def get_compartments(self, penetration_id: str):
"""Get compartments for each point in `penetration_id`."""
if not self.has_penetration(penetration_id):
return
ccf_coord = self.get_coordinates(
penetration_id) # loads this penetration
annotation_volume = self.cache.load_annotation_volume()
tree = StructureTree(self.cache.load_structure_graph())
i, j, k = (ccf_coord.T / self.settings.system.resolution).astype(
np.int)
cids = annotation_volume[i, j, k]
structures = tree.get_structures_by_id(cids)
return [self._jsonify_compartment(s) for s in structures]
def get_compartment_tree(self):
"""Get the entire compartment hierarchy."""
def populate_children(tr: StructureTree, node: dict):
# make corrections to field names
node = self._jsonify_compartment(node)
node["children"] = []
for child in tr.children([node["id"]])[0]:
node["children"].append(populate_children(tr, child))
return node
tree = StructureTree(self.cache.load_structure_graph())
root = tree.get_structures_by_id([997])[0]
root["rgb_triplet"] = 3 * [135]
root = populate_children(tree, root)
return root
# this is a string which contains the name of the latest ccf version
annotation_version = MouseConnectivityApi.CCF_VERSION_DEFAULT
mcapi = MouseConnectivityApi()
#Next line commented because the annotation volume is already downloaded
mcapi.download_annotation_volume(annotation_version, 10, annotation_path)
annotation, meta = nrrd.read(annotation_path)
swapped_ann = np.swapaxes(annotation, 1, 2)
swapped_ann = swapped_ann[:, :, ::
-1] #Revert the z axis so the 0 is the ventral part
rsp = ReferenceSpace(tree, swapped_ann, [10, 10, 10])
root_path = "E:\\Histology\\brain_structures_half_not_close_10\\"
##Here comes the obj creation
for struct in structure_graph[:1]:
path_parent = ""
for parent_id in struct["structure_id_path"][:-1]:
name_parent = tree.get_structures_by_id([parent_id])[0]["acronym"]
name_parent = name_parent.replace("/", "-")
path_parent = path_parent + name_parent + "\\"
struct_id = struct["id"]
name = tree.get_structures_by_id(
[struct_id])[0]["name"] + " (" + tree.get_structures_by_id(
[struct_id])[0]["acronym"] + ")"
name = name.replace("/", "-")
export_obj(struct_id, name, root_path + path_parent)
print(struct["name"])
