if not os.path.exists(weights_path):
os.makedirs(weights_path)
if not os.path.exists(training_output_path):
os.makedirs(training_output_path)
if not os.path.exists(dir_output):
os.makedirs(dir_output)
if not os.path.exists(dir_temp):
os.makedirs(dir_temp)
nvideo = len(list_Exp_ID) # number of videos used for cross validation
# Get and check the dimensions of all the videos
list_Dimens = np.zeros((nvideo, 3), dtype='uint16')
for (eid, Exp_ID) in enumerate(list_Exp_ID):
h5_video = os.path.join(dir_video, Exp_ID + '.h5')
h5_file = h5py.File(h5_video, 'r')
dset = find_dataset(h5_file)
list_Dimens[eid] = h5_file[dset].shape
h5_file.close()
nframes = np.unique(list_Dimens[:, 0])
Lx = np.unique(list_Dimens[:, 1])
Ly = np.unique(list_Dimens[:, 2])
if len(Lx) * len(Ly) != 1:
ValueError(
'''The lateral dimensions of all the training videos must be the same in this version.
Use another version if training videos have different dimensions''')
nframes = nframes.min()
rows = Lx[0]
cols = Ly[0]
rowspad = math.ceil(rows / 8) * 8 # size of the network input and output
def preprocess_video_online(dir_video:str, Exp_ID:str, Params:dict, frames_init=10**6,
dir_network_input:str = None, useSF=False, useTF=True, useSNR=True, \
med_subtract=False, update_baseline=False, prealloc=True, display=True):
'''Pre-process the registered video "Exp_ID" in "dir_video" into an SNR video "network_input".
The process includes spatial filter, temporal filter, and SNR normalization. Each step is optional.
The function does some preparations, including pre-allocating memory space (optional), FFT planing,
and setting filter kernels, before loading the video.
Inputs:
dir_video (str): The folder containing the input video.
Each file must be a ".h5" file.
The video dataset can have any name, but cannot be under any group.
Exp_ID (str): The filer name of the input video.
Params (dict): Parameters for pre-processing.
Params['gauss_filt_size'] (float): The standard deviation of the spatial Gaussian filter in pixels
Params['Poisson_filt'] (1D numpy.ndarray of float32): The temporal filter kernel
Params['num_median_approx'] (int): Number of frames used to compute
the median and median-based standard deviation
Params['nn'] (int): Number of frames at the beginning of the video to be processed.
The remaining video is not considered a part of the input video.
frames_init (int, default to a very large number): Median and median-based standard deviation are
calculate from the first "frames_init" frames (before temporal filtering) of the video
dir_network_input (str, default to None): The folder to save the SNR video (network_input) in hard drive.
If dir_network_input == None, then the SNR video is not stored in hard drive
useSF (bool, default to True): True if spatial filtering is used.
useTF (bool, default to True): True if temporal filtering is used.
useSNR (bool, default to True): True if pixel-by-pixel SNR normalization filtering is used.
med_subtract (bool, default to False): True if the spatial median of every frame is subtracted before temporal filtering.
Can only be used when spatial filtering is not used.
update_baseline (bool, default to False): True if the median and median-based std is updated every "frames_init" frames.
prealloc (bool, default to True): True if pre-allocate memory space for large variables.
Achieve faster speed at the cost of higher memory occupation.
Outputs:
network_input (numpy.ndarray of float32, shape = (T,Lx,Ly)): the SNR video obtained after pre-processing.
The shape is (T,Lx,Ly), where T is shorter than T0 due to temporal filtering,
and Lx and Ly are Lx0 and Ly0 padded to multiples of 8, so that the images can be process by the shallow U-Net.
start (float): the starting time of the pipline (after the data is loaded into memory)
In addition, the SNR video is saved in "dir_network_input" as a "(Exp_ID).h5" file containing a dataset "network_input".
'''
nn = Params['nn']
if useSF:
gauss_filt_size = Params['gauss_filt_size']
Poisson_filt = Params['Poisson_filt']
# num_median_approx = Params['num_median_approx']
h5_video = os.path.join(dir_video, Exp_ID + '.h5')
h5_file = h5py.File(h5_video, 'r')
dset = find_dataset(h5_file)
(nframes, rows, cols) = h5_file[dset].shape
# Make the lateral number of pixels a multiple of 8, so that the CNN can process them
rowspad = math.ceil(rows / 8) * 8
colspad = math.ceil(cols / 8) * 8
# Only keep the first "nn" frames to process
nframes = min(nframes, nn)
if useSF:
# lateral dimensions slightly larger than the raw video but faster for FFT
rows1 = cv2.getOptimalDFTSize(rows)
cols1 = cv2.getOptimalDFTSize(cols)
if display:
print(rows, cols, nn, '->', rows1, cols1, nn)
start_plan = time.time()
# if the learned wisdom files have been saved, load them. Otherwise, learn wisdom later
Length_data = str((nn, rows1, cols1))
cc = load_wisdom_txt('wisdom\\' + Length_data)
if cc:
pyfftw.import_wisdom(cc)
# FFT planning
bb, bf, fft_object_b, fft_object_c = plan_fft(nn, (rows1, cols1),
prealloc)
if display:
end_plan = time.time()
print('FFT planning: {} s'.format(end_plan - start_plan))
# %% Initialization: Calculate the spatial filter and set variables.
mask2 = plan_mask2((rows, cols), (rows1, cols1), gauss_filt_size)
else:
bb = np.zeros((nframes, rowspad, colspad), dtype='float32')
fft_object_b = None
fft_object_c = None
bf = None
end_plan = time.time()
mask2 = None
# %% Initialization: Set variables.
if useTF:
leng_tf = Poisson_filt.size
nframesf = nframes - leng_tf + 1 # Number of frames after temporal filtering
else:
nframesf = nframes
frames_initf = frames_init - leng_tf + 1
if prealloc:
network_input = np.ones((nframesf, rowspad, colspad), dtype='float32')
med_frame2 = np.ones((rowspad, colspad, 2), dtype='float32')
else:
network_input = np.zeros((nframesf, rowspad, colspad), dtype='float32')
med_frame2 = np.zeros((rowspad, colspad, 2), dtype='float32')
# median_decimate = max(1,nframes//num_median_approx)
if display:
end_init = time.time()
print('Initialization: {} s'.format(end_init - end_plan))
# %% Load the raw video into "bb"
for t in range(nframes): # use this one to save memory
bb[t, :rows, :cols] = np.array(h5_file[dset][t])
h5_file.close()
if display:
end_load = time.time()
print('data loading: {} s'.format(end_load - end_init))
start = time.time(
) # The pipline starts after the video is loaded into memory
network_input = preprocess_complete_online(bb, (rowspad,colspad), network_input, med_frame2, \
Poisson_filt, mask2, bf, fft_object_b, fft_object_c, useSF, useTF, useSNR, \
med_subtract, update_baseline, frames_initf, frames_init, prealloc, display)
if display:
end = time.time()
print('total per frame: {} ms'.format((end - start) / nframes * 1000))
# if "dir_network_input" is not None, save network_input to an ".h5" file
if dir_network_input:
f = h5py.File(os.path.join(dir_network_input, Exp_ID + ".h5"), "w")
f.create_dataset("network_input", data=network_input)
f.close()
if display:
end_saving = time.time()
print('Network_input saving: {} s'.format(end_saving - end))
return network_input, start