added static files

doc/source/_static/example/load_tracking.py

+import os.path as osp
+import sys
+import argparse
+
+import numpy as np
+from skimage.io import imread
+import tifffile as tifff
+
+
+def parse_args(args=None):
+    """
+    Parse arguments for main()
+    """
+
+    parser = argparse.ArgumentParser()
+
+    parser.add_argument('data_dir',
+                        help='path of the data directory')
+
+    parsed_args = parser.parse_args(args)
+
+    return parsed_args
+
+
+def main(args=None):
+    """ 
+    Main function to extract images from dataset and save it as a tiff stack
+    Freely inspired from napari tutorial: https://napari.org/tutorials/applications/cell_tracking.html
+    """
+
+    # number of images
+    NUM_IMAGES = 195
+
+    # load and check argument
+    args = sys.argv[1:] if args is None else args
+    parsed_args = parse_args(args)
+
+    data_dir = osp.realpath(parsed_args.data_dir)
+
+    if not osp.exists(data_dir):
+        raise Exception("ERROR: the passed data directory does not exist. Aborting...")
+
+    if not osp.isdir(data_dir):
+        raise Exception("ERROR: the passed data directory is not a directory. Aborting...")
+
+    # extract images
+    stack = np.asarray([imread(osp.join(data_dir, '01', f't{i:0>3}.tif')) for i in range(NUM_IMAGES)])
+
+    #save_image
+    tifff.imsave(osp.join(data_dir,'stack.tif'), stack)
+
+
+if __name__ == '__main__':
+    main()
+
+

doc/source/developer_guide/index.rst

+.. Track Analyzer - Quantification and visualization of tracking data
+    Authors: Arthur Michaut                                                
+    Copyright 2016-2019 Harvard Medical School and Brigham and             
+                             Women's Hospital                              
+    Copyright 2019-2021 Institut Pasteur and CNRS–UMR3738                  
+    See the COPYRIGHT file for details                                     
+                                                                           
+    This file is part of Track Analyzer package.                           
+                                                                           
+    Track Analyzer is free software: you can redistribute it and/or modify 
+    it under the terms of the GNU General Public License as published by   
+    the Free Software Foundation, either version 3 of the License, or      
+    (at your option) any later version.                                    
+                                                                           
+    Track Analyzer is distributed in the hope that it will be useful,      
+    but WITHOUT ANY WARRANTY; without even the implied warranty of         
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the           
+    GNU General Public License for more details .                          
+                                                                           
+    You should have received a copy of the GNU General Public License      
+    along with Track Analyzer (COPYING).                                   
+    If not, see <https://www.gnu.org/licenses/>.     
+
+===============
+Developer Guide
+===============
+
+Under construction
\ No newline at end of file