diff imagej2_enhance_contrast_jython_script.py @ 0:ab54024c0a88 draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/imagej2_enhance_contrast_jython_script.py	Tue Sep 17 17:02:18 2019 -0400
@@ -0,0 +1,42 @@
+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 ]
+
+# 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()
+bit_depth = image_processor_copy.getBitDepth()
+
+# Set the options
+options = []
+# If equalize_histogram, saturated_pixels and normalize are ignored.
+if equalize_histogram:
+    options.append( 'equalize' )
+else:
+    if saturated_pixels not in [ None, 'None' ]:
+        # Fiji allows only a single decimal place for this value.
+        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 ) )