Package net.preibisch.mvrecon.fiji.plugin

Class Apply_Transformation

java.lang.Object

net.preibisch.mvrecon.fiji.plugin.Apply_Transformation

All Implemented Interfaces:

ij.plugin.PlugIn

public class Apply_Transformation
extends Object
implements ij.plugin.PlugIn

Field Summary

Fields

Modifier and Type	Field	Description
static String[]	applyToChoice
String[]	axesChoice
static int	defaultApplyTo
static int[]	defaultAxis
static int	defaultDefineAs
static double[]	defaultDegrees
static int	defaultModel
static ArrayList<double[]>	defaultModels
static boolean	defaultSameModelAngles
static boolean	defaultSameModelChannels
static boolean	defaultSameModelIlluminations
static boolean	defaultSameModelTiles
static boolean	defaultSameModelTimePoints
static String[]	defineAsChoice
static String[]	modelChoice

Constructor Summary

Constructors

Constructor	Description
Apply_Transformation()

Method Summary

Modifier and Type	Method	Description
static void	applyAxis(mpicbg.spim.data.SpimData data)
static void	applyAxisGrouped(mpicbg.spim.data.SpimData data)
static void	applyAxisGrouped(mpicbg.spim.data.SpimData data, boolean moveToOrigin)
void	applyModels(mpicbg.spim.data.SpimData spimData, double minResolution, int applyTo, Map<mpicbg.spim.data.sequence.ViewDescription,ImgLib2Temp.Pair<double[],String>> modelLinks)
static double[]	getCenterOfMass(Collection<ImgLib2Temp.Pair<net.imglib2.Dimensions,net.imglib2.realtransform.AffineGet>> views)
static void	main(String[] args)
protected static final double[]	parseString(String entry, int numValues)
static void	preConcatenateTransform(mpicbg.spim.data.SpimData spimData, mpicbg.spim.data.sequence.ViewId viewId, net.imglib2.realtransform.AffineTransform3D model, String name)
Map<mpicbg.spim.data.sequence.ViewDescription,ImgLib2Temp.Pair<double[],String>>	queryBigDataViewer(mpicbg.spim.data.SpimData data, List<mpicbg.spim.data.sequence.ViewId> viewIds, ApplyParameters params)
final ApplyParameters	queryParams(mpicbg.spim.data.SpimData data, List<mpicbg.spim.data.sequence.ViewId> viewIds)
Map<mpicbg.spim.data.sequence.ViewDescription,ImgLib2Temp.Pair<double[],String>>	queryRotationAxis(mpicbg.spim.data.SpimData data, List<mpicbg.spim.data.sequence.ViewId> viewIds, ApplyParameters params)
Map<mpicbg.spim.data.sequence.ViewDescription,ImgLib2Temp.Pair<double[],String>>	queryString(mpicbg.spim.data.SpimData data, List<mpicbg.spim.data.sequence.ViewId> viewIds, ApplyParameters params)
static net.imglib2.realtransform.AffineTransform3D	rotationAngleAxis(double angle, double[] axis)
void	run(String arg0)
static void	setModelToCalibration(mpicbg.spim.data.SpimData spimData, mpicbg.spim.data.sequence.ViewId viewId, double minResolution)
static void	setModelToIdentity(mpicbg.spim.data.SpimData spimData, mpicbg.spim.data.sequence.ViewId viewId)
static double[]	toUnit(double[] vec)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details

defaultSameModelTimePoints

public static boolean defaultSameModelTimePoints

defaultSameModelChannels

public static boolean defaultSameModelChannels

defaultSameModelIlluminations

public static boolean defaultSameModelIlluminations

defaultSameModelAngles

public static boolean defaultSameModelAngles

defaultSameModelTiles

public static boolean defaultSameModelTiles

defaultModel

public static int defaultModel

defaultDefineAs

public static int defaultDefineAs

defaultApplyTo

public static int defaultApplyTo

applyToChoice

public static String[] applyToChoice

modelChoice

public static String[] modelChoice

defineAsChoice

public static String[] defineAsChoice

axesChoice

public String[] axesChoice

defaultAxis

public static int[] defaultAxis

defaultDegrees

public static double[] defaultDegrees

defaultModels

public static ArrayList<double[]> defaultModels

Constructor Details

Apply_Transformation

public Apply_Transformation()

Method Details

run

public void run(String arg0)

Specified by:

run in interface ij.plugin.PlugIn

queryParams

public final ApplyParameters queryParams(mpicbg.spim.data.SpimData data,
 List<mpicbg.spim.data.sequence.ViewId> viewIds)

queryBigDataViewer

public Map<mpicbg.spim.data.sequence.ViewDescription,ImgLib2Temp.Pair<double[],String>> queryBigDataViewer(mpicbg.spim.data.SpimData data,
 List<mpicbg.spim.data.sequence.ViewId> viewIds,
 ApplyParameters params)

queryRotationAxis

public Map<mpicbg.spim.data.sequence.ViewDescription,ImgLib2Temp.Pair<double[],String>> queryRotationAxis(mpicbg.spim.data.SpimData data,
 List<mpicbg.spim.data.sequence.ViewId> viewIds,
 ApplyParameters params)

queryString

public Map<mpicbg.spim.data.sequence.ViewDescription,ImgLib2Temp.Pair<double[],String>> queryString(mpicbg.spim.data.SpimData data,
 List<mpicbg.spim.data.sequence.ViewId> viewIds,
 ApplyParameters params)

applyModels

public void applyModels(mpicbg.spim.data.SpimData spimData,
 double minResolution,
 int applyTo,
 Map<mpicbg.spim.data.sequence.ViewDescription,ImgLib2Temp.Pair<double[],String>> modelLinks)

parseString

protected static final double[] parseString(String entry,
 int numValues)

preConcatenateTransform

public static void preConcatenateTransform(mpicbg.spim.data.SpimData spimData,
 mpicbg.spim.data.sequence.ViewId viewId,
 net.imglib2.realtransform.AffineTransform3D model,
 String name)

setModelToCalibration

public static void setModelToCalibration(mpicbg.spim.data.SpimData spimData,
 mpicbg.spim.data.sequence.ViewId viewId,
 double minResolution)

setModelToIdentity

public static void setModelToIdentity(mpicbg.spim.data.SpimData spimData,
 mpicbg.spim.data.sequence.ViewId viewId)

applyAxis

public static void applyAxis(mpicbg.spim.data.SpimData data)

rotationAngleAxis

public static net.imglib2.realtransform.AffineTransform3D rotationAngleAxis(double angle,
 double[] axis)

toUnit

public static double[] toUnit(double[] vec)

applyAxisGrouped

public static void applyAxisGrouped(mpicbg.spim.data.SpimData data)

applyAxisGrouped

public static void applyAxisGrouped(mpicbg.spim.data.SpimData data,
 boolean moveToOrigin)

getCenterOfMass

public static double[] getCenterOfMass(Collection<ImgLib2Temp.Pair<net.imglib2.Dimensions,net.imglib2.realtransform.AffineGet>> views)

main

public static void main(String[] args)