Mercurial > repos > imgteam > imagej2_smooth
comparison imagej2_crop_jython_script.py @ 3:c11777ffe5b1 draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
author | imgteam |
---|---|
date | Wed, 25 Sep 2024 16:05:45 +0000 |
parents | |
children |
comparison
equal
deleted
inserted
replaced
2:6d7dd2194b4c | 3:c11777ffe5b1 |
---|---|
1 import sys | |
2 | |
3 from ij import IJ | |
4 from ij.plugin import Duplicator | |
5 | |
6 # Fiji Jython interpreter implements Python 2.5 which does not | |
7 # provide support for argparse. | |
8 input_file = sys.argv[-13] | |
9 xleft = int(sys.argv[-12]) | |
10 width = int(sys.argv[-11]) | |
11 ytop = int(sys.argv[-10]) | |
12 height = int(sys.argv[-9]) | |
13 first_channel = int(sys.argv[-8]) | |
14 last_channel = int(sys.argv[-7]) | |
15 first_slice = int(sys.argv[-6]) | |
16 last_slice = int(sys.argv[-5]) | |
17 first_frame = int(sys.argv[-4]) | |
18 last_frame = int(sys.argv[-3]) | |
19 output_filename = sys.argv[-2] | |
20 output_datatype = sys.argv[-1] | |
21 | |
22 # Open the input image file. | |
23 input_image_plus = IJ.openImage(input_file) | |
24 | |
25 # Get image dimensions (width, height, nChannels, nSlices, nFrames) | |
26 image_dims = input_image_plus.getDimensions() | |
27 | |
28 # Create a copy of the image. | |
29 input_image_plus_copy = input_image_plus.duplicate() | |
30 | |
31 # Determine if crop in XY is needed: | |
32 if xleft != 0 or width != 0 or ytop != 0 or height != 0: | |
33 # Need to define a ROI | |
34 if width == 0: | |
35 width = image_dims[0] - xleft | |
36 if height == 0: | |
37 height = image_dims[1] - ytop | |
38 input_image_plus_copy.setRoi(xleft, ytop, width, height) | |
39 | |
40 # Replace 0's with default: | |
41 if last_channel == 0: | |
42 last_channel = image_dims[2] | |
43 if last_slice == 0: | |
44 last_slice = image_dims[3] | |
45 if last_frame == 0: | |
46 last_frame = image_dims[4] | |
47 print("Original dimensions:") | |
48 print(image_dims) | |
49 # This will also crop in XY is a ROI has been set | |
50 input_image_plus_copy = Duplicator().run(input_image_plus_copy, first_channel, last_channel, first_slice, last_slice, first_frame, last_frame) | |
51 print("Final dimensions:") | |
52 print(input_image_plus_copy.getDimensions()) | |
53 | |
54 # Save the ImagePlus object as a new image. | |
55 IJ.saveAs(input_image_plus_copy, output_datatype, output_filename) |