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Adding option to disable generation of gui elements for neuron
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Addresses part of NeuroML/jNeuroML#11
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@pgleeson
pgleeson committed Jun 10, 2014
1 parent 7f7849b commit 71ce848
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Showing 2 changed files with 115 additions and 46 deletions.
20 changes: 20 additions & 0 deletions src/main/java/org/neuroml/export/Utils.java
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Original file line number Diff line number Diff line change
Expand Up @@ -22,6 +22,7 @@
import org.lemsml.jlems.core.type.QuantityReader;
import org.lemsml.jlems.core.type.Unit;
import org.lemsml.jlems.core.xml.XMLException;
import org.lemsml.jlems.io.IOUtil;
import org.lemsml.jlems.io.reader.JarResourceInclusionReader;
import org.lemsml.jlems.io.util.FileUtil;
import org.lemsml.jlems.io.util.JUtil;
Expand Down Expand Up @@ -313,6 +314,25 @@ public static AbstractList reorderAlphabetically(AbstractList list, boolean asce
return list;
}

public static void runLemsFile(File f) throws ContentError, ParseError, ParseException, BuildException, XMLException, ConnectionError, RuntimeError {
loadLemsFile(f, true);
}

public static void loadLemsFile(File f, boolean run) throws ContentError, ParseError, ParseException, BuildException, XMLException, ConnectionError, RuntimeError {

Sim sim = Utils.readLemsNeuroMLFile(f);
sim.build();

if (run) {
sim.run();
IOUtil.saveReportAndTimesFile(sim);
E.info("Finished reading, building, running and displaying LEMS model");
} else {
E.info("Finished reading and building LEMS model");
}

}


public static void main(String[] args) throws Exception {

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141 changes: 95 additions & 46 deletions src/main/java/org/neuroml/export/neuron/NeuronWriter.java
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Original file line number Diff line number Diff line change
Expand Up @@ -18,7 +18,11 @@
import org.lemsml.export.dlems.DLemsWriter;
import org.lemsml.jlems.core.expression.ParseError;
import org.lemsml.jlems.core.logging.E;
import org.lemsml.jlems.core.run.ConnectionError;
import org.lemsml.jlems.core.run.RuntimeError;
import org.lemsml.jlems.core.sim.ContentError;
import org.lemsml.jlems.core.sim.ParseException;
import org.lemsml.jlems.core.type.BuildException;
import org.lemsml.jlems.core.type.Component;
import org.lemsml.jlems.core.type.Dimension;
import org.lemsml.jlems.core.type.DimensionalQuantity;
Expand All @@ -42,6 +46,7 @@
import org.lemsml.jlems.core.type.dynamics.StateVariable;
import org.lemsml.jlems.core.type.dynamics.TimeDerivative;
import org.lemsml.jlems.core.type.dynamics.Transition;
import org.lemsml.jlems.core.xml.XMLException;
import org.lemsml.jlems.io.util.FileUtil;
import org.neuroml.export.LEMSQuantityPath;
import org.neuroml.export.Utils;
Expand All @@ -64,13 +69,31 @@ public class NeuronWriter extends BaseWriter {
private File dirForMods;

ArrayList<File> allGeneratedFiles = new ArrayList<File>();
boolean nogui = false;
static boolean debug = false;


public enum ChannelConductanceOption {
FIXED_REVERSAL_POTENTIAL, USE_NERNST, USE_GHK;
float erev;

};



public static void exportToNeuron(File lemsFile, boolean nogui, boolean run) throws ContentError, ParseError, ConnectionError, BuildException, BuildException, RuntimeError, ParseException, XMLException, GenerationException, NeuroMLException, IOException {

Lems lems = Utils.readLemsNeuroMLFile(lemsFile).getLems();

NeuronWriter nw = new NeuronWriter(lems);
nw.nogui = nogui;
String nrn = nw.getMainScript();

File nrnFile = new File(lemsFile.getParentFile(), lemsFile.getName().replaceAll(".xml", "_nrn.py"));
E.info("Writing to: " + nrnFile.getAbsolutePath());

FileUtil.writeStringToFile(nrn, nrnFile);
}

public NeuronWriter(Lems l) {
super(l, NRNConst.NEURON_FORMAT);
Expand All @@ -90,6 +113,16 @@ protected void addComment(StringBuilder sb, String comment) {
private void reset() {
allGeneratedFiles.clear();
}

public void setNoGui(boolean nogui) {
this.nogui = nogui;
}

public boolean isNoGui() {
return nogui;
}



public ArrayList<File> generateMainScriptAndMods(File mainFile)
throws ContentError, ParseError, IOException, JAXBException,
Expand Down Expand Up @@ -131,7 +164,7 @@ private static String getStateVarName(String sv) {
private static String checkForBinaryOperators(String expr) {
return expr.replace("\\.gt\\.", ">").replace("\\.geq\\.", ">=")
.replace("\\.lt\\.", "<").replace("\\.leq\\.", "<=")
.replace("\\.and\\.", "&&");
.replace("\\.and\\.", "&&").replace("\\.neq\\.", "!=");
}

private static String checkForStateVarsAndNested(String expr,
Expand All @@ -151,6 +184,7 @@ private static String checkForStateVarsAndNested(String expr,
newExpr = newExpr.replaceAll("\\.leq\\.", "<=");
newExpr = newExpr.replaceAll("\\.lt\\.", "<=");
newExpr = newExpr.replaceAll("\\.eq\\.", "==");
newExpr = newExpr.replaceAll("\\.neq\\.", "!=");
newExpr = newExpr.replaceAll("\\.and.", "&&");

newExpr = newExpr.replaceAll(" ln\\(", " log(");
Expand Down Expand Up @@ -196,7 +230,12 @@ public String generate(File pdirForMods) throws NeuroMLException,

main.append("import neuron\n");
main.append("h = neuron.h\n");
main.append("h.load_file(\"nrngui.hoc\")\n\n");
if (nogui) {
main.append("h.load_file(\"stdlib.hoc\")\n\n");
main.append("h.load_file(\"stdgui.hoc\")\n\n");
} else {
main.append("h.load_file(\"nrngui.hoc\")\n\n");
}
main.append("h(\"objref p\")\n");
main.append("h(\"p = new PythonObject()\")\n\n");

Expand Down Expand Up @@ -584,42 +623,44 @@ public String generate(File pdirForMods) throws NeuroMLException,
ArrayList<String> displayGraphs = new ArrayList<String>();
HashMap<String, ArrayList<String>> plots = new HashMap<String, ArrayList<String>>();

for (Component dispComp : simCpt.getAllChildren()) {
if (dispComp.getName().indexOf("Display") >= 0) {
if (!nogui) {
for (Component dispComp : simCpt.getAllChildren()) {
if (dispComp.getName().indexOf("Display") >= 0) {

String dispId = dispComp.getID();
int plotColour = 1;
String dispId = dispComp.getID();
int plotColour = 1;

String dispGraph = "display_" + dispId;
if (!displayGraphs.contains(dispGraph)) {
displayGraphs.add(dispGraph);
}
String dispGraph = "display_" + dispId;
if (!displayGraphs.contains(dispGraph)) {
displayGraphs.add(dispGraph);
}

for (Component lineComp : dispComp.getAllChildren()) {
if (lineComp.getName().indexOf("Line") >= 0) {
for (Component lineComp : dispComp.getAllChildren()) {
if (lineComp.getName().indexOf("Line") >= 0) {

String quantity = lineComp.getStringValue("quantity");
String scale = lineComp.getStringValue("scale");

LEMSQuantityPathNeuron lqp = new LEMSQuantityPathNeuron(quantity, scale, targetComp, compMechNamesHoc, popsOrComponents, compIdsVsCells, lems);

if (plots.get(dispGraph) == null)
plots.put(dispGraph, new ArrayList<String>());
String quantity = lineComp.getStringValue("quantity");
String scale = lineComp.getStringValue("scale");

plots.get(dispGraph).add("# Line, plotting: " + lqp.getQuantity());
//plots.get(dispGraph).add("# compMechNamesHoc: " + compMechNamesHoc);
//plots.get(dispGraph).add("# " + lqp.toString().replaceAll("\n", "\n# "));
LEMSQuantityPathNeuron lqp = new LEMSQuantityPathNeuron(quantity, scale, targetComp, compMechNamesHoc, popsOrComponents, compIdsVsCells, lems);

plots.get(dispGraph).add(dispGraph + ".addexpr(\"" + lqp.getNeuronVariableReference() + "\", \"" + lqp.getNeuronVariableReference() + "\", " + plotColour + ", 1, 0.8, 0.9, 2)");
plotColour++;
if (plotColour > 10) {
plotColour = 1;
}
if (plots.get(dispGraph) == null)
plots.put(dispGraph, new ArrayList<String>());

}
}
}
}
plots.get(dispGraph).add("# Line, plotting: " + lqp.getQuantity());
//plots.get(dispGraph).add("# compMechNamesHoc: " + compMechNamesHoc);
//plots.get(dispGraph).add("# " + lqp.toString().replaceAll("\n", "\n# "));

plots.get(dispGraph).add(dispGraph + ".addexpr(\"" + lqp.getNeuronVariableReference() + "\", \"" + lqp.getNeuronVariableReference() + "\", " + plotColour + ", 1, 0.8, 0.9, 2)");
plotColour++;
if (plotColour > 10) {
plotColour = 1;
}

}
}
}
}
}
main.append(toRec);

String len = simCpt.getStringValue("length");
Expand All @@ -640,18 +681,20 @@ public String generate(File pdirForMods) throws NeuroMLException,
main.append("h.dt = " + dt + "\n\n");
main.append("h.steps_per_ms = " + (float) (1d / Double.parseDouble(dt)) + "\n\n");

// main.append("objref SampleGraph\n");
for (String dg : displayGraphs) {
addComment(main, "Display: " + dg);
main.append(dg + " = h.Graph(0)\n");
main.append(dg + ".size(0,h.tstop,-80.0,50.0)\n");
main.append(dg + ".view(0, -80.0, h.tstop, 130.0, 80, 330, 330, 250)\n");
main.append("h.graphList[0].append(" + dg + ")\n");
for (String plot : plots.get(dg)) {
main.append(plot + "\n");
}
main.append("\n");
}

if (!nogui) {
for (String dg : displayGraphs) {
addComment(main, "Display: " + dg);
main.append(dg + " = h.Graph(0)\n");
main.append(dg + ".size(0,h.tstop,-80.0,50.0)\n");
main.append(dg + ".view(0, -80.0, h.tstop, 130.0, 80, 330, 330, 250)\n");
main.append("h.graphList[0].append(" + dg + ")\n");
for (String plot : plots.get(dg)) {
main.append(plot + "\n");
}
main.append("\n");
}
}

main.append("\n\n");

Expand Down Expand Up @@ -734,7 +777,7 @@ public String generate(File pdirForMods) throws NeuroMLException,

main.append("\n\n");

main.append("h.nrncontrolmenu()\n");
if (!nogui) main.append("h.nrncontrolmenu()\n");

main.append("h.run()\n\n");

Expand Down Expand Up @@ -764,6 +807,9 @@ public String generate(File pdirForMods) throws NeuroMLException,
}

main.append("print \"Done\"\n\n");
if (nogui) {
main.append("quit()\n");
}

return main.toString();
}
Expand Down Expand Up @@ -2101,6 +2147,7 @@ public static void main(String[] args) throws Exception {
lemsFiles.add(new File("../NeuroML2/LEMSexamples/LEMS_NML2_Ex0_IaF.xml"));
lemsFiles.add(new File("../NeuroML2/LEMSexamples/LEMS_NML2_Ex5_DetCell.xml"));
lemsFiles.add(new File("../NeuroML2/LEMSexamples/LEMS_NML2_Ex9_FN.xml"));
/*
lemsFiles.add(new File("../neuroConstruct/osb/cerebellum/cerebellar_granule_cell/GranuleCell/neuroConstruct/generatedNeuroML2/LEMS_GranuleCell.xml"));
lemsFiles.add(new File("../neuroConstruct/osb/invertebrate/lobster/PyloricNetwork/neuroConstruct/generatedNeuroML2/LEMS_PyloricPacemakerNetwork.xml"));
lemsFiles.add(new File("../neuroConstruct/osb/invertebrate/celegans/CElegansNeuroML/CElegans/pythonScripts/c302/LEMS_c302_A_Syns.xml"));
Expand All @@ -2109,7 +2156,7 @@ public static void main(String[] args) throws Exception {
lemsFiles.add(new File("src/test/resources/BIOMD0000000185_LEMS.xml"));
lemsFiles.add(new File("../neuroConstruct/osb/cerebral_cortex/networks/ACnet2/neuroConstruct/generatedNeuroML2/LEMS_ACnet2.xml"));
//lemsFiles.add(new File("../neuroConstruct/osb/hippocampus/networks/nc_superdeep/neuroConstruct/generatedNeuroML2/LEMS_nc_superdeep.xml"));
//lemsFiles.add(new File("../neuroConstruct/osb/hippocampus/networks/nc_superdeep/neuroConstruct/generatedNeuroML2/LEMS_nc_superdeep.xml"));*/

NeuronWriter nw = null;
String testScript = "";
Expand All @@ -2119,6 +2166,7 @@ public static void main(String[] args) throws Exception {
File mainFile = new File(lemsFile.getParentFile(), lemsFile.getName().replaceAll(".xml", "_nrn.py"));

nw = new NeuronWriter(lems);
nw.setNoGui(true);
ArrayList<File> ff = nw.generateMainScriptAndMods(mainFile);
for (File f : ff) {
System.out.println("Generated: " + f.getAbsolutePath());
Expand All @@ -2128,7 +2176,8 @@ public static void main(String[] args) throws Exception {
testScript += "echo\n";
testScript += "cd "+lemsFile.getParentFile().getCanonicalPath()+"\n";
testScript += "nrnivmodl\n";
testScript += "nrngui -python "+lemsFile.getName().replaceAll(".xml", "_nrn.py")+" \n";
String nrn = nw.isNoGui() ? "nrniv" : "nrngui";
testScript += nrn+" -python "+lemsFile.getName().replaceAll(".xml", "_nrn.py")+" \n";
testScript += "\n";
}
File t = new File("test.sh");
Expand Down

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