allensdk.core.reference_space_cache module¶
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class
allensdk.core.reference_space_cache.ReferenceSpaceCache(resolution, reference_space_key, **kwargs)[source]¶ Bases:
allensdk.api.warehouse_cache.cache.Cache-
ANNOTATION_KEY= 'ANNOTATION'¶
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MANIFEST_VERSION= 1.2¶
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REFERENCE_SPACE_VERSION_KEY= 'REFERENCE_SPACE_VERSION'¶
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STRUCTURES_KEY= 'STRUCTURES'¶
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STRUCTURE_MASK_KEY= 'STRUCTURE_MASK'¶
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STRUCTURE_MESH_KEY= 'STRUCTURE_MESH'¶
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STRUCTURE_TREE_KEY= 'STRUCTURE_TREE'¶
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TEMPLATE_KEY= 'TEMPLATE'¶
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add_manifest_paths(self, manifest_builder)[source]¶ Construct a manifest for this Cache class and save it in a file.
Parameters: - file_name: string
File location to save the manifest.
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get_annotation_volume(self, file_name=None)[source]¶ Read the annotation volume. Download it first if it doesn’t exist.
Parameters: - file_name: string
File name to store the annotation volume. If it already exists, it will be read from this file. If file_name is None, the file_name will be pulled out of the manifest. Default is None.
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get_reference_space(self, structure_file_name=None, annotation_file_name=None)[source]¶ Build a ReferenceSpace from this cache’s annotation volume and structure tree. The ReferenceSpace does operations that relate brain structures to spatial domains.
Parameters: - structure_file_name: string
File name to save/read the structures table. If file_name is None, the file_name will be pulled out of the manifest. If caching is disabled, no file will be saved. Default is None.
- annotation_file_name: string
File name to store the annotation volume. If it already exists, it will be read from this file. If file_name is None, the file_name will be pulled out of the manifest. Default is None.
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get_structure_mask(self, structure_id, file_name=None, annotation_file_name=None)[source]¶ Read a 3D numpy array shaped like the annotation volume that has non-zero values where voxels belong to a particular structure. This will take care of identifying substructures.
Parameters: - structure_id: int
ID of a structure.
- file_name: string
File name to store the structure mask. If it already exists, it will be read from this file. If file_name is None, the file_name will be pulled out of the manifest. Default is None.
- annotation_file_name: string
File name to store the annotation volume. If it already exists, it will be read from this file. If file_name is None, the file_name will be pulled out of the manifest. Default is None.
Notes
This method downloads structure masks from the Allen Institute. To make your own locally, see ReferenceSpace.many_structure_masks.
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get_structure_mesh(self, structure_id, file_name=None)[source]¶ Obtain a 3D mesh specifying the surface of an annotated structure.
Parameters: - structure_id: int
ID of a structure.
- file_name: string
File name to store the structure mesh. If it already exists, it will be read from this file. If file_name is None, the file_name will be pulled out of the manifest. Default is None.
Returns: - vertices : np.ndarray
Dimensions are (nSamples, nCoordinates=3). Locations in the reference space of vertices
- vertex_normals : np.ndarray
Dimensions are (nSample, nElements=3). Vectors normal to vertices.
- face_vertices : np.ndarray
Dimensions are (sample, nVertices=3). References are given in indices (0-indexed here, but 1-indexed in the file) of vertices that make up each face.
- face_normals : np.ndarray
Dimensions are (sample, nNormals=3). References are given in indices (0-indexed here, but 1-indexed in the file) of vertex normals that make up each face.
Notes
These meshes are meant for 3D visualization and as such have been smoothed. If you are interested in performing quantative analyses, we recommend that you use the structure masks instead.
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get_structure_tree(self, file_name=None, structure_graph_id=1)[source]¶ Read the list of adult mouse structures and return an StructureTree instance.
Parameters: - file_name: string
File name to save/read the structures table. If file_name is None, the file_name will be pulled out of the manifest. If caching is disabled, no file will be saved. Default is None.
- structure_graph_id: int
Build a tree using structure only from the identified structure graph.
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get_template_volume(self, file_name=None)[source]¶ Read the template volume. Download it first if it doesn’t exist.
Parameters: - file_name: string
File name to store the template volume. If it already exists, it will be read from this file. If file_name is None, the file_name will be pulled out of the manifest. Default is None.
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