R6289/preprocessing.py
6862d18c2c4dmaster

preprocessing.py
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			#@String parameter_file

			from ij import IJ, ImagePlus
			from ij.io import Opener, FileSaver
			from ij.plugin import RGBStackMerge, StackCombiner, Resizer
			from ij.process import ImageConverter
			from ij.plugin import Resizer

			import json
			import os

			#import file paths
			json_file = open(parameter_file,'r')
			text = json_file.read()
			files = json.loads(text)
			json_file.close()

			#Instanciate necessary classes
			opener = Opener()
			RGB_stack_merge = RGBStackMerge()
			stack_combiner = StackCombiner()
			resizer = Resizer()


			#Open images
			unregistered_GC6s_info = opener.getTiffFileInfo(files['GC6s_input'])
			unregistered_GC6s_imp = opener.openTiffStack(unregistered_GC6s_info)

			unregistered_tdTom_info = opener.getTiffFileInfo(files['tdTom_input'])
			unregistered_tdTom_imp = opener.openTiffStack(unregistered_tdTom_info)

			#Remove dispensable slices from unregistered stacks
			IJ.run(unregistered_GC6s_imp, "Slice Remover", files['slices_removed'])
			IJ.run(unregistered_tdTom_imp, "Slice Remover", files['slices_removed'])

			#Create output directory if it does not exist
			if not os.path.exists(files['output_dir']):
			os.makedirs(files['output_dir'])

			#Save result
			file_saver_GC6s_image = FileSaver(unregistered_GC6s_imp)
			file_saver_GC6s_image.saveAsTiffStack(files['output_dir']+'/GC6s_preprocessed.tif')
			file_saver_tdTom_image = FileSaver(unregistered_tdTom_imp)
			file_saver_tdTom_image.saveAsTiffStack(files['output_dir']+'/tdTom_preprocessed.tif')