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remove duplicate intro #1443

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108 changes: 0 additions & 108 deletions docs/gallery/general/file.py
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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 <https://nwb-schema.readthedocs.io>`_, 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:
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