java.lang.Object
- java.lang.Thread
- - gov.nih.mipav.model.algorithms.AlgorithmBase
  - - gov.nih.mipav.model.algorithms.AlgorithmTransform

All Implemented Interfaces:

java.awt.event.ActionListener, java.awt.event.WindowListener, java.lang.Runnable, java.util.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
  java.lang.Thread.State, java.lang.Thread.UncaughtExceptionHandler

Field Summary

Fields
Modifier and Type	Field	Description
`private static int[]`	`axisOrient`	DOCUMENT ME!
`static int`	`BILINEAR`	Biilinear interpolation.
`static int`	`BSPLINE3`	Cubic bspline interpolation.
`static int`	`BSPLINE4`	Quadratic bspline interpolation.
`private int`	`bufferFactor`	DOCUMENT ME!
`private WildMagic.LibFoundation.Mathematics.Vector3f`	`center`	DOCUMENT ME!
`private boolean`	`clip`	DOCUMENT ME!
`static 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 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 int`	`interp`	DOCUMENT ME!
`private boolean`	`isSATransform`	flag for determining if the transform is for scanner anatomical (->AXIAL).
`private int`	`iTdim`
`private int`	`iXdim`	DOCUMENT ME!
`private float`	`iXres`	DOCUMENT ME!
`private 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 int`	`NEAREST_NEIGHBOR`	Nearest neighbor interpolation.
`private int`	`oTdim`	DOCUMENT ME!
`private int[]`	`oUnits`	DOCUMENT ME!
`private int`	`oXdim`	DOCUMENT ME!
`private float`	`oXres`	DOCUMENT ME!
`private int`	`oYdim`	DOCUMENT ME!
`private float`	`oYres`	DOCUMENT ME!
`private int`	`oZdim`	DOCUMENT ME!
`private float`	`oZres`
`private boolean`	`pad`	DOCUMENT ME!
`static 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 TransMatrix`	`transMatrix`	DOCUMENT ME!
`static int`	`TRILINEAR`	Trilinear interpolation.
`private static boolean`	`updateOrigin`	DOCUMENT ME!
`static 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

All Methods Static Methods Instance Methods Concrete Methods Deprecated Methods
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 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 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 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 void`	`transformBilinear(float[] imgBuf, ModelImage transformedImg, TransMatrix trans, int iXdim, int iYdim, float iXres, float iYres, ViewJProgressBar progressBar)`	Transforms using bilinear interpolation.
`static 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 void`	`transformBilinear(ModelImage image, ModelImage transformedImg, TransMatrix trans, ViewJProgressBar progressBar)`	Transforms using bilinear interpolation.
`static void`	`transformBilinear(ModelImage image, ModelImage transformedImg, TransMatrix trans, ViewJProgressBar progressBar, boolean activeImage)`	Transforms using bilinear interpolation.
`static 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 void`	`transformBilinearC(ModelImage image, ModelImage transformedImg, TransMatrix trans, int oXdim, int oYdim, float oXres, float oYres)`	Used on color images.
`static 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 void`	`transformNearestNeighbor2D(float[] imgBuf, float[] tImgBuf, TransMatrix trans, int xdim, int ydim)`	Transforms using Nearest neighbor interpolation.
`static 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 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 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 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 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 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 void`	`transformTrilinear(ModelImage image, ModelImage transformedImg, TransMatrix trans, ViewJProgressBar progressBar)`	Transforms and resamples volume using trilinear interpolation.
`static void`	`transformTrilinear(ModelImage image, ModelImage transformedImg, TransMatrix trans, ViewJProgressBar progressBar, boolean activeImage)`	Transforms and resamples volume using trilinear interpolation.
`static 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 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 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, join, join, join, onSpinWait, resume, setContextClassLoader, setDaemon, setDefaultUncaughtExceptionHandler, setName, setPriority, setUncaughtExceptionHandler, sleep, sleep, start, stop, suspend, toString, yield

Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail
- 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 Detail

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 Detail

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