Mercurial > repos > imgteam > imagej2_bunwarpj_convert_to_raw
view imagej2_math_jython_script.py @ 2:0cdd96322600 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
author | imgteam |
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date | Sun, 05 Nov 2023 11:00:42 +0000 |
parents | 7f9840d3b7e7 |
children | bd2aadf0f589 |
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import sys from ij import IJ # Fiji Jython interpreter implements Python 2.5 which does not # provide support for argparse. error_log = sys.argv[-8] input_file = sys.argv[-7] operation = sys.argv[-6] expression = sys.argv[-5] if sys.argv[-4] in [None, "None"]: bin_constant = None else: bin_constant = int(sys.argv[-4]) if sys.argv[-3] in [None, "None"]: float_constant = None else: float_constant = float(sys.argv[-3]) tmp_output_path = sys.argv[-2] output_datatype = sys.argv[-1] print("\nerror_log: %s\n" % str(error_log)) print("\ninput_file: %s\n" % str(input_file)) print("\noperation: %s\n" % str(operation)) print("\nexpression: %s\n" % str(expression)) print("\nbin_constant: %s\n" % str(bin_constant)) print("\nfloat_constant: %s\n" % str(float_constant)) print("\ntmp_output_path: %s\n" % str(tmp_output_path)) print("\noutput_datatype: %s\n" % str(output_datatype)) # Open the input image file. input_image_plus = IJ.openImage(input_file) # Create a copy of the image. input_image_plus_copy = input_image_plus.duplicate() image_processor_copy = input_image_plus_copy.getProcessor() bit_depth = image_processor_copy.getBitDepth() if operation.find("_") > 0: # Square_Root. new_operation = operation.replace("_", " ") elif operation in ["Square", "Log", "Exp", "Abs", "Reciprocal"]: # Unfortunately some ImageJ commands require a "..." ending # while others do not. There seems to be no pattern. new_operation = "%s" % operation else: new_operation = "%s..." % operation if operation == "Macro": # Apply the macro code to the image via a call to it's # ImageProcessor since this option does not work using # the IJ.run() method. new_expression = expression.lstrip('"').rstrip('"') options = "code=%s" % new_expression image_processor_copy.applyMacro(new_expression) elif operation == "Min": # Min does not work without using the ImageProcessor. image_processor_copy.min(float_constant) elif operation == "Max": # Max does not work without using the ImageProcessor. image_processor_copy.max(float_constant) elif operation == "Abs": if bit_depth not in [16, 32]: # Convert the image to 32-bit. IJ.run(input_image_plus_copy, "32-bit", "") IJ.run(input_image_plus_copy, new_operation, "") elif operation == "Reciprocal": if bit_depth != 32: # Convert the image to 32 bit. IJ.run(input_image_plus_copy, "32-bit", "") IJ.run(input_image_plus_copy, new_operation, "") else: if operation in ["AND", "OR", "XOR"]: # Value is a binary number. options = "value=%d" % bin_constant elif operation in ["Log", "Exp", "Square", "Square_Root"]: # No constant value. options = "" else: # Value is a floating point number. options = "value=%.3f" % float_constant IJ.run(input_image_plus_copy, "%s" % new_operation, "%s" % options) # Save the ImagePlus object as a new image. IJ.saveAs(input_image_plus_copy, output_datatype, tmp_output_path)