diff imagej2_adjust_threshold_binary_jython_script.py @ 0:6840ce593a91 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_adjust_threshold_binary_jython_script.py	Tue Sep 17 17:08:47 2019 -0400
@@ -0,0 +1,49 @@
+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 ] )
+# 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 ]
+
+# 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()
+
+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 ) )