diff imagej2_binary_to_edm_jython_script.py @ 1:2be338fc671e draft default tip

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
author imgteam
date Mon, 28 Sep 2020 16:44:56 +0000
parents 1bffabc15695
children
line wrap: on
line diff
--- a/imagej2_binary_to_edm_jython_script.py	Tue Sep 17 16:55:25 2019 -0400
+++ b/imagej2_binary_to_edm_jython_script.py	Mon Sep 28 16:44:56 2020 +0000
@@ -1,44 +1,40 @@
-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 ]
+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 )
+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,
-                                               iterations=iterations,
-                                               count=count,
-                                               pad_edges_when_eroding=pad_edges_when_eroding )
-    IJ.run( input_image_plus_copy, "Options...", options )
+# 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", "" )
+# 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 ) )
+# 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)