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

.. only:: html

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

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

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

.. _sphx_glr_gallery_auto_examples_analysis_plot_iris.py:


2D-IRIS analysis example
=========================

In this example, we perform the 2D IRIS analysis of CO adsorption on a sulfide catalyst.

.. GENERATED FROM PYTHON SOURCE LINES 15-17

.. code-block:: default

    import spectrochempy as scp








.. GENERATED FROM PYTHON SOURCE LINES 18-20

Uploading dataset
-----------------

.. GENERATED FROM PYTHON SOURCE LINES 20-22

.. code-block:: default

    X = scp.read("irdata/CO@Mo_Al2O3.SPG")








.. GENERATED FROM PYTHON SOURCE LINES 23-26

`X` has two coordinates:
* `wavenumbers` named "x"
* and `timestamps` (*i.e.,* the time of recording) named "y".

.. GENERATED FROM PYTHON SOURCE LINES 26-29

.. code-block:: default


    print(X.coordset)





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

 .. code-block:: none

    CoordSet: [x:wavenumbers, y:acquisition timestamp (GMT)]




.. GENERATED FROM PYTHON SOURCE LINES 30-38

Setting new coordinates
-----------------------

The `y` coordinates of the dataset is the acquisition timestamp.
However, each spectrum has been recorded with a given pressure of CO
in the infrared cell.

Hence, it would be interesting to add pressure coordinates to the `y` dimension:

.. GENERATED FROM PYTHON SOURCE LINES 38-63

.. code-block:: default


    pressures = [
        0.003,
        0.004,
        0.009,
        0.014,
        0.021,
        0.026,
        0.036,
        0.051,
        0.093,
        0.150,
        0.203,
        0.300,
        0.404,
        0.503,
        0.602,
        0.702,
        0.801,
        0.905,
        1.004,
    ]

    c_pressures = scp.Coord(pressures, title="pressure", units="torr")








.. GENERATED FROM PYTHON SOURCE LINES 64-65

Now we can set multiple coordinates:

.. GENERATED FROM PYTHON SOURCE LINES 65-70

.. code-block:: default


    c_times = X.y.copy()  # the original coordinate
    X.y = [c_times, c_pressures]
    print(X.y)





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

 .. code-block:: none

    CoordSet: [_1:acquisition timestamp (GMT), _2:pressure]




.. GENERATED FROM PYTHON SOURCE LINES 71-73

To get a detailed
a rich display of these coordinates. In a jupyter notebook, just type:

.. GENERATED FROM PYTHON SOURCE LINES 73-76

.. code-block:: default


    X.coordset






.. 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'><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;  '> 3112</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'>[    4000     3999 ...     1001    999.9] 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;  '> 19</td><tr>
    <tr><td style='padding-right:5px; padding-bottom:0px; padding-top:0px; width:124px'><strong>          (_1)</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;  '> 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'>[1.477e+09 1.477e+09 ... 1.477e+09 1.477e+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'>         [[  2016-10-18 13:49:35+00:00   2016-10-18 13:54:06+00:00 ...   2016-10-18 16:01:33+00:00   2016-10-18 16:06:37+00:00]<br/>          [  *Résultat de Soustraction:04_Mo_Al2O3_calc_0.003torr_LT_after sulf_Oct 18 15:46:42 2016 (GMT+02:00)<br/>             *Résultat de Soustraction:04_Mo_Al2O3_calc_0.004torr_LT_after sulf_Oct 18 15:51:12 2016 (GMT+02:00) ...<br/>             *Résultat de Soustraction:04_Mo_Al2O3_calc_0.905torr_LT_after sulf_Oct 18 17:58:42 2016 (GMT+02:00)<br/>             *Résultat de Soustraction:04_Mo_Al2O3_calc_1.004torr_LT_after sulf_Oct 18 18:03:41 2016 (GMT+02:00)]]</font></div></td><tr>
    <tr><td style='padding-right:5px; padding-bottom:0px; padding-top:0px; width:124px'><strong>          (_2)</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;  '> pressure</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'>[   0.003    0.004 ...    0.905    1.004] torr</font></div></td><tr>
    </table>
    </div>
    <br />
    <br />

.. GENERATED FROM PYTHON SOURCE LINES 77-80

By default, the current coordinate is the first one (here `c_times` ).
For example, it will be used by default for
plotting:

.. GENERATED FROM PYTHON SOURCE LINES 80-86

.. code-block:: default


    prefs = X.preferences
    prefs.figure.figsize = (7, 3)
    _ = X.plot(colorbar=True)
    _ = X.plot_map(colorbar=True)




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


    *

      .. image-sg:: /gallery/auto_examples/analysis/images/sphx_glr_plot_iris_001.png
         :alt: plot iris
         :srcset: /gallery/auto_examples/analysis/images/sphx_glr_plot_iris_001.png
         :class: sphx-glr-multi-img

    *

      .. image-sg:: /gallery/auto_examples/analysis/images/sphx_glr_plot_iris_002.png
         :alt: plot iris
         :srcset: /gallery/auto_examples/analysis/images/sphx_glr_plot_iris_002.png
         :class: sphx-glr-multi-img





.. GENERATED FROM PYTHON SOURCE LINES 87-89

To seamlessly work with the second coordinates (pressures), we can change the default
coordinate:

.. GENERATED FROM PYTHON SOURCE LINES 89-93

.. code-block:: default


    X.y.select(2)  # to select coordinate `_2`
    X.y.default






.. 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'>         size</font> </td><td style='text-align:left; padding-bottom:0px; padding-top:0px; border:.5px solid lightgray;  '> 19</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;  '> pressure</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'>[   0.003    0.004 ...    0.905    1.004] torr</font></div></td><tr>
    </table>
    </div>
    <br />
    <br />

.. GENERATED FROM PYTHON SOURCE LINES 94-95

Let's now plot the spectral range of interest. The default coordinate is now used:

.. GENERATED FROM PYTHON SOURCE LINES 95-100

.. code-block:: default

    X_ = X[:, 2250.0:1950.0]
    print(X_.y.default)
    _ = X_.plot()
    _ = X_.plot_map()




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


    *

      .. image-sg:: /gallery/auto_examples/analysis/images/sphx_glr_plot_iris_003.png
         :alt: plot iris
         :srcset: /gallery/auto_examples/analysis/images/sphx_glr_plot_iris_003.png
         :class: sphx-glr-multi-img

    *

      .. image-sg:: /gallery/auto_examples/analysis/images/sphx_glr_plot_iris_004.png
         :alt: plot iris
         :srcset: /gallery/auto_examples/analysis/images/sphx_glr_plot_iris_004.png
         :class: sphx-glr-multi-img


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

 .. code-block:: none

    Coord: [float64] torr (size: 19)




.. GENERATED FROM PYTHON SOURCE LINES 101-105

IRIS analysis without regularization
------------------------------------
Perform IRIS without regularization (the loglevel can be set to `INFO` to have
information on the running process)

.. GENERATED FROM PYTHON SOURCE LINES 105-107

.. code-block:: default

    iris1 = scp.IRIS(log_level="INFO")








.. GENERATED FROM PYTHON SOURCE LINES 108-109

first we compute the kernel object

.. GENERATED FROM PYTHON SOURCE LINES 109-111

.. code-block:: default

    K = scp.IrisKernel(X_, "langmuir", q=[-8, -1, 50])





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

 .. code-block:: none

     Creating Kernel...
     Kernel now ready as IrisKernel().kernel!




.. GENERATED FROM PYTHON SOURCE LINES 112-113

The actual kernel is given by the `kernel` attribute

.. GENERATED FROM PYTHON SOURCE LINES 113-116

.. code-block:: default

    kernel = K.kernel
    kernel






.. 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;  '> langmuir kernel matrix</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-az626-878</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;  '> 2023-06-06 01:27:35+00:00</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;  '> coverage</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'>         [[ 0.06424   0.1265 ... 0.001332 0.0005778]<br/>          [  0.0659   0.1303 ...  0.00177 0.0007683]<br/>          ...<br/>          [  0.0714   0.1428 ...   0.1056  0.05078]<br/>          [  0.0714   0.1428 ...   0.1084  0.05227]]</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:19, x:50)</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;  '> 50</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;  '> $\Delta_{ads}G^{0}/RT$</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'>[      -8   -7.857 ...   -1.143       -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;  '> 19</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;  '> pressure</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'>[   0.003    0.004 ...    0.905    1.004] torr</font></div></td><tr>
    </table>
    </div>
    <br />
    <br />

.. GENERATED FROM PYTHON SOURCE LINES 117-118

Now we fit the model - we can pass either the Kernel object or the kernel NDDataset

.. GENERATED FROM PYTHON SOURCE LINES 118-120

.. code-block:: default

    iris1.fit(X_, K)





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

 .. code-block:: none

     Build S matrix (sharpness)
     ... done
     Solving for 312 channels and 19 observations, no regularization
     -->  residuals = 1.09e-01    curvature = 9.14e+04
     Done.

    <spectrochempy.analysis.iris.IRIS object at 0x7f15af6cb070>



.. GENERATED FROM PYTHON SOURCE LINES 121-122

Plots the results

.. GENERATED FROM PYTHON SOURCE LINES 122-125

.. code-block:: default

    iris1.plotdistribution()
    _ = iris1.plotmerit()




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


    *

      .. image-sg:: /gallery/auto_examples/analysis/images/sphx_glr_plot_iris_005.png
         :alt: plot iris
         :srcset: /gallery/auto_examples/analysis/images/sphx_glr_plot_iris_005.png
         :class: sphx-glr-multi-img

    *

      .. image-sg:: /gallery/auto_examples/analysis/images/sphx_glr_plot_iris_006.png
         :alt: 2D IRIS merit plot, $\lambda$ = 0.00e+00
         :srcset: /gallery/auto_examples/analysis/images/sphx_glr_plot_iris_006.png
         :class: sphx-glr-multi-img





.. GENERATED FROM PYTHON SOURCE LINES 126-129

With regularization and a manual search
---------------------------------------
Perform  IRIS with regularization, manual search

.. GENERATED FROM PYTHON SOURCE LINES 129-131

.. code-block:: default

    iris2 = scp.IRIS(reg_par=[-10, 1, 12])








.. GENERATED FROM PYTHON SOURCE LINES 132-133

We keep the same kernel object as previously - performs the fit.

.. GENERATED FROM PYTHON SOURCE LINES 133-139

.. code-block:: default

    iris2.fit(X_, K)

    iris2.plotlcurve(title="L curve, manual search")
    iris2.plotdistribution(-7)
    _ = iris2.plotmerit(-7)




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


    *

      .. image-sg:: /gallery/auto_examples/analysis/images/sphx_glr_plot_iris_007.png
         :alt: L curve, manual search
         :srcset: /gallery/auto_examples/analysis/images/sphx_glr_plot_iris_007.png
         :class: sphx-glr-multi-img

    *

      .. image-sg:: /gallery/auto_examples/analysis/images/sphx_glr_plot_iris_008.png
         :alt: plot iris
         :srcset: /gallery/auto_examples/analysis/images/sphx_glr_plot_iris_008.png
         :class: sphx-glr-multi-img

    *

      .. image-sg:: /gallery/auto_examples/analysis/images/sphx_glr_plot_iris_009.png
         :alt: 2D IRIS merit plot, $\lambda$ = 0.00e+00
         :srcset: /gallery/auto_examples/analysis/images/sphx_glr_plot_iris_009.png
         :class: sphx-glr-multi-img





.. GENERATED FROM PYTHON SOURCE LINES 140-144

Automatic search
----------------
%%
Now try an automatic search of the regularization parameter:

.. GENERATED FROM PYTHON SOURCE LINES 144-149

.. code-block:: default


    iris3 = scp.IRIS(reg_par=[-10, 1])
    iris3.fit(X_, K)
    iris3.plotlcurve(title="L curve, automated search")




.. image-sg:: /gallery/auto_examples/analysis/images/sphx_glr_plot_iris_010.png
   :alt: L curve, automated search
   :srcset: /gallery/auto_examples/analysis/images/sphx_glr_plot_iris_010.png
   :class: sphx-glr-single-img


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

 .. code-block:: none


    <Axes: title={'center': 'L curve, automated search'}, xlabel='Residuals', ylabel='Curvature'>



.. GENERATED FROM PYTHON SOURCE LINES 150-152

The data corresponding to the largest curvature of the L-curve
are at the second last position of output data.

.. GENERATED FROM PYTHON SOURCE LINES 152-158

.. code-block:: default


    # sphinx_gallery_thumbnail_number = 11

    iris3.plotdistribution(-2)
    _ = iris3.plotmerit(-2)




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


    *

      .. image-sg:: /gallery/auto_examples/analysis/images/sphx_glr_plot_iris_011.png
         :alt: plot iris
         :srcset: /gallery/auto_examples/analysis/images/sphx_glr_plot_iris_011.png
         :class: sphx-glr-multi-img

    *

      .. image-sg:: /gallery/auto_examples/analysis/images/sphx_glr_plot_iris_012.png
         :alt: 2D IRIS merit plot, $\lambda$ = 1.00e-03
         :srcset: /gallery/auto_examples/analysis/images/sphx_glr_plot_iris_012.png
         :class: sphx-glr-multi-img





.. GENERATED FROM PYTHON SOURCE LINES 159-161

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

.. GENERATED FROM PYTHON SOURCE LINES 163-165

.. code-block:: default


    # scp.show()








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

   **Total running time of the script:** ( 0 minutes  8.614 seconds)


.. _sphx_glr_download_gallery_auto_examples_analysis_plot_iris.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_iris.py <plot_iris.py>`

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

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


.. only:: html

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

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