exec_postprocessingΒΆ
This section contains the exec_postprocessing script.
Download file: exec_postprocessing.py
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# (C) 2016 Elettra - Sincrotrone Trieste S.C.p.A.. All rights reserved. #
# #
# #
# This file is part of STP-Core, the Python core of SYRMEP Tomo Project, #
# a software tool for the reconstruction of experimental CT datasets. #
# #
# STP-Core is free software: you can redistribute it and/or modify it #
# under the terms of the GNU General Public License as published by the #
# Free Software Foundation, either version 3 of the License, or (at your #
# option) any later version. #
# #
# STP-Core is distributed in the hope that it will be useful, but WITHOUT #
# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or #
# FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License #
# for more details. #
# #
# You should have received a copy of the GNU General Public License #
# along with STP-Core. If not, see <http://www.gnu.org/licenses/>. #
# #
###########################################################################
#
# Author: Francesco Brun
# Last modified: July, 8th 2016
#
from sys import argv, exit
from glob import glob
from os import linesep
from os.path import sep, basename, exists
from time import time
from multiprocessing import Process, Lock
# pystp-specific:
from stp_core.postprocess.postprocess import postprocess
from tifffile import imread, imsave
def _write_log(lock, fname, logfilename, cputime, iotime):
lock.acquire()
try:
# Print out execution time:
log = open(logfilename,"a")
log.write(linesep + "\t%s processed (CPU: %0.3f sec - I/O: %0.3f sec)." % (basename(fname), cputime, iotime))
log.close()
finally:
lock.release()
def _process(lock, int_from, int_to, files, outpath, convert_opt, crop_opt, outprefix, logfilename):
# Process the required subset of images:
for i in range(int_from, int_to + 1):
# Read i-th slice:
t0 = time()
im = imread(files[i])
t1 = time()
# Post process the image:
im = postprocess(im, convert_opt, crop_opt)
# Write down post-processed slice:
t2 = time()
fname = outpath + outprefix + '_' + str(i).zfill(4) + '.tif'
imsave(fname, im)
t3 = time()
# Write log (atomic procedure - lock used):
_write_log(lock, fname, logfilename, t2 - t1, (t3 - t2) + (t1 - t0) )
def main(argv):
"""To do...
Usage
-----
Parameters
---------
Example
--------------------------
The following line processes the first ten TIFF files of input path
"/home/in" and saves the processed files to "/home/out" with the
application of the Boin and Haibel filter with smoothing via a Butterworth
filter of order 4 and cutoff frequency 0.01:
reconstruct 0 4 C:\Temp\Dullin_Aug_2012\sino_noflat C:\Temp\Dullin_Aug_2012\sino_noflat\output
9.0 10.0 0.0 0.0 0.0 true sino slice C:\Temp\Dullin_Aug_2012\sino_noflat\tomo_conv flat dark
"""
lock = Lock()
# Get the from and to number of files to process:
int_from = int(argv[0])
int_to = int(argv[1])
# Get input and output paths:
inpath = argv[2]
outpath = argv[3]
if not inpath.endswith(sep): inpath += sep
if not outpath.endswith(sep): outpath += sep
# Get parameters:
convert_opt = argv[4]
crop_opt = argv[5]
outprefix = argv[6]
# Number of threads to use and logfile:
nr_threads = int(argv[7])
logfilename = argv[8]
# Get the files in infile:
log = open(logfilename,"w")
log.write(linesep + "\tInput TIFF folder: %s" % (inpath))
log.write(linesep + "\tOutput TIFF folder: %s" % (outpath))
log.write(linesep + "\t--------------")
if (int_to != -1):
log.write(linesep + "\tThe subset [%d,%d] of the input files will be considered." % (int_from, int_to))
log.write(linesep + "\tCropping:")
crop_opt_num = crop_opt.split(":")
log.write(linesep + "\t\tTop: %s pixels" % (crop_opt_num[0]))
log.write(linesep + "\t\tBottom: %s pixels" % (crop_opt_num[1]))
log.write(linesep + "\t\tLeft: %s pixels" % (crop_opt_num[2]))
log.write(linesep + "\t\tRight: %s pixels" % (crop_opt_num[3]))
conv_method, conv_args = convert_opt.split(":", 1)
if (conv_method == "linear8"):
min, max = conv_args.split(";")
log.write(linesep + "\tConversion to 8-bit by remapping range [%s,%s] to [0,255]." % (min, max))
elif (conv_method == "linear"):
min, max = conv_args.split(";")
log.write(linesep + "\tConversion to 16-bit by remapping range [%s,%s] to [0,65535]." % (min, max))
log.write(linesep + "\t--------------")
log.write(linesep + "\tBrowsing input folder...")
log.close()
files = sorted(glob(inpath + '*.tif*'))
num_files = len(files)
if ((int_to >= num_files) or (int_to == -1)):
int_to = num_files - 1
# Log infos:
log = open(logfilename,"a")
log.write(linesep + "\tInput folder browsed correctly.")
log.close()
# Run several threads for independent computation without waiting for threads completion:
for num in range(nr_threads):
start = ( (int_to - int_from + 1) / nr_threads)*num + int_from
if (num == nr_threads - 1):
end = int_to
else:
end = ( (int_to - int_from + 1) / nr_threads)*(num + 1) + int_from - 1
Process(target=_process, args=(lock, start, end, files, outpath, convert_opt, crop_opt, outprefix, logfilename )).start()
#start = 0
#end = num_files - 1
#process(lock, start, end, files, outpath, convert_opt, crop_opt, outprefix, logfilename )
#0 -1 C:\Temp\BrunGeorgos C:\Temp\BrunGeorgos\slice_8 linear8:-0.01;0.01 10:10:10:20 slice C:\Temp\log_00_conv.txt
if __name__ == "__main__":
main(argv[1:])
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