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def __init__(self):
# get mouse connectivity cache and structure tree
self.mcc = MouseConnectivityCache(
manifest_file=os.path.join(
self.mouse_connectivity_cache, "manifest.json"
)
)
self.structure_tree = self.mcc.get_structure_tree()
# get ontologies API and brain structures sets
self.oapi = OntologiesApi()
# get reference space
self.space = ReferenceSpaceApi()
self.spacecache = ReferenceSpaceCache(
manifest=os.path.join(
self.annotated_volume_fld, "manifest.json"
), # downloaded files are stored relative to here
resolution=int(self.resolution[0]),
reference_space_key="annotation/ccf_2017", # use the latest version of the CCF
)
self.annotated_volume, _ = self.spacecache.get_annotation_volume()
# mouse connectivity API [used for tractography]
self.mca = MouseConnectivityApi()
# Get tree search api
def __init__(self):
SvgApi.__init__(
self
) # https://github.com/AllenInstitute/AllenSDK/blob/master/allensdk/api/queries/svg_api.py
ImageDownloadApi.__init__(
self
) # https://github.com/AllenInstitute/AllenSDK/blob/master/allensdk/api/queries/image_download_api.py
self.annsetsapi = (
AnnotatedSectionDataSetsApi()
) # https://github.com/AllenInstitute/AllenSDK/blob/master/allensdk/api/queries/annotated_section_data_sets_api.py
self.oapi = (
OntologiesApi()
) # https://github.com/AllenInstitute/AllenSDK/blob/master/allensdk/api/queries/ontologies_api.py
# Get metadata about atlases
self.atlases = pd.DataFrame(self.oapi.get_atlases_table())
self.atlases_names = sorted(list(self.atlases["name"].values))
self.mouse_coronal_atlas_id = int(
self.atlases.loc[
self.atlases["name"] == self.mouse_coronal
].id.values[0]
)
self.mouse_sagittal_atlas_id = int(
self.atlases.loc[
self.atlases["name"] == self.mouse_sagittal
].id.values[0]
)
def __init__(self, base_dir=None, **kwargs):
BrainGlobeAtlasBase.__init__(self, base_dir=base_dir, **kwargs)
# get mouse connectivity cache and structure tree
self.mcc = MouseConnectivityCache(
manifest_file=os.path.join(
self.mouse_connectivity_cache, "manifest.json"
)
)
self.structure_tree = self.mcc.get_structure_tree()
# get ontologies API and brain structures sets
self.oapi = OntologiesApi()
# get reference space
self.space = ReferenceSpaceApi()
self.spacecache = ReferenceSpaceCache(
manifest=os.path.join(
self.annotated_volume_fld, "manifest.json"
), # downloaded files are stored relative to here
resolution=self.resolution,
reference_space_key="annotation/ccf_2017", # use the latest version of the CCF
)
self.annotated_volume, _ = self.spacecache.get_annotation_volume()
# mouse connectivity API [used for tractography]
self.mca = MouseConnectivityApi()
# Get tree search api