allensdk.brain_observatory.session_analysis module

class allensdk.brain_observatory.session_analysis.SessionAnalysis(nwb_path, save_path)

Bases: object

Run all of the stimulus-specific analyses associated with a single experiment session.

Parameters:

nwb_path: string, path to NWB file

save_path: string, path to HDF5 file to store outputs. Recommended NOT to modify the NWB file.

append_experiment_metrics(metrics)

Extract stimulus-agnostic metrics from an experiment into a dictionary

append_metadata(df)

Append the metadata fields from the NWB file as columns to a pd.DataFrame

append_metrics_drifting_grating(metrics, dg)

Extract metrics from the DriftingGratings peak response table into a dictionary.

append_metrics_locally_sparse_noise(metrics, lsn)

Extract metrics from the LocallySparseNoise peak response table into a dictionary.

append_metrics_natural_movie_one(metrics, nma)

Extract metrics from the NaturalMovie(stimulus_info.NATURAL_MOVIE_ONE) peak response table into a dictionary.

append_metrics_natural_movie_three(metrics, nma)

Extract metrics from the NaturalMovie(stimulus_info.NATURAL_MOVIE_THREE) peak response table into a dictionary.

append_metrics_natural_movie_two(metrics, nma)

Extract metrics from the NaturalMovie(stimulus_info.NATURAL_MOVIE_TWO) peak response table into a dictionary.

append_metrics_natural_scene(metrics, ns)

Extract metrics from the NaturalScenes peak response table into a dictionary.

append_metrics_static_grating(metrics, sg)

Extract metrics from the StaticGratings peak response table into a dictionary.

save_session_a(dg, nm1, nm3, peak)

Save the output of session A analysis to self.save_path.

Parameters:

dg: DriftingGratings instance

nm1: NaturalMovie instance

This NaturalMovie instance should have been created with movie_name = stimulus_info.NATURAL_MOVIE_ONE

nm3: NaturalMovie instance

This NaturalMovie instance should have been created with movie_name = stimulus_info.NATURAL_MOVIE_THREE

peak: pd.DataFrame

The combined peak response property table created in self.session_a().

save_session_b(sg, nm1, ns, peak)

Save the output of session B analysis to self.save_path.

Parameters:

sg: StaticGratings instance

nm1: NaturalMovie instance

This NaturalMovie instance should have been created with movie_name = stimulus_info.NATURAL_MOVIE_ONE

ns: NaturalScenes instance

peak: pd.DataFrame

The combined peak response property table created in self.session_b().

save_session_c(lsn, nm1, nm2, peak)

Save the output of session C analysis to self.save_path.

Parameters:

lsn: LocallySparseNoise instance

nm1: NaturalMovie instance

This NaturalMovie instance should have been created with movie_name = stimulus_info.NATURAL_MOVIE_ONE

nm2: NaturalMovie instance

This NaturalMovie instance should have been created with movie_name = stimulus_info.NATURAL_MOVIE_TWO

peak: pd.DataFrame

The combined peak response property table created in self.session_c().

save_session_c2(lsn4, lsn8, nm1, nm2, peak)

Save the output of session C2 analysis to self.save_path.

Parameters:

lsn4: LocallySparseNoise instance

This LocallySparseNoise instance should have been created with self.stimulus = stimulus_info.LOCALLY_SPARSE_NOISE_4DEG.

lsn8: LocallySparseNoise instance

This LocallySparseNoise instance should have been created with self.stimulus = stimulus_info.LOCALLY_SPARSE_NOISE_8DEG.

nm1: NaturalMovie instance

This NaturalMovie instance should have been created with movie_name = stimulus_info.NATURAL_MOVIE_ONE

nm2: NaturalMovie instance

This NaturalMovie instance should have been created with movie_name = stimulus_info.NATURAL_MOVIE_TWO

peak: pd.DataFrame

The combined peak response property table created in self.session_c2().

session_a(plot_flag=False, save_flag=True)

Run stimulus-specific analysis for natural movie one, natural movie three, and drifting gratings. The input NWB be for a stimulus_info.THREE_SESSION_A experiment.

Parameters:

plot_flag: bool

Whether to generate brain_observatory_plotting work plots after running analysis.

save_flag: bool

Whether to save the output of analysis to self.save_path upon completion.

session_b(plot_flag=False, save_flag=True)

Run stimulus-specific analysis for natural scenes, static gratings, and natural movie one. The input NWB be for a stimulus_info.THREE_SESSION_B experiment.

Parameters:

plot_flag: bool

Whether to generate brain_observatory_plotting work plots after running analysis.

save_flag: bool

Whether to save the output of analysis to self.save_path upon completion.

session_c(plot_flag=False, save_flag=True)

Run stimulus-specific analysis for natural movie one, natural movie two, and locally sparse noise. The input NWB be for a stimulus_info.THREE_SESSION_C experiment.

Parameters:

plot_flag: bool

Whether to generate brain_observatory_plotting work plots after running analysis.

save_flag: bool

Whether to save the output of analysis to self.save_path upon completion.

session_c2(plot_flag=False, save_flag=True)

Run stimulus-specific analysis for locally sparse noise (4 deg.), locally sparse noise (8 deg.), natural movie one, and natural movie two. The input NWB be for a stimulus_info.THREE_SESSION_C2 experiment.

Parameters:

plot_flag: bool

Whether to generate brain_observatory_plotting work plots after running analysis.

save_flag: bool

Whether to save the output of analysis to self.save_path upon completion.

verify_roi_lists_equal(roi1, roi2)

TODO: replace this with simpler numpy comparisons

allensdk.brain_observatory.session_analysis.main(*args, **kwargs)

allensdk.brain_observatory.session_analysis.multi_dataframe_merge(dfs)

merge a number of pd.DataFrames into a single dataframe on their index columns. If any columns are duplicated, prefer the first occuring instance of the column

allensdk.brain_observatory.session_analysis.run_session_analysis(nwb_path, save_path, plot_flag=False, save_flag=True)

Inspect an NWB file to determine which experiment session was run and compute all stimulus-specific analyses.

Parameters:

nwb_path: string

Path to NWB file.

save_path: string

path to save results. Recommended NOT to use NWB file.

plot_flag: bool

Whether to save brain_observatory_plotting work plots.

save_flag: bool

Whether to save results to save_path.