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 crop_and_mask(infile, temp_dir, thumb, prev_crop=False, prev_mask=False):
"""initiates the interactive cropping and masking of the video"""
image = Image(thumb, prev_crop=prev_crop)
crop = image.crop()
silent_remove(os.path.join(temp_dir, "crop.tiff"))
ffmpeg = Ffmpeg(infile, os.path.join(temp_dir, "crop.tiff"))
ffmpeg.pix_fmt = "gray8"
ffmpeg.vframes = "1"
ffmpeg.ss = "150"
ffmpeg.filter = "crop=" + crop
ffmpeg.run()
image = Image(os.path.join(temp_dir, "crop.tiff"), prev_mask=prev_mask)
mask = image.mask()
return crop, mask
def get_borders(borders, temp_dir, v):
thumb = 'thumb.tiff'
thumb = os.path.join(temp_dir, thumb)
silent_remove(thumb)
ffmpeg = Ffmpeg(v, os.path.join(thumb))
ffmpeg.pix_fmt = "gray8"
ffmpeg.vframes = "1"
ffmpeg.ss = "150"
ffmpeg.run()
image = Image(thumb, scaling=4)
border = image.set_border()
border = int(np.mean((border[0][1], border[1][1])))
borders.append(border)
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)
def main():
"""main function to track larvae"""
args = get_arguments()
# get all file names and directories ready
infile = os.path.abspath(args.in_path)
video_name = os.path.basename(infile)
video_name_base = os.path.splitext(video_name)[0]
out_dir = os.path.abspath(args.out_path)
prep_outfile(out_dir)
if not out_dir.endswith('/'):
out_dir += '/'
# make directory for temporary results
temp_dirs = []
seg_paths = []
for i in range(args.number):
temp_dirs.append(os.path.join(out_dir, "temp_" + str(i) + "/"))
# segmentation path does not include file extension,
# it will be appended in FIJI macro
seg_paths.append(os.path.join(out_dir, "SEG_" + str(i) + '_' + video_name_base))
cropped_video = "cropped_" + video_name_base + ".avi"
thumb = 'thumb.tiff'
start_frame = None
end_frame = None
for temp_dir in temp_dirs:
if not os.path.exists(temp_dir):
os.makedirs(temp_dir)
crops = []
masks = []
silent_remove(os.path.join(temp_dirs[0], "thumb.tiff"))
ffmpeg = Ffmpeg(infile, os.path.join(temp_dirs[0], thumb))
ffmpeg.pix_fmt = "gray8"
ffmpeg.vframes = "1"
ffmpeg.ss = "150"
ffmpeg.run()
thumb = os.path.join(temp_dirs[0], thumb)
if not args.manual_crop and args.number == 24:
# crop the image into 24 parts
# let the user choose the region in which the wells are.
image = Image(thumb)
crops = image.auto_crop()
prev_mask = False
for i in range(len(crops)):
crop = crops[i]
temp_dir = temp_dirs[i]
silent_remove(os.path.join(temp_dir, "crop.tiff"))
ffmpeg = Ffmpeg(infile, os.path.join(temp_dir, "crop.tiff"))
ffmpeg.pix_fmt = "gray8"
ffmpeg.vframes = "1"
ffmpeg.ss = "150"
ffmpeg.filter = "crop=" + crop
ffmpeg.run()
image = Image(os.path.join(temp_dir, "crop.tiff"), prev_mask=prev_mask)
prev_mask = image.mask()
masks.append(prev_mask)
else:
m = (0, 0)
for i in range(len(temp_dirs)):
# prepare cropping and masking
temp_dir = temp_dirs[i]
if len(crops) == 0:
c, m = crop_and_mask(infile, temp_dir, thumb)
crops.append(c)
masks.append(m)
else:
c, m = crop_and_mask(infile, temp_dir, thumb, crops[-1], m)
crops.append(c)
masks.append(m)
for i in range(len(temp_dirs)):
temp_dir = temp_dirs[i]
crop = crops[i]
prepare_vid(cropped_video, infile, temp_dir, crop)
for i in range(len(temp_dirs)):
# track the segmented video
temp_dir = temp_dirs[i]
mask = masks[i]
vid = Video(temp_dir + cropped_video)
tracks = vid.track()
outer_tracks = []
inner_tracks = []
for track in tracks:
outer_track, inner_track = (split_tracks(mask, track))
outer_tracks += outer_track
inner_tracks += inner_track
analysis = Analysis(outer_tracks, inner_tracks)
analysis.analyze(out_dir + 'stats.txt', i)
if args.save_track_image:
analysis.save_track_image(temp_dirs[i], out_dir, i)
if args.save_track:
# save track points to file
analysis.save_track(out_dir, i)
if not args.keep_temp:
for temp_dir in temp_dirs:
shutil.rmtree(temp_dir)
def main():
"""main function to track larvae"""
start = datetime.now()
parser = argparse.ArgumentParser(
description="Tracks larvae for thigmotaxis experiment")
# add options for argument parser
parser.add_argument("in_path", help="Path to the video.")
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("-t",
"--only_tracking",
action="store_true",
help="Only perform tracking step.")
parser.add_argument("-n",
"--number",
type=int,
default=24,
help="Number of wells to track, default is 24")
parser.add_argument("-i",
"--save_track_image",
action="store_true",
help="Save images of tracked paths.")
parser.add_argument("-m",
"--manual_crop",
action="store_true",
help="Manually select the wells to be tracked.")
parser.add_argument("-s",
"--save_track",
action="store_true",
help="Save track points to file.")
parser.add_argument(
"--median",
action="store_true",
help="Use median intensity projection for segmentation.")
parser.add_argument("-c",
"--cpu",
type=int,
default=1,
help="Set number of threads for multi core machines.")
parser.add_argument(
"--big",
action="store_true",
help=
"Reduces memory usage for very large video files (time intensive, not recommended)."
)
# parse arguments from command line
args = parser.parse_args()
# get all file names and directories ready
infile = os.path.abspath(args.in_path)
video_name = os.path.basename(infile)
video_name_base = os.path.splitext(video_name)[0]
out_dir = os.path.abspath(args.out_path)
with open(os.path.join(out_dir, 'stats.txt'), 'w') as out:
out.write('well\t')
out.write('time in outer region\t')
out.write('distance in outer region\t')
out.write('time in inner region\t')
out.write(' distance in inner region\t')
out.write(' % of time in outer region\t')
out.write(' % of distance in outer region\n')
if not out_dir.endswith('/'):
out_dir += '/'
# make directory for temporary results
temp_dirs = []
seg_paths = []
for i in range(args.number):
temp_dirs.append(os.path.join(out_dir, "temp_" + str(i) + "/"))
# segmentation path does not include file extension,
# it will be appended in FIJI macro
seg_paths.append(
os.path.join(out_dir, "SEG_" + str(i) + '_' + video_name_base))
cropped_video = "cropped_" + video_name_base + ".avi"
thumb = 'thumb.tiff'
mask_paths = []
start_frame = False
end_frame = False
for temp_dir in temp_dirs:
if not os.path.exists(temp_dir):
os.makedirs(temp_dir)
mask_paths.append(os.path.join(temp_dir, "mask.tiff"))
crops = []
if not args.only_tracking:
silent_remove(os.path.join(temp_dirs[0], "thumb.tiff"))
ffmpeg = Ffmpeg(infile, os.path.join(temp_dirs[0], thumb))
ffmpeg.pix_fmt = "gray8"
ffmpeg.vframes = "1"
ffmpeg.ss = "150"
ffmpeg.run()
thumb = os.path.join(temp_dirs[0], thumb)
if not args.manual_crop and args.number == 24:
# crop the image into 24 parts
# let the user choose the region in which the wells are.
image = Image(thumb)
crops = image.auto_crop()
prev_mask = False
for i in range(len(crops)):
crop = crops[i]
temp_dir = temp_dirs[i]
mask_path = mask_paths[i]
silent_remove(os.path.join(temp_dir, "crop.tiff"))
ffmpeg = Ffmpeg(infile, os.path.join(temp_dir, "crop.tiff"))
ffmpeg.pix_fmt = "gray8"
ffmpeg.vframes = "1"
ffmpeg.ss = "150"
ffmpeg.filter = "crop=" + crop
ffmpeg.run()
image = Image(os.path.join(temp_dir, "crop.tiff"),
prev_mask=prev_mask)
prev_mask = image.mask(mask_path)
else:
m = (0, 0)
for i in range(len(temp_dirs)):
# prepare cropping and masking
temp_dir = temp_dirs[i]
mask_path = mask_paths[i]
if len(crops) == 0:
c, m = crop_and_mask(infile, mask_path, temp_dir, thumb)
crops.append(c)
else:
c, m = crop_and_mask(infile, mask_path, temp_dir, thumb,
crops[-1], m)
crops.append(c)
i = 0
while i < len(temp_dirs):
threads = {}
for thread in range(args.cpu):
try:
temp_dir = temp_dirs[i]
crop = crops[i]
# prepare the video for segmentation
threads[thread] = Thread(
target=prepare_vid,
args=[cropped_video, infile, temp_dir, crop])
threads[thread].start()
i += 1
except IndexError:
break
for thread in threads:
threads[thread].join()
while not start_frame:
try:
start_frame = int(input("First frame to keep: "))
except ValueError:
start_frame = False
while not end_frame:
try:
end_frame = int(input("Last frame to keep: ")) + 1
except ValueError:
end_frame = False
for i in range(len(temp_dirs)):
# segment the video
temp_dir = temp_dirs[i]
mask_path = mask_paths[i]
seg_path = seg_paths[i]
# run the segmentation macro
if args.median:
fiji = ImageJMacro("segmentation_median")
else:
fiji = ImageJMacro("segmentation")
fiji.run([
temp_dir + cropped_video,
str(start_frame),
str(end_frame), seg_path, mask_path
])
for i in range(len(seg_paths)):
# track outer region
seg_path = seg_paths[i]
if args.big:
outer = Video(seg_path + "_outer.tiff", big=True)
else:
outer = Video(seg_path + "_outer.tiff")
outer_tracks = outer.track()
del outer
# track inner region
if args.big:
inner = Video(seg_path + "_inner.tiff", big=True)
else:
inner = Video(seg_path + "_inner.tiff")
inner_tracks = inner.track()
del inner
analysis = Analysis(outer_tracks, inner_tracks)
analysis.analyze(out_dir + 'stats.txt', i)
if args.save_track_image:
analysis.save_track_image(temp_dirs[i], out_dir, i)
if args.save_track:
# save track points to file
analysis.save_track(out_dir, i)
if not args.keep_temp:
for temp_dir in temp_dirs:
shutil.rmtree(temp_dir)
for i in range(args.number):
silent_remove(
os.path.join(
out_dir,
"SEG_" + str(i) + '_' + video_name_base + "_outer.tiff"))
silent_remove(
os.path.join(
out_dir,
"SEG_" + str(i) + '_' + video_name_base + "_inner.tiff"))
end = datetime.now()
print("Executed in " + str(end - start))