allensdk.core package¶
Subpackages¶
Submodules¶
- allensdk.core.auth_config module
- allensdk.core.authentication module
- allensdk.core.brain_observatory_cache module
- allensdk.core.brain_observatory_nwb_data_set module
BrainObservatoryNwbDataSetBrainObservatoryNwbDataSet.FILE_METADATA_MAPPINGBrainObservatoryNwbDataSet.MOTION_CORRECTION_DATASETSBrainObservatoryNwbDataSet.PIPELINE_DATASETBrainObservatoryNwbDataSet.STIMULUS_TABLE_TYPESBrainObservatoryNwbDataSet.SUPPORTED_PIPELINE_VERSIONBrainObservatoryNwbDataSet.get_cell_specimen_ids()BrainObservatoryNwbDataSet.get_cell_specimen_indices()BrainObservatoryNwbDataSet.get_corrected_fluorescence_traces()BrainObservatoryNwbDataSet.get_demixed_traces()BrainObservatoryNwbDataSet.get_dff_traces()BrainObservatoryNwbDataSet.get_fluorescence_timestamps()BrainObservatoryNwbDataSet.get_fluorescence_traces()BrainObservatoryNwbDataSet.get_locally_sparse_noise_stimulus_template()BrainObservatoryNwbDataSet.get_max_projection()BrainObservatoryNwbDataSet.get_metadata()BrainObservatoryNwbDataSet.get_motion_correction()BrainObservatoryNwbDataSet.get_neuropil_r()BrainObservatoryNwbDataSet.get_neuropil_traces()BrainObservatoryNwbDataSet.get_pupil_location()BrainObservatoryNwbDataSet.get_pupil_size()BrainObservatoryNwbDataSet.get_roi_ids()BrainObservatoryNwbDataSet.get_roi_mask()BrainObservatoryNwbDataSet.get_roi_mask_array()BrainObservatoryNwbDataSet.get_running_speed()BrainObservatoryNwbDataSet.get_session_type()BrainObservatoryNwbDataSet.get_stimulus()BrainObservatoryNwbDataSet.get_stimulus_epoch_table()BrainObservatoryNwbDataSet.get_stimulus_table()BrainObservatoryNwbDataSet.get_stimulus_template()BrainObservatoryNwbDataSet.list_stimuli()BrainObservatoryNwbDataSet.number_of_cellsBrainObservatoryNwbDataSet.save_analysis_arrays()BrainObservatoryNwbDataSet.save_analysis_dataframes()BrainObservatoryNwbDataSet.stimulus_search
align_running_speed()get_epoch_mask_list()
- allensdk.core.cache_method_utilities module
- allensdk.core.cell_types_cache module
CellTypesCacheCellTypesCache.CELLS_KEYCellTypesCache.EPHYS_DATA_KEYCellTypesCache.EPHYS_FEATURES_KEYCellTypesCache.EPHYS_SWEEPS_KEYCellTypesCache.MANIFEST_VERSIONCellTypesCache.MARKER_KEYCellTypesCache.MORPHOLOGY_FEATURES_KEYCellTypesCache.RECONSTRUCTION_KEYCellTypesCache.build_manifest()CellTypesCache.get_all_features()CellTypesCache.get_cells()CellTypesCache.get_ephys_data()CellTypesCache.get_ephys_features()CellTypesCache.get_ephys_sweeps()CellTypesCache.get_morphology_features()CellTypesCache.get_reconstruction()CellTypesCache.get_reconstruction_markers()
ReporterStatus
- allensdk.core.dat_utilities module
- allensdk.core.dataframe_utils module
- allensdk.core.exceptions module
- allensdk.core.h5_utilities module
- allensdk.core.json_utilities module
- allensdk.core.mouse_connectivity_cache module
MouseConnectivityCacheMouseConnectivityCache.ALIGNMENT3D_KEYMouseConnectivityCache.DATA_MASK_KEYMouseConnectivityCache.DEFAULT_STRUCTURE_SET_IDSMouseConnectivityCache.DEFORMATION_FIELD_HEADER_KEYMouseConnectivityCache.DEFORMATION_FIELD_VOXEL_KEYMouseConnectivityCache.DFMFLD_RESOLUTIONSMouseConnectivityCache.EXPERIMENTS_KEYMouseConnectivityCache.INJECTION_DENSITY_KEYMouseConnectivityCache.INJECTION_FRACTION_KEYMouseConnectivityCache.MANIFEST_VERSIONMouseConnectivityCache.PROJECTION_DENSITY_KEYMouseConnectivityCache.STRUCTURE_UNIONIZES_KEYMouseConnectivityCache.SUMMARY_STRUCTURE_SET_IDMouseConnectivityCache.add_manifest_paths()MouseConnectivityCache.default_structure_idsMouseConnectivityCache.filter_experiments()MouseConnectivityCache.filter_structure_unionizes()MouseConnectivityCache.get_affine_parameters()MouseConnectivityCache.get_data_mask()MouseConnectivityCache.get_deformation_field()MouseConnectivityCache.get_experiment_structure_unionizes()MouseConnectivityCache.get_experiments()MouseConnectivityCache.get_injection_density()MouseConnectivityCache.get_injection_fraction()MouseConnectivityCache.get_projection_density()MouseConnectivityCache.get_projection_matrix()MouseConnectivityCache.get_structure_unionizes()MouseConnectivityCache.rank_structures()
- allensdk.core.nwb_data_set module
NwbDataSetNwbDataSet.DEPRECATED_SPIKE_TIMESNwbDataSet.SPIKE_TIMESNwbDataSet.fill_sweep_responses()NwbDataSet.get_experiment_sweep_numbers()NwbDataSet.get_pipeline_version()NwbDataSet.get_spike_times()NwbDataSet.get_sweep()NwbDataSet.get_sweep_metadata()NwbDataSet.get_sweep_numbers()NwbDataSet.set_spike_times()NwbDataSet.set_sweep()
- allensdk.core.obj_utilities module
- allensdk.core.ontology module
- allensdk.core.ophys_experiment_session_id_mapping module
- allensdk.core.pickle_utils module
- allensdk.core.reference_space module
ReferenceSpaceReferenceSpace.check_and_write()ReferenceSpace.check_coverage()ReferenceSpace.direct_voxel_counts()ReferenceSpace.direct_voxel_mapReferenceSpace.downsample()ReferenceSpace.export_itksnap_labels()ReferenceSpace.get_slice_image()ReferenceSpace.make_structure_mask()ReferenceSpace.many_structure_masks()ReferenceSpace.remove_unassigned()ReferenceSpace.return_mask_cb()ReferenceSpace.total_voxel_counts()ReferenceSpace.total_voxel_mapReferenceSpace.validate_structures()ReferenceSpace.write_itksnap_labels()
- allensdk.core.reference_space_cache module
ReferenceSpaceCacheReferenceSpaceCache.ANNOTATION_KEYReferenceSpaceCache.MANIFEST_VERSIONReferenceSpaceCache.REFERENCE_SPACE_VERSION_KEYReferenceSpaceCache.STRUCTURES_KEYReferenceSpaceCache.STRUCTURE_MASK_KEYReferenceSpaceCache.STRUCTURE_MESH_KEYReferenceSpaceCache.STRUCTURE_TREE_KEYReferenceSpaceCache.TEMPLATE_KEYReferenceSpaceCache.add_manifest_paths()ReferenceSpaceCache.get_annotation_volume()ReferenceSpaceCache.get_reference_space()ReferenceSpaceCache.get_structure_mask()ReferenceSpaceCache.get_structure_mesh()ReferenceSpaceCache.get_structure_tree()ReferenceSpaceCache.get_template_volume()ReferenceSpaceCache.validate_structure_id()ReferenceSpaceCache.validate_structure_ids()
- allensdk.core.simple_tree module
SimpleTreeSimpleTree.ancestor_ids()SimpleTree.ancestors()SimpleTree.child_ids()SimpleTree.children()SimpleTree.descendant_ids()SimpleTree.descendants()SimpleTree.filter_nodes()SimpleTree.node()SimpleTree.node_ids()SimpleTree.nodes()SimpleTree.nodes_by_property()SimpleTree.parent()SimpleTree.parent_id()SimpleTree.parent_ids()SimpleTree.parents()SimpleTree.value_map()
- allensdk.core.sitk_utilities module
- allensdk.core.structure_tree module
StructureTreeStructureTree.clean_structures()StructureTree.collect_sets()StructureTree.data_transforms()StructureTree.export_label_description()StructureTree.get_ancestor_id_map()StructureTree.get_colormap()StructureTree.get_id_acronym_map()StructureTree.get_name_map()StructureTree.get_structure_sets()StructureTree.get_structures_by_acronym()StructureTree.get_structures_by_id()StructureTree.get_structures_by_name()StructureTree.get_structures_by_set_id()StructureTree.has_overlaps()StructureTree.hex_to_rgb()StructureTree.path_to_list()StructureTree.renames()StructureTree.structure_descends_from()StructureTree.whitelist()
- allensdk.core.swc module
CompartmentMarkerMorphologyMorphology.APICAL_DENDRITEMorphology.AXONMorphology.BASAL_DENDRITEMorphology.DENDRITEMorphology.NODE_TYPESMorphology.SOMAMorphology.append()Morphology.apply_affine()Morphology.change_parent()Morphology.children_of()Morphology.compartment_indexMorphology.compartment_index_by_type()Morphology.compartment_listMorphology.compartment_list_by_type()Morphology.convert_type()Morphology.delete_tree()Morphology.find()Morphology.node()Morphology.num_nodesMorphology.num_treesMorphology.parent_of()Morphology.rootMorphology.save()Morphology.somaMorphology.sparsify()Morphology.strip_all_other_types()Morphology.strip_type()Morphology.stumpify_axon()Morphology.tree()Morphology.write()
read_marker_file()read_swc()
- allensdk.core.typing module
- allensdk.core.utilities module