diff imagej2_enhance_contrast.xml @ 0:edfc597fb180 draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/imagej2_enhance_contrast.xml	Tue Sep 17 17:01:04 2019 -0400
@@ -0,0 +1,93 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<tool id="imagej2_enhance_contrast" name="Enhance contrast" version="@WRAPPER_VERSION@.0">
+    <description></description>
+    <macros>
+        <import>imagej2_macros.xml</import>
+    </macros>
+    <expand macro="fiji_requirements" />
+    <command>
+<![CDATA[
+    python $__tool_directory__/imagej2_enhance_contrast.py
+    --input "$input"
+    --input_datatype $input.ext
+    --equalize_histogram $equalize_histogram_cond.equalize_histogram
+    #if $equalize_histogram_cond.equalize_histogram == 'no':
+        --saturated_pixels $equalize_histogram_cond.saturated_pixels
+        --normalize $equalize_histogram_cond.normalize
+    #end if
+    --jython_script $__tool_directory__/imagej2_enhance_contrast_jython_script.py
+    --output_datatype $output.ext
+    --output "$output"
+]]>
+    </command>
+    <inputs>
+        <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="input" type="data" label="Select image"/>
+        <conditional name="equalize_histogram_cond">
+            <param name="equalize_histogram" type="select" label="Equalize histogram?">
+                <option value="no" selected="True">No</option>
+                <option value="yes">Yes</option>
+            </param>
+            <when value="no">
+                <param name="saturated_pixels" type="float" value="0.3" min="0.0" max="100.0" label="Saturated pixels pct" help="Value is percentage of total number of pixels">
+                    <validator type="in_range" min="0" exclude_min="true" max="100" />
+                </param>
+                <param name="normalize" type="select" label="Normalize?">
+                    <option value="no" selected="True">No</option>
+                    <option value="yes">Yes</option>
+                </param>
+            </when>
+            <when value="yes"/>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="output" format_source="input" label="${tool.name} on ${on_string}"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="blobs.gif" />
+            <param name="equalize_histogram" value="yes" />
+            <output name="output" file="blobs_equalize.gif" compare="sim_size" />
+        </test>
+        <test>
+            <param name="input" value="blobs.gif" />
+            <param name="saturated_pixels" value="6.2" />
+            <output name="output" file="blobs_saturate.gif" compare="sim_size" />
+        </test>
+        <test>
+            <param name="input" value="blobs.gif" />
+            <param name="saturated_pixels" value="13.0" />
+            <param name="normalize" value="yes" />
+            <output name="output" file="blobs_normalize.gif" compare="sim_size" />
+        </test>
+    </tests>
+    <help>
+
+**What it does**
+
+<![CDATA[
+
+Enhances image contrast by using either normalization (contrast stretching) or histogram
+equalization.
+
+Normalization (i.e., contrast stretching) attempts to improve the contrast in an image by
+stretching the range of intensity values it contains to span a desired range of values
+(e.g. the the full range of pixel values that the image type allows).  It differs from the
+more sophisticated histogram equalization in that it can only apply a linear scaling function
+to the image pixel values.  As a result the enhancement is less harsh.
+
+Histogram equalization provides a sophisticated method for modifying the dynamic range and
+contrast of an image by altering the image such that its intensity histogram has a desired
+shape.  Unlike contrast stretching, histogram modeling operators may employ non-linear and
+non-monotonic transfer functions to map between pixel intensity values in the input and output
+images.  Histogram equalization re-assigns the intensity values of pixels in the input image
+such that the output image contains a uniform distribution of intensities (i.e. a flat histogram).
+
+- **Equalize histogram** - Enhances the image using histogram equalization.  Choosing this option eliminates the "Saturated pixels pct" and "Normalize" options.
+- **Saturated pixels pct** - Determines the number of pixels in the image that are allowed to become saturated.  Increasing this value increases contrast.  This value should be greater than zero to prevent a few outlying pixels from causing the histogram stretch to not work as intended.
+- **Normalize** - Recalculates the pixel values of the image so the range is equal to the maximum range for the data type, or 0-1.0 for float images. The maximum range is 0-255 for 8-bit images and 0-65535 for 16-bit images.  Normalization of RGB images is not supported, so selecting "yes" is ignored for this image type.
+
+]]>
+
+    </help>
+    <expand macro="fiji_headless_citations" />
+</tool>