def exportToNML(cells):
nml_net_file = "../NeuroML2/GranuleCells/Exported/GCnet%iG.net.nml" % len(cells)
export_to_neuroml2(None,
nml_net_file,
includeBiophysicalProperties=False,
separateCellFiles=True)
# Rename files so their cell GIDs are preserved
for gcid in cells.keys():
fileId = cells[gcid]['index']
oldFile = '../NeuroML2/GranuleCells/Exported/Granule_0_%i.cell.nml' % fileId
newFile = '../NeuroML2/GranuleCells/Exported/Granule_0_%i.cell.nml_TEMP' % gcid
# Using TEMP files to avoid naming conflicts
os.rename(oldFile, newFile)
# Remove temp files after all have been renamed
for gcid in cells.keys():
oldFile = '../NeuroML2/GranuleCells/Exported/Granule_0_%i.cell.nml_TEMP' % gcid
newFile = '../NeuroML2/GranuleCells/Exported/Granule_0_%i.cell.nml' % gcid
os.rename(oldFile, newFile)
for gcid in cells.keys():
cell, nml_doc, nml_cell_file = readGCnml(gcid)
print("Loaded GC cell %i with %i segments"%(gcid, len(cell.morphology.segments)))
# Change cell ID to preserve GCID
cell.id = "Granule_0_%i" % gcid
# Change segment ids to start at 0 and increment
exportHelper.resetRoot(cell)
# Replace ModelViewParmSubset_N groups with all, axon, soma, dendrite groups
buildStandardSegmentGroups(cell)
# Add channel placeholders
nml_doc.includes.append(neuroml.IncludeType(href="channelIncludesPLACEHOLDER"))
cell.biophysical_properties = neuroml.BiophysicalProperties(id="biophysPLACEHOLDER")
cell.morphology.segments.append(neuroml.Segment(id="spinePLACEHOLDER"))
# Save the new NML
pynml.write_neuroml2_file(nml_doc, nml_cell_file)
# Replace placeholders with contents from GranuleCell...xml files
replaceChannelPlaceholders(nml_cell_file)
cell, nml_doc, nml_cell_file = readGCnml(gcid)
# Fix the fractionAlong parent segment bug ( https://github.com/NeuroML/org.neuroml.export/issues/46 )
exportHelper.splitSegmentAlongFraction(cell, "Seg0_priden", "priden", 0.8, "Seg0_priden2_0")
# Orient cell along the versor
versor = granules.granule_position_orientation(gcid)[1]
for seg in cell.morphology.segments:
segLength = seg.length
if seg.parent is not None:
parentDistal = [parent for parent in cell.morphology.segments if parent.id == seg.parent.segments][0].distal
seg.proximal.x = parentDistal.x
seg.proximal.y = parentDistal.y
seg.proximal.z = parentDistal.z
seg.distal = setAlongVersor(seg.distal, versor, seg.proximal, segLength)
# Make sure spine is in the all group
[group for group in cell.morphology.segment_groups if group.id == 'all'][0]\
.includes\
.append(neuroml.Include(segment_groups='spine_group'))\
# and Dendrite group
[group for group in cell.morphology.segment_groups if group.id == 'dendrite_group'][0]\
.includes\
.append(neuroml.Include(segment_groups='spine_group'))
# Save orientation
pynml.write_neuroml2_file(nml_doc, nml_cell_file)
print(nml_cell_file)
def export(num_cells_to_export=5):
cells = []
for mgid in range(num_cells_to_export):
print mgid
cells.append(mkmitral(mgid))
nml_net_file = "../NeuroML2/MitralCells/Exported/PartialBulb_%iMTCells.net.nml" % num_cells_to_export
export_to_neuroml2(None,
nml_net_file,
includeBiophysicalProperties=False,
separateCellFiles=True)
for i in range(num_cells_to_export):
print("Processing cell %i out of %i" % (i, num_cells_to_export))
nml_cell_file = "../NeuroML2/MitralCells/Exported/Mitral_0_%i.cell.nml" % i
nml_doc = pynml.read_neuroml2_file(nml_cell_file)
cell = nml_doc.cells[0]
soma_seg = next(seg for seg in cell.morphology.segments
if seg.name == "Seg0_soma")
initial_seg = next(seg for seg in cell.morphology.segments
if seg.name == "Seg0_initialseg")
hillock_seg = next(seg for seg in cell.morphology.segments
if seg.name == "Seg0_hillock")
# Ensure hillock parent is soma
hillock_seg.parent.segments = soma_seg.id
# Fix initial and hillock segs by moving them to the soma
hillock_seg.proximal = pointMovedByOffset(hillock_seg.proximal,
soma_seg.distal)
hillock_seg.distal = pointMovedByOffset(hillock_seg.distal,
soma_seg.distal)
initial_seg.proximal = pointMovedByOffset(initial_seg.proximal,
soma_seg.distal)
initial_seg.distal = pointMovedByOffset(initial_seg.distal,
soma_seg.distal)
# Set root to id=0 and increment others
exportHelper.resetRoot(cell)
# TODO: cell.position(x,y,z) used for cell positioning in networks does not work as expected
# See: https://github.com/NeuroML/jNeuroML/issues/55
# Skipping the translation for now
# # Move everything back to the origin
# originOffset = type("", (), dict(x = -soma_seg.proximal.x, y = -soma_seg.proximal.y, z = -soma_seg.proximal.z ))()
#
# for seg in cell.morphology.segments:
# seg.proximal = pointMovedByOffset(seg.proximal, originOffset)
# seg.distal = pointMovedByOffset(seg.distal, originOffset)
# Replace ModelViewParmSubset_N groups with all, axon, soma, dendrite groups
buildStandardSegmentGroups(cell)
# Add channel placeholders
nml_doc.includes.append(
neuroml.IncludeType(href="channelIncludesPLACEHOLDER"))
cell.biophysical_properties = neuroml.BiophysicalProperties(
id="biophysPLACEHOLDER")
# Save the new NML
pynml.write_neuroml2_file(nml_doc, nml_cell_file)
# Replace placeholders with contents from MitralCell...xml files
replaceChannelPlaceholders(nml_cell_file)
print("COMPLETED: " + nml_cell_file)
print("DONE")
def __main__():
num_cells_to_export = 1
cells = []
for mgid in range(num_cells_to_export):
print mgid
cells.append(mkmitral(mgid))
nml_net_file = "../NeuroML2/MitralCells/Exported/PartialBulb_%iMTCells.net.nml" % num_cells_to_export
export_to_neuroml2(None,
nml_net_file,
includeBiophysicalProperties=False,
separateCellFiles=True)
for i in range(num_cells_to_export):
print("Processing cell %i out of %i"%(i, num_cells_to_export))
nml_cell_file = "../NeuroML2/MitralCells/Exported/Mitral_0_%i.cell.nml" % i
nml_doc = pynml.read_neuroml2_file(nml_cell_file)
cell = nml_doc.cells[0]
import pydevd
pydevd.settrace('10.211.55.3', port=4200, stdoutToServer=True, stderrToServer=True, suspend=True)
# Set root to id=0 and increment others
exportHelper.resetRoot(cell)
somaSeg = [seg for seg in cell.morphology.segments if seg.name == "Seg0_soma"][0]
initialSeg = [seg for seg in cell.morphology.segments if seg.name == "Seg0_initialseg"][0]
hillockSeg = [seg for seg in cell.morphology.segments if seg.name == "Seg0_hillock"][0]
# Fix initial and hillock segs by moving them to the soma
hillockSeg.proximal = pointMovedByOffset(hillockSeg.proximal, somaSeg.distal)
hillockSeg.distal = pointMovedByOffset(hillockSeg.distal, somaSeg.distal)
initialSeg.proximal = pointMovedByOffset(initialSeg.proximal, somaSeg.distal)
initialSeg.distal = pointMovedByOffset(initialSeg.distal, somaSeg.distal)
# Move everything back to the origin
originOffset = type("", (), dict(x = -somaSeg.proximal.x, y = -somaSeg.proximal.y, z = -somaSeg.proximal.z ))()
for seg in cell.morphology.segments:
seg.proximal = pointMovedByOffset(seg.proximal, originOffset)
seg.distal = pointMovedByOffset(seg.distal, originOffset)
# Replace ModelViewParmSubset_N groups with all, axon, soma, dendrite groups
buildStandardSegmentGroups(cell)
# Add channel placeholders
nml_doc.includes.append(neuroml.IncludeType(href="channelIncludesPLACEHOLDER"))
cell.biophysical_properties = neuroml.BiophysicalProperties(id="biophysPLACEHOLDER")
# Save the new NML
pynml.write_neuroml2_file(nml_doc, nml_cell_file)
# Replace placeholders with contents from MitralCell...xml files
replaceChannelPlaceholders(nml_cell_file)
print("COMPLETED: " + nml_cell_file)
print("DONE")
