error_log = sys.argv[ -5 ] input = sys.argv[ -4 ] black_background = jython_utils.asbool( 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() try: # Set binary options. options = jython_utils.get_binary_options( black_background=black_background ) IJ.run( input_image_plus_copy, "Options...", options ) # Convert image to binary if necessary. if not image_processor_copy.isBinary(): # Convert the image to binary grayscale. IJ.run( input_image_plus_copy, "Make Binary", "" ) # Run the command. IJ.run( input_image_plus_copy, "Watershed", "" ) # 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 ) )
error_log = sys.argv[-5] input = sys.argv[-4] black_background = jython_utils.asbool(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() try: # Set binary options. options = jython_utils.get_binary_options( black_background=black_background) IJ.run(input_image_plus_copy, "Options...", options) # Convert image to binary if necessary. if not image_processor_copy.isBinary(): # Convert the image to binary grayscale. IJ.run(input_image_plus_copy, "Make Binary", "") # Run the command. IJ.run(input_image_plus_copy, "Skeletonize (2D/3D)", "") # 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))
input = sys.argv[ -7 ] iterations = int( sys.argv[ -6 ] ) count = int( sys.argv[ -5 ] ) black_background = jython_utils.asbool( sys.argv[ -4 ] ) pad_edges_when_eroding = jython_utils.asbool( 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() try: # Set binary options. options = jython_utils.get_binary_options( black_background=black_background, iterations=iterations, count=count, pad_edges_when_eroding=pad_edges_when_eroding ) IJ.run( input_image_plus_copy, "Options...", options ) # Run the command. IJ.run( input_image_plus_copy, "Make Binary", "" ) # 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 ) )