diff imagej2_adjust_threshold_binary_jython_script.py @ 1:e2622ebb5ce4 draft

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

--- a/imagej2_adjust_threshold_binary_jython_script.py	Tue Sep 17 17:01:44 2019 -0400
+++ b/imagej2_adjust_threshold_binary_jython_script.py	Mon Sep 28 16:49:43 2020 +0000
@@ -1,49 +1,46 @@
-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[ -10 ]
-input = sys.argv[ -9 ]
-threshold_min = float( sys.argv[ -8 ] )
-threshold_max = float( sys.argv[ -7 ] )
-method = sys.argv[ -6 ]
-display = sys.argv[ -5 ]
-black_background = jython_utils.asbool( sys.argv[ -4 ] )
+error_log = sys.argv[-10]
+input_file = sys.argv[-9]
+threshold_min = float(sys.argv[-8])
+threshold_max = float(sys.argv[-7])
+method = sys.argv[-6]
+display = sys.argv[-5]
+black_background = sys.argv[-4] == "yes"
 # TODO: this is not being used.
-stack_histogram = jython_utils.asbool( sys.argv[ -3 ] )
-tmp_output_path = sys.argv[ -2 ]
-output_datatype = sys.argv[ -1 ]
+stack_histogram = 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:
-    # 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","iterations=1 count=1 edm=Overwrite do=Nothing" )
-    # Set the options.
-    if black_background:
-        method_str = "%s dark" % method
-    else:
-        method_str = method
-    IJ.setAutoThreshold( input_image_plus_copy, method_str )
-    if display == "red":
-        display_mode = "Red"
-    elif display == "bw":
-        display_mode = "Black & White"
-    elif display == "over_under":
-        display_mode = "Over/Under"
-    IJ.setThreshold( input_image_plus_copy, threshold_min, threshold_max, display_mode )
-    # Run the command.
-    IJ.run( input_image_plus_copy, "threshold", "" )
-    # 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 ) )
+# 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", "iterations=1 count=1 edm=Overwrite do=Nothing")
+# Set the options.
+if black_background:
+    method_str = "%s dark" % method
+else:
+    method_str = method
+IJ.setAutoThreshold(input_image_plus_copy, method_str)
+if display == "red":
+    display_mode = "Red"
+elif display == "bw":
+    display_mode = "Black & White"
+elif display == "over_under":
+    display_mode = "Over/Under"
+IJ.setThreshold(input_image_plus_copy, threshold_min, threshold_max, display_mode)
+# Run the command.
+IJ.run(input_image_plus_copy, "threshold", "")
+# Save the ImagePlus object as a new image.
+IJ.saveAs(input_image_plus_copy, output_datatype, output_filename)