def savefile(im, imname, plugin, compress='false'):
attemptcount = 0
imname = tiffextend(imname)
print('Saving ', imname, im.width, im.height)
if compress.lower() != 'true':
IJ.saveAs(im, "tiff", imname)
else:
while attemptcount < 5:
try:
plugin.arg = "outfile=" + imname + " windowless=true compression=LZW saveROI=false"
exporter = Exporter(plugin, im)
exporter.run()
print('Succeeded after attempt ', attemptcount)
return
except:
attemptcount += 1
print('failed 5 times at saving')
def bfexporter(imp, savepath, useLOCI=True):
if useLOCI:
paramstring = "outfile=[" + savepath + "] windowless=true compression=Uncompressed saveROI=false"
plugin = LociExporter()
plugin.arg = paramstring
exporter = Exporter(plugin, imp)
exporter.run()
# save as OME-TIFF using BioFormats library using the IJ.run method
if not useLOCI:
# 2019-04-25: This does not seem to work in headless anymore
paramstring = "save=[" + savepath + "] compression=Uncompressed"
IJ.run(imp, "Bio-Formats Exporter", paramstring)
return paramstring
# run image analysis pipeline
filtered_image = run(IMAGEPATH,
useBF=True,
series=0)
# get time at the end and calc duration of processing
end = time.clock()
log.info('Duration of whole Processing : ' + str(end - start))
###########################################################
start = time.clock()
# create the argument string for the BioFormats Exporter and save as OME.TIFF
paramstring = "outfile=" + outputimagepath + " " + "windowless=true compression=Uncompressed saveROI=false"
plugin = LociExporter()
plugin.arg = paramstring
exporter = Exporter(plugin, filtered_image)
exporter.run()
# get time at the end and calc duration of processing
end = time.clock()
log.info('Duration of saving as OME-TIFF : ' + str(end - start))
# show the image
filtered_image.show()
# finish
log.info('Done.')
