT_S_PER_MHZ = 7/2993. # s / MHz
16
17BIN_WIDTH = 0.001
@@ -106,27 +111,31 @@
27
28VOLUME = 4/3.*math.pi*(0.2**3-0.1**3)
29
-
30def expected(e):
+
+
30def expected(e):
31 if EMIN <= e <= EMAX:
32 return SCORED_IN_BIN/(VOLUME*BIN_WIDTH)
33 return 0
34
-
35def compare_results(egslst, inp_name):
+
+
+
35def compare_results(egslst, inp_name):
36
37 energies, counts, uncs = read_csv_spectrum(inp_name+".voxelflu.csv")
38
39 for e, c in zip(energies, counts):
-
40 exp = expected(e)
+
40 exp = expected(e)
41 if (exp > 0 and not values_close(c, exp, 0.005)) or (exp == 0 and c > 0.01):
42 return False, "Fluence at E = %f MeV was %f" %(e, c), "Expected %f" % exp
43
44 return True, [], []
-
eb_tests.spec_vox.test.expected
def expected(e)
Definition: test.py:30
-
eb_tests.utils
Definition: utils.py:1
+
+
eb_tests.spec_vox.test.expected
expected(e)
Definition test.py:30
+
eb_tests.utils
Definition utils.py:1
-Generated by doxygen 1.9.5 +Generated by doxygen 1.9.8
diff --git a/docs/spectra_8md.html b/docs/spectra_8md.html index 77d15fbc..a56a786f 100644 --- a/docs/spectra_8md.html +++ b/docs/spectra_8md.html @@ -3,7 +3,7 @@ - + EGS Brachy: spectra.md File Reference @@ -30,7 +30,7 @@ - + @@ -30,7 +30,7 @@ - + @@ -30,7 +30,7 @@ - + +
-Generated by doxygen 1.9.5 +Generated by doxygen 1.9.8
diff --git a/docs/stepped__source_2test_8py.html b/docs/stepped__source_2test_8py.html index a3d52930..1144598e 100644 --- a/docs/stepped__source_2test_8py.html +++ b/docs/stepped__source_2test_8py.html @@ -3,9 +3,9 @@ - + -EGS Brachy: /Users/marc/dev/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/eb_tests/stepped_source/test.py File Reference +EGS Brachy: /Users/marc/Developer/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/eb_tests/stepped_source/test.py File Reference @@ -30,7 +30,7 @@ - + @@ -30,7 +30,7 @@ - + +
12from eb_tests.utils import (compare_3ddose_files, doses_approx_equal,
13 extract_all_doses, read3ddose)
14
-
15EGSINP = "stepped.egsinp"
+
15EGSINP = "stepped.egsinp"
16TIME_LIMIT_S_PER_MHZ = 1000/2993. # s / MHz
17NCOMPARE = 20
18
-
19def get_n_highest_dose_pairs(dose1, dose2, n=NCOMPARE):
+
+
19def get_n_highest_dose_pairs(dose1, dose2, n=NCOMPARE):
20 return sorted(zip(dose1, dose2))[-NCOMPARE:]
21
-
22def compare_results(egslst, inp_name):
+
+
+
22def compare_results(egslst, inp_name):
23
24 gold_standard = read3ddose(os.path.join(os.path.dirname(os.path.abspath(__file__)), "gold_standard.3ddose"))
25 run_doses = read3ddose(inp_name+".phantom.3ddose")
26
-
27 dose_pairs = get_n_highest_dose_pairs(gold_standard['doses'], run_doses['doses'])
+
27 dose_pairs = get_n_highest_dose_pairs(gold_standard['doses'], run_doses['doses'])
28
29 dose_diff = [abs((a-b)/a) for a, b in dose_pairs]
30
@@ -112,12 +120,13 @@
33 rd, gs = list(zip(*dose_pairs))
34 return doses_close, rd, gs
35
-
eb_tests.stepped_source.test.get_n_highest_dose_pairs
def get_n_highest_dose_pairs(dose1, dose2, n=NCOMPARE)
Definition: test.py:19
-
eb_tests.utils
Definition: utils.py:1
+
+
eb_tests.stepped_source.test.get_n_highest_dose_pairs
get_n_highest_dose_pairs(dose1, dose2, n=NCOMPARE)
Definition test.py:19
+
eb_tests.utils
Definition utils.py:1
-Generated by doxygen 1.9.5 +Generated by doxygen 1.9.8
diff --git a/docs/structGeomRegionInfo-members.html b/docs/structGeomRegionInfo-members.html index 333971e2..bcb1120a 100644 --- a/docs/structGeomRegionInfo-members.html +++ b/docs/structGeomRegionInfo-members.html @@ -3,7 +3,7 @@ - + EGS Brachy: Member List @@ -30,7 +30,7 @@ - + @@ -30,7 +30,7 @@ - + @@ -30,7 +30,7 @@ - + +
-Generated by doxygen 1.9.5 +Generated by doxygen 1.9.8
diff --git a/docs/tg43mode_2test_8py.html b/docs/tg43mode_2test_8py.html index 5c07b0a8..d27ccd78 100644 --- a/docs/tg43mode_2test_8py.html +++ b/docs/tg43mode_2test_8py.html @@ -3,9 +3,9 @@ - + -EGS Brachy: /Users/marc/dev/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/eb_tests/tg43mode/test.py File Reference +EGS Brachy: /Users/marc/Developer/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/eb_tests/tg43mode/test.py File Reference @@ -30,7 +30,7 @@ - + @@ -30,7 +30,7 @@ - + +
11from eb_tests.utils import (compare_3ddose_files, doses_approx_equal,
12 extract_all_doses, read3ddose)
13
-
14EGSINP = "tg43mode.egsinp"
+
14EGSINP = "tg43mode.egsinp"
15TIME_LIMIT_S_PER_MHZ = 2000/2993. # s / MHz
16NCOMPARE = 100
17
-
18def get_n_highest_dose_pairs(dose1, dose2, n=NCOMPARE):
+
+
18def get_n_highest_dose_pairs(dose1, dose2, n=NCOMPARE):
19 return sorted(zip(dose1, dose2))[-NCOMPARE:]
20
-
21def compare_results(egslst, inp_name):
+
+
+
21def compare_results(egslst, inp_name):
22
23 gold_standard = read3ddose(os.path.join(os.path.dirname(os.path.abspath(__file__)), "gold_standard.3ddose"))
24 run_doses = read3ddose(inp_name+".phantom.3ddose")
25
-
26 dose_pairs = get_n_highest_dose_pairs(gold_standard['doses'], run_doses['doses'])
+
26 dose_pairs = get_n_highest_dose_pairs(gold_standard['doses'], run_doses['doses'])
27
28 dose_diff = [abs(a-b)/a for a, b in dose_pairs]
29
@@ -111,12 +119,13 @@
32 rd, gs = list(zip(*dose_pairs))
33 return doses_close, rd, gs
34
-
eb_tests.tg43mode.test.get_n_highest_dose_pairs
def get_n_highest_dose_pairs(dose1, dose2, n=NCOMPARE)
Definition: test.py:18
-
eb_tests.utils
Definition: utils.py:1
+
+
eb_tests.tg43mode.test.get_n_highest_dose_pairs
get_n_highest_dose_pairs(dose1, dose2, n=NCOMPARE)
Definition test.py:18
+
eb_tests.utils
Definition utils.py:1
-Generated by doxygen 1.9.5 +Generated by doxygen 1.9.8
diff --git a/docs/tg43mode__recycle_2____init_____8py.html b/docs/tg43mode__recycle_2____init_____8py.html index 04e96acd..3f326c9a 100644 --- a/docs/tg43mode__recycle_2____init_____8py.html +++ b/docs/tg43mode__recycle_2____init_____8py.html @@ -3,9 +3,9 @@ - + -EGS Brachy: /Users/marc/dev/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/eb_tests/tg43mode_recycle/__init__.py File Reference +EGS Brachy: /Users/marc/Developer/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/eb_tests/tg43mode_recycle/__init__.py File Reference @@ -30,7 +30,7 @@ - + @@ -30,7 +30,7 @@ - + +
-Generated by doxygen 1.9.5 +Generated by doxygen 1.9.8
diff --git a/docs/tg43mode__recycle_2test_8py.html b/docs/tg43mode__recycle_2test_8py.html index 04811383..86942232 100644 --- a/docs/tg43mode__recycle_2test_8py.html +++ b/docs/tg43mode__recycle_2test_8py.html @@ -3,9 +3,9 @@ - + -EGS Brachy: /Users/marc/dev/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/eb_tests/tg43mode_recycle/test.py File Reference +EGS Brachy: /Users/marc/Developer/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/eb_tests/tg43mode_recycle/test.py File Reference @@ -30,7 +30,7 @@ - + @@ -30,7 +30,7 @@ - + +
11from eb_tests.utils import (compare_3ddose_files, doses_approx_equal,
12 extract_all_doses, read3ddose)
13
-
14EGSINP = "tg43mode_recycling.egsinp"
+
14EGSINP = "tg43mode_recycling.egsinp"
15TIME_LIMIT_S_PER_MHZ = 1000/2993. # s / MHz
16NCOMPARE = 50
17
-
18def get_n_highest_dose_pairs(dose1, dose2, n=NCOMPARE):
+
+
18def get_n_highest_dose_pairs(dose1, dose2, n=NCOMPARE):
19 return sorted(zip(dose1, dose2))[-NCOMPARE:]
20
-
21def compare_results(egslst, inp_name):
+
+
+
21def compare_results(egslst, inp_name):
22
23 gold_standard = read3ddose(os.path.join(os.path.dirname(os.path.abspath(__file__)), "gold_standard.3ddose"))
24 run_doses = read3ddose(inp_name+".phantom.3ddose")
25
-
26 dose_pairs = get_n_highest_dose_pairs(gold_standard['doses'], run_doses['doses'])
+
26 dose_pairs = get_n_highest_dose_pairs(gold_standard['doses'], run_doses['doses'])
27
28 dose_diff = [abs(a-b)/a for a, b in dose_pairs]
29
@@ -111,12 +119,13 @@
32 rd, gs = list(zip(*dose_pairs))
33 return doses_close, rd, gs
34
-
eb_tests.tg43mode_recycle.test.get_n_highest_dose_pairs
def get_n_highest_dose_pairs(dose1, dose2, n=NCOMPARE)
Definition: test.py:18
-
eb_tests.utils
Definition: utils.py:1
+
+
eb_tests.tg43mode_recycle.test.get_n_highest_dose_pairs
get_n_highest_dose_pairs(dose1, dose2, n=NCOMPARE)
Definition test.py:18
+
eb_tests.utils
Definition utils.py:1
-Generated by doxygen 1.9.5 +Generated by doxygen 1.9.8
diff --git a/docs/tg43mode__zeroweight_2____init_____8py.html b/docs/tg43mode__zeroweight_2____init_____8py.html index 5b752c77..cc364548 100644 --- a/docs/tg43mode__zeroweight_2____init_____8py.html +++ b/docs/tg43mode__zeroweight_2____init_____8py.html @@ -3,9 +3,9 @@ - + -EGS Brachy: /Users/marc/dev/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/eb_tests/tg43mode_zeroweight/__init__.py File Reference +EGS Brachy: /Users/marc/Developer/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/eb_tests/tg43mode_zeroweight/__init__.py File Reference @@ -30,7 +30,7 @@ - + @@ -30,7 +30,7 @@ - + +
-Generated by doxygen 1.9.5 +Generated by doxygen 1.9.8
diff --git a/docs/tg43mode__zeroweight_2test_8py.html b/docs/tg43mode__zeroweight_2test_8py.html index 55eeab75..222d1f75 100644 --- a/docs/tg43mode__zeroweight_2test_8py.html +++ b/docs/tg43mode__zeroweight_2test_8py.html @@ -3,9 +3,9 @@ - + -EGS Brachy: /Users/marc/dev/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/eb_tests/tg43mode_zeroweight/test.py File Reference +EGS Brachy: /Users/marc/Developer/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/eb_tests/tg43mode_zeroweight/test.py File Reference @@ -30,7 +30,7 @@ - + @@ -30,7 +30,7 @@ - + +
6Gold standard dose distribution was generated with egs_brachy and gold_standard.egsinp
7
8"""
-
9
-
10import math
-
11import os
-
12import re
-
13
-
14from eb_tests.utils import (compare_3ddose_files, doses_approx_equal,
-
15 extract_all_doses, read3ddose)
-
16
-
17EGSINP = "tg43mode_zeroweight.egsinp"
+
9
+
10import math
+
11import os
+
12import re
+
13
+
14from eb_tests.utils import (compare_3ddose_files, doses_approx_equal,
+
15 extract_all_doses, read3ddose)
+
16
+
17EGSINP = "tg43mode_zeroweight.egsinp"
18TIME_LIMIT_S_PER_MHZ = 2000/2993. # s / MHz
19NCOMPARE = 10
20
-
21def get_n_highest_dose_pairs(dose1, dose2, n=NCOMPARE):
+
+
21def get_n_highest_dose_pairs(dose1, dose2, n=NCOMPARE):
22 return list(sorted(zip(dose1, dose2)))[-n:]
23
-
24def compare_results(egslst, inp_name):
+
+
+
24def compare_results(egslst, inp_name):
25
26 gold_standard = read3ddose(os.path.join(os.path.dirname(os.path.abspath(__file__)), "gold_standard.3ddose"))
27 run_doses = read3ddose(inp_name+".phantom.3ddose")
@@ -111,7 +119,7 @@
32
33 # make sure energy deposition and tlen doses roughly equal
34 run_doses_edep = read3ddose(inp_name+".phantom.edep.3ddose")
-
35 dose_pairs_edep = get_n_highest_dose_pairs(run_doses['doses'], run_doses_edep['doses'],n=5)
+
35 dose_pairs_edep = get_n_highest_dose_pairs(run_doses['doses'], run_doses_edep['doses'],n=5)
36 dose_diff_edep = [abs(a-b)/a for a, b in dose_pairs_edep]
37 doses_close_edep = max(dose_diff_edep) < 0.10
38
@@ -126,11 +134,13 @@
47 }
48 return doses_close and doses_close_edep, actual, expected
49
-
eb_tests.tg43mode_zeroweight.test.get_n_highest_dose_pairs
def get_n_highest_dose_pairs(dose1, dose2, n=NCOMPARE)
Definition: test.py:21
+
+
eb_tests.tg43mode_zeroweight.test.get_n_highest_dose_pairs
get_n_highest_dose_pairs(dose1, dose2, n=NCOMPARE)
Definition test.py:21
+
eb_tests.utils
Definition utils.py:1
-Generated by doxygen 1.9.5 +Generated by doxygen 1.9.8
diff --git a/docs/timing_8h.html b/docs/timing_8h.html index b2cb8f8c..d5ad4fc4 100644 --- a/docs/timing_8h.html +++ b/docs/timing_8h.html @@ -3,9 +3,9 @@ - + -EGS Brachy: /Users/marc/dev/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/timing.h File Reference +EGS Brachy: /Users/marc/Developer/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/timing.h File Reference @@ -30,7 +30,7 @@ - + @@ -30,7 +30,7 @@ - + +
-
/Users/marc/dev/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/timing.h
+
/Users/marc/Developer/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/timing.h
Go to the documentation of this file.
1/*
@@ -119,6 +124,7 @@
44#include "egs_timer.h"
45
46
+
47class EB_Timer {
48
49 string name;
@@ -128,60 +134,84 @@
53 int nested_level;
54
55public:
+
56 EB_Timer(string tname, int level) {
57 nested_level = level;
58 name = tname;
59 start_time = -1;
60 stop_time = -1;
61 }
+
62
+
63 void start() {
64 timer.start();
65 start_time = timer.time();
66 }
+
67
+
68 void stop() {
69 stop_time = timer.time();
70 }
+
71
+
72 EGS_Float getElapsedTime() {
73 return timer.time();
74 }
+
75
+
76 EGS_Float getStartTime() {
77 return start_time;
78 }
+
79
+
80 EGS_Float getStop() {
81 return stop_time;
82 }
+
83
+
84 EGS_Float getDuration() {
85 if (stop_time >= 0 && start_time >=0) {
86 return stop_time - start_time;
87 }
88 return -1;
89 }
+
90
+
91 string getName() {
92 return name;
93 }
+
94
+
95 bool isStopped() {
96 return getStop() >=0;
97 }
+
98
+
99 bool isRunning() {
100 return !isStopped();
101 }
+
102
+
103 int getLevel() {
104 return nested_level;
105 }
+
106
107};
+
108
109
+
110class EB_TimingTree {
111
112 vector<EB_Timer *> running_blocks;
@@ -192,6 +222,7 @@
117public:
118 EB_TimingTree(): level(0) {};
119
+
120 ~EB_TimingTree() {
121 for (vector<EB_Timer *>::iterator it = running_blocks.begin() ; it != running_blocks.end(); ++it) {
122 delete(*it);
@@ -203,14 +234,18 @@
128 }
129 stopped_blocks.clear();
130 }
+
131
+
132 void addTimer(string name) {
133 EB_Timer *timer = new EB_Timer(name, level);
134 timer->start();
135 running_blocks.push_back(timer);
136 level++;
137 }
+
138
+
139 void stopTimer() {
140 if (running_blocks.empty()) {
141 level = 0;
@@ -230,7 +265,9 @@
155 }
156
157 }
+
158
+
159 void outputInfo() {
160 string sep(80, '=');
161 egsInformation("\n\nTiming Blocks\n%s\n", sep.c_str());
@@ -257,40 +294,42 @@
182 egsInformation("%s\n", output.str().c_str());
183 }
184 }
+
185
186};
+
187
188#endif
-
EB_Timer
Definition: timing.h:47
-
EB_Timer::getDuration
EGS_Float getDuration()
Definition: timing.h:84
-
EB_Timer::getName
string getName()
Definition: timing.h:91
-
EB_Timer::name
string name
Definition: timing.h:49
-
EB_Timer::start_time
EGS_Float start_time
Definition: timing.h:51
-
EB_Timer::stop_time
EGS_Float stop_time
Definition: timing.h:52
-
EB_Timer::isRunning
bool isRunning()
Definition: timing.h:99
-
EB_Timer::timer
EGS_Timer timer
Definition: timing.h:50
-
EB_Timer::start
void start()
Definition: timing.h:63
-
EB_Timer::getStop
EGS_Float getStop()
Definition: timing.h:80
-
EB_Timer::stop
void stop()
Definition: timing.h:68
-
EB_Timer::getLevel
int getLevel()
Definition: timing.h:103
-
EB_Timer::EB_Timer
EB_Timer(string tname, int level)
Definition: timing.h:56
-
EB_Timer::getElapsedTime
EGS_Float getElapsedTime()
Definition: timing.h:72
-
EB_Timer::getStartTime
EGS_Float getStartTime()
Definition: timing.h:76
-
EB_Timer::nested_level
int nested_level
Definition: timing.h:53
-
EB_Timer::isStopped
bool isStopped()
Definition: timing.h:95
-
EB_TimingTree
Definition: timing.h:110
-
EB_TimingTree::level
int level
Definition: timing.h:115
-
EB_TimingTree::stopTimer
void stopTimer()
Definition: timing.h:139
-
EB_TimingTree::running_blocks
vector< EB_Timer * > running_blocks
Definition: timing.h:112
-
EB_TimingTree::~EB_TimingTree
~EB_TimingTree()
Definition: timing.h:120
-
EB_TimingTree::stopped_blocks
vector< EB_Timer * > stopped_blocks
Definition: timing.h:113
-
EB_TimingTree::outputInfo
void outputInfo()
Definition: timing.h:159
-
EB_TimingTree::addTimer
void addTimer(string name)
Definition: timing.h:132
-
EB_TimingTree::EB_TimingTree
EB_TimingTree()
Definition: timing.h:118
+
EB_Timer
Definition timing.h:47
+
EB_Timer::getDuration
EGS_Float getDuration()
Definition timing.h:84
+
EB_Timer::getName
string getName()
Definition timing.h:91
+
EB_Timer::name
string name
Definition timing.h:49
+
EB_Timer::start_time
EGS_Float start_time
Definition timing.h:51
+
EB_Timer::stop_time
EGS_Float stop_time
Definition timing.h:52
+
EB_Timer::isRunning
bool isRunning()
Definition timing.h:99
+
EB_Timer::timer
EGS_Timer timer
Definition timing.h:50
+
EB_Timer::start
void start()
Definition timing.h:63
+
EB_Timer::getStop
EGS_Float getStop()
Definition timing.h:80
+
EB_Timer::stop
void stop()
Definition timing.h:68
+
EB_Timer::getLevel
int getLevel()
Definition timing.h:103
+
EB_Timer::EB_Timer
EB_Timer(string tname, int level)
Definition timing.h:56
+
EB_Timer::getElapsedTime
EGS_Float getElapsedTime()
Definition timing.h:72
+
EB_Timer::getStartTime
EGS_Float getStartTime()
Definition timing.h:76
+
EB_Timer::nested_level
int nested_level
Definition timing.h:53
+
EB_Timer::isStopped
bool isStopped()
Definition timing.h:95
+
EB_TimingTree
Definition timing.h:110
+
EB_TimingTree::level
int level
Definition timing.h:115
+
EB_TimingTree::stopTimer
void stopTimer()
Definition timing.h:139
+
EB_TimingTree::running_blocks
vector< EB_Timer * > running_blocks
Definition timing.h:112
+
EB_TimingTree::~EB_TimingTree
~EB_TimingTree()
Definition timing.h:120
+
EB_TimingTree::stopped_blocks
vector< EB_Timer * > stopped_blocks
Definition timing.h:113
+
EB_TimingTree::outputInfo
void outputInfo()
Definition timing.h:159
+
EB_TimingTree::addTimer
void addTimer(string name)
Definition timing.h:132
+
EB_TimingTree::EB_TimingTree
EB_TimingTree()
Definition timing.h:118
-Generated by doxygen 1.9.5 +Generated by doxygen 1.9.8
diff --git a/docs/transport_8md.html b/docs/transport_8md.html index e760bacb..55955e36 100644 --- a/docs/transport_8md.html +++ b/docs/transport_8md.html @@ -3,7 +3,7 @@ - + EGS Brachy: transport.md File Reference @@ -30,7 +30,7 @@
- + @@ -30,7 +30,7 @@ - + @@ -30,7 +30,7 @@ - + +
Go to the documentation of this file.
1import math
2import re
3
-
4REG_DOSE_UNC_RE = "\s+(\d)+\s+\d+\s+\d+\..*?\s+(.*?)\s+\+/-\s+(.*?)%\s+(.*?)\s+\+/-\s+(.*?)%"
+
4REG_DOSE_UNC_RE = "\s+(\d)+\s+\d+\s+\d+\..*?\s+(.*?)\s+\+/-\s+(.*?)%\s+(.*?)\s+\+/-\s+(.*?)%"
5
6
-
7def extract_all_doses(egslst):
+
+
7def extract_all_doses(egslst):
8 """return all regions and doses from egslst file. This may
-
9 include doses from more than one phantom"""
-
10
-
11 # regex to match scientific notation +[+-]?(?:0|[1-9]\d*)(?:\.\d*)?(?:[eE][+\-]?\d+)
+
9 include doses from more than one phantom"""
+
10
+
11 # regex to match scientific notation +[+-]?(?:0|[1-9]\d*)(?:\.\d*)?(?:[eE][+\-]?\d+)
12 sci_not = r"[+-]?(?:0|[1-9]\d*)(?:\.\d*)?(?:[eE][+\-]?\d+)"
13
-
14 r = re.compile(r"""\s+(\d+) # region number
-
15 \s+\d+ # medium number
-
16 \s+{sci_not}\({sci_not}\)\s+\+\/\-\s+\d+\.\d+% # volume, correction and error
-
17 \s+({sci_not})\s+\+\/\-\s+(\d+\.\d+)% # tlen dose and unc
-
18 \s+\(.*\)
-
19 \s+({sci_not})\s+\+\/\-\s+(\d+\.\d+)% # edep dose and unc
-
20 """.format(sci_not=sci_not), re.X)
-
21
-
22 return sorted(r.findall(egslst))
+
14 r = re.compile(r"""\s+(\d+) # region number
+
15 \s+\d+ # medium number
+
16 \s+{sci_not}\‍({sci_not}\‍)\s+\+\/\-\s+\d+\.\d+% # volume, correction and error
+
17 \s+({sci_not})\s+\+\/\-\s+(\d+\.\d+)% # tlen dose and unc
+
18 \s+\‍(.*\‍)
+
19 \s+({sci_not})\s+\+\/\-\s+(\d+\.\d+)% # edep dose and unc
+
20 """.format(sci_not=sci_not), re.X)
+
21
+
22 return sorted(r.findall(egslst))
23
-
24def values_close(a, b, max_percent_diff=0.001):
+
+
+
24def values_close(a, b, max_percent_diff=0.001):
25 if a == 0:
-
26 return values_close_abs(a, b, max_percent_diff)
+
26 return values_close_abs(a, b, max_percent_diff)
27 return abs((a-b)/a) < max_percent_diff
28
29
-
30def values_close_abs(a, b, max_diff=0.001):
+
+
+
30def values_close_abs(a, b, max_diff=0.001):
31 return abs(a-b) < max_diff
32
-
33def read_csv_spectrum(fname):
+
+
+
33def read_csv_spectrum(fname):
34 f = open(fname, "r")
35 header = f.readline()
36 energies = []
@@ -125,7 +137,9 @@
46 return energies, counts, unc
47
48
-
49def doses_approx_equal(d1, d1_unc, d2, d2_unc, max_percent_diff=None, compare_unc=True, max_unc_percent_diff=None):
+
+
+
49def doses_approx_equal(d1, d1_unc, d2, d2_unc, max_percent_diff=None, compare_unc=True, max_unc_percent_diff=None):
50 if max_percent_diff is None:
51 max_percent_diff = max(d1_unc, d2_unc)
52
@@ -134,14 +148,16 @@
55
56 vc = values_close(d1, d2, max_percent_diff)
57 if compare_unc:
-
58 uc = values_close_abs(d1_unc, d2_unc, max_unc_percent_diff)
+
58 uc = values_close_abs(d1_unc, d2_unc, max_unc_percent_diff)
59 else:
60 uc = True
61
62 return vc and uc
63
64
-
65def read3ddose(fname):
+
+
+
65def read3ddose(fname):
66
67 with open(fname, 'r') as f:
68 dat = f.readlines()
@@ -165,7 +181,9 @@
86 }
87
88
-
89def compare_3ddose_files(f1, f2, max_percent_diff=None):
+
+
+
89def compare_3ddose_files(f1, f2, max_percent_diff=None):
90
91 d1 = read3ddose(f1)
92 d2 = read3ddose(f2)
@@ -185,11 +203,12 @@
106
107 return doses_close
108
-
eb_tests.utils.values_close_abs
def values_close_abs(a, b, max_diff=0.001)
Definition: utils.py:30
+
+
eb_tests.utils.values_close_abs
values_close_abs(a, b, max_diff=0.001)
Definition utils.py:30
-Generated by doxygen 1.9.5 +Generated by doxygen 1.9.8
diff --git a/docs/variable__activity_2____init_____8py.html b/docs/variable__activity_2____init_____8py.html index 25f0c781..569e17fd 100644 --- a/docs/variable__activity_2____init_____8py.html +++ b/docs/variable__activity_2____init_____8py.html @@ -3,9 +3,9 @@ - + -EGS Brachy: /Users/marc/dev/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/eb_tests/variable_activity/__init__.py File Reference +EGS Brachy: /Users/marc/Developer/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/eb_tests/variable_activity/__init__.py File Reference @@ -30,7 +30,7 @@ - + @@ -30,7 +30,7 @@ - + +
-Generated by doxygen 1.9.5 +Generated by doxygen 1.9.8
diff --git a/docs/variable__activity_2test_8py.html b/docs/variable__activity_2test_8py.html index d143c2ca..d6cd3067 100644 --- a/docs/variable__activity_2test_8py.html +++ b/docs/variable__activity_2test_8py.html @@ -3,9 +3,9 @@ - + -EGS Brachy: /Users/marc/dev/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/eb_tests/variable_activity/test.py File Reference +EGS Brachy: /Users/marc/Developer/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/eb_tests/variable_activity/test.py File Reference @@ -30,7 +30,7 @@ - + @@ -30,7 +30,7 @@ - + +
12from eb_tests.utils import (doses_approx_equal, extract_all_doses, read3ddose,
13 values_close)
14
-
15EGSINP = "variable.egsinp"
+
15EGSINP = "variable.egsinp"
16TIME_LIMIT_S_PER_MHZ = 100/2993. # s / MHz
17
18
-
19def compare_results(egslst, inp_name):
+
+
19def compare_results(egslst, inp_name):
20
21 gold_standard = os.path.join(os.path.dirname(os.path.abspath(__file__)), "gold_standard.3ddose")
22 run_doses_file = inp_name+".phantom.3ddose"
@@ -108,11 +114,12 @@
29
30
31 return all(close), run_doses, gold_doses
-
eb_tests.utils
Definition: utils.py:1
+
+
eb_tests.utils
Definition utils.py:1
-Generated by doxygen 1.9.5 +Generated by doxygen 1.9.8
diff --git a/docs/variable__w__recycling_2____init_____8py.html b/docs/variable__w__recycling_2____init_____8py.html index 4ba3c759..79481e75 100644 --- a/docs/variable__w__recycling_2____init_____8py.html +++ b/docs/variable__w__recycling_2____init_____8py.html @@ -3,9 +3,9 @@ - + -EGS Brachy: /Users/marc/dev/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/eb_tests/variable_w_recycling/__init__.py File Reference +EGS Brachy: /Users/marc/Developer/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/eb_tests/variable_w_recycling/__init__.py File Reference @@ -30,7 +30,7 @@ - + @@ -30,7 +30,7 @@ - + +
-Generated by doxygen 1.9.5 +Generated by doxygen 1.9.8
diff --git a/docs/variable__w__recycling_2test_8py.html b/docs/variable__w__recycling_2test_8py.html index 310ded22..231a5095 100644 --- a/docs/variable__w__recycling_2test_8py.html +++ b/docs/variable__w__recycling_2test_8py.html @@ -3,9 +3,9 @@ - + -EGS Brachy: /Users/marc/dev/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/eb_tests/variable_w_recycling/test.py File Reference +EGS Brachy: /Users/marc/Developer/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/eb_tests/variable_w_recycling/test.py File Reference @@ -30,7 +30,7 @@ - + @@ -30,7 +30,7 @@ - + +
15from eb_tests.utils import (compare_3ddose_files, doses_approx_equal,
16 extract_all_doses, read3ddose)
17
-
18EGSINP = "variable_w_recycling.egsinp"
+
18EGSINP = "variable_w_recycling.egsinp"
19TIME_LIMIT_S_PER_MHZ = 15/2993. # s / MHz
20
21# benchmark doses calcualted using egs_brachy and gold_standard.egsinp
22BENCHMARK_DOSES = [(1.061E-13, 0.0001), (1.644E-13, 0.0001)]
23
24
-
25def compare_results(egslst, inp_name):
+
+
25def compare_results(egslst, inp_name):
26
27 gold_standard = os.path.join(os.path.dirname(os.path.abspath(__file__)), "gold_standard.3ddose")
28 run_doses = inp_name+".phantom.3ddose"
@@ -110,11 +116,12 @@
31 gold_standard, run_doses, max_percent_diff=0.0015)
32
33 return doses_close, read3ddose(run_doses), read3ddose(gold_standard)
-
eb_tests.utils
Definition: utils.py:1
+
+
eb_tests.utils
Definition utils.py:1
-Generated by doxygen 1.9.5 +Generated by doxygen 1.9.8
diff --git a/docs/volume__correction_2____init_____8py.html b/docs/volume__correction_2____init_____8py.html index 0b4a5dc0..28ff4e9f 100644 --- a/docs/volume__correction_2____init_____8py.html +++ b/docs/volume__correction_2____init_____8py.html @@ -3,9 +3,9 @@ - + -EGS Brachy: /Users/marc/dev/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/eb_tests/volume_correction/__init__.py File Reference +EGS Brachy: /Users/marc/Developer/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/eb_tests/volume_correction/__init__.py File Reference @@ -30,7 +30,7 @@ - + @@ -30,7 +30,7 @@ - + +
-Generated by doxygen 1.9.5 +Generated by doxygen 1.9.8
diff --git a/docs/volume__correction_2test_8py.html b/docs/volume__correction_2test_8py.html index 2cb03f7a..259c16f5 100644 --- a/docs/volume__correction_2test_8py.html +++ b/docs/volume__correction_2test_8py.html @@ -3,9 +3,9 @@ - + -EGS Brachy: /Users/marc/dev/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/eb_tests/volume_correction/test.py File Reference +EGS Brachy: /Users/marc/Developer/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/eb_tests/volume_correction/test.py File Reference @@ -30,7 +30,7 @@ - + @@ -30,7 +30,7 @@ - + +
Go to the documentation of this file.
1"""
2
3A test of the egs_brachy Monte Carlo volume correction routines. The volume of
-
4phantom voxels overlapped by sources and other phantoms are calculated by
-
5egs_brachy and compared with analytical values.
-
6
+
4phantom voxels overlapped by sources and other phantoms are calculated by
+
5egs_brachy and compared with analytical values.
+
6
7"""
-
8
-
9import csv
-
10import math
-
11import re
-
12
-
13EGSINP = "vc.egsinp"
-
14TIME_LIMIT_S_PER_MHZ = 1 / 2993.# s / MHz
-
15
-
16expected_volumes = {
-
17 "source_volume": 4/3.*math.pi*0.1**3,
+
8
+
9import csv
+
10import math
+
11import re
+
12
+
13EGSINP = "vc.egsinp"
+
14TIME_LIMIT_S_PER_MHZ = 1 / 2993.# s / MHz
+
15
+
16expected_volumes = {
+
17 "source_volume": 4/3.*math.pi*0.1**3,
18 "bounding_shape_volume": 4/3.*math.pi*0.11**3,
19 "extra_bounding_shape_vol": 8**3,
20 "box_reg_0": 10**3 - 6**3,
@@ -104,16 +109,19 @@
25}
26
27
-
28def approx_equal( a, b, eps=0.001 ):
+
+
28def approx_equal( a, b, eps=0.001 ):
29 same_sign = a*b >= 0
30 return same_sign and abs(math.log( a ) - math.log(b)) <= eps
31
32
-
33def read_vols(phant, inp_name):
+
+
+
33def read_vols(phant, inp_name):
34 """Read voxel values for the phanton named 'phant' and
-
35 return the region volumes for that phantom"""
-
36
-
37 path = "%s.%s.voxels" % (inp_name, phant)
+
35 return the region volumes for that phantom"""
+
36
+
37 path = "%s.%s.voxels" % (inp_name, phant)
38 f = open(path, "r")
39 dialect = csv.Sniffer().sniff(f.read(1024))
40 f.seek(0)
@@ -126,11 +134,13 @@
47 return reg_vols
48
49
-
50def compare_results(egslst, inp_name):
+
+
+
50def compare_results(egslst, inp_name):
51
-
52 box_vols = read_vols("box", inp_name)
-
53 phant_vols = read_vols("phantom", inp_name)
-
54 sph_phant_vols = read_vols("sph_phantom", inp_name)
+
52 box_vols = read_vols("box", inp_name)
+
53 phant_vols = read_vols("phantom", inp_name)
+
54 sph_phant_vols = read_vols("sph_phantom", inp_name)
55
56 vsource = float(re.findall("Volume of Source\s*=\s*(.*)\s*cm", egslst, re.IGNORECASE)[0])
57 bounding_vols = list(map(float, re.findall("Bounding shape volume\s*=\s*(.*)\s*cm", egslst, re.IGNORECASE)))
@@ -148,17 +158,18 @@
69
70 all_close = True
71 for k,v in list(expected_volumes.items()):
-
72 if not approx_equal(v, actual[k]):
+
72 if not approx_equal(v, actual[k]):
73 print(("Vol comparison failed for %s: Actual=%E Expected=%E" % (k, actual[k], v)))
74 all_close = False
75
76 return all_close, actual, expected_volumes
-
eb_tests.volume_correction.test.read_vols
def read_vols(phant, inp_name)
Definition: test.py:33
-
eb_tests.volume_correction.test.approx_equal
def approx_equal(a, b, eps=0.001)
Definition: test.py:28
+
+
eb_tests.volume_correction.test.approx_equal
approx_equal(a, b, eps=0.001)
Definition test.py:28
+
eb_tests.volume_correction.test.read_vols
read_vols(phant, inp_name)
Definition test.py:33
-Generated by doxygen 1.9.5 +Generated by doxygen 1.9.8