allensdk.internal.core.mouse_connectivity_cache_prerelease module¶
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class
allensdk.internal.core.mouse_connectivity_cache_prerelease.
MouseConnectivityCachePrerelease
(resolution=None, cache=True, manifest_file='mouse_connectivity_manifest_prerelease.json', ccf_version=None, version=None, cache_storage_directories=True, storage_directories_file_name=None)[source]¶ Bases:
allensdk.core.mouse_connectivity_cache.MouseConnectivityCache
Extends MouseConnectivityCache to use prereleased data from lims.
Parameters: - resolution: int
Resolution of grid data to be downloaded when accessing projection volume, the annotation volume, and the annotation volume. Must be one of (10, 25, 50, 100). Default is 25.
- ccf_version: string
Desired version of the Common Coordinate Framework. This affects the annotation volume (get_annotation_volume) and structure masks (get_structure_mask). Must be one of (MouseConnectivityApi.CCF_2015, MouseConnectivityApi.CCF_2016). Default: MouseConnectivityApi.CCF_2016
- cache: boolean
Whether the class should save results of API queries to locations specified in the manifest file. Queries for files (as opposed to metadata) must have a file location. If caching is disabled, those locations must be specified in the function call (e.g. get_projection_density(file_name=’file.nrrd’)).
- manifest_file: string
File name of the manifest to be read. Default is “mouse_connectivity_manifest.json”.
Attributes: - resolution: int
Resolution of grid data to be downloaded when accessing projection volume, the annotation volume, and the annotation volume. Must be one of (10, 25, 50, 100). Default is 25.
- api: MouseConnectivityApiPrerelease instance
Used internally to make API queries.
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EXPERIMENTS_PRERELEASE_KEY
= 'EXPERIMENTS_PRERELEASE'¶
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STORAGE_DIRECTORIES_PRERELEASE_KEY
= 'STORAGE_DIRECTORIES_PRERELEASE'¶
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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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filter_experiments
(self, experiments, cre=None, injection_structure_ids=None, age=None, gender=None, workflow_state=None, workflows=None, project_code=None)[source]¶ Take a list of experiments and filter them by cre status and injection structure.
Parameters: - cre: boolean or list
If True, return only cre-positive experiments. If False, return only cre-negative experiments. If None, return all experients. If list, return all experiments with cre line names in the supplied list. Default None.
- injection_structure_ids: list
Only return experiments that were injected in the structures provided here. If None, return all experiments. Default None.
- age : list
Only return experiments with specimens with ages provided here. If None, returna all experiments. Default None.
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get_experiments
(self, dataframe=False, file_name=None, cre=None, injection_structure_ids=None, age=None, gender=None, workflow_state=None, workflows=None, project_code=None)[source]¶ Read a list of experiments.
If caching is enabled, this will save the whole (unfiltered) list of experiments to a file.
Parameters: - dataframe: boolean
Return the list of experiments as a Pandas DataFrame. If False, return a list of dictionaries. Default False.
- 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.