<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>
    </macros>
    <edam_operations>
        <edam_operation>operation_3443</edam_operation>
    </edam_operations>
    <xrefs>
        <xref type="bio.tools">imagej</xref>
        <xref type="biii">imagej2</xref>
    </xrefs>
    <expand macro="fiji_requirements"/>
    <command detect_errors="exit_code"><![CDATA[
#import os
#set input_sans_ext = $os.path.splitext($os.path.basename($input.file_name))[0]
#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' &&
ImageJ --ij2 --headless --debug
--jython '$__tool_directory__/imagej2_noise_jython_script.py'
'$input_with_ext'
'$input.ext'
'$noise_cond.noise'
#if $noise_cond.noise == 'add_specified_noise':
    $noise_cond.standard_deviation
#else:
    'None'
#end if
#if $noise_cond.noise == 'remove_outliers':
    $noise_cond.radius
    $noise_cond.threshold
    '$noise_cond.which_outliers'
#else:
    'None'
    'None'
    'None'
#end if
'$output_filename'
&& mv '$output_filename' '$output';
]]></command>
    <inputs>
        <expand macro="param_input"/>
        <conditional name="noise_cond">
            <param name="noise" type="select" label="Noise">
                <option value="add_noise" selected="True">Add Random Noise</option>
                <option value="add_specified_noise">Add Specified Noise</option>
                <option value="salt_and_pepper">Salt and Pepper</option>
                <option value="despeckle">Despeckle</option>
                <option value="remove_outliers">Remove Outliers</option>
                <option value="remove_nans">Remove NaNs</option>
                <option value="rof_denoise">ROF Denoise</option>
            </param>
            <when value="add_noise"/>
            <when value="add_specified_noise">
                <param name="standard_deviation" type="float" value="25.0" label="Standard deviation" help="Floating point number"/>
            </when>
            <when value="salt_and_pepper"/>
            <when value="despeckle"/>
            <when value="remove_outliers">
                <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>
                </param>
            </when>
            <when value="remove_nans"/>
            <when value="rof_denoise"/>
        </conditional>
    </inputs>
    <outputs>
        <data name="output" format_source="input"/>
    </outputs>
    <tests>
        <test>
            <param name="input" value="blobs.gif"/>
            <param name="noise" value="add_specified_noise"/>
            <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" compare="image_diff"/>
        </test>
        <test>
            <param name="input" value="blobs.gif"/>
            <param name="noise" value="remove_outliers"/>
            <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>
**What it does**

<![CDATA[
Adds noise to or removes noise from images.

- **Add Random Noise** - Adds random noise to the image. The noise is Gaussian (normally) distributed with a mean of zero and standard deviation of 25.
- **Add Specified Noise** - Adds Gaussian noise with a mean of zero and a chosen standard deviation.
- **Salt and Pepper** - Adds salt and pepper noise to the image by randomly replacing 2.5% of the pixels with black pixels and 2.5% with white pixels. This command only works with 8-bit images.
- **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.
]]>
    </help>
    <expand macro="fiji_headless_citations"/>
</tool>