def load_neurohdf(filename, hdf5path, memmapped=False):
""" Loads the circuit from a NeuroHDF file as exported from CATMAID
Parameters
----------
filename : str
Path to the NeuroHDF file
hdfpath : str
HDF5 path to the irregular dataset containing the circuit
e.g. /Microcircuit
"""
if memmapped:
raise NotImplementedError('Memmapped HDF5 reading not yet implemented')
circuit = Circuit()
f = h5py.File(filename, 'r')
circuitdata_group=f[hdf5path]
vertices_group = circuitdata_group.get('vertices')
connectivity_group = circuitdata_group.get('connectivity')
metadata_group = circuitdata_group.get('metadata')
def helpdict(v):
helpdict = dict.fromkeys( v.attrs.keys() )
for k in helpdict:
helpdict[k] = v.attrs.get(k)
return helpdict
for k,v in vertices_group.items():
if k == 'id':
circuit.vertices = vertices_group[k].value
else:
circuit.vertices_properties[k] = dict.fromkeys( [const.DATA, const.METADATA] )
circuit.vertices_properties[k][const.DATA] = v.value
circuit.vertices_properties[k][const.METADATA] = helpdict(v)
print('Added vertices {0}'.format(k))
for k,v in connectivity_group.items():
if k == 'id':
circuit.connectivity = connectivity_group[k].value
else:
circuit.connectivity_properties[k] = dict.fromkeys( [const.DATA, const.METADATA] )
circuit.connectivity_properties[k][const.DATA] = v.value
circuit.connectivity_properties[k][const.METADATA] = helpdict(v)
print('Added connectivity {0}'.format(k))
if metadata_group:
for k,v in metadata_group.items():
circuit.metadata[k] = dict.fromkeys( [const.DATA, const.METADATA] )
circuit.metadata[k][const.DATA] = v.value
circuit.metadata[k][const.METADATA] = helpdict(v)
print('Added metadata {0}'.format(k))
circuit._remap_vertices_id2indices()
f.close()
return circuit
