Mercurial > repos > imgteam > imagej2_enhance_contrast
view imagej2_math_jython_script.py @ 0:edfc597fb180 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 17:01:04 -0400 |
parents | |
children | ef3de3e84817 |
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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 ) )