diff imagej2_enhance_contrast_jython_script.py @ 1:29a4d422f32a 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 16:41:15 +0000
parents f1ba33cd9edf
children
line wrap: on
line diff
--- a/imagej2_enhance_contrast_jython_script.py	Tue Sep 17 17:09:25 2019 -0400
+++ b/imagej2_enhance_contrast_jython_script.py	Mon Sep 28 16:41:15 2020 +0000
@@ -1,19 +1,19 @@
-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[ -7 ]
-input = sys.argv[ -6 ]
-equalize_histogram = jython_utils.asbool( sys.argv[ -5 ] )
-saturated_pixels = sys.argv[ -4 ]
-normalize = jython_utils.asbool( sys.argv[ -3 ] )
-tmp_output_path = sys.argv[ -2 ]
-output_datatype = sys.argv[ -1 ]
+error_log = sys.argv[-7]
+input = sys.argv[-6]
+equalize_histogram = sys.argv[-5] == "yes"
+saturated_pixels = sys.argv[-4]
+normalize = 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)
 
 # Create a copy of the image.
 input_image_plus_copy = input_image_plus.duplicate()
@@ -24,19 +24,16 @@
 options = []
 # If equalize_histogram, saturated_pixels and normalize are ignored.
 if equalize_histogram:
-    options.append( 'equalize' )
+    options.append('equalize')
 else:
-    if saturated_pixels not in [ None, 'None' ]:
+    if saturated_pixels not in [None, 'None']:
         # Fiji allows only a single decimal place for this value.
-        options.append( 'saturated=%.3f' % float( saturated_pixels ) )
+        options.append('saturated=%.3f' % float(saturated_pixels))
     # Normalization of RGB images is not supported.
     if bit_depth != 24 and normalize:
-        options.append( 'normalize' )
-try:
-    # Run the command.
-    options = "%s" % ' '.join( options )
-    IJ.run( input_image_plus_copy, "Enhance Contrast...", options )
-    # 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 ) )
+        options.append('normalize')
+# Run the command.
+options = "%s" % ' '.join(options)
+IJ.run(input_image_plus_copy, "Enhance Contrast...", options)
+# Save the ImagePlus object as a new image.
+IJ.saveAs(input_image_plus_copy, output_datatype, tmp_output_path)