def header_from_knossos_file(self, bable_anno, in_fname):
bable_anno.header = Header(None, None, None)
bable_anno.header.additional_meta = AdditionalHeader()
xml_str = self._get_knossos_file_annotation_xml(in_fname)
root = cet.fromstring(xml_str)
parameters_e = root.find('parameters')
for cur_tag_name, cur_tag_attrs, cur_targets in header_tags:
cur_tag_e = parameters_e.find(cur_tag_name)
ret = parse_attributes(cur_tag_e, cur_tag_attrs)
if len(cur_targets) == 1 and len(ret) > 1:
ret = [ret]
for cur_target, cur_ret in zip(cur_targets, ret):
setattr(bable_anno.header, cur_target, cur_ret)
for cur_tag_name, cur_tag_attrs, cur_targets in additional_header_tags:
cur_tag_e = parameters_e.find(cur_tag_name)
ret = parse_attributes(cur_tag_e, cur_tag_attrs)
if len(cur_targets) == 1 and len(ret) > 1:
ret = [ret]
for cur_target, cur_ret in zip(cur_targets, ret):
setattr(bable_anno.header.additional_meta, cur_target, cur_ret)
bable_anno.header.source = 'Knossos'
def read(self, bable_anno, source, scaling=None):
"""
Add skeleton annotations from a knossos file. Node and graph IDs are
not preserved from the file.
"""
if scaling is None:
raise Exception('Must specifiy scaling to read knossos file.')
self.header_from_knossos_file(bable_anno, source)
xml_str = self._get_knossos_file_annotation_xml(source)
root = cet.fromstring(xml_str)
# This dictionary temporarily holds the mapping from node IDs local
# to the current knossos file to unique IDs given out while loading.
# We make no attempt to preserve node IDs.
local_node_id_to_unique_id = dict()
local_graph_id_to_unique_id = dict()
local_node_id_to_node = dict()
for cur_graph_e in root.findall('thing'):
graph_id, r, g, b, a, comment = parse_attributes(
cur_graph_e, XMLSkeletons.thing_tag_attrs)
cur_graph_id = bable_anno._graph_unique_id.get_id()
cur_graph = Graph(
graph_id=cur_graph_id, additional_meta=None)
cur_graph.additional_meta = AdditionalGraph(
color=(r, g, b, a), comment=comment)
bable_anno._graphs.append(cur_graph)
local_graph_id_to_unique_id[graph_id] = cur_graph_id
cur_nodes_e = cur_graph_e.find('nodes')
for cur_node_e in cur_nodes_e.findall('node'):
node_id, radius, x, y, z, in_vp, in_mag, timestamp = \
parse_attributes(cur_node_e, XMLSkeletons.node_tag_attrs)
cur_node_id = bable_anno._node_unique_id.get_id()
local_node_id_to_unique_id[node_id] = cur_node_id
cur_node = Node(
node_id=cur_node_id,
graph_id=cur_graph_id,
coord=(x, y, z),
scaling=scaling)
cur_node.additional_meta = AdditionalNode(
radius=radius,
in_vp=in_vp,
in_mag=in_mag,
time=timestamp, )
bable_anno._nodes.append(cur_node)
local_node_id_to_node[node_id] = cur_node
# It is important to read edges after reading nodes, since otherwise
# the edges could refer to nodes that have not yet been encountered,
# since they can be between different things (graphs). This is a design
# issue in the Knossos skeleton XML format (NML).
for cur_graph_e in root.findall('thing'):
graph_id, _, _, _, _, _ = parse_attributes(
cur_graph_e, XMLSkeletons.thing_tag_attrs)
cur_graph_id = local_graph_id_to_unique_id[graph_id]
cur_edges_e = cur_graph_e.find('edges')
for cur_edge_e in cur_edges_e.findall('edge'):
source_node_id, target_node_id = parse_attributes(
cur_edge_e, XMLSkeletons.edge_tag_attrs)
try:
cur_edge = Edge(
graph_id=cur_graph_id,
from_id=local_node_id_to_unique_id[source_node_id],
to_id=local_node_id_to_unique_id[target_node_id])
except KeyError:
raise InvalidFormatException(
'File %s contains edge with non-existant node: (%d, '
'%d).' % (source, source_node_id, target_node_id, ))
bable_anno._edges.append(cur_edge)
for comment_e in root.iter('comment'):
node_id, content = parse_attributes(
comment_e, XMLSkeletons.comment_tag_attrs)
try:
n = local_node_id_to_node[node_id]
except KeyError:
print('Skipping comment on non-existing node %d' % (node_id, ))
continue
n.additional_meta.comment = content
for branchpoint_e in root.iter('branchpoint'):
node_id, = parse_attributes(
branchpoint_e, XMLSkeletons.branchpoint_tag_attrs)
try:
n = local_node_id_to_node[node_id]
except KeyError:
print('Skipping branchpoint flag on non-existing node %d' % (
node_id, ))
continue
n.is_branchpoint = True
