def main():
root = myDir.getPath() # get the root out the java file object
print(root)
import os, glob
# set up bioformats
from loci.plugins import BF
from loci.plugins.in import ImporterOptions
options = ImporterOptions()
options.setColorMode(ImporterOptions.COLOR_MODE_COMPOSITE)
options.setGroupFiles(True) # if the files are named logically if will group them into a stack
# this will do the maximum intensity projection
from ij.plugin import ZProjector
Zproj = ZProjector()
for path, subdirs, files in os.walk(root):
print(path)
# just get the one of the files that matches your image pattern
flist = glob.glob(os.path.join(path,"*.tif"))
print(len(flist))
if( flist ):
file = flist[0]
print("Processing {}".format(file))
options.setId(file)
imp = BF.openImagePlus(options)[0]
# show the image if you want to see it
IJ.run(imp, "Grays", "")
imp.show()
imp_max = Zproj.run(imp,'max')
IJ.run(imp_max, "Grays", "")
imp_max.show()
# save the Z projection
IJ.save(imp_max,file.rsplit('_',1)[0]+'_processed.tif')
