brain_locations_visualizer.plotting_functions

This module contains functions for generating the main figures

Module Contents

Functions

generate_side_figure(config_parser, sl_list, str_im, ...)

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

generate_coronal_figure(config_parser, sl_list, w, h, ...)

plots the location of the fibers in the striatum from the coronal view
brain_locations_visualizer.plotting_functions.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

Parameters:

  • config_parser (module with global variables) – module from config_parser.py

  • sl_list (list) – location of the slices to show as dotted lines

  • str_im (Image) – image to use

  • X (array) – array with x coordinates of the fibers

  • Y (array) – array with y coordinates of the fibers

  • mask_1 (logical array) – mask for locations of fibers from the first group

  • mask_2 (logical array) – mask for locations of fibers from the second group

  • mask_other (logical array) – mask for locations of fibers from other groups

  • ff_mask (logical array) – mask for locations of fibers from flat fibers

  • tf_mask (logical array) – mask for locations of fibers from tapered fibers

  • ff_marker (str) – type of marker for flat fibers

  • tf_marker (str) – type of marker for tapered fibers

  • parent (str or Path) – path to the parent directory

brain_locations_visualizer.plotting_functions.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

Parameters:

  • config_parser (module with global variables) – module from config_parser.py

  • sl_list (list) – location of the slices to show as dotted lines

  • w (int) – width of the individual slices

  • h (int) – height of the individual slices

  • atlas (Image) – atlas to use

  • X (array) – array with x coordinates of the fibers

  • Y (array) – array with y coordinates of the fibers

  • Z (array) – array with z coordinates of the fibers

  • mask_1 (logical array) – mask for locations of fibers from the first group

  • mask_2 (logical array) – mask for locations of fibers from the second group

  • mask_other (logical array) – mask for locations of fibers from other groups

  • ff_mask (logical array) – mask for locations of fibers from flat fibers

  • tf_mask (logical array) – mask for locations of fibers from tapered fibers

  • ff_marker (str) – type of marker for flat fibers

  • tf_marker (str) – type of marker for tapered fibers

  • parent (str or Path) – path to the parent directory