Merge pull request #1 from CNS-OIST/py2py3

python2/python3 compatibility

Author: FrancescoCasalegno

manual_tutorials/HH_APprop/HH_APprop.py

@@ -34,6 +34,7 @@
 # # # # # # # # # # # # # # # # # # # IMPORTS # # # # # # # # # # # # # # # # # #
 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
 
+from __future__ import print_function
 import steps.model as smodel
 import steps.geom as sgeom
 import steps.rng as srng
@@ -272,14 +273,14 @@
 for i in range(mesh.nverts):
 	if ((mesh.getVertex(i)[2] < (mesh.getBoundMin()[2]+0.1e-6))):
 		injverts.append(i)
-print "Found ", injverts.__len__(), "I_inject vertices"
+print("Found ", injverts.__len__(), "I_inject vertices")
 
 facetris = []
 for i in range(mesh.ntris):
 	tri = mesh.getTri(i) 
 	if ((tri[0] in injverts) and (tri[1] in injverts) and (tri[2] in injverts)):
 		facetris.append(i)
-print "Found ", facetris.__len__(), "triangles on bottom face"
+print("Found ", facetris.__len__(), "triangles on bottom face")
 
 memb_tris = list(mesh.getSurfTris()) 
 
@@ -404,7 +405,7 @@
 
 # Run the simulation
 for l in range(N_timepoints):
-    print "\nTpnt: ", l,
+    print("\nTpnt: ", l,)
 
     sim.run(DT_sim*l)
 

manual_tutorials/HH_APprop/HH_APprop_tetode.py

@@ -34,6 +34,7 @@
 # # # # # # # # # # # # # # # # # # # IMPORTS # # # # # # # # # # # # # # # # # #
 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
 
+from __future__ import print_function
 import steps.model as smodel
 import steps.geom as sgeom
 import steps.rng as srng
@@ -272,14 +273,14 @@
 for i in range(mesh.nverts):
 	if ((mesh.getVertex(i)[2] < (mesh.getBoundMin()[2]+0.1e-6))):
 		injverts.append(i)
-print "Found ", injverts.__len__(), "I_inject vertices"
+print("Found ", injverts.__len__(), "I_inject vertices")
 
 facetris = []
 for i in range(mesh.ntris):
 	tri = mesh.getTri(i) 
 	if ((tri[0] in injverts) and (tri[1] in injverts) and (tri[2] in injverts)):
 		facetris.append(i)
-print "Found ", facetris.__len__(), "triangles on bottom face"
+print("Found ", facetris.__len__(), "triangles on bottom face")
 
 memb_tris = list(mesh.getSurfTris()) 
 
@@ -404,7 +405,7 @@
 
 # Run the simulation
 for l in range(N_timepoints):
-    print "\nTpnt: ", l,
+    print("\nTpnt: ", l,)
 
     sim.run(DT_sim*l)
 

manual_tutorials/HH_APprop/HH_APprop_tetopsplit.py

@@ -33,6 +33,7 @@
 # # # # # # # # # # # # # # # # # # # IMPORTS # # # # # # # # # # # # # # # # # #
 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
 
+from __future__ import print_function
 import steps.model as smodel
 import steps.geom as sgeom
 import steps.rng as srng
@@ -279,14 +280,14 @@
 for i in range(mesh.nverts):
 	if ((mesh.getVertex(i)[2] < (mesh.getBoundMin()[2]+0.1e-6))):
 		injverts.append(i)
-if steps.mpi.rank ==0: print "Found ", injverts.__len__(), "I_inject vertices"
+if steps.mpi.rank ==0: print("Found ", injverts.__len__(), "I_inject vertices")
 
 facetris = []
 for i in range(mesh.ntris):
 	tri = mesh.getTri(i) 
 	if ((tri[0] in injverts) and (tri[1] in injverts) and (tri[2] in injverts)):
 		facetris.append(i)
-if steps.mpi.rank ==0: print "Found ", facetris.__len__(), "triangles on bottom face"
+if steps.mpi.rank ==0: print("Found ", facetris.__len__(), "triangles on bottom face")
 
 memb_tris = list(mesh.getSurfTris()) 
 
@@ -385,7 +386,7 @@
 
 # Run the simulation
 for l in range(N_timepoints):
-    if steps.mpi.rank ==0: print "Tpnt: ", l,"/", N_timepoints
+    if steps.mpi.rank ==0: print("Tpnt: ", l,"/", N_timepoints)
 
     sim.run(DT_sim*l)
 

manual_tutorials/HH_APprop/runHH_APprop.py

@@ -30,6 +30,7 @@
 
 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #  
 
+from __future__ import print_function
 from pylab import *
 
 from HH_APprop import *
@@ -42,7 +43,7 @@
 
 def plotVz(tidx):
     if (tidx >= tpnt.size): 
-        print 'Time index out of range'
+        print('Time index out of range')
         return
     plot(results[1]*1e6, results[0][tidx], \
          label=str(1e3*tidx*DT_sim)+'ms', linewidth=3)
@@ -56,7 +57,7 @@ def plotVz(tidx):
 
 def plotIz(tidx, plotstyles = ['-', '--']):
     if (tidx >= tpnt.size): 
-        print 'Time index out of range'
+        print('Time index out of range')
         return
     plot(results[4]*1e6, results[2][tidx], plotstyles[0],\
          label = 'Na: '+str(1e3*tidx*DT_sim)+'ms', linewidth=3)

manual_tutorials/HH_APprop/runHH_APprop_tetode.py

@@ -30,6 +30,7 @@
 
 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #  
 
+from __future__ import print_function
 from pylab import *
 
 from HH_APprop_tetode import *
@@ -42,7 +43,7 @@
 
 def plotVz(tidx):
     if (tidx >= tpnt.size): 
-        print 'Time index out of range'
+        print('Time index out of range')
         return
     plot(results[1]*1e6, results[0][tidx], \
          label=str(1e3*tidx*DT_sim)+'ms', linewidth=3)

manual_tutorials/diffusion/diffusion.py

@@ -27,6 +27,7 @@
 
 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
 
+from __future__ import print_function
 import math
 import numpy
 import pylab
@@ -50,10 +51,10 @@
 INT = 0.101
 
 # The number of molecules to be injected into the centre
-NINJECT = 10000	
+NINJECT = 10000    
 
 # The number of tetrahedral elements to sample data from. 
-SAMPLE = 2000	
+SAMPLE = 2000    
 
 # The diffusion constant for our diffusing species (m^2/s)
 DCST= 20.0e-12
@@ -70,13 +71,13 @@
 
 def printtime(end_time):
 
-	totsecs = int(end_time-beg_time)
-	sec = totsecs%60
-	totmin = totsecs/60
-	min = totmin%60
-	hours = totmin/60
-	
-	print 'Simulation time: %d h, %d min, %d sec' %(hours, min, sec)
+    totsecs = int(end_time-beg_time)
+    sec = totsecs%60
+    totmin = totsecs/60
+    min = totmin%60
+    hours = totmin/60
+    
+    print('Simulation time: %d h, %d min, %d sec' %(hours, min, sec))
 
 ########################################################################
 
@@ -92,17 +93,17 @@ def gen_model():
 
 def gen_geom():
 
-    print "Loading mesh..."
+    print("Loading mesh...")
     mesh = smeshio.loadMesh('meshes/sphere_rad10_11Ktets')[0]
-    print "Mesh Loaded"
+    print("Mesh Loaded")
 
-    # Find the total number of tetrahedrons in the mesh	
+    # Find the total number of tetrahedrons in the mesh    
     ntets = mesh.countTets()
     # Create a compartment containing all tetrahedron
     comp = stetmesh.TmComp('cyto', mesh, range(ntets))
     comp.addVolsys('cytosolv')
 
-    print "Finding tetrahedron samples..."
+    print("Finding tetrahedron samples...")
     # Fetch the central tetrahedron index and store:
     ctetidx = mesh.findTetByPoint([0.0, 0.0, 0.0])
     tetidxs[0] = ctetidx
@@ -155,7 +156,7 @@ def gen_geom():
         # Store the radial distance (in microns):
         tetrads[i] = r*1.0e6
 
-    print "Tetrahedron samples found"
+    print("Tetrahedron samples found")
 
     return mesh
 
@@ -181,57 +182,57 @@ def gen_geom():
 
 # Run NITER number of iterations:
 for i in range(NITER):
-	sim.reset()
-	print "Running iteration", i
+    sim.reset()
+    print("Running iteration", i)
     # Inject all molecules into the central tet:
-	sim.setTetCount(ctetidx, 'A', NINJECT)
-	for j in range(ntpnts):
-		sim.run(tpnts[j])
+    sim.setTetCount(ctetidx, 'A', NINJECT)
+    for j in range(ntpnts):
+        sim.run(tpnts[j])
         # Loop over the tetrahedrons we are saving data for
-		for k in range(SAMPLE):
+        for k in range(SAMPLE):
             # Save the concentration in the tetrahedron, in uM
-			res[i, j, k] = sim.getTetConc(int(tetidxs[k]), 'A')*1.0e6
-	printtime(time.time())
+            res[i, j, k] = sim.getTetConc(int(tetidxs[k]), 'A')*1.0e6
+    printtime(time.time())
 
 res_mean = numpy.mean(res, axis = 0)
 
 ########################################################################
 
 def plotres(tidx):
-	if (tidx >= INT/DT):
-		print "Time index is out of range."
-		return
-	
-	pylab.scatter(tetrads, res_mean[tidx], s=2)
-	pylab.xlabel('Radial distance of tetrahedron ($\mu$m)')			
-	pylab.ylabel('Concentration in tetrahedron ($\mu$M)')
-	t = tpnts[tidx]
-	pylab.title('Unbounded diffusion. Time: ' + str(t) + 's')
-	plotanlyt(t)
-	pylab.xlim(0.0, 10.0)
-	pylab.ylim(0.0)
-	pylab.show()
+    if (tidx >= INT/DT):
+        print("Time index is out of range.")
+        return
+    
+    pylab.scatter(tetrads, res_mean[tidx], s=2)
+    pylab.xlabel('Radial distance of tetrahedron ($\mu$m)')            
+    pylab.ylabel('Concentration in tetrahedron ($\mu$M)')
+    t = tpnts[tidx]
+    pylab.title('Unbounded diffusion. Time: ' + str(t) + 's')
+    plotanlyt(t)
+    pylab.xlim(0.0, 10.0)
+    pylab.ylim(0.0)
+    pylab.show()
 
 ########################################################################
 
-def plotanlyt(t): 	
-	segs = 100 	
-	anlytconc = numpy.zeros((segs)) 	
-	radialds = numpy.zeros((segs)) 	
-	maxrad = 0.0 	
-	for i in tetrads: 		
-		if (i > maxrad): maxrad = i 	
-	maxrad *= 1e-6 	
-	intervals = maxrad/segs 	
-	rad = 0.0 	
-	for i in range((segs)): 		
-		# Find the conc from analytical solution, and convert to mol/L 		
-		anlytconc[i]=1.0e3*(1/6.022e23)* \
-            ((NINJECT/(math.pow((4*math.pi*DCST*t),1.5)))* \
-             (math.exp((-1.0*(rad*rad))/(4*DCST*t)))) 		
-                radialds[i] = rad*1e6 		
-                rad += intervals 	
-	pylab.plot(radialds, anlytconc, color = 'red')
+def plotanlyt(t):     
+    segs = 100     
+    anlytconc = numpy.zeros((segs))     
+    radialds = numpy.zeros((segs))     
+    maxrad = 0.0     
+    for i in tetrads:         
+        if (i > maxrad): maxrad = i     
+    maxrad *= 1e-6     
+    intervals = maxrad/segs     
+    rad = 0.0     
+    for i in range((segs)):         
+        # Find the conc from analytical solution, and convert to mol/L         
+        anlytconc[i]=1.0e3*(1/6.022e23)* \
+                ((NINJECT/(math.pow((4*math.pi*DCST*t),1.5)))* \
+                (math.exp((-1.0*(rad*rad))/(4*DCST*t))))         
+        radialds[i] = rad*1e6         
+        rad += intervals     
+    pylab.plot(radialds, anlytconc, color = 'red')
 
 ########################################################################
 

manual_tutorials/diffusion_boundary/diffusion_boundary.py

@@ -27,6 +27,7 @@
 
 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
 
+from __future__ import print_function
 import steps.model as smodel
 import steps.geom as sgeom
 import steps.rng as srng
@@ -151,7 +152,7 @@ def gen_geom():
 
 def plot_binned(t_idx, bin_n = 100):
     if (t_idx > tpnts.size):
-        print "Time index is out of range."
+        print("Time index is out of range.")
         return
 
     z_tets = numpy.zeros(ntets)  

manual_tutorials/directional_dcst/boundary_directional_dcst.py

@@ -2,6 +2,7 @@
 
 """ Example of directional dcst."""
 
+from __future__ import print_function
 import random
 import steps.model as smodel
 import steps.geom as sgeom
@@ -36,23 +37,23 @@
 
 solver = solv.Tetexact(model, mesh, rng)
 
-print "Set directonal dcst from comp1 to comp2, and from comp2 to comp1 to 0..."
+print("Set directonal dcst from comp1 to comp2, and from comp2 to comp1 to 0...")
 solver.setCompCount("comp1", "A", 100)
 solver.setCompCount("comp2", "A", 20)
 solver.setDiffBoundaryDcst("boundary", "A", 0)
-print "V1 Count: ", solver.getCompCount("comp1", "A")
-print "V2 Count: ", solver.getCompCount("comp2", "A")
+print("V1 Count: ", solver.getCompCount("comp1", "A"))
+print("V2 Count: ", solver.getCompCount("comp2", "A"))
 solver.run(1)
-print "V1 Count: ", solver.getCompCount("comp1", "A")
-print "V2 Count: ", solver.getCompCount("comp2", "A")
+print("V1 Count: ", solver.getCompCount("comp1", "A"))
+print("V2 Count: ", solver.getCompCount("comp2", "A"))
 
-print "Set directonal dcst from comp1 to comp2 to 1/10 of DCST, and 0 from comp2 to comp1..."
+print("Set directonal dcst from comp1 to comp2 to 1/10 of DCST, and 0 from comp2 to comp1...")
 solver.reset()
 solver.setCompCount("comp1", "A", 100)
 solver.setDiffBoundaryDcst("boundary", "A", DCST / 10, "comp2")
 solver.setDiffBoundaryDcst("boundary", "A", 0.0, "comp1")
-print "V1 Count: ", solver.getCompCount("comp1", "A")
-print "V2 Count: ", solver.getCompCount("comp2", "A")
+print("V1 Count: ", solver.getCompCount("comp1", "A"))
+print("V2 Count: ", solver.getCompCount("comp2", "A"))
 solver.run(1)
-print "V1 Count: ", solver.getCompCount("comp1", "A")
-print "V2 Count: ", solver.getCompCount("comp2", "A")
+print("V1 Count: ", solver.getCompCount("comp1", "A"))
+print("V2 Count: ", solver.getCompCount("comp2", "A"))