allensdk.core.brain_observatory_cache module¶
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class
allensdk.core.brain_observatory_cache.BrainObservatoryCache(cache=True, manifest_file=None, base_uri=None, api=None)[source]¶ Bases:
allensdk.api.cache.CacheCache class for storing and accessing data from the Brain Observatory. By default, this class will cache any downloaded metadata or files in well known locations defined in a manifest file. This behavior can be disabled.
Parameters: - 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_ophys_experiment_data(file_name=’file.nwb’)).
- manifest_file: string
File name of the manifest to be read. Default is “brain_observatory_manifest.json”.
Attributes: - api: BrainObservatoryApi instance
The object used for making API queries related to the Brain Observatory.
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ANALYSIS_DATA_KEY= 'ANALYSIS_DATA'¶
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CELL_SPECIMENS_KEY= 'CELL_SPECIMENS'¶
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EVENTS_DATA_KEY= 'EVENTS_DATA'¶
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EXPERIMENTS_KEY= 'EXPERIMENTS'¶
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EXPERIMENT_CONTAINERS_KEY= 'EXPERIMENT_CONTAINERS'¶
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EXPERIMENT_DATA_KEY= 'EXPERIMENT_DATA'¶
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EYE_GAZE_DATA_KEY= 'EYE_GAZE_DATA'¶
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MANIFEST_VERSION= '1.3'¶
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STIMULUS_MAPPINGS_KEY= 'STIMULUS_MAPPINGS'¶
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build_manifest(self, file_name)[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_all_targeted_structures(self)[source]¶ Return a list of all targeted structures in the data set.
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get_cell_specimens(self, file_name=None, ids=None, experiment_container_ids=None, include_failed=False, simple=True, filters=None)[source]¶ Return cell specimens that have certain properies.
Parameters: - file_name: string
File name to save/read the cell specimens. 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.
- ids: list
List of cell specimen ids.
- experiment_container_ids: list
List of experiment container ids.
- include_failed: bool
Whether to include cells from failed experiment containers
- simple: boolean
Whether or not to simplify the dictionary properties returned by this method to a more concise subset.
- filters: list of dicts
List of filter dictionaries. The Allen Brain Observatory web site can generate filters in this format to reproduce a filtered set of cells found there. To see what these look like, visit http://observatory.brain-map.org/visualcoding, perform a cell search and apply some filters (e.g. find cells in a particular area), then click the “view these cells in the AllenSDK” link on the bottom-left of the search results page. This will take you to a page that contains a code sample you can use to apply those same filters via this argument. For more detail on the filter syntax, see BrainObservatoryApi.dataframe_query.
Returns: - list of dictionaries
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get_experiment_containers(self, file_name=None, ids=None, targeted_structures=None, imaging_depths=None, cre_lines=None, reporter_lines=None, transgenic_lines=None, include_failed=False, simple=True)[source]¶ Get a list of experiment containers matching certain criteria.
Parameters: - file_name: string
File name to save/read the experiment containers. 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.
- ids: list
List of experiment container ids.
- targeted_structures: list
List of structure acronyms. Must be in the list returned by BrainObservatoryCache.get_all_targeted_structures().
- imaging_depths: list
List of imaging depths. Must be in the list returned by BrainObservatoryCache.get_all_imaging_depths().
- cre_lines: list
List of cre lines. Must be in the list returned by BrainObservatoryCache.get_all_cre_lines().
- reporter_lines: list
List of reporter lines. Must be in the list returned by BrainObservatoryCache.get_all_reporter_lines().
- transgenic_lines: list
List of transgenic lines. Must be in the list returned by BrainObservatoryCache.get_all_cre_lines() or. BrainObservatoryCache.get_all_reporter_lines().
- include_failed: boolean
Whether or not to include failed experiment containers.
- simple: boolean
Whether or not to simplify the dictionary properties returned by this method to a more concise subset.
Returns: - list of dictionaries
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get_ophys_experiment_analysis(self, ophys_experiment_id, stimulus_type, file_name=None)[source]¶ Download the h5 analysis file for a stimulus set, for a particular ophys_experiment (if it hasn’t already been downloaded) and return a data accessor object.
Parameters: - file_name: string
File name to save/read the data set. 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.
- ophys_experiment_id: int
id of the ophys_experiment to retrieve
- stimulus_name: str
stimulus type; should be an element of self.list_stimuli()
Returns: - BrainObservatoryNwbDataSet
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get_ophys_experiment_data(self, ophys_experiment_id, file_name=None)[source]¶ Download the NWB file for an ophys_experiment (if it hasn’t already been downloaded) and return a data accessor object.
Parameters: - file_name: string
File name to save/read the data set. 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.
- ophys_experiment_id: integer
id of the ophys_experiment to retrieve
Returns: - BrainObservatoryNwbDataSet
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get_ophys_experiment_events(self, ophys_experiment_id, file_name=None)[source]¶ Download the npz events file for an ophys_experiment if it hasn’t already been downloaded and return the events array.
Parameters: - file_name: string
File name to save/read the data set. 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.
- ophys_experiment_id: int
id of the ophys_experiment to retrieve events for
- Returns
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- events: numpy.ndarray
[N_cells,N_times] array of events.
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get_ophys_experiment_stimuli(self, experiment_id)[source]¶ For a single experiment, return the list of stimuli present in that experiment.
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get_ophys_experiments(self, file_name=None, ids=None, experiment_container_ids=None, targeted_structures=None, imaging_depths=None, cre_lines=None, reporter_lines=None, transgenic_lines=None, stimuli=None, session_types=None, cell_specimen_ids=None, include_failed=False, require_eye_tracking=False, simple=True)[source]¶ Get a list of ophys experiments matching certain criteria.
Parameters: - file_name: string
File name to save/read the ophys experiments. 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.
- ids: list
List of ophys experiment ids.
- experiment_container_ids: list
List of experiment container ids.
- targeted_structures: list
List of structure acronyms. Must be in the list returned by BrainObservatoryCache.get_all_targeted_structures().
- imaging_depths: list
List of imaging depths. Must be in the list returned by BrainObservatoryCache.get_all_imaging_depths().
- cre_lines: list
List of cre lines. Must be in the list returned by BrainObservatoryCache.get_all_cre_lines().
- reporter_lines: list
List of reporter lines. Must be in the list returned by BrainObservatoryCache.get_all_reporter_lines().
- transgenic_lines: list
List of transgenic lines. Must be in the list returned by BrainObservatoryCache.get_all_cre_lines() or. BrainObservatoryCache.get_all_reporter_lines().
- stimuli: list
List of stimulus names. Must be in the list returned by BrainObservatoryCache.get_all_stimuli().
- session_types: list
List of stimulus session type names. Must be in the list returned by BrainObservatoryCache.get_all_session_types().
- cell_specimen_ids: list
Only include experiments that contain cells with these ids.
- include_failed: boolean
Whether or not to include experiments from failed experiment containers.
- simple: boolean
Whether or not to simplify the dictionary properties returned by this method to a more concise subset.
- require_eye_tracking: boolean
If True, only return experiments that have eye tracking results. Default: False.
Returns: - list of dictionaries
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get_ophys_pupil_data(self, ophys_experiment_id: int, file_name: str = None, suppress_pupil_data: bool = True) → pandas.core.frame.DataFrame[source]¶ Download the h5 eye gaze mapping file for an ophys_experiment if it hasn’t already been downloaded and return it as a pandas.DataFrame.
Parameters: - file_name: string
File name to save/read the data set. 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.
- ophys_experiment_id: int
id of the ophys_experiment to retrieve pupil data for.
- suppress_pupil_data: bool
Whether or not to suppress pupil data from dataset. Default is True.
Returns: