diff --git a/docs/gallery/general/file.py b/docs/gallery/general/file.py index 40195b419..4fc9fb90d 100644 --- a/docs/gallery/general/file.py +++ b/docs/gallery/general/file.py @@ -85,114 +85,6 @@ More commonly, you will be creating instances of classes that extend this class. -.. seealso:: - - For your reference, NWB defines the following main analysis :py:class:`~pynwb.core.NWBDataInterface` subtypes: - - * **Behavior:** :py:class:`~pynwb.behavior.BehavioralEpochs`, - :py:class:`~pynwb.behavior.BehavioralEvents`, - :py:class:`~pynwb.behavior.BehavioralTimeSeries`, - :py:class:`~pynwb.behavior.CompassDirection`, - :py:class:`~pynwb.behavior.PupilTracking`, - :py:class:`~pynwb.behavior.Position`, - :py:class:`~pynwb.behavior.EyeTracking`. - - * **Extracellular electrophysiology:** :py:class:`~pynwb.ecephys.EventDetection`, - :py:class:`~pynwb.ecephys.EventWaveform`, - :py:class:`~pynwb.ecephys.FeatureExtraction`, - :py:class:`~pynwb.ecephys.FilteredEphys`, - :py:class:`~pynwb.ecephys.LFP`. - - * **Optical physiology:** :py:class:`~pynwb.ophys.DfOverF`, - :py:class:`~pynwb.ophys.Fluorescence`, - :py:class:`~pynwb.ophys.ImageSegmentation`, - :py:class:`~pynwb.ophys.MotionCorrection`. - - * **Others:** :py:class:`~pynwb.retinotopy.ImagingRetinotopy`, - :py:class:`~pynwb.base.Images`. - - * **TimeSeries:** Any :ref:`timeseries_overview` is also a subclass of :py:class:`~pynwb.core.NWBDataInterface` - and can be used anywhere :py:class:`~pynwb.core.NWBDataInterface` is allowed. - -.. note:: - - In addition to :py:class:`~pynwb.core.NWBContainer`, which functions as a common base type for Group objects, - :py:class:`~pynwb.core.NWBData` provides a common base for the specification of datasets in the NWB format. - -.. _basics_background: - -Background: Basic concepts --------------------------- - -In the `NWB Format `_, each experimental session is typically -represented by a separate NWB file. NWB files are represented in PyNWB by :py:class:`~pynwb.file.NWBFile` -objects which provide functionality for creating and retrieving: - - * :ref:`timeseries_overview` datasets, i.e., objects for storing time series data - * :ref:`modules_overview`, i.e., objects for storing and grouping analyses, and - * experimental metadata and other metadata related to data provenance. - -The following sections describe the :py:class:`~pynwb.base.TimeSeries` and :py:class:`~pynwb.base.ProcessingModules` -classes in further detail. - -.. _timeseries_overview: - -TimeSeries -^^^^^^^^^^ - -:py:class:`~pynwb.base.TimeSeries` objects store time series data and correspond to the *TimeSeries* specifications -provided by the `NWB Format`_ . Like the NWB specification, :py:class:`~pynwb.base.TimeSeries` Python objects -follow an object-oriented inheritance pattern, i.e., the class :py:class:`~pynwb.base.TimeSeries` -serves as the base class for all other :py:class:`~pynwb.base.TimeSeries` types, such as, -:py:class:`~pynwb.ecephys.ElectricalSeries`, which itself may have further subtypes, e.g., -:py:class:`~pynwb.ecephys.SpikeEventSeries`. - -.. seealso:: - - For your reference, NWB defines the following main :py:class:`~pynwb.base.TimeSeries` subtypes: - - * **Extracellular electrophysiology:** - :py:class:`~pynwb.ecephys.ElectricalSeries`, :py:class:`~pynwb.ecephys.SpikeEventSeries` - - * **Intracellular electrophysiology:** - :py:class:`~pynwb.icephys.PatchClampSeries` is the base type for all intracellular time series, which - is further refined into subtypes depending on the type of recording: - :py:class:`~pynwb.icephys.CurrentClampSeries`, - :py:class:`~pynwb.icephys.IZeroClampSeries`, - :py:class:`~pynwb.icephys.CurrentClampStimulusSeries`, - :py:class:`~pynwb.icephys.VoltageClampSeries`, - :py:class:`~pynwb.icephys.VoltageClampStimulusSeries`. - - * **Optical physiology and imaging:** :py:class:`~pynwb.image.ImageSeries` is the base type - for image recordings and is further refined by the - :py:class:`~pynwb.image.ImageMaskSeries`, - :py:class:`~pynwb.image.OpticalSeries`, and - :py:class:`~pynwb.ophys.TwoPhotonSeries` types. - Other related time series types are: - :py:class:`~pynwb.image.IndexSeries` and - :py:class:`~pynwb.ophys.RoiResponseSeries`. - - * **Others** :py:class:`~pynwb.ogen.OptogeneticSeries`, - :py:class:`~pynwb.behavior.SpatialSeries`, - :py:class:`~pynwb.misc.DecompositionSeries`, - :py:class:`~pynwb.misc.AnnotationSeries`, - :py:class:`~pynwb.misc.AbstractFeatureSeries`, and - :py:class:`~pynwb.misc.IntervalSeries`. - - -.. _modules_overview: - -Processing Modules -^^^^^^^^^^^^^^^^^^ - -Processing modules are objects that group together common analyses done during processing of data. -Processing module objects are unique collections of analysis results. To standardize the storage of -common analyses, NWB provides the concept of an :py:class:`~pynwb.core.NWBDataInterface`, where the output of -common analyses are represented as objects that extend the :py:class:`~pynwb.core.NWBDataInterface` class. -In most cases, you will not need to interact with the :py:class:`~pynwb.core.NWBDataInterface` class directly. -More commonly, you will be creating instances of classes that extend this class. - - .. seealso:: For your reference, NWB defines the following main analysis :py:class:`~pynwb.core.NWBDataInterface` subtypes: