:py:mod:`brain_locations_visualizer.plotting_functions`
=======================================================

.. py:module:: brain_locations_visualizer.plotting_functions

.. autoapi-nested-parse::

   This module contains functions for generating the main figures



Module Contents
---------------


Functions
~~~~~~~~~

.. autoapisummary::

   brain_locations_visualizer.plotting_functions.generate_side_figure
   brain_locations_visualizer.plotting_functions.generate_coronal_figure



.. py:function:: generate_side_figure(config_parser, sl_list, str_im, X, Y, mask_1, mask_2, mask_other, ff_mask, tf_mask, ff_marker, tf_marker, parent)

   Plots the location of the fibers in the striatum from the side

   :param config_parser: module from config_parser.py
   :type config_parser: module with global variables
   :param sl_list: location of the slices to show as dotted lines
   :type sl_list: list
   :param str_im: image to use
   :type str_im: Image
   :param X: array with x coordinates of the fibers
   :type X: array
   :param Y: array with y coordinates of the fibers
   :type Y: array
   :param mask_1: mask for locations of fibers from the first group
   :type mask_1: logical array
   :param mask_2: mask for locations of fibers from the second group
   :type mask_2: logical array
   :param mask_other: mask for locations of fibers from other groups
   :type mask_other: logical array
   :param ff_mask: mask for locations of fibers from flat fibers
   :type ff_mask: logical array
   :param tf_mask: mask for locations of fibers from tapered fibers
   :type tf_mask: logical array
   :param ff_marker: type of marker for flat fibers
   :type ff_marker: str
   :param tf_marker: type of marker for tapered fibers
   :type tf_marker: str
   :param parent: path to the parent directory
   :type parent: str or Path


.. py:function:: generate_coronal_figure(config_parser, sl_list, w, h, atlas, X, Y, Z, mask_1, mask_2, mask_other, ff_mask, tf_mask, ff_marker, tf_marker, parent)

   plots the location of the fibers in the striatum from the coronal view

   :param config_parser: module from config_parser.py
   :type config_parser: module with global variables
   :param sl_list: location of the slices to show as dotted lines
   :type sl_list: list
   :param w: width of the individual slices
   :type w: int
   :param h: height of the individual slices
   :type h: int
   :param atlas: atlas to use
   :type atlas: Image
   :param X: array with x coordinates of the fibers
   :type X: array
   :param Y: array with y coordinates of the fibers
   :type Y: array
   :param Z: array with z coordinates of the fibers
   :type Z: array
   :param mask_1: mask for locations of fibers from the first group
   :type mask_1: logical array
   :param mask_2: mask for locations of fibers from the second group
   :type mask_2: logical array
   :param mask_other: mask for locations of fibers from other groups
   :type mask_other: logical array
   :param ff_mask: mask for locations of fibers from flat fibers
   :type ff_mask: logical array
   :param tf_mask: mask for locations of fibers from tapered fibers
   :type tf_mask: logical array
   :param ff_marker: type of marker for flat fibers
   :type ff_marker: str
   :param tf_marker: type of marker for tapered fibers
   :type tf_marker: str
   :param parent: path to the parent directory
   :type parent: str or Path