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

.. only:: html

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

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

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

.. _sphx_glr_examples_convert_to_nwb.py:


Converting to NWB using Neo
===========================

.. GENERATED FROM PYTHON SOURCE LINES 6-59

.. code-block:: Python


    from urllib.request import urlretrieve
    from urllib.parse import quote
    from neo.io import get_io


    dataset_url = "https://object.cscs.ch/v1/AUTH_63ea6845b1d34ad7a43c8158d9572867/hbp-d000017_PatchClamp-GranuleCells_pub"

    folder = "GrC_Subject15_180116"

    # filenames = ["180116_0004 IV -70.abf", "180116_0005 CC step.abf", "180116_0006 EPSP.abf"]
    filenames = ["180116_0005 CC step.abf"]

    for filename in filenames:
        datafile_url = f"{dataset_url}/{folder}/{quote(filename)}"
        local_file = urlretrieve(datafile_url, filename)


    reader = get_io("180116_0005 CC step.abf")
    data = reader.read()

    global_metadata = {
        "session_start_time": data[0].rec_datetime,
        "identifier": data[0].file_origin,
        "session_id": "180116_0005",
        "institution": "University of Pavia",
        "lab": "D'Angelo Lab",
        "related_publications": "https://doi.org/10.1038/s42003-020-0953-x",
    }

    # data[0].annotate(**global_metadata)

    signal_metadata = {
        "nwb_group": "acquisition",
        "nwb_neurodata_type": ("pynwb.icephys", "PatchClampSeries"),
        "nwb_electrode": {
            "name": "patch clamp electrode",
            "description": "The patch-clamp pipettes were pulled from borosilicate glass capillaries "
            "(Hilgenberg, Malsfeld, Germany) and filled with intracellular solution "
            "(K-gluconate based solution)",
            "device": {"name": "patch clamp electrode"},
        },
        "nwb:gain": 1.0,
    }

    for segment in data[0].segments:
        signal = segment.analogsignals[0]
        signal.annotate(**signal_metadata)

    from neo.io import NWBIO

    writer = NWBIO("GrC_Subject15_180116.nwb", mode="w", **global_metadata)
    writer.write(data)


.. _sphx_glr_download_examples_convert_to_nwb.py:

.. only:: html

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

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

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

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

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


.. only:: html

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

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