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

.. only:: html

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

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

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

.. _sphx_glr_examples_plot_read_files_neo_rawio.py:


Reading files with neo.rawio
============================

compare with read_files_neo_io.py

.. GENERATED FROM PYTHON SOURCE LINES 9-11

First we import a RawIO from neo.rawio
For this example we will use PlexonRawIO

.. GENERATED FROM PYTHON SOURCE LINES 11-15

.. code-block:: Python


    import urllib
    from neo.rawio import PlexonRawIO








.. GENERATED FROM PYTHON SOURCE LINES 16-17

Get Plexon files

.. GENERATED FROM PYTHON SOURCE LINES 17-29

.. code-block:: Python


    # We will be pulling these files down, but if you have a local file
    # then all you need to do is specify the file location on your
    # computer. NeuralEnsemble keeps a wide variety of freely accesible, small
    # test files that can be used. So for this example we will take advantage of that
    # fact.

    url_repo = "https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/"
    distantfile = url_repo + "plexon/File_plexon_3.plx"
    localfile = "File_plexon_3.plx"
    urllib.request.urlretrieve(distantfile, localfile)





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

 .. code-block:: none


    ('File_plexon_3.plx', <http.client.HTTPMessage object at 0x772688ad0c50>)



.. GENERATED FROM PYTHON SOURCE LINES 30-31

Create a reader

.. GENERATED FROM PYTHON SOURCE LINES 31-43

.. code-block:: Python


    # All it takes to create a reader is giving the filename (or dirname)
    # Then we need to do the slow step of parsing the header with the
    # `parse_header` function. This collects metadata as well as
    # make all future steps much faster for us

    reader = PlexonRawIO(filename="File_plexon_3.plx")
    reader.parse_header()
    print(reader)
    # we can view metadata in the header
    print(reader.header)





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

 .. code-block:: none

    PlexonRawIO: File_plexon_3.plx
    nb_block: 1
    nb_segment:  [1]
    signal_streams: [V (chans: 1)]
    signal_channels: [V1]
    spike_channels: [Wspk1u, Wspk2u, Wspk4u, Wspk5u ... Wspk29u , Wspk30u , Wspk31u , Wspk32u]
    event_channels: []

    {'nb_block': 1, 'nb_segment': [1], 'signal_buffers': array([], dtype=[('name', '<U64'), ('id', '<U64')]), 'signal_streams': array([('V', 'V', '')],
          dtype=[('name', '<U64'), ('id', '<U64'), ('buffer_id', '<U64')]), 'signal_channels': array([('V1', '0', 1000., 'int16', '', 2.44140625, 0., 'V', '')],
          dtype=[('name', '<U64'), ('id', '<U64'), ('sampling_rate', '<f8'), ('dtype', '<U16'), ('units', '<U64'), ('gain', '<f8'), ('offset', '<f8'), ('stream_id', '<U64'), ('buffer_id', '<U64')]), 'spike_channels': array([('Wspk1u', 'ch1#0', '', 7.32421875e-05, 0., -1, 30000.),
           ('Wspk2u', 'ch2#0', '', 7.32421875e-05, 0., -1, 30000.),
           ('Wspk4u', 'ch3#0', '', 7.32421875e-05, 0., -1, 30000.),
           ('Wspk5u', 'ch4#0', '', 7.32421875e-05, 0., -1, 30000.),
           ('Wspk6u', 'ch5#0', '', 7.32421875e-05, 0., -1, 30000.),
           ('Wspk7u', 'ch6#0', '', 7.32421875e-05, 0., -1, 30000.),
           ('Wspk8u', 'ch7#0', '', 7.32421875e-05, 0., -1, 30000.),
           ('Wspk9u', 'ch8#0', '', 7.32421875e-05, 0., -1, 30000.),
           ('Wspk10u', 'ch9#0', '', 7.32421875e-05, 0., -1, 30000.),
           ('Wspk11u', 'ch10#0', '', 7.32421875e-05, 0., -1, 30000.),
           ('Wspk12u', 'ch11#0', '', 7.32421875e-05, 0., -1, 30000.),
           ('Wspk13u', 'ch12#0', '', 7.32421875e-05, 0., -1, 30000.),
           ('Wspk14u', 'ch13#0', '', 7.32421875e-05, 0., -1, 30000.),
           ('Wspk15u', 'ch14#0', '', 7.32421875e-05, 0., -1, 30000.),
           ('Wspk16u', 'ch15#0', '', 7.32421875e-05, 0., -1, 30000.),
           ('Wspk17u', 'ch16#0', '', 7.32421875e-05, 0., -1, 30000.),
           ('Wspk19u', 'ch18#0', '', 7.32421875e-05, 0., -1, 30000.),
           ('Wspk20u', 'ch19#0', '', 7.32421875e-05, 0., -1, 30000.),
           ('Wspk21u', 'ch20#0', '', 7.32421875e-05, 0., -1, 30000.),
           ('Wspk22u', 'ch21#0', '', 7.32421875e-05, 0., -1, 30000.),
           ('Wspk23u', 'ch22#0', '', 7.32421875e-05, 0., -1, 30000.),
           ('Wspk24u', 'ch23#0', '', 7.32421875e-05, 0., -1, 30000.),
           ('Wspk25u', 'ch24#0', '', 7.32421875e-05, 0., -1, 30000.),
           ('Wspk26u', 'ch25#0', '', 7.32421875e-05, 0., -1, 30000.),
           ('Wspk27u', 'ch26#0', '', 7.32421875e-05, 0., -1, 30000.),
           ('Wspk28u', 'ch27#0', '', 7.32421875e-05, 0., -1, 30000.),
           ('Wspk29u', 'ch28#0', '', 7.32421875e-05, 0., -1, 30000.),
           ('Wspk30u', 'ch29#0', '', 7.32421875e-05, 0., -1, 30000.),
           ('Wspk31u', 'ch30#0', '', 7.32421875e-05, 0., -1, 30000.),
           ('Wspk32u', 'ch31#0', '', 7.32421875e-05, 0., -1, 30000.)],
          dtype=[('name', '<U64'), ('id', '<U64'), ('wf_units', '<U64'), ('wf_gain', '<f8'), ('wf_offset', '<f8'), ('wf_left_sweep', '<i8'), ('wf_sampling_rate', '<f8')]), 'event_channels': array([], dtype=[('name', '<U64'), ('id', '<U64'), ('type', 'S5')])}




.. GENERATED FROM PYTHON SOURCE LINES 44-51

Read signal chunks
This is how we read raw data. We choose indices that we want or
we can use None to mean look at all channels. We also need to
specify the block of data (block_index) as well as the segment
(seg_index). Then we give the index start and stop. Since we
often think in time: to go from time to index would just require
the sample rate (so index = time / sampling_rate)

.. GENERATED FROM PYTHON SOURCE LINES 51-65

.. code-block:: Python


    channel_indexes = None  # could be channel_indexes = [0]
    raw_sigs = reader.get_analogsignal_chunk(
        block_index=0, seg_index=0, i_start=1024, i_stop=2048, channel_indexes=channel_indexes
    )

    # raw_sigs are not voltages so to convert to voltages we do the follwing
    float_sigs = reader.rescale_signal_raw_to_float(raw_sigs, dtype="float64")

    # We can see that the shapes are the same, but that the datatypes
    # are different once we've rescaled our data
    print("Raw Data: ", raw_sigs.shape, raw_sigs.dtype)
    print("Scaled Data: ", float_sigs.shape, float_sigs.dtype)





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

 .. code-block:: none

    Raw Data:  (1024, 1) int16
    Scaled Data:  (1024, 1) float64




.. GENERATED FROM PYTHON SOURCE LINES 66-69

Each rawio gives you access to lots of information about your data
some of this information comes from functions
other information is stored as metadata in the reader.header

.. GENERATED FROM PYTHON SOURCE LINES 69-79

.. code-block:: Python


    sampling_rate = reader.get_signal_sampling_rate()
    # Like above we need to indicate the block and segment
    t_start = reader.get_signal_t_start(block_index=0, seg_index=0)
    units = reader.header["signal_channels"][0]["units"]

    # and we can display all of this information
    print(f"{sampling_rate=}, {t_start=}, {units=}")






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

 .. code-block:: none

    sampling_rate=1000.0, t_start=0.0, units=np.str_('')




.. GENERATED FROM PYTHON SOURCE LINES 80-83

Some rawio's and file formats also provide information about spikes
If a rawio can't read this data it will raise an error, but lucky
for us PlexonRawIO does have spikes data!!

.. GENERATED FROM PYTHON SOURCE LINES 83-101

.. code-block:: Python


    # Count units and spikes per unit
    nb_unit = reader.spike_channels_count()
    print(f"nb_unit: {nb_unit}\n")  # nb_unit stands for number of units
    print("spike_channel_index     nb_spike")
    for spike_channel_index in range(nb_unit):
        nb_spike = reader.spike_count(block_index=0, seg_index=0, spike_channel_index=spike_channel_index)
        print(f"{spike_channel_index}: {nb_spike}\n")

    # Read spike times and rescale (just like analogsignal above)
    spike_timestamps = reader.get_spike_timestamps(
        block_index=0, seg_index=0, spike_channel_index=0, t_start=0.0, t_stop=10.0
    )

    print(f"{spike_timestamps.shape=}\n{spike_timestamps.dtype=}\n{spike_timestamps[:5]=}\n")
    spike_times = reader.rescale_spike_timestamp(spike_timestamps, dtype="float64")
    print(f"{spike_times.shape=}\n{spike_times.dtype=}\n{spike_times[:5]}\n")





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

 .. code-block:: none

    nb_unit: 30

    spike_channel_index     nb_spike
    0: 701

    1: 716

    2: 69

    3: 12

    4: 95

    5: 37

    6: 25

    7: 15

    8: 33

    9: 392

    10: 337

    11: 333

    12: 85

    13: 13

    14: 20

    15: 750

    16: 3

    17: 1345

    18: 826

    19: 818

    20: 744

    21: 753

    22: 34

    23: 36

    24: 30

    25: 19

    26: 2

    27: 42

    28: 15

    29: 51

    spike_timestamps.shape=(424,)
    spike_timestamps.dtype=dtype('int64')
    spike_timestamps[:5]=array([  90,  420,  708, 1020, 1310])

    spike_times.shape=(424,)
    spike_times.dtype=dtype('float64')
    [0.003      0.014      0.0236     0.034      0.04366667]





.. GENERATED FROM PYTHON SOURCE LINES 102-105

Some file formats can also give waveform information. We are lucky
again our file has waveform data!! We forms are a 3d dataset of
(nb_spike, nb_channel, nb_sample)

.. GENERATED FROM PYTHON SOURCE LINES 105-114

.. code-block:: Python


    # Read spike waveforms
    raw_waveforms = reader.get_spike_raw_waveforms(
        block_index=0, seg_index=0, spike_channel_index=0, t_start=0.0, t_stop=10.0
    )
    print(f"{raw_waveforms.shape=}\n{raw_waveforms.dtype=}\n{raw_waveforms[0, 0, :4]=}\n")
    float_waveforms = reader.rescale_waveforms_to_float(raw_waveforms, dtype="float32", spike_channel_index=0)
    print(f"{float_waveforms.shape=}\n{float_waveforms.dtype=}{float_waveforms[0, 0, :4]=}\n")





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

 .. code-block:: none

    raw_waveforms.shape=(424, 1, 64)
    raw_waveforms.dtype=dtype('int16')
    raw_waveforms[0, 0, :4]=array([-449, -206,   34,   40], dtype=int16)

    float_waveforms.shape=(424, 1, 64)
    float_waveforms.dtype=dtype('float32')float_waveforms[0, 0, :4]=array([-0.03288574, -0.01508789,  0.00249023,  0.00292969], dtype=float32)





.. GENERATED FROM PYTHON SOURCE LINES 115-117

RawIOs can also read event timestamps. But looks like our luck ran out
let's grab a new file to see this feature

.. GENERATED FROM PYTHON SOURCE LINES 117-123

.. code-block:: Python


    # Read event timestamps and times (take another file)
    distantfile = url_repo + "plexon/File_plexon_2.plx"
    localfile = "File_plexon_2.plx"
    urllib.request.urlretrieve(distantfile, localfile)





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

 .. code-block:: none


    ('File_plexon_2.plx', <http.client.HTTPMessage object at 0x772688a7fb50>)



.. GENERATED FROM PYTHON SOURCE LINES 124-126

Since this is a new file we need to read initialize our reader as well
as parse the header

.. GENERATED FROM PYTHON SOURCE LINES 126-132

.. code-block:: Python


    reader = PlexonRawIO(filename="File_plexon_2.plx")
    reader.parse_header()
    # if we look at this header we see it is different than the header above
    print(reader.header)





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

 .. code-block:: none

    {'nb_block': 1, 'nb_segment': [1], 'signal_buffers': array([], dtype=[('name', '<U64'), ('id', '<U64')]), 'signal_streams': array([], dtype=[('name', '<U64'), ('id', '<U64'), ('buffer_id', '<U64')]), 'signal_channels': array([],
          dtype=[('name', '<U64'), ('id', '<U64'), ('sampling_rate', '<f8'), ('dtype', '<U16'), ('units', '<U64'), ('gain', '<f8'), ('offset', '<f8'), ('stream_id', '<U64'), ('buffer_id', '<U64')]), 'spike_channels': array([('sig001', 'ch1#1', '', 0.00073242, 0., -1, 0.),
           ('sig001', 'ch1#2', '', 0.00073242, 0., -1, 0.),
           ('sig001', 'ch1#3', '', 0.00073242, 0., -1, 0.),
           ('sig002', 'ch2#1', '', 0.00073242, 0., -1, 0.),
           ('sig002', 'ch2#2', '', 0.00073242, 0., -1, 0.),
           ('sig002', 'ch2#3', '', 0.00073242, 0., -1, 0.)],
          dtype=[('name', '<U64'), ('id', '<U64'), ('wf_units', '<U64'), ('wf_gain', '<f8'), ('wf_offset', '<f8'), ('wf_left_sweep', '<i8'), ('wf_sampling_rate', '<f8')]), 'event_channels': array([('Event001', '1', b'event'), ('Event002', '2', b'event'),
           ('Event003', '3', b'event'), ('Event004', '4', b'event'),
           ('Event005', '5', b'event'), ('Event006', '6', b'event'),
           ('Event007', '7', b'event'), ('Event008', '8', b'event'),
           ('Event009', '9', b'event'), ('Event010', '10', b'event'),
           ('Event011', '11', b'event'), ('Event012', '12', b'event'),
           ('Event013', '13', b'event'), ('Event014', '14', b'event'),
           ('Event015', '15', b'event'), ('Event016', '16', b'event'),
           ('Strobed', '257', b'event'), ('Start\x0018', '258', b'event'),
           ('Stop\x00019', '259', b'event'), ('Keyboard1', '101', b'event'),
           ('Keyboard2', '102', b'event'), ('Keyboard3', '103', b'event'),
           ('Keyboard4', '104', b'event'), ('Keyboard5', '105', b'event'),
           ('Keyboard6', '106', b'event'), ('Keyboard7', '107', b'event'),
           ('Keyboard8', '108', b'event'), ('Keyboard9', '109', b'event')],
          dtype=[('name', '<U64'), ('id', '<U64'), ('type', 'S5')])}




.. GENERATED FROM PYTHON SOURCE LINES 133-135

Now let's look at some event data. This could be things like stimuli applied
during the course of an ephys recording

.. GENERATED FROM PYTHON SOURCE LINES 135-144

.. code-block:: Python


    nb_event_channel = reader.event_channels_count()
    print(f"nb_event_channel: {nb_event_channel}")
    # now iterate through the channels
    for chan_index in range(nb_event_channel):
        nb_event = reader.event_count(block_index=0, seg_index=0, event_channel_index=chan_index)
        print(f"chan_index: {chan_index} nb_event: {nb_event}\n")






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

 .. code-block:: none

    nb_event_channel: 28
    chan_index: 0 nb_event: 1

    chan_index: 1 nb_event: 0

    chan_index: 2 nb_event: 0

    chan_index: 3 nb_event: 0

    chan_index: 4 nb_event: 0

    chan_index: 5 nb_event: 0

    chan_index: 6 nb_event: 0

    chan_index: 7 nb_event: 0

    chan_index: 8 nb_event: 0

    chan_index: 9 nb_event: 0

    chan_index: 10 nb_event: 0

    chan_index: 11 nb_event: 0

    chan_index: 12 nb_event: 0

    chan_index: 13 nb_event: 0

    chan_index: 14 nb_event: 0

    chan_index: 15 nb_event: 0

    chan_index: 16 nb_event: 0

    chan_index: 17 nb_event: 1

    chan_index: 18 nb_event: 0

    chan_index: 19 nb_event: 0

    chan_index: 20 nb_event: 0

    chan_index: 21 nb_event: 0

    chan_index: 22 nb_event: 0

    chan_index: 23 nb_event: 0

    chan_index: 24 nb_event: 0

    chan_index: 25 nb_event: 0

    chan_index: 26 nb_event: 0

    chan_index: 27 nb_event: 0





.. GENERATED FROM PYTHON SOURCE LINES 145-149

Finally we can get our actual event timestamps. Some file formats provide the
real timestamps (timestamps in s/ms) others have raw timestamps (in samples)
so we can do the same style of functions as above. Get the raw timestamps
and convert to real times with a rescale function.

.. GENERATED FROM PYTHON SOURCE LINES 149-156

.. code-block:: Python


    ev_timestamps, ev_durations, ev_labels = reader.get_event_timestamps(
        block_index=0, seg_index=0, event_channel_index=0, t_start=None, t_stop=None
    )
    print(f"{ev_timestamps=}\n{ev_durations=}\n{ev_labels=}\n")
    ev_times = reader.rescale_event_timestamp(ev_timestamps, dtype="float64")
    print(f"{ev_times=}\n")




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

 .. code-block:: none

    ev_timestamps=array([1268])
    ev_durations=None
    ev_labels=array(['0'], dtype='<U5')

    ev_times=array([0.0317])






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

   **Total running time of the script:** (1 minutes 8.673 seconds)


.. _sphx_glr_download_examples_plot_read_files_neo_rawio.py:

.. only:: html

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

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

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

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

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

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

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


.. only:: html

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

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