Document how different entities are to be referenced

[sanjayankur31]

Most are to be referred in the /../.../... form following the document hierarchy. Some components where a size is provided are to be referenced using the [..] index notation. It'll be good to document this somewhere so it is clear to users.

[sanjayankur31]

I'm not sure if this is consistent. When using NEURON, one must use the /../ form, it does not accept the `[ ]/' form at all.

This works:

    simulation.add_column_to_output_file("output0",
                                         column_id="pop0_0_v_Seg1_dend_1",
                                         quantity="pop0/0/olm/7/v")

but this does not:

    simulation.add_column_to_output_file("output0",
                                         column_id="pop0_0_v_Seg1_dend_1",
                                         quantity="pop0[0]/olm/7/v")

It results in a NEURON writer error, so either there's a bug in the writer class, or there's another reason why this doesn't work:

Exception in thread "main" java.lang.NullPointerException
        at org.neuroml.export.neuron.LEMSQuantityPathNeuron.getExposure(LEMSQuantityPathNeuron.java:91)
        at org.neuroml.export.neuron.LEMSQuantityPathNeuron.getExposure(LEMSQuantityPathNeuron.java:117)
        at org.neuroml.export.neuron.LEMSQuantityPathNeuron.getDimension(LEMSQuantityPathNeuron.java:151)
        at org.neuroml.export.neuron.NeuronWriter.getMainScript(NeuronWriter.java:1400)
        at org.neuroml.export.neuron.NeuronWriter.generateMainScriptAndMods(NeuronWriter.java:277)
        at org.neuroml.export.neuron.NeuronWriter.generateAndRun(NeuronWriter.java:155)
        at org.neuroml.JNeuroML.main(JNeuroML.java:517)

I'm also unclear why one has to mention the name of the cell component (olm) in this case here.

[sanjayankur31]

Using [0] works fine in the izhikevich example, even with NEURON, so it looks like it works for cells that do not have multiple compartments. Again, not sure if this is a LEMS thing or an export bug.

[sanjayankur31]

@pgleeson, using indexing without the cell name does not work. So here's what I have so far. Noting this here so I can remove it from the example in the docs.

    simulation.add_column_to_output_file("output0",
                                         column_id="pop0_0_v_Seg1_dend_1",
                                         quantity="pop0/0/olm/7/v")
    # TODO: why does the name of the cell component have to be included? This
    # does not work, for example.
    """
    simulation.add_column_to_output_file("output0",
                                         column_id="pop0_0_v_Seg1_dend_1",
                                         quantity="pop0/0/7/v")
    """
    # TODO: why does indexing not work in this population?
    """
    simulation.add_column_to_output_file("output0",
                                         column_id="pop0_0_v_Seg1_dend_1",
                                         quantity="pop0[0]/olm/7/v")


    """
    # TODO: this does not work
    """
    simulation.add_column_to_output_file("output0",
                                         column_id="pop0_0_v_Seg1_dend_1",
                                         quantity="pop0[0]/7/v")
    """

All the cases that do not work give errors of this form:

Exception in thread "main" java.lang.NullPointerException
        at org.neuroml.export.neuron.LEMSQuantityPathNeuron.getExposure(LEMSQuantityPathNeuron.java:91)
        at org.neuroml.export.neuron.LEMSQuantityPathNeuron.getExposure(LEMSQuantityPathNeuron.java:117)
        at org.neuroml.export.neuron.LEMSQuantityPathNeuron.getDimension(LEMSQuantityPathNeuron.java:151)
        at org.neuroml.export.neuron.NeuronWriter.getMainScript(NeuronWriter.java:1400)
        at org.neuroml.export.neuron.NeuronWriter.generateMainScriptAndMods(NeuronWriter.java:277)
        at org.neuroml.export.neuron.NeuronWriter.generateAndRun(NeuronWriter.java:155)
        at org.neuroml.JNeuroML.main(JNeuroML.java:517)

[sanjayankur31]

Duplicate of #15