Mercurial > repos > imgteam > imagej2_skeletonize3d
diff imagej2_math_jython_script.py @ 0:f6df6830d5ec draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
author | imgteam |
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date | Tue, 17 Sep 2019 16:57:15 -0400 |
parents | |
children | 768825d9034a |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/imagej2_math_jython_script.py Tue Sep 17 16:57:15 2019 -0400 @@ -0,0 +1,78 @@ +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' ]: + 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 ] + +# Open the input image file. +input_image_plus = IJ.openImage( input ) + +# 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 == '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 ) +except Exception, e: + jython_utils.handle_error( error_log, str( e ) )