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"

0:ab54024c0a88

<?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>
    <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"/>
        <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="yes">Yes</option>
            </param>
            <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"/>
            </when>
        </conditional>
        <param name="min_scale_def" type="select" label="Initial deformation">
            <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="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" />
        </param>
        <param name="source_out_datatype" type="select" label="Save registered source image as format">
            <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="save_transformation">Save calculated transformations</option>
            </param>
            <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 ${on_string}: Registered source image">
            <actions>
                <action type="format">
                    <option type="from_param" name="source_out_datatype" />
                </action>
            </actions>
        </data>
        <data name="target_out" format="png"  label="${tool.name} on ${on_string}: Registered target image">
            <filter>advanced_options_cond['advanced_options'] != "mono"</filter>
            <actions>
                <action type="format">
                    <option type="from_param" name="target_out_datatype" />
                </action>
            </actions>
        </data>
        <data format="txt" name="source_trans_out" label="${tool.name} on ${on_string}: Direct source transformation matrix">
            <filter>advanced_options_cond['advanced_options'] == "save_transformation"</filter>
        </data>
        <data format="txt" name="target_trans_out" label="${tool.name} on ${on_string}: Inverse target transformation matrix">
            <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" />
        </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" />
        </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" />
        </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" />
</tool>

1:e9243cad1d67

<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 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>
        <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="yes">Yes</option>
            </param>
            <when value="no"/>
            <when value="yes">
                <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="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="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"/>
        </param>
        <param name="source_out_datatype" type="select" label="Save registered source image as format">
            <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="save_transformation">Save calculated transformations</option>
            </param>
            <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} (registered source)  ${on_string}">
            <actions>
                <action type="format">
                    <option type="from_param" name="source_out_datatype"/>
                </action>
            </actions>
        </data>
        <data name="target_out" format="png"  label="${tool.name} (registered target) ${on_string}">
            <filter>advanced_options_cond['advanced_options'] != "mono"</filter>
            <actions>
                <action type="format">
                    <option type="from_param" name="target_out_datatype"/>
                </action>
            </actions>
        </data>
        <data format="txt" name="source_trans_out" label="${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} (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 -->
            <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 -->
            <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 -->
            <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>
**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"/>
</tool>