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comparison imagej2_math_jython_script.py @ 0:db3066ae9b09 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 imgteam
date Wed, 25 Sep 2024 16:28:45 +0000
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-1:000000000000 0:db3066ae9b09
1 import sys
2
3 from ij import IJ
4
5 # Fiji Jython interpreter implements Python 2.5 which does not
6 # provide support for argparse.\
7 input_file = sys.argv[-7]
8 operation = sys.argv[-6]
9 expression = sys.argv[-5]
10 if sys.argv[-4] in [None, "None"]:
11 bin_constant = None
12 else:
13 bin_constant = int(sys.argv[-4])
14 if sys.argv[-3] in [None, "None"]:
15 float_constant = None
16 else:
17 float_constant = float(sys.argv[-3])
18 tmp_output_path = sys.argv[-2]
19 output_datatype = sys.argv[-1]
20
21 print("\ninput_file: %s\n" % str(input_file))
22 print("\noperation: %s\n" % str(operation))
23 print("\nexpression: %s\n" % str(expression))
24 print("\nbin_constant: %s\n" % str(bin_constant))
25 print("\nfloat_constant: %s\n" % str(float_constant))
26 print("\ntmp_output_path: %s\n" % str(tmp_output_path))
27 print("\noutput_datatype: %s\n" % str(output_datatype))
28
29 # Open the input image file.
30 input_image_plus = IJ.openImage(input_file)
31
32 # Create a copy of the image.
33 input_image_plus_copy = input_image_plus.duplicate()
34 image_processor_copy = input_image_plus_copy.getProcessor()
35 bit_depth = image_processor_copy.getBitDepth()
36
37 if operation.find("_") > 0:
38 # Square_Root.
39 new_operation = operation.replace("_", " ")
40 elif operation in ["Square", "Log", "Exp", "Abs", "Reciprocal"]:
41 # Unfortunately some ImageJ commands require a "..." ending
42 # while others do not. There seems to be no pattern.
43 new_operation = "%s" % operation
44 else:
45 new_operation = "%s..." % operation
46
47 if operation == "Macro":
48 # Apply the macro code to the image via a call to it's
49 # ImageProcessor since this option does not work using
50 # the IJ.run() method.
51 new_expression = expression.lstrip('"').rstrip('"')
52 options = "code=%s" % new_expression
53 image_processor_copy.applyMacro(new_expression)
54 elif operation == "Min":
55 # Min does not work without using the ImageProcessor.
56 image_processor_copy.min(float_constant)
57 elif operation == "Max":
58 # Max does not work without using the ImageProcessor.
59 image_processor_copy.max(float_constant)
60 elif operation == "Abs":
61 if bit_depth not in [16, 32]:
62 # Convert the image to 32-bit.
63 IJ.run(input_image_plus_copy, "32-bit", "")
64 IJ.run(input_image_plus_copy, new_operation, "")
65 elif operation == "Reciprocal":
66 if bit_depth != 32:
67 # Convert the image to 32 bit.
68 IJ.run(input_image_plus_copy, "32-bit", "")
69 IJ.run(input_image_plus_copy, new_operation, "")
70 else:
71 if operation in ["AND", "OR", "XOR"]:
72 # Value is a binary number.
73 options = "value=%d" % bin_constant
74 elif operation in ["Log", "Exp", "Square", "Square_Root"]:
75 # No constant value.
76 options = ""
77 else:
78 # Value is a floating point number.
79 options = "value=%.3f" % float_constant
80 IJ.run(input_image_plus_copy, "%s" % new_operation, "%s" % options)
81 # Save the ImagePlus object as a new image.
82 IJ.saveAs(input_image_plus_copy, output_datatype, tmp_output_path)