Mercurial > repos > bgruening > imagej2_crop

comparison imagej2_analyze_particles_binary_jython_script.py @ 0:018144807556 draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
author bgruening
date Tue, 24 Sep 2024 17:12:52 +0000
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-1:000000000000 0:018144807556
1 import sys
2
3 from ij import IJ, Prefs
4 from ij.plugin.filter import Analyzer
5
6 OPTIONS = ["edm=Overwrite", "iterations=1", "count=1"]
7
8 # Fiji Jython interpreter implements Python 2.5 which does not
9 # provide support for argparse.
10 roi_coordinate_file = sys.argv[-13]
11 input_file = sys.argv[-12]
12 black_background = sys.argv[-11] == "yes"
13 size = sys.argv[-10]
14 circularity_min = float(sys.argv[-9])
15 circularity_max = float(sys.argv[-8])
16 show = sys.argv[-7]
17 display_results = sys.argv[-6] == "yes"
18 exclude_edges = sys.argv[-5] == "yes"
19 include_holes = sys.argv[-4] == "yes"
20 output_filename = sys.argv[-3]
21 output_datatype = sys.argv[-2]
22 results_path = sys.argv[-1]
23
24
25 if black_background:
26 Prefs.blackBackground = True
27 else:
28 Prefs.blackBackground = False
29
30 # Open the input image file.
31 input_image_plus = IJ.openImage(input_file)
32
33 # Create a copy of the image.
34 input_image_plus_copy = input_image_plus.duplicate()
35 image_processor_copy = input_image_plus_copy.getProcessor()
36 analyzer = Analyzer(input_image_plus_copy)
37
38 # Set binary options.
39 options_list = OPTIONS
40 if black_background:
41 options_list.append("black")
42 options = " ".join(options_list)
43 IJ.run(input_image_plus_copy, "Options...", options)
44
45 if not image_processor_copy.isBinary():
46 # Convert the image to binary grayscale.
47 IJ.run(input_image_plus_copy, "Make Binary", "")
48
49 # Set the options.
50 options = ["size=%s" % size, "stack"]
51 circularity_str = "%.3f-%.3f" % (circularity_min, circularity_max)
52 options.append("circularity=%s" % circularity_str)
53 if exclude_edges:
54 options.append("exclude")
55 if include_holes:
56 options.append("include")
57
58 # If you need the coordinates of ROIs we compute it twice
59 if len(roi_coordinate_file) > 0:
60 options2 = list(options)
61 options2.append("show=Overlay")
62 IJ.run(input_image_plus_copy, "Analyze Particles...", " ".join(options2))
63 ov = input_image_plus_copy.getOverlay()
64 with open(roi_coordinate_file, 'w') as fo:
65 fo.write("shape\tpoints\tlabel\tt\tz\n")
66 for i, roi in enumerate(ov):
67 if roi.getName() is None:
68 roi.name = "ROI_%d" % i
69 poly = roi.getPolygon()
70 x_values = poly.xpoints
71 y_values = poly.ypoints
72 points_coo = ",".join(["(%d,%d)" % (x, y) for x, y in zip(x_values, y_values)])
73 fo.write("Polygon\t%s\t%s\t%d\t%d\n" % (points_coo, roi.getName(), roi.getTPosition(), roi.getZPosition()))
74 analyzer.resetCounter()
75
76 if show.find("_") >= 0:
77 show_str = "[%s]" % show.replace("_", " ")
78 else:
79 show_str = show
80 options.append("show=%s" % show_str)
81 if display_results:
82 options.append("display")
83 # Always run "in_situ".
84 options.append("in_situ")
85
86 # Run the command.
87 IJ.run(input_image_plus_copy, "Analyze Particles...", " ".join(options))
88
89 # Save outputs.
90 if len(output_filename) > 0:
91 # Save the ImagePlus object as a new image.
92 IJ.saveAs(input_image_plus_copy, output_datatype, output_filename)
93 if len(results_path) > 0:
94 results_table = analyzer.getResultsTable()
95 results_table.saveAs(results_path)