diff imagej2_skeletonize3d_jython_script.py @ 1:c8bb47840c8d draft

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

--- a/imagej2_skeletonize3d_jython_script.py	Tue Sep 17 16:59:39 2019 -0400
+++ b/imagej2_skeletonize3d_jython_script.py	Mon Sep 28 16:51:33 2020 +0000
@@ -1,36 +1,36 @@
-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[ -5 ]
-input = sys.argv[ -4 ]
-black_background = jython_utils.asbool( sys.argv[ -3 ] )
-tmp_output_path = sys.argv[ -2 ]
-output_datatype = sys.argv[ -1 ]
+error_log = sys.argv[-5]
+input_file = sys.argv[-4]
+black_background = sys.argv[-3] == 'yes'
+tmp_output_path = sys.argv[-2]
+output_datatype = sys.argv[-1]
 
 # Open the input image file.
-input_image_plus = IJ.openImage( input )
+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()
 
-try:
-    # Set binary options.
-    options = jython_utils.get_binary_options( black_background=black_background )
-    IJ.run( input_image_plus_copy, "Options...", options )
+# Set binary options.
+options = ['edm=Overwrite', 'iterations=1', 'count=1']
+if (black_background):
+    options.append('black')
+options = " ".join(options)
+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", "" )
+# 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)", "" )
+# 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 ) )
+# Save the ImagePlus object as a new image.
+IJ.saveAs(input_image_plus_copy, output_datatype, tmp_output_path)