--- a/imagej2_bunwarpj_align.xml	Tue Sep 17 17:02:18 2019 -0400
+++ b/imagej2_bunwarpj_align.xml	Mon Sep 28 16:40:20 2020 +0000
@@ -1,67 +1,120 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <tool id="imagej2_bunwarpj_align" name="Align two images" version="@WRAPPER_VERSION@.0">
     <description>with bUnwarpJ</description>
     <macros>
         <import>imagej2_macros.xml</import>
     </macros>
-    <expand macro="fiji_requirements" />
-    <command>
-<![CDATA[
-    python $__tool_directory__/imagej2_bunwarpj_align.py
-    --target_image "$target_image"
-    --target_image_format $target_image.ext
-    --source_image "$source_image"
-    --source_image_format $source_image.ext
-    #if $align_with_mask_cond.align_with_mask == 'yes':
-        --target_mask "$target_mask"
-        --target_mask_format $target_mask.ext
-        --source_mask "$source_mask"
-        --source_mask_format $source_mask.ext
-    #end if
-    --min_scale_def $min_scale_def
-    --max_scale_def $max_scale_def
-    --max_subsamp_fact $max_subsamp_fact
-    --divergence_weight $divergence_weight
-    --curl_weight $curl_weight
-    --image_weight $image_weight
-    --consistency_weight $consistency_weight
-    #if $advanced_options_cond.advanced_options == 'landmarks':
-        --landmarks_weight $advanced_options_cond.landmarks_weight
-        --landmarks_file "$advanced_options_cond.landmarks_file"
-    #else if $advanced_options_cond.advanced_options == 'affine':
-        --target_affine_file "$advanced_options_cond.target_affine_file"
-        --source_affine_file "$advanced_options_cond.source_affine_file"
-    #else if $advanced_options_cond.advanced_options == 'mono':
-        --mono "true"
-    #else if $advanced_options_cond.advanced_options == 'save_transformation':
-        --target_trans_out "$target_trans_out"
-        --source_trans_out "$source_trans_out"
-    #end if
-    --source_out "$source_out"
-    --source_out_datatype $source_out_datatype
-    #if $advanced_options_cond.advanced_options != 'mono':
-        --target_out "$target_out"
-        --target_out_datatype $target_out_datatype
-    #end if
-    --jython_script $__tool_directory__/imagej2_bunwarpj_align_jython_script.py
-]]>
-    </command>
+    <expand macro="fiji_requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+#import os
+#set error_log = 'output_log.txt'
+touch '$error_log';
+
+## ImageJ2 requires file extensions to be valid image data types.
+#set source_out_suffix = '.' + str($source_out_datatype)
+#set target_out_suffix = '.' + str($target_out_datatype)
+#set source_image_sans_ext = $os.path.splitext($os.path.basename($source_image.file_name))[0]
+#set source_image_with_ext = '.'.join([$source_image_sans_ext, $source_image.ext])
+ln -s '$source_image.file_name' '$source_image_with_ext';
+#set target_image_sans_ext = $os.path.splitext($os.path.basename($target_image.file_name))[0]
+#set target_image_with_ext = '.'.join([$target_image_sans_ext, $target_image.ext])
+ln -s '$target_image.file_name' '$target_image_with_ext';
+
+#set save_transformation = str($advanced_options_cond.advanced_options) == 'save_transformation'
+#set mono = str($advanced_options_cond.advanced_options) == 'mono'
+#set landmarks = str($advanced_options_cond.advanced_options) == 'landmarks'
+#set affine = str($advanced_options_cond.advanced_options) == 'affine'
+
+#if str($align_with_mask_cond.align_with_mask) == 'yes':
+    #set source_mask_sans_ext = $os.path.splitext($os.path.basename($align_with_mask_cond.source_mask.file_name))[0]
+    #set source_mask_with_ext = '.'.join([$source_mask_sans_ext, $source_mask.ext])
+    #set source_mask = $source_mask_with_ext
+    ln -s '$align_with_mask_cond.source_mask.file_name' '$source_mask_with_ext';
+    #set target_mask_sans_ext = $os.path.splitext($os.path.basename($align_with_mask_cond.target_mask.file_name))[0]
+    #set target_mask_with_ext = '.'.join([$target_mask_sans_ext, $target_mask.ext])
+    #set target_mask = $target_mask_with_ext
+    ln -s '$align_with_mask_cond.target_mask.file_name' '$target_mask_with_ext';
+#else:
+    #set source_mask = 'NULL'
+    #set target_mask = 'NULL'
+#end if
+
+#if not $mono:
+    #set tmp_target_out = 'tmp_target_out' + $target_out_suffix
+    touch '$tmp_target_out';
+
+    ## bUnwarpJ automatically names the transformation files based
+    ## on the names of the source and target image file names.
+    #set tmp_target_out_transf_name_sans_ext = $os.path.splitext($target_out.file_name)[0]
+    #set tmp_target_out_transf_name = $tmp_target_out_transf_name_sans_ext + '_transf.txt'
+    touch '$tmp_target_out_transf_name';
+#end if
+#set tmp_source_out = 'tmp_source_out' + $source_out_suffix
+touch '$tmp_source_out';
+
+## bUnwarpJ automatically names the transformation files based
+## on the names of the source and target image file names.
+#set tmp_source_out_transf_name_sans_ext = $os.path.splitext($source_out.file_name)[0]
+#set tmp_source_out_transf_name = $tmp_source_out_transf_name_sans_ext + '_transf.txt'
+touch '$tmp_source_out_transf_name';
+
+## Align the two images using bUnwarpJ.
+bunwarpj -align
+'$target_image_with_ext'
+'$target_mask'
+'$source_image_with_ext'
+'$source_mask'
+$min_scale_def
+$max_scale_def
+$max_subsamp_fact
+$divergence_weight
+$curl_weight
+$image_weight
+$consistency_weight
+'$source_out'
+#if not $mono:
+    '$target_out'
+#end if
+#if $landmarks:
+    '-landmarks'
+    $advanced_options_cond.landmarks_weight
+    '$landmarks_file'
+#end if
+#if $affine:
+    '-affine'
+    '$advanced_options_cond.target_affine_file'
+    '$advanced_options_cond.source_affine_file'
+#end if
+#if $mono:
+    '-mono'
+#end if
+#if $save_transformation:
+    '-save_transformation'
+#end if
+&>'$error_log';
+#if $save_transformation:
+    mv '$tmp_source_out_transf_name' '$source_trans_out';
+    mv '$tmp_target_out_transf_name' '$target_trans_out';
+#end if
+if [[ $? -ne 0 ]]; then
+    cat '$error_log' >&2;
+fi
+]]></command>
     <inputs>
-        <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="target_image" type="data" label="Target image"/>
-        <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="source_image" type="data" label="Source image"/>
+        <expand macro="param_target_image"/>
+        <expand macro="param_source_image"/>
         <conditional name="align_with_mask_cond">
             <param name="align_with_mask" type="select" label="Align with masks?" help="Source and target mask can be any image format.">
-                <option value="no" selected="True">No</option>
+                <option value="no" selected="true">No</option>
                 <option value="yes">Yes</option>
             </param>
-            <when value="no" />
+            <when value="no"/>
             <when value="yes">
-                <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="target_mask" type="data" label="Target mask"/>
-                <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="source_mask" type="data" label="Source mask"/>
+                <expand macro="param_target_mask"/>
+                <expand macro="param_source_mask"/>
             </when>
         </conditional>
         <param name="min_scale_def" type="select" label="Initial deformation">
-            <option value="0" selected="True">Very Coarse</option>
+            <option value="0" selected="true">Very Coarse</option>
             <option value="1">Coarse</option>
             <option value="2">Fine</option>
             <option value="3">Very Fine</option>
@@ -69,7 +122,7 @@
         <param name="max_scale_def" type="select" label="Final deformation">
             <option value="0">Very Coarse</option>
             <option value="1">Coarse</option>
-            <option value="2" selected="True">Fine</option>
+            <option value="2" selected="true">Fine</option>
             <option value="3">Very Fine</option>
         </param>
         <param name="max_subsamp_fact" type="integer" value="0" min="0" label="Image sub-sample factor" help="Power of 2: [0, 1, 2 .. 7]"/>
@@ -78,10 +131,10 @@
         <param name="image_weight" type="float" label="Weight of the image term" value="1.0" help="Value is a floating point number"/>
         <param name="consistency_weight" type="float" label="Weight of the deformation consistency" value="10.0" help="Value is a floating point number"/>
         <param name="target_out_datatype" type="select" label="Save registered target image as format">
-            <expand macro="image_datatypes" />
+            <expand macro="image_datatypes"/>
         </param>
         <param name="source_out_datatype" type="select" label="Save registered source image as format">
-            <expand macro="image_datatypes" />
+            <expand macro="image_datatypes"/>
         </param>
         <!--
         The following additional options can be added to the advanced_options select
@@ -105,10 +158,10 @@
         -->
         <conditional name="advanced_options_cond">
             <param name="advanced_options" type="select" label="Advanced options" help="These are mutually exclusive for each execution">
-                <option value="none" selected="True">None</option>
+                <option value="none" selected="true">None</option>
                 <option value="save_transformation">Save calculated transformations</option>
             </param>
-            <when value="none" />
+            <when value="none"/>
             <!--
             <when value="landmarks">
                 <param name="landmarks_weight" type="float" label="Landmark weight" value="0.0" help="Value is a floating point number"/>
@@ -124,81 +177,55 @@
         </conditional>
     </inputs>
     <outputs>
-        <data name="source_out" format="png" label="${tool.name} on ${on_string}: Registered source image">
+        <data name="source_out" format="png" label="${tool.name} (registered source)  ${on_string}">
             <actions>
                 <action type="format">
-                    <option type="from_param" name="source_out_datatype" />
+                    <option type="from_param" name="source_out_datatype"/>
                 </action>
             </actions>
         </data>
-        <data name="target_out" format="png"  label="${tool.name} on ${on_string}: Registered target image">
+        <data name="target_out" format="png"  label="${tool.name} (registered target) ${on_string}">
             <filter>advanced_options_cond['advanced_options'] != "mono"</filter>
             <actions>
                 <action type="format">
-                    <option type="from_param" name="target_out_datatype" />
+                    <option type="from_param" name="target_out_datatype"/>
                 </action>
             </actions>
         </data>
-        <data format="txt" name="source_trans_out" label="${tool.name} on ${on_string}: Direct source transformation matrix">
+        <data format="txt" name="source_trans_out" label="${tool.name} (source transf matrix)  ${on_string}">
             <filter>advanced_options_cond['advanced_options'] == "save_transformation"</filter>
         </data>
-        <data format="txt" name="target_trans_out" label="${tool.name} on ${on_string}: Inverse target transformation matrix">
+        <data format="txt" name="target_trans_out" label="${tool.name} (target transf matrix) ${on_string}">
             <filter>advanced_options_cond['advanced_options'] == "save_transformation"</filter>
         </data>
     </outputs>
     <tests>
         <test>
             <!-- Align two images without landmarks or mask and not saving transformation matrices -->
-            <param name="target_image" value="dotblot.jpg" />
-            <param name="source_image" value="blobs.gif" />
-            <param name="min_scale_def" value="0" />
-            <param name="max_scale_def" value="2" />
-            <param name="max_subsamp_fact" value="1" />
-            <param name="divergence_weight" value="0.0" />
-            <param name="curl_weight" value="0.0" />
-            <param name="image_weight" value="1.0" />
-            <param name="consistency_weight" value="10.0" />
-            <param name="target_out_datatype" value="png" />
-            <param name="source_out_datatype" value="png" />
-            <output name="source_out" file="registered_source1.png" compare="sim_size" />
-            <output name="target_out" file="registered_target1.png" compare="sim_size" />
+            <expand macro="test_target_source_images"/>
+            <param name="max_subsamp_fact" value="1"/>
+            <output name="source_out" file="registered_source1.png" compare="sim_size"/>
+            <output name="target_out" file="registered_target1.png" compare="sim_size"/>
         </test>
         <test>
             <!-- Align two images without landmarks or mask, but saving transformation matrices -->
-            <param name="target_image" value="dotblot.jpg" />
-            <param name="source_image" value="blobs.gif" />
-            <param name="min_scale_def" value="0" />
-            <param name="max_scale_def" value="2" />
-            <param name="max_subsamp_fact" value="1" />
-            <param name="divergence_weight" value="0.0" />
-            <param name="curl_weight" value="0.0" />
-            <param name="image_weight" value="1.0" />
-            <param name="consistency_weight" value="10.0" />
-            <param name="target_out_datatype" value="png" />
-            <param name="source_out_datatype" value="png" />
-            <param name="advanced_options" value="save_transformation" />
-            <output name="source_out" file="registered_source1.png" compare="sim_size" />
-            <output name="target_out" file="registered_target1.png" compare="sim_size" />
-            <output name="source_trans_out" file="source_elastic_transformation.txt" />
-            <output name="target_trans_out" file="target_elastic_transformation.txt" />
+            <expand macro="test_target_source_images"/>
+            <param name="max_subsamp_fact" value="1"/>
+            <param name="advanced_options" value="save_transformation"/>
+            <output name="source_out" file="registered_source1.png" compare="sim_size"/>
+            <output name="target_out" file="registered_target1.png" compare="sim_size"/>
+            <output name="source_trans_out" file="source_elastic_transformation_out.txt" compare="contains"/>
+            <output name="target_trans_out" file="target_elastic_transformation_out.txt" compare="contains"/>
         </test>
         <test>
             <!-- Align two images without landmarks but with mask, not saving transformation matrices -->
-            <param name="target_image" value="dotblot.jpg" />
-            <param name="source_image" value="blobs.gif" />
-            <param name="target_mask" value="mask_white.png" />
-            <param name="source_mask" value="mask_ramp.gif" />
-            <param name="min_scale_def" value="0" />
-            <param name="max_scale_def" value="2" />
-            <param name="max_subsamp_fact" value="1" />
-            <param name="divergence_weight" value="0.0" />
-            <param name="curl_weight" value="0.0" />
-            <param name="image_weight" value="1.0" />
-            <param name="consistency_weight" value="10.0" />
-            <param name="target_out_datatype" value="png" />
-            <param name="source_out_datatype" value="png" />
-            <output name="source_out" file="registered_source2.png" compare="sim_size" />
-            <output name="target_out" file="registered_target2.png" compare="sim_size" />
+            <expand macro="test_target_source_images"/>
+            <param name="align_with_mask" value="yes"/>
+            <param name="target_mask" value="mask_white.png"/>
+            <param name="source_mask" value="mask_ramp.gif"/>
+            <param name="max_subsamp_fact" value="1"/>
+            <output name="source_out" file="registered_source2.png" compare="sim_size"/>
+            <output name="target_out" file="registered_target2.png" compare="sim_size"/>
         </test>
     </tests>
     <help>
@@ -243,5 +270,5 @@
 ]]>
 
     </help>
-    <expand macro="bunwarpj_citations" />
+    <expand macro="bunwarpj_citations"/>
 </tool>