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)
def createMorphoMlFile(fileName, cell):
'''
Convert to new neuroml structures and write
'''
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.distal_point is None:
p = None
else:
p = cvt_pt(seg1.position.distal_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.name = "Test neuroML document"
doc.cells.append(nml_cell)
doc.id = fileName
writers.NeuroMLWriter.write(doc, "Output/%s.nml" % fileName)
def createMorphoMlFile(fileName, cell):
'''
Convert to new neuroml structures and write
'''
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.distal_point is None:
p = None
else:
p = cvt_pt(seg1.position.distal_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.name = "Test neuroML document"
doc.cells.append(nml_cell)
doc.id = fileName
writers.NeuroMLWriter.write(doc, "Output/%s.nml" % fileName)
def neuroml_network(cells, response):
""" Write a list of Cell instances.
cells: a list of Cell instances.
response: somewhere to write to, like an HttpResponse
Returns nothing.
"""
doc = NeuroMLDocument()
doc.cells.extend(cells)
doc.id = "NeuroMLDocument"
namespacedef = 'xmlns="http://www.neuroml.org/schema/neuroml2"' \
+ ' xmlns:xi="http://www.w3.org/2001/XInclude"' \
+ ' xmlns:xs="http://www.w3.org/2001/XMLSchema"' \
+ ' xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"' \
+ ' xsi:schemaLocation="http://www.w3.org/2001/XMLSchema"'
doc.export( response, 0, name_="neuroml", namespacedef_=namespacedef)
return response
def neuroml_network(cells, response):
""" Write a list of Cell instances.
cells: a list of Cell instances.
response: somewhere to write to, like an HttpResponse
Returns nothing.
"""
doc = NeuroMLDocument()
doc.cells.extend(cells)
doc.id = "NeuroMLDocument"
namespacedef = 'xmlns="http://www.neuroml.org/schema/neuroml2"' \
+ ' xmlns:xi="http://www.w3.org/2001/XInclude"' \
+ ' xmlns:xs="http://www.w3.org/2001/XMLSchema"' \
+ ' xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"' \
+ ' xsi:schemaLocation="http://www.w3.org/2001/XMLSchema"'
doc.export(response, 0, name_="neuroml", namespacedef_=namespacedef)
return response
