def parse_channel_property(property_root):
children = list(property_root)
if len(children) > 0:
version_element = children[0]
version = float("".join(version_element.itertext()))
if version == 2:
channel, colour = parse_channel_property_version_2(children)
else:
raise MBFXMLException(
"XML format violation channel property has unknown version '{0}'."
.format(version))
else:
raise MBFXMLException(
"XML format violation channel property has no children.")
return MBFPropertyChannel(version, channel, colour)
def parse_punctum_property(property_root):
children = list(property_root)
if len(children) > 0:
version_element = children[0]
version = float("".join(version_element.itertext()))
if version == 4:
spread, mean_luminance, surface_area, voxel_count, flag_2d, \
volume, location, colocalized_fraction, proximal_fraction = parse_punctum_property_version_4(children)
else:
raise MBFXMLException(
"XML format violation punctum property has unknown version '{0}'."
.format(version))
else:
raise MBFXMLException(
"XML format violation punctum property has no children.")
return MBFPropertyPunctum(version, spread, mean_luminance, surface_area, voxel_count, flag_2d, \
volume, location, colocalized_fraction, proximal_fraction)
def _property_text(property_root):
children = list(property_root)
if len(children) > 0:
element = children[0]
text = "".join(element.itertext())
else:
raise MBFXMLException(
"XML format violation text property has no children.")
return text
def parse_nodes(nodes_root):
nodes = []
for child in nodes_root:
raw_tag = get_raw_tag(child)
if raw_tag == "node":
nodes.append(parse_node(child))
else:
raise MBFXMLException(
"XML format violation unknown tag '{0}'.".format(raw_tag))
return nodes
def parse_fill_density_property(property_root):
children = list(property_root)
if len(children) > 0:
fill_density_element = children[0]
fill_density_string = "".join(fill_density_element.itertext())
fill_density = float(fill_density_string)
else:
raise MBFXMLException(
"XML format violation fill density property has no children.")
return MBFPropertyFillDensity(fill_density)
def parse_volume_rle_property(property_root):
children = list(property_root)
if len(children) > 0:
volume_element = children[0]
volume_string = "".join(volume_element.itertext())
volume_description = volume_string.split(" ")
else:
raise MBFXMLException(
"XML format violation volume rle property has no children.")
return MBFPropertyVolumeRLE(volume_description)
def parse_edgelists(edgelists_root):
edgelists = []
for child in edgelists_root:
raw_tag = get_raw_tag(child)
if raw_tag == "edgelist":
edgelists.append(parse_edgelist(child))
else:
raise MBFXMLException(
"XML format violation unknown tag '{0}'.".format(raw_tag))
return edgelists
def parse_node(node_root):
node = {
'id': node_root.attrib['id'],
}
data = None
for child in node_root:
raw_tag = get_raw_tag(child)
if raw_tag == "point":
data = _create_mbf_point(child)
else:
raise MBFXMLException(
"XML format violation unknown tag '{0}'.".format(raw_tag))
if data is None:
raise MBFXMLException(
"XML format violation no point tag for node with id '{0}'.".format(
node['id']))
node['data'] = data
return node
def parse_edge(edge_root):
edge = {'id': edge_root.attrib['id']}
data = []
for child in edge_root:
raw_tag = get_raw_tag(child)
if raw_tag == "point":
data.append(_create_mbf_point(child))
else:
raise MBFXMLException(
"XML format violation unknown tag {0}".format(raw_tag))
edge['data'] = data
return edge
def parse_channels(channels_root):
channels = NeurolucidaChannels(channels_root.attrib['merge'])
for child in channels_root:
raw_tag = get_raw_tag(child)
if raw_tag == "channel":
channels.add_channel(
NeurolucidaChannel(child.attrib['id'], child.attrib['source']))
else:
raise MBFXMLException(
"XML format violation unknown tag {0} in channels.".format(
raw_tag))
return channels
def _parse_tree_structure(tree_root):
tree = {'points': [], 'properties': []}
for child in tree_root:
raw_tag = get_raw_tag(child)
if raw_tag == "point":
tree['points'].append(_create_mbf_point(child))
elif raw_tag == "branch":
tree['points'].append(_parse_tree_structure(child))
elif raw_tag == "property":
tree['properties'].append(parse_property(child))
else:
raise MBFXMLException(
"XML format violation unknown tag '{0}'.".format(raw_tag))
return tree
def parse_property(property_root) -> MBFProperty:
name = property_root.attrib['name']
if name == "Channel":
return parse_channel_property(property_root)
elif name == "Punctum":
return parse_punctum_property(property_root)
elif name == "VolumeRLE":
return parse_volume_rle_property(property_root)
elif name == "Set":
return parse_set_property(property_root)
elif name == "TraceAssociation":
return parse_trace_association_property(property_root)
elif name == "GUID":
return parse_guid_property(property_root)
elif name == "FillDensity":
return parse_fill_density_property(property_root)
elif name == "zSmear":
pass
else:
raise MBFXMLException("Unhandled property '{0}'".format(name))
def parse_contour(contour_root):
contour = {
'colour': contour_root.attrib['color'],
'rgb': hex_to_rgb(contour_root.attrib['color']),
'closed': contour_root.attrib['closed'] == 'true',
'name': contour_root.attrib['name'],
'properties': []
}
data = []
for child in contour_root:
raw_tag = get_raw_tag(child)
if raw_tag == "point":
data.append(_create_mbf_point(child))
elif raw_tag == "property":
contour['properties'].append(parse_property(child))
elif raw_tag == "resolution":
pass
else:
raise MBFXMLException(
"XML format violation unknown tag '{0}'.".format(raw_tag))
contour['data'] = data
return contour
def parse_marker(marker_root):
marker = {
'colour': marker_root.attrib['color'],
'rgb': hex_to_rgb(marker_root.attrib['color']),
'name': marker_root.attrib['name'],
'type': marker_root.attrib['type'],
'varicosity': marker_root.attrib['varicosity'] == "true",
'properties': []
}
data = []
for child in marker_root:
raw_tag = get_raw_tag(child)
if raw_tag == "point":
data.append(_create_mbf_point(child))
elif raw_tag == "property":
marker['properties'].append(parse_property(child))
else:
raise MBFXMLException(
"XML format violation unknown tag '{0}'.".format(raw_tag))
marker['data'] = data
return marker