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Improve error reporting when things go wrong while generating NEURON code: to enable the use to have some idea of where to look #106

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Improve error reporting when things go wrong while generating NEURON code: to enable the use to have some idea of where to look #106

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e6021af
chore(lems-quantity-path-neuron): print out super info on new line
sanjayankur31 Aug 25, 2023
0c86e27
feat(neuron-writer): print out what quantity path errors happen on
sanjayankur31 Aug 25, 2023
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2 changes: 1 addition & 1 deletion src/main/java/org/neuroml/export/neuron/LEMSQuantityPathNeuron.java
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Original file line number Diff line number Diff line change
Expand Up @@ -427,7 +427,7 @@ public String toString()
ref = "=== Unable to determine reference: " + ex;
}

ref += super.toString()
ref += "\n" + super.toString()
+ "\n ** Neuron ref: " + ref
+ "\n popsOrComponents: " + popsOrComponents
+ "\n targetComp: " + targetComp
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48 changes: 32 additions & 16 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 @@ -1277,6 +1277,7 @@ else if(cc.getComponentType().isOrExtends(NeuroMLElements.CONTINUOUS_CONNECTION_
processInputLists(main, targetComp);
processExplicitInputs(main, targetComp);

E.info("Setting up recorders...");
main.append(bIndent+"trec = h.Vector()\n");
main.append(bIndent+"trec.record(h._ref_t)\n\n");

Expand Down Expand Up @@ -1439,28 +1440,43 @@ else if(cc.getComponentType().isOrExtends(NeuroMLElements.CONTINUOUS_CONNECTION_
String quantity = colComp.getStringValue("quantity");
String scale = "1";

LEMSQuantityPathNeuron lqp = new LEMSQuantityPathNeuron(quantity, scale, targetComp, compMechNamesHoc, popsOrComponents, compIdsVsCells, hocRefsVsInputs, lems);
LEMSQuantityPathNeuron lqp = null;
try
{
lqp = new LEMSQuantityPathNeuron(quantity, scale, targetComp, compMechNamesHoc, popsOrComponents, compIdsVsCells, hocRefsVsInputs, lems);

//System.out.println("lqp: "+lqp);
//System.out.println("lqp: "+lqp);

columnsPre.get(outfileId).add(bIndent+"# Column: " + lqp.getQuantity());
columnsPre.get(outfileId).add(bIndent+"h(' objectvar v_" + colId + " ')");
columnsPre.get(outfileId).add(bIndent+"h(' { v_" + colId + " = new Vector() } ')");
columnsPre.get(outfileId).add(bIndent+"h(' { v_" + colId + ".record(&" + lqp.getNeuronVariableReference() + ") } ')");
columnsPre.get(outfileId).add(bIndent+"if self.abs_tol is None or self.rel_tol is None:\n");
columnsPre.get(outfileId).add(bIndent+" h.v_" + colId + ".resize((h.tstop * h.steps_per_ms) + 1)");
columnsPre.get(outfileId).add(bIndent+"# Column: " + lqp.getQuantity());
columnsPre.get(outfileId).add(bIndent+"h(' objectvar v_" + colId + " ')");
columnsPre.get(outfileId).add(bIndent+"h(' { v_" + colId + " = new Vector() } ')");
columnsPre.get(outfileId).add(bIndent+"h(' { v_" + colId + ".record(&" + lqp.getNeuronVariableReference() + ") } ')");
columnsPre.get(outfileId).add(bIndent+"if self.abs_tol is None or self.rel_tol is None:\n");
columnsPre.get(outfileId).add(bIndent+" h.v_" + colId + ".resize((h.tstop * h.steps_per_ms) + 1)");

float conv = NRNUtils.getNeuronUnitFactor(lqp.getDimension().getName());
String factor = (conv == 1) ? "" : " / " + conv;
float conv = NRNUtils.getNeuronUnitFactor(lqp.getDimension().getName());
String factor = (conv == 1) ? "" : " / " + conv;

columnsPost0.get(outfileId).add(bIndent+
"py_v_" + colId + " = [ float(x " + factor + ") for x in h.v_" + colId + ".to_python() ] # Convert to Python list for speed, variable has dim: " + lqp.getDimension().getName());
columnsPost0.get(outfileId).add(bIndent+
"py_v_" + colId + " = [ float(x " + factor + ") for x in h.v_" + colId + ".to_python() ] # Convert to Python list for speed, variable has dim: " + lqp.getDimension().getName());

/*columnsPostTraces.get(outfileId).add(
" + '%e\\t'%(py_v_" + colId + "[i]) ");*/
/*columnsPostTraces.get(outfileId).add(
" + '%e\\t'%(py_v_" + colId + "[i]) ");*/

columnsPostTraces.get(outfileId).add("%e\\t");
writingVariables.get(outfileId).add("py_v_" + colId + "[i], ");
columnsPostTraces.get(outfileId).add("%e\\t");
writingVariables.get(outfileId).add("py_v_" + colId + "[i], ");
}
catch(NullPointerException e){
String err = "Error processing outputfile quantity: " + quantity + "\n";
try {
err += "Reference: " + lqp + "\n";
throw new ContentError(err + e);
}
catch(NullPointerException ex)
{
throw new ContentError(err + ex);
}
}

}
}
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