Search found 37 matches
- Sat Sep 21, 2019 10:02 am
- Forum: Adding new mechanisms and functions to NEURON
- Topic: Filter Mechanism params by NMODL PARAMETER
- Replies: 8
- Views: 3724
Re: Filter Mechanism params by NMODL PARAMETER
Here is the today's solution. Thank you again! ms = h.MechanismStandard(mech_name, 1) param_name = h.ref('') param_names = [] for i in range(ms.count()): ms.name(param_name, i) param_names.append(param_name[0]) param_names = [name.split('_' + mech_name)[0] for name in param_names]
- Fri Sep 20, 2019 3:22 pm
- Forum: Adding new mechanisms and functions to NEURON
- Topic: Filter Mechanism params by NMODL PARAMETER
- Replies: 8
- Views: 3724
Re: Filter Mechanism params by NMODL PARAMETER
Thank you so much for so many options. I will try the old way tomorrow as it looks very neat. Today I've ended up with this solution: from neuron import h from nmodl import dsl mech_type = h.MechanismType(0) mech_type.select('hh') code = mech_type.code() driver = dsl.NmodlDriver() modast = driver.pa...
- Thu Sep 19, 2019 2:24 pm
- Forum: Adding new mechanisms and functions to NEURON
- Topic: Filter Mechanism params by NMODL PARAMETER
- Replies: 8
- Views: 3724
Re: Filter Mechanism params by NMODL PARAMETER
That is brilliant! Thank you!
- Thu Sep 19, 2019 12:27 pm
- Forum: Adding new mechanisms and functions to NEURON
- Topic: Filter Mechanism params by NMODL PARAMETER
- Replies: 8
- Views: 3724
Re: Filter Mechanism params by NMODL PARAMETER
If to be that precise, lets take this example: soma = h.Section(name='soma') soma.insert('hh') for seg in soma: for mech in seg: if mech.name() == 'hh': filtered = [] for n in dir(mech): v = getattr(mech, n) if n.startswith('__') or n in ('next', 'name', 'is_ion', 'segment',): continue filtered.appe...
- Thu Sep 19, 2019 7:25 am
- Forum: Adding new mechanisms and functions to NEURON
- Topic: Filter Mechanism params by NMODL PARAMETER
- Replies: 8
- Views: 3724
Filter Mechanism params by NMODL PARAMETER
Hello! I'm collecting all cell's mechanisms in Python like this: soma = h.Section(name='soma') // soma.insert( lots of mechanisms ) for seg in soma: for mech in seg: print(mech) mech contains parameters like 'gbar', 'g', 'ica' and so on. How can I filter them to get only those that are in 'PARAMETER...
- Wed Sep 11, 2019 12:07 pm
- Forum: Anatomically detailed models
- Topic: Export to .hoc with CellBuilder from Python
- Replies: 2
- Views: 7708
Re: Export to .hoc with CellBuilder from Python
Thank you for the response.
- Tue Sep 10, 2019 12:32 pm
- Forum: Anatomically detailed models
- Topic: Export to .hoc with CellBuilder from Python
- Replies: 2
- Views: 7708
Export to .hoc with CellBuilder from Python
Hi! I'm trying now for a week to properly export the currently loaded neuron model. There is only one loaded model in my namespace that I loaded like this. h.load_file('Cell_Scnn1a.hoc') cell_hoc = h.Cell_Scnn1a('/morphologies', 'Scnn1a_473845048_m.swc') It is absolutely properly exported to nml by ...
- Wed Sep 04, 2019 6:42 am
- Forum: Anatomically detailed models
- Topic: Save model's biophysics and morphology programmatically to .hoc
- Replies: 3
- Views: 7507
Re: Save model's biophysics and morphology programmatically to .hoc
I've managed to export it into a single nml file. h.load_file('Cell_Scnn1a.hoc') cell_hoc = h.Cell_Scnn1a('/morphologies', 'Scnn1a_473845048_m.swc') h.load_file("mview.hoc") mv = h.ModelView(0) mv_xml = h.ModelViewXML(mv) export_filepath = os.path.join('.', 'test.nml') mv_xml.exportNeuroML...
- Tue Sep 03, 2019 3:26 pm
- Forum: Anatomically detailed models
- Topic: Save model's biophysics and morphology programmatically to .hoc
- Replies: 3
- Views: 7507
Re: Save model's biophysics and morphology programmatically to .hoc
Am I correct that I would need to call proc exportNeuroML from share/lib/hoc/mview/mviewxml.hoc ?
- Tue Sep 03, 2019 11:25 am
- Forum: Anatomically detailed models
- Topic: Save model's biophysics and morphology programmatically to .hoc
- Replies: 3
- Views: 7507
Save model's biophysics and morphology programmatically to .hoc
Hi! I couldn't find the answer in similar topics: https://www.neuron.yale.edu/phpBB/viewtopic.php?t=1855 , https://www.neuron.yale.edu/phpBB/viewtopic.php?t=364 . I have a model loaded from this kind of template: {load_file("stdrun.hoc")} {load_file("import3d.hoc")} begintemplate...
- Thu Aug 22, 2019 3:34 am
- Forum: NEURON + Python
- Topic: Does Section have something like `id` attribute?
- Replies: 2
- Views: 4388
Re: Does Section have something like `id` attribute?
Thank you for such a thorough answer! By any chance, do you have an example of identifying sections in parallel environment?
- Wed Aug 21, 2019 12:16 pm
- Forum: NEURON + Python
- Topic: Does Section have something like `id` attribute?
- Replies: 2
- Views: 4388
Does Section have something like `id` attribute?
Hello everyone! I'm trying to launch a Sonata network in NEURON. According to their documentation they store synapses locations as some section id. I suspect that it is a Section's index in h.allsec() collection. I've looked over Section's documentation and have some questions. 1. Am I correct that ...
- Thu Aug 15, 2019 1:43 pm
- Forum: NEURON + Python
- Topic: Convert Python to Hoc
- Replies: 4
- Views: 2450
Re: Convert Python to Hoc
For now I couldn't do it. Currently jNeuroML does not support json files. I have to make it by hands unfortunately, can't waste time on this anymore.
- Thu Aug 15, 2019 6:45 am
- Forum: NEURON + Python
- Topic: Convert Python to Hoc
- Replies: 4
- Views: 2450
Re: Convert Python to Hoc
Seems that https://github.com/NeuroML/jNeuroML is a way to go.
- Wed Aug 14, 2019 2:24 pm
- Forum: NEURON + Python
- Topic: Convert Python to Hoc
- Replies: 4
- Views: 2450
Convert Python to Hoc
Hello! There is a model https://senselab.med.yale.edu/ModelDB/showmodel.cshtml?model=184187 . It exists in NeuroML2 and standalone Python versions. Is it possible to convert any of these into Hoc? What would you suggest? Would it be simpler just to recreate Hoc file from scratch? My circumstances ar...