idMap = SectionIndexerWithOffsetDF(morph=morph, offset=offset)()
idMap[ morph.getDummySection() ] = dummyOffset
if regionname_to_int_map is None:
regionname_to_int_map = AutoRegionToIntMapTable()
region_type_map = dict( (s,0) if not s.region else (s,regionname_to_int_map.regionNameToInt(s.region.name)) for s in morph )
context = [{ 'morph':morph, 'ids':idMap, 'region_type_map':region_type_map }]
newOP = Template(swc_templ, context ).respond()
output += newOP
offset += len( idMap )
return output
MorphologyExporter.register("toSWCFile", lambda filename,morphology: SWCTreeWriter.toFile(filename=filename, morph=morphology), allow_override=False, from_type=MorphologyTree )
MorphologyExporter.register("toSWCStr", lambda morphology: SWCTreeWriter.toStr(morph=morphology), allow_override=False, from_type=MorphologyTree )
# Root Vertex:
data = [vertex_to_data(morphology._dummy_vertex_index, None, 0)]
# Add Each Vertex
for (conn_index,
(v_index, v_index_parent)) in enumerate(morphology._connectivity):
rgn = morphology._section_types[conn_index]
data.append(vertex_to_data(v_index, v_index_parent, rgn))
# Save the file:
if op:
np.savetxt(op, np.array(data), fmt=fmt)
else:
op = StringIO()
np.savetxt(op, np.array(data), fmt=fmt)
return op.getvalue()
# Wrapper function to avoid binding error:
def _export_single_swc(morphology, **kwargs):
return ExportArray_SWC._export_single_swc(morphology=morphology, **kwargs)
MorphologyExporter.register('toSWC',
_export_single_swc,
allow_override=False,
from_type=MorphologyArray)
@classmethod
def export_single(cls, morphology, swc_vertex_offset = 1, op=None, fmt='%d %d %0.2f %0.2f %0.2f %0.2f %d'):
def vertexToData(v_index, v_index_parent, rgn):
x,y,z,r = morphology._vertices[v_index,:]
return [ v_index+swc_vertex_offset, rgn, x, y, z, r, v_index_parent+swc_vertex_offset if v_index_parent is not None else -1 ]
#Root Vertex:
data = [ vertexToData(morphology._dummy_vertex_index, None, 0) ]
# Add Each Vertex
for conn_index,(v_index, v_index_parent) in enumerate(morphology._connectivity):
rgn = morphology._section_types[conn_index]
data.append( vertexToData(v_index, v_index_parent, rgn) )
# Save the file:
if op:
np.savetxt(op, np.array(data), fmt=fmt )
else:
op = StringIO()
np.savetxt(op, np.array(data), fmt=fmt )
return op.getvalue()
#Wrapper function to avoid binding error:
def export_single( morphology, **kwargs):
return ExportArray_SWC.export_single(morphology=morphology, **kwargs)
MorphologyExporter.register("toSWC",export_single, allow_override=False, from_type=MorphologyArray )
id_map[morph.get_dummy_section()] = dummy_offset
if regionname_to_int_map is None:
regionname_to_int_map = AutoRegionToIntMapTable()
region_type_map = dict((s, 0) if not s.region else (
s, regionname_to_int_map.region_name_to_int(s.region.name))
for s in morph)
context = [{
'morph': morph,
'ids': id_map,
'region_type_map': region_type_map
}]
new_op = Template(swc_templ, context).respond()
output += new_op
offset += len(id_map)
return output
MorphologyExporter.register("toSWCFile",
lambda filename, morphology: SWCTreeWriter.to_file(
filename=filename, morph=morphology),
allow_override=False,
from_type=MorphologyTree)
MorphologyExporter.register(
"toSWCStr",
lambda morphology: SWCTreeWriter.to_str(morph=morphology),
allow_override=False,
from_type=MorphologyTree)
def vertex_to_data(v_index, v_index_parent, rgn):
(x, y, z, r) = morphology._vertices[v_index, :]
return [v_index + swc_vertex_offset, rgn, x, y, z, r, v_index_parent + swc_vertex_offset if v_index_parent is not None else -1]
# Root Vertex:
data = [vertex_to_data(morphology._dummy_vertex_index, None, 0)]
# Add Each Vertex
for (conn_index, (v_index, v_index_parent)) in enumerate(morphology._connectivity):
rgn = morphology._section_types[conn_index]
data.append(vertex_to_data(v_index, v_index_parent, rgn))
# Save the file:
if op:
np.savetxt(op, np.array(data), fmt=fmt)
else:
op = StringIO()
np.savetxt(op, np.array(data), fmt=fmt)
return op.getvalue()
# Wrapper function to avoid binding error:
def _export_single_swc(morphology, **kwargs):
return ExportArray_SWC._export_single_swc(morphology=morphology, **kwargs)
MorphologyExporter.register('toSWC', _export_single_swc,
allow_override=False,
from_type=MorphologyArray)
