Mercurial > repos > imgteam > imagej2_bunwarpj_convert_to_raw
view imagej2_crop_jython_script.py @ 3:bd2aadf0f589 draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
author | imgteam |
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date | Wed, 25 Sep 2024 16:03:19 +0000 |
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import sys from ij import IJ from ij.plugin import Duplicator # Fiji Jython interpreter implements Python 2.5 which does not # provide support for argparse. input_file = sys.argv[-13] xleft = int(sys.argv[-12]) width = int(sys.argv[-11]) ytop = int(sys.argv[-10]) height = int(sys.argv[-9]) first_channel = int(sys.argv[-8]) last_channel = int(sys.argv[-7]) first_slice = int(sys.argv[-6]) last_slice = int(sys.argv[-5]) first_frame = int(sys.argv[-4]) last_frame = int(sys.argv[-3]) output_filename = sys.argv[-2] output_datatype = sys.argv[-1] # Open the input image file. input_image_plus = IJ.openImage(input_file) # Get image dimensions (width, height, nChannels, nSlices, nFrames) image_dims = input_image_plus.getDimensions() # Create a copy of the image. input_image_plus_copy = input_image_plus.duplicate() # Determine if crop in XY is needed: if xleft != 0 or width != 0 or ytop != 0 or height != 0: # Need to define a ROI if width == 0: width = image_dims[0] - xleft if height == 0: height = image_dims[1] - ytop input_image_plus_copy.setRoi(xleft, ytop, width, height) # Replace 0's with default: if last_channel == 0: last_channel = image_dims[2] if last_slice == 0: last_slice = image_dims[3] if last_frame == 0: last_frame = image_dims[4] print("Original dimensions:") print(image_dims) # This will also crop in XY is a ROI has been set input_image_plus_copy = Duplicator().run(input_image_plus_copy, first_channel, last_channel, first_slice, last_slice, first_frame, last_frame) print("Final dimensions:") print(input_image_plus_copy.getDimensions()) # Save the ImagePlus object as a new image. IJ.saveAs(input_image_plus_copy, output_datatype, output_filename)