def createMorphoMlFile(fileName):
'''
Create MorphoMl for every cell from cells collection
'''
neuroMlwriter = NeuroMlWriter(fileName)
for cell in neurons:
neuroMlwriter.addCell(cell)
neuroMlwriter.writeDocumentToFile()
def createMorphoMlFile(fileName):
'''
Create MorphoMl File with all cells from neurons
'''
neuroMlwriter = NeuroMlWriter(fileName)
for cell in neurons:
neuroMlwriter.addCell(cell)
neuroMlwriter.writeDocumentToFile()
print "%s neurons was successful imported"%len(neurons)
def createMorphoMlFile(fileName, cell):
'''
Convert to new neuroml structures and write
'''
if not muscle_dict.has_key(cell.name):
neuroMlwriter = NeuroMlWriter(fileName, cell.name)
neuroMlwriter.addCell(cell)
neuroMlwriter.writeDocumentToFile()
return
#
# Incomplete code to use the neuroml interface to write the file,
# used for muscles, doesn't produce good enough result on neurons yet.
#
seg0 = cell.segments[0].position
soma = Segment(proximal=cvt_pt(seg0.proximal_point),
distal=cvt_pt(seg0.distal_point))
soma.name = 'Soma'
soma.id = 0
axon_segments = []
for seg1 in cell.segments[1:]:
parent = SegmentParent(segments=seg1.parent)
if seg1.position.proximal_point is None:
p = None
else:
p = cvt_pt(seg1.position.proximal_point)
axon_segment = Segment(proximal = p,
distal = cvt_pt(seg1.position.distal_point),
parent = parent)
axon_segment.id = seg1.id
axon_segment.name = seg1.name
axon_segments.append(axon_segment)
morphology = Morphology()
morphology.segments.append(soma)
morphology.segments += axon_segments
morphology.id = 'morphology_' + cell.name
nml_cell = neuroml_Cell()
nml_cell.id = cell.name
nml_cell.morphology = morphology
doc = NeuroMLDocument()
doc.cells.append(nml_cell)
#addCell(doc, cell)
doc.id = "TestNeuroMLDocument"
writers.NeuroMLWriter.write(doc, "Output/%s.nml" % fileName)
def createMorphoMlFile(fileName, cell):
'''
Convert to new neuroml structures and write
'''
if not muscle_dict.has_key(cell.name):
neuroMlwriter = NeuroMlWriter(fileName, cell.name)
neuroMlwriter.addCell(cell)
neuroMlwriter.writeDocumentToFile()
return
#
# Incomplete code to use the neuroml interface to write the file,
# used for muscles, doesn't produce good enough result on neurons yet.
#
seg0 = cell.segments[0].position
soma = Segment(proximal=cvt_pt(seg0.proximal_point),
distal=cvt_pt(seg0.distal_point))
soma.name = 'Soma'
soma.id = 0
axon_segments = []
for seg1 in cell.segments[1:]:
parent = SegmentParent(segments=seg1.parent)
if seg1.position.proximal_point is None:
p = None
else:
p = cvt_pt(seg1.position.proximal_point)
axon_segment = Segment(proximal=p,
distal=cvt_pt(seg1.position.distal_point),
parent=parent)
axon_segment.id = seg1.id
axon_segment.name = seg1.name
axon_segments.append(axon_segment)
morphology = Morphology()
morphology.segments.append(soma)
morphology.segments += axon_segments
morphology.id = 'morphology_' + cell.name
nml_cell = neuroml_Cell()
nml_cell.id = cell.name
nml_cell.morphology = morphology
doc = NeuroMLDocument()
doc.cells.append(nml_cell)
#addCell(doc, cell)
doc.id = "TestNeuroMLDocument"
writers.NeuroMLWriter.write(doc, "Output/%s.nml" % fileName)