--- a/imagej2_noise.xml	Sun Nov 05 10:57:39 2023 +0000
+++ b/imagej2_noise.xml	Wed Sep 25 16:16:10 2024 +0000
@@ -1,13 +1,7 @@
-<tool id="imagej2_noise" name="Add or remove noise" version="@WRAPPER_VERSION@.1">
+<tool id="imagej2_noise" name="Add or remove noise" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
     <description>with ImageJ2</description>
     <macros>
         <import>imagej2_macros.xml</import>
-        <xml name="insertion_select">
-            <param name="insertion" type="select" label="Insertion">
-                <option value="additive" selected="True">Additive</option>
-                <option value="multiplicative">Multiplicative</option>
-            </param>
-        </xml>
     </macros>
     <edam_operations>
         <edam_operation>operation_3443</edam_operation>
@@ -19,21 +13,13 @@
     <expand macro="fiji_requirements"/>
     <command detect_errors="exit_code"><![CDATA[
 #import os
-#set error_log = 'output_log.txt'
-#if str($noise_cond.noise) == 'randomj':
-    #set randomj_value = $noise_cond.randomj_cond.randomj
-#else:
-    #set randomj_value = None
-#end if
 #set input_sans_ext = $os.path.splitext($os.path.basename($input.file_name))[0]
-#set input_with_ext = '.'.join([input_sans_ext, $input.ext])
+#set input_with_ext = './' + '.'.join([input_sans_ext, $input.ext])
 ln -s '$input.file_name' '$input_with_ext' &&
 #set output_filename = '.'.join(['output', $input.ext])
 touch '$output_filename' &&
-touch '$error_log' &&
 ImageJ --ij2 --headless --debug
 --jython '$__tool_directory__/imagej2_noise_jython_script.py'
-'$error_log'
 '$input_with_ext'
 '$input.ext'
 '$noise_cond.noise'
@@ -51,54 +37,8 @@
     'None'
     'None'
 #end if
-'$randomj_value'
-#if $randomj_value == 'randomj_binomial':
-    $noise_cond.randomj_cond.trials
-    $noise_cond.randomj_cond.probability
-#else:
-    'None'
-    'None'
-#end if
-#if $randomj_value == 'randomj_exponential':
-    $noise_cond.randomj_cond.lammbda
-#else:
-    'None'
-#end if
-#if $randomj_value == 'randomj_gamma':
-    $noise_cond.randomj_cond.order
-#else:
-    'None'
-#end if
-#if $randomj_value in['randomj_gaussian', 'randomj_poisson']:
-    $noise_cond.randomj_cond.mean
-    #if $randomj_value == 'randomj_gaussian':
-        $noise_cond.randomj_cond.sigma
-    #else:
-        'None'
-    #end if
-#else:
-    'None'
-    'None'
-#end if
-#if $randomj_value == 'randomj_uniform':
-    $noise_cond.randomj_cond.min
-    $noise_cond.randomj_cond.max
-#else:
-    'None'
-    'None'
-#end if
-#if str($randomj_value) != 'None':
-    '$noise_cond.randomj_cond.insertion'
-#else:
-    'None'
-#end if
 '$output_filename'
-&>'$error_log';
-if [[ $? -ne 0 ]]; then
-    cat '$error_log' >&2;
-else
-    mv '$output_filename' '$output';
-fi
+&& mv '$output_filename' '$output';
 ]]></command>
     <inputs>
         <expand macro="param_input"/>
@@ -111,7 +51,6 @@
                 <option value="remove_outliers">Remove Outliers</option>
                 <option value="remove_nans">Remove NaNs</option>
                 <option value="rof_denoise">ROF Denoise</option>
-                <option value="randomj">RandomJ</option>
             </param>
             <when value="add_noise"/>
             <when value="add_specified_noise">
@@ -123,51 +62,12 @@
                 <param name="radius" type="float" value="2.0" label="Radius" help="pixels"/>
                 <param name="threshold" type="float" value="50.0" label="Threshold"/>
                 <param name="which_outliers" type="select" label="Which Outliers">
-                    <option value="bright" selected="True">Bright</option>
-                    <option value="dark">Dark</option>
+                    <option value="Bright" selected="True">Bright</option>
+                    <option value="Dark">Dark</option>
                 </param>
             </when>
             <when value="remove_nans"/>
             <when value="rof_denoise"/>
-            <when value="randomj">
-                <conditional name="randomj_cond">
-                    <param name="randomj" type="select" label="RandomJ">
-                        <option value="randomj_binomial" selected="True">RandomJ Binomial</option>
-                        <option value="randomj_exponential">RandomJ Exponential</option>
-                        <option value="randomj_gamma">RandomJ Gamma</option>
-                        <option value="randomj_gaussian">RandomJ Gaussian</option>
-                        <option value="randomj_poisson">RandomJ Poisson</option>
-                        <option value="randomj_uniform">RandomJ Uniform</option>
-                    </param>
-                    <when value="randomj_binomial">
-                        <param name="trials" type="float" value="1.0" label="Trials"/>
-                        <param name="probability" type="float" value="0.5" label="Probability"/>
-                        <expand macro="insertion_select"/>
-                    </when>
-                    <when value="randomj_exponential">
-                        <param name="lammbda" type="float" value="0.5" label="Lambda"/>
-                        <expand macro="insertion_select"/>
-                    </when>
-                    <when value="randomj_gamma">
-                        <param name="order" type="integer" value="1" label="Order"/>
-                        <expand macro="insertion_select"/>
-                    </when>
-                    <when value="randomj_gaussian">
-                        <param name="mean" type="float" value="0.0" label="Mean"/>
-                        <param name="sigma" type="float" value="1.0" label="Sigma"/>
-                        <expand macro="insertion_select"/>
-                    </when>
-                    <when value="randomj_poisson">
-                        <param name="mean" type="float" value="1.0" label="Mean"/>
-                        <expand macro="insertion_select"/>
-                    </when>
-                    <when value="randomj_uniform">
-                        <param name="min" type="float" value="0.0" label="Min"/>
-                        <param name="max" type="float" value="1.0" label="Max"/>
-                        <expand macro="insertion_select"/>
-                    </when>
-                </conditional>
-            </when>
         </conditional>
     </inputs>
     <outputs>
@@ -177,17 +77,26 @@
         <test>
             <param name="input" value="blobs.gif"/>
             <param name="noise" value="add_specified_noise"/>
-            <output name="output" file="add_specified_noise.gif"/>
+            <param name="standard_deviation" value="5" />
+            <!-- Cannot use image_diff as the noise is random -->
+            <output name="output" file="add_specified_noise.gif" compare="sim_size"/>
         </test>
         <test>
             <param name="input" value="blobs.gif"/>
             <param name="noise" value="despeckle"/>
-            <output name="output" file="despeckle.gif"/>
+            <output name="output" file="despeckle.gif" compare="image_diff"/>
         </test>
         <test>
             <param name="input" value="blobs.gif"/>
             <param name="noise" value="remove_outliers"/>
-            <output name="output" file="remove_outliers.gif"/>
+            <param name="radius" value="10.0"/>
+            <param name="threshold" value="1"/>
+            <param name="which_outliers" value="Bright"/>
+            <output name="output" file="remove_outliers.gif" compare="image_diff"/>
+        </test>
+        <test expect_failure="true">
+            <param name="input" value="blobs.gif"/>
+            <param name="noise" value="remove_nans"/>
         </test>
     </tests>
     <help>
@@ -202,12 +111,6 @@
 - **Despeckle** - Replaces each pixel with the median value in its 3 × 3 neighborhood. This is a time consuming operation because for each pixel, the nine pixels in the 3 × 3 neighborhood must be sorted and the center pixel replaced with the median value (the fifth).
 - **Remove Outliers** - Replaces a pixel by the median of the pixels in the surrounding if it deviates from the median by more than a certain value (the threshold).
 - **Remove NaNs** - Replaces NaN (Not-a-Number) pixels in 32-bit images by the median of the neighbors inside the circular kernel area defined by Radius. It does not remove patches of NaNs larger than the kernel size, however.
-- **RandonJ Binomial** - Contaminates image with random numbers generated using a binomial random variable
-- **RandonJ Exponential** - Contaminates image with random numbers generated using an exponential random variable.
-- **RandonJ Gamma** - Contaminates image with random numbers generated using a gamma random variable.
-- **RandonJ Gaussian** - Contaminates image with random numbers generated using a Gaussian random variable.
-- **RandonJ Poisson** - Contaminates image with random numbers generated using a Poisson random variable.
-- **RandonJ Uniform** - Contaminates image with random numbers generated using a uniform random variable.
 ]]>
     </help>
     <expand macro="fiji_headless_citations"/>