Mercurial > repos > imgteam > imagej2_bunwarpj_align
diff imagej2_math_jython_script.py @ 1:e9243cad1d67 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
author | imgteam |
---|---|
date | Mon, 28 Sep 2020 16:40:20 +0000 |
parents | ab54024c0a88 |
children | 0a0d2dfd17e0 |
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--- a/imagej2_math_jython_script.py Tue Sep 17 17:02:18 2019 -0400 +++ b/imagej2_math_jython_script.py Mon Sep 28 16:40:20 2020 +0000 @@ -1,78 +1,84 @@ -import jython_utils 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 = sys.argv[ -7 ] -operation = sys.argv[ -6 ] -expression = sys.argv[ -5 ] -if sys.argv[ -4 ] in [ None, 'None' ]: +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' ]: + 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 ] + 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 ) +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() -try: - 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.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, "" ) +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: - 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 ) -except Exception, e: - jython_utils.handle_error( error_log, str( e ) ) + # 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)