Run ashlar on windows machines, output is ome-tiff with flat field and dark field corrected

ashlar-pyramid-output-with-ffc-dfc.py

import os
from datetime import datetime

dirPath = 'D:\i074_40b_132a'
outputFileName = 'i074_40b_132a'
fileExt = 'rcpnl'

os.chdir(dirPath)

files = os.listdir(dirPath)
targetedFiles = [file for file in files if fileExt in file]

print 'Start generating ffp and dfp '
print datetime.now().strftime('%Y-%m-%d %H:%M:%S')

for file in targetedFiles:
    fileName = file.split('.')[0]
    print fileName
    os.system("C:\Users\Public\Downloads\Fiji.app\ImageJ-win64.exe --ij2 --headless --run C:\Users\Public\Downloads\Fiji.app\plugins\imagej_basic_ashlar.py \"filename='%s.rcpnl', output_dir='.\\', experiment_name='%s'\"" %(fileName, fileName))

print 'End generating ffp and dfp '
print datetime.now().strftime('%Y-%m-%d %H:%M:%S')

files = os.listdir(dirPath)
rcpnls = ' '.join(targetedFiles)
ffps = ' '.join([file for file in files if 'ffp' in file])
dfps = ' '.join([file for file in files if 'dfp' in file])

pyramidFName = outputFileName if outputFileName else datetime.now().strftime('%Y%m%d-%H%M%S')

command = 'ashlar ' + rcpnls + ' -o .\ -f ' + pyramidFName + '.ome.tif --pyramid --ffp ' + ffps + ' --dfp ' + dfps
 
print 'Start stitching and generating pyramid '
print datetime.now().strftime('%Y-%m-%d %H:%M:%S')
    
os.system(command)

print 'End stitching and generating pyramid '
print datetime.now().strftime('%Y-%m-%d %H:%M:%S')

Read .csv config file with the list of slides (a slide is a folder of files from different cycles)
User run python THE_SCRIPT.py CONFIG.csv START_SLIDE_NUM END_SLIDE_NUM