--- a/jython_script.py	Sun Oct 11 13:30:50 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,84 +0,0 @@
-import sys
-from ij import IJ
-from ij import ImagePlus
-import jython_utils
-
-# Fiji Jython interpreter implements Python 2.5 which does not
-# provide support for argparse.
-error_log = sys.argv[ -19 ]
-input = sys.argv[ -18 ]
-image_datatype = sys.argv[ -17 ]
-noise = sys.argv[ -16 ]
-standard_deviation = sys.argv[ -15 ]
-radius = sys.argv[ -14 ]
-threshold = sys.argv[ -13 ]
-which_outliers = sys.argv[ -12 ]
-randomj = sys.argv[ -11 ]
-trials = sys.argv[ -10 ]
-probability = sys.argv[ -9 ]
-# Note the spelling - so things don't get confused due to Python lambda function.
-lammbda = sys.argv[ -8 ]
-order = sys.argv[ -7 ]
-mean = sys.argv[ -6 ]
-sigma = sys.argv[ -5 ]
-min = sys.argv[ -4 ]
-max = sys.argv[ -3 ]
-insertion = sys.argv[ -2 ]
-tmp_output_path = sys.argv[ -1 ]
-
-error = False
-
-# Open the input image file.
-image_plus = IJ.openImage( input )
-bit_depth = image_plus.getBitDepth()
-image_type = image_plus.getType()
-# Create an ImagePlus object for the image.
-image_plus_copy = image_plus.duplicate()
-# Make a copy of the image.
-image_processor_copy = image_plus_copy.getProcessor()
-
-# Perform the analysis on the ImagePlus object.
-if noise == 'add_noise':
-    IJ.run( image_plus_copy, "Add Noise", "" )
-elif noise == 'add_specified_noise':
-    IJ.run( image_plus_copy, "Add Specified Noise", "standard=&standard_deviation" )
-elif noise == 'salt_and_pepper':
-    IJ.run( image_plus_copy, "Salt and Pepper", "" )
-elif noise == 'despeckle':
-    IJ.run( image_plus_copy, "Despeckle", "" )
-elif noise == 'remove_outliers':
-    IJ.run( image_plus_copy, "Remove Outliers", "radius=&radius threshold=&threshold which=&which_outliers" )
-elif noise == 'remove_nans':
-    if bit_depth == 32:
-        IJ.run( image_plus_copy, "Remove NaNs", "" )
-    else:
-        # When Galaxy metadata for images is enhanced to include information like this,
-        # we'll be able to write tool validators rather than having to stop the job in
-        # an error state.
-        msg = "Remove NaNs requires a 32-bit image, the selected image is %d-bit" % bit_depth
-        jython_utils.handle_error( error_log, msg )
-        error = True
-elif noise == 'rof_denoise':
-    if image_type == ImagePlus.GRAY32:
-        IJ.run( image_plus_copy, "ROF Denoise", "" )
-    else:
-        msg = "ROF Denoise requires an image of type 32-bit grayscale, the selected image is %d-bit" % ( bit_depth )
-        jython_utils.handle_error( error_log, msg )
-        error = True
-elif noise == 'randomj':
-    if randomj == 'randomj_binomial':
-        IJ.run( image_plus_copy, "RandomJ Binomial", "trials=&trials probability=&probability insertion=&insertion" )
-    elif randomj == 'randomj_exponential':
-        IJ.run( image_plus_copy, "RandomJ Exponential", "lambda=&lammbda insertion=&insertion" )
-    elif randomj == 'randomj_gamma':
-        IJ.run( image_plus_copy, "RandomJ Gamma", "order=&order insertion=&insertion" )
-    elif randomj == 'randomj_gaussian':
-        IJ.run( image_plus_copy, "RandomJ Gaussian", "mean=&mean sigma=&sigma insertion=&insertion" )
-    elif randomj == 'randomj_poisson':
-        IJ.run( image_plus_copy, "RandomJ Poisson", "mean=&mean insertion=&insertion" )
-    elif randomj == 'randomj_uniform':
-        IJ.run( image_plus_copy, "RandomJ Uniform", "min=&min max=&max insertion=&insertion" )
-
-if not error:
-    # Save the ImagePlus object as a new image.
-    IJ.saveAs( image_plus_copy, image_datatype, tmp_output_path )