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

.. only:: html

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

        Click :ref:`here <sphx_glr_download_auto_examples_plot_fibers_in_striatum_side_view.py>`
        to download the full example code

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

.. _sphx_glr_auto_examples_plot_fibers_in_striatum_side_view.py:


plot_fibers_in_striatum_side_view.py
====================================
generates a side view of the striatum with the fiber tips

1. Import required packages
~~~~~~~~~~~~~~~~~~~~~~~~~~~

.. GENERATED FROM PYTHON SOURCE LINES 9-16

.. code-block:: default


    import pandas as pd
    import numpy as np
    from pathlib import Path
    from brain_locations_visualizer import config_parser
    from brain_locations_visualizer.plotting_functions import generate_side_figure








.. GENERATED FROM PYTHON SOURCE LINES 17-19

2. Get the configuration file and define variables
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

.. GENERATED FROM PYTHON SOURCE LINES 19-26

.. code-block:: default


    # use the default config file for the documentation
    config_file = Path("config_for_documentation.json")

    # variables are assigned in the config_parser function
    config_parser.config_parser(config_file)








.. GENERATED FROM PYTHON SOURCE LINES 27-29

plot with a different marker the flat fibers and the tapered fibers
(this is specified in the mouse name)

.. GENERATED FROM PYTHON SOURCE LINES 29-32

.. code-block:: default

    ff_marker = "_"
    tf_marker = "|"








.. GENERATED FROM PYTHON SOURCE LINES 33-34

define the output directory as the parent of the config file

.. GENERATED FROM PYTHON SOURCE LINES 34-36

.. code-block:: default

    parent = Path(config_file).parent








.. GENERATED FROM PYTHON SOURCE LINES 37-38

read the file of points

.. GENERATED FROM PYTHON SOURCE LINES 38-43

.. code-block:: default

    coords = pd.read_csv(config_parser.file_path, header=0)
    X = coords.x
    Y = coords.y
    Animal_Name = coords.Mouse_name








.. GENERATED FROM PYTHON SOURCE LINES 44-46

select only the fibers used in the analysis
animals that are not included have a # in front of their name

.. GENERATED FROM PYTHON SOURCE LINES 46-51

.. code-block:: default

    animal_mask = [not an.startswith("#") for an in Animal_Name]
    X = np.array(list(X[animal_mask])).astype(float)
    Y = np.array(list(Y[animal_mask])).astype(float)
    Animal_Name = np.array(list(Animal_Name[animal_mask]))








.. GENERATED FROM PYTHON SOURCE LINES 52-54

plot slices location evenly if the precise slices are not specified
in the config file

.. GENERATED FROM PYTHON SOURCE LINES 54-69

.. code-block:: default

    if config_parser.sl_list == []:
        step = int(
            np.floor(
                (config_parser.z_limits[1] - config_parser.z_limits[0])
                / config_parser.n_images
            )
        )
        sl_list = list(
            range(config_parser.z_limits[0], config_parser.z_limits[1], step)
        )
        sl_list = sl_list[-config_parser.n_images :]

    else:
        sl_list = config_parser.sl_list








.. GENERATED FROM PYTHON SOURCE LINES 70-71

separate animals

.. GENERATED FROM PYTHON SOURCE LINES 71-80

.. code-block:: default

    mask_1 = [x.startswith(config_parser.id_1) for x in Animal_Name]
    mask_2 = [x.startswith(config_parser.id_2) for x in Animal_Name]
    mask_other = np.logical_and(
        [not e for e in mask_1], [not e for e in mask_2]
    )

    ff_mask = [x.endswith("_flat") for x in Animal_Name]
    tf_mask = [not x for x in ff_mask]








.. GENERATED FROM PYTHON SOURCE LINES 81-83

2. Generate the figure
~~~~~~~~~~~~~~~~~~~~~~

.. GENERATED FROM PYTHON SOURCE LINES 83-98

.. code-block:: default

    generate_side_figure(
        config_parser,
        sl_list,
        X,
        Y,
        mask_1,
        mask_2,
        mask_other,
        ff_mask,
        tf_mask,
        ff_marker,
        tf_marker,
        parent,
    )




.. image-sg:: /auto_examples/images/sphx_glr_plot_fibers_in_striatum_side_view_001.png
   :alt: plot fibers in striatum side view
   :srcset: /auto_examples/images/sphx_glr_plot_fibers_in_striatum_side_view_001.png
   :class: sphx-glr-single-img


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

 .. code-block:: none

    /mnt/c/Users/herny/Documents/GitHub/brain-locations-visualizer/brain_locations_visualizer/plotting_functions.py:103: UserWarning: FixedFormatter should only be used together with FixedLocator
      ax.set_xticklabels(a, fontsize=18)
    /mnt/c/Users/herny/Documents/GitHub/brain-locations-visualizer/brain_locations_visualizer/plotting_functions.py:106: UserWarning: FixedFormatter should only be used together with FixedLocator
      ax.set_yticklabels(a, fontsize=18)





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

   **Total running time of the script:** ( 0 minutes  2.160 seconds)


.. _sphx_glr_download_auto_examples_plot_fibers_in_striatum_side_view.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_fibers_in_striatum_side_view.py <plot_fibers_in_striatum_side_view.py>`

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

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


.. only:: html

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

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