imagej2_bunwarpj_align: imagej2_bunwarpj

comparison imagej2_bunwarpj_align.xml @ 1:e9243cad1d67 draft

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

author	imgteam
date	Mon, 28 Sep 2020 16:40:20 +0000
parents	ab54024c0a88
children	0a0d2dfd17e0

comparison

equal deleted inserted replaced

-:ab54024c0a88
+:e9243cad1d67
-<?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" />
+<expand macro="fiji_requirements"/>
-<command>
+<command detect_errors="exit_code"><![CDATA[
-<![CDATA[
+#import os
-python $__tool_directory__/imagej2_bunwarpj_align.py
+#set error_log = 'output_log.txt'
---target_image "$target_image"
+touch '$error_log';
---target_image_format $target_image.ext
---source_image "$source_image"
+## ImageJ2 requires file extensions to be valid image data types.
---source_image_format $source_image.ext
+#set source_out_suffix = '.' + str($source_out_datatype)
-#if $align_with_mask_cond.align_with_mask == 'yes':
+#set target_out_suffix = '.' + str($target_out_datatype)
---target_mask "$target_mask"
+#set source_image_sans_ext = $os.path.splitext($os.path.basename($source_image.file_name))[0]
---target_mask_format $target_mask.ext
+#set source_image_with_ext = '.'.join([$source_image_sans_ext, $source_image.ext])
---source_mask "$source_mask"
+ln -s '$source_image.file_name' '$source_image_with_ext';
---source_mask_format $source_mask.ext
+#set target_image_sans_ext = $os.path.splitext($os.path.basename($target_image.file_name))[0]
-#end if
+#set target_image_with_ext = '.'.join([$target_image_sans_ext, $target_image.ext])
---min_scale_def $min_scale_def
+ln -s '$target_image.file_name' '$target_image_with_ext';
---max_scale_def $max_scale_def
---max_subsamp_fact $max_subsamp_fact
+#set save_transformation = str($advanced_options_cond.advanced_options) == 'save_transformation'
---divergence_weight $divergence_weight
+#set mono = str($advanced_options_cond.advanced_options) == 'mono'
---curl_weight $curl_weight
+#set landmarks = str($advanced_options_cond.advanced_options) == 'landmarks'
---image_weight $image_weight
+#set affine = str($advanced_options_cond.advanced_options) == 'affine'
---consistency_weight $consistency_weight
-#if $advanced_options_cond.advanced_options == 'landmarks':
+#if str($align_with_mask_cond.align_with_mask) == 'yes':
---landmarks_weight $advanced_options_cond.landmarks_weight
+#set source_mask_sans_ext = $os.path.splitext($os.path.basename($align_with_mask_cond.source_mask.file_name))[0]
---landmarks_file "$advanced_options_cond.landmarks_file"
+#set source_mask_with_ext = '.'.join([$source_mask_sans_ext, $source_mask.ext])
-#else if $advanced_options_cond.advanced_options == 'affine':
+#set source_mask = $source_mask_with_ext
---target_affine_file "$advanced_options_cond.target_affine_file"
+ln -s '$align_with_mask_cond.source_mask.file_name' '$source_mask_with_ext';
---source_affine_file "$advanced_options_cond.source_affine_file"
+#set target_mask_sans_ext = $os.path.splitext($os.path.basename($align_with_mask_cond.target_mask.file_name))[0]
-#else if $advanced_options_cond.advanced_options == 'mono':
+#set target_mask_with_ext = '.'.join([$target_mask_sans_ext, $target_mask.ext])
---mono "true"
+#set target_mask = $target_mask_with_ext
-#else if $advanced_options_cond.advanced_options == 'save_transformation':
+ln -s '$align_with_mask_cond.target_mask.file_name' '$target_mask_with_ext';
---target_trans_out "$target_trans_out"
+#else:
---source_trans_out "$source_trans_out"
+#set source_mask = 'NULL'
-#end if
+#set target_mask = 'NULL'
---source_out "$source_out"
+#end if
---source_out_datatype $source_out_datatype
-#if $advanced_options_cond.advanced_options != 'mono':
+#if not $mono:
---target_out "$target_out"
+#set tmp_target_out = 'tmp_target_out' + $target_out_suffix
---target_out_datatype $target_out_datatype
+touch '$tmp_target_out';
-#end if
---jython_script $__tool_directory__/imagej2_bunwarpj_align_jython_script.py
+## bUnwarpJ automatically names the transformation files based
-]]>
+## on the names of the source and target image file names.
-</command>
+#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"/>
+<expand macro="param_target_image"/>
-<param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="source_image" type="data" label="Source 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"/>
+<expand macro="param_target_mask"/>
-<param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="source_mask" type="data" label="Source 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>
 </param>
 <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]"/>
 <param name="divergence_weight" type="float" value="0.0" label="Weight of the divergence term" help="Value is a floating point number"/>
 <param name="curl_weight" type="float" label="Weight of the curl term" value="0.0" help="Value is a floating point number"/>
 <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
 list as soon as appropriate.  Their use is supported in the imagej2_bunwarp_align.py
 wrapper.
 results from the ImageJ GUI and in headless mode from the command line.
 <option value="mono">Unidirectional registration (source to target)</option>
 -->
 <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"/>
 <param format="txt" name="landmarks_file" type="data" label="Landmark file"/>
 </when>
 -->
 <when value="save_transformation"/>
 </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" />
+<expand macro="test_target_source_images"/>
-<param name="source_image" value="blobs.gif" />
+<param name="max_subsamp_fact" value="1"/>
-<param name="min_scale_def" value="0" />
+<output name="source_out" file="registered_source1.png" compare="sim_size"/>
-<param name="max_scale_def" value="2" />
+<output name="target_out" file="registered_target1.png" compare="sim_size"/>
-<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" />
 </test>
 <test>
 <!-- Align two images without landmarks or mask, but saving transformation matrices -->
-<param name="target_image" value="dotblot.jpg" />
+<expand macro="test_target_source_images"/>
-<param name="source_image" value="blobs.gif" />
+<param name="max_subsamp_fact" value="1"/>
-<param name="min_scale_def" value="0" />
+<param name="advanced_options" value="save_transformation"/>
-<param name="max_scale_def" value="2" />
+<output name="source_out" file="registered_source1.png" compare="sim_size"/>
-<param name="max_subsamp_fact" value="1" />
+<output name="target_out" file="registered_target1.png" compare="sim_size"/>
-<param name="divergence_weight" value="0.0" />
+<output name="source_trans_out" file="source_elastic_transformation_out.txt" compare="contains"/>
-<param name="curl_weight" value="0.0" />
+<output name="target_trans_out" file="target_elastic_transformation_out.txt" compare="contains"/>
-<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" />
 </test>
 <test>
 <!-- Align two images without landmarks but with mask, not saving transformation matrices -->
-<param name="target_image" value="dotblot.jpg" />
+<expand macro="test_target_source_images"/>
-<param name="source_image" value="blobs.gif" />
+<param name="align_with_mask" value="yes"/>
-<param name="target_mask" value="mask_white.png" />
+<param name="target_mask" value="mask_white.png"/>
-<param name="source_mask" value="mask_ramp.gif" />
+<param name="source_mask" value="mask_ramp.gif"/>
-<param name="min_scale_def" value="0" />
+<param name="max_subsamp_fact" value="1"/>
-<param name="max_scale_def" value="2" />
+<output name="source_out" file="registered_source2.png" compare="sim_size"/>
-<param name="max_subsamp_fact" value="1" />
+<output name="target_out" file="registered_target2.png" compare="sim_size"/>
-<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" />
 </test>
 </tests>
 <help>
 **What it does**
 the registerd source and target images: the direct transformation matrix of A and the inverse transformation
 matrix of B.
 ]]>
 </help>
-<expand macro="bunwarpj_citations" />
+<expand macro="bunwarpj_citations"/>
 </tool>

Mercurial > repos > imgteam > imagej2_bunwarpj_align

comparison imagej2_bunwarpj_align.xml @ 1:e9243cad1d67 draft