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Weina Ji
authored
SimulationConfig: remove amp_end from pulse input (#358)
To follow the change in SONATA specs: BlueBrain/sonata-extension#56
1 parent c1e6f17 commit bcdcaeb

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4 files changed

+14
-22
lines changed

4 files changed

+14
-22
lines changed

‎include/bbp/sonata/config.h

-2
Original file line numberDiff line numberDiff line change
@@ -476,8 +476,6 @@ class SONATA_API SimulationConfig
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struct InputPulse: public InputBase {
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/// The amount of current initially injected (nA)
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double ampStart{};
479-
/// The final current when a stimulus concludes (nA)
480-
double ampEnd{};
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/// The length of time each pulse lasts (ms)
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double width{};
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/// The frequency of pulse trains (Hz)

‎python/bindings.cpp

-3
Original file line numberDiff line numberDiff line change
@@ -844,9 +844,6 @@ PYBIND11_MODULE(_libsonata, m) {
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.def_readonly("amp_start",
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&SimulationConfig::InputPulse::ampStart,
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DOC_SIMULATIONCONFIG(InputPulse, ampStart))
847-
.def_readonly("amp_end",
848-
&SimulationConfig::InputPulse::ampEnd,
849-
DOC_SIMULATIONCONFIG(InputPulse, ampEnd))
850847
.def_readonly("width",
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&SimulationConfig::InputPulse::width,
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DOC_SIMULATIONCONFIG(InputPulse, width))

‎python/generated/docstrings.h

+14-16
Original file line numberDiff line numberDiff line change
@@ -794,14 +794,14 @@ static const char *__doc_bbp_sonata_SimulationConfig_InputAbsoluteShotNoise_rand
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R"doc(Override the random seed to introduce correlations between cells,
795795
default = None)doc";
796796

797+
static const char *__doc_bbp_sonata_SimulationConfig_InputAbsoluteShotNoise_representsPhysicalElectrode = R"doc(Whether this input represents a physical electrode. Default is false)doc";
798+
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static const char *__doc_bbp_sonata_SimulationConfig_InputAbsoluteShotNoise_reversal = R"doc(Reversal potential for conductance injection in mV. Default is 0)doc";
798800

799801
static const char *__doc_bbp_sonata_SimulationConfig_InputAbsoluteShotNoise_riseTime = R"doc(The rise time of the bi-exponential shots (ms))doc";
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801803
static const char *__doc_bbp_sonata_SimulationConfig_InputAbsoluteShotNoise_sigma = R"doc(signal std dev in nA (current_clamp) or uS (conductance).)doc";
802804

803-
static const char *__doc_bbp_sonata_SimulationConfig_InputAbsoluteShotNoise_representsPhysicalElectrode = R"doc(Whether this input represents a physical electrode. Default is false)doc";
804-
805805
static const char *__doc_bbp_sonata_SimulationConfig_InputBase = R"doc()doc";
806806

807807
static const char *__doc_bbp_sonata_SimulationConfig_InputBase_InputType = R"doc()doc";
@@ -878,12 +878,12 @@ static const char *__doc_bbp_sonata_SimulationConfig_InputNoise_meanPercent =
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R"doc(The mean value of current to inject as a percentage of threshold
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current, default = None)doc";
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881+
static const char *__doc_bbp_sonata_SimulationConfig_InputNoise_representsPhysicalElectrode = R"doc(Whether this input represents a physical electrode. Default is false)doc";
882+
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static const char *__doc_bbp_sonata_SimulationConfig_InputNoise_variance =
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R"doc(State var to track whether the value of injected noise current is mean
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or mean_percent)doc";
884886

885-
static const char *__doc_bbp_sonata_SimulationConfig_InputNoise_representsPhysicalElectrode = R"doc(Whether this input represents a physical electrode. Default is false)doc";
886-
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static const char *__doc_bbp_sonata_SimulationConfig_InputOrnsteinUhlenbeck = R"doc()doc";
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static const char *__doc_bbp_sonata_SimulationConfig_InputOrnsteinUhlenbeck_dt = R"doc(Timestep of generated signal in ms. Default is 0.25 ms)doc";
@@ -894,26 +894,24 @@ static const char *__doc_bbp_sonata_SimulationConfig_InputOrnsteinUhlenbeck_rand
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R"doc(Override the random seed to introduce correlations between cells,
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default = None)doc";
896896

897+
static const char *__doc_bbp_sonata_SimulationConfig_InputOrnsteinUhlenbeck_representsPhysicalElectrode = R"doc(Whether this input represents a physical electrode. Default is false)doc";
898+
897899
static const char *__doc_bbp_sonata_SimulationConfig_InputOrnsteinUhlenbeck_reversal = R"doc(Reversal potential for conductance injection in mV. Default is 0)doc";
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static const char *__doc_bbp_sonata_SimulationConfig_InputOrnsteinUhlenbeck_sigma = R"doc(Signal std dev in nA (current_clamp) or uS (conductance))doc";
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901903
static const char *__doc_bbp_sonata_SimulationConfig_InputOrnsteinUhlenbeck_tau = R"doc(Relaxation time constant in ms)doc";
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903-
static const char *__doc_bbp_sonata_SimulationConfig_InputOrnsteinUhlenbeck_representsPhysicalElectrode = R"doc(Whether this input represents a physical electrode. Default is false)doc";
904-
905905
static const char *__doc_bbp_sonata_SimulationConfig_InputPulse = R"doc()doc";
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907-
static const char *__doc_bbp_sonata_SimulationConfig_InputPulse_ampEnd = R"doc(The final current when a stimulus concludes (nA))doc";
908-
909907
static const char *__doc_bbp_sonata_SimulationConfig_InputPulse_ampStart = R"doc(The amount of current initially injected (nA))doc";
910908

911909
static const char *__doc_bbp_sonata_SimulationConfig_InputPulse_frequency = R"doc(The frequency of pulse trains (Hz))doc";
912910

913-
static const char *__doc_bbp_sonata_SimulationConfig_InputPulse_width = R"doc(The length of time each pulse lasts (ms))doc";
914-
915911
static const char *__doc_bbp_sonata_SimulationConfig_InputPulse_representsPhysicalElectrode = R"doc(Whether this input represents a physical electrode. Default is false)doc";
916912

913+
static const char *__doc_bbp_sonata_SimulationConfig_InputPulse_width = R"doc(The length of time each pulse lasts (ms))doc";
914+
917915
static const char *__doc_bbp_sonata_SimulationConfig_InputRelativeLinear = R"doc()doc";
918916

919917
static const char *__doc_bbp_sonata_SimulationConfig_InputRelativeLinear_percentEnd = R"doc(The percentage of a cell's threshold current to inject at the end)doc";
@@ -934,6 +932,8 @@ static const char *__doc_bbp_sonata_SimulationConfig_InputRelativeOrnsteinUhlenb
934932
R"doc(Override the random seed to introduce correlations between cells,
935933
default = None)doc";
936934

935+
static const char *__doc_bbp_sonata_SimulationConfig_InputRelativeOrnsteinUhlenbeck_representsPhysicalElectrode = R"doc(Whether this input represents a physical electrode. Default is false)doc";
936+
937937
static const char *__doc_bbp_sonata_SimulationConfig_InputRelativeOrnsteinUhlenbeck_reversal = R"doc(Reversal potential for conductance injection in mV. Default is 0)doc";
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939939
static const char *__doc_bbp_sonata_SimulationConfig_InputRelativeOrnsteinUhlenbeck_sdPercent =
@@ -942,8 +942,6 @@ R"doc(Signal std dev as percentage of a cell’s threshold current
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943943
static const char *__doc_bbp_sonata_SimulationConfig_InputRelativeOrnsteinUhlenbeck_tau = R"doc(Relaxation time constant in ms)doc";
944944

945-
static const char *__doc_bbp_sonata_SimulationConfig_InputRelativeOrnsteinUhlenbeck_representsPhysicalElectrode = R"doc(Whether this input represents a physical electrode. Default is false)doc";
946-
947945
static const char *__doc_bbp_sonata_SimulationConfig_InputRelativeShotNoise = R"doc()doc";
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949947
static const char *__doc_bbp_sonata_SimulationConfig_InputRelativeShotNoise_ampCv = R"doc(The coefficient of variation (sd/mean) of gamma-distributed amplitudes)doc";
@@ -960,6 +958,8 @@ static const char *__doc_bbp_sonata_SimulationConfig_InputRelativeShotNoise_rand
960958
R"doc(Override the random seed to introduce correlations between cells,
961959
default = None)doc";
962960

961+
static const char *__doc_bbp_sonata_SimulationConfig_InputRelativeShotNoise_representsPhysicalElectrode = R"doc(Whether this input represents a physical electrode. Default is false)doc";
962+
963963
static const char *__doc_bbp_sonata_SimulationConfig_InputRelativeShotNoise_reversal = R"doc(Reversal potential for conductance injection in mV. Default is 0)doc";
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965965
static const char *__doc_bbp_sonata_SimulationConfig_InputRelativeShotNoise_riseTime = R"doc(The rise time of the bi-exponential shots (ms))doc";
@@ -968,8 +968,6 @@ static const char *__doc_bbp_sonata_SimulationConfig_InputRelativeShotNoise_sdPe
968968
R"doc(signal std dev as percentage of a cell’s threshold current
969969
(current_clamp) or inverse input resistance (conductance).)doc";
970970

971-
static const char *__doc_bbp_sonata_SimulationConfig_InputRelativeShotNoise_representsPhysicalElectrode = R"doc(Whether this input represents a physical electrode. Default is false)doc";
972-
973971
static const char *__doc_bbp_sonata_SimulationConfig_InputSeclamp = R"doc()doc";
974972

975973
static const char *__doc_bbp_sonata_SimulationConfig_InputSeclamp_seriesResistance = R"doc(The series resistance (Mohm), default is 0.01 Mohm)doc";
@@ -996,12 +994,12 @@ default = None)doc";
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997995
static const char *__doc_bbp_sonata_SimulationConfig_InputShotNoise_rate = R"doc(Rate of Poisson events (Hz))doc";
998996

997+
static const char *__doc_bbp_sonata_SimulationConfig_InputShotNoise_representsPhysicalElectrode = R"doc(Whether this input represents a physical electrode. Default is false)doc";
998+
999999
static const char *__doc_bbp_sonata_SimulationConfig_InputShotNoise_reversal = R"doc(Reversal potential for conductance injection in mV. Default is 0)doc";
10001000

10011001
static const char *__doc_bbp_sonata_SimulationConfig_InputShotNoise_riseTime = R"doc(The rise time of the bi-exponential shots (ms))doc";
10021002

1003-
static const char *__doc_bbp_sonata_SimulationConfig_InputShotNoise_representsPhysicalElectrode = R"doc(Whether this input represents a physical electrode. Default is false)doc";
1004-
10051003
static const char *__doc_bbp_sonata_SimulationConfig_InputSubthreshold = R"doc()doc";
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10071005
static const char *__doc_bbp_sonata_SimulationConfig_InputSubthreshold_percentLess = R"doc(A percentage adjusted from 100 of a cell's threshold current)doc";

‎src/config.cpp

-1
Original file line numberDiff line numberDiff line change
@@ -432,7 +432,6 @@ SimulationConfig::Input parseInputModule(const nlohmann::json& valueIt,
432432
parseMandatory(valueIt, "amp_start", debugStr, ret.ampStart);
433433
parseMandatory(valueIt, "width", debugStr, ret.width);
434434
parseMandatory(valueIt, "frequency", debugStr, ret.frequency);
435-
parseOptional(valueIt, "amp_end", ret.ampEnd, {ret.ampStart});
436435
parseOptional(valueIt,
437436
"represents_physical_electrode",
438437
ret.representsPhysicalElectrode,

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