import numpy as np import matplotlib.pyplot as plt import image_marker as im import tracking_result as tr import os import glob import argparse from IPython import embed #1. Tankkoordinaten def tankcoordinates(video, dontask=False): redo = True if os.path.exists('tankcoordinates.py'): from tankcoordinates import bottom_left, bottom_right, top_left, top_right print("Found tank coordinates top left: %s, top right: %s" % (top_left, top_right)) if dontask: return bottom_left, top_left, top_right, bottom_right answer = input('Redo markers? y/n') if answer == 'y' or answer == 'Y': redo = True else: redo = False if redo: tank_task = im.MarkerTask("tank limits", ["bottom left corner", "top left corner", "top right corner", "bottom right corner"], "Mark tank corners") image_marker = im.ImageMarker([tank_task]) marker_positions = image_marker.mark_movie(video, 100) bottom_right = marker_positions[0]['bottom right corner'] bottom_left = marker_positions[0]['bottom left corner'] top_right = marker_positions[0]['top right corner'] top_left = marker_positions[0]['top left corner'] with open('tankcoordinates.py', 'w') as f: f.write('bottom_left = %s\n' % str(marker_positions[0]['bottom left corner'])) f.write('top_left = %s\n' % str(marker_positions[0]['top left corner'])) f.write('top_right = %s\n' % str(marker_positions[0]['top right corner'])) f.write('bottom_right = %s\n' % str(marker_positions[0]['bottom right corner'])) return bottom_left, top_left, top_right, bottom_right #2. Feederkoordinaten #3. dark_light Koordinaten def dark_light_coordinates(video, dontask=False): redo = True if os.path.exists('dark_light_coordinates.py'): from dark_light_coordinates import left, right, dark_center print("Found dark_light_coordinates left: %s, right: %s, dark_center: %s" % (left, right, dark_center)) if dontask: return left, right, dark_center answer = input('Redo markers? y/n') if answer == 'y' or answer == 'Y': redo = True else: redo = False if redo: dark_light_task = im.MarkerTask('Dark side', ['left', 'right', 'dark_center'], 'Mark light dark separator line') image_marker = im.ImageMarker([dark_light_task]) marker_positions = image_marker.mark_movie(video, 100) right = tr.coordinate_transformation(marker_positions[0]['right']) left = tr.coordinate_transformation(marker_positions[0]['left']) dark_center = tr.coordinate_transformation(marker_positions[0]['dark_center']) with open('dark_light_coordinates.py', 'w') as f: f.write('left = %s\n' % str(left)) f.write('right = %s\n' % str(right)) f.write('dark_center = %s\n' % str(dark_center)) return left, right, dark_center #4. Laden der Trackingresults def load_tracking_results(dlc_results_file): trs = tr.TrackingResult(dlc_results_file) t, x, y, l, name = trs.position_values(bodypart="snout", framerate=30) return t, x, y, l #5. Wie lange hält sich der Fisch im Hellen/Dunklen auf? # Anzahl Frames in der Fisch in definiertem, dunklen Bereich ist, bzw. in der der Fisch nicht im Hellen ist def aufenthaltsort(left, center, fish_y): top_is_dark=left[1]>=center[1] #bei wie vielen Frames ist der Fisch im Hellen? if top_is_dark: hell_count = len(fish_y[fish_y >= left[1]]) else: hell_count = len(fish_y[fish_y < left[1]]) dark_count=len(fish_y) - hell_count total_count = len(fish_y) return hell_count, dark_count, total_count def analysiere_video(v, dlc, left, center): t, fish_x, fish_y, likelihood = load_tracking_results(dlc) hc, dc, tc = aufenthaltsort(left, center, fish_y) print('Der Fisch hat sich %.2f %% im Dunklen aufgehalten.'%(dc/tc*100)) return (dc/tc*100) def main(): parser = argparse.ArgumentParser(description="") parser.add_argument("day", type=str, help="The day you want to work on") parser.add_argument("-f", "--folder", type=str, default="/data/boldness/labeled_videos", help="The base folder in which the labeled videos are stored. Default is /data/boldness/labeled_videos") parser.add_argument("-a", "--animal", type=str, default="*", help="The animal id, default is * for all animals") parser.add_argument("-e", "--extension", type=str, default=".mp4", help="The video file extension, default is .mp4") parser.add_argument("-na", "--noask", action="store_true", help="do not ask for coordinates") args = parser.parse_args() videos = sorted(glob.glob(os.path.join(args.folder, args.day, '*%s*%s' % (args.animal, args.extension)))) dlc_files = sorted(glob.glob(os.path.join(args.folder, args.day, '*%s*%s' % (args.animal, '.h5')))) results = {} if len(videos) > 0: left, right, center = dark_light_coordinates(videos[0], args.noask) # bl, tl, tr, br = tankcoordinates(v, args.noask) for video, dlc_file in zip(videos, dlc_files): animal = video.split(os.sep)[-1].split('_')[1] p_dark = analysiere_video(video, dlc_file, left, center) results[animal] = p_dark np.save('results_%s.npy' % args.day, results) print(results) if __name__ == '__main__': main()