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

.. only:: html

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

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

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

.. _sphx_glr_auto_examples_howto_quickstart_plot_meshseries.py:


Read mesh from file (vtu or xdmf) into pyvista mesh
=====================================================

.. GENERATED FROM PYTHON SOURCE LINES 8-12

.. code-block:: Python

    import numpy as np

    from ogstools import examples








.. GENERATED FROM PYTHON SOURCE LINES 13-20

To read your own data as a MeshSeries you can do:

..  code-block:: python

  from ogstools.meshlib import MeshSeries
  mesh_series = MeshSeries("filepath/filename_pvd_or_xdmf")


.. GENERATED FROM PYTHON SOURCE LINES 22-25

MeshSeries takes as mandatory argument a str OR pathlib.Path that represents
the location of the pvd or xdmf file. Here, we load example data and print
the meta information:

.. GENERATED FROM PYTHON SOURCE LINES 27-31

.. code-block:: Python

    ms = examples.load_meshseries_HT_2D_XDMF()
    ms






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

 .. code-block:: none


    <ogstools.meshlib.mesh_series.MeshSeries object at 0x780b38d4d000>



.. GENERATED FROM PYTHON SOURCE LINES 32-37

Accessing time values
=====================
Time values (and spatial coordinates) can be unit transformed via
:meth:`~ogstools.meshlib.mesh_series.MeshSeries.scale`. Either pass a tuple
to convert from the first to the second unit or pass a scaling factor.

.. GENERATED FROM PYTHON SOURCE LINES 39-45

.. code-block:: Python

    print(f"First 3 time values are: {ms.timevalues[:3]} s.")
    ms = ms.scale(time=("s", "h"))
    print(f"Last time value is: {ms.timevalues[-1]} h.")
    ms = ms.scale(time=3600.0)
    print(f"Last time value is: {ms.timevalues[-1]} s.")





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

 .. code-block:: none

    First 3 time values are: [   0.  900. 1800.] s.
    Last time value is: 24.0 h.
    Last time value is: 86400.0 s.




.. GENERATED FROM PYTHON SOURCE LINES 46-53

Accessing meshes
================
To get a single mesh at a specified timestep you can use the mesh() method of
a MeshSeries object (in this example: ms). Another way to to do so is by
indexing the MeshSeries object with brackets (ms[timestep]).
Besides custom ogstools functions you can use all available pyvista
functions. Here we use pyvista's plot function.

.. GENERATED FROM PYTHON SOURCE LINES 55-58

.. code-block:: Python

    mesh_ts10 = ms.mesh(10)  # or ms[10]
    mesh_ts10.plot(show_edges=True)








.. tab-set::



   .. tab-item:: Static Scene



            
     .. image-sg:: /auto_examples/howto_quickstart/images/sphx_glr_plot_meshseries_001.png
        :alt: plot meshseries
        :srcset: /auto_examples/howto_quickstart/images/sphx_glr_plot_meshseries_001.png
        :class: sphx-glr-single-img
     


   .. tab-item:: Interactive Scene



       .. offlineviewer:: /builds/ogs/tools/ogstools/docs/auto_examples/howto_quickstart/images/sphx_glr_plot_meshseries_001.vtksz






.. GENERATED FROM PYTHON SOURCE LINES 59-74

Indexing
========
`MeshSeries.values("<variable_name>")`` returns a
`numpy ndarray <https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html>`_.
It allows `multidimensional indexing on ndarrays
<https://numpy.org/doc/stable/user/basics.indexing.html>`_.

Typically, the first dimension is the time step, second dimension is the
number of points/cells, and the last dimension is the number of components of
the variable.

By default, ``values`` would read the entire dataset. If only a subset of the
MeshSeries should be read you can select the relevant timesteps by indexing /
slicing the MeshSeries directly. This selection will also be adhered to if you
read individual meshes.

.. GENERATED FROM PYTHON SOURCE LINES 76-84

.. code-block:: Python

    ms = examples.load_meshseries_HT_2D_XDMF()
    # Temperature is a scalar, Darcy velocity is a vector with 2 components.
    # Both are defined at points.

    print("Entire dataset:", np.shape(ms.values("temperature")))
    print("Every second timestep:", np.shape(ms[::2].values("temperature")))
    print("Last two steps:", np.shape(ms[-2:].values("darcy_velocity")))





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

 .. code-block:: none

    Entire dataset: (97, 190)
    Every second timestep: (49, 190)
    Last two steps: (2, 190, 2)




.. GENERATED FROM PYTHON SOURCE LINES 85-87

To select points or cells you can use the ``extract`` method to specify the
corresponding ids.

.. GENERATED FROM PYTHON SOURCE LINES 89-93

.. code-block:: Python

    temp_at_points = ms.extract([2, 3, 4]).values("temperature")
    print("Data on extracted points:", np.shape(temp_at_points))
    print("Temperatures at last timestep:", temp_at_points[-1])





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

 .. code-block:: none

    Data on extracted points: (97, 3)
    Temperatures at last timestep: [352.9994477  303.         353.00000001]




.. GENERATED FROM PYTHON SOURCE LINES 94-96

You can also use pyvista dataset filters to ``transform`` the domain for the
entire MeshSeries.

.. GENERATED FROM PYTHON SOURCE LINES 98-104

.. code-block:: Python

    ms_right_half = ms.transform(
        lambda mesh: mesh.clip("x", mesh.center, crinkle=True)
    )
    temp_right_half = ms_right_half.values("temperature")
    print("Data on clipped domain:", np.shape(temp_right_half))





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

 .. code-block:: none

    Data on clipped domain: (97, 114)




.. GENERATED FROM PYTHON SOURCE LINES 105-106

Let's plot the last timestep of the transformed MeshSeries.

.. GENERATED FROM PYTHON SOURCE LINES 108-109

.. code-block:: Python

    fig = ms_right_half[-1].plot_contourf("temperature")



.. image-sg:: /auto_examples/howto_quickstart/images/sphx_glr_plot_meshseries_002.png
   :alt: plot meshseries
   :srcset: /auto_examples/howto_quickstart/images/sphx_glr_plot_meshseries_002.png
   :class: sphx-glr-single-img






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

   **Total running time of the script:** (0 minutes 1.633 seconds)


.. _sphx_glr_download_auto_examples_howto_quickstart_plot_meshseries.py:

.. only:: html

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

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

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

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

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

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

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