Saving and loading NeuroML file

When Python is the interpreter, what is a good
design for the interface to the basic NEURON
concepts.

Moderator: hines

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mattions
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Joined: Tue Jul 15, 2008 11:21 am
Location: EMBL-EBI Cambridge UK

Saving and loading NeuroML file

Post by mattions » Thu Apr 01, 2010 10:09 am

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:

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h.save_to_NeuroML('filename.xml', level=1) # For saving. Level keyword to choose the NeuroML level
h.load_NeuroML('filename.xml')
A quick example how I would like to use it:
Saving:

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from neuron import h
soma = h.Section()
h.save_to_NeuroML('filename.xml', level=1)
Loading:

Code: Select all

from neuron import h
h.load_NeuroML('filename.xml')
print h.soma.diam

hines
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Re: Saving and loading NeuroML file

Post by hines » Fri Apr 02, 2010 2:01 pm

neurondemo -python
from neuron import h
h.demo(2)
h.load_file("mview.hoc")
h.ModelViewXML(h.ModelView(0)).xportLevel2('temp.xml')

hines
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Re: Saving and loading NeuroML file

Post by hines » Fri Apr 02, 2010 2:19 pm

forgot the load example (note that xml import does not work for the demo(2) above since that demo has
inhomogeneities within a section. Try above with demo(3).)

nrngui -python
from neuron import h
h.load_file('celbild.hoc')
cb = h.CellBuild(0)
cb.manage.neuroml('temp.xml')
cb.cexport(1)

ted
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Re: Saving and loading NeuroML file

Post by ted » Fri Apr 02, 2010 9:31 pm

hines wrote:neurondemo -python
from neuron import h
h.demo(2)
h.load_file("mview.hoc")
h.ModelViewXML(h.ModelView(0)).xportLevel2('temp.xml')
From which is it correct to infer that the hoc way (once a model exists) would be

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load_file("mview.hoc")
objref foo
foo = new ModelView(0)
objref bar
bar = new ModelViewXML(foo)
bar.xportLevel2("temp.xml")
?

The hoc code for xml import seems almost identical to the Python--

Code: Select all

load_file("celbild.hoc")
objref cb
cb = new CellBuild(0)
cb.manage.neuroml("temp.xml")
cb.export(1)

mattions
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Joined: Tue Jul 15, 2008 11:21 am
Location: EMBL-EBI Cambridge UK

Re: Saving and loading NeuroML file

Post by mattions » Tue Apr 06, 2010 5:40 am

Hi, thanks for the answers.

I managed to export a NeuroML file using the python interpreter doing this:

Saving

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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)

modelView = h.ModelView(0)
modelXml = h.ModelViewXML(modelView)
modelXml.xportLevel1("temp.xml")
However when I load that file, using the Cellbuilder I get this error:

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NameError: name 'rdxml' is not defined
The whole log:

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mattions@triton:Neuronvisio(local)$ ipython -pylab
Python 2.6.4 (r264:75706, Dec  7 2009, 18:45:15) 
Type "copyright", "credits" or "license" for more information.

IPython 0.10 -- An enhanced Interactive Python.
?         -> Introduction and overview of IPython's features.
%quickref -> Quick reference.
help      -> Python's own help system.
object?   -> Details about 'object'. ?object also works, ?? prints more.

  Welcome to pylab, a matplotlib-based Python environment.
  For more information, type 'help(pylab)'.

In [1]: import neuron.gui
NEURON -- Release 7.1 (359:7f113b76a94b) 2009-10-26
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2008
See http://www.neuron.yale.edu/credits.html

	1 

In [2]: ---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)

/usr/lib/pymodules/python2.6/IPython/FakeModule.pyc in <module>()
----> 1 
      2 
      3 
      4 
      5 

ImportError: No module named rdxml
---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)

/usr/lib/pymodules/python2.6/IPython/FakeModule.pyc in <module>()
----> 1 
      2 
      3 
      4 
      5 

NameError: name 'rdxml' is not defined
NEURON: No attribute: rdxml
 near line 0
 {neuroml1()}
             ^
        CellManage[0].neuroml("./exported_neuroml.xml")
      CellManage[0].neuroml1()
    doNotify()
Exception in thread Thread-2:
Traceback (most recent call last):
  File "/usr/lib/python2.6/threading.py", line 525, in __bootstrap_inner
    self.run()
  File "/usr/local/lib/python2.6/dist-packages/neuron/gui.py", line 36, in run
    self.fun()
  File "/usr/local/lib/python2.6/dist-packages/neuron/gui.py", line 17, in process_events
    h.doNotify()
RuntimeError: hoc error
Loading

ted
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Re: Saving and loading NeuroML file

Post by ted » Tue Apr 06, 2010 9:46 am

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

mattions
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Location: EMBL-EBI Cambridge UK

Re: Saving and loading NeuroML file

Post by mattions » Tue Apr 06, 2010 10:08 am

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..

hines
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Re: Saving and loading NeuroML file

Post by hines » Tue Apr 06, 2010 4:53 pm

The xml readers require 3-d points. Before constructing the ModelView in your example you need
h.define_shape()
Then you can write a model which will be readable.
It works in my hands.
for writing
ipython
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)
h.define_shape()

modelView = h.ModelView(0)
modelXml = h.ModelViewXML(modelView)
modelXml.xportLevel1("temp.xml")

for reading
ipython
from neuron import h
h.load_file('celbild.hoc')
cb = h.CellBuild(0)
cb.manage.neuroml('temp.xml')
cb.cexport(1)

mattions
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Joined: Tue Jul 15, 2008 11:21 am
Location: EMBL-EBI Cambridge UK

Re: Saving and loading NeuroML file

Post by mattions » Tue Apr 06, 2010 5:30 pm

I guess I have a problem with the CellBuilder:

this is the dir of the neuroml object:

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In [21]: dir(cb.manage.neuroml )
Out[21]: 
['Section',
 '__call__',
 '__class__',
 '__delattr__',
 '__delitem__',
 '__doc__',
 '__format__',
 '__getattribute__',
 '__getitem__',
 '__hash__',
 '__init__',
 '__iter__',
 '__len__',
 '__new__',
 '__nonzero__',
 '__reduce__',
 '__reduce_ex__',
 '__repr__',
 '__setattr__',
 '__setitem__',
 '__sizeof__',
 '__str__',
 '__subclasshook__',
 'allsec',
 'baseattr',
 'cas',
 'classname',
 'egeom',
 'emem',
 'esub',
 'etop',
 'hocobjptr',
 'neuroml',
 'next',
 'pr',
 'ref',
 'save_classbody',
 'save_data',
 'setpointer',
 'toplevel',
 'update',
 'xmlwrite']
There is not rdxml attribute.

Do you have one in your version? (I'm running 7.1, not svn)

mattions
Posts: 65
Joined: Tue Jul 15, 2008 11:21 am
Location: EMBL-EBI Cambridge UK

Re: Saving and loading NeuroML file

Post by mattions » Thu Apr 08, 2010 5:12 am

Dear all,

I think I found the problem.

The rdxml.py file is in the source http://www.neuron.yale.edu/hg/neuron/nr ... n/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 rdxml fails badly because it can't find the module.

Copying the module inside the directory or adding it to the path makes everything working. Both from gui and code.

Thanks,
Michele.

hines
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Re: Saving and loading NeuroML file

Post by hines » Fri Apr 09, 2010 1:13 pm

Are you sure about that. When I 'make install' I see
<prefix>/share/nrn/lib/python/rdxml.py
and when I launch python and
from neuron import h
I see that path in sys.path (the above path is supposed to be automatically added when
neuron is imported).

mattions
Posts: 65
Joined: Tue Jul 15, 2008 11:21 am
Location: EMBL-EBI Cambridge UK

Re: Saving and loading NeuroML file

Post by mattions » Fri Apr 09, 2010 1:33 pm

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

I found the file here:

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/usr/local/nrn/share/nrn/lib/python/rdxml.py
instead should be here

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/usr/local/share/nrn/lib/python/rdxml.py
my prefix is the standard:

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/usr/local

hines
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Re: Saving and loading NeuroML file

Post by hines » Fri Apr 09, 2010 1:55 pm

The default prefix is /usr/local/nrn
Do you use an explicit --prefix=/usr/local? That should create a /usr/local/share, /usr/local/include, and /usr/local/i686.
Of course that makes uninstallation via rm -r -f not so easy.

mattions
Posts: 65
Joined: Tue Jul 15, 2008 11:21 am
Location: EMBL-EBI Cambridge UK

Re: Saving and loading NeuroML file

Post by mattions » Fri Apr 09, 2010 2:27 pm

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.

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