Package gov.nih.mipav.model.algorithms

Class AlgorithmTransform

java.lang.Object

java.lang.Thread

gov.nih.mipav.model.algorithms.AlgorithmBase

gov.nih.mipav.model.algorithms.AlgorithmTransform

All Implemented Interfaces:

ActionListener, WindowListener, Runnable, EventListener

public class AlgorithmTransform
extends AlgorithmBase

Transforms Volume by resampling using transformation matrix and the choice of nearest-neighbor, trilinear interpolation, 3rd order Bspline, 4th order Bspline, cubic Lagrangian, quintic Lagrangian, heptic Lagrangian, or windowed sinc. Must indicate output volume's desired resolutions and dimensions.

Also includes static methods to transform images. Once caution - these static methods are NOT run in a separate thread. Consequently, if a progress bar is sent into the method to update progress, it should not include a cancel button because the user is unable to cancel a static transformation. If we want a transformation to have the ability to be cancelled, we should NOT use the static method, but rather construct a new AlgorithmTransform and run the algorithm using the standard .run() method.

NOTE for possible improvements in the future. To move images into "mm" space we presently multiple by voxel resolutions as we loop through the dimensions. A more efficent method is to modify the scale values of the the transformation matrix (i.e. the diagonals). This would speed the process by reducing the number of mults and divisions. Not sure how much but faster is better. Change should happen here and in the JDialogTransform interface.

This version of AlgorithmTransform includes a flag (passed as the last parameter) indicating whether to pad the image volume.

Version:

0.1 Nov, 1999

Author:

Delia McGarry, William Gandler, Matthew McAuliffe, Zohara Cohen

Nested Class Summary

Nested classes/interfaces inherited from class java.lang.Thread

Thread.Builder, Thread.State, Thread.UncaughtExceptionHandler

Field Summary

Fields

Modifier and Type	Field	Description
private static int[]	axisOrient	DOCUMENT ME!
static final int	BILINEAR	Biilinear interpolation.
static final int	BSPLINE3	Cubic bspline interpolation.
static final int	BSPLINE4	Quadratic bspline interpolation.
private int	bufferFactor	DOCUMENT ME!
private WildMagic.LibFoundation.Mathematics.Vector3f	center	DOCUMENT ME!
private boolean	clip	DOCUMENT ME!
static final int	CUBIC_LAGRANGIAN	Cubic lagrangian interpolation.
private ModelImage	destImage	DOCUMENT ME!
private float[]	destResolutions	DOCUMENT ME!
private int	DIM	DOCUMENT ME!
private static int[]	direct	DOCUMENT ME!
private boolean	do25D	DOCUMENT ME!
private boolean	doCenter	DOCUMENT ME!
private float	fillValue	Used for out of bounds values in the transformation routines.
private boolean	haveCentered
static final int	HEPTIC_LAGRANGIAN	Heptic lagrangian interpolation.
private double[]	imgBuf	DOCUMENT ME!
private float[]	imgBuf2	DOCUMENT ME!
private int	imgLength	DOCUMENT ME!
private int	imgLength2	DOCUMENT ME!
private static int	imgOrient	DOCUMENT ME!
private static float[]	imgOrigin	DOCUMENT ME!
private final int	interp	DOCUMENT ME!
private boolean	isSATransform	flag for determining if the transform is for scanner anatomical (->AXIAL).
private int	iTdim
private final int	iXdim	DOCUMENT ME!
private float	iXres	DOCUMENT ME!
private final int	iYdim	DOCUMENT ME!
private float	iYres	DOCUMENT ME!
private int	iZdim
private float	iZres
private static int[]	margins	DOCUMENT ME!
private ModelImage	maskImage	DOCUMENT ME!
static final int	NEAREST_NEIGHBOR	Nearest neighbor interpolation.
private int	oTdim	DOCUMENT ME!
private final int[]	oUnits	DOCUMENT ME!
private int	oXdim	DOCUMENT ME!
private final float	oXres	DOCUMENT ME!
private int	oYdim	DOCUMENT ME!
private final float	oYres	DOCUMENT ME!
private int	oZdim	DOCUMENT ME!
private float	oZres
private boolean	pad	DOCUMENT ME!
static final int	QUINTIC_LAGRANGIAN	Quintic lagrangian interpolation.
private ModelImage	srcImage	DOCUMENT ME!
private static float	startPos	DOCUMENT ME!
private static float	startTime
private boolean	suppressProgressBar
private boolean	transformVOI	DOCUMENT ME!
private final TransMatrix	transMatrix	DOCUMENT ME!
static final int	TRILINEAR	Trilinear interpolation.
private static boolean	updateOrigin	DOCUMENT ME!
static final int	WSINC	Windowed sinc interpolation.

Fields inherited from class gov.nih.mipav.model.algorithms.AlgorithmBase

destFlag, image25D, mask, maxProgressValue, minProgressValue, multiThreadingEnabled, nthreads, progress, progressModulus, progressStep, runningInSeparateThread, separable, threadStopped

Fields inherited from class java.lang.Thread

MAX_PRIORITY, MIN_PRIORITY, NORM_PRIORITY

Constructor Summary

Constructors

Constructor	Description
AlgorithmTransform(ModelImage _srcImage, TransMatrix xfrm, int interp, float _oXres, float _oYres, float _oZres, int _oXdim, int _oYdim, int _oZdim, boolean tVOI, boolean clip, boolean pad)	3D constructor for transformation algorithm.
AlgorithmTransform(ModelImage _srcImage, TransMatrix xfrm, int interp, float _oXres, float _oYres, float _oZres, int _oXdim, int _oYdim, int _oZdim, int[] units, boolean tVOI, boolean clip, boolean pad)	Creates a new $class.name$ object.
AlgorithmTransform(ModelImage _srcImage, TransMatrix xfrm, int interp, float _oXres, float _oYres, float _oZres, int _oXdim, int _oYdim, int _oZdim, int[] units, boolean tVOI, boolean clip, boolean pad, boolean doCenter, WildMagic.LibFoundation.Mathematics.Vector3f center)	Creates a new $class.name$ object.
AlgorithmTransform(ModelImage srcImage, TransMatrix xfrm, int interp, float oXres, float oYres, int oXdim, int oYdim, boolean tVOI, boolean clip, boolean pad)	2D constructor for transformation algorithm.
AlgorithmTransform(ModelImage srcImage, TransMatrix xfrm, int interp, float oXres, float oYres, int oXdim, int oYdim, int[] units, boolean tVOI, boolean clip, boolean pad)	Creates a new AlgorithmTransform object.
AlgorithmTransform(ModelImage srcImage, TransMatrix xfrm, int interp, float oXres, float oYres, int oXdim, int oYdim, int[] units, boolean tVOI, boolean clip, boolean pad, boolean doCenter, WildMagic.LibFoundation.Mathematics.Vector3f center)	Creates a new AlgorithmTransform object.

Method Summary

Modifier and Type	Method	Description
static ModelImage	bspline(ModelImage image, ModelImage resultImage, int degree, TransMatrix xfrm, ViewJProgressBar progressBar)	Performs bspline interpolation on black and white image data.
static ModelImage	bspline4D(ModelImage image, ModelImage resultImage, int degree, TransMatrix xfrm, ViewJProgressBar progressBar)	Performs bspline interpolation on black and white image data in 4D image.
static ModelImage	bsplineC(ModelImage image, ModelImage resultImage, int degree, TransMatrix xfrm, ViewJProgressBar progressBar)	Performs bspline interpolation on color image data.
static ModelImage	bsplineC4D(ModelImage image, ModelImage resultImage, int degree, TransMatrix xfrm, ViewJProgressBar progressBar)	Performs bspline interpolation on color image data in 4D image.
void	disposeLocal()	Dispose of local variables that may be taking up lots of room.
void	finalize()	Prepares this class for destruction.
private int[]	getImageMargins(ModelImage srcImage, TransMatrix transMatrix, float dxOut, float dyOut)	Calculate necessary padding for image given applied transform.
static int[]	getImageMargins(ModelImage srcImage, TransMatrix transMatrix, float dxOut, float dyOut, float dzOut)	Calculate necessary padding for image given applied transform.
ModelImage	getTransformedImage()	Returns transformed volume.
static final TransMatrix	matrixtoInverseArray(TransMatrix transMatrix)	Converts matrix to inverse array.
void	runAlgorithm()	Starts the program.
void	setCenter(WildMagic.LibFoundation.Mathematics.Vector3f center)	DOCUMENT ME!
void	setDoCenter(boolean doCenter)	DOCUMENT ME!
void	setFillValue(float fillValue)	Set value for out of bounds transformation values.
void	setPadValue(float padValue)	Deprecated. The value is not just used for padding.
void	setSuppressProgressBar(boolean suppressProgressBar)
void	setUpdateOriginFlag(boolean originFlag)	Sets the origin flag used indicated that origin should be changed based using the supplied transformation matrix.
void	setUseScannerAnatomical(boolean useSA)	Sets the tranform to set orientation to AXIAL (this is a scanner anatomical transform).
private void	transform()	Creates buffer for new image, prepares transformation matrix, and calls transform function for interpolation specified.
private void	transform25DVOI(ModelImage image, double[] imgBuffer, TransMatrix kTM)	Transforms and resamples a 3D VOI using nearest neighbor interpolation.
private void	transform2DVOI(ModelImage image, double[] imgBuffer, TransMatrix kTM)	Transforms and resamples a 2D VOI using nearest neighbor interpolation.
private void	transform3DVOI(ModelImage image, double[] imgBuffer, TransMatrix kTM)	Transforms and resamples a 3D VOI using nearest neighbor interpolation.
private void	transform3DVOIByte(ModelImage image, byte[] imgBuffer, TransMatrix kTM)	Transforms and resamples a 3D VOI using nearest neighbor interpolation.
private void	transformAlgorithmBspline2D(double[] imgBuf, TransMatrix kTM, int degree)	Transforms and resamples volume using Bspline interpolation.
private void	transformAlgorithmBspline2DC(double[] imgBuf, TransMatrix kTM, int degree)	Transforms and resamples volume using Bspline interpolation.
private void	transformAlgorithmBspline3D(double[] imgBuf, TransMatrix kTM, int degree)	Transforms and resamples volume using Bspline interpolation.
private void	transformAlgorithmBspline3DC(double[] imgBuf, TransMatrix kTM, int degree)	Transforms and resamples volume using Bspline interpolation.
private void	transformAlgorithmBspline4D(double[] imgBuf, TransMatrix kTM, int degree)	Transforms and resamples volume using Bspline interpolation.
private void	transformAlgorithmBspline4DC(double[] imgBuf, TransMatrix kTM, int degree)	Transforms and resamples color volume using Bspline interpolation.
private void	transformBilinear(double[] imgBuf, TransMatrix kTM)	Transforms and resamples volume using bilinear interpolation.
static final void	transformBilinear(float[] imgBuf, float[] tImgBuf, TransMatrix trans, int iXdim, int iYdim, float iXres, float iYres, int oXdim, int oYdim, float oXres, float oYres, ViewJProgressBar progressBar)	Transforms using bilinear interpolation.
static final void	transformBilinear(float[] imgBuf, float[] tImgBuf, TransMatrix trans, int iXdim, int iYdim, float iXres, float iYres, int oXdim, int oYdim, float oXres, float oYres, ViewJProgressBar progressBar, boolean activeImage)	Transforms using bilinear interpolation.
static final void	transformBilinear(float[] imgBuf, ModelImage transformedImg, TransMatrix trans, int iXdim, int iYdim, float iXres, float iYres, ViewJProgressBar progressBar)	Transforms using bilinear interpolation.
static final void	transformBilinear(float[] imgBuf, ModelImage transformedImg, TransMatrix trans, int iXdim, int iYdim, float iXres, float iYres, ViewJProgressBar progressBar, boolean activeImage)	Transforms using bilinear interpolation.
static final void	transformBilinear(ModelImage image, ModelImage transformedImg, TransMatrix trans, ViewJProgressBar progressBar)	Transforms using bilinear interpolation.
static final void	transformBilinear(ModelImage image, ModelImage transformedImg, TransMatrix trans, ViewJProgressBar progressBar, boolean activeImage)	Transforms using bilinear interpolation.
static final void	transformBilinear(ModelImage image, ModelImage transformedImg, TransMatrix trans, ViewJProgressBar progressBar, boolean activeImage, float fillValue)	Transforms using bilinear interpolation.
private void	transformBilinear3D(double[] imgBuf, TransMatrix kTM)	Transforms and resamples volume using bilinear interpolation.
private void	transformBilinear3DC(double[] imgBuf, float[] imgBuf2, TransMatrix kTM)	Transforms and resamples volume using bilinear interpolation (2.5D) This version used with color images.
private void	transformBilinear4D(double[] imgBuf, TransMatrix kTM)	Transforms and resamples volume using bilinear interpolation (2.5D) Used as a slice only algorithm on 3D images.
private void	transformBilinear4DC(double[] imgBuf, float[] imgBuf2, TransMatrix kTM)	Transforms and resamples volume using bilinear interpolation This version used with color images This alogorithm used on a slice by slice basis on 4D images.
private void	transformBilinearC(double[] imgBuf, float[] imgBuf2, TransMatrix kTM)	Transforms and resamples volume using bilinear interpolation.
static final void	transformBilinearC(ModelImage image, ModelImage transformedImg, TransMatrix trans, int oXdim, int oYdim, float oXres, float oYres)	Used on color images.
static final void	transformBilinearC(ModelImage image, ModelImage transformedImg, TransMatrix trans, int oXdim, int oYdim, float oXres, float oYres, float fillValue)	Used on color images.
private void	transformCubicLagrangian2D(double[] imgBuf, TransMatrix kTM, boolean clip)	Transforms and resamples volume using cubic Lagrangian interpolation.
private void	transformCubicLagrangian2DC(double[] imgBuf, float[] imgBuf2, TransMatrix kTM, boolean clip)	Transforms and resamples volume using cubic Lagrangian interpolation.
private void	transformCubicLagrangian3D(double[] imgBuf, TransMatrix kTM, boolean clip)	Transforms and resamples volume using cubic Lagrangian interpolation.
private void	transformCubicLagrangian3DC(double[] imgBuf, float[] imgBuf2, TransMatrix kTM, boolean clip)	Transforms and resamples volume using cubic Lagrangian interpolation.
private void	transformCubicLagrangian3Dim2D(double[] imgBuf, TransMatrix kTM, boolean clip)	Transforms and resamples volume using cubic Lagrangian interpolation Does a slice by slice cubic Lagrangian interpolation on a 3 dimensional object.
private void	transformCubicLagrangian3Dim2DC(double[] imgBuf, float[] imgBuf2, TransMatrix kTM, boolean clip)	Transforms and resamples volume using cubic Lagrangian interpolation This version used with color images This version performs a slice by slice algorithm on a 3 dimensional object.
private void	transformCubicLagrangian4D(double[] imgBuf, TransMatrix kTM, boolean clip)	Transforms and resamples 4 dimensional object using 3D cubic Lagrangian interpolation.
private void	transformCubicLagrangian4DC(double[] imgBuf, float[] imgBuffer2, TransMatrix kTM, boolean clip)	Transforms and resamples 4 dimensional object using 3D cubic Lagrangian interpolation.
private void	transformCubicLagrangian4Dim2D(double[] imgBuf, TransMatrix kTM, boolean clip)	Transforms and resamples volume using cubic Lagrangian interpolation Does a slice by slice cubic Lagrangian interpolation on a 4 dimensional object.
private void	transformCubicLagrangian4Dim2DC(double[] imgBuf, float[] imgBuf2, TransMatrix kTM, boolean clip)	Transforms and resamples volume using cubic Lagrangian interpolation This version used with color images This version performs a slice by slice algorithm on a 4 dimensional object.
private void	transformHepticLagrangian2D(double[] imgBuf, TransMatrix kTM, boolean clip)	Transforms and resamples volume using heptic Lagrangian interpolation.
private void	transformHepticLagrangian2DC(double[] imgBuf, float[] imgBuf2, TransMatrix kTM, boolean clip)	Transforms and resamples volume using heptic Lagrangian interpolation This version used with color images.
private void	transformHepticLagrangian3D(double[] imgBuf, TransMatrix kTM, boolean clip)	Transforms and resamples volume using heptic Lagrangian interpolation.
private void	transformHepticLagrangian3DC(double[] imgBuf, float[] imgBuf2, TransMatrix kTM, boolean clip)	Transforms and resamples volume using heptic Lagrangian interpolation This version used with color images.
private void	transformHepticLagrangian3Dim2D(double[] imgBuf, TransMatrix kTM, boolean clip)	Transforms and resamples volume using heptic Lagrangian interpolation Does a slice by slice heptic Lagrangian interpolation on a 3 dimensional object.
private void	transformHepticLagrangian3Dim2DC(double[] imgBuf, float[] imgBuf2, TransMatrix kTM, boolean clip)	Transforms and resamples volume using heptic Lagrangian interpolation This version used with color images This version performs a slice by slice algorithm on a 3 dimensional object.
private void	transformHepticLagrangian4D(double[] imgBuf, TransMatrix kTM, boolean clip)	transforms and resamples 4 dimensional object using 3D heptic Lagrangian interpolation.
private void	transformHepticLagrangian4DC(double[] imgBuf, float[] imgBuffer2, TransMatrix kTM, boolean clip)	transforms and resamples 4 dimensional object using 3D heptic Lagrangian interpolation.
private void	transformHepticLagrangian4Dim2D(double[] imgBuf, TransMatrix kTM, boolean clip)	Transforms and resamples volume using heptic Lagrangian interpolation Does a slice by slice heptic Lagrangian interpolation on a 4 dimensional object.
private void	transformHepticLagrangian4Dim2DC(double[] imgBuf, float[] imgBuf2, TransMatrix kTM, boolean clip)	Transforms and resamples volume using heptic Lagrangian interpolation This version used with color images This version performs a slice by slice algorithm on a 4 dimensional object.
private void	transformNearestNeighbor2D(double[] imgBuf, TransMatrix kTM)	Transforms and resamples volume using nearest neighbor interpolation.
static final void	transformNearestNeighbor2D(float[] imgBuf, float[] tImgBuf, TransMatrix trans, int xdim, int ydim)	Transforms using Nearest neighbor interpolation.
static final void	transformNearestNeighbor2D(float[] imgBuf, float[] tImgBuf, TransMatrix trans, int iXdim, int iYdim, float iXres, float iYres, int oXdim, int oYdim, float oXres, float oYres)	Transforms using Nearest neighbor interpolation.
private void	transformNearestNeighbor2DC(double[] imgBuf, float[] imgBuf2, TransMatrix kTM)	Transforms and resamples volume using nearest neighbor interpolation.
private void	transformNearestNeighbor3D(double[] imgBuf, TransMatrix kTM)	Transforms and resamples volume using nearest neighbor interpolation.
static final void	transformNearestNeighbor3D(float[] imgBuf, ModelImage transformedImg, int Xdim, int Ydim, int Zdim, TransMatrix trans)	Transforms and resamples volume using nearest neighbor interpolation.
private void	transformNearestNeighbor3DC(double[] imgBuf, float[] imgBuf2, TransMatrix kTM)	Transforms and resamples volume using nearest neighbor interpolation.
private void	transformNearestNeighbor3Dim2D(double[] imgBuf, TransMatrix kTM)	Transforms and resamples volume using nearest neighbor interpolation.
private void	transformNearestNeighbor3Dim2DC(double[] imgBuf, float[] imgBuf2, TransMatrix kTM)	Transforms and resamples volume using nearest neighbor interpolation.
private void	transformNearestNeighbor4D(double[] imgBuf, TransMatrix kTM)	Transforms and resamples 4 dimensional object using 3D algorithm using nearest neighbor interpolation.
private void	transformNearestNeighbor4DC(double[] imgBuf, float[] imgBuffer2, TransMatrix kTM)	Transforms and resamples 4 dimensional object using 3D algorithm using nearest neighbor interpolation.
private void	transformNearestNeighbor4Dim2D(double[] imgBuf, TransMatrix kTM)	Transforms and resamples volume using nearest neighbor interpolation.
private void	transformNearestNeighbor4Dim2DC(double[] imgBuf, float[] imgBuf2, TransMatrix kTM)	Transforms and resamples volume using nearest neighbor interpolation.
private void	transformQuinticLagrangian2D(double[] imgBuf, TransMatrix kTM, boolean clip)	Transforms and resamples volume using quintic Lagrangian interpolation.
private void	transformQuinticLagrangian2DC(double[] imgBuf, float[] imgBuf2, TransMatrix kTM, boolean clip)	Transforms and resamples volume using quintic Lagrangian interpolation This version used with color images.
private void	transformQuinticLagrangian3D(double[] imgBuf, TransMatrix kTM, boolean clip)	Transforms and resamples volume using quintic Lagrangian interpolation.
private void	transformQuinticLagrangian3DC(double[] imgBuf, float[] imgBuf2, TransMatrix kTM, boolean clip)	Transforms and resamples volume using quintic Lagrangian interpolation This version used with color images.
private void	transformQuinticLagrangian3Dim2D(double[] imgBuf, TransMatrix kTM, boolean clip)	Transforms and resamples volume using quintic Lagrangian interpolation Does a slice by slice quintic Lagrangian interpolation on a 3 dimensional object.
private void	transformQuinticLagrangian3Dim2DC(double[] imgBuf, float[] imgBuf2, TransMatrix kTM, boolean clip)	Transforms and resamples volume using quintic Lagrangian interpolation This version used with color images This version performs a slice by slice algorithm on a 3 dimensional object.
private void	transformQuinticLagrangian4D(double[] imgBuf, TransMatrix kTM, boolean clip)	Transforms and resamples 4 dimensional object using 3D quintic Lagrangian interpolation.
private void	transformQuinticLagrangian4DC(double[] imgBuf, float[] imgBuffer2, TransMatrix kTM, boolean clip)	Transforms and resamples 4 dimensional color object using 3D quintic Lagrangian interpolation.
private void	transformQuinticLagrangian4Dim2D(double[] imgBuf, TransMatrix kTM, boolean clip)	Transforms and resamples volume using quintic Lagrangian interpolation Does a slice by slice quintic Lagrangian interpolation on a 4 dimensional object.
private void	transformQuinticLagrangian4Dim2DC(double[] imgBuf, float[] imgBuf2, TransMatrix kTM, boolean clip)	Transforms and resamples volume using quintic Lagrangian interpolation This version used with color images This version performs a slice by slice algorithm on a 4 dimensional object.
private void	transformTrilinear(double[] imgBuffer, TransMatrix kTM)	Transforms and resamples a 3D volume using trilinear interpolation.
static final void	transformTrilinear(float[] imgBuffer, float[] tImgBuf, TransMatrix trans, int iXdim, int iYdim, int iZdim, float iXres, float iYres, float iZres, int oXdim, int oYdim, int oZdim, float oXres, float oYres, float oZres, ViewJProgressBar progressBar)	Transforms and resamples volume using trilinear interpolation.
static final void	transformTrilinear(float[] imgBuffer, float[] tImgBuf, TransMatrix trans, int iXdim, int iYdim, int iZdim, float iXres, float iYres, float iZres, int oXdim, int oYdim, int oZdim, float oXres, float oYres, float oZres, ViewJProgressBar progressBar, boolean activeImage)	Transforms and resamples volume using trilinear interpolation.
static final void	transformTrilinear(float[] imgBuffer, ModelImage transformedImg, TransMatrix trans, int iXdim, int iYdim, int iZdim, float iXres, float iYres, float iZres, ViewJProgressBar progressBar)	Transforms and resamples volume using trilinear interpolation.
static final void	transformTrilinear(float[] imgBuffer, ModelImage transformedImg, TransMatrix trans, int iXdim, int iYdim, int iZdim, float iXres, float iYres, float iZres, ViewJProgressBar progressBar, boolean activeImage)	Transforms and resamples volume using trilinear interpolation.
static final void	transformTrilinear(ModelImage image, ModelImage transformedImg, TransMatrix trans, ViewJProgressBar progressBar)	Transforms and resamples volume using trilinear interpolation.
static final void	transformTrilinear(ModelImage image, ModelImage transformedImg, TransMatrix trans, ViewJProgressBar progressBar, boolean activeImage)	Transforms and resamples volume using trilinear interpolation.
static final void	transformTrilinear(ModelImage image, ModelImage transformedImg, TransMatrix trans, ViewJProgressBar progressBar, boolean activeImage, float fillValue)	Transforms and resamples volume using trilinear interpolation.
private void	transformTrilinear4D(double[] imgBuffer, TransMatrix kTM)	Transforms and resamples 4 dimensional object using trilinear interpolation.
static ModelImage	transformTrilinear4D(ModelImage image, ModelImage resultImage, TransMatrix xfrm, ViewJProgressBar progressBar)	Performs trilinear interpolation on black and white image data in a 4D image.
private void	transformTrilinear4DByteC(byte[] imgBuffer, byte[] imgBuffer2, TransMatrix kTM)	Transforms and resamples 4 dimensional color ARGB object using trilinear interpolation.
private void	transformTrilinear4DC(double[] imgBuffer, float[] imgBuffer2, TransMatrix kTM)	Transforms and resamples 4 dimensional color object using trilinear interpolation.
private void	transformTrilinearByteC(byte[] imgBuffer, byte[] imgBuffer2, TransMatrix kTM)	Transforms and resamples volume using trilinear interpolation This version is used with ARGB color images.
private void	transformTrilinearC(double[] imgBuffer, float[] imgBuffer2, TransMatrix kTM)	Transforms and resamples volume using trilinear interpolation This version is used with color images.
static ModelImage	transformTrilinearC(ModelImage image, ModelImage resultImage, float[] imgBuffer, TransMatrix xfrm, ViewJProgressBar progressBar)	Performs trilinear interpolation on color image data.
static final void	transformTrilinearC(ModelImage image, ModelImage transformedImg, TransMatrix trans, int oXdim, int oYdim, int oZdim, float oXres, float oYres, float oZres)	Transforms and resamples volume using trilinear interpolation Use on color images USE THIS IF OUTPUT IMAGE HAS DIFFERENT DIM/RES THAN INPUT IMAGE.
static final void	transformTrilinearC(ModelImage image, ModelImage transformedImg, TransMatrix trans, int oXdim, int oYdim, int oZdim, float oXres, float oYres, float oZres, float fillValue)	Transforms and resamples volume using trilinear interpolation Use on color images USE THIS IF OUTPUT IMAGE HAS DIFFERENT DIM/RES THAN INPUT IMAGE.
static ModelImage	transformTrilinearC4D(ModelImage image, ModelImage resultImage, TransMatrix xfrm, ViewJProgressBar progressBar)	Performs trilinear interpolation on color image data in a 4D image.
private void	transformWSinc2D(double[] imgBuf, TransMatrix kTM, boolean clip)	Transforms and resamples volume using windowed sinc interpolation.
private void	transformWSinc2DC(double[] imgBuf, float[] imgBuf2, TransMatrix kTM, boolean clip)	Transforms and resamples volume using windowed sinc interpolation This version used with color images.
private void	transformWSinc3D(double[] imgBuf, TransMatrix kTM, boolean clip)	Transforms and resamples volume using windowed sinc interpolation.
private void	transformWSinc3DC(double[] imgBuf, float[] imgBuf2, TransMatrix kTM, boolean clip)	Transforms and resamples volume using windowed sinc interpolation This version used with color images.
private void	transformWSinc3Dim2D(double[] imgBuf, TransMatrix kTM, boolean clip)	Transforms and resamples volume using windowed sinc interpolation Does a slice by slice windowed sinc interpolation on a 3 dimensional object.
private void	transformWSinc3Dim2DC(double[] imgBuf, float[] imgBuf2, TransMatrix kTM, boolean clip)	Transforms and resamples volume using windowed sinc interpolation This version used with color images This version performs a slice by slice algorithm on a 3 dimensional object.
private void	transformWSinc4D(double[] imgBuf, TransMatrix kTM, boolean clip)	Transforms and resamples 4 dimensional object using 3D windowed sinc interpolation.
private void	transformWSinc4DC(double[] imgBuf, float[] imgBuffer2, TransMatrix kTM, boolean clip)	Transforms and resamples 4 dimensional object using 3D windowed sinc interpolation.
private void	transformWSinc4Dim2D(double[] imgBuf, TransMatrix kTM, boolean clip)	Transforms and resamples volume using windowed sinc interpolation Does a slice by slice windowed sinc interpolation on a 4 dimensional object.
private void	transformWSinc4Dim2DC(double[] imgBuf, float[] imgBuf2, TransMatrix kTM, boolean clip)	Transforms and resamples volume using windowed sinc interpolation This version used with color images This version performs a slice by slice algorithm on a 4 dimensional object.
private static void	updateFileInfo(ModelImage image, ModelImage resultImage, float[] resolutions, int[] units, TransMatrix matrix, boolean useSATransform, AlgorithmBase srcAlg)	Copy important file information to resultant image structure.
private void	updateOrigin()	Translate the image origin from image space to patient space (scanner space).
private static void	updateOrigin(TransMatrix xfrm)	Update origin.
private void	updateOriginMargins()	Update origin to reflect padding.
private void	updateOriginMargins2D()	Update origin to reflect padding.

Methods inherited from class gov.nih.mipav.model.algorithms.AlgorithmBase

actionPerformed, addListener, addProgressChangeListener, calculateImageSize, calculatePrincipleAxis, computeElapsedTime, computeElapsedTime, convertIntoFloat, delinkProgressToAlgorithm, delinkProgressToAlgorithmMulti, displayError, errorCleanUp, fireProgressStateChanged, fireProgressStateChanged, fireProgressStateChanged, fireProgressStateChanged, fireProgressStateChanged, generateProgressValues, getDestImage, getElapsedTime, getMask, getMaxProgressValue, getMinProgressValue, getNumberOfThreads, getProgress, getProgressChangeListener, getProgressChangeListeners, getProgressModulus, getProgressStep, getProgressValues, getSrcImage, isCompleted, isImage25D, isMultiThreadingEnabled, isRunningInSeparateThread, isThreadStopped, linkProgressToAlgorithm, linkProgressToAlgorithm, makeProgress, notifyListeners, removeListener, removeProgressChangeListener, run, setCompleted, setImage25D, setMask, setMaxProgressValue, setMinProgressValue, setMultiThreadingEnabled, setNumberOfThreads, setProgress, setProgressModulus, setProgressStep, setProgressValues, setProgressValues, setRunningInSeparateThread, setSrcImage, setStartTime, setThreadStopped, startMethod, windowActivated, windowClosed, windowClosing, windowDeactivated, windowDeiconified, windowIconified, windowOpened

Methods inherited from class java.lang.Thread

activeCount, checkAccess, clone, countStackFrames, currentThread, dumpStack, enumerate, getAllStackTraces, getContextClassLoader, getDefaultUncaughtExceptionHandler, getId, getName, getPriority, getStackTrace, getState, getThreadGroup, getUncaughtExceptionHandler, holdsLock, interrupt, interrupted, isAlive, isDaemon, isInterrupted, isVirtual, join, join, join, join, ofPlatform, ofVirtual, onSpinWait, resume, setContextClassLoader, setDaemon, setDefaultUncaughtExceptionHandler, setName, setPriority, setUncaughtExceptionHandler, sleep, sleep, sleep, start, startVirtualThread, stop, suspend, threadId, toString, yield

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Details

TRILINEAR

public static final int TRILINEAR

Trilinear interpolation.

See Also:

• Constant Field Values

BILINEAR

public static final int BILINEAR

Biilinear interpolation.

See Also:

• Constant Field Values

NEAREST_NEIGHBOR

public static final int NEAREST_NEIGHBOR

Nearest neighbor interpolation.

See Also:

• Constant Field Values

BSPLINE3

public static final int BSPLINE3

Cubic bspline interpolation.

See Also:

• Constant Field Values

BSPLINE4

public static final int BSPLINE4

Quadratic bspline interpolation.

See Also:

• Constant Field Values

CUBIC_LAGRANGIAN

public static final int CUBIC_LAGRANGIAN

Cubic lagrangian interpolation.

See Also:

• Constant Field Values

QUINTIC_LAGRANGIAN

public static final int QUINTIC_LAGRANGIAN

Quintic lagrangian interpolation.

See Also:

• Constant Field Values

HEPTIC_LAGRANGIAN

public static final int HEPTIC_LAGRANGIAN

Heptic lagrangian interpolation.

See Also:

• Constant Field Values

WSINC

public static final int WSINC

Windowed sinc interpolation.

See Also:

• Constant Field Values

updateOrigin

private static boolean updateOrigin

DOCUMENT ME!

imgOrigin

private static float[] imgOrigin

DOCUMENT ME!

imgOrient

private static int imgOrient

DOCUMENT ME!

axisOrient

private static int[] axisOrient

DOCUMENT ME!

direct

private static int[] direct

DOCUMENT ME!

margins

private static int[] margins

DOCUMENT ME!

startPos

private static float startPos

DOCUMENT ME!

startTime

private static float startTime

bufferFactor

private int bufferFactor

DOCUMENT ME!

center

private WildMagic.LibFoundation.Mathematics.Vector3f center

DOCUMENT ME!

clip

private boolean clip

DOCUMENT ME!

destResolutions

private float[] destResolutions

DOCUMENT ME!

DIM

private int DIM

DOCUMENT ME!

do25D

private boolean do25D

DOCUMENT ME!

doCenter

private boolean doCenter

DOCUMENT ME!

imgBuf

private double[] imgBuf

DOCUMENT ME!

imgBuf2

private float[] imgBuf2

DOCUMENT ME!

imgLength

private int imgLength

DOCUMENT ME!

imgLength2

private int imgLength2

DOCUMENT ME!

interp

private final int interp

DOCUMENT ME!

isSATransform

private boolean isSATransform

flag for determining if the transform is for scanner anatomical (->AXIAL).

iXdim

private final int iXdim

DOCUMENT ME!

iYdim

private final int iYdim

DOCUMENT ME!

iZdim

private int iZdim

iTdim

private int iTdim

iXres

private float iXres

DOCUMENT ME!

iYres

private float iYres

DOCUMENT ME!

iZres

private float iZres

oUnits

private final int[] oUnits

DOCUMENT ME!

oXdim

private int oXdim

DOCUMENT ME!

oYdim

private int oYdim

DOCUMENT ME!

oZdim

private int oZdim

DOCUMENT ME!

oTdim

private int oTdim

DOCUMENT ME!

oXres

private final float oXres

DOCUMENT ME!

oYres

private final float oYres

DOCUMENT ME!

oZres

private float oZres

pad

private boolean pad

DOCUMENT ME!

fillValue

private float fillValue

Used for out of bounds values in the transformation routines. Set to (float)srcImage.getMin() in the constructors.

srcImage

private ModelImage srcImage

DOCUMENT ME!

destImage

private ModelImage destImage

DOCUMENT ME!

maskImage

private ModelImage maskImage

DOCUMENT ME!

transformVOI

private boolean transformVOI

DOCUMENT ME!

transMatrix

private final TransMatrix transMatrix

DOCUMENT ME!

haveCentered

private boolean haveCentered

suppressProgressBar

private boolean suppressProgressBar

Constructor Details

AlgorithmTransform

public AlgorithmTransform(ModelImage srcImage,
 TransMatrix xfrm,
 int interp,
 float oXres,
 float oYres,
 int oXdim,
 int oYdim,
 boolean tVOI,
 boolean clip,
 boolean pad)

2D constructor for transformation algorithm. Also used for 2.5D algorithms on 3D and 4D images.

Parameters:

srcImage - ModelImage to be transformed

xfrm - Transformation matrix to be applied

interp - Type of interpolation (NEAREST_NEIGHBOR, BILINEAR, BSPLINE3, BSPLINE4, etc)

oXres - X resolution of output image

oYres - Y resolution of output image

oXdim - X dimension of output image

oYdim - Y dimension of output image

tVOI - if true the VOI should be transformed with the volume

clip - if true output range is clipped to input range

pad - if true output image is padded so that none of the image is clipped

AlgorithmTransform

public AlgorithmTransform(ModelImage srcImage,
 TransMatrix xfrm,
 int interp,
 float oXres,
 float oYres,
 int oXdim,
 int oYdim,
 int[] units,
 boolean tVOI,
 boolean clip,
 boolean pad)

Creates a new AlgorithmTransform object.

Parameters:

srcImage - ModelImage to be transformed

xfrm - Transformation matrix to be applied

interp - Type of interpolation (NEAREST_NEIGHBOR, BILINEAR, BSPLINE3, BSPLINE4, etc)

oXres - X resolution of output image

oYres - Y resolution of output image

oXdim - X dimension of output image

oYdim - Y dimension of output image

units - DOCUMENT ME!

tVOI - if true the VOI should be transformed with the volume

clip - if true output range is clipped to input range

pad - if true output image is padded so that none of the image is clipped

AlgorithmTransform

public AlgorithmTransform(ModelImage srcImage,
 TransMatrix xfrm,
 int interp,
 float oXres,
 float oYres,
 int oXdim,
 int oYdim,
 int[] units,
 boolean tVOI,
 boolean clip,
 boolean pad,
 boolean doCenter,
 WildMagic.LibFoundation.Mathematics.Vector3f center)

Creates a new AlgorithmTransform object.

Parameters:

srcImage - DOCUMENT ME!

xfrm - DOCUMENT ME!

interp - DOCUMENT ME!

oXres - DOCUMENT ME!

oYres - DOCUMENT ME!

oXdim - DOCUMENT ME!

oYdim - DOCUMENT ME!

units - DOCUMENT ME!

tVOI - DOCUMENT ME!

clip - DOCUMENT ME!

pad - DOCUMENT ME!

doCenter -

center -

AlgorithmTransform

public AlgorithmTransform(ModelImage _srcImage,
 TransMatrix xfrm,
 int interp,
 float _oXres,
 float _oYres,
 float _oZres,
 int _oXdim,
 int _oYdim,
 int _oZdim,
 boolean tVOI,
 boolean clip,
 boolean pad)

3D constructor for transformation algorithm. Also used for 3D algorithms on 4D images.

Parameters:

_srcImage - ModelImage to be transformed

xfrm - Transformation matrix to be applied

interp - Type of interpolation (NEAREST_NEIGHBOR, TRILINEAR, BSPLINE3, BSPLINE4, etc)

_oXres - X resolution of output image

_oYres - Y resolution of output image

_oZres - Z resolution of output image

_oXdim - X dimension of output image

_oYdim - Y dimension of output image

_oZdim - Z dimension of output image

tVOI - if true the VOI should be transformed with the volume

clip - if true output range is clipped to input range

pad - if true output image is padded so that none of the image is clipped

AlgorithmTransform

public AlgorithmTransform(ModelImage _srcImage,
 TransMatrix xfrm,
 int interp,
 float _oXres,
 float _oYres,
 float _oZres,
 int _oXdim,
 int _oYdim,
 int _oZdim,
 int[] units,
 boolean tVOI,
 boolean clip,
 boolean pad)

Creates a new $class.name$ object.

Parameters:

_srcImage - DOCUMENT ME!

xfrm - DOCUMENT ME!

interp - DOCUMENT ME!

_oXres - DOCUMENT ME!

_oYres - DOCUMENT ME!

_oZres - DOCUMENT ME!

_oXdim - DOCUMENT ME!

_oYdim - DOCUMENT ME!

_oZdim - DOCUMENT ME!

units - DOCUMENT ME!

tVOI - DOCUMENT ME!

clip - DOCUMENT ME!

pad - DOCUMENT ME!

AlgorithmTransform

public AlgorithmTransform(ModelImage _srcImage,
 TransMatrix xfrm,
 int interp,
 float _oXres,
 float _oYres,
 float _oZres,
 int _oXdim,
 int _oYdim,
 int _oZdim,
 int[] units,
 boolean tVOI,
 boolean clip,
 boolean pad,
 boolean doCenter,
 WildMagic.LibFoundation.Mathematics.Vector3f center)

Creates a new $class.name$ object.

Parameters:

_srcImage - DOCUMENT ME!

xfrm - DOCUMENT ME!

interp - DOCUMENT ME!

_oXres - DOCUMENT ME!

_oYres - DOCUMENT ME!

_oZres - DOCUMENT ME!

_oXdim - DOCUMENT ME!

_oYdim - DOCUMENT ME!

_oZdim - DOCUMENT ME!

units - DOCUMENT ME!

tVOI - DOCUMENT ME!

clip - DOCUMENT ME!

pad - DOCUMENT ME!

doCenter -

center -

Method Details

setSuppressProgressBar

public void setSuppressProgressBar(boolean suppressProgressBar)

Parameters:

suppressProgressBar -

bspline

public static ModelImage bspline(ModelImage image,
 ModelImage resultImage,
 int degree,
 TransMatrix xfrm,
 ViewJProgressBar progressBar)

Performs bspline interpolation on black and white image data.

Parameters:

image - Image from which the data is derived

resultImage - Image to put result in; can be null.

degree - Degree of the spline algorithm, either 3 or 4.

xfrm - Transformation to apply.

progressBar - Buffer containing image data.

Returns:

DOCUMENT ME!

bspline4D

public static ModelImage bspline4D(ModelImage image,
 ModelImage resultImage,
 int degree,
 TransMatrix xfrm,
 ViewJProgressBar progressBar)

Performs bspline interpolation on black and white image data in 4D image. Works time slice by time slice.

Parameters:

image - Image from which the data is derived

resultImage - Image to put result in; can be null.

degree - Degree of the spline algorithm, either 3 or 4.

xfrm - Transformation to apply.

progressBar - Buffer containing image data.

Returns:

DOCUMENT ME!

bsplineC

public static ModelImage bsplineC(ModelImage image,
 ModelImage resultImage,
 int degree,
 TransMatrix xfrm,
 ViewJProgressBar progressBar)

Performs bspline interpolation on color image data.

Parameters:

image - Image from which the data is derived

resultImage - Image to put result in; can be null.

degree - Degree of the spline algorithm, either 3 or 4.

xfrm - Transformation to apply.

progressBar - Buffer containing image data.

Returns:

DOCUMENT ME!

bsplineC4D

public static ModelImage bsplineC4D(ModelImage image,
 ModelImage resultImage,
 int degree,
 TransMatrix xfrm,
 ViewJProgressBar progressBar)

Performs bspline interpolation on color image data in 4D image. Works time slice by time slice.

Parameters:

image - Image from which the data is derived

resultImage - Image to put result in; can be null.

degree - Degree of the spline algorithm, either 3 or 4.

xfrm - Transformation to apply.

progressBar - Buffer containing image data.

Returns:

DOCUMENT ME!

getImageMargins

public static int[] getImageMargins(ModelImage srcImage,
 TransMatrix transMatrix,
 float dxOut,
 float dyOut,
 float dzOut)

Calculate necessary padding for image given applied transform.

Parameters:

srcImage - DOCUMENT ME!

transMatrix - array with transformation matrix

dxOut - DOCUMENT ME!

dyOut - DOCUMENT ME!

dzOut - DOCUMENT ME!

Returns:

DOCUMENT ME!

matrixtoInverseArray

public static final TransMatrix matrixtoInverseArray(TransMatrix transMatrix)

Converts matrix to inverse array.

Parameters:

transMatrix - Matrix to convert.

Returns:

The inverted array.

transformBilinear

public static final void transformBilinear(ModelImage image,
 ModelImage transformedImg,
 TransMatrix trans,
 ViewJProgressBar progressBar)

Transforms using bilinear interpolation.

Parameters:

image - Image to be transformed

transformedImg - Transformed image

trans - Transformation matrix to be applied

progressBar - Progress bar to update. Can be null. Should NOT have cancel button.

transformBilinear

public static final void transformBilinear(ModelImage image,
 ModelImage transformedImg,
 TransMatrix trans,
 ViewJProgressBar progressBar,
 boolean activeImage)

Transforms using bilinear interpolation.

Parameters:

image - Image to be transformed

transformedImg - Transformed image

trans - Transformation matrix to be applied

progressBar - Progress bar to update. Can be null. Should NOT have cancel button.

activeImage - true if the algorithm is being run in a separate thread, false otherwise, to control progress bar repainting

transformBilinear

public static final void transformBilinear(ModelImage image,
 ModelImage transformedImg,
 TransMatrix trans,
 ViewJProgressBar progressBar,
 boolean activeImage,
 float fillValue)

Transforms using bilinear interpolation.

Parameters:

image - Image to be transformed

transformedImg - Transformed image

trans - Transformation matrix to be applied

progressBar - Progress bar to update. Can be null. Should NOT have cancel button.

activeImage - true if the algorithm is being run in a separate thread, false otherwise, to control progress bar repainting

fillValue - value used for out of bounds pixels

transformBilinear

public static final void transformBilinear(float[] imgBuf,
 ModelImage transformedImg,
 TransMatrix trans,
 int iXdim,
 int iYdim,
 float iXres,
 float iYres,
 ViewJProgressBar progressBar)

Transforms using bilinear interpolation.

Parameters:

imgBuf - Image buffer to be transformed

transformedImg - Transformed image

trans - Transformation matrix to be applied

iXdim - X dimension of input image

iYdim - Y dimension of input image

iXres - X resolution of input image

iYres - Y resolution of input image

progressBar - Progress bar to update. Can be null. Should NOT have cancel button.

transformBilinear

public static final void transformBilinear(float[] imgBuf,
 ModelImage transformedImg,
 TransMatrix trans,
 int iXdim,
 int iYdim,
 float iXres,
 float iYres,
 ViewJProgressBar progressBar,
 boolean activeImage)

Transforms using bilinear interpolation.

Parameters:

imgBuf - Image buffer to be transformed

transformedImg - Transformed image

trans - Transformation matrix to be applied

iXdim - X dimension of input image

iYdim - Y dimension of input image

iXres - X resolution of input image

iYres - Y resolution of input image

progressBar - Progress bar to update. Can be null. Should NOT have cancel button.

activeImage - true if the algorithm is being run in a separate thread, false otherwise, to control progress bar repainting

transformBilinear

public static final void transformBilinear(float[] imgBuf,
 float[] tImgBuf,
 TransMatrix trans,
 int iXdim,
 int iYdim,
 float iXres,
 float iYres,
 int oXdim,
 int oYdim,
 float oXres,
 float oYres,
 ViewJProgressBar progressBar)

Transforms using bilinear interpolation.

Parameters:

imgBuf - Image buffer to be transformed

tImgBuf - Transformed image

trans - Transformation matrix to be applied

iXdim - X dimension of input image

iYdim - Y dimension of input image

iXres - X resolution of input image

iYres - Y resolution of input image

oXdim - X dimension of output image

oYdim - Y dimension of output image

oXres - X resolution of output image

oYres - Y resolution of output image

progressBar - Progress bar to be updated. Can be null. Should NOT have cancel button.

transformBilinear

public static final void transformBilinear(float[] imgBuf,
 float[] tImgBuf,
 TransMatrix trans,
 int iXdim,
 int iYdim,
 float iXres,
 float iYres,
 int oXdim,
 int oYdim,
 float oXres,
 float oYres,
 ViewJProgressBar progressBar,
 boolean activeImage)

Transforms using bilinear interpolation.

Parameters:

imgBuf - Image buffer to be transformed

tImgBuf - Transformed image

trans - Transformation matrix to be applied

iXdim - X dimension of input image

iYdim - Y dimension of input image

iXres - X resolution of input image

iYres - Y resolution of input image

oXdim - X dimension of output image

oYdim - Y dimension of output image

oXres - X resolution of output image

oYres - Y resolution of output image

progressBar - Progress bar to be updated. Can be null. Should NOT have cancel button.

activeImage - true if the algorithm is being run in a separate thread, false otherwise, to control progress bar repainting

transformBilinearC

public static final void transformBilinearC(ModelImage image,
 ModelImage transformedImg,
 TransMatrix trans,
 int oXdim,
 int oYdim,
 float oXres,
 float oYres)

Used on color images. USE THIS IF OUTPUT IMAGE HAS DIFFERENT DIM/RES THAN INPUT IMAGE

Parameters:

image - Input image to be transformed

transformedImg - Transformed image

trans - Transformation matrix to be applied

oXdim - Dimensions of output image

oYdim - Dimensions of output image

oXres - Resolutions of output image

oYres - Resolutions of output image

transformBilinearC

public static final void transformBilinearC(ModelImage image,
 ModelImage transformedImg,
 TransMatrix trans,
 int oXdim,
 int oYdim,
 float oXres,
 float oYres,
 float fillValue)

Used on color images. USE THIS IF OUTPUT IMAGE HAS DIFFERENT DIM/RES THAN INPUT IMAGE

Parameters:

image - Input image to be transformed

transformedImg - Transformed image

trans - Transformation matrix to be applied

oXdim - Dimensions of output image

oYdim - Dimensions of output image

oXres - Resolutions of output image

oYres - Resolutions of output image

fillValue - value used for out of bounds pixel transformations

transformNearestNeighbor2D

public static final void transformNearestNeighbor2D(float[] imgBuf,
 float[] tImgBuf,
 TransMatrix trans,
 int xdim,
 int ydim)

Transforms using Nearest neighbor interpolation.

Parameters:

imgBuf - Image buffer to be transformed

tImgBuf - Transformed image buffer

trans - Transformation matrix to be applied

xdim - X dimension of input AND output image

ydim - Y dimension of input AND output image

transformNearestNeighbor2D

public static final void transformNearestNeighbor2D(float[] imgBuf,
 float[] tImgBuf,
 TransMatrix trans,
 int iXdim,
 int iYdim,
 float iXres,
 float iYres,
 int oXdim,
 int oYdim,
 float oXres,
 float oYres)

Transforms using Nearest neighbor interpolation.

Parameters:

imgBuf - Image buffer to be transformed

tImgBuf - Transformed image buffer

trans - Transformation matrix to be applied

iXdim - X dimension of input image

iYdim - Y dimension of input image

iXres - X resolution of input image

iYres - Y resolution of input image

oXdim - X dimension of output image

oYdim - Y dimension of output image

oXres - X resolution of output image

oYres - Y resolution of output image

transformNearestNeighbor3D

public static final void transformNearestNeighbor3D(float[] imgBuf,
 ModelImage transformedImg,
 int Xdim,
 int Ydim,
 int Zdim,
 TransMatrix trans)

Transforms and resamples volume using nearest neighbor interpolation.

Parameters:

imgBuf - Image array to transform

transformedImg - Transformed image.

Xdim - X dimension of input image

Ydim - Y dimension of input image

Zdim - Z dimension of input image

trans - Transformation matrix to be applied

transformTrilinear

public static final void transformTrilinear(ModelImage image,
 ModelImage transformedImg,
 TransMatrix trans,
 ViewJProgressBar progressBar)

Transforms and resamples volume using trilinear interpolation.

Parameters:

image - Image to transform

transformedImg - Transformed image.

trans - Transformation matrix to be applied

progressBar - The progress bar. Can be null. Should NOT have a cancel button.

transformTrilinear

public static final void transformTrilinear(ModelImage image,
 ModelImage transformedImg,
 TransMatrix trans,
 ViewJProgressBar progressBar,
 boolean activeImage)

Transforms and resamples volume using trilinear interpolation.

Parameters:

image - Image to transform

transformedImg - Transformed image.

trans - Transformation matrix to be applied

progressBar - The progress bar. Can be null. Should NOT have a cancel button.

activeImage - true if the algorithm is being run in a separate thread, false otherwise, to control progress bar repainting

transformTrilinear

public static final void transformTrilinear(ModelImage image,
 ModelImage transformedImg,
 TransMatrix trans,
 ViewJProgressBar progressBar,
 boolean activeImage,
 float fillValue)

Transforms and resamples volume using trilinear interpolation.

Parameters:

image - Image to transform

transformedImg - Transformed image.

trans - Transformation matrix to be applied

progressBar - The progress bar. Can be null. Should NOT have a cancel button.

activeImage - true if the algorithm is being run in a separate thread, false otherwise, to control progress bar repainting

fillValue - value used if transformed pixel is out of bounds

transformTrilinear

public static final void transformTrilinear(float[] imgBuffer,
 ModelImage transformedImg,
 TransMatrix trans,
 int iXdim,
 int iYdim,
 int iZdim,
 float iXres,
 float iYres,
 float iZres,
 ViewJProgressBar progressBar)

Transforms and resamples volume using trilinear interpolation.

Parameters:

imgBuffer - Image array

transformedImg - Image after transform

trans - Transformation matrix to be applied

iXdim - X dimension of input image

iYdim - Y dimension of input image

iZdim - Z dimension of input image

iXres - X resolution of input image

iYres - Y resolution of input image

iZres - Z resolution of input image

progressBar - Progress bar to update. Can be null. Should NOT have a cancel button.

transformTrilinear

public static final void transformTrilinear(float[] imgBuffer,
 ModelImage transformedImg,
 TransMatrix trans,
 int iXdim,
 int iYdim,
 int iZdim,
 float iXres,
 float iYres,
 float iZres,
 ViewJProgressBar progressBar,
 boolean activeImage)

Transforms and resamples volume using trilinear interpolation.

Parameters:

imgBuffer - Image array

transformedImg - Image after transform

trans - Transformation matrix to be applied

iXdim - X dimension of input image

iYdim - Y dimension of input image

iZdim - Z dimension of input image

iXres - X resolution of input image

iYres - Y resolution of input image

iZres - Z resolution of input image

progressBar - Progress bar to update. Can be null. Should NOT have a cancel button.

activeImage - true if the algorithm is being run in a separate thread, false otherwise, to control progress bar repainting

transformTrilinear

public static final void transformTrilinear(float[] imgBuffer,
 float[] tImgBuf,
 TransMatrix trans,
 int iXdim,
 int iYdim,
 int iZdim,
 float iXres,
 float iYres,
 float iZres,
 int oXdim,
 int oYdim,
 int oZdim,
 float oXres,
 float oYres,
 float oZres,
 ViewJProgressBar progressBar)

Transforms and resamples volume using trilinear interpolation.

Parameters:

imgBuffer - Image buffer to be transformed

tImgBuf - Transformed image

trans - Transformation matrix to be applied

iXdim - X dimension of input image

iYdim - Y dimension of input image

iZdim - Z dimension of input image

iXres - X resolution of input image

iYres - Y resolution of input image

iZres - Z resolution of input image

oXdim - X dimension of output image

oYdim - Y dimension of output image

oZdim - Z dimension of output image

oXres - X resolution of output image

oYres - Y resolution of output image

oZres - Z resolution of output image

progressBar - Progress bar. Can be null. Should NOT have cancel button.

transformTrilinear

public static final void transformTrilinear(float[] imgBuffer,
 float[] tImgBuf,
 TransMatrix trans,
 int iXdim,
 int iYdim,
 int iZdim,
 float iXres,
 float iYres,
 float iZres,
 int oXdim,
 int oYdim,
 int oZdim,
 float oXres,
 float oYres,
 float oZres,
 ViewJProgressBar progressBar,
 boolean activeImage)

Transforms and resamples volume using trilinear interpolation.

Parameters:

imgBuffer - Image buffer to be transformed

tImgBuf - Transformed image

trans - Transformation matrix to be applied

iXdim - X dimension of input image

iYdim - Y dimension of input image

iZdim - Z dimension of input image

iXres - X resolution of input image

iYres - Y resolution of input image

iZres - Z resolution of input image

oXdim - X dimension of output image

oYdim - Y dimension of output image

oZdim - Z dimension of output image

oXres - X resolution of output image

oYres - Y resolution of output image

oZres - Z resolution of output image

progressBar - Progress bar. Can be null. Should NOT have cancel button.

activeImage - true if the algorithm is being run in a separate thread, false otherwise, to control progress bar repainting

transformTrilinear4D

public static ModelImage transformTrilinear4D(ModelImage image,
 ModelImage resultImage,
 TransMatrix xfrm,
 ViewJProgressBar progressBar)

Performs trilinear interpolation on black and white image data in a 4D image. Works time slice by time slice

Parameters:

image - Image from which the data is derived

resultImage - Image to put result in; can be null.

xfrm - Transformation to apply.

progressBar - Buffer containing image data.

Returns:

DOCUMENT ME!

transformTrilinearC

public static ModelImage transformTrilinearC(ModelImage image,
 ModelImage resultImage,
 float[] imgBuffer,
 TransMatrix xfrm,
 ViewJProgressBar progressBar)

Performs trilinear interpolation on color image data.

Parameters:

image - Image from which the data is derived

resultImage - Image to put result in; can be null.

imgBuffer - Buffer containing image data.

xfrm - Transformation to apply.

progressBar - DOCUMENT ME!

Returns:

DOCUMENT ME!

transformTrilinearC

public static final void transformTrilinearC(ModelImage image,
 ModelImage transformedImg,
 TransMatrix trans,
 int oXdim,
 int oYdim,
 int oZdim,
 float oXres,
 float oYres,
 float oZres)

Transforms and resamples volume using trilinear interpolation Use on color images USE THIS IF OUTPUT IMAGE HAS DIFFERENT DIM/RES THAN INPUT IMAGE.

Parameters:

image - Image to transform

transformedImg - Result image.

trans - Transformation matrix to be applied

oXdim - DOCUMENT ME!

oYdim - DOCUMENT ME!

oZdim - DOCUMENT ME!

oXres - DOCUMENT ME!

oYres - DOCUMENT ME!

oZres - DOCUMENT ME!

transformTrilinearC

public static final void transformTrilinearC(ModelImage image,
 ModelImage transformedImg,
 TransMatrix trans,
 int oXdim,
 int oYdim,
 int oZdim,
 float oXres,
 float oYres,
 float oZres,
 float fillValue)

Transforms and resamples volume using trilinear interpolation Use on color images USE THIS IF OUTPUT IMAGE HAS DIFFERENT DIM/RES THAN INPUT IMAGE.

Parameters:

image - Image to transform

transformedImg - Result image.

trans - Transformation matrix to be applied

oXdim - DOCUMENT ME!

oYdim - DOCUMENT ME!

oZdim - DOCUMENT ME!

oXres - DOCUMENT ME!

oYres - DOCUMENT ME!

oZres - DOCUMENT ME!

fillValue - value if transformed pixel is out of bounds

transformTrilinearC4D

public static ModelImage transformTrilinearC4D(ModelImage image,
 ModelImage resultImage,
 TransMatrix xfrm,
 ViewJProgressBar progressBar)

Performs trilinear interpolation on color image data in a 4D image. Works time slice by time slice.

Parameters:

image - Image from which the data is derived

resultImage - Image to put result in; can be null.

xfrm - Transformation to apply.

progressBar - Buffer containing image data.

Returns:

DOCUMENT ME!

disposeLocal

public void disposeLocal()

Dispose of local variables that may be taking up lots of room.

finalize

public void finalize()

Prepares this class for destruction.

Overrides:

finalize in class AlgorithmBase

getImageMargins

private int[] getImageMargins(ModelImage srcImage,
 TransMatrix transMatrix,
 float dxOut,
 float dyOut)

Calculate necessary padding for image given applied transform.

Parameters:

srcImage - DOCUMENT ME!

transMatrix - array with transformation matrix

dxOut - DOCUMENT ME!

dyOut - DOCUMENT ME!

Returns:

DOCUMENT ME!

getTransformedImage

public ModelImage getTransformedImage()

Returns transformed volume.

Returns:

destImage

runAlgorithm

public void runAlgorithm()

Starts the program.

Specified by:

runAlgorithm in class AlgorithmBase

setCenter

public void setCenter(WildMagic.LibFoundation.Mathematics.Vector3f center)

DOCUMENT ME!

Parameters:

center - DOCUMENT ME!

setDoCenter

public void setDoCenter(boolean doCenter)

DOCUMENT ME!

Parameters:

doCenter - DOCUMENT ME!

setFillValue

public void setFillValue(float fillValue)

Set value for out of bounds transformation values. Set in constructors to a default of srcImage.getMin().

Parameters:

fillValue -

setPadValue

@Deprecated
public void setPadValue(float padValue)

Deprecated.

The value is not just used for padding. Please use setFillValue().

Set value for out of bounds transformation values. Set in constructors to a default of srcImage.getMin().

Parameters:

padValue -

setUpdateOriginFlag

public void setUpdateOriginFlag(boolean originFlag)

Sets the origin flag used indicated that origin should be changed based using the supplied transformation matrix.

Parameters:

originFlag - if true sets the updateOrigin flag to true

setUseScannerAnatomical

public void setUseScannerAnatomical(boolean useSA)

Sets the tranform to set orientation to AXIAL (this is a scanner anatomical transform).

Parameters:

useSA - set to axial orientation

updateFileInfo

private static void updateFileInfo(ModelImage image,
 ModelImage resultImage,
 float[] resolutions,
 int[] units,
 TransMatrix matrix,
 boolean useSATransform,
 AlgorithmBase srcAlg)

Copy important file information to resultant image structure.

Parameters:

image - Source image.

resultImage - Resultant image.

resolutions - DOCUMENT ME!

units - DOCUMENT ME!

matrix - DOCUMENT ME!

useSATransform - DOCUMENT ME!

m -

updateOrigin

private static void updateOrigin(TransMatrix xfrm)

Update origin. Translate the image origin from image space to patient space (scanner space). The basic ideas, tranlate the (0,0,0) point from scaner space to image space, then subtract the original image origin. The (0, 0, 0) point is the upper left corner of the scanner space's image.

Parameters:

xfrm - DOCUMENT ME!

updateOrigin

private void updateOrigin()

Translate the image origin from image space to patient space (scanner space). The basic ideas, tranlate the (0,0,0) point from scaner space to image space, then multiply the resolution, and subtract the image origin. The (0, 0, 0) point is the upper left corner of the scanner space's image.

transform

private void transform()

Creates buffer for new image, prepares transformation matrix, and calls transform function for interpolation specified.

transform2DVOI

private void transform2DVOI(ModelImage image,
 double[] imgBuffer,
 TransMatrix kTM)

Transforms and resamples a 2D VOI using nearest neighbor interpolation.

For each VOI in VOIVector:
1. Export VOIs as a mask image
2. Transform mask
3. Extract VOI contours from mask image and put in new image.

Parameters:

image - Image where VOIs are stored

imgBuffer - Image array

xfrm - Transformation matrix to be applied

transform25DVOI

private void transform25DVOI(ModelImage image,
 double[] imgBuffer,
 TransMatrix kTM)

Transforms and resamples a 3D VOI using nearest neighbor interpolation.

1. Export VOIs as a mask image
2. Transform mask
3. Extract VOI contours from mask image and put in new image.

Parameters:

image - Image where VOIs are stored

imgBuffer - Image array

kTM - Transformation matrix to be applied

transform3DVOI

private void transform3DVOI(ModelImage image,
 double[] imgBuffer,
 TransMatrix kTM)

Transforms and resamples a 3D VOI using nearest neighbor interpolation.

1. Export VOIs as a mask image
2. Transform mask
3. Extract VOI contours from mask image and put in new image.

Parameters:

image - Image where VOIs are stored

imgBuffer - Image array

kTM - Transformation matrix to be applied

transform3DVOIByte

private void transform3DVOIByte(ModelImage image,
 byte[] imgBuffer,
 TransMatrix kTM)

Transforms and resamples a 3D VOI using nearest neighbor interpolation.

1. Export VOIs as a mask image
2. Transform mask
3. Extract VOI contours from mask image and put in new image.

Parameters:

image - Image where VOIs are stored

imgBuffer - Image array

kTM - Transformation matrix to be applied use byte imgBuffer to save a factor of 4 in memory in 3D ARGB color images.

transformBilinear

private void transformBilinear(double[] imgBuf,
 TransMatrix kTM)

Transforms and resamples volume using bilinear interpolation.

Parameters:

imgBuf - Image array

kTM - Matrix to be applied

transformBilinear3D

private void transformBilinear3D(double[] imgBuf,
 TransMatrix kTM)

Transforms and resamples volume using bilinear interpolation. Used as a slice-only algorithm on 3D images.

Parameters:

imgBuf - Image array

kTM - Matrix to be applied

transformBilinear3DC

private void transformBilinear3DC(double[] imgBuf,
 float[] imgBuf2,
 TransMatrix kTM)

Transforms and resamples volume using bilinear interpolation (2.5D) This version used with color images. This alogorithm used on a slice by slice basis on 3D images.

Parameters:

imgBuf - Input image array

imgBuf2 - Output image array

kTM - Matrix to be applied

transformBilinear4D

private void transformBilinear4D(double[] imgBuf,
 TransMatrix kTM)

Transforms and resamples volume using bilinear interpolation (2.5D) Used as a slice only algorithm on 3D images.

Parameters:

imgBuf - Image array

kTM - Transformation matrix to be applied

transformBilinear4DC

private void transformBilinear4DC(double[] imgBuf,
 float[] imgBuf2,
 TransMatrix kTM)

Transforms and resamples volume using bilinear interpolation This version used with color images This alogorithm used on a slice by slice basis on 4D images.

Parameters:

imgBuf - Input image array

imgBuf2 - Output image array

kTM - Matrix to be applied

transformBilinearC

private void transformBilinearC(double[] imgBuf,
 float[] imgBuf2,
 TransMatrix kTM)

Transforms and resamples volume using bilinear interpolation. This version used with color images

Parameters:

imgBuf - Input image array

imgBuf2 - Output image array

kTM - Matrix to be applied

transformAlgorithmBspline2D

private void transformAlgorithmBspline2D(double[] imgBuf,
 TransMatrix kTM,
 int degree)

Transforms and resamples volume using Bspline interpolation.

Parameters:

imgBuf - image array

kTM - transformation matrix to be applied

degree - degree of polynomial

transformAlgorithmBspline2DC

private void transformAlgorithmBspline2DC(double[] imgBuf,
 TransMatrix kTM,
 int degree)

Transforms and resamples volume using Bspline interpolation.

Parameters:

imgBuf - image array

kTM - transformation matrix to be applied

degree - degree of polynomial

transformAlgorithmBspline3D

private void transformAlgorithmBspline3D(double[] imgBuf,
 TransMatrix kTM,
 int degree)

Transforms and resamples volume using Bspline interpolation.

Parameters:

imgBuf - image array

kTM - transformation matrix to be applied

degree - degree of polynomial

transformAlgorithmBspline3DC

private void transformAlgorithmBspline3DC(double[] imgBuf,
 TransMatrix kTM,
 int degree)

Transforms and resamples volume using Bspline interpolation.

Parameters:

imgBuf - image array

kTM - transformation matrix to be applied

degree - degree of polynomial

transformAlgorithmBspline4D

private void transformAlgorithmBspline4D(double[] imgBuf,
 TransMatrix kTM,
 int degree)

Transforms and resamples volume using Bspline interpolation.

Parameters:

imgBuf - image array

kTM - transformation matrix to be applied

degree - degree of polynomial

transformAlgorithmBspline4DC

private void transformAlgorithmBspline4DC(double[] imgBuf,
 TransMatrix kTM,
 int degree)

Transforms and resamples color volume using Bspline interpolation.

Parameters:

imgBuf - image array

kTM - transformation matrix to be applied

degree - degree of polynomial

transformCubicLagrangian2D

private void transformCubicLagrangian2D(double[] imgBuf,
 TransMatrix kTM,
 boolean clip)

Transforms and resamples volume using cubic Lagrangian interpolation.

Parameters:

imgBuf - Image array

kTM - Transformation matrix to be applied

clip - if true clip output values to be within input range

transformCubicLagrangian2DC

private void transformCubicLagrangian2DC(double[] imgBuf,
 float[] imgBuf2,
 TransMatrix kTM,
 boolean clip)

Transforms and resamples volume using cubic Lagrangian interpolation. This version used with color images

Parameters:

imgBuf - Input image array

imgBuf2 - Output image array

kTM - Transformation matrix to be applied

clip - if true clip output values to be within input range

transformCubicLagrangian3D

private void transformCubicLagrangian3D(double[] imgBuf,
 TransMatrix kTM,
 boolean clip)

Transforms and resamples volume using cubic Lagrangian interpolation.

Parameters:

imgBuf - Image array

kTM - Transformation matrix to be applied

clip - If true clip output values to be within input range

transformCubicLagrangian3DC

private void transformCubicLagrangian3DC(double[] imgBuf,
 float[] imgBuf2,
 TransMatrix kTM,
 boolean clip)

Transforms and resamples volume using cubic Lagrangian interpolation. This version used with color images

Parameters:

imgBuf - Input image array

imgBuf2 - Output image array

kTM - Transformation matrix to be applied

clip - If true clip output values to be within input range

transformCubicLagrangian3Dim2D

private void transformCubicLagrangian3Dim2D(double[] imgBuf,
 TransMatrix kTM,
 boolean clip)

Transforms and resamples volume using cubic Lagrangian interpolation Does a slice by slice cubic Lagrangian interpolation on a 3 dimensional object.

Parameters:

imgBuf - Image array

kTM - Transformation matrix to be applied

clip - If true clip output values to be within input range

transformCubicLagrangian3Dim2DC

private void transformCubicLagrangian3Dim2DC(double[] imgBuf,
 float[] imgBuf2,
 TransMatrix kTM,
 boolean clip)

Transforms and resamples volume using cubic Lagrangian interpolation This version used with color images This version performs a slice by slice algorithm on a 3 dimensional object.

Parameters:

imgBuf - Input image array

imgBuf2 - Output image array

kTM - Transformation matrix to be applied

clip - If true clip output values to be within input range

transformCubicLagrangian4D

private void transformCubicLagrangian4D(double[] imgBuf,
 TransMatrix kTM,
 boolean clip)

Transforms and resamples 4 dimensional object using 3D cubic Lagrangian interpolation.

Parameters:

imgBuf - Image array

kTM - Transformation matrix to be applied

clip - if true clip output values to be within input range

transformCubicLagrangian4DC

private void transformCubicLagrangian4DC(double[] imgBuf,
 float[] imgBuffer2,
 TransMatrix kTM,
 boolean clip)

Transforms and resamples 4 dimensional object using 3D cubic Lagrangian interpolation.

Parameters:

imgBuf - Image array

imgBuffer2 -

kTM - Transformation matrix to be applied

clip - if true clip output values to be within input range

transformCubicLagrangian4Dim2D

private void transformCubicLagrangian4Dim2D(double[] imgBuf,
 TransMatrix kTM,
 boolean clip)

Transforms and resamples volume using cubic Lagrangian interpolation Does a slice by slice cubic Lagrangian interpolation on a 4 dimensional object.

Parameters:

imgBuf - Image array

kTM - Transformation matrix to be applied

clip - If true clip output values to be within input range

transformCubicLagrangian4Dim2DC

private void transformCubicLagrangian4Dim2DC(double[] imgBuf,
 float[] imgBuf2,
 TransMatrix kTM,
 boolean clip)

Transforms and resamples volume using cubic Lagrangian interpolation This version used with color images This version performs a slice by slice algorithm on a 4 dimensional object.

Parameters:

imgBuf - Input image array

imgBuf2 - Output image array

kTM - Transformation matrix to be applied

clip - If true clip output values to be within input range

transformHepticLagrangian2D

private void transformHepticLagrangian2D(double[] imgBuf,
 TransMatrix kTM,
 boolean clip)

Transforms and resamples volume using heptic Lagrangian interpolation.

Parameters:

imgBuf - Image array

kTM - Transformation matrix to be applied

clip - If true clip output values to be within input range

transformHepticLagrangian2DC

private void transformHepticLagrangian2DC(double[] imgBuf,
 float[] imgBuf2,
 TransMatrix kTM,
 boolean clip)

Transforms and resamples volume using heptic Lagrangian interpolation This version used with color images.

Parameters:

imgBuf - Input image array

imgBuf2 - Output image array

kTM - Transformation matrix to be applied

clip - If true clip output values to be within input range

transformHepticLagrangian3D

private void transformHepticLagrangian3D(double[] imgBuf,
 TransMatrix kTM,
 boolean clip)

Transforms and resamples volume using heptic Lagrangian interpolation.

Parameters:

imgBuf - Image array

kTM - Transformation matrix to be applied

clip - If true clip output values to be within input range

transformHepticLagrangian3DC

private void transformHepticLagrangian3DC(double[] imgBuf,
 float[] imgBuf2,
 TransMatrix kTM,
 boolean clip)

Transforms and resamples volume using heptic Lagrangian interpolation This version used with color images.

Parameters:

imgBuf - Input image array

imgBuf2 - Output image array

kTM - Transformation matrix to be applied

clip - If true clip output values to be within input range

transformHepticLagrangian3Dim2D

private void transformHepticLagrangian3Dim2D(double[] imgBuf,
 TransMatrix kTM,
 boolean clip)

Transforms and resamples volume using heptic Lagrangian interpolation Does a slice by slice heptic Lagrangian interpolation on a 3 dimensional object.

Parameters:

imgBuf - Image array

kTM - Transformation matrix to be applied

clip - If true clip output values to be within input range

transformHepticLagrangian3Dim2DC

private void transformHepticLagrangian3Dim2DC(double[] imgBuf,
 float[] imgBuf2,
 TransMatrix kTM,
 boolean clip)

Transforms and resamples volume using heptic Lagrangian interpolation This version used with color images This version performs a slice by slice algorithm on a 3 dimensional object.

Parameters:

imgBuf - Input image array

imgBuf2 - Output image array

kTM - Transformation matrix to be applied

clip - If true clip output values to be within input range

transformHepticLagrangian4D

private void transformHepticLagrangian4D(double[] imgBuf,
 TransMatrix kTM,
 boolean clip)

transforms and resamples 4 dimensional object using 3D heptic Lagrangian interpolation.

Parameters:

imgBuf - image array

kTM - transformation matrix to be applied

clip - if true clip output values to be within input range

transformHepticLagrangian4DC

private void transformHepticLagrangian4DC(double[] imgBuf,
 float[] imgBuffer2,
 TransMatrix kTM,
 boolean clip)

transforms and resamples 4 dimensional object using 3D heptic Lagrangian interpolation.

Parameters:

imgBuf - image array

imgBuffer2 -

kTM - transformation matrix to be applied

clip - if true clip output values to be within input range

transformHepticLagrangian4Dim2D

private void transformHepticLagrangian4Dim2D(double[] imgBuf,
 TransMatrix kTM,
 boolean clip)

Transforms and resamples volume using heptic Lagrangian interpolation Does a slice by slice heptic Lagrangian interpolation on a 4 dimensional object.

Parameters:

imgBuf - Image array

kTM - Transformation matrix to be applied

clip - If true clip output values to be within input range

transformHepticLagrangian4Dim2DC

private void transformHepticLagrangian4Dim2DC(double[] imgBuf,
 float[] imgBuf2,
 TransMatrix kTM,
 boolean clip)

Transforms and resamples volume using heptic Lagrangian interpolation This version used with color images This version performs a slice by slice algorithm on a 4 dimensional object.

Parameters:

imgBuf - Input image array

imgBuf2 - Output image array

kTM - Transformation matrix to be applied

clip - If true clip output values to be within input range

transformNearestNeighbor2D

private void transformNearestNeighbor2D(double[] imgBuf,
 TransMatrix kTM)

Transforms and resamples volume using nearest neighbor interpolation.

Parameters:

imgBuf - image array

kTM - transformation matrix to be applied

transformNearestNeighbor2DC

private void transformNearestNeighbor2DC(double[] imgBuf,
 float[] imgBuf2,
 TransMatrix kTM)

Transforms and resamples volume using nearest neighbor interpolation.

Parameters:

imgBuf - input image array

imgBuf2 - output image array

kTM - transformation matrix to be applied

transformNearestNeighbor3D

private void transformNearestNeighbor3D(double[] imgBuf,
 TransMatrix kTM)

Transforms and resamples volume using nearest neighbor interpolation.

Parameters:

imgBuf - image array

kTM - transformation matrix to be applied

transformNearestNeighbor3DC

private void transformNearestNeighbor3DC(double[] imgBuf,
 float[] imgBuf2,
 TransMatrix kTM)

Transforms and resamples volume using nearest neighbor interpolation.

Parameters:

imgBuf - input image array

imgBuf2 - output image array

kTM - transformation matrix to be applied

transformNearestNeighbor3Dim2D

private void transformNearestNeighbor3Dim2D(double[] imgBuf,
 TransMatrix kTM)

Transforms and resamples volume using nearest neighbor interpolation.

Parameters:

imgBuf - image array

kTM - transformation matrix to be applied

transformNearestNeighbor3Dim2DC

private void transformNearestNeighbor3Dim2DC(double[] imgBuf,
 float[] imgBuf2,
 TransMatrix kTM)

Transforms and resamples volume using nearest neighbor interpolation.

Parameters:

imgBuf - input image array

imgBuf2 - output image array

kTM - transformation matrix to be applied

transformNearestNeighbor4D

private void transformNearestNeighbor4D(double[] imgBuf,
 TransMatrix kTM)

Transforms and resamples 4 dimensional object using 3D algorithm using nearest neighbor interpolation.

Parameters:

imgBuf - image array

kTM - transformation matrix to be applied

transformNearestNeighbor4DC

private void transformNearestNeighbor4DC(double[] imgBuf,
 float[] imgBuffer2,
 TransMatrix kTM)

Transforms and resamples 4 dimensional object using 3D algorithm using nearest neighbor interpolation.

Parameters:

imgBuf - image array

kTM - transformation matrix to be applied

imgBufffer2 -

transformNearestNeighbor4Dim2D

private void transformNearestNeighbor4Dim2D(double[] imgBuf,
 TransMatrix kTM)

Transforms and resamples volume using nearest neighbor interpolation.

Parameters:

imgBuf - image array

kTM - transformation matrix to be applied

transformNearestNeighbor4Dim2DC

private void transformNearestNeighbor4Dim2DC(double[] imgBuf,
 float[] imgBuf2,
 TransMatrix kTM)

Transforms and resamples volume using nearest neighbor interpolation.

Parameters:

imgBuf - input image array

imgBuf2 - output image array

kTM - transformation matrix to be applied

transformQuinticLagrangian2D

private void transformQuinticLagrangian2D(double[] imgBuf,
 TransMatrix kTM,
 boolean clip)

Transforms and resamples volume using quintic Lagrangian interpolation.

Parameters:

imgBuf - Image array

kTM - Transformation matrix to be applied

clip - If true clip output values to be within input range

transformQuinticLagrangian2DC

private void transformQuinticLagrangian2DC(double[] imgBuf,
 float[] imgBuf2,
 TransMatrix kTM,
 boolean clip)

Transforms and resamples volume using quintic Lagrangian interpolation This version used with color images.

Parameters:

imgBuf - Input image array

imgBuf2 - Output image array

kTM - Transformation matrix to be applied

clip - If true clip output values to be within input range

transformQuinticLagrangian3D

private void transformQuinticLagrangian3D(double[] imgBuf,
 TransMatrix kTM,
 boolean clip)

Transforms and resamples volume using quintic Lagrangian interpolation.

Parameters:

imgBuf - Image array

kTM - Transformation matrix to be applied

clip - If true clip output values to be within input range

transformQuinticLagrangian3DC

private void transformQuinticLagrangian3DC(double[] imgBuf,
 float[] imgBuf2,
 TransMatrix kTM,
 boolean clip)

Transforms and resamples volume using quintic Lagrangian interpolation This version used with color images.

Parameters:

imgBuf - Input image array

imgBuf2 - Output image array

kTM - Transformation matrix to be applied

clip - If true clip output values to be within input range

transformQuinticLagrangian3Dim2D

private void transformQuinticLagrangian3Dim2D(double[] imgBuf,
 TransMatrix kTM,
 boolean clip)

Transforms and resamples volume using quintic Lagrangian interpolation Does a slice by slice quintic Lagrangian interpolation on a 3 dimensional object.

Parameters:

imgBuf - Image array

kTM - Transformation matrix to be applied

clip - If true clip output values to be within input range

transformQuinticLagrangian3Dim2DC

private void transformQuinticLagrangian3Dim2DC(double[] imgBuf,
 float[] imgBuf2,
 TransMatrix kTM,
 boolean clip)

Transforms and resamples volume using quintic Lagrangian interpolation This version used with color images This version performs a slice by slice algorithm on a 3 dimensional object.

Parameters:

imgBuf - Input image array

imgBuf2 - Output image array

kTM - Transformation matrix to be applied

clip - If true clip output values to be within input range

transformQuinticLagrangian4DC

private void transformQuinticLagrangian4DC(double[] imgBuf,
 float[] imgBuffer2,
 TransMatrix kTM,
 boolean clip)

Transforms and resamples 4 dimensional color object using 3D quintic Lagrangian interpolation.

Parameters:

imgBuf - Image array

kTM - Transformation matrix to be applied

clip - If true clip output values to be within input range

imgBuf2 -

transformQuinticLagrangian4D

private void transformQuinticLagrangian4D(double[] imgBuf,
 TransMatrix kTM,
 boolean clip)

Transforms and resamples 4 dimensional object using 3D quintic Lagrangian interpolation.

Parameters:

imgBuf - Image array

kTM - Transformation matrix to be applied

clip - If true clip output values to be within input range

transformQuinticLagrangian4Dim2D

private void transformQuinticLagrangian4Dim2D(double[] imgBuf,
 TransMatrix kTM,
 boolean clip)

Transforms and resamples volume using quintic Lagrangian interpolation Does a slice by slice quintic Lagrangian interpolation on a 4 dimensional object.

Parameters:

imgBuf - Image array

kTM - Transformation matrix to be applied

clip - If true clip output values to be within input range

transformQuinticLagrangian4Dim2DC

private void transformQuinticLagrangian4Dim2DC(double[] imgBuf,
 float[] imgBuf2,
 TransMatrix kTM,
 boolean clip)

Transforms and resamples volume using quintic Lagrangian interpolation This version used with color images This version performs a slice by slice algorithm on a 4 dimensional object.

Parameters:

imgBuf - Input image array

imgBuf2 - Output image array

kTM - Transformation matrix to be applied

clip - if true clip output values to be within input range

transformTrilinear

private void transformTrilinear(double[] imgBuffer,
 TransMatrix kTM)

Transforms and resamples a 3D volume using trilinear interpolation.

Parameters:

imgBuffer - Image array

kTM - Transformation matrix to be applied

transformTrilinear4D

private void transformTrilinear4D(double[] imgBuffer,
 TransMatrix kTM)

Transforms and resamples 4 dimensional object using trilinear interpolation.

Parameters:

imgBuffer - Image array

kTM - Transformation matrix to be applied

transformTrilinear4DByteC

private void transformTrilinear4DByteC(byte[] imgBuffer,
 byte[] imgBuffer2,
 TransMatrix kTM)

Transforms and resamples 4 dimensional color ARGB object using trilinear interpolation.

Parameters:

imgBuffer - Image array

kTM - Transformation matrix to be applied Byte buffers are used to reduce memory requirements by a factor of 4

imgBuf2 -

transformTrilinear4DC

private void transformTrilinear4DC(double[] imgBuffer,
 float[] imgBuffer2,
 TransMatrix kTM)

Transforms and resamples 4 dimensional color object using trilinear interpolation.

Parameters:

imgBuffer - Image array

kTM - Transformation matrix to be applied

imgBuf2 -

transformTrilinearC

private void transformTrilinearC(double[] imgBuffer,
 float[] imgBuffer2,
 TransMatrix kTM)

Transforms and resamples volume using trilinear interpolation This version is used with color images.

Parameters:

imgBuffer - Input image array

imgBuffer2 - Output image array

kTM - Transformation matrix to be applied

transformTrilinearByteC

private void transformTrilinearByteC(byte[] imgBuffer,
 byte[] imgBuffer2,
 TransMatrix kTM)

Transforms and resamples volume using trilinear interpolation This version is used with ARGB color images. Use byte[] rather than float[] to save memory

Parameters:

imgBuffer - Input image array

imgBuffer2 - Output image array

kTM - Transformation matrix to be applied

transformWSinc2D

private void transformWSinc2D(double[] imgBuf,
 TransMatrix kTM,
 boolean clip)

Transforms and resamples volume using windowed sinc interpolation.

Parameters:

imgBuf - Image array

kTM - Transformation matrix to be applied

clip - If true clip output values to be within input range

transformWSinc2DC

private void transformWSinc2DC(double[] imgBuf,
 float[] imgBuf2,
 TransMatrix kTM,
 boolean clip)

Transforms and resamples volume using windowed sinc interpolation This version used with color images.

Parameters:

imgBuf - Input image array

imgBuf2 - Output image array

kTM - Transformation matrix to be applied

clip - If true clip output values to be within input range

transformWSinc3D

private void transformWSinc3D(double[] imgBuf,
 TransMatrix kTM,
 boolean clip)

Transforms and resamples volume using windowed sinc interpolation.

Parameters:

imgBuf - Image array

kTM - Transformation matrix to be applied

clip - If true clip output values to be within input range

transformWSinc3DC

private void transformWSinc3DC(double[] imgBuf,
 float[] imgBuf2,
 TransMatrix kTM,
 boolean clip)

Transforms and resamples volume using windowed sinc interpolation This version used with color images.

Parameters:

imgBuf - Input image array

imgBuf2 - Output image array

kTM - Transformation matrix to be applied

clip - If true clip output values to be within input range

transformWSinc3Dim2D

private void transformWSinc3Dim2D(double[] imgBuf,
 TransMatrix kTM,
 boolean clip)

Transforms and resamples volume using windowed sinc interpolation Does a slice by slice windowed sinc interpolation on a 3 dimensional object.

Parameters:

imgBuf - Image array

kTM - Transformation matrix to be applied

clip - If true clip output values to be within input range

transformWSinc3Dim2DC

private void transformWSinc3Dim2DC(double[] imgBuf,
 float[] imgBuf2,
 TransMatrix kTM,
 boolean clip)

Transforms and resamples volume using windowed sinc interpolation This version used with color images This version performs a slice by slice algorithm on a 3 dimensional object.

Parameters:

imgBuf - Input image array

imgBuf2 - Output image array

kTM - Transformation matrix to be applied

clip - If true clip output values to be within input range

transformWSinc4D

private void transformWSinc4D(double[] imgBuf,
 TransMatrix kTM,
 boolean clip)

Transforms and resamples 4 dimensional object using 3D windowed sinc interpolation.

Parameters:

imgBuf - Image array

kTM - Transformation matrix to be applied

clip - If true clip output values to be within input range

transformWSinc4DC

private void transformWSinc4DC(double[] imgBuf,
 float[] imgBuffer2,
 TransMatrix kTM,
 boolean clip)

Transforms and resamples 4 dimensional object using 3D windowed sinc interpolation.

Parameters:

imgBuf - Image array

imgBuffer2 -

kTM - Transformation matrix to be applied

clip - If true clip output values to be within input range

transformWSinc4Dim2D

private void transformWSinc4Dim2D(double[] imgBuf,
 TransMatrix kTM,
 boolean clip)

Transforms and resamples volume using windowed sinc interpolation Does a slice by slice windowed sinc interpolation on a 4 dimensional object.

Parameters:

imgBuf - Image array

kTM - Transformation matrix to be applied

clip - If true clip output values to be within input range

transformWSinc4Dim2DC

private void transformWSinc4Dim2DC(double[] imgBuf,
 float[] imgBuf2,
 TransMatrix kTM,
 boolean clip)

Transforms and resamples volume using windowed sinc interpolation This version used with color images This version performs a slice by slice algorithm on a 4 dimensional object.

Parameters:

imgBuf - Input image array

imgBuf2 - Output image array

kTM - Transformation matrix to be applied

clip - If true clip output values to be within input range

updateOriginMargins

private void updateOriginMargins()

Update origin to reflect padding.

updateOriginMargins2D

private void updateOriginMargins2D()

Update origin to reflect padding.