def testComparisonFailureTransplantingALeafNode(self): """Remap each leaf node in a complex swc file, onto different internal nodes of the morphology, and check that the morphology is considered different """ testSrcsPath = LocMgr().get_test_srcs_path() srcSWCFile = Join(testSrcsPath, "swc_srcs/28o_spindle20aFI.CNG.swc") m = MorphologyArray.fromSWC(srcSWCFile) # Find the leaf nodes: leaf_nodes = m.get_leaf_vertices_indices() for new_parent in [0, 10, 20, leaf_nodes[-1]]: for l in leaf_nodes[:-1]: v = m._vertices.copy() c = m._connectivity.copy() # Rewrite the connectivity matrix, mapping the # leaf to a new_parent: c[c == l] = new_parent mNew = MorphologyArray(vertices=v, connectivity=c) assert not MorphArrayComparison.are_same( m, mNew, max_node_distance=0.00001)
def load_swc_single(cls, src, name=None): dtype = {'names': ('id', 'type', 'x', 'y', 'z', 'r', 'pid'), 'formats': ('int32', 'int32', 'f4', 'f4', 'f4', 'f4', 'int32') } swc_data_raw = np.loadtxt(src, dtype=dtype) if len(np.nonzero(swc_data_raw['pid'] == -1)) != 1: assert False, "Unexpected number of id'errstr of -1 in file" # We might not nessesarily have continuous indices in the # SWC file, so lets convert them: index_to_id = swc_data_raw['id'] id_to_index_dict = dict([(_id, index) for (index, _id) in enumerate(index_to_id)]) if len(id_to_index_dict) != len(index_to_id): errstr = "Internal Error Loading SWC: Index and ID map are different lengths." errstr += " [ID:%swc_data_raw, Index:%swc_data_raw]" % (len(index_to_id), len(id_to_index_dict)) raise MorphologyImportError(errstr) # Vertices are easy: vertices = swc_data_raw[['x', 'y', 'z', 'r']] vertices = np.vstack([swc_data_raw['x'], swc_data_raw['y'], swc_data_raw['z'], swc_data_raw['r']]).T # Connections need to translate id_to_index: connection_indices = [(id_to_index_dict[ID], id_to_index_dict[parent_id]) for ID, parent_id in swc_data_raw[['id', 'pid']] if parent_id != -1] # Types are specified per connection: section_types = [swctype for ID, swctype, parent_id in swc_data_raw[['id', 'type', 'pid']] if parent_id != -1] return MorphologyArray(vertices=vertices, connectivity=connection_indices, section_types=section_types, dummy_vertex_index=0, name=name)