www.neuron.yale.edu

Sorry. I misunderstood the context. The implmentation for reading is incomplete as I see in nrn/share/lib/hoc/celbild/celtopol.hoc that the name is ignored and substituted with "d" in sscanf(cab.name_, "%s[%d]", s.s, &nx) //printf("i=%d id=%d %s[%d]\n", i, cab.id_,...

Are you going to apply this modification (and the one before) to the source of NEURON?

I'm saving only the anatomy and working on the single cell right now so NeuroML should be enough for the time being.

I just want to make clear what I'm looking for: my goal is to save all the info about the geometry in the NeuroML format and write them on a file. Then I want to reload the geometry info in memory, using the NeuroML file as the source of my model. The model back in memory and loaded in NEURON should...

There are any plans to support multiple cells?
For now I have only one cell in my model, so that would be good enough for the time being.

How can I accomplish that?

It is also possible to put the name of the cell in front of it? This is my system: In [3]: h.topology() |-| MSP_Cell[0].soma(0-1) `| MSP_Cell[0].dend1(0-1) `| MSP_Cell[0].dend1_1[0](0-1) `----------| MSP_Cell[0].dend1_1[1](0-1) `----------| MSP_Cell[0].dend1_1[2](0-1) `| MSP_Cell[0].dend1_2[0](0-1) ...

My fault.

Used with classic GNU program I though ./configure would use /usr/local by default not /usr/local/nrn.
I need to update my PYTHONPATH with this location, then should be ok.

Consider this code: from neuron import h import neuron.gui # To not freeze the GUI h.load_file('mview.hoc') # Bunch of sections, just for testing purpose. sec1 = h.Section() sec2 = h.Section() sec2.diam=1000 sec1.connect(sec2) print sec1.name(), sec2.name() h.define_shape() modelView = h.ModelView(0...

I think that maybe there is a nrn directory that should not be there.

I found the file here: instead should be here my prefix is the standard:

I've tried to export a model in neuroML but I just noticed that the name of the sections change http://www.neuron.yale.edu/hg/neuron/nrn/file/cbc0331180f8/share/lib/hoc/mview/mviewxml.hoc#l301 I think would be better if the real name of the section will be exported, so it's possible to attach to it ...

Dear all, I think I found the problem. The rdxml.py file is in the source http://www.neuron.yale.edu/hg/neuron/nrn/file/cbc0331180f8/share/lib/python/rdxml.py but it doesn't get installed in the proper location. Therefore is not in the PYTHONPATH so when CellBuilder try to read the xml, loading rdxm...

I guess I have a problem with the CellBuilder: this is the dir of the neuroml object: In [21]: dir(cb.manage.neuroml ) Out[21]: ['Section', '__call__', '__class__', '__delattr__', '__delitem__', '__doc__', '__format__', '__getattribute__', '__getitem__', '__hash__', '__init__', '__iter__', '__len__'...

ted wrote:The problem occurs with Level 1 NeuroML. Level 2 NeuroML seems to import OK.

I'm getting the same error also using Level 2..

Hi, thanks for the answers. I managed to export a NeuroML file using the python interpreter doing this: Saving from neuron import h import neuron.gui # To not freeze the GUI h.load_file('mview.hoc') # Bunch of sections, just for testing purpose. sec1 = h.Section() sec2 = h.Section() sec2.diam=1000 s...

Hello, I would like to know if there is a way to save and load NeuroML file using python and not the GUI. Is somewhere on the Programmer's Reference? Proposed API would be something like: h.save_to_NeuroML('filename.xml', level=1) # For saving. Level keyword to choose the NeuroML level h.load_NeuroM...

Hi there, the logic I use in Neuronvisio http://mattions.github.com/neuronvisio/ is to check if the section has that variable as attribute: (Have a look to the following code: from neuron import h soma = h.Section() if hasattr(soma, 'v'): print "Variable v present" It worked pretty well so...