def track_tails(self, make_video=False):
""" processes the video and locates the tails """
# initialize the video
self.load_video(make_video)
# process first _frame to find objects
tails = self.process_first_frame()
# initialize the result structure
tail_trajectories = collections.defaultdict(dict)
# iterate through all frames
iterator = display_progress(self.video)
for self.frame_id, self._frame in enumerate(iterator, self.frame_start):
self._frame_cache = {} #< delete cache per _frame
if make_video:
self.set_video_background(tails)
# adapt the object outlines
tails = self.adapt_tail_contours(tails)
# store tail data in the result
for tail_id, tail in enumerate(tails):
tail_trajectories[tail_id][self.frame_id] = tail
# update the debug output
if make_video:
self.update_video_output(tails, show_measurement_line=False)
# save the data and close the videos
self.result['tail_trajectories'] = tail_trajectories
self.save_result()
self.close()
def reduce_video(video, function, initial_value=None):
""" applies function to consecutive frames """
result = initial_value
for frame in display_progress(video):
if result is None:
result = frame
else:
result = function(frame, result)
return result
def measure_mean(video):
"""
measures the mean of each movie pixel over time
"""
mean = np.zeros(video.shape[1:])
for n, frame in enumerate(display_progress(video)):
mean = mean*n/(n + 1) + frame/(n + 1)
return mean
def _iterate_over_video(self, video):
""" internal function doing the heavy lifting by iterating over the video """
# load data from previous passes
ground_profile = self.data['pass2/ground_profile']
background_frame_offset = self.data['pass1/video/background_frame_offset']
# create the video iterator with preprocessing that will be done in a
# separate thread to speed up computations
video_iter = VideoPreprocessor(
video, functions={'gradient_strength': self.get_gradient_strenght},
use_threads=self.params['use_threads']
)
video_iter = display_progress(video_iter)
# iterate over the video and analyze it
for background_id, data in enumerate(video_iter):
# extract the images from the preprocessed data
frame = data['raw']
gradient_strength = data['gradient_strength']
# calculate _frame id in the original video
self.frame_id = (background_frame_offset
+ background_id * self.params['output/video/period'])
# copy _frame to debug video
if 'video' in self.debug:
self.debug['video'].set_frame(frame, copy=False)
# retrieve data for current _frame
self.ground = ground_profile.get_ground_profile(self.frame_id)
# write the mouse trail to the mouse mask
self.update_mouse_mask()
# find the changes in the background
if self.params['burrows/enabled_pass4']:
self.find_burrows_using_active_contour(frame, gradient_strength)
# store some debug information
self.debug_process_frame(frame)
if background_id % 1000 == 0:
self.logger.debug('Analyzed _frame %d', self.frame_id)
def measure_mean_std(video):
"""
measures the mean and the standard deviation of each movie pixel over time
Uses https://en.wikipedia.org/wiki/Algorithms_for_calculating_variance#Incremental_algorithm
"""
mean = np.zeros(video.shape[1:])
M2 = np.zeros(video.shape[1:])
for n, frame in enumerate(display_progress(video)):
delta = frame - mean
mean = mean + delta/(n + 1)
M2 = M2 + delta*(frame - mean)
if (n < 2):
return frame, 0
return mean, np.sqrt(M2/n)
def determine_average_frame_brightness(video_file_or_pattern,
output_hdf5_file=None):
""" iterates a video and determines its intensity, which will be stored
in a hdf5 file, if the respective file name is given"""
# read video data
with closing(load_any_video(video_file_or_pattern)) as video:
brightness = np.empty(video.frame_count, np.double)
for k, frame in enumerate(display_progress(video)):
brightness[k] = frame.mean()
# restrict the result to the number of actual frames read
if k < video.frame_count:
brightness = brightness[:k + 1]
# write brightness data
if output_hdf5_file:
with h5py.File(output_hdf5_file, "w") as fd:
fd.create_dataset("brightness", data=brightness)
return brightness
def determine_average_frame_brightness(video_file_or_pattern,
output_hdf5_file=None):
""" iterates a video and determines its intensity, which will be stored
in a hdf5 file, if the respective file name is given"""
# read video data
with closing(load_any_video(video_file_or_pattern)) as video:
brightness = np.empty(video.frame_count, np.double)
for k, frame in enumerate(display_progress(video)):
brightness[k] = frame.mean()
# restrict the result to the number of actual frames read
if k < video.frame_count:
brightness = brightness[:k + 1]
# write brightness data
if output_hdf5_file:
with h5py.File(output_hdf5_file, "w") as fd:
fd.create_dataset("brightness", data=brightness)
return brightness
def _iterate_over_video(self, video):
""" internal function doing the heavy lifting by iterating over the video """
# load data from previous passes
mouse_track = self.data['pass2/mouse_trajectory']
ground_profile = self.data['pass2/ground_profile']
frame_offset = self.result['video/frames'][0]
if frame_offset is None:
frame_offset = 0
# iterate over the video and analyze it
for self.frame_id, frame in enumerate(display_progress(video),
frame_offset):
# adapt the background to current _frame
adaptation_rate = self.params['background/adaptation_rate']
self.background += adaptation_rate * (frame - self.background)
# copy _frame to debug video
if 'video' in self.debug:
self.debug['video'].set_frame(frame, copy=False)
# retrieve data for current _frame
try:
self.mouse_pos = mouse_track.pos[self.frame_id, :]
except IndexError:
# Sometimes the mouse trail has not been calculated till the end
self.mouse_pos = (np.nan, np.nan)
self.ground = ground_profile.get_ground_profile(self.frame_id)
if self.params['burrows/enabled_pass3']:
# find the burrow from the mouse trail
self.find_burrows()
# find out where the mouse currently is
self.classify_mouse_state(mouse_track)
# store some information in the debug dictionary
self.debug_process_frame(frame, mouse_track)
if self.frame_id % 1000 == 0:
self.logger.debug('Analyzed _frame %d', self.frame_id)
def _iterate_over_video(self, video):
""" internal function doing the heavy lifting by iterating over the video """
# load data from previous passes
mouse_track = self.data['pass2/mouse_trajectory']
ground_profile = self.data['pass2/ground_profile']
frame_offset = self.result['video/frames'][0]
if frame_offset is None:
frame_offset = 0
# iterate over the video and analyze it
for self.frame_id, frame in enumerate(display_progress(video), frame_offset):
# adapt the background to current _frame
adaptation_rate = self.params['background/adaptation_rate']
self.background += adaptation_rate*(frame - self.background)
# copy _frame to debug video
if 'video' in self.debug:
self.debug['video'].set_frame(frame, copy=False)
# retrieve data for current _frame
try:
self.mouse_pos = mouse_track.pos[self.frame_id, :]
except IndexError:
# Sometimes the mouse trail has not been calculated till the end
self.mouse_pos = (np.nan, np.nan)
self.ground = ground_profile.get_ground_profile(self.frame_id)
if self.params['burrows/enabled_pass3']:
# find the burrow from the mouse trail
self.find_burrows()
# find out where the mouse currently is
self.classify_mouse_state(mouse_track)
# store some information in the debug dictionary
self.debug_process_frame(frame, mouse_track)
if self.frame_id % 1000 == 0:
self.logger.debug('Analyzed _frame %d', self.frame_id)
def copy(self, dtype=np.uint8, disp=True):
"""
Creates a copy of the current video and returns a VideoMemory instance.
"""
# prevent circular import by lazy importing
from .memory import VideoMemory
logger.debug('Copy a video stream and store it in memory')
# copy the data into a numpy array
data = np.empty(self.shape, dtype)
if disp:
iterator = display_progress(self)
else:
iterator = self
for k, val in enumerate(iterator):
data[k, ...] = val
# construct the memory object without copying the data
return VideoMemory(data, fps=self.fps, copy_data=False)
def copy(self, dtype=np.uint8, disp=True):
"""
Creates a copy of the current video and returns a VideoMemory instance.
"""
# prevent circular import by lazy importing
from .memory import VideoMemory
logger.debug('Copy a video stream and store it in memory')
# copy the data into a numpy array
data = np.empty(self.shape, dtype)
if disp:
iterator = display_progress(self)
else:
iterator = self
for k, val in enumerate(iterator):
data[k, ...] = val
# construct the memory object without copying the data
return VideoMemory(data, fps=self.fps, copy_data=False)
def do_linescans(self, make_video=True):
""" do the line scans for all current_tails """
# initialize the video
self.load_video(make_video)
self.load_result()
# load the previously track tail data
try:
tail_trajectories = self.result['tail_trajectories']
except KeyError:
raise ValueError('Tails have to be tracked before line scans can '
'be done.')
current_tails = None
# collect all line scans in a structure
linescans = collections.defaultdict(list)
# iterate through all frames and collect the line scans
iterator = display_progress(self.video)
for self.frame_id, self._frame in enumerate(iterator, self.frame_start):
self._frame_cache = {} #< delete cache per _frame
if make_video:
self.set_video_background(current_tails)
# do the line scans in each object
current_tails = []
for tail_id, tail_trajectory in tail_trajectories.iteritems():
try:
tail = tail_trajectory[self.frame_id]
except KeyError:
logging.debug('Could not find any information on tails '
'for _frame %d', self.frame_id)
break
# get the line scan left and right of the centerline
linescan_data= self.measure_single_tail(self._frame, tail)
# append it to the temporary structure
linescans[tail_id].append(linescan_data)
current_tails.append(tail) #< safe for video output
# update the debug output
if make_video:
self.update_video_output(current_tails,
show_measurement_line=True)
# create the kymographs from the line scans
kymographs = collections.defaultdict(dict)
# iterate over all tails found in the movie
for tail_id, linescan_trajectory in linescans.iteritems():
# transpose data to have data for each side of the center line
line_scans = zip(*linescan_trajectory)
# iterate over all line scans (ventral and dorsal)
for side_id, data in enumerate(line_scans):
kymograph = Kymograph(data)
side = tail.line_names[side_id]
kymographs[tail_id][side] = kymograph
# save the data and close the videos
self.result['kymographs'] = kymographs
self.save_result()
self.close()
def produce_video(self):
""" prepares everything for the debug output """
# load parameters for video output
video_extension = self.params['output/video/extension']
video_codec = self.params['output/video/codec']
video_bitrate = self.params['output/video/bitrate']
if self.video is None:
self.load_video()
filename = self.get_filename('video' + video_extension, 'video')
video = VideoComposer(filename, size=self.video.size,
fps=self.video.fps, is_color=True,
output_period=self.params['output/output_period'],
codec=video_codec, bitrate=video_bitrate)
mouse_track = self.data['pass2/mouse_trajectory']
ground_profile = self.data['pass2/ground_profile']
self.logger.info('Pass 2 - Start producing final video with %d frames', len(self.video))
# we used the first frame to determine the cage dimensions in the first pass
source_video = self.video[1:]
track_first = 0
tracks = self.data['pass1/objects/tracks']
tracks.sort(key=lambda track: track.start)
burrow_tracks = self.data['pass1/burrows/tracks']
for frame_id, frame in enumerate(display_progress(source_video)):
# set real video as background
video.set_frame(frame)
# plot the ground profile
ground_line = ground_profile.get_groundline(frame_id)
video.add_line(ground_line, is_closed=False,
mark_points=False, color='y')
# indicate burrow centerline
for burrow in burrow_tracks.find_burrows(frame_id):
ground = GroundProfile(ground_line)
video.add_line(burrow.get_centerline(ground),
'k', is_closed=False, width=2)
# indicate all moving objects
# find the first track which is still active
while tracks[track_first].end < frame_id:
track_first += 1
# draw all tracks that are still active
for track in tracks[track_first:]:
if track.start > frame_id:
# this is the last track that can possibly be active
break
elif track.start <= frame_id <= track.end:
video.add_circle(track.get_pos(frame_id),
self.params['mouse/model_radius'],
'0.5', thickness=1)
# indicate the mouse position
if np.all(np.isfinite(mouse_track.pos[frame_id])):
video.add_circle(mouse_track.pos[frame_id],
self.params['mouse/model_radius'],
'w', thickness=2)
# # add additional debug information
video.add_text(str(frame_id), (20, 20), anchor='top')
# video.add_text(str(self.frame_id/self.fps), (20, 20), anchor='top')
video.close()
def make_cropped_video(result_file, output_video=None,
display='{time} [{frame}]', scale_bar=True,
border_buffer_cm=0, frame_compression=1,
time_duration=None, progress=True):
""" function that crops a video to an antfarm.
`result_file` is the file where the results from the video analysis are
stored. This is usually a *.yaml file
`output_video` denotes the filename where the result video should be
written to.
`display` determines what information is displayed. There are several
variables that would be replaced by data:
{time} the current time stamp
{frame} the current frame number
`scale_bar` determines whether a scale bar is shown
`border_buffer_cm` sets the extra space (in units of cm) around the cropping
rectangle that is included in the analysis
`frame_compression` sets the compression factor that determines how many
frames are dropped compared to the original video
`time_duration` sets the maximal number of seconds the video is supposed to
last. Additional frames will not be written.
`progress` flag that determines whether the progress is displayed
"""
logging.info('Analyze video `%s`', result_file)
# load the respective result file
analyzer = load_result_file(result_file)
# load the full original video
video_info = analyzer.load_video(frames=(0, None))
# crop the video to the cage
video_input = analyzer.video
cropping_cage = analyzer.data['pass1/video/cropping_cage']
border_buffer_px = int(border_buffer_cm / analyzer.length_scale_mag)
# change rectangle size if necessary
if border_buffer_px != 0:
cropping_rect = Rectangle.from_list(cropping_cage)
video_rect = Rectangle(0, 0, video_input.width - 1,
video_input.height - 1)
cropping_rect.buffer(border_buffer_px)
cropping_rect.intersect(video_rect)
cropping_cage = cropping_rect.to_list()
if cropping_cage:
# size_alignment=2 makes sure that the width and height are even numbers
video_input = FilterCrop(video_input, rect=cropping_cage,
size_alignment=2)
if frame_compression is not None and frame_compression != 1:
video_input = FilterDropFrames(video_input,
compression=frame_compression)
if time_duration is not None:
index_max = int(time_duration * video_input.fps)
video_input = video_input[:index_max]
# determine the filename of the output video
if output_video is None:
# determine the complete filename automatically
movie_ext = analyzer.params['output/video/extension']
filename = 'cropped'
output_video = analyzer.get_filename(filename + movie_ext, 'video')
elif '.' not in output_video:
# determine the extension automatically
movie_ext = analyzer.params['output/video/extension']
output_video = output_video + movie_ext
logging.info('Write output to `%s`', output_video)
# create the video writer
video_codec = analyzer.params['output/video/codec']
video_bitrate = analyzer.params['output/video/crop_bitrate']
if video_bitrate is None:
video_bitrate = analyzer.params['output/video/bitrate']
fps = video_input.fps
video_output = VideoComposer(
output_video, size=video_input.size, fps=fps,
is_color=video_input.is_color, codec=video_codec, bitrate=video_bitrate,
)
# time label position
label_pos = video_input.width // 2, 30
# calculate size of scale bar and the position of its label
pixel_size_cm = analyzer.data['pass2/pixel_size_cm']
scale_bar_size_cm = 10
scale_bar_size_px = np.round(scale_bar_size_cm / pixel_size_cm)
scale_bar_rect = Rectangle(30, 50, scale_bar_size_px, 5)
scale_bar_pos = (30 + scale_bar_size_px//2, 30)
if progress:
video_input = display_progress(video_input)
for frame_id, frame in enumerate(video_input):
video_output.set_frame(frame, copy=True)
if scale_bar:
# show a scale bar
video_output.add_rectangle(scale_bar_rect, width=-1)
video_output.add_text(str('%g cm' % scale_bar_size_cm),
scale_bar_pos, color='w',
anchor='upper center')
# gather data about this frame
frame_data = {'frame': frame_id}
# calculate time stamp
time_secs, time_frac = divmod(frame_id, fps)
time_msecs = int(1000 * time_frac / fps)
dt = datetime.timedelta(seconds=time_secs,
milliseconds=time_msecs)
frame_data['time'] = str(dt)
# output the display data
if display:
display_text = display.format(**frame_data)
video_output.add_text(display_text, label_pos, color='w',
anchor='upper center')
# show summary
frames_total = video_info['frames'][1] - video_info['frames'][0]
frames_written = video_output.frames_written
logging.info('%d (%d%%) of %d frames written', frames_written,
100 * frames_written // frames_total, frames_total)
# close and finalize video
try:
video_output.close()
except IOError:
logging.exception('Error while writing out the debug video `%s`',
video_output)
def make_underground_video(result_file, output_video=None,
display='{time} [{frame}]', scale_bar=True,
min_duration=60, blank_duration=5,
bouts_slice=slice(None, None), video_part=None):
""" main routine of the program
`result_file` is the file where the results from the video analysis are
stored. This is usually a *.yaml file
`output_video` denotes the filename where the result video should be
written to.
`display` determines what information is displayed. There are several
variables that would be replaced by data:
{time} the current time stamp
{frame} the current frame number
`scale_bar` determines whether a scale bar is shown
`min_duration` determines how many frames the mouse has to be below ground
for the bout to be included in the video
`blank_duration` determines who many white frames are displayed between
time intervals where the mouse is underground
`bouts_slice` is a slice object that determines which bouts are included in
the video.
`video_part` determines which part of a longer video will be produced
"""
logging.info('Analyze video `%s`', result_file)
# load the respective result file
analyzer = load_result_file(result_file)
# determine the bouts of this video
bouts = get_underground_bouts(analyzer, bouts_slice, video_part)
if len(bouts) == 0:
raise RuntimeError('There are no bouts that could be turned into a '
'video. This could be a problem with finding the '
'mouse trajectory in the analysis or it could '
'indicate that the requested bouts_slice or '
'video_part resulted in empty data.')
# load the original video
video_info = analyzer.load_video()
frame_offset = video_info['frames'][0]
# crop the video to the cage
video_input = analyzer.video
cropping_cage = analyzer.data['pass1/video/cropping_cage']
if cropping_cage:
video_input = FilterCrop(video_input, rect=cropping_cage)
# determine the filename of the output video
if output_video is None:
# determine the complete filename automatically
movie_ext = analyzer.params['output/video/extension']
if video_part is None:
filename = 'underground'
else:
filename = 'underground_%d' % video_part
output_video = analyzer.get_filename(filename + movie_ext,
'video_underground')
elif '.' not in output_video:
# determine the extension automatically
movie_ext = analyzer.params['output/video/extension']
output_video = output_video + movie_ext
logging.info('Write output to `%s`', output_video)
# create the video writer
video_codec = analyzer.params['output/video/codec']
video_bitrate = analyzer.params['output/video/bitrate']
fps = video_input.fps
video_output = VideoComposer(
output_video, size=video_input.size, fps=fps, is_color=False,
codec=video_codec, bitrate=video_bitrate,
)
# create blank frame with mean color of video
blank_frame = np.full(video_input.shape[1:], video_input[0].mean(),
dtype=np.uint8)
# time label position
label_pos = video_input.width // 2, 30
# calculate size of scale bar and the position of its label
pixel_size_cm = analyzer.data['pass2/pixel_size_cm']
scale_bar_size_cm = 10
scale_bar_size_px = np.round(scale_bar_size_cm / pixel_size_cm)
scale_bar_rect = Rectangle(30, 50, scale_bar_size_px, 5)
scale_bar_pos = (30 + scale_bar_size_px//2, 30)
# iterate over all bouts
for start, finish in display_progress(bouts):
duration = finish - start + 1
# check whether bout is long enough
if duration < min_duration:
continue
if video_output.frames_written > 1:
# write blank frame
for _ in xrange(blank_duration):
video_output.set_frame(blank_frame)
video_bout = video_input[start - frame_offset :
finish - frame_offset + 1]
for frame_id, frame in enumerate(video_bout, start):
video_output.set_frame(frame, copy=True)
if scale_bar:
# show a scale bar
video_output.add_rectangle(scale_bar_rect, width=-1)
video_output.add_text(str('%g cm' % scale_bar_size_cm),
scale_bar_pos, color='w',
anchor='upper center')
# gather data about this frame
frame_data = {'frame': frame_id}
# calculate time stamp
time_secs, time_frac = divmod(frame_id, fps)
time_msecs = int(1000 * time_frac / fps)
dt = datetime.timedelta(seconds=time_secs,
milliseconds=time_msecs)
frame_data['time'] = str(dt)
# output the display data
if display:
display_text = display.format(**frame_data)
video_output.add_text(display_text, label_pos, color='w',
anchor='upper center')
# show summary
frames_total = video_info['frames'][1] - video_info['frames'][0]
frames_written = video_output.frames_written
logging.info('%d (%d%%) of %d frames written', frames_written,
100 * frames_written // frames_total, frames_total)
# close and finalize video
try:
video_output.close()
except IOError:
logging.exception('Error while writing out the debug video `%s`',
video_output)
def main():
""" main routine of the program """
# parse the command line arguments
parser = argparse.ArgumentParser(description='Analyze antfarm polygons')
parser.add_argument('-c', '--result_csv', dest='result_csv', type=str,
metavar='FILE.csv',
help='csv file to which statistics about the burrows '
'are written')
parser.add_argument('-p', '--result_pkl', dest='result_pkl', type=str,
metavar='FILE.pkl',
help='python pickle file to which all results from the '
'algorithm are written')
parser.add_argument('-l', '--load_pkl', dest='load_pkl', type=str,
metavar='FILE.pkl',
help='python pickle file from which data is loaded')
parser.add_argument('-f', '--folder', dest='folder', type=str,
help='folder where output images will be written to')
parser.add_argument('--scale', dest='scale', type=float,
default=default_parameters['scale_bar/length_cm'],
help='length of the scale bar in cm')
flags = parser.add_mutually_exclusive_group(required=False)
flags.add_argument('-m', '--multi-processing', dest='multiprocessing',
action='store_true', help='turns on multiprocessing')
flags.add_argument('-d', '--debug', dest='debug', action='store_true',
help='does debug output')
parser.add_argument('files', metavar='FILE', type=str, nargs='*',
help='files to analyze')
# parse the command line arguments
args = parser.parse_args()
if args.debug:
logging.getLogger().setLevel(logging.DEBUG)
if args.folder:
ensure_directory_exists(args.folder)
if args.load_pkl:
# load file from pickled data
logging.info('Loading data from file `%s`.' % args.load_pkl)
with open(args.load_pkl, "rb") as fp:
results = pickle.load(fp)
else:
# get files to analyze
files = args.files
logging.info('Analyzing %d files.' % len(files))
# collect burrows from all files
if args.multiprocessing:
# use multiple processes to analyze data
job_func = functools.partial(process_polygon_file,
output_folder=args.folder,
suppress_exceptions=True,
scale=args.scale)
pool = mp.Pool()
results = pool.map(job_func, files)
else:
# analyze data in the current process
job_func = functools.partial(process_polygon_file,
output_folder=args.folder,
suppress_exceptions=False,
debug=args.debug, scale=args.scale)
# iterate over all files
results = []
for path in misc.display_progress(files):
results.append(job_func(path))
# filter results
results = [res for res in results if res is not None]
# write complete results as pickle file if requested
if args.result_pkl:
with open(args.result_pkl, "wb") as fp:
pickle.dump(results, fp)
# write burrow results as csv file if requested
if args.result_csv:
# create a dictionary of lists
table = collections.defaultdict(list)
# iterate through all experiments and save information about the burrows
for data in results:
if data:
# sort the burrows from left to right
burrows = sorted(data['burrows'],
key=operator.itemgetter('pos_x'))
# create a single row per burrow
for burrow_id, properties in enumerate(burrows, 1):
properties['burrow_id'] = burrow_id
properties['experiment'] = data['name']
# iterate over all burrow properties
for k, v in properties.iteritems():
table[k].append(v)
# write the data to a csv file
first_columns = ['experiment', 'burrow_id']
data_structures.misc.save_dict_to_csv(table, args.result_csv,
first_columns=first_columns)