.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "tutorials/general/add_remove_containers.py"
.. LINE NUMBERS ARE GIVEN BELOW.

.. only:: html

    .. note::
        :class: sphx-glr-download-link-note

        :ref:`Go to the end <sphx_glr_download_tutorials_general_add_remove_containers.py>`
        to download the full example code.

.. rst-class:: sphx-glr-example-title

.. _sphx_glr_tutorials_general_add_remove_containers.py:


.. _modifying_data:

Adding/Removing Containers from an NWB File
============================================

This tutorial explains how to add and remove containers from an existing NWB file and either write the data back to the
same file or export the data to a new file.

.. GENERATED FROM PYTHON SOURCE LINES 12-24

Adding objects to an NWB file in read/write mode
----------------------------------------------------
PyNWB supports adding container objects to an existing NWB file - that is, reading data from an NWB file, adding a
container object, such as a new :py:class:`~pynwb.base.TimeSeries` object, and writing the modified
:py:class:`~pynwb.file.NWBFile` back to the same file path on disk. To do so:

1. open the file with an :py:class:`~pynwb.NWBHDF5IO` object in read/write mode (``mode='r+'`` or ``mode='a'``)
2. read the :py:class:`~pynwb.file.NWBFile`
3. add container objects to the :py:class:`~pynwb.file.NWBFile` object
4. write the modified :py:class:`~pynwb.file.NWBFile` using the same :py:class:`~pynwb.NWBHDF5IO` object

For example:

.. GENERATED FROM PYTHON SOURCE LINES 24-62

.. code-block:: Python


    import datetime

    import numpy as np

    from pynwb import NWBHDF5IO, NWBFile, TimeSeries

    # first, write a test NWB file
    nwbfile = NWBFile(
        session_description="demonstrate adding to an NWB file",
        identifier="NWB123",
        session_start_time=datetime.datetime.now(datetime.timezone.utc),
    )

    filename = "nwbfile.nwb"
    with NWBHDF5IO(filename, "w") as io:
        io.write(nwbfile)

    # open the NWB file in r+ mode
    with NWBHDF5IO(filename, "r+") as io:
        read_nwbfile = io.read()

        # create a TimeSeries and add it to the file under the acquisition group
        data = list(range(100, 200, 10))
        timestamps = np.arange(10, dtype=float)
        test_ts = TimeSeries(
            name="test_timeseries", data=data, unit="m", timestamps=timestamps
        )
        read_nwbfile.add_acquisition(test_ts)

        # write the modified NWB file
        io.write(read_nwbfile)

    # confirm the file contains the new TimeSeries in acquisition
    with NWBHDF5IO(filename, "r") as io:
        read_nwbfile = io.read()
        print(read_nwbfile)


.. GENERATED FROM PYTHON SOURCE LINES 64-67

.. note::

  You cannot remove objects from an NWB file using the above method.

.. GENERATED FROM PYTHON SOURCE LINES 69-89

Modifying an NWB file in this way has limitations. The destination file path must be the same as the source
file path, and it is not possible to remove objects from an NWB file. You can use the
:py:meth:`NWBHDF5IO.export <pynwb.NWBHDF5IO.export>` method, detailed below, to modify an NWB file in these ways.

Exporting a written NWB file to a new file path
-----------------------------------------------
Use the :py:meth:`NWBHDF5IO.export <pynwb.NWBHDF5IO.export>` method to read data from an existing NWB file,
modify the data, and write the modified data to a new file path. Modifications to the data can be additions or
removals of objects, such as :py:class:`~pynwb.base.TimeSeries` objects. This is especially useful if you
have raw data and processed data in the same NWB file and you want to create a new NWB file with all the contents of
the original file except for the raw data for sharing with collaborators.

To remove existing containers, use the :py:meth:`~hdmf.utils.LabelledDict.pop` method on any
:py:class:`~hdmf.utils.LabelledDict` object, such as ``NWBFile.acquisition``, ``NWBFile.processing``,
``NWBFile.analysis``, ``NWBFile.processing``, ``NWBFile.scratch``, ``NWBFile.devices``, ``NWBFile.stimulus``,
``NWBFile.stimulus_template``, ``NWBFile.electrode_groups``, ``NWBFile.imaging_planes``,
``NWBFile.icephys_electrodes``, ``NWBFile.ogen_sites``, ``NWBFile.lab_meta_data``,
and :py:class:`~pynwb.base.ProcessingModule` objects.

For example:

.. GENERATED FROM PYTHON SOURCE LINES 89-150

.. code-block:: Python


    # first, create a test NWB file with a TimeSeries in the acquisition group
    nwbfile = NWBFile(
        session_description="demonstrate export of an NWB file",
        identifier="NWB123",
        session_start_time=datetime.datetime.now(datetime.timezone.utc),
    )
    data1 = list(range(100, 200, 10))
    timestamps1 = np.arange(10, dtype=float)
    test_ts1 = TimeSeries(
        name="test_timeseries1", data=data1, unit="m", timestamps=timestamps1
    )
    nwbfile.add_acquisition(test_ts1)

    # then, create a processing module for processed behavioral data
    nwbfile.create_processing_module(
        name="behavior", description="processed behavioral data"
    )
    data2 = list(range(100, 200, 10))
    timestamps2 = np.arange(10, dtype=float)
    test_ts2 = TimeSeries(
        name="test_timeseries2", data=data2, unit="m", timestamps=timestamps2
    )
    nwbfile.processing["behavior"].add(test_ts2)

    # write these objects to an NWB file
    filename = "nwbfile.nwb"
    with NWBHDF5IO(filename, "w") as io:
        io.write(nwbfile)

    # read the written file
    export_filename = "exported_nwbfile.nwb"
    with NWBHDF5IO(filename, mode="r") as read_io:
        read_nwbfile = read_io.read()

        # add a new TimeSeries to the behavior processing module
        data3 = list(range(100, 200, 10))
        timestamps3 = np.arange(10, dtype=float)
        test_ts3 = TimeSeries(
            name="test_timeseries3", data=data3, unit="m", timestamps=timestamps3
        )
        read_nwbfile.processing["behavior"].add(test_ts3)

        # use the pop method to remove the original TimeSeries from the acquisition group
        read_nwbfile.acquisition.pop("test_timeseries1")

        # use the pop method to remove a TimeSeries from a processing module
        read_nwbfile.processing["behavior"].data_interfaces.pop("test_timeseries2")

        # call the export method to write the modified NWBFile instance to a new file path.
        # the original file is not modified
        with NWBHDF5IO(export_filename, mode="w") as export_io:
            export_io.export(src_io=read_io, nwbfile=read_nwbfile)

    # confirm the exported file does not contain TimeSeries with names 'test_timeseries1' or 'test_timeseries2'
    # but does contain a new TimeSeries in processing['behavior'] with name 'test_timeseries3'
    with NWBHDF5IO(export_filename, "r") as io:
        read_nwbfile = io.read()
        print(read_nwbfile)
        print(read_nwbfile.processing["behavior"])


.. GENERATED FROM PYTHON SOURCE LINES 151-156

.. note::

  :py:class:`~pynwb.epoch.TimeIntervals` objects, such as ``NWBFile.epochs``, ``NWBFile.trials``,
  ``NWBFile.invalid_times``, and custom :py:class:`~pynwb.epoch.TimeIntervals` objects cannot be
  removed (popped) from ``NWBFile.intervals``.

.. GENERATED FROM PYTHON SOURCE LINES 158-166

.. warning::

  Removing an object from an NWBFile may break links and references within the file and across files.
  This is analogous to having shortcuts/aliases to a file on your filesystem and then deleting the file.
  Extra caution should be taken when removing heavily referenced items such as
  :py:class:`~pynwb.device.Device` objects,
  :py:class:`~pynwb.ecephys.ElectrodeGroup` objects, the electrodes table, and the
  :py:class:`~pynwb.ophys.PlaneSegmentation` table.

.. GENERATED FROM PYTHON SOURCE LINES 168-175

Exporting with new object IDs
---------------------------------
When exporting a read NWB file to a new file path, the object IDs within the original NWB file will be copied to the
new file. To make the exported NWB file contain a new set of object IDs, call
:py:meth:`~hdmf.container.AbstractContainer.generate_new_id` on your :py:class:`~pynwb.file.NWBFile` object.
This will generate a new object ID for the :py:class:`~pynwb.file.NWBFile` object and all of the objects within
the NWB file.

.. GENERATED FROM PYTHON SOURCE LINES 175-184

.. code-block:: Python


    export_filename = "exported_nwbfile.nwb"
    with NWBHDF5IO(filename, mode="r") as read_io:
        read_nwbfile = read_io.read()
        read_nwbfile.generate_new_id()

        with NWBHDF5IO(export_filename, mode="w") as export_io:
            export_io.export(src_io=read_io, nwbfile=read_nwbfile)


.. GENERATED FROM PYTHON SOURCE LINES 185-189

For more information about the export functionality, see :ref:`export`
and the PyNWB documentation for :py:meth:`NWBHDF5IO.export <pynwb.NWBHDF5IO.export>`.

For more information about editing a file in place, see :ref:`editing`.


.. _sphx_glr_download_tutorials_general_add_remove_containers.py:

.. only:: html

  .. container:: sphx-glr-footer sphx-glr-footer-example

    .. container:: sphx-glr-download sphx-glr-download-jupyter

      :download:`Download Jupyter notebook: add_remove_containers.ipynb <add_remove_containers.ipynb>`

    .. container:: sphx-glr-download sphx-glr-download-python

      :download:`Download Python source code: add_remove_containers.py <add_remove_containers.py>`

    .. container:: sphx-glr-download sphx-glr-download-zip

      :download:`Download zipped: add_remove_containers.zip <add_remove_containers.zip>`


.. only:: html

 .. rst-class:: sphx-glr-signature

    `Gallery generated by Sphinx-Gallery <https://sphinx-gallery.github.io>`_