def doit(input_fname,
subtract_frame,
start=None,
stop=None,
gain=1.0,
offset=0.0,
):
output_fname = os.path.splitext(input_fname)[0]+'.sub.fmf'
in_fmf = FMF.FlyMovie(input_fname)
input_format = in_fmf.get_format()
input_is_color = imops.is_coding_color(input_format)
if not subtract_frame.endswith('.fmf'):
raise NotImplementedError('only fmf supported for --subtract-frame')
tmp_fmf = FMF.FlyMovie(subtract_frame)
if input_is_color:
tmp_frame, tmp_timestamp = tmp_fmf.get_next_frame()
subtract_frame = imops.to_rgb8(tmp_fmf.get_format(),tmp_frame)
subtract_frame = subtract_frame.astype(np.float32) # force upconversion to float
else:
tmp_frame, tmp_timestamp = tmp_fmf.get_next_frame()
subtract_frame = imops.to_mono8(tmp_fmf.get_format(),tmp_frame)
subtract_frame = subtract_frame.astype(np.float32) # force upconversion to float
if input_is_color:
output_format = 'RGB8'
else:
output_format = 'MONO8'
out_fmf = FMF.FlyMovieSaver(output_fname,
version=3,
format=output_format,
)
try:
if stop is None:
stop = in_fmf.get_n_frames()-1
if start is None:
start = 0
n_frames = stop-start+1
n_samples = max(30,n_frames)
for fno in np.linspace(start,stop,n_samples):
fno = int(round(fno))
in_fmf.seek(fno)
frame,timestamp = in_fmf.get_next_frame()
if input_is_color:
frame = imops.to_rgb8(input_format,frame)
new_frame = frame-subtract_frame
else:
frame = np.atleast_3d(frame)
new_frame = frame-subtract_frame
new_frame = np.clip(new_frame*gain + offset,0,255)
new_frame = new_frame.astype(np.uint8)
out_fmf.add_frame(new_frame,timestamp)
out_fmf.close()
except:
os.unlink(output_fname)
raise
in_fmf.close()
def fmf2images(filename, imgformat='png',
startframe=0,endframe=-1,interval=1,
prefix=None,outdir=None,progress=False):
base,ext = os.path.splitext(filename)
if ext != '.fmf':
print 'fmf_filename does not end in .fmf'
sys.exit()
path,base = os.path.split(base)
if prefix is not None:
base = prefix
if outdir is None:
outdir = path
fly_movie = FlyMovieFormat.FlyMovie(filename)
fmf_format = fly_movie.get_format()
n_frames = fly_movie.get_n_frames()
if endframe < 0 or endframe >= n_frames:
endframe = n_frames - 1
fly_movie.seek(startframe)
frames = range(startframe,endframe+1,interval)
n_frames = len(frames)
if progress:
import progressbar
widgets=['fmf2bmps', progressbar.Percentage(), ' ',
progressbar.Bar(), ' ', progressbar.ETA()]
pbar=progressbar.ProgressBar(widgets=widgets,
maxval=n_frames).start()
else:
pbar = None
for count,frame_number in enumerate(frames):
if pbar is not None:
pbar.update(count)
frame,timestamp = fly_movie.get_frame(frame_number)
mono=False
if (fmf_format in ['RGB8','RGB32f','ARGB8','YUV411','YUV422'] or
fmf_format.startswith('MONO8:') or
fmf_format.startswith('MONO32f:')):
save_frame = imops.to_rgb8(fmf_format,frame)
else:
if fmf_format not in ['MONO8','MONO16']:
warnings.warn('converting unknown fmf format %s to mono'%(
fmf_format,))
save_frame = imops.to_mono8(fmf_format,frame)
mono=True
h,w=save_frame.shape[:2]
if mono:
im = Image.fromstring('L',(w,h),save_frame.tostring())
else:
im = Image.fromstring('RGB',(w,h),save_frame.tostring())
f='%s_%08d.%s'%(os.path.join(outdir,base),frame_number,imgformat)
im.save(f)
if pbar is not None:
pbar.finish()
def convert(frame,format):
if format in ['RGB8','ARGB8','YUV411','YUV422']:
frame = imops.to_rgb8(format,frame)
elif format in ['MONO8','MONO16']:
frame = imops.to_mono8(format,frame)
elif (format.startswith('MONO8:') or
format.startswith('MONO32f:')):
# bayer
frame = imops.to_rgb8(format,frame)
return frame
def _convert_to_displayable(self,frame):
if self.format in ['RGB8','ARGB8','YUV411','YUV422']:
frame = imops.to_rgb8(self.format,frame)
elif self.format in ['MONO8','MONO16']:
frame = imops.to_mono8(self.format,frame)
elif (self.format.startswith('MONO8:') or
self.format.startswith('MONO32f:')):
# bayer
frame = imops.to_rgb8(self.format,frame)
#frame = self.convert_to_matplotlib(frame)
return frame
def main():
try:
filename = sys.argv[1]
except:
print 'Usage: %s fmf_filename' % sys.argv[0]
sys.exit()
path,ext = os.path.splitext(filename)
if ext != '.fmf':
print 'fmf_filename does not end in .fmf'
sys.exit()
fly_movie = FlyMovieFormat.FlyMovie(filename)
n_frames = fly_movie.get_n_frames()
fmf_format = fly_movie.get_format()
fmf = fly_movie
delays = numpy.array([])
for frame_number in range(n_frames):
frame,timestamp = fmf.get_frame(frame_number)
mono=False
if (fmf_format in ['RGB8','ARGB8','YUV411','YUV422'] or
fmf_format.startswith('MONO8:') or
fmf_format.startswith('MONO32f:')):
save_frame = imops.to_rgb8(fmf_format, frame)
else:
if fmf_format not in ['MONO8','MONO16']:
warnings.warn('converting unknown fmf format %s to mono'%(
fmf_format,))
save_frame = imops.to_mono8(fmf_format,frame)
mono=True
h, w = save_frame.shape[:2]
if mono:
im = Image.fromstring('L',(w,h),save_frame.tostring())
else:
im = Image.fromstring('RGB',(w,h),save_frame.tostring())
f = '%s_%08d.%s'%(os.path.join("./", "zbartmp"), frame_number, 'bmp')
im.save(f)
try:
TS = subprocess.check_output(['zbarimg', '-q', f])
ts = float(TS[8:].strip())
except OSError:
raise
except:
ts = float('nan')
delay = timestamp-ts
delays = numpy.append(delays,[delay])
print "ds: % 14.6f cam: % 14.6f delay: % 8.6f" % (ts, timestamp, delay)
os.unlink(f)
print "delay mean: % 8.6f std: % 8.6f" % (delays[~numpy.isnan(delays)].mean(),delays[~numpy.isnan(delays)].std())
print "delay max: % 8.6f min: % 8.6f" % (delays[~numpy.isnan(delays)].max(),delays[~numpy.isnan(delays)].min())
print "%i of %i frames used" % (len(delays[numpy.isnan(delays)]),len(delays[~numpy.isnan(delays)]))
def _convert_to_displayable(self, frame):
if self.format in ["RGB8", "ARGB8", "YUV411", "YUV422", "RGB32f"]:
frame = imops.to_rgb8(self.format, frame)
elif self.format in ["MONO8", "MONO16"]:
frame = imops.to_mono8(self.format, frame)
elif self.format.startswith("MONO8:") or self.format.startswith("MONO32f:") or self.format.startswith("RAW8:"):
# bayer
frame = imops.to_rgb8(self.format, frame)
else:
warnings.warn('unknown format "%s" conversion to displayable' % self.format)
# frame = self.convert_to_matplotlib(frame)
return frame
def _convert_to_displayable(self,frame):
if self.format in ['RGB8','ARGB8','YUV411','YUV422','RGB32f']:
frame = imops.to_rgb8(self.format,frame)
elif self.format in ['MONO8','MONO16']:
frame = imops.to_mono8(self.format,frame)
elif (self.format.startswith('MONO8:') or
self.format.startswith('MONO32f:')):
# bayer
frame = imops.to_rgb8(self.format,frame)
else:
warnings.warn('unknown format "%s" conversion to displayable'%
self.format)
#frame = self.convert_to_matplotlib(frame)
return frame
def main():
usage = """%prog FILE [options]
Example:
fmf2bmps myvideo.fmf --start=10 --stop=100 --extension=jpg --outdir=tmp
"""
parser = OptionParser(usage)
parser.add_option('--start',type='int',default=0,help='first frame to save')
parser.add_option('--stop',type='int',default=-1,help='last frame to save')
parser.add_option('--interval',type='int',default=1,help='save every Nth frame')
parser.add_option('--extension',type='string',default='bmp',
help='image extension (default: bmp)')
parser.add_option('--outdir',type='string',default=None,
help='directory to save images (default: same as fmf)')
parser.add_option('--progress',action='store_true',default=False,
help='show progress bar')
parser.add_option('--prefix',default=None,type='str',
help='prefix for image filenames')
(options, args) = parser.parse_args()
if len(args)<1:
parser.print_help()
return
filename = args[0]
startframe = options.start
endframe = options.stop
interval = options.interval
assert interval >= 1
imgformat = options.extension
base,ext = os.path.splitext(filename)
if ext != '.fmf':
print 'fmf_filename does not end in .fmf'
sys.exit()
path,base = os.path.split(base)
if options.prefix is not None:
base = options.prefix
if options.outdir is None:
outdir = path
else:
outdir = options.outdir
fly_movie = FlyMovieFormat.FlyMovie(filename)
fmf_format = fly_movie.get_format()
n_frames = fly_movie.get_n_frames()
if endframe < 0 or endframe >= n_frames:
endframe = n_frames - 1
fly_movie.seek(startframe)
frames = range(startframe,endframe+1,interval)
n_frames = len(frames)
if options.progress:
import progressbar
widgets=['fmf2bmps', progressbar.Percentage(), ' ',
progressbar.Bar(), ' ', progressbar.ETA()]
pbar=progressbar.ProgressBar(widgets=widgets,
maxval=n_frames).start()
else:
pbar = None
for count,frame_number in enumerate(frames):
if pbar is not None:
pbar.update(count)
frame,timestamp = fly_movie.get_frame(frame_number)
mono=False
if (fmf_format in ['RGB8','ARGB8','YUV411','YUV422'] or
fmf_format.startswith('MONO8:') or
fmf_format.startswith('MONO32f:')):
save_frame = imops.to_rgb8(fmf_format,frame)
else:
if fmf_format not in ['MONO8','MONO16']:
warnings.warn('converting unknown fmf format %s to mono'%(
fmf_format,))
save_frame = imops.to_mono8(fmf_format,frame)
mono=True
h,w=save_frame.shape[:2]
if mono:
im = Image.fromstring('L',(w,h),save_frame.tostring())
else:
im = Image.fromstring('RGB',(w,h),save_frame.tostring())
f='%s_%08d.%s'%(os.path.join(outdir,base),frame_number,imgformat)
im.save(f)
if pbar is not None:
pbar.finish()
def doit(
movie_fname=None,
reconstructor_fname=None,
h5_fname=None,
cam_id=None,
dest_dir=None,
transform=None,
start=None,
stop=None,
h5start=None,
h5stop=None,
show_obj_ids=False,
obj_only=None,
image_format=None,
subtract_frame=None,
save_framelist_fname=None,
):
if dest_dir is None:
dest_dir = os.curdir
if movie_fname is None:
raise NotImplementedError('')
if image_format is None:
image_format = 'png'
if cam_id is None:
raise NotImplementedError('')
if movie_fname.lower().endswith('.fmf'):
movie = fmf_mod.FlyMovie(movie_fname)
else:
movie = ufmf_mod.FlyMovieEmulator(movie_fname)
if start is None:
start = 0
if stop is None:
stop = movie.get_n_frames() - 1
ca = core_analysis.get_global_CachingAnalyzer()
(obj_ids, unique_obj_ids, is_mat_file, data_file, extra) = \
ca.initial_file_load(h5_fname)
if obj_only is not None:
unique_obj_ids = obj_only
dynamic_model_name = extra['dynamic_model_name']
if dynamic_model_name.startswith('EKF'):
dynamic_model_name = dynamic_model_name[4:]
if reconstructor_fname is None:
reconstructor = flydra_core.reconstruct.Reconstructor(data_file)
else:
reconstructor = flydra_core.reconstruct.Reconstructor(
reconstructor_fname)
fix_w = movie.get_width()
fix_h = movie.get_height()
is_color = imops.is_coding_color(movie.get_format())
if subtract_frame is not None:
if not subtract_frame.endswith('.fmf'):
raise NotImplementedError(
'only fmf supported for --subtract-frame')
tmp_fmf = fmf_mod.FlyMovie(subtract_frame)
if is_color:
tmp_frame, tmp_timestamp = tmp_fmf.get_next_frame()
subtract_frame = imops.to_rgb8(tmp_fmf.get_format(), tmp_frame)
subtract_frame = subtract_frame.astype(
np.float32) # force upconversion to float
else:
tmp_frame, tmp_timestamp = tmp_fmf.get_next_frame()
subtract_frame = imops.to_mono8(tmp_fmf.get_format(), tmp_frame)
subtract_frame = subtract_frame.astype(
np.float32) # force upconversion to float
if save_framelist_fname is not None:
save_framelist_fd = open(save_framelist_fname, mode='w')
movie_fno_count = 0
for movie_fno in range(start, stop + 1):
movie.seek(movie_fno)
image, timestamp = movie.get_next_frame()
h5_frame = extra['time_model'].timestamp2framestamp(timestamp)
if h5start is not None:
if h5_frame < h5start:
continue
if h5stop is not None:
if h5_frame > h5stop:
continue
if is_color:
image = imops.to_rgb8(movie.get_format(), image)
else:
image = imops.to_mono8(movie.get_format(), image)
if subtract_frame is not None:
new_image = np.clip(image - subtract_frame, 0, 255)
image = new_image.astype(np.uint8)
warnings.warn('not implemented: interpolating data')
h5_frame = int(round(h5_frame))
if save_framelist_fname is not None:
save_framelist_fd.write('%d\n' % h5_frame)
movie_fno_count += 1
if 0:
# save starting from frame 1
save_fname_path = os.path.splitext(movie_fname)[
0] + '_frame%06d.%s' % (movie_fno_count, image_format)
else:
# frame is frame in movie file
save_fname_path = os.path.splitext(
movie_fname)[0] + '_frame%06d.%s' % (movie_fno, image_format)
save_fname_path = os.path.join(dest_dir, save_fname_path)
if transform in ['rot 90', 'rot -90']:
device_rect = (0, 0, fix_h, fix_w)
canv = benu.Canvas(save_fname_path, fix_h, fix_w)
else:
device_rect = (0, 0, fix_w, fix_h)
canv = benu.Canvas(save_fname_path, fix_w, fix_h)
user_rect = (0, 0, image.shape[1], image.shape[0])
show_points = []
with canv.set_user_coords(device_rect, user_rect, transform=transform):
canv.imshow(image, 0, 0)
for obj_id in unique_obj_ids:
try:
data = ca.load_data(
obj_id,
data_file,
frames_per_second=extra['frames_per_second'],
dynamic_model_name=dynamic_model_name,
)
except core_analysis.NotEnoughDataToSmoothError:
continue
cond = data['frame'] == h5_frame
idxs = np.nonzero(cond)[0]
if not len(idxs):
continue # no data at this frame for this obj_id
assert len(idxs) == 1
idx = idxs[0]
row = data[idx]
# circle over data point
xyz = row['x'], row['y'], row['z']
x2d, y2d = reconstructor.find2d(cam_id, xyz, distorted=True)
radius = 10
canv.scatter([x2d], [y2d],
color_rgba=green,
markeredgewidth=3,
radius=radius)
if 1:
# z line to XY plane through origin
xyz0 = row['x'], row['y'], 0
x2d_z0, y2d_z0 = reconstructor.find2d(cam_id,
xyz0,
distorted=True)
warnings.warn('not distorting Z line')
if 1:
xdist = x2d - x2d_z0
ydist = y2d - y2d_z0
dist = np.sqrt(xdist**2 + ydist**2)
start_frac = radius / dist
if radius > dist:
start_frac = 0
x2d_r = x2d - xdist * start_frac
y2d_r = y2d - ydist * start_frac
else:
x2d_r = x2d
y2d_r = y2d
canv.plot([x2d_r, x2d_z0], [y2d_r, y2d_z0],
color_rgba=green,
linewidth=3)
if show_obj_ids:
show_points.append((obj_id, x2d, y2d))
for show_point in show_points:
obj_id, x2d, y2d = show_point
x, y = canv.get_transformed_point(x2d,
y2d,
device_rect,
user_rect,
transform=transform)
canv.text(
'obj_id %d' % obj_id,
x,
y,
color_rgba=(0, 1, 0, 1),
font_size=20,
)
canv.save()
def doit(
h5_filename=None,
output_h5_filename=None,
ufmf_filenames=None,
kalman_filename=None,
start=None,
stop=None,
view=None,
erode=0,
save_images=False,
save_image_dir=None,
intermediate_thresh_frac=None,
final_thresh=None,
stack_N_images=None,
stack_N_images_min=None,
old_sync_timestamp_source=False,
do_rts_smoothing=True,
):
"""
Copy all data in .h5 file (specified by h5_filename) to a new .h5
file in which orientations are set based on image analysis of
.ufmf files. Tracking data to associate 2D points from subsequent
frames is read from the .h5 kalman file specified by
kalman_filename.
"""
if view is None:
view = ["orig" for f in ufmf_filenames]
else:
assert len(view) == len(ufmf_filenames)
if intermediate_thresh_frac is None or final_thresh is None:
raise ValueError("intermediate_thresh_frac and final_thresh must be "
"set")
filename2view = dict(zip(ufmf_filenames, view))
ca = core_analysis.get_global_CachingAnalyzer()
obj_ids, use_obj_ids, is_mat_file, data_file, extra = ca.initial_file_load(
kalman_filename)
try:
ML_estimates_2d_idxs = data_file.root.ML_estimates_2d_idxs[:]
except tables.exceptions.NoSuchNodeError as err1:
# backwards compatibility
try:
ML_estimates_2d_idxs = data_file.root.kalman_observations_2d_idxs[:]
except tables.exceptions.NoSuchNodeError as err2:
raise err1
if os.path.exists(output_h5_filename):
raise RuntimeError("will not overwrite old file '%s'" %
output_h5_filename)
with open_file_safe(output_h5_filename, delete_on_error=True,
mode="w") as output_h5:
if save_image_dir is not None:
if not os.path.exists(save_image_dir):
os.mkdir(save_image_dir)
with open_file_safe(h5_filename, mode="r") as h5:
fps = result_utils.get_fps(h5, fail_on_error=True)
for input_node in h5.root._f_iter_nodes():
# copy everything from source to dest
input_node._f_copy(output_h5.root, recursive=True)
print("done copying")
# Clear values in destination table that we may overwrite.
dest_table = output_h5.root.data2d_distorted
for colname in [
"x",
"y",
"area",
"slope",
"eccentricity",
"cur_val",
"mean_val",
"sumsqf_val",
]:
if colname == "cur_val":
fill_value = 0
else:
fill_value = np.nan
clear_col(dest_table, colname, fill_value=fill_value)
dest_table.flush()
print("done clearing")
camn2cam_id, cam_id2camns = result_utils.get_caminfo_dicts(h5)
cam_id2fmfs = collections.defaultdict(list)
cam_id2view = {}
for ufmf_filename in ufmf_filenames:
fmf = ufmf.FlyMovieEmulator(
ufmf_filename,
# darken=-50,
allow_no_such_frame_errors=True,
)
timestamps = fmf.get_all_timestamps()
cam_id = get_cam_id_from_filename(fmf.filename,
cam_id2camns.keys())
cam_id2fmfs[cam_id].append(
(fmf, result_utils.Quick1DIndexer(timestamps)))
cam_id2view[cam_id] = filename2view[fmf.filename]
# associate framenumbers with timestamps using 2d .h5 file
data2d = h5.root.data2d_distorted[:] # load to RAM
data2d_idxs = np.arange(len(data2d))
h5_framenumbers = data2d["frame"]
h5_frame_qfi = result_utils.QuickFrameIndexer(h5_framenumbers)
fpc = realtime_image_analysis.FitParamsClass(
) # allocate FitParamsClass
for obj_id_enum, obj_id in enumerate(use_obj_ids):
print("object %d of %d" % (obj_id_enum, len(use_obj_ids)))
# get all images for this camera and this obj_id
obj_3d_rows = ca.load_dynamics_free_MLE_position(
obj_id, data_file)
this_obj_framenumbers = collections.defaultdict(list)
if save_images:
this_obj_raw_images = collections.defaultdict(list)
this_obj_mean_images = collections.defaultdict(list)
this_obj_absdiff_images = collections.defaultdict(list)
this_obj_morphed_images = collections.defaultdict(list)
this_obj_morph_failures = collections.defaultdict(list)
this_obj_im_coords = collections.defaultdict(list)
this_obj_com_coords = collections.defaultdict(list)
this_obj_camn_pt_no = collections.defaultdict(list)
for this_3d_row in obj_3d_rows:
# iterate over each sample in the current camera
framenumber = this_3d_row["frame"]
if start is not None:
if not framenumber >= start:
continue
if stop is not None:
if not framenumber <= stop:
continue
h5_2d_row_idxs = h5_frame_qfi.get_frame_idxs(framenumber)
frame2d = data2d[h5_2d_row_idxs]
frame2d_idxs = data2d_idxs[h5_2d_row_idxs]
obs_2d_idx = this_3d_row["obs_2d_idx"]
kobs_2d_data = ML_estimates_2d_idxs[int(obs_2d_idx)]
# Parse VLArray.
this_camns = kobs_2d_data[0::2]
this_camn_idxs = kobs_2d_data[1::2]
# Now, for each camera viewing this object at this
# frame, extract images.
for camn, camn_pt_no in zip(this_camns, this_camn_idxs):
# find 2D point corresponding to object
cam_id = camn2cam_id[camn]
movie_tups_for_this_camn = cam_id2fmfs[cam_id]
cond = (frame2d["camn"] == camn) & (
frame2d["frame_pt_idx"] == camn_pt_no)
idxs = np.nonzero(cond)[0]
assert len(idxs) == 1
idx = idxs[0]
orig_data2d_rownum = frame2d_idxs[idx]
if not old_sync_timestamp_source:
# Change the next line to 'timestamp' for old
# data (before May/June 2009 -- the switch to
# fview_ext_trig)
frame_timestamp = frame2d[idx][
"cam_received_timestamp"]
else:
# previous version
frame_timestamp = frame2d[idx]["timestamp"]
found = None
for fmf, fmf_timestamp_qi in movie_tups_for_this_camn:
fmf_fnos = fmf_timestamp_qi.get_idxs(
frame_timestamp)
if not len(fmf_fnos):
continue
assert len(fmf_fnos) == 1
# should only be one .ufmf with this frame and cam_id
assert found is None
fmf_fno = fmf_fnos[0]
found = (fmf, fmf_fno)
if found is None:
print(
"no image data for frame timestamp %s cam_id %s"
% (repr(frame_timestamp), cam_id))
continue
fmf, fmf_fno = found
image, fmf_timestamp = fmf.get_frame(fmf_fno)
mean_image = fmf.get_mean_for_timestamp(fmf_timestamp)
coding = fmf.get_format()
if imops.is_coding_color(coding):
image = imops.to_rgb8(coding, image)
mean_image = imops.to_rgb8(coding, mean_image)
else:
image = imops.to_mono8(coding, image)
mean_image = imops.to_mono8(coding, mean_image)
xy = (
int(round(frame2d[idx]["x"])),
int(round(frame2d[idx]["y"])),
)
maxsize = (fmf.get_width(), fmf.get_height())
# Accumulate cropped images. Note that the region
# of the full image that the cropped image
# occupies changes over time as the tracked object
# moves. Thus, averaging these cropped-and-shifted
# images is not the same as simply averaging the
# full frame.
roiradius = 25
warnings.warn(
"roiradius hard-coded to %d: could be set "
"from 3D tracking" % roiradius)
tmp = clip_and_math(image, mean_image, xy, roiradius,
maxsize)
im_coords, raw_im, mean_im, absdiff_im = tmp
max_absdiff_im = absdiff_im.max()
intermediate_thresh = intermediate_thresh_frac * max_absdiff_im
absdiff_im[absdiff_im <= intermediate_thresh] = 0
if erode > 0:
morphed_im = scipy.ndimage.grey_erosion(absdiff_im,
size=erode)
## morphed_im = scipy.ndimage.binary_erosion(absdiff_im>1).astype(np.float32)*255.0
else:
morphed_im = absdiff_im
y0_roi, x0_roi = scipy.ndimage.center_of_mass(
morphed_im)
x0 = im_coords[0] + x0_roi
y0 = im_coords[1] + y0_roi
if 1:
morphed_im_binary = morphed_im > 0
labels, n_labels = scipy.ndimage.label(
morphed_im_binary)
morph_fail_because_multiple_blobs = False
if n_labels > 1:
x0, y0 = np.nan, np.nan
# More than one blob -- don't allow image.
if 1:
# for min flattening
morphed_im = np.empty(morphed_im.shape,
dtype=np.uint8)
morphed_im.fill(255)
morph_fail_because_multiple_blobs = True
else:
# for mean flattening
morphed_im = np.zeros_like(morphed_im)
morph_fail_because_multiple_blobs = True
this_obj_framenumbers[camn].append(framenumber)
if save_images:
this_obj_raw_images[camn].append(
(raw_im, im_coords))
this_obj_mean_images[camn].append(mean_im)
this_obj_absdiff_images[camn].append(absdiff_im)
this_obj_morphed_images[camn].append(morphed_im)
this_obj_morph_failures[camn].append(
morph_fail_because_multiple_blobs)
this_obj_im_coords[camn].append(im_coords)
this_obj_com_coords[camn].append((x0, y0))
this_obj_camn_pt_no[camn].append(orig_data2d_rownum)
if 0:
fname = "obj%05d_%s_frame%07d_pt%02d.png" % (
obj_id,
cam_id,
framenumber,
camn_pt_no,
)
plot_image_subregion(
raw_im,
mean_im,
absdiff_im,
roiradius,
fname,
im_coords,
view=filename2view[fmf.filename],
)
# Now, all the frames from all cameras for this obj_id
# have been gathered. Do a camera-by-camera analysis.
for camn in this_obj_absdiff_images:
cam_id = camn2cam_id[camn]
image_framenumbers = np.array(this_obj_framenumbers[camn])
if save_images:
raw_images = this_obj_raw_images[camn]
mean_images = this_obj_mean_images[camn]
absdiff_images = this_obj_absdiff_images[camn]
morphed_images = this_obj_morphed_images[camn]
morph_failures = np.array(this_obj_morph_failures[camn])
im_coords = this_obj_im_coords[camn]
com_coords = this_obj_com_coords[camn]
camn_pt_no_array = this_obj_camn_pt_no[camn]
all_framenumbers = np.arange(image_framenumbers[0],
image_framenumbers[-1] + 1)
com_coords = np.array(com_coords)
if do_rts_smoothing:
# Perform RTS smoothing on center-of-mass coordinates.
# Find first good datum.
fgnz = np.nonzero(~np.isnan(com_coords[:, 0]))
com_coords_smooth = np.empty(com_coords.shape,
dtype=np.float)
com_coords_smooth.fill(np.nan)
if len(fgnz[0]):
first_good = fgnz[0][0]
RTS_com_coords = com_coords[first_good:, :]
# Setup parameters for Kalman filter.
dt = 1.0 / fps
A = np.array(
[
[1, 0, dt, 0], # process update
[0, 1, 0, dt],
[0, 0, 1, 0],
[0, 0, 0, 1],
],
dtype=np.float,
)
C = np.array(
[[1, 0, 0, 0], [0, 1, 0, 0]
], # observation matrix
dtype=np.float,
)
Q = 0.1 * np.eye(4) # process noise
R = 1.0 * np.eye(2) # observation noise
initx = np.array(
[
RTS_com_coords[0, 0], RTS_com_coords[0, 1],
0, 0
],
dtype=np.float,
)
initV = 2 * np.eye(4)
initV[0, 0] = 0.1
initV[1, 1] = 0.1
y = RTS_com_coords
xsmooth, Vsmooth = adskalman.adskalman.kalman_smoother(
y, A, C, Q, R, initx, initV)
com_coords_smooth[first_good:] = xsmooth[:, :2]
# Now shift images
image_shift = com_coords_smooth - com_coords
bad_cond = np.isnan(image_shift[:, 0])
# broadcast zeros to places where no good tracking
image_shift[bad_cond, 0] = 0
image_shift[bad_cond, 1] = 0
shifted_morphed_images = [
shift_image(im, xy)
for im, xy in zip(morphed_images, image_shift)
]
results = flatten_image_stack(
image_framenumbers,
shifted_morphed_images,
im_coords,
camn_pt_no_array,
N=stack_N_images,
)
else:
results = flatten_image_stack(
image_framenumbers,
morphed_images,
im_coords,
camn_pt_no_array,
N=stack_N_images,
)
# The variable fno (the first element of the results
# tuple) is guaranteed to be contiguous and to span
# the range from the first to last frames available.
for (
fno,
av_im,
lowerleft,
orig_data2d_rownum,
orig_idx,
orig_idxs_in_average,
) in results:
# Clip image to reduce moment arms.
av_im[av_im <= final_thresh] = 0
fail_fit = False
fast_av_im = FastImage.asfastimage(
av_im.astype(np.uint8))
try:
(x0_roi, y0_roi, area, slope,
eccentricity) = fpc.fit(fast_av_im)
except realtime_image_analysis.FitParamsError as err:
fail_fit = True
this_morph_failures = morph_failures[
orig_idxs_in_average]
n_failed_images = np.sum(this_morph_failures)
n_good_images = stack_N_images - n_failed_images
if n_good_images >= stack_N_images_min:
n_images_is_acceptable = True
else:
n_images_is_acceptable = False
if fail_fit:
x0_roi = np.nan
y0_roi = np.nan
area, slope, eccentricity = np.nan, np.nan, np.nan
if not n_images_is_acceptable:
x0_roi = np.nan
y0_roi = np.nan
area, slope, eccentricity = np.nan, np.nan, np.nan
x0 = x0_roi + lowerleft[0]
y0 = y0_roi + lowerleft[1]
if 1:
for row in dest_table.iterrows(
start=orig_data2d_rownum,
stop=orig_data2d_rownum + 1):
row["x"] = x0
row["y"] = y0
row["area"] = area
row["slope"] = slope
row["eccentricity"] = eccentricity
row.update() # save data
if save_images:
# Display debugging images
fname = "av_obj%05d_%s_frame%07d.png" % (
obj_id,
cam_id,
fno,
)
if save_image_dir is not None:
fname = os.path.join(save_image_dir, fname)
raw_im, raw_coords = raw_images[orig_idx]
mean_im = mean_images[orig_idx]
absdiff_im = absdiff_images[orig_idx]
morphed_im = morphed_images[orig_idx]
raw_l, raw_b = raw_coords[:2]
imh, imw = raw_im.shape[:2]
n_ims = 5
if 1:
# increase contrast
contrast_scale = 2.0
av_im_show = np.clip(av_im * contrast_scale, 0,
255)
margin = 10
scale = 3
# calculate the orientation line
yintercept = y0 - slope * x0
xplt = np.array([
lowerleft[0] - 5,
lowerleft[0] + av_im_show.shape[1] + 5,
])
yplt = slope * xplt + yintercept
if 1:
# only send non-nan values to plot
plt_good = ~np.isnan(xplt) & ~np.isnan(yplt)
xplt = xplt[plt_good]
yplt = yplt[plt_good]
top_row_width = scale * imw * n_ims + (
1 + n_ims) * margin
SHOW_STACK = True
if SHOW_STACK:
n_stack_rows = 4
rw = scale * imw * stack_N_images + (
1 + n_ims) * margin
row_width = max(top_row_width, rw)
col_height = (n_stack_rows * scale * imh +
(n_stack_rows + 1) * margin)
stack_margin = 20
else:
row_width = top_row_width
col_height = scale * imh + 2 * margin
stack_margin = 0
canv = benu.Canvas(
fname,
row_width,
col_height + stack_margin,
color_rgba=(1, 1, 1, 1),
)
if SHOW_STACK:
for (stacki, s_orig_idx
) in enumerate(orig_idxs_in_average):
(s_raw_im,
s_raw_coords) = raw_images[s_orig_idx]
s_raw_l, s_raw_b = s_raw_coords[:2]
s_imh, s_imw = s_raw_im.shape[:2]
user_rect = (s_raw_l, s_raw_b, s_imw,
s_imh)
x_display = (stacki + 1) * margin + (
scale * imw) * stacki
for show in ["raw", "absdiff", "morphed"]:
if show == "raw":
y_display = scale * imh + 2 * margin
elif show == "absdiff":
y_display = 2 * scale * imh + 3 * margin
elif show == "morphed":
y_display = 3 * scale * imh + 4 * margin
display_rect = (
x_display,
y_display + stack_margin,
scale * raw_im.shape[1],
scale * raw_im.shape[0],
)
with canv.set_user_coords(
display_rect,
user_rect,
transform=cam_id2view[cam_id],
):
if show == "raw":
s_im = s_raw_im.astype(
np.uint8)
elif show == "absdiff":
tmp = absdiff_images[
s_orig_idx]
s_im = tmp.astype(np.uint8)
elif show == "morphed":
tmp = morphed_images[
s_orig_idx]
s_im = tmp.astype(np.uint8)
canv.imshow(s_im, s_raw_l, s_raw_b)
sx0, sy0 = com_coords[s_orig_idx]
X = [sx0]
Y = [sy0]
# the raw coords in red
canv.scatter(X,
Y,
color_rgba=(1, 0.5,
0.5, 1))
if do_rts_smoothing:
sx0, sy0 = com_coords_smooth[
s_orig_idx]
X = [sx0]
Y = [sy0]
# the RTS smoothed coords in green
canv.scatter(
X,
Y,
color_rgba=(0.5, 1, 0.5,
1))
if s_orig_idx == orig_idx:
boxx = np.array([
s_raw_l,
s_raw_l,
s_raw_l + s_imw,
s_raw_l + s_imw,
s_raw_l,
])
boxy = np.array([
s_raw_b,
s_raw_b + s_imh,
s_raw_b + s_imh,
s_raw_b,
s_raw_b,
])
canv.plot(
boxx,
boxy,
color_rgba=(0.5, 1, 0.5,
1),
)
if show == "morphed":
canv.text(
"morphed %d" %
(s_orig_idx - orig_idx, ),
display_rect[0],
(display_rect[1] +
display_rect[3] +
stack_margin - 20),
font_size=font_size,
color_rgba=(1, 0, 0, 1),
)
# Display raw_im
display_rect = (
margin,
margin,
scale * raw_im.shape[1],
scale * raw_im.shape[0],
)
user_rect = (raw_l, raw_b, imw, imh)
with canv.set_user_coords(
display_rect,
user_rect,
transform=cam_id2view[cam_id],
):
canv.imshow(raw_im.astype(np.uint8), raw_l,
raw_b)
canv.plot(
xplt, yplt,
color_rgba=(0, 1, 0,
0.5)) # the orientation line
canv.text(
"raw",
display_rect[0],
display_rect[1] + display_rect[3],
font_size=font_size,
color_rgba=(0.5, 0.5, 0.9, 1),
shadow_offset=1,
)
# Display mean_im
display_rect = (
2 * margin + (scale * imw),
margin,
scale * mean_im.shape[1],
scale * mean_im.shape[0],
)
user_rect = (raw_l, raw_b, imw, imh)
with canv.set_user_coords(
display_rect,
user_rect,
transform=cam_id2view[cam_id],
):
canv.imshow(mean_im.astype(np.uint8), raw_l,
raw_b)
canv.text(
"mean",
display_rect[0],
display_rect[1] + display_rect[3],
font_size=font_size,
color_rgba=(0.5, 0.5, 0.9, 1),
shadow_offset=1,
)
# Display absdiff_im
display_rect = (
3 * margin + (scale * imw) * 2,
margin,
scale * absdiff_im.shape[1],
scale * absdiff_im.shape[0],
)
user_rect = (raw_l, raw_b, imw, imh)
absdiff_clip = np.clip(absdiff_im * contrast_scale,
0, 255)
with canv.set_user_coords(
display_rect,
user_rect,
transform=cam_id2view[cam_id],
):
canv.imshow(absdiff_clip.astype(np.uint8),
raw_l, raw_b)
canv.text(
"absdiff",
display_rect[0],
display_rect[1] + display_rect[3],
font_size=font_size,
color_rgba=(0.5, 0.5, 0.9, 1),
shadow_offset=1,
)
# Display morphed_im
display_rect = (
4 * margin + (scale * imw) * 3,
margin,
scale * morphed_im.shape[1],
scale * morphed_im.shape[0],
)
user_rect = (raw_l, raw_b, imw, imh)
morphed_clip = np.clip(morphed_im * contrast_scale,
0, 255)
with canv.set_user_coords(
display_rect,
user_rect,
transform=cam_id2view[cam_id],
):
canv.imshow(morphed_clip.astype(np.uint8),
raw_l, raw_b)
if 0:
canv.text(
"morphed",
display_rect[0],
display_rect[1] + display_rect[3],
font_size=font_size,
color_rgba=(0.5, 0.5, 0.9, 1),
shadow_offset=1,
)
# Display time-averaged absdiff_im
display_rect = (
5 * margin + (scale * imw) * 4,
margin,
scale * av_im_show.shape[1],
scale * av_im_show.shape[0],
)
user_rect = (
lowerleft[0],
lowerleft[1],
av_im_show.shape[1],
av_im_show.shape[0],
)
with canv.set_user_coords(
display_rect,
user_rect,
transform=cam_id2view[cam_id],
):
canv.imshow(
av_im_show.astype(np.uint8),
lowerleft[0],
lowerleft[1],
)
canv.plot(
xplt, yplt,
color_rgba=(0, 1, 0,
0.5)) # the orientation line
canv.text(
"stacked/flattened",
display_rect[0],
display_rect[1] + display_rect[3],
font_size=font_size,
color_rgba=(0.5, 0.5, 0.9, 1),
shadow_offset=1,
)
canv.text(
"%s frame % 7d: eccentricity % 5.1f, min N images %d, actual N images %d"
% (
cam_id,
fno,
eccentricity,
stack_N_images_min,
n_good_images,
),
0,
15,
font_size=font_size,
color_rgba=(0.6, 0.7, 0.9, 1),
shadow_offset=1,
)
canv.save()
# Save results to new table
if 0:
recarray = np.rec.array(list_of_rows_of_data2d,
dtype=Info2DCol_description)
dest_table.append(recarray)
dest_table.flush()
dest_table.attrs.has_ibo_data = True
data_file.close()
fmf_fno = fmf_fnos[0]
found = (fmf, fmf_fno )
if found is None:
print 'no image data for frame timestamp %s cam_id %s'%(
repr(frame_timestamp),cam_id)
continue
fmf, fmf_fno = found
image, fmf_timestamp = fmf.get_frame( fmf_fno )
mean_image = fmf.get_mean_for_timestamp(fmf_timestamp)
coding = fmf.get_format()
if imops.is_coding_color(coding):
image = imops.to_rgb8(coding,image)
mean_image = imops.to_rgb8(coding,mean_image)
else:
image = imops.to_mono8(coding,image)
mean_image = imops.to_mono8(coding,mean_image)
xy = (int(round(frame2d[idx]['x'])),
int(round(frame2d[idx]['y'])))
maxsize = (fmf.get_width(), fmf.get_height())
# Accumulate cropped images. Note that the region
# of the full image that the cropped image
# occupies changes over time as the tracked object
# moves. Thus, averaging these cropped-and-shifted
# images is not the same as simply averaging the
# full frame.
roiradius = 25
warnings.warn('roiradius hard-coded to %d: could be set '
def get_similar_direction_graphs(
fmf,
frame,
use="raw",
return_early=False,
debug_line_finding=False,
aspect_ratio=1.0,
direction_eps_radians=None,
chess_preview=False,
ncorners_h=None,
ncorners_v=None,
):
bg_im, tmp = fmf.get_frame(0)
bg_im = imops.to_mono8(fmf.get_format(), bg_im)
imnx_orig, tmp = fmf.get_frame(frame)
imnx_orig = imops.to_mono8(fmf.get_format(), imnx_orig)
imnx_no_bg = get_non_background(imnx_orig, bg_im)
imnx_binary = binarize(imnx_no_bg)
imnx_rawbinary = binarize(imnx_orig)
if use == "no_bg":
imnx_use = imnx_no_bg
elif use == "binary":
imnx_use = imnx_binary
elif use == "rawbinary":
imnx_use = imnx_rawbinary
elif use == "raw":
imnx_use = imnx_orig
else:
raise ValueError("unknown use image")
if chess_preview:
pylab.imshow(imnx_use)
pylab.title("preview of chessboard finding image - close to continue")
pylab.show()
x, y = extract_corners(imnx_use, ncorners_h=ncorners_h, ncorners_v=ncorners_v)
if len(x) == 0:
raise ValueError("extract corners found no corners. cannot continue")
if chess_preview:
pylab.imshow(imnx_use)
pylab.plot(x, y, "wo")
pylab.title("found corners")
pylab.show()
show_clusters_frame = frame
graph, nodes = points2graph(
x, y, show_clusters=debug_line_finding, show_clusters_frame=show_clusters_frame, aspect_ratio=aspect_ratio
)
if return_early:
print "returning early with entire super-graph"
similar_direction_graphs = [graph]
return (similar_direction_graphs, imnx_orig, imnx_no_bg, imnx_binary, imnx_use, imnx_rawbinary)
similar_direction_graphs = [] # collection of all the graphs of similar directions
for node in nodes:
subgraph = find_subgraph_similar_direction(
graph, source=node, direction_eps_radians=direction_eps_radians, already_done=similar_direction_graphs
)
if subgraph is not None:
similar_direction_graphs.append(subgraph)
if 0:
print "backwards search?!"
# do again to get other direction
subgraph = find_subgraph_similar_direction(
graph, source=node, direction_eps_radians=direction_eps_radians, already_done=similar_direction_graphs
)
if subgraph is not None:
similar_direction_graphs.append(subgraph)
# filter to force 2 or more edges in graph
similar_direction_graphs = [graph for graph in similar_direction_graphs if len(graph.edges()) >= 2]
if debug_line_finding:
print "edges in each subgraph (frame %d)" % frame, "-" * 40
for graph in similar_direction_graphs:
print graph.edges()
print "-" * 40
print
return (similar_direction_graphs, imnx_orig, imnx_no_bg, imnx_binary, imnx_use, imnx_rawbinary)