added trackmate ready option

setup.py

@@ -59,6 +59,7 @@ setup(name='track_analyzer',
           'console_scripts': [
               'traj_analysis=track_analyzer.scripts.analyze_tracks:main',
               'map_analysis=track_analyzer.scripts.analyze_maps:main',
+              'TA_config=track_analyzer.scripts.make_default_config:main',
           ]
       }
       )

track_analyzer/prepare.py

@@ -652,7 +652,7 @@ def get_info(data_dir):
 
 
 def get_data(data_dir, df=None, refresh=False, split_traj=False, set_origin_=False, image=None, reset_dim=['x', 'y'],
-             invert_axes=[], custom_var={}):
+             invert_axes=[], custom_var={}, trackmate_input=False):
     """
     Main function to import data and perform the initial processing (scaling and computing of time derivatives).
     It saves the database as a pickle object.
@@ -678,6 +678,8 @@ def get_data(data_dir, df=None, refresh=False, split_traj=False, set_origin_=Fal
     :type invert_axes: list
     :param custom_var: dict of custom variables: {'var_i':{'name':'var_name','unit':'var_unit'}}
     :type custom_var: dict
+    :param trackmate_input: True if input file is a trackmate (v7) csv file
+    :type trackmate_input: bool
     :return: dict with dataframe and key info
     :rtype: dict
     """
@@ -700,7 +702,16 @@ def get_data(data_dir, df=None, refresh=False, split_traj=False, set_origin_=Fal
             data_file = osp.join(data_dir, 'positions.csv')
             sep = info["separator"] if "separator" in info.keys() else ','  # by default comma separated
             sep = '\t' if sep == 'tab' else sep
-            df = pd.read_csv(data_file, sep=sep)  # columns must be ['x','y','z','frame','track']
+            if osp.exists(data_file):
+                df = pd.read_csv(data_file, sep=sep)  # columns must be ['x','y','z','frame','track']
+            else: 
+                raise Exception("""data file does not exist, it must be named 'positions.csv' or 'positions.txt'""")
+
+        # trackmate specific case
+        if trackmate_input: 
+            df = df[['POSITION_X','POSITION_Y','POSITION_Z','FRAME','TRACK_ID']]
+            df.columns = ['x', 'y', 'z', 'frame', 'track']
+            df = df.loc[3:]
 
         # check data type
         df = df.apply(pd.to_numeric, errors='ignore')
@@ -1495,6 +1506,7 @@ def make_data_config(data_dir=None, export_config=True):
               'set_origin_': False,  # to reset origin of coordinates with dict with dimensions as key and coordinates as values
               'reset_dim': ['x', 'y'],  # list of dimensions to reset, as set_origin_ contains coordinates along all dimensions
               'invert_axes': [],  # list of dimensions to invert (change sign)
+              'trackmate_input': False,  # if the input file is a trackmate (v7) csv file
              }
 
     if export_config: 

track_analyzer/scripts/analyze_maps.py

@@ -53,7 +53,8 @@ def map_analysis(data_dir, data=None, image=None, refresh=False, parallelize=Fal
             data_config[k] = data_config_default[k]
     if data is None: 
         data = tpr.get_data(data_dir, refresh=refresh, split_traj=data_config["split_traj"], set_origin_=data_config["set_origin_"], 
-                            image=image, reset_dim=data_config["reset_dim"], invert_axes=data_config["invert_axes"])
+                            image=image, reset_dim=data_config["reset_dim"], invert_axes=data_config["invert_axes"], 
+                            trackmate_input=data_config["trackmate_input"])
 
     df = data['df']
     dimensions = data['dimensions']
@@ -242,13 +243,9 @@ def parse_args(args=None):
     parse arguments for main()
     """
 
-    #    description = """Analyze trajectories
-    #                Argument :
-    #                -
-    #                """
-
-    #    parser = argparse.ArgumentParser(formatter_class=argparse.RawDescriptionHelpFormatter, description=description)
-    parser = argparse.ArgumentParser()
+    parser = argparse.ArgumentParser(description="""
+        Run the map analysis module in the data_dir directory
+        """)
 
     parser.add_argument('data_dir',
                         help='path of the data directory')

track_analyzer/scripts/analyze_tracks.py

@@ -53,7 +53,8 @@ def traj_analysis(data_dir, data=None, image=None, refresh=False, parallelize=Fa
             data_config[k] = data_config_default[k]
     if data is None: 
         data = tpr.get_data(data_dir, refresh=refresh, split_traj=data_config["split_traj"], set_origin_=data_config["set_origin_"], 
-                            image=image, reset_dim=data_config["reset_dim"], invert_axes=data_config["invert_axes"])
+                            image=image, reset_dim=data_config["reset_dim"], invert_axes=data_config["invert_axes"], 
+                            trackmate_input=data_config["trackmate_input"])
 
     df = data['df']
     dim = data['dim']
@@ -290,13 +291,9 @@ def parse_args(args=None):
     parse arguments for main()
     """
 
-    #    description = """Analyze trajectories
-    #                Argument :
-    #                -
-    #                """
-
-    #    parser = argparse.ArgumentParser(formatter_class=argparse.RawDescriptionHelpFormatter, description=description)
-    parser = argparse.ArgumentParser()
+    parser = argparse.ArgumentParser(description="""
+        Run the trajectory analysis module in the data_dir directory
+        """)
 
     parser.add_argument('data_dir',
                         help='path of the data directory')

track_analyzer/scripts/make_default_config.py

+##########################################################################
+# Track Analyzer - Quantification and visualization of tracking data     #
+# Authors: Arthur Michaut                                                #
+# Copyright 2016-2019 Harvard Medical School and Brigham and             #
+#                          Women's Hospital                              #
+# Copyright 2019-2022 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/>.                           #
+##########################################################################
+
+import os.path as osp
+import sys
+import argparse
+
+from track_analyzer import prepare as tpr
+from track_analyzer import plotting as tpl
+from track_analyzer import calculate as tca
+
+
+def make_default_config(data_dir):
+    """Make default config and export it to data_dir"""
+
+    config_dir = osp.join(data_dir, 'config')
+    tpr.safe_mkdir(config_dir)
+
+   
+    data_config = tpr.make_data_config(data_dir=data_dir, export_config=True)
+    plot_config = tpl.make_plot_config(data_dir=data_dir, export_config=True)
+    traj_config = tpr.make_traj_config(data_dir=data_dir, export_config=True)
+    map_config = tpr.make_map_config(data_dir=data_dir, export_config=True)
+
+    config = {'data_config':data_config, 
+            'plot_config':plot_config, 
+            'traj_config':traj_config, 
+            'map_config':map_config, 
+            }
+
+    return config
+
+
+def parse_args(args=None):
+    """
+    parse arguments for main()
+    """
+
+    parser = argparse.ArgumentParser(description="""
+        Make a default set of config files and save it to data_dir
+        """)
+
+    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 run traj_analysis from command line"""
+
+    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...")
+
+    # make config
+    make_default_config(data_dir)
+
+
+if __name__ == '__main__':
+    main()