biswebnode/winbin/bw_thresholdimage.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>Threshold</title>
	<description>This element will threshold an image -- values between the thresholds will be considered 'input' and values outside will be considered 'out'</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 Threshold</name>
			<label>Low Threshold</label>
			<description>The threshold below which values will be classified as 'out'</description>
			<longflag>--low</longflag>
			<default>1</default>
		</double>
		<double>
			<name>High Threshold</name>
			<label>High Threshold</label>
			<description>The value above which values will be classified as 'out'</description>
			<longflag>--high</longflag>
			<default>2</default>
		</double>
	</parameters>
	<parameters advanced="true">
		<label>Advanced</label>
		<description>Advanced Parameters</description>
		<string-enumeration>
			<name>Replace 'in'</name>
			<label>Replace 'in'</label>
			<description>If true, values classified as 'in' will be replaced by 'in value'</description>
			<longflag>--replacein</longflag>
			<default>false</default>
			<element>true</element>
			<element>false</element>
		</string-enumeration>
		<string-enumeration>
			<name>Replace 'out'</name>
			<label>Replace 'out'</label>
			<description>If true, values classified as 'out' will be replaced by 'out value'</description>
			<longflag>--replaceout</longflag>
			<default>true</default>
			<element>true</element>
			<element>false</element>
		</string-enumeration>
		<string-enumeration>
			<name>'in' Value</name>
			<label>'in' Value</label>
			<description>Value to replace 'in' values with, -1 is mapped to the maximum value in the image</description>
			<longflag>--inval</longflag>
			<default>1</default>
			<element>0</element>
			<element>1</element>
			<element>100</element>
			<element>-1</element>
		</string-enumeration>
		<string-enumeration>
			<name>'out' Value</name>
			<label>'out' Value</label>
			<description>Value to replace 'out' values with, -1 is mapped to the minimum value in the image</description>
			<longflag>--outval</longflag>
			<default>0</default>
			<element>0</element>
			<element>1</element>
			<element>100</element>
			<element>-1</element>
		</string-enumeration>
		<string-enumeration>
			<name>Output Type</name>
			<label>Output Type</label>
			<description>Output Type</description>
			<longflag>--outtype</longflag>
			<default>Same</default>
			<element>Same</element>
			<element>UChar</element>
			<element>Short</element>
		</string-enumeration>
		<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>