def prepare_vid(cropped_video, infile, temp_dir, crop):
"""get FIJI compatible avi from video"""
ffmpeg = Ffmpeg(infile, temp_dir + cropped_video)
ffmpeg.pix_fmt = "nv12"
ffmpeg.f = "avi"
ffmpeg.vcodec = "rawvideo"
ffmpeg.filter = "crop=" + crop
ffmpeg.run()
def main():
"""main function to track fish"""
parser = argparse.ArgumentParser(description="Tracks adult fish")
# add options for argument parser
parser.add_argument("in_path",
help="Path to the video directory.")
parser.add_argument("out_path",
help="Directory for results. Should be empty.")
parser.add_argument("-x", "--keep_temp", action="store_true",
help="Keep temporary folder after execution.")
parser.add_argument("--visual", action="store_true",
help="shows a visual representation of the tracking progress.")
# parse arguments from command line
args = parser.parse_args()
# get all file names and directories ready
out_dir, temp_dir, video_bases, videos = housekeeping(args)
borders = []
for i in range(len(videos)):
v = videos[i]
get_borders(borders, temp_dir, v)
for i in range(len(videos)):
vbn = video_bases[i]
v = videos[i]
scaled_video = "scaled_" + vbn + ".avi"
ffmpeg = Ffmpeg(v, os.path.join(temp_dir, scaled_video))
ffmpeg.f = "avi"
ffmpeg.vcodec = "libx264rgb"
ffmpeg.width = 480
ffmpeg.run()
for i in range(len(videos)):
vbn = video_bases[i]
pts = tracker(args, temp_dir, vbn)
border = borders[i]
tracks_lower, tracks_upper = split_tracks(border, pts)
analysis = Analysis(tracks_lower, tracks_upper, px_size=0.06)
analysis.analyze(os.path.join(out_dir, 'stats.txt'), vbn, vel=True)
if not args.keep_temp:
shutil.rmtree(temp_dir)