preprocessing.py
No OneTemporary
Actions

Subscribers

None

File Metadata

	#@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')