def main():
args = parse_args()
infile = InputFile(args.input_file)
infile.channel = args.c
total_byte_size = np.asscalar(np.prod(infile.shape) * infile.dtype.itemsize)
bigtiff = total_byte_size > 2 ** 31 - 1
n = int(total_byte_size // (psutil.virtual_memory().available * 0.9)) + 1
try:
os.remove(args.output_file)
except FileNotFoundError:
pass
curr_z = 0
part_height = infile.nfrms // n
end_loop = False
while True:
end_z = curr_z + part_height
if end_z >= infile.shape[0]:
end_z = infile.shape[0]
end_loop = True
logger.info('loading \tz=[{}:{}]'.format(curr_z, end_z))
img = infile[curr_z:end_z]
logger.info('saving to {}'.format(args.output_file))
tiff.imsave(args.output_file, img, append=True, bigtiff=bigtiff)
curr_z = end_z
if end_loop:
break
def main():
args = parse_args()
infile = InputFile(args.input_file)
if args.channel is not None:
infile.channel = args.channel
total_byte_size = np.asscalar(np.prod(infile.shape) * infile.dtype.itemsize)
bigtiff = total_byte_size > 2 ** 31 - 1
ram = psutil.virtual_memory().available * 0.5
n_of_parts = ceil(total_byte_size / ram)
try:
os.remove(args.output_file)
except FileNotFoundError:
pass
curr_z = 0
part_height = infile.nfrms // n_of_parts
end_loop = False
mip = np.zeros(infile.shape[1:], dtype=infile.dtype)
tiff.imsave(args.output_file, mip)
while True:
end_z = curr_z + part_height
if end_z >= infile.shape[0]:
end_z = infile.shape[0]
end_loop = True
logger.info('loading \tz=[{}:{}]'.format(curr_z, end_z))
img = infile[curr_z:end_z]
logger.info('Computing MIP...')
mip = np.maximum(np.max(img, axis=0), mip)
del img
curr_z = end_z
if end_loop:
break
logger.info('saving to {}'.format(args.output_file))
if args.channel is None and infile.nchannels > 1:
mip = np.moveaxis(mip, -3, -1)
tiff.imsave(args.output_file, mip)
def main():
args = parse_args()
infile = InputFile(args.input_file)
if args.channel != -1:
infile.channel = args.channel
os.makedirs(args.output_directory, exist_ok=True)
n_of_digits = math.ceil(math.log10(infile.nfrms))
output_filename_fmt = '{:0' + str(n_of_digits) + '}.tiff'
for z in range(infile.nfrms):
a = infile[z]
if infile.nchannels != 1 and infile.channel == -1:
a = np.moveaxis(a, -3, -1)
output_filename = os.path.join(args.output_directory,
output_filename_fmt.format(z))
logger.info('saving to {}'.format(output_filename))
tiff.imsave(output_filename, a, compress=args.compression)