NetPyNE to NeuroML 2 conversion

[pgleeson]

Work on this is happening in this branch: https://github.com/Neurosim-lab/netpyne/tree/neuroml_export

NetPyNE -> NeuroML 2

See sim.py

• Handle export of NetStims when noise = 1
• Handle export of NetStims when 0 < noise < 1
• Solve issue with mapping izhikevich
• Export geom to *.cell.nml file
• Better export of only what has been requested to be saved/plotted

Importing NeuroML cells/synapses in NetPyNE

• * Add importNeuroML2Cell() in NetPyNE
• Add importNeuroML2Synapse() in NetPyNE

NeuroML 2 -> NetPyNE

See NetPyNEWriter.java, run.vm

• import of generic nml2 cells into NetPyNE (dependent on * above)
• generation of explicit lists of connections in netpyne from lists in nml

[salvadord]

@pgleeson - as mentioned I just released a version that make some changes to the netParams and simConfig structures: they are now objects of class NetParams and SimConfig, so can use the object methods to add stuff easily.
Also, all the inner structures (popParams, cellParams etc) are now orderedDicts (for consistency).
All the tuts, examples and most of documentation is already updated.
Sorry about the format changes, we are hoping this will be the last major change for a while. I'm happy to update the neuroml export/import funcs.

[pgleeson]

Ok, I'll look at the changes and make the updates in the nml import/export. I have a simple example of import working here: https://github.com/Neurosim-lab/netpyne/blob/c9794646cf7af138581b48d288bda3015c2d9f1c/examples/NeuroMLImport/SimpleNet_import.py

[salvadord]

@pgleeson - I was trying to test the neuroml export examples in the neuroml_export branch, but I don't get any new files, and last line says:
pyNeuroML >>> Unable to find file: /u/salvadord/Documents/ISB/Models/netpyne_repo/examples/HHTut/HH.cell.nml!

anything I'm missing or doing wrong?

Update: Actually I did get a new file: HHTut.net.nml, so guess just missing HH.cell.nml?

[pgleeson]

Working on generating the required NML <cell>/<izhikevich2007Cell> elements now... Previously I had manually placed a HH.cell.nml etc. there for testing.

[pgleeson]

@salvadord your issue above is solved in the latest version

[salvadord]

That's great, thanks!