.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "examples/ex_06_import_export_to_file.py"
.. LINE NUMBERS ARE GIVEN BELOW.

.. only:: html

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

        :ref:`Go to the end <sphx_glr_download_examples_ex_06_import_export_to_file.py>`
        to download the full example code.

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

.. _sphx_glr_examples_ex_06_import_export_to_file.py:


Import/export functions
-----------------------

`probeinterface` has its own format based on JSON.
The format can handle several probes in one file.
It has a 'probes' key that can contain a list of probes.

Each probe field in the json format contains the `Probe` class attributes.

It also supports reading (and sometimes writing) from these formats:

  * PRB (.prb) : used by klusta/spyking-circus/tridesclous
  * CSV (.csv): 2 or 3 columns locations in text file
  * mearec (.h5) : mearec handles the geometry
  * spikeglx (.meta) : spikeglx also handles the geometry

.. GENERATED FROM PYTHON SOURCE LINES 21-22

Import

.. GENERATED FROM PYTHON SOURCE LINES 22-32

.. code-block:: Python


    import numpy as np
    import matplotlib.pyplot as plt

    from probeinterface import Probe, ProbeGroup
    from probeinterface.plotting import plot_probe, plot_probegroup
    from probeinterface import generate_dummy_probe
    from probeinterface import write_probeinterface, read_probeinterface
    from probeinterface import write_prb, read_prb








.. GENERATED FROM PYTHON SOURCE LINES 33-35

Let's first generate 2 dummy probes and combine them
into a ProbeGroup

.. GENERATED FROM PYTHON SOURCE LINES 35-44

.. code-block:: Python


    probe0 = generate_dummy_probe(elec_shapes='square')
    probe1 = generate_dummy_probe(elec_shapes='circle')
    probe1.move([250, -90])

    probegroup = ProbeGroup()
    probegroup.add_probe(probe0)
    probegroup.add_probe(probe1)








.. GENERATED FROM PYTHON SOURCE LINES 45-47

With the `write_probeinterface` and `read_probeinterface` functions we can
write to and read from the json-based probeinterface format:

.. GENERATED FROM PYTHON SOURCE LINES 47-53

.. code-block:: Python


    write_probeinterface('my_two_probe_setup.json', probegroup)

    probegroup2 = read_probeinterface('my_two_probe_setup.json')
    plot_probegroup(probegroup2)




.. image-sg:: /examples/images/sphx_glr_ex_06_import_export_to_file_001.png
   :alt: ex 06 import export to file
   :srcset: /examples/images/sphx_glr_ex_06_import_export_to_file_001.png
   :class: sphx-glr-single-img





.. GENERATED FROM PYTHON SOURCE LINES 54-55

The format looks like this:

.. GENERATED FROM PYTHON SOURCE LINES 55-61

.. code-block:: Python


    with open('my_two_probe_setup.json', mode='r') as f:
        txt = f.read()

    print(txt[:600], '...')





.. rst-class:: sphx-glr-script-out

 .. code-block:: none

    {
        "specification": "probeinterface",
        "version": "0.3.2",
        "probes": [
            {
                "ndim": 2,
                "si_units": "um",
                "annotations": {
                    "manufacturer": "me"
                },
                "contact_annotations": {
                    "quality": [
                        1000.0,
                        1000.0,
                        1000.0,
                        1000.0,
                        1000.0,
                        1000.0,
                        1000.0,
                        1000.0,
                        1000.0,
                        1000.0,
                        1000.0,
      ...




.. GENERATED FROM PYTHON SOURCE LINES 62-72

PRB is an historical format introduced by the Klusta team and it is also
used by SpikeInterface, Spyking-circus, and Tridesclous.
The format is in fact a python script that describes a dictionary.
This format handles:
  * multiple groups (multi-shank or multi-probe)
  * contact_positions with 'geometry'
  * device_channel_indices with 'channels'

Here is an example of a .prb file with 2 channel groups of 4 channels each.
It can be easily loaded and plotted with `probeinterface`

.. GENERATED FROM PYTHON SOURCE LINES 72-104

.. code-block:: Python



    prb_two_tetrodes = """
    channel_groups = {
        0: {
                'channels' : [0,1,2,3],
                'geometry': {
                    0: [0, 50],
                    1: [50, 0],
                    2: [0, -50],
                    3: [-50, 0],
                }
        },
        1: {
                'channels' : [4,5,6,7],
                'geometry': {
                    4: [0, 50],
                    5: [50, 0],
                    6: [0, -50],
                    7: [-50, 0],
                }
        }
    }
    """

    with open('two_tetrodes.prb', 'w') as f:
        f.write(prb_two_tetrodes)

    two_tetrode = read_prb('two_tetrodes.prb')
    plot_probegroup(two_tetrode, same_axes=False, with_contact_id=True)

    plt.show()



.. image-sg:: /examples/images/sphx_glr_ex_06_import_export_to_file_002.png
   :alt: ex 06 import export to file
   :srcset: /examples/images/sphx_glr_ex_06_import_export_to_file_002.png
   :class: sphx-glr-single-img






.. rst-class:: sphx-glr-timing

   **Total running time of the script:** (0 minutes 0.151 seconds)


.. _sphx_glr_download_examples_ex_06_import_export_to_file.py:

.. only:: html

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

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

      :download:`Download Jupyter notebook: ex_06_import_export_to_file.ipynb <ex_06_import_export_to_file.ipynb>`

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

      :download:`Download Python source code: ex_06_import_export_to_file.py <ex_06_import_export_to_file.py>`

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

      :download:`Download zipped: ex_06_import_export_to_file.zip <ex_06_import_export_to_file.zip>`


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