def extractInstances(self, netpyne_model, netpyne_geppetto_library,
geppetto_model):
instance = pygeppetto.Variable(id='network')
instance.types.append(netpyne_geppetto_library.types[0])
geppetto_model.variables.append(instance)
pass
def extractPopulations(self, netpyne_model, netpyne_geppetto_library, geppetto_model):
# Initialise network
network = pygeppetto.CompositeType(id='network_netpyne', name='network_netpyne')
netpyne_geppetto_library.types.append(network)
# Create intermediate population structure for easy access (by key)
populations = {}
for index, cell in enumerate(netpyne_model.net.allCells):
# This will be only executed the first time for each population
if cell['tags']['pop'] not in populations:
# Create CellType, VisualType, ArrayType, ArrayVariable and append to netpyne library
if 'cellType' in cell['tags']:
composite_id = cell['tags']['cellType']
else:
composite_id = cell['tags']['pop'] + "_cell"
cellType = pygeppetto.CompositeType(id=str(composite_id), name=str(composite_id), abstract= False)
visualType = pygeppetto.CompositeVisualType(id='cellMorphology', name='cellMorphology')
cellType.visualType = visualType
defaultValue = ArrayValue(elements=[])
arrayType = pygeppetto.ArrayType(size=0,
arrayType=cellType,
id=str(cell['tags']['pop']),
name=str(cell['tags']['pop']),
defaultValue= defaultValue)
arrayVariable = pygeppetto.Variable(id=str(cell['tags']['pop']))
arrayVariable.types.append(arrayType)
network.variables.append(arrayVariable)
netpyne_geppetto_library.types.append(cellType)
netpyne_geppetto_library.types.append(visualType)
netpyne_geppetto_library.types.append(arrayType)
# Save in intermediate structure
populations[cell['tags']['pop']] = arrayType
# Note: no need to check if pt3d since already done via netpyne sim.net.defineCellShapes() in instantiateNetPyNEModel
secs = cell['secs']
# Iterate sections creating spheres and cylinders
if hasattr(secs, 'items'):
for sec_name, sec in list(secs.items()):
if 'pt3d' in sec['geom']:
points = sec['geom']['pt3d']
for i in range(len(points) - 1):
# draw soma as a cylinder, not as a sphere (more accurate representation of 3d pts)
visualType.variables.append(self.factory.createCylinder(str(sec_name),
bottomRadius=float(points[i][3] / 2),
topRadius=float(points[i + 1][3] / 2),
position=Point(x=float(points[i][0]),y=float(points[i][1]), z=float(points[i][2])),
distal=Point(x=float(points[i + 1][0]), y=float(points[i + 1][1]), z=float(points[i + 1][2]))))
# Save the cell position and update elements in defaultValue and size
populations[cell['tags']['pop']].size = populations[cell['tags']['pop']].size + 1
populations[cell['tags']['pop']].defaultValue.elements.append(ArrayElement(index=len(populations[cell['tags']['pop']].defaultValue.elements) , position=Point(x=float(cell['tags']['x']), y=-float(cell['tags']['y']), z=float(cell['tags']['z']))))