comparison imagej2_binary_to_edm_jython_script.py @ 1:768825d9034a draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"

0:f6df6830d5ec

import jython_utils
import sys
from ij import IJ
from ij import ImagePlus
from ij.plugin.filter import Analyzer
from ij.plugin.filter import EDM

# Fiji Jython interpreter implements Python 2.5 which does not
# provide support for argparse.
error_log = sys.argv[ -8 ]
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 )

    # 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, "Distance Map", "" )
    # 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 ) )

1:768825d9034a

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_file = sys.argv[-7]
iterations = int(sys.argv[-6])
count = int(sys.argv[-5])
black_background = sys.argv[-4] == "yes"
pad_edges_when_eroding = sys.argv[-3] == "yes"
output_filename = sys.argv[-2]
output_datatype = sys.argv[-1]

# Open the input image file.
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()

# Set binary options.
options_list = ['edm=Overwrite', 'iterations=%d' % iterations, 'count=%d' % count]
if black_background:
    options_list.append("black")
if pad_edges_when_eroding:
    options_list.append("pad")
options = " ".join(options_list)
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, "Distance Map", "")
# Save the ImagePlus object as a new image.
IJ.saveAs(input_image_plus_copy, output_datatype, output_filename)