compressiontools/batch_bfconvertJetraw.py at main · Pitt-IshiharaLab/compressiontools · GitHub

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import os, glob
import shutil
import platform

flag_jetraw = True
flag_omecompanion = True

# for macOS
dldir = '/Users/keisuke/Downloads'
path_bftools = '/Users/keisuke/bftools'

# # for Windows
dldir = 'D:\\JetrawTesting'
path_bftools = 'C:\\Users\\ishihara\\bftools'

stacks = '-S%sC%c'
if platform.system() == 'Windows':
	stacks = stacks.replace("%", "%%")

inputdir = os.path.join(dldir, 'M44test')
inputdir = os.path.join(dldir, '230509_JETRAW_M44_TEST')
outdir = os.path.join(dldir, 'out')

# prepare output directory
if os.path.exists(outdir):
	shutil.rmtree(outdir)
os.makedirs(outdir)

ext_in = '.vsi'

files = sorted(glob.glob(os.path.join(inputdir, '*' + ext_in)))

# Nfiles = len(files)
# for file in files:
# 	print(file)

file = files[0]

fnme = os.path.basename(file).replace(ext_in, '') # filename minus extension

# arguments - common for all files
bfconvert = os.path.join(path_bftools, 'bfconvert')
series    = '-series 0 '
if flag_jetraw:
	jetraw = '-compression Jetraw -jetraw-identifier 000391_standard -tilex 2304 -tiley 2304'
else:
	jetraw = ''
# overwr    = '-overwrite' # the overwrite parameter is not working in macOS or Windows, file size adds to pre-existing files

# arguments - file specific
if flag_omecompanion:
	companion = '-option ometiff.companion ' + os.path.join(dldir, 'out', fnme + '.companion.ome')
	ext_out   = '.ome.tif'
else:
	companion = ''
	ext_out   = '.tif'

myin  = os.path.join(inputdir, fnme + ext_in)
myout = os.path.join(outdir,   fnme + stacks + ext_out)

mylist = [bfconvert, series, jetraw, companion, myin, myout]
cmdstr = ' '.join(mylist)

# print(cmdstr)
os.system(cmdstr)