Python get_binary_optionsの例

コード例 #1

ファイル: imagej2_watershed_binary_jython_script.py プロジェクト: BIMSBbioinfo/galaxytools

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 ) )

コード例 #2

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))

コード例 #3

ファイル: imagej2_make_binary_jython_script.py プロジェクト: pvanheus/galaxytools

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 ) )