biswebnode/bin/bw_normalizeimage.xml

A node.js implementation of BioImage Suite Web command line tools in Javascript and WebAssembly

<?xml version="1.0" encoding="utf-8"?>
<executable>
	<category>BisWEB</category>
	<title>Normalize</title>
	<description>This element will normalize an image by setting the value below the low threshold to zero and setting the value about the high threshold to the max value.</description>
	<version>1.3.0b2</version>
	<documentation-url>https://bioimagesuiteweb.github.io/bisweb-manual</documentation-url>
	<license>GPL v2</license>
	<contributor>Zach Saltzman and Xenios Papademetris</contributor>

<acknowledgements>Funding for this work was provided by the NIH Brain Initiative under grant R24 MH114805.</acknowledgements>
	<parameters>
		<label>Standard</label>
		<description>Standard Parameters</description>
		<double>
			<name>Low</name>
			<label>Low</label>
			<description>The percentage of the cumulative histogram to threshold below</description>
			<longflag>--perlow</longflag>
			<default>0.02</default>
			<constraints>
				<minimum>0</minimum>
				<maximum>0.7</maximum>
			</constraints>
		</double>
		<double>
			<name>High</name>
			<label>High</label>
			<description>The percentage of the cumulative histogram to saturate above</description>
			<longflag>--perhigh</longflag>
			<default>0.98</default>
			<constraints>
				<minimum>0.75</minimum>
				<maximum>1</maximum>
			</constraints>
		</double>
		<integer>
			<name>Max Value</name>
			<label>Max Value</label>
			<description>Maximum value for the normalized image</description>
			<longflag>--maxval</longflag>
			<default>255</default>
			<constraints>
				<minimum>16</minimum>
				<maximum>255</maximum>
			</constraints>
		</integer>
	</parameters>
	<parameters advanced="true">
		<label>Advanced</label>
		<description>Advanced Parameters</description>
		<string-enumeration>
			<name>Debug</name>
			<label>Debug</label>
			<description>Toggles debug logging</description>
			<longflag>--debug</longflag>
			<default>false</default>
			<element>true</element>
			<element>false</element>
		</string-enumeration>
		<string-enumeration>
			<name>SlicerProgress</name>
			<label>SlicerProgress</label>
			<description>Enables progress xml outputs for Slicer</description>
			<longflag>--slicerprogress</longflag>
			<default>true</default>
			<element>true</element>
			<element>false</element>
		</string-enumeration>
	</parameters>
	<parameters>
		<label>Inputs</label>
		<description>Input Objects</description>
		<image fileExtensions=".nii.gz,.nii">
			<name>Input Image</name>
			<label>Input Image</label>
			<description>The filename for the image to be processed</description>
			<longflag>--input</longflag>
    			<channel>input</channel>
		</image>
	</parameters>
	<parameters>
		<label>Outputs</label>
		<description>Output Objects</description>
		<image fileExtensions=".nii.gz,.nii">
			<name>Output Image</name>
			<label>Output Image</label>
			<description>The output image filename</description>
			<longflag>--output</longflag>
    			<channel>output</channel>
		</image>
	</parameters>

</executable>