Comments (4)
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.
from documentation.
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.
from documentation.
@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)
from documentation.
Duplicate of #15
from documentation.
Related Issues (20)
- As a user, I want a page that lists what validation tests are run by NeuroML
- Minor typo in 'Getting Started' documentation HOT 3
- Document when one should use NeuroML for creating new ComponentTypes, and when one should use LEMS
- Update editorial board
- Add bluepyopt to docs
- Schema docs: add a new tab that quotes the type definition from the XSD HOT 1
- Add HBP SWC viewer
- Add some pages on working with existing NeuroML models in the "getting started with .." section
- Note HDF5 export somewhere
- Binder not using latest main for notebooks (neither is Colab) HOT 4
- Add page on for Harmony 2024 HOT 1
- Investigate SNT for NeuroML support
- Script and notebook on "A two population network of regular spiking Izhikevich neurons" failing to simulate HOT 8
- Issue on page /Userdocs/Software/pyNeuroML.html: update to list extras provided by the python package
- Add basic info on HH formalism---useful for channel conversions
- Document usage on Powershell
- In introductory tutorials, maybe start with playing with a cell model and doing things
- Issue on page /Userdocs/LEMS_elements/Dynamics.html: add LEMS schema to inform users of right order
- IncludeType is not in our schema documentation
- Docs site for nml reference has updated apparance - intended? HOT 1
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from documentation.