Version 0.1.5

Fixed numpy.float error: error and solution found by Christopher Tinkey.
Fixed np.int0 usage, found by Maria Kisch.
Fixed argrelextrema_groupby call, might need future improvements.
Fixed spelling mistakes
Updated copyright info

setup.py

@@ -17,10 +17,10 @@
 NAME = 'ysmr'
 DESCRIPTION = 'Bacterial video tracking and analysis.'
 URL = 'https://github.com/schwanbeck/YSMR'
-EMAIL = '[email protected]'
+EMAIL = '[email protected]'
 AUTHOR = 'Julian Schwanbeck'
 REQUIRES_PYTHON = '>=3.6.0'
-VERSION = '0.1.4'
+VERSION = '0.1.5'
 
 # What packages are required for this module to be executed?
 REQUIRED = [

ysmr.py

@@ -2,7 +2,7 @@
 # -*- coding: utf-8 -*-
 
 """
-Copyright 2019 Julian Schwanbeck ([email protected])
+Copyright 2019 Julian Schwanbeck ([email protected])
 https://github.com/schwanbeck/YSMR
 ##Explanation
 This file starts YSMR.

ysmr/__version__.py

@@ -8,6 +8,6 @@
    #     ####   ####       ####  #      ### #    #     #    # ######        #    #  ####   ####  #    # #####
 or YoghurtYetis Software for Motility Recognition
 """
-VERSION = (0, 1, 4)
+VERSION = (0, 1, 5)
 
 __version__ = '.'.join(map(str, VERSION))

ysmr/gsff.py

@@ -2,7 +2,7 @@
 #  -*- coding: utf-8 -*-
 
 """
-Copyright 2019, 2020 Jerôme Dretzke and Julian Schwanbeck ([email protected])
+Copyright 2019, 2020 Jerôme Dretzke and Julian Schwanbeck ([email protected])
 https://github.com/schwanbeck/YSMR
 Original Idea and Equations from Pak, JM: Gaussian Sum FIR Filtering for 2D Target Tracking
 (DOI: 10.1007/s12555-018-0938-4)

ysmr/helper_file.py

@@ -2,7 +2,7 @@
 # -*- coding: utf-8 -*-
 
 """
-Copyright 2019, 2020 Julian Schwanbeck ([email protected])
+Copyright 2019, 2020 Julian Schwanbeck ([email protected])
 https://github.com/schwanbeck/YSMR
 ##Explanation
 This file contains various functions used by YSMR.
@@ -39,7 +39,7 @@
 def argrelextrema_groupby(group, comparator=np.greater_equal, order=10, shift_range=4, fill_value=0):
     """Find local minima/maxima in range of order (depending on comparator).
     When shift is not 0, will only return one result in range of shift.
-    Returns array with non-extrema replaced by fil_value
+    Returns array with non-extrema replaced by fill_value
 
     :param group: array like
     :param comparator: numpy comparator or equivalent
@@ -63,7 +63,8 @@ def argrelextrema_groupby(group, comparator=np.greater_equal, order=10, shift_ra
                 (query == 1),
                 0, result))
     result = np.where(result == 1, group_intermediate, fill_value)
-    result = pd.Series(result, index=group.index)
+    # @todo: check if we can skip the series conversion while using this with df .transform instead of .apply
+    result = pd.Series(result, index=group.index)  # .reindex_like(group)
     return result
 
 
@@ -1200,7 +1201,8 @@ def logging_listener(settings):
             print('Problem:', file=sys.stderr)
             traceback.print_exc(file=sys.stderr)
             try:
-                traceback.print_exc(file=settings['log file path'])
+                with open(file=settings['log file path'], mode='w+') as file:
+                    traceback.print_exc(file=file)
             except (FileNotFoundError, PermissionError):
                 pass
             break

ysmr/main.py

@@ -2,7 +2,7 @@
 # -*- coding: utf-8 -*-
 
 """
-Copyright 2019, 2020 Julian Schwanbeck ([email protected])
+Copyright 2019, 2020 Julian Schwanbeck ([email protected])
 https://github.com/schwanbeck/YSMR
 ##Explanation
 This file starts YSMR.

ysmr/plot_functions.py

@@ -2,7 +2,7 @@
 # -*- coding: utf-8 -*-
 
 """
-Copyright 2019, 2020 Julian Schwanbeck ([email protected])
+Copyright 2019, 2020 Julian Schwanbeck ([email protected])
 https://github.com/schwanbeck/YSMR
 ##Explanation
 This file contains functions which create plots for YSMR.

ysmr/track_eval.py

@@ -2,7 +2,7 @@
 # -*- coding: utf-8 -*-
 
 """
-Copyright 2019, 2020 Julian Schwanbeck ([email protected])
+Copyright 2019, 2020 Julian Schwanbeck ([email protected])
 https://github.com/schwanbeck/YSMR
 ##Explanation
 This file contains the main functions used by YSMR.
@@ -288,7 +288,7 @@ def track_bacteria(video_path, settings=None, result_folder=None):
             # cv2.minAreaRect returns ((x, y), (w, h), degrees)
 
             if settings['include luminosity in tracking calculation']:
-                box = np.int0(cv2.boxPoints(reichtangle))
+                box = np.intp(cv2.boxPoints(reichtangle))
                 # must be generated for each object as cv2.fillpoly() changes it's input
                 mask = np.zeros((frame_height, frame_width), dtype=np.uint8)
                 cv2.fillPoly(mask, [box], 255)
@@ -304,7 +304,7 @@ def track_bacteria(video_path, settings=None, result_folder=None):
                 # reshape_result(tuple_of_tuples) returns ((x, y[, *args]), (w, h, degrees_orientation))
 
             if settings['display video analysis']:  # or settings['save video']:  # Display bounding boxes
-                box = np.int0(cv2.boxPoints(reichtangle))
+                box = np.intp(cv2.boxPoints(reichtangle))
                 # Box: 4 x/y coordinates
                 cv2.drawContours(frame, [box], -1, (255, 0, 0), 0)
 
@@ -973,7 +973,9 @@ def evaluate_tracks(path_to_file, results_directory, df=None, settings=None, fps
     df['y_norm'] = (df['POSITION_Y'].sub(df.groupby('TRACK_ID')['POSITION_Y'].transform('first'))) / px_to_micrometre
 
     # get local maxima
-    df['turn_points'] = df.groupby('TRACK_ID')['turn_points'].apply(argrelextrema_groupby)
+    df['turn_points'] = df.groupby('TRACK_ID')['turn_points'].transform(
+        argrelextrema_groupby
+    )
     # Convert to binary
     df['turn_points'] = np.where(df['turn_points'] == 0, 0, 1).astype(np.int8)
     # start counts as TP so we can later group by TPs
@@ -1198,9 +1200,10 @@ def evaluate_tracks(path_to_file, results_directory, df=None, settings=None, fps
     df_stats_seaborne.dropna(subset=[cut_off_category], inplace=True)
 
     # Exchange int values in 'Categories' for correct labels
-    df_stats_seaborne[cut_off_category].replace(  # name_all_categories is not present and can be skipped
+    df_stats_seaborne[cut_off_category] = df_stats_seaborne[cut_off_category].replace(
+        # name_all_categories is not present and can be skipped
         {value: key for key, value in zip([i for (_, _, i) in cut_off_list[1:]], range(1, len(cut_off_list)))},
-        inplace=True)
+    )
 
     # Put name_all_categories and assigned categories in one df
     df_stats_seaborne = pd.concat([df_stats, df_stats_seaborne], ignore_index=True)

ysmr/tracker.py

@@ -2,7 +2,7 @@
 # -*- coding: utf-8 -*-
 
 """
-Copyright 2019, 2020  Julian Schwanbeck ([email protected])
+Copyright 2019, 2020  Julian Schwanbeck ([email protected])
 Original Idea by Adrian Rosebrock ([email protected])
 https://www.pyimagesearch.com/2018/07/23/simple-object-tracking-with-opencv/
 ##Explanation