biswebnode/bin/bw_nonlinearpointregistration.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>nonLinear RPM Registration</title>
	<description>Computes a linear point registration between the reference point set and target point set. Returns a matrix transformation.</description>
	<version>1.3.0b2</version>
	<documentation-url>https://bioimagesuiteweb.github.io/bisweb-manual</documentation-url>
	<license>GPL v2</license>
	<contributor>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>
		<string>
			<name>NumLandmarks</name>
			<label>NumLandmarks</label>
			<description>Maximum Number of Landmarks</description>
			<longflag>--numlandmarks</longflag>
			<default>1000</default>
		</string>
		<double>
			<name>Init Temp</name>
			<label>Init Temp</label>
			<description>Initial Temperature for RPM</description>
			<longflag>--initialtemp</longflag>
			<default>10</default>
			<constraints>
				<minimum>0.1</minimum>
				<maximum>20</maximum>
			</constraints>
		</double>
		<double>
			<name>Fin Temp</name>
			<label>Fin Temp</label>
			<description>Final Temperature for RPM</description>
			<longflag>--finaltemp</longflag>
			<default>3</default>
			<constraints>
				<minimum>0.1</minimum>
				<maximum>20</maximum>
			</constraints>
		</double>
		<double>
			<name>Init cps</name>
			<label>Init cps</label>
			<description>Initial control point spacing</description>
			<longflag>--initialcps</longflag>
			<default>40</default>
			<constraints>
				<minimum>1</minimum>
				<maximum>80</maximum>
			</constraints>
		</double>
		<double>
			<name>Final cps</name>
			<label>Final cps</label>
			<description>Final control point spacing</description>
			<longflag>--finalcps</longflag>
			<default>20</default>
			<constraints>
				<minimum>0.5</minimum>
				<maximum>80</maximum>
			</constraints>
		</double>
		<double>
			<name>Init smoothness</name>
			<label>Init smoothness</label>
			<description>Initial Smoothness</description>
			<longflag>--initialsmoothness</longflag>
			<default>1</default>
			<constraints>
				<minimum>0.01</minimum>
				<maximum>5</maximum>
			</constraints>
		</double>
		<double>
			<name>Final smoothness</name>
			<label>Final smoothness</label>
			<description>Final Smoothness</description>
			<longflag>--finalsmoothness</longflag>
			<default>0.1</default>
			<constraints>
				<minimum>0.01</minimum>
				<maximum>5</maximum>
			</constraints>
		</double>
		<string-enumeration>
			<name>LinMode</name>
			<label>LinMode</label>
			<description>Linear Mode</description>
			<longflag>--linmode</longflag>
			<default>Affine</default>
			<element>None</element>
			<element>Rigid</element>
			<element>Similarity</element>
			<element>Affine</element>
		</string-enumeration>
	</parameters>
	<parameters advanced="true">
		<label>Advanced</label>
		<description>Advanced Parameters</description>
		<string-enumeration>
			<name>Warp</name>
			<label>Warp</label>
			<description>If true, also output a warped reference surface using the current transform</description>
			<longflag>--dowarp</longflag>
			<default>false</default>
			<element>true</element>
			<element>false</element>
		</string-enumeration>
		<integer>
			<name>IterPerTemp</name>
			<label>IterPerTemp</label>
			<description>Number of Iterations at Each Temperature</description>
			<longflag>--iterpertemp</longflag>
			<default>5</default>
			<constraints>
				<minimum>1</minimum>
				<maximum>10</maximum>
			</constraints>
		</integer>
		<double>
			<name>Anneal Rate</name>
			<label>Anneal Rate</label>
			<description>Anneal Rate</description>
			<longflag>--annealrate</longflag>
			<default>0.93</default>
			<constraints>
				<minimum>0.5</minimum>
				<maximum>0.99</maximum>
			</constraints>
		</double>
		<string-enumeration>
			<name>MatchMode</name>
			<label>MatchMode</label>
			<description>Match Mode</description>
			<longflag>--matchmode</longflag>
			<default>RPM</default>
			<element>ICP</element>
			<element>Mixture</element>
			<element>RPM</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>
		<file>
			<name>Reference Surface</name>
			<label>Reference Surface</label>
			<description>The reference surface</description>
			<longflag>--reference</longflag>
    			<channel>input</channel>
		</file>
		<file>
			<name>Target Surface</name>
			<label>Target Surface</label>
			<description>The surface to register</description>
			<longflag>--target</longflag>
    			<channel>input</channel>
		</file>
		<file>
			<name>Initial Xform</name>
			<label>Initial Xform</label>
			<description>The initial transformation (optional)</description>
			<longflag>--initial</longflag>
    			<channel>input</channel>
		</file>
	</parameters>
	<parameters>
		<label>Outputs</label>
		<description>Output Objects</description>
		<file>
			<name>Output Transformation</name>
			<label>Output Transformation</label>
			<description>The output transformation</description>
			<longflag>--output</longflag>
    			<channel>output</channel>
		</file>
		<file>
			<name>Warped Surface</name>
			<label>Warped Surface</label>
			<description>The warped surface</description>
			<longflag>--warped</longflag>
    			<channel>output</channel>
		</file>
	</parameters>

</executable>