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

.. only:: html

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

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

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

.. _sphx_glr_gettingstarted_examples_gallery_auto_examples_core_c_importer_plot_generic_read.py:


Reading datasets
================

In this example, we show the use of the generic `read` method to create dataset
either from local or remote files.

.. GENERATED FROM PYTHON SOURCE LINES 17-18

First we need to import the spectrochempy API package

.. GENERATED FROM PYTHON SOURCE LINES 18-20

.. code-block:: default

    import spectrochempy as scp








.. GENERATED FROM PYTHON SOURCE LINES 21-25

Import dataset from local files
-------------------------------
Read a IR data recorded in Omnic format (``.spg`` extension).
We just pass the file name as parameter.

.. GENERATED FROM PYTHON SOURCE LINES 25-28

.. code-block:: default

    dataset = scp.read("irdata/nh4y-activation.spg")
    dataset






.. raw:: html

    <div class="output_subarea output_html rendered_html output_result">
    <table style='background:transparent'>
    <tr><td style='padding-right:5px; padding-bottom:0px; padding-top:0px; width:124px'><font color='green'>         name</font> </td><td style='text-align:left; padding-bottom:0px; padding-top:0px; border:.5px solid lightgray;  '> nh4y-activation</td><tr>
    <tr><td style='padding-right:5px; padding-bottom:0px; padding-top:0px; width:124px'><font color='green'>       author</font> </td><td style='text-align:left; padding-bottom:0px; padding-top:0px; border:.5px solid lightgray;  '> runner@fv-az1152-754</td><tr>
    <tr><td style='padding-right:5px; padding-bottom:0px; padding-top:0px; width:124px'><font color='green'>      created</font> </td><td style='text-align:left; padding-bottom:0px; padding-top:0px; border:.5px solid lightgray;  '> 2024-03-08 00:59:42+00:00</td><tr>
    <tr><td style='padding-right:5px; padding-bottom:0px; padding-top:0px; width:124px'><font color='green'>  description</font> </td><td style='text-align:left; padding-bottom:0px; padding-top:0px; border:.5px solid lightgray;  '> <div>Omnic title: NH4Y-activation.SPG<br/>               Omnic filename: /home/runner/.spectrochempy/testdata/irdata/nh4y-activation.spg</div></td><tr>
    <tr><td style='padding-right:5px; padding-bottom:0px; padding-top:0px; width:124px'><font color='green'>      history</font> </td><td style='text-align:left; padding-bottom:0px; padding-top:0px; border:.5px solid lightgray;  '> <div>2024-03-08 00:59:42+00:00> Imported from spg file /home/runner/.spectrochempy/testdata/irdata/nh4y-activation.spg.<br/>               2024-03-08 00:59:42+00:00> Sorted by date</div></td><tr>
    <tr><td style='padding-right:5px; padding-bottom:0px; padding-top:0px; width:124px'><strong>          DATA </strong></td><td style='text-align:left; padding-bottom:0px; padding-top:0px; padding-top:10px; '><hr/></td><tr>
    <tr><td style='padding-right:5px; padding-bottom:0px; padding-top:0px; width:124px'><font color='green'>        title</font> </td><td style='text-align:left; padding-bottom:0px; padding-top:0px; border:.5px solid lightgray;  '> absorbance</td><tr>
    <tr><td style='padding-right:5px; padding-bottom:0px; padding-top:0px; width:124px'><font color='green'>       values</font> </td><td style='text-align:left; padding-bottom:0px; padding-top:0px; border:.5px solid lightgray;  '> <div><font color='blue'>         [[   2.057    2.061 ...    2.013    2.012]<br/>          [   2.033    2.037 ...    1.913    1.911]<br/>          ...<br/>          [   1.794    1.791 ...    1.198    1.198]<br/>          [   1.816    1.815 ...     1.24    1.238]] a.u.</font></div></td><tr>
    <tr><td style='padding-right:5px; padding-bottom:0px; padding-top:0px; width:124px'><font color='green'>        shape</font> </td><td style='text-align:left; padding-bottom:0px; padding-top:0px; border:.5px solid lightgray;  '> (y:55, x:5549)</td><tr>
    <tr><td style='padding-right:5px; padding-bottom:0px; padding-top:0px; width:124px'><strong>     DIMENSION `x`</strong></td><td style='text-align:left; padding-bottom:0px; padding-top:0px; padding-top:10px; '><hr/></td><tr>
    <tr><td style='padding-right:5px; padding-bottom:0px; padding-top:0px; width:124px'><font color='green'>         size</font> </td><td style='text-align:left; padding-bottom:0px; padding-top:0px; border:.5px solid lightgray;  '> 5549</td><tr>
    <tr><td style='padding-right:5px; padding-bottom:0px; padding-top:0px; width:124px'><font color='green'>        title</font> </td><td style='text-align:left; padding-bottom:0px; padding-top:0px; border:.5px solid lightgray;  '> wavenumbers</td><tr>
    <tr><td style='padding-right:5px; padding-bottom:0px; padding-top:0px; width:124px'><font color='green'>  coordinates</font> </td><td style='text-align:left; padding-bottom:0px; padding-top:0px; border:.5px solid lightgray;  '> <div><font color='blue'>[    6000     5999 ...    650.9    649.9] cm⁻¹</font></div></td><tr>
    <tr><td style='padding-right:5px; padding-bottom:0px; padding-top:0px; width:124px'><strong>     DIMENSION `y`</strong></td><td style='text-align:left; padding-bottom:0px; padding-top:0px; padding-top:10px; '><hr/></td><tr>
    <tr><td style='padding-right:5px; padding-bottom:0px; padding-top:0px; width:124px'><font color='green'>         size</font> </td><td style='text-align:left; padding-bottom:0px; padding-top:0px; border:.5px solid lightgray;  '> 55</td><tr>
    <tr><td style='padding-right:5px; padding-bottom:0px; padding-top:0px; width:124px'><font color='green'>        title</font> </td><td style='text-align:left; padding-bottom:0px; padding-top:0px; border:.5px solid lightgray;  '> acquisition timestamp (GMT)</td><tr>
    <tr><td style='padding-right:5px; padding-bottom:0px; padding-top:0px; width:124px'><font color='green'>  coordinates</font> </td><td style='text-align:left; padding-bottom:0px; padding-top:0px; border:.5px solid lightgray;  '> <div><font color='blue'>[1.468e+09 1.468e+09 ... 1.468e+09 1.468e+09] s</font></div></td><tr>
    <tr><td style='padding-right:5px; padding-bottom:0px; padding-top:0px; width:124px'><font color='green'>       labels</font> </td><td style='text-align:left; padding-bottom:0px; padding-top:0px; border:.5px solid lightgray;  '> <div><font color='darkcyan'>         [[  2016-07-06 19:03:14+00:00   2016-07-06 19:13:14+00:00 ...   2016-07-07 04:03:17+00:00   2016-07-07 04:13:17+00:00]<br/>          [  vz0466.spa, Wed Jul 06 21:00:38 2016 (GMT+02:00)   vz0467.spa, Wed Jul 06 21:10:38 2016 (GMT+02:00) ...<br/>             vz0520.spa, Thu Jul 07 06:00:41 2016 (GMT+02:00)   vz0521.spa, Thu Jul 07 06:10:41 2016 (GMT+02:00)]]</font></div></td><tr>
    </table>
    </div>
    <br />
    <br />

.. GENERATED FROM PYTHON SOURCE LINES 29-31

.. code-block:: default

    _ = dataset.plot(style="paper")




.. image-sg:: /gettingstarted/examples/gallery/auto_examples_core/c_importer/images/sphx_glr_plot_generic_read_001.png
   :alt: plot generic read
   :srcset: /gettingstarted/examples/gallery/auto_examples_core/c_importer/images/sphx_glr_plot_generic_read_001.png
   :class: sphx-glr-single-img





.. GENERATED FROM PYTHON SOURCE LINES 32-33

When using `read`, we can pass filename as a `str` or a `~pathlib.Path` object.

.. GENERATED FROM PYTHON SOURCE LINES 33-38

.. code-block:: default

    from pathlib import Path

    filename = Path("irdata/nh4y-activation.spg")
    dataset = scp.read(filename)








.. GENERATED FROM PYTHON SOURCE LINES 39-41

Note that is the file is not found in the current working directory, `SpectroChemPy`
will try to find it in the ``datadir`` directory defined in `preferences` :

.. GENERATED FROM PYTHON SOURCE LINES 41-44

.. code-block:: default

    datadir = scp.preferences.datadir
    datadir





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

 .. code-block:: none


    PosixPath('/home/runner/.spectrochempy/testdata')



.. GENERATED FROM PYTHON SOURCE LINES 45-50

If the supplied argument is a directory, then the whole directory is read at once.
By default, the different files will be merged along the first dimension (y).
However, for this to work, the second dimension (x) must be compatible (same size)
or else a WARNING appears. To avoid the warning and get individual spectra, you can
set ``merge`` to `False` .

.. GENERATED FROM PYTHON SOURCE LINES 50-53

.. code-block:: default

    dataset_list = scp.read("irdata", merge=False)
    dataset_list





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

 .. code-block:: none


    [NDDataset: [float64] a.u. (shape: (y:19, x:3112)), NDDataset: [float64] a.u. (shape: (y:55, x:5549)), NDDataset: [float64] unitless (shape: (y:1, x:3736))]



.. GENERATED FROM PYTHON SOURCE LINES 54-56

to get full details on the parameters that can be used, look at the API documentation:
`spectrochempy.read` .

.. GENERATED FROM PYTHON SOURCE LINES 58-61

Import dataset from remote files
--------------------------------
To download and read file from remote server you can use urls.

.. GENERATED FROM PYTHON SOURCE LINES 61-62

.. code-block:: default

    dataset_list = scp.read("http://www.eigenvector.com/data/Corn/corn.mat")







.. GENERATED FROM PYTHON SOURCE LINES 63-65

In this case the matlab data contains 7 arrays that have been automatically
transformed to `NDDataset` .

.. GENERATED FROM PYTHON SOURCE LINES 65-68

.. code-block:: default

    for nd in dataset_list:
        print(f"{nd.name} : {nd.shape}")





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

 .. code-block:: none

    m5nbs : (3, 700)
    mp5nbs : (4, 700)
    mp6nbs : (4, 700)
    propvals : (80, 4)
    m5spec : (80, 700)
    mp5spec : (80, 700)
    mp6spec : (80, 700)




.. GENERATED FROM PYTHON SOURCE LINES 69-73

The `eigenvector.com <eigenvector.com>`__ website contains the same data in a
compressed (zipped) format:
`corn.mat_.zip <https://eigenvector.com/wp-content/uploads/2019/06/corn.mat_.zip>`__ .
This can also be used by the `read` method.

.. GENERATED FROM PYTHON SOURCE LINES 73-81

.. code-block:: default

    dataset_list = scp.read(
        "https://eigenvector.com/wp-content/uploads/2019/06/corn.mat_.zip"
    )
    _ = dataset_list[-1].plot()
    _ = dataset_list[-2].plot()
    _ = dataset_list[-3].plot()
    _ = dataset_list[-4].plot()




.. rst-class:: sphx-glr-horizontal


    *

      .. image-sg:: /gettingstarted/examples/gallery/auto_examples_core/c_importer/images/sphx_glr_plot_generic_read_002.png
         :alt: plot generic read
         :srcset: /gettingstarted/examples/gallery/auto_examples_core/c_importer/images/sphx_glr_plot_generic_read_002.png
         :class: sphx-glr-multi-img

    *

      .. image-sg:: /gettingstarted/examples/gallery/auto_examples_core/c_importer/images/sphx_glr_plot_generic_read_003.png
         :alt: plot generic read
         :srcset: /gettingstarted/examples/gallery/auto_examples_core/c_importer/images/sphx_glr_plot_generic_read_003.png
         :class: sphx-glr-multi-img

    *

      .. image-sg:: /gettingstarted/examples/gallery/auto_examples_core/c_importer/images/sphx_glr_plot_generic_read_004.png
         :alt: plot generic read
         :srcset: /gettingstarted/examples/gallery/auto_examples_core/c_importer/images/sphx_glr_plot_generic_read_004.png
         :class: sphx-glr-multi-img

    *

      .. image-sg:: /gettingstarted/examples/gallery/auto_examples_core/c_importer/images/sphx_glr_plot_generic_read_005.png
         :alt: plot generic read
         :srcset: /gettingstarted/examples/gallery/auto_examples_core/c_importer/images/sphx_glr_plot_generic_read_005.png
         :class: sphx-glr-multi-img





.. GENERATED FROM PYTHON SOURCE LINES 82-84

This ends the example ! The following line can be uncommented if no plot shows when
running the .py script with python

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.. code-block:: default


    # scp.show()








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

   **Total running time of the script:** ( 0 minutes  3.803 seconds)


.. _sphx_glr_download_gettingstarted_examples_gallery_auto_examples_core_c_importer_plot_generic_read.py:

.. only:: html

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




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

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

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

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


.. only:: html

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

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