def score(self, ref_path, hyp_path):
from sklearn.metrics import f1_score
ref = skv.vread(ref_path)
hyp = skv.vread(hyp_path)
score = f1_score(
np.any(ref, axis=-1).flatten(),
np.any(hyp, axis=-1).flatten())
print(score)
def _calc_psnr(r_vid, c_vid):
# calculate PSNR
np_r_vid = sk.vread(r_vid)
np_c_vid = sk.vread(c_vid)
psnr = PSNR(data_range=255).calc_video(np_r_vid, np_c_vid)
return psnr
def _calc_ssim(r_vid, c_vid):
# calculate SSIM Guassian
np_r_vid = sk.vread(r_vid)
np_c_vid = sk.vread(c_vid)
ssim = SSIM(data_range=255, multichannel=True,
gaussian_weights=True).calc_video(np_r_vid, np_c_vid)
return ssim
def _get_video_batch(self, x_paths, as_grey=False, reduce_frames=True, verbose=False):
"""
Returns ndarray of shape (batch_size, num_frames, width, height, channels).
If as_grey, then channels dimension is squeezed out.
"""
videos = []
failed = []
for row in x_paths.itertuples():
filepath = row.filepath
obf_id = row.Index
try:
# load
video = skv.vread(filepath, as_grey=as_grey)
except:
try:
# try again
print("trying again to load id:\t", obf_id)
video = skv.vread(filepath, as_grey=as_grey)
except:
if verbose:
print("FAILED TO LOAD:", filepath)
print("faild to load id:\t", obf_id)
failed.append(obf_id)
first_row = False
x_paths_removed_fault = x_paths.drop(row.Index)
x_paths_removed_fault = pd.concat([x_paths_removed_fault, \
x_paths_removed_fault.ix[np.random.random_integers(0, self.batch_size -2, 1)]])
return self._get_video_batch(x_paths_removed_fault, as_grey, reduce_frames, verbose)
# fill video if neccessary
if video.shape[0] < self.num_frames:
video = self._fill_video(video)
# reduce
if reduce_frames:
step_size = int(video.shape[0] / 90)
frames = np.arange(random.randint(0,step_size-1), video.shape[0], step_size)
try:
video = video[frames, :, :] #.squeeze()
videos.append(video)
except IndexError:
if verbose:
print("FAILED TO REDUCE:", filepath)
print("failed to reduce id:\t", obf_id)
failed.append(obf_id)
return np.array(videos), failed
def readImages(ims, thresholdParam=0.95):
images = skv.vread(ims)
count = 0
temp = images[0]
temp = cv.cvtColor(temp, cv.COLOR_BGR2GRAY)
numberOfFrames, a, b, c = images.shape
finalImages = np.zeros((numberOfFrames, a, b))
finalImages[0] = temp
d = []
for image in images:
image = cv.cvtColor(image, cv.COLOR_BGR2GRAY)
score = m.compare_ssim(temp, image)
d.append(score)
if score < thresholdParam:
finalImages[count] = image
temp = image
count += 1
finalImages = finalImages[:count]
del images, temp, d
return finalImages, count
def data_aug(video_path, num_of_aug, aug_dict=data_aug_dict):
"""
Augment all frames in the video and creates num_of_aug new videos.
:param video_path: Path to video
:param num_of_aug: Number of different augmentations
:param aug_dict: Augmentation dictionary
:return: New videos
"""
new_videos = []
video = vread(video_path)
for aug_i in range(num_of_aug): # run over augmentations
str_data_aug = 'data_aug_' + str(aug_i)
new_video = []
# run over frames
for frame_idx in range(video.shape[0]): # frames
frame = video[frame_idx, :, :, :]
aug_frame = aug_dict[str(str_data_aug)](frame)
# # for debug:
# plt.figure()
# plt.imshow(aug_frame)
# plt.show()
# #
new_video.append(aug_frame)
new_video = np.stack(new_video)
new_videos.append(new_video)
return new_videos
def compressvideo(filepath : str, output: str, ylabelval: float, xkey: str, ykey: str):
# Reading
vid = vio.vread(filepath)
# Writing
with h5py.File(output, 'w') as wfile:
wfile.create_dataset(xkey, data=vid)
wfile.create_dataset(ykey, data=ylabelval)
def GetFrames(fileName, skipLength=1, debug=False):
'''
Get video frames after skipping
Args:
fileName: full fileName to read
skipLength: Number of skips to perform
Returns:
Numpy array of frames
'''
if debug:
print "Started creating Frame List for file", fileName
try:
frameList = vread(fileName)
except:
return None
if debug:
print 'The video shape is', frameList.shape
print 'The array type is', frameList.dtype
frameList = frameList[range(0, frameList.shape[0], skipLength), :, :, :]
# Skip frames according to skipLength
if debug:
print 'The new shape after skipping', skipLength, 'is', frameList.shape
print "Finished creating Frame List"
return frameList
def __getitem__(self, index):
""" Get a sample from the dataset
"""
if self.videos is not None:
# If dataset is preloaded
video = self.videos[index]
label = self.labels[index]
else:
# If on-demand data loading
video_fn, label = self.filenames[index]
video = vp.vread(video_fn)
video = np.reshape(video, (video.shape[3], video.shape[0],
video.shape[1], video.shape[2]))
if self.spatial_transform is not None:
self.spatial_transform.randomize_parameters()
video = video.reshape((video.shape[1], video.shape[2],
video.shape[3], video.shape[0]))
clip = [
self.spatial_transform(Image.fromarray(img)) for img in video
]
video = torch.stack(clip, 0).permute(1, 0, 2, 3)
# return video and label
return video, label
def load_frames(idx, video_files, data_mode, data_path, zips_list,
in_which_zip):
"""Load the video frames"""
if data_mode == 'json':
vid_path = video_files[idx]
if not os.path.isabs(vid_path):
vid_path = os.path.join(data_path, vid_path)
# Deal with multiple possible extensions
path_base, path_ext = os.path.splitext(vid_path)
if path_ext == '.csv':
vid_path = path_base + '.mp4'
elif path_ext == '':
vid_path = vid_path + '.mp4'
frames = vread(vid_path)
elif data_mode == 'npz':
vid_path = os.path.dirname(video_files[idx])
right_zip = zips_list[in_which_zip[idx]]
zip_path = os.path.join(data_path, right_zip) # type: str
zip_path = zip_path.split('_meta.zip')[0] + '_video.zip'
with zipfile.ZipFile(zip_path) as my_zip:
frames = np.zeros((100, 100, 100, 3), dtype=np.uint8)
for i in range(100):
img_path = os.path.join(vid_path, '%04d.jpg' % i)
img_path = os.path.normpath(img_path).replace('\\', '/')
file = my_zip.read(img_path)
image = np.array(Image.open(BytesIO(file), ))
image = np.dstack((image, image, image))
frames[i, ...] = image
else:
raise Exception('Data mode must be either json or npz')
return frames
def __getitem__(self, index):
"""
Args:
index (int): Index
Returns:
tuple: (image, target) where target is class_index of the target class.
"""
path = self.data[index]['video']
clip_name = path.rstrip().split('/')[-1].split('.')[0]
try:
clip_numpy = vp.vread(path)
except:
print(path)
raise
n_frames = clip_numpy.shape[0]
frame_indices = [x for x in range(n_frames)]
if self.temporal_transform is not None:
frame_indices = self.temporal_transform(frame_indices)
# clip = [Image.fromarray(clip_numpy[i]) for i in frame_indices]
clip = [clip_numpy[i] for i in frame_indices]
# path = self.data[index]['video']
#
# frame_indices = self.data[index]['frame_indices']
# clip = self.loader(path, frame_indices)
if self.spatial_transforms is not None:
self.spatial_transforms[self.annotationDict[clip_name]].randomize_parameters()
clip = [self.spatial_transforms[self.annotationDict[clip_name]](img) for img in clip]
clip = torch.stack(clip, 0).permute(1, 0, 2, 3)
target = self.data[index]
if self.target_transform is not None:
target = self.target_transform(target)
return clip, target, path
def extract(video_path, positions):
if not isinstance(positions, (list, tuple)):
raise RuntimeError('expect list or tuple, get {}.'.format(
type(positions)))
capture = cv2.VideoCapture(video_path)
frames = []
for pos in positions:
total_len = capture.get(cv2.CAP_PROP_FRAME_COUNT) / capture.get(
cv2.CAP_PROP_FPS)
if pos >= total_len:
continue
capture.set(cv2.CAP_PROP_POS_MSEC, pos * 1000)
ok, img = capture.read()
if not ok:
img = vread(video_path)[math.floor(
capture.get(cv2.CAP_PROP_FPS) * pos)]
img = cv2.cvtColor(img, cv2.COLOR_RGB2BGR)
# raise RuntimeError(video_path, pos)
if img.shape[0] > img.shape[1] > 224:
img = cv2.resize(img,
(224, round(img.shape[0] / img.shape[1] * 224)),
interpolation=cv2.INTER_CUBIC)
elif img.shape[1] > img.shape[0] > 224:
img = cv2.resize(img,
(round(img.shape[1] / img.shape[0] * 224), 224),
interpolation=cv2.INTER_CUBIC)
frames.append(img)
capture.release()
return frames
def file_check(label_path):
for video in os.listdir(label_path):
try:
vid = io.vread(os.path.join(label_path, video))
except:
print("video: {} in class: {} doesn't open".format(video, label_path))
print('Finished {}'.format(label_path))
def predict(data_dir, output_dir, checkpoint, batch_size):
in_place, output_video_t = build_forward(INPUT_SIZE, NUM_FRAMES,
tf.estimator.ModeKeys.PREDICT)
saver = tf.train.Saver()
with tf.Session() as sess:
try:
saver.restore(sess, 'weights/{}_best'.format(checkpoint))
except Exception as e:
print('{}: {} is not a valid checkpoint to restore from.'.format(e, checkpoint))
prediction_folder = os.path.join(output_dir, 'output')
# check that prediction folder exists
if not os.path.exists(prediction_folder):
os.mkdir(prediction_folder)
input_videos = glob.glob(os.path.join(data_dir, '/*.mp4'))
for ivf in input_videos:
in_video = vidio.vread(ivf)
out_video = sess.run([output_video_t],
{ in_place : in_video[:NUM_FRAMES, :INPUT_SIZE, :INPUT_SIZE] })
base_filename = ivf.split('/')[-1]
out_filename = os.path.join(prediction_folder, base_filename)
writer = vidio.FFmpegWriter(out_filename)
for i in range(out_video.shape[0]):
writer.writeFrame(out_video[i,...])
writer.close()
def _get_frames(self, index):
# return frames (t, H, W ,C)
# numpy video data
video_frames = sk.vread(self.video_file_names[index])
return video_frames
def __getitem__(self, index):
""" Get a sample from the dataset
"""
if self.videos is not None:
# If dataset is preloaded
video = self.videos[index]
label = self.labels[index]
else:
# If on-demand data loading
video_fn, label = self.filenames[index]
video = vp.vread(video_fn)
if self.spatial_transform is not None:
self.spatial_transform.randomize_parameters()
if self.resize is not None:
video = [
cv2.resize(img, literal_eval(self.resize)) for img in video
]
clip = [
self.spatial_transform(Image.fromarray(img)) for img in video
]
video = torch.stack(clip, 0).permute(1, 0, 2, 3)
self.logger.debug((video.shape, label))
# return video and label
return video, label
def extract_frames(fname):
meta = skvio.ffprobe(fname)
fps = int(meta['video']['@r_frame_rate'].split('/')[0])
size = (int(meta['video']['@width']), int(meta['video']['@height']))
assert fps > 0, 'Broken video %s' % fname
frames = list(skvio.vread(fname))
return frames, fps, size
def process_file(filepath):
filename = os.path.basename(filepath)
video = vreader.vread(filepath)
metadata = {
'total_frames': video.shape[0],
'rows': video.shape[1],
'cols': video.shape[2],
'channels': video.shape[3]
}
extras = vreader.ffprobe(filepath).get('video', {})
metadata['frame_rate'] = extras.get('@avg_frame_rate', '')
metadata['duration'] = extras.get('@duration', '')
payload = {'video_id': filename}
# now we would send each video in frames
for idx, frame in enumerate(video):
metadata['id'] = idx
img_str = base64.b64encode(frame.flatten()).decode(
'utf8') # decode to plane string
payload['data'] = img_str
payload['metadata'] = metadata
print('%s, sending frame: %s' % (filename, idx))
producer.send(TOPIC, json.dumps(payload).encode('utf8'))
print('%s, sent frame: %s' % (filename, idx))
#once done move the file to
print('%s, moving to completed folder' % (filename, ))
shutil.move(filepath, COMPLETED_DIR)
def __init__(self):
filename = 'serve.mp4'
height = 24
width = 40
self.action_space = spaces.Discrete(2)
self.observation_space = spaces.Box(0, 1, [height * width])
self._seed()
#self._reset()
self.__videodata = None
try:
self.__videodata = skio.vread(filename)
except FileNotFoundError:
print(filename + ' could not be opened')
return False
with open(filename.split(".")[0] + ".labels",
encoding='utf-8') as file:
l = file.readlines()
self.__labels = [x.strip() for x in l]
self.__nb_frames, _, _, _ = self.__videodata.shape
self.__w = width
self.__h = height
self.__index = 0
self.__correct = 0
self.__action = 1
def visualize(video: str, subtitle: str):
video = vread(video)
ax = plt.subplot(111)
ax.spines["top"].set_visible(False)
ax.spines["bottom"].set_visible(False)
ax.spines["right"].set_visible(False)
ax.spines["left"].set_visible(False)
plt.axis('off')
text = plt.text(0.5,
0.1,
"",
ha='center',
va='center',
transform=ax.transAxes,
fontdict={
'fontsize': 14,
'color': 'yellow',
'fontweight': 500
})
text.set_path_effects([
path_effects.Stroke(linewidth=3, foreground='black'),
path_effects.Normal()
])
subs = subtitle.split()
inc = max(len(video) / (len(subs) + 1), 0.01)
img = None
for i, frame in enumerate(video):
gray = cv2.cvtColor(frame, cv2.COLOR_BGR2GRAY)
detected = detector(gray, 1)
shape = predictor(
gray, detected[0]
) # detected[0] ensures only first detected face is chosen for further processing
shape = face_utils.shape_to_np(
shape
) # shape predictor outputs 68 coordinate pairs, each responsible for a particular landmark
mouth_points = shape[48:68]
hull = cv2.convexHull(mouth_points) # draw convex hull around mouth
frame = cv2.drawContours(frame, [hull], -1, (100, 255, 0), 3)
# cv2.imshow('test', frame)
# cv2.waitKey(10)
video[i] = frame
for i, frame in enumerate(video):
sub = " ".join(subs[:int(i / inc)])
text.set_text(sub)
if img is None:
img = plt.imshow(frame)
else:
img.set_data(frame)
plt.pause(1 / 250)
plt.show()
def load_reduce_pipeline(path):
vid = skv.vread(path)
vid = block_reduce(vid, (1, 5, 5, 1), func=np.max)
vid = vid[:, :, 100:324, :]
return np.pad(vid, ((0, 0), (4, 4), (0, 0), (0, 0)),
"constant",
constant_values=(0))
def extract_video(video_path):
from skvideo.io import vread
try:
ret = vread(video_path)
except Exception as e:
print("reading failed on ", video_path, e)
ret = np.array([])
return ret
def _get_video_batch(self,
x_paths,
is_training,
as_grey=False,
reduce_frames=True,
verbose=False,
y=None):
"""
Returns ndarray of shape (batch_size, num_frames, width, height, channels).
If as_grey, then channels dimension is squeezed out.
"""
videos = []
#failed = []
i = 0
for f in x_paths:
filepath = 'micro/' + f
assert x_paths[i] == f
# load
video = skv.vread(filepath, as_grey=as_grey)
# fill video if neccessary
if video.shape[0] < self.num_frames:
video = self._fill_video(video)
#videos.append(video)
# reduce
if reduce_frames:
frames = np.arange(0, video.shape[0], 2)
try:
video = video[frames, :, :] #.squeeze()
videos.append(self.augment(video))
#print(video.shape)
#videos.append(video)
except IndexError:
if verbose:
print("FAILED TO REDUCE: {filepath}")
print("id:\t{obf_id}")
failed.append(obf_id)
else:
#videos.append(video)
if is_training:
if (y[i, self.classmap['blank']] == 1
or y[i, self.classmap['duiker']] == 1
or y[i, self.classmap['other (primate)']] == 1
or y[i, self.classmap['human']] == 1):
videos.append(video)
else:
videos.append(self.augment(video.astype(np.float32)))
else:
videos.append(video)
i += 1
return np.array(videos)
def try_load_avi(the_path):
vid = skvid.vread(the_path)
print('asdf')
pass
# the_path = '/fast/gabras/dots/dataset_avi/train/scale/14023.avi'
# try_load_avi(the_path)
def load_video(vid_path):
try:
video = vread(vid_path)
return video
except:
log_fail = open('fail_crop1.txt','a')
log_fail.write(vid_path + '\n')
log_fail.close()
return []
def main():
# parse the arguments
parser = argparse.ArgumentParser(description='Retouch video partially.')
parser.add_argument('--src_path',
type=str,
default='../originals',
help='source path')
parser.add_argument('--dst_path',
type=str,
default='../retouch_temporal_videos',
help='destination path')
parser.add_argument('--intensity',
type=str,
default='strong',
help='strong or weak')
args = parser.parse_args()
SRC_PATH = args.src_path
DST_PATH = args.dst_path
INTENSITY = args.intensity
methods = ["blur", "median", "noise"]
fnames = glob(join(SRC_PATH, "*.mp4"))
for fname in fnames:
vOriginal = np.array(vio.vread(fname, inputdict={}))
vRetouched = np.zeros(vOriginal.shape)
fn, w, h, c = vOriginal.shape
start_fn = int(fn / 3)
end_fn = int(fn * 2 / 3)
for method in methods:
print("processing {}".format(
join(DST_PATH, INTENSITY, method,
fname.split("\\")[-1])))
for idx in range(fn):
if idx >= start_fn and idx <= end_fn:
vRetouched[idx] = manipulate(vOriginal[idx],
method,
intensity=INTENSITY)
else:
vRetouched[idx] = vOriginal[idx]
write_option['-b:v'] = "800k"
writer = vio.FFmpegWriter(filename=join(DST_PATH, INTENSITY,
method,
fname.split("\\")[-1]),
inputdict={'-r': fps},
outputdict=write_option)
for frame in vRetouched:
writer.writeFrame(frame)
writer.close()
def load_video(vid_path):
try:
video = vread(vid_path)
return video
except:
log_fail = open('fail_crop1.txt', 'a')
log_fail.write(vid_path + '\n')
log_fail.close()
return []
def loadDicom(self, path):
if path is None:
return
start_time = time.time()
self.image_path = path
self.image_dir = osp.dirname(osp.abspath(path))
self.image_suffix = osp.splitext(path)[1]
if str.lower(self.image_suffix) in ['.mp4', '.avi', '.flv', '.wmv']:
img_nda = skio.vread(path)
img_nda = img_nda.astype('float32')
self.image_type = 'video'
self._channel = img_nda.shape[3]
self._spacing = (1, 1, 1)
self._dims = (img_nda.shape[1], img_nda.shape[0], img_nda.shape[2])
print(img_nda.shape)
output = self.numpy_array_as_vtk_image_data(img_nda)
else:
img_itk = sitk.ReadImage(path)
spacing = img_itk.GetSpacing()
dims = img_itk.GetSize()
channel = img_itk.GetNumberOfComponentsPerPixel()
frame_count = 1 if len(dims) == 2 else dims[2]
spacing_z = 1 if len(dims) == 2 else spacing[2]
self._dims = (dims[0], dims[1], frame_count)
self._spacing = (spacing[0], spacing[1], spacing_z)
self._channel = channel
self.image_type = 'image' if frame_count == 1 else 'volume'
img_nda = sitk.GetArrayFromImage(img_itk)
img_nda = img_nda.astype('float32')
importer = vtk.vtkImageImport()
importer.SetDataScalarTypeToFloat()
importer.SetNumberOfScalarComponents(self._channel)
importer.SetDataExtent(0, self._dims[0] - 1, 0, self._dims[1] - 1,
0, self._dims[2] - 1)
importer.SetWholeExtent(0, self._dims[0] - 1, 0, self._dims[1] - 1,
0, self._dims[2] - 1)
importer.SetDataSpacing(self._spacing[0], self._spacing[1],
self._spacing[2])
importer.CopyImportVoidPointer(img_nda, img_nda.nbytes)
importer.Update()
output = importer.GetOutput()
# print(output)
self.image_data.DeepCopy(output)
print("---laod dicom: %s seconds ---" % (time.time() - start_time))
print("image dims ", self._dims)
print("image spacing ", self._spacing)
print("image channel ", self._channel)
# print('load image info:')
# print(output)
return self.image_data
def read_video(path, face_predictor_path, verbose=False):
if verbose:
print("loading: " + path)
video = vread(path)
frames = np.array([frame for frame in video])
detector = dlib.get_frontal_face_detector()
predictor = dlib.shape_predictor(face_predictor_path)
mouth_video = get_frames_mouth(detector, predictor, frames)
return np.array(mouth_video)
def load(fname: str) -> np.ndarray:
vid = skvio.vread(fname)
n, h, w, depth = vid.shape
if depth != 3:
print('You need to provide a colored video!')
sys.exit(2)
log.info('loaded video with %d frames and resulution %d, %d', n, h, w)
return vid
def write_video_tf_record(video_path,
video_name,
video_class,
tfwriter,
error_files,
success_file,
format=".mp4",
num_channels=3,
num_frames_keep=None):
"""Write video to _tf_record file
:param video_path: Path of the video, string
:param video_name: name of the video file
:param video_class: string, class of video
:param tfwriter: tf.python_io.TFRecordWriter() object
:param num_channels: integer, specifies number of video channels, 3 for RGB by default
"""
try:
vid = sk.vread(video_path)
except:
print('RUNTIME ERROR')
with open(error_files, 'a') as f:
f.write(video_path)
f.write("\n")
f.close()
return
#import ipdb;
#ipdb.set_trace()
num_frames_total = vid.shape[0]
height = vid.shape[1]
width = vid.shape[2]
# make list of frame indexes to keep
if (num_frames_keep is not None):
num_frames = num_frames_keep
frame_list = np.linspace(0,
num_frames_total - 1,
num=num_frames,
dtype='int')
video_np = vid[frame_list, :, :, :]
else:
num_frames = num_frames_total
video_np = vid
video_string = video_np.tobytes() #convert from np array to bytes array
example = build_tf_example_basic(video_string, str.encode(video_name),
height, width, video_class, num_frames)
tfwriter.write(example.SerializeToString())
with open(success_file, 'a') as f:
f.write(video_path + "\n")
f.close()
return
def __getitem__(self, index):
annotation = self.annotation[index]
video_path = annotation['path']
clazz = annotation['class']
metadata = ffprobe(video_path)
duration = float(metadata["video"]["@duration"])
output_parameter = self.base_parameter
if self.clip_duration > 0:
sta = int(random() * max((duration - self.clip_duration), 0.))
output_parameter.update({
"-ss": "{}".format(sta),
"-t": "{}".format(min(self.clip_duration, duration - sta))
})
video_data = vread(video_path, outputdict=output_parameter)
if self.transform:
video_data = self.transform(video_data)
return video_data, clazz