Mercurial > repos > imgteam > imagej2_find_maxima
comparison imagej2_adjust_threshold_binary_jython_script.py @ 0:29b39f5b0e69 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
author | imgteam |
---|---|
date | Tue, 17 Sep 2019 17:01:44 -0400 |
parents | |
children | e2622ebb5ce4 |
comparison
equal
deleted
inserted
replaced
-1:000000000000 | 0:29b39f5b0e69 |
---|---|
1 import jython_utils | |
2 import sys | |
3 from ij import IJ | |
4 | |
5 # Fiji Jython interpreter implements Python 2.5 which does not | |
6 # provide support for argparse. | |
7 error_log = sys.argv[ -10 ] | |
8 input = sys.argv[ -9 ] | |
9 threshold_min = float( sys.argv[ -8 ] ) | |
10 threshold_max = float( sys.argv[ -7 ] ) | |
11 method = sys.argv[ -6 ] | |
12 display = sys.argv[ -5 ] | |
13 black_background = jython_utils.asbool( sys.argv[ -4 ] ) | |
14 # TODO: this is not being used. | |
15 stack_histogram = jython_utils.asbool( sys.argv[ -3 ] ) | |
16 tmp_output_path = sys.argv[ -2 ] | |
17 output_datatype = sys.argv[ -1 ] | |
18 | |
19 # Open the input image file. | |
20 input_image_plus = IJ.openImage( input ) | |
21 | |
22 # Create a copy of the image. | |
23 input_image_plus_copy = input_image_plus.duplicate() | |
24 image_processor_copy = input_image_plus_copy.getProcessor() | |
25 | |
26 try: | |
27 # Convert image to binary if necessary. | |
28 if not image_processor_copy.isBinary(): | |
29 # Convert the image to binary grayscale. | |
30 IJ.run( input_image_plus_copy, "Make Binary","iterations=1 count=1 edm=Overwrite do=Nothing" ) | |
31 # Set the options. | |
32 if black_background: | |
33 method_str = "%s dark" % method | |
34 else: | |
35 method_str = method | |
36 IJ.setAutoThreshold( input_image_plus_copy, method_str ) | |
37 if display == "red": | |
38 display_mode = "Red" | |
39 elif display == "bw": | |
40 display_mode = "Black & White" | |
41 elif display == "over_under": | |
42 display_mode = "Over/Under" | |
43 IJ.setThreshold( input_image_plus_copy, threshold_min, threshold_max, display_mode ) | |
44 # Run the command. | |
45 IJ.run( input_image_plus_copy, "threshold", "" ) | |
46 # Save the ImagePlus object as a new image. | |
47 IJ.saveAs( input_image_plus_copy, output_datatype, tmp_output_path ) | |
48 except Exception, e: | |
49 jython_utils.handle_error( error_log, str( e ) ) |