java.lang.Object
- WildMagic.LibFoundation.Mathematics.Matrix4f
- - gov.nih.mipav.model.structures.TransMatrix

All Implemented Interfaces:: java.io.Serializable

public class TransMatrix
extends WildMagic.LibFoundation.Mathematics.Matrix4f

Transformation matrix class is an affine homogeneous class that can be used to rotate objects like images and VOIs. It can constructed as a 2D(3x3) or 3D(4x4) homogeneous matrix for transform (rotation, translation, skew and zoom) images/VOIs. Skew is not commonly used.

The MIPAV 3D model for 4 X 4 transformations is:

         [ m00 m01 m02 m03 ]   [ x ]   [ x' ]
         [ m10 m11 m12 m13 ] . [ y ] = [ y' ]
         [ m20 m21 m22 m23 ]   [ z ]   [ z' ]
         [ m30 m31 m32 m33 ]   [ w ]   [ w' ]
 
         x' = m00*x + m01*y + m02*z + m03*w
         y' = m10*x + m11*y + m12*z + m13*w
         z' = m20*x + m21*y + m22*z + m23*w
         w' = m30*x + m31*y + m32*z + m33*w

However, because the transform type is limited, we can always set the third row to [ 0 0 0 1] and write instead:

         [ m00 m01 m02 ]   [ x ]   [ t0 ]   [ x' ]
         [ m10 m11 m12 ] . [ y ] + [ t1 ] = [ y' ]
         [ m20 m21 m22 ]   [ z ]   [ t2 ]   [ z' ]
 
         x' = m00*x + m01*y + m02*z + t0
         y' = m10*x + m11*y + m12*z + t1
         z' = m20*x + m21*y + m22*z + t2

We still represent 4x4 m with a WildMagic Matrix4f, because of the existing implementations that assume a 4x4 matrix, and the use of the upper 3x3 matrix as a 2D transform.

We considered representing m with a WildMagic Matrix3f, and t with a Vector3f, as encapsulated in the WildMagic Transformation class, but it does not match typical Mipav usage.

ORDER OF TRANSFORMATIONS = TRANSLATE, ROTATE, ZOOM or TRANSLATE, ROTATE, SKEW, ZOOM
Row, Col format - right hand rule
2D Example

          zoom_x    theta    tx
          theta     zoom_y   ty
          0         0         1
 represented in 3D by leaving Z the identity transform:
          zoom_x    theta    0    tx
          theta     zoom_y   0    ty
          0         0        1    0
          0         0        0    1

Note that for 2D, the tx and ty components are stored in M02 and M12, and not in M03 and M13, as might be guessed by the use of a Matrix4f to store both 2D and 3D transforms.

Note for 3D - ref. Foley, Van Dam p. 214

          Axis of rotation            Direction of positive rotation is
              x                               y to z
              y                               z to x
              z                               x to y

          Order of rotation is important (i.e. not commutative)
          Rx Ry Ry != Ry Rx Rz

Version:: 2, July 24, 2008, original 0.1 Nov 15, 1997
Author:: Matthew J. McAuliffe, Ph.D., changes Aron Helser, Geometric Tools
See Also:: Serialized Form

Nested Class Summary

Nested Classes
Modifier and Type Class Description

private static class TransMatrix.DataFileV2Keys

Field Summary

Fields
Modifier and Type	Field	Description
`static int`	`DEGREES`	used for setting rotation
`private boolean`	`m_Is2D`	Transform was constructed to transform 2D vectors, instead of 3D
`private boolean`	`m_IsNIFTI`	boolean indicating whether this matrix is associated with a NIFTI image (special case handling)
`private boolean`	`m_IsQform`	If true, nifti matrix codes for a qform matrix If false, nifti matrix codes for a sform matrix Value has no effect if not a nifti matrix
`private int`	`m_TransformID`	Transform ID associated with the matrix.
`private static java.lang.String`	`MIPAV_DATA_FILE_V2_HEADER`
`static int`	`RADIANS`	used for setting rotation
`private static long`	`serialVersionUID`	Use serialVersionUID for interoperability.
`static int`	`TRANSFORM_ANOTHER_DATASET`	Another Dataset transform ID.
`static int`	`TRANSFORM_COMPOSITE`	Composite, dynamically generated matrix type
`private static java.lang.String[]`	`TRANSFORM_ID_STR`	Array of transform ID strings.
`static int`	`TRANSFORM_MNI_152`	MNI 152 transform ID.
`static int`	`TRANSFORM_NIFTI_SCANNER_ANATOMICAL`	Scanner anatomical matrix associated with NIFTI type
`static int`	`TRANSFORM_SCANNER_ANATOMICAL`	Scanner Anatomical transform ID.
`static int`	`TRANSFORM_TALAIRACH_TOURNOUX`	Talairach Tournoux transform ID.
`static int`	`TRANSFORM_UNKNOWN`	Composite transform ID.

Fields inherited from class WildMagic.LibFoundation.Mathematics.Matrix4f
IDENTITY, M00, M01, M02, M03, M10, M11, M12, M13, M20, M21, M22, M23, M30, M31, M32, M33, ZERO

Constructor Summary

Constructors
Constructor	Description
`TransMatrix(int dim)`	Construct a transformation matrix.
`TransMatrix(int dim, int id)`
`TransMatrix(int dim, int id, boolean is_nifti, boolean isQform)`
`TransMatrix(TransMatrix rkTM)`	copy constructor.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods Deprecated Methods
Modifier and Type	Method	Description
`TransMatrix`	`clone()`
`void`	`Copy(TransMatrix rkTM)`	copy, overwrite this.
`void`	`copyMatrix(double[][] newMatrix)`	Copies provided transformation matrix.
`private static TransMatrix`	`createMatrixFromAfni(java.util.ArrayList<java.lang.Float> d)`
`private void`	`decodeLine(java.io.RandomAccessFile raFile, int row, WildMagic.LibFoundation.Mathematics.Matrix4f matrix)`	Decodes the line in the matrix file.
`private static void`	`decodeLine(java.io.RandomAccessFile raFile, int row, WildMagic.LibFoundation.Mathematics.Matrix4f matrix, int dim)`	Reads a row of the matrix from file
`private void`	`decodeLine(java.lang.String str, int row, WildMagic.LibFoundation.Mathematics.Matrix4f matrix)`	Decodes the line in the matrix file.
`void`	`decodeMatrixString(java.lang.String str)`	Decodes the matrix from a string into the matrix array.
`boolean`	`decomposeMatrix(WildMagic.LibFoundation.Mathematics.Vector3f rotate, WildMagic.LibFoundation.Mathematics.Vector3f trans, WildMagic.LibFoundation.Mathematics.Vector3f scale, WildMagic.LibFoundation.Mathematics.Vector3f shear)`	Decomposing a matrix into simple transformations TransMatrix transformation sequence: Scale(Sx, Sy, Sz)ShearXYShearXZShearYZ RotateXRotateYRotateZTranslate(tx, ty, tz) ( Perspective(Px, Py, Pz, Pw), no longer supported)
`private boolean`	`getBooleanProperty(java.util.Properties props, java.lang.String key)`
`void`	`getColumn(int r, double[] column)`	Copy our data into the provided double array
`int`	`getDim()`	Return dimension passed to constructor.
`private float`	`getFloatProperty(java.util.Properties props, java.lang.String key)`
`private int`	`getIntProperty(java.util.Properties props, java.lang.String key)`
`private java.lang.String`	`getProperty(java.util.Properties props, java.lang.String key)`
`int`	`getTransformID()`	Returns the transform ID associated with the matrix.
`static int`	`getTransformIDFromStr(java.lang.String s)`	Returns the transform ID associated with a string.
`static java.lang.String[]`	`getTransformIDStr()`	Return the list of transform ID strings (for edit attributes combo box.
`static java.lang.String`	`getTransformIDStr(int m)`	Return the string associated with the matrix transform ID.
`void`	`Inverse()`	Matrix inversion that replaces this objects matrix with an inverted matrix.
`boolean`	`isIdentity()`	Reports whether transform is Identity transform, to within a small epsilon.
`boolean`	`isNIFTI()`	Tells whether this matrix is associated with a NIFTI image this only matters when the matrix is being saved/when the composite matrix is being generated in MatrixHolder
`boolean`	`isQform()`	Tells whether a NIFTI matrix is a qform matrix or a sform matrix
`static boolean`	`isV2MatrixDataFile(java.io.File f)`
`java.lang.String`	`matrixToString(int w, int d)`	Produces a string of the matrix values.
`static TransMatrix`	`readAfniMatrix(java.io.RandomAccessFile raFile)`	Reads AFNI-style matrix and does processing to generate TransMatrix result
`private void`	`readLegacyFileParameters(java.io.RandomAccessFile raFile, int[] interp, float[] oXres, float[] oYres, float[] oZres, int[] oXdim, int[] oYdim, int[] oZdim, boolean[] tVOI, boolean[] clip, boolean[] pad)`
`void`	`readMatrix(java.io.RandomAccessFile raFile, boolean composite)`	Reads transformation matrix to a text file.
`boolean`	`readMatrix(java.io.RandomAccessFile raFile, int[] interp, float[] sourceXres, float[] sourceYres, float[] sourceZres, float[] targetXres, float[] targetYres, float[] targetZres, int[] sourceXdim, int[] sourceYdim, int[] sourceZdim, int[] targetXdim, int[] targetYdim, int[] targetZdim, boolean[] tVOI, boolean[] clip, boolean[] pad, boolean composite)`	Reads transformation matrix to a text file.
`void`	`readMatrix(java.io.RandomAccessFile raFile, int[] interp, float[] oXres, float[] oYres, float[] oZres, int[] oXdim, int[] oYdim, int[] oZdim, boolean[] tVOI, boolean[] clip, boolean[] pad, boolean composite)`	Deprecated.
`static TransMatrix[]`	`readMultiMatrix(java.io.RandomAccessFile raFile)`	Reads a file containing a list of multiple TransMatrix values.
`void`	`saveMatrix(java.io.RandomAccessFile raFile)`	Saves transformation matrix to a text file MIPAV format.
`void`	`saveMatrix(java.io.RandomAccessFile raFile, int interp, float sourceXres, float sourceYres, float sourceZres, float targetXres, float targetYres, float targetZres, int sourceXdim, int sourceYdim, int sourceZdim, int targetXdim, int targetYdim, int targetZdim, boolean tVOI, boolean clip, boolean pad, java.lang.String message)`	Saves transformation matrix to a text file MIPAV format.
`void`	`saveMatrix(java.io.RandomAccessFile raFile, int interp, float oXres, float oYres, float oZres, int oXdim, int oYdim, int oZdim, boolean tVOI, boolean clip, boolean pad, java.lang.String message)`	Saves transformation matrix to a text file MIPAV format
`void`	`saveMatrix(java.io.RandomAccessFile raFile, java.lang.String message)`	Saves transformation matrix to a text file MIPAV format.
`void`	`saveMatrix(java.lang.String fileName)`	Saves transformation matrix to a text file MIPAV format
`void`	`saveMatrix(java.lang.String fileName, int interp, float sourceXres, float sourceYres, float sourceZres, float targetXres, float targetYres, float targetZres, int sourceXdim, int sourceYdim, int sourceZdim, int targetXdim, int targetYdim, int targetZdim, boolean tVOI, boolean clip, boolean pad, java.lang.String message)`
`void`	`saveMatrix(java.lang.String fileName, int interp, float oXres, float oYres, float oZres, int oXdim, int oYdim, int oZdim, boolean tVOI, boolean clip, boolean pad, java.lang.String message)`
`void`	`saveMatrix(java.lang.String fileName, java.lang.String message)`	Saves transformation matrix to a text file MIPAV format
`void`	`saveXFMMatrix(java.io.RandomAccessFile raFile)`	Saves transformation matrix to McGill XFM format
`TransMatrix`	`set(int r, int c, double val)`
`private void`	`setBooleanProperty(java.util.Properties props, java.lang.String key, boolean val)`
`private void`	`setFloatProperty(java.util.Properties props, java.lang.String key, float val)`
`private void`	`setIntProperty(java.util.Properties props, java.lang.String key, int val)`
`void`	`setIsNIFTI(boolean is_NIFTI)`	Accessor that sets whether or not the matrix is a NIFTI matrix.
`void`	`setIsQform(boolean is_Qform)`	Accessor that sets whether a nifti matrix is a qform matrix or a sform matrix.
`void`	`setMatrix(double[][] X)`	Set a submatrix.
`void`	`setMatrix(int i0, int i1, int j0, int j1, double[][] X)`	Set a submatrix.
`void`	`setRotate(double theta)`	Sets the rotation (2D) of transformation matrix.
`void`	`setRotate(double thetaX, double thetaY, double thetaZ, int degreeORradian)`	Sets rotation (3D) of transformation matrix.
`void`	`setRotate(WildMagic.LibFoundation.Mathematics.Vector3f alpha, WildMagic.LibFoundation.Mathematics.Vector3f beta, WildMagic.LibFoundation.Mathematics.Vector3f gamma)`	Sets rotation (3D) of transformation matrix.
`void`	`setSkew(double x, double y)`	Sets skew part of 2D matrix.
`void`	`setSkew(double x, double y, double z)`	Sets the skew parts of 3D matrix (4D Homogenous).
`void`	`setTransform(double tX, double tY, double r)`	Sets 2D transformation matrix.
`void`	`setTransform(double tX, double tY, double tZ, double rX, double rY, double rZ)`	Sets the 3D transformation matrix [4x4].
`void`	`setTransform(double tX, double tY, double tZ, double rX, double rY, double rZ, double sX, double sY, double sZ, double skX, double skY, double skZ)`	Sets the 3D transformation matrix [4x4].
`void`	`setTransformID(int t_id)`	Sets the transform ID for the matrix.
`void`	`setTranslate(double x, double y)`	Sets translation parts of 2D matrix.
`void`	`setTranslate(double x, double y, double z)`	Sets the translation parts of 3D matrix (4D Homogenous).
`void`	`setZoom(double sx, double sy)`	Sets the zoom parts of 2D matrix.
`void`	`setZoom(double sx, double sy, double sz)`	Sets the zoom parts of 3D matrix.
`java.lang.String`	`toDialogString()`	Produces a string of the matrix values, rows separated by tabs.
`java.lang.String`	`toString()`	ToString method that includes the matrix printout as well as the transform ID of the transmatrix
`void`	`transform(double[] pt, double[] tPt)`	Takes a 3D or 2D point (as a double array) and premultiplies it by the 3D transformation matrix.
`void`	`transform(double x, double y, double[] tPt)`	Takes double components of a 2D point and premultiplies it by the 2d transformation matrix.
`void`	`transform(double x, double y, double z, double[] tPt)`	Takes the double components of a 3D point and premultiplies it by the 3D transformation matrix.
`void`	`transform(float[] pt, float[] tPt)`	Takes a 3D point, as a float array, and premultiplies it by the 3D transformation matrix.
`void`	`transform(float x, float y, float[] tPt)`	Takes float components of a 2D point and premultiplies it by the 2d transformation matrix.
`void`	`transform(float x, float y, float z, float[] tPt)`	Takes the float components of a 3D point and premultiplies it by the 3D transformation matrix.
`java.awt.Polygon`	`transform(java.awt.Polygon gon)`	Tranforms a Polygon (2D).
`void`	`transformAsPoint2Df(WildMagic.LibFoundation.Mathematics.Vector2f[] vects, WildMagic.LibFoundation.Mathematics.Vector2f[] tVects)`	Takes an array of Point2Df 2D vectors and multiplies them with the 2d transformation matrix.
`void`	`transformAsPoint3Df(WildMagic.LibFoundation.Mathematics.Vector3f pt, WildMagic.LibFoundation.Mathematics.Vector3f tPt)`	Takes a Point3Df 3D point and multiplies it by the 3D transformation matrix.
`void`	`transformAsVector3Df(VOIBase vects, WildMagic.LibFoundation.Mathematics.Vector3f[] tVects)`	Takes an array of Vector3Df 2D vectors and multiplies them with the 2d transformation matrix.
`void`	`transformAsVector3Df(WildMagic.LibFoundation.Mathematics.Vector3f[] vects, WildMagic.LibFoundation.Mathematics.Vector3f[] tVects)`	Takes an array of Vector3Df 2D vectors and multiplies them with the 2d transformation matrix.

Methods inherited from class WildMagic.LibFoundation.Mathematics.Matrix4f
adjoint, copy, determinant, equals, get, getColumnMajor, getData, identity, inverse, inverse, makeObliqueProjection, makePerspectiveProjection, makeReflection, makeZero, mult, mult, mult, mult, multLeft, multLeft, multLeft, multRight, multRight, qForm, set, set, timesTranspose, transpose, transpose, transposeTimes, transposeTimes

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

Field Detail
- serialVersionUID
```
private static final long serialVersionUID
```
  Use serialVersionUID for interoperability.
  
  See Also:
  
  Constant Field Values
- TRANSFORM_UNKNOWN
```
public static final int TRANSFORM_UNKNOWN
```
  Composite transform ID.
  
  See Also:
  
  Constant Field Values
- TRANSFORM_SCANNER_ANATOMICAL
```
public static final int TRANSFORM_SCANNER_ANATOMICAL
```
  Scanner Anatomical transform ID.
  
  See Also:
  
  Constant Field Values
- TRANSFORM_ANOTHER_DATASET
```
public static final int TRANSFORM_ANOTHER_DATASET
```
  Another Dataset transform ID.
  
  See Also:
  
  Constant Field Values
- TRANSFORM_TALAIRACH_TOURNOUX
```
public static final int TRANSFORM_TALAIRACH_TOURNOUX
```
  Talairach Tournoux transform ID.
  
  See Also:
  
  Constant Field Values
- TRANSFORM_MNI_152
```
public static final int TRANSFORM_MNI_152
```
  MNI 152 transform ID.
  
  See Also:
  
  Constant Field Values
- TRANSFORM_COMPOSITE
```
public static final int TRANSFORM_COMPOSITE
```
  Composite, dynamically generated matrix type
  
  See Also:
  
  Constant Field Values
- TRANSFORM_NIFTI_SCANNER_ANATOMICAL
```
public static final int TRANSFORM_NIFTI_SCANNER_ANATOMICAL
```
  Scanner anatomical matrix associated with NIFTI type
  
  See Also:
  
  Constant Field Values
- TRANSFORM_ID_STR
```
private static final java.lang.String[] TRANSFORM_ID_STR
```
  Array of transform ID strings.
- DEGREES
```
public static final int DEGREES
```
  used for setting rotation
  
  See Also:
  
  Constant Field Values
- RADIANS
```
public static final int RADIANS
```
  used for setting rotation
  
  See Also:
  
  Constant Field Values
- m_TransformID
```
private int m_TransformID
```
  Transform ID associated with the matrix.
- m_IsNIFTI
```
private boolean m_IsNIFTI
```
  boolean indicating whether this matrix is associated with a NIFTI image (special case handling)
- m_IsQform
```
private boolean m_IsQform
```
  If true, nifti matrix codes for a qform matrix If false, nifti matrix codes for a sform matrix Value has no effect if not a nifti matrix
- m_Is2D
```
private boolean m_Is2D
```
  Transform was constructed to transform 2D vectors, instead of 3D
- MIPAV_DATA_FILE_V2_HEADER
```
private static final java.lang.String MIPAV_DATA_FILE_V2_HEADER
```
  See Also:
  
  Constant Field Values

Constructor Detail

TransMatrix
```
public TransMatrix(int dim)
```
Construct a transformation matrix.

Parameters:

dim - should be 3 or 4 (square matrix)

TransMatrix

public TransMatrix(int dim,
                   int id)

TransMatrix

public TransMatrix(int dim,
                   int id,
                   boolean is_nifti,
                   boolean isQform)

TransMatrix
```
public TransMatrix(TransMatrix rkTM)
```
copy constructor.

Parameters:

rkTM - matrix to copy

Method Detail

getDim
```
public int getDim()
```
Return dimension passed to constructor.

Returns:

3 for 2D transform, 4 for 3D transform.

clone
```
public TransMatrix clone()
```
Overrides:

clone in class java.lang.Object

Returns:

deep copy of this.

Copy
```
public void Copy(TransMatrix rkTM)
```
copy, overwrite this.

Parameters:

rkTM - matrix to copy

decodeMatrixString
```
public void decodeMatrixString(java.lang.String str)
```
Decodes the matrix from a string into the matrix array.

Parameters:

str - Matrix represented as a string.

decomposeMatrix
```
public boolean decomposeMatrix(WildMagic.LibFoundation.Mathematics.Vector3f rotate,
                               WildMagic.LibFoundation.Mathematics.Vector3f trans,
                               WildMagic.LibFoundation.Mathematics.Vector3f scale,
                               WildMagic.LibFoundation.Mathematics.Vector3f shear)
```
Decomposing a matrix into simple transformations TransMatrix transformation sequence: Scale(Sx, Sy, Sz)*ShearXY*ShearXZ*ShearYZ* RotateX*RotateY*RotateZ*Translate(tx, ty, tz) ( *Perspective(Px, Py, Pz, Pw), no longer supported)

Parameters:

rotate - rotation about x, y, z axis, in radians

trans - translation

scale - scale, for each dimension

shear - shear.X is XY, shear.Y is XZ, shear.Z is YZ

Returns:

true if decompose was successful.

isIdentity
```
public boolean isIdentity()
```
Reports whether transform is Identity transform, to within a small epsilon.

Returns:

true iff identity

isNIFTI
```
public boolean isNIFTI()
```
Tells whether this matrix is associated with a NIFTI image this only matters when the matrix is being saved/when the composite matrix is being generated in MatrixHolder

Returns:

is this a nifti matrix

setIsNIFTI
```
public void setIsNIFTI(boolean is_NIFTI)
```
Accessor that sets whether or not the matrix is a NIFTI matrix.

Parameters:

is_NIFTI - val to set

isQform
```
public boolean isQform()
```
Tells whether a NIFTI matrix is a qform matrix or a sform matrix

Returns:

true if qform, false if sform.

setIsQform
```
public void setIsQform(boolean is_Qform)
```
Accessor that sets whether a nifti matrix is a qform matrix or a sform matrix.

Parameters:

is_Qform - val to set

readMatrix

public void readMatrix(java.io.RandomAccessFile raFile,
                       boolean composite)

Reads transformation matrix to a text file.

This method reads two formats MIPAV format

 4                    // number of rows in matrix 
 4                    // number of cols in matrix 
 0.234 0.33 0.22 5.0  // matrix info separated by a space 
 0.234 0.33 0.22 10.0 // matrix info separated by a space 
 0.234 0.33 0.22 12.0 // matrix info separated by a space 
 0.0 0.0 0.0 1.0      // matrix info separated by a space.

Note the above is a homogenous transformation matrix

FSL or alternate format supported

 0.234  0.33  0.22  5.0 // matrix info separated by 2 spaces 
 0.234  0.33  0.22  5.0 // matrix info separated by 2 spaces 
 0.234  0.33  0.22  5.0 // matrix info separated by 2 spaces
 0  0  0  1             // matrix info separated by 2 spaces

also note integer values

Parameters:: raFile - random access file pointer; composite - if true make a composite matrix of the by multipling this matrix with the one to be read from the file. If false replace this object matrix with a new matrix read from the file.

readMatrix

public void readMatrix(java.io.RandomAccessFile raFile,
                       int[] interp,
                       float[] oXres,
                       float[] oYres,
                       float[] oZres,
                       int[] oXdim,
                       int[] oYdim,
                       int[] oZdim,
                       boolean[] tVOI,
                       boolean[] clip,
                       boolean[] pad,
                       boolean composite)

Deprecated.

Reads transformation matrix to a text file.

This method reads two formats MIPAV format

 4                    // number of rows in matrix 
 4                    // number of cols in matrix 
 0.234 0.33 0.22 5.0  // matrix info separated by a space 
 0.234 0.33 0.22 10.0 // matrix info separated by a space 
 0.234 0.33 0.22 12.0 // matrix info separated by a space 
 0.0 0.0 0.0 1.0      // matrix info separated by a space.

Note the above is a homogenous transformation matrix

FSL or alternate format supported

 0.234  0.33  0.22  5.0 // matrix info separated by 2 spaces 
 0.234  0.33  0.22  5.0 // matrix info separated by 2 spaces 
 0.234  0.33  0.22  5.0 // matrix info separated by 2 spaces
 0  0  0  1             // matrix info separated by 2 spaces

also note integer values

Parameters:: raFile - random access file pointer; composite - if true make a composite matrix of the by multipling this matrix with the one to be read from the file. If false replace this object matrix with a new matrix read from the file.

readLegacyFileParameters

private void readLegacyFileParameters(java.io.RandomAccessFile raFile,
                                      int[] interp,
                                      float[] oXres,
                                      float[] oYres,
                                      float[] oZres,
                                      int[] oXdim,
                                      int[] oYdim,
                                      int[] oZdim,
                                      boolean[] tVOI,
                                      boolean[] clip,
                                      boolean[] pad)
                               throws java.io.IOException

Throws:: java.io.IOException

readMatrix

public boolean readMatrix(java.io.RandomAccessFile raFile,
                          int[] interp,
                          float[] sourceXres,
                          float[] sourceYres,
                          float[] sourceZres,
                          float[] targetXres,
                          float[] targetYres,
                          float[] targetZres,
                          int[] sourceXdim,
                          int[] sourceYdim,
                          int[] sourceZdim,
                          int[] targetXdim,
                          int[] targetYdim,
                          int[] targetZdim,
                          boolean[] tVOI,
                          boolean[] clip,
                          boolean[] pad,
                          boolean composite)

Reads transformation matrix to a text file.

This method reads version 2 MIPAV matrix data files (including legacy versions of these files)

 MIPAV Matrix Data File v2
 rows = 4             // number of rows in matrix (r0..rows-1 matrix keys below)
 cols = 4             // number of cols in matrix 
 r0 = 0.234 0.33 0.22 5.0  // matrix info separated by a space
 r1 = 0.234 0.33 0.22 10.0 // matrix info separated by a space 
 r2 = 0.234 0.33 0.22 12.0 // matrix info separated by a space 
 r3 = 0.0 0.0 0.0 1.0      // matrix info separated by a space.
 \n // newline
 interpolation = 0 // 0 for trilinear interpolation, 2 for nearest neighbor, 3 for cubic bspline, 4 for quadratic bspline
 sourceXres = 0.5 // source x resolution
 sourceYres = 0.5 // source y resolution
 sourceZres = 0.2 // source z resolution
 targetXres = 0.5 // target x resolution
 targetYres = 0.5 // target y resolution
 targetZres = 0.2 // target z resolution
 sourceXdim = 256 // source x dimension
 sourceYdim = 256 // source y dimension
 sourceZdim = 128 // source z dimension
 targetXdim = 256 // target x dimension
 targetYdim = 256 // target y dimension
 targetZdim = 128 // target z dimension
 voi = true             // transformVOI (true or false)
 clip = false   // clip (true or false) output image range is clipped to input image range
 pad = true             // pad (true of false) output image is padded so that all of the original image is present

Note the above is a homogenous transformation matrix

FSL or alternate format supported

 0.234  0.33  0.22  5.0 // matrix info separated by 2 spaces 
 0.234  0.33  0.22  5.0 // matrix info separated by 2 spaces 
 0.234  0.33  0.22  5.0 // matrix info separated by 2 spaces
 0  0  0  1             // matrix info separated by 2 spaces

also note integer values

Parameters:: raFile - random access file pointer; composite - if true make a composite matrix of the by multipling this matrix with the one to be read from the file. If false replace this object matrix with a new matrix read from the file.

isV2MatrixDataFile

public static boolean isV2MatrixDataFile(java.io.File f)

getProperty

private java.lang.String getProperty(java.util.Properties props,
                                     java.lang.String key)
                              throws java.lang.Exception

Throws:: java.lang.Exception

getIntProperty

private int getIntProperty(java.util.Properties props,
                           java.lang.String key)
                    throws java.lang.Exception

Throws:: java.lang.Exception

getFloatProperty

private float getFloatProperty(java.util.Properties props,
                               java.lang.String key)
                        throws java.lang.Exception

Throws:: java.lang.Exception

getBooleanProperty

private boolean getBooleanProperty(java.util.Properties props,
                                   java.lang.String key)
                            throws java.lang.Exception

Throws:: java.lang.Exception

setIntProperty

private void setIntProperty(java.util.Properties props,
                            java.lang.String key,
                            int val)

setFloatProperty

private void setFloatProperty(java.util.Properties props,
                              java.lang.String key,
                              float val)

setBooleanProperty

private void setBooleanProperty(java.util.Properties props,
                                java.lang.String key,
                                boolean val)

readMultiMatrix
```
public static TransMatrix[] readMultiMatrix(java.io.RandomAccessFile raFile)
```
Reads a file containing a list of multiple TransMatrix values. Returns the new TransMatrix array. Format is rows (int) columns (int) Matrix line 1 Matrix line 2 Matrix line 3 Matrix line 4 (optional) new line

Parameters:

raFile -

Returns:

readAfniMatrix
```
public static TransMatrix readAfniMatrix(java.io.RandomAccessFile raFile)
```
Reads AFNI-style matrix and does processing to generate TransMatrix result

createMatrixFromAfni

private static TransMatrix createMatrixFromAfni(java.util.ArrayList<java.lang.Float> d)

saveMatrix
```
public void saveMatrix(java.lang.String fileName)
```
Saves transformation matrix to a text file MIPAV format

Parameters:

fileName - - file name, including the path

See Also:

saveMatrix(java.io.RandomAccessFile)

saveMatrix
```
public void saveMatrix(java.lang.String fileName,
                       java.lang.String message)
```
Saves transformation matrix to a text file MIPAV format

Parameters:

fileName - - file name, including the path

message - String, may be null for no message.

See Also:

saveMatrix(java.io.RandomAccessFile,java.lang.String)

saveMatrix

public void saveMatrix(java.io.RandomAccessFile raFile)

Saves transformation matrix to a text file MIPAV format. The format is:

 4                    // number of rows in matrix 
 4                    // number of cols in matrix 
 0.234 0.33 0.22 5.0  // matrix info separated by a space 
 0.234 0.33 0.22 10.0 // matrix info separated by a space 
 0.234 0.33 0.22 12.0 // matrix info separated by a space 
 0.0 0.0 0.0 1.0      // matrix info separated by a space.

Parameters:: raFile - random access file pointer
See Also:: saveMatrix(java.io.RandomAccessFile,java.lang.String)

saveMatrix

public void saveMatrix(java.io.RandomAccessFile raFile,
                       java.lang.String message)

Saves transformation matrix to a text file MIPAV format. The format is:

 4                    // number of rows in matrix 
 4                    // number of cols in matrix 
 0.234 0.33 0.22 5.0  // matrix info separated by a space 
 0.234 0.33 0.22 10.0 // matrix info separated by a space 
 0.234 0.33 0.22 12.0 // matrix info separated by a space 
 0.0 0.0 0.0 1.0      // matrix info separated by a space.

Parameters:: raFile - random access file pointer; message - String, may be null for no message.

saveMatrix

public void saveMatrix(java.lang.String fileName,
                       int interp,
                       float oXres,
                       float oYres,
                       float oZres,
                       int oXdim,
                       int oYdim,
                       int oZdim,
                       boolean tVOI,
                       boolean clip,
                       boolean pad,
                       java.lang.String message)

saveMatrix

public void saveMatrix(java.lang.String fileName,
                       int interp,
                       float sourceXres,
                       float sourceYres,
                       float sourceZres,
                       float targetXres,
                       float targetYres,
                       float targetZres,
                       int sourceXdim,
                       int sourceYdim,
                       int sourceZdim,
                       int targetXdim,
                       int targetYdim,
                       int targetZdim,
                       boolean tVOI,
                       boolean clip,
                       boolean pad,
                       java.lang.String message)

saveMatrix

public void saveMatrix(java.io.RandomAccessFile raFile,
                       int interp,
                       float oXres,
                       float oYres,
                       float oZres,
                       int oXdim,
                       int oYdim,
                       int oZdim,
                       boolean tVOI,
                       boolean clip,
                       boolean pad,
                       java.lang.String message)

Saves transformation matrix to a text file MIPAV format

 4                    // number of rows in matrix 
 4                    // number of cols in matrix 
 0.234 0.33 0.22 5.0  // matrix info separated by a space 
 0.234 0.33 0.22 10.0 // matrix info separated by a space 
 0.234 0.33 0.22 12.0 // matrix info separated by a space 
 0.0 0.0 0.0 1.0      // matrix info separated by a space.
 \n // newline
 Have transform parameters
 0 // 0 for trilinear interpolation, 2 for nearest neighbor, 3 for cubic bspline, 4 for quadratic bspline
 0.5 // output x resolution
 0.5 // output y resolution
 0.2 // output z resolution
 256 // output x dimension
 256 // output y dimension
 128 // output z dimension
 true // transformVOI (true or false)
 false // clip (true or false) output image range is clipped to input image range
 true // pad (true of false) output image is padded so that all of the original image is present

Parameters:: raFile - random access file pointer; interp -; oXres -; oYres -; oZres -; oXdim -; oYdim -; oZdim -; tVOI -; clip -; pad -; message - String, may be null for no message.

saveMatrix

public void saveMatrix(java.io.RandomAccessFile raFile,
                       int interp,
                       float sourceXres,
                       float sourceYres,
                       float sourceZres,
                       float targetXres,
                       float targetYres,
                       float targetZres,
                       int sourceXdim,
                       int sourceYdim,
                       int sourceZdim,
                       int targetXdim,
                       int targetYdim,
                       int targetZdim,
                       boolean tVOI,
                       boolean clip,
                       boolean pad,
                       java.lang.String message)

Saves transformation matrix to a text file MIPAV format. The format is an enhanced format with format version as well as name, value pairs. Matrix read functions are aware of both legacy and enhanced formats and will be able to read both formats properly.

 MIPAV Matrix Data File v2
 rows = 4             // number of rows in matrix (r0..rows-1 matrix keys below)
 cols = 4             // number of cols in matrix 
 r0 = 0.234 0.33 0.22 5.0  // matrix info separated by a space
 r1 = 0.234 0.33 0.22 10.0 // matrix info separated by a space 
 r2 = 0.234 0.33 0.22 12.0 // matrix info separated by a space 
 r3 = 0.0 0.0 0.0 1.0      // matrix info separated by a space.
 interpolation = 0 // 0 for trilinear interpolation, 2 for nearest neighbor, 3 for cubic bspline, 4 for quadratic bspline
 sourceXres = 0.5 // source x resolution
 sourceYres = 0.5 // source y resolution
 sourceZres = 0.2 // source z resolution
 targetXres = 0.5 // target x resolution
 targetYres = 0.5 // target y resolution
 targetZres = 0.2 // target z resolution
 sourceXdim = 256 // source x dimension
 sourceYdim = 256 // source y dimension
 sourceZdim = 128 // source z dimension
 targetXdim = 256 // target x dimension
 targetYdim = 256 // target y dimension
 targetZdim = 128 // target z dimension
 voi = true             // transformVOI (true or false)
 clip = false   // clip (true or false) output image range is clipped to input image range
 pad = true             // pad (true of false) output image is padded so that all of the original image is present

saveXFMMatrix
```
public void saveXFMMatrix(java.io.RandomAccessFile raFile)
```
Saves transformation matrix to McGill XFM format

Parameters:

raFile - random access file pointer

copyMatrix
```
public void copyMatrix(double[][] newMatrix)
```
Copies provided transformation matrix.

Parameters:

newMatrix - 2D array to copy, 3x3 or 4x4

getColumn
```
public void getColumn(int r,
                      double[] column)
```
Copy our data into the provided double array

Parameters:

r - row to copy

column - place to put column data, length 3 or 4

set

public TransMatrix set(int r,
                       int c,
                       double val)

setMatrix
```
public void setMatrix(int i0,
                      int i1,
                      int j0,
                      int j1,
                      double[][] X)
```
Set a submatrix. Borrowed from Jama, useful for copying a Jama matrix M by passing in M.getArray() for param X

Parameters:

i0 - Initial row index

i1 - Final row index

j0 - Initial column index

j1 - Final column index

X - A(i0:i1,j0:j1)

Throws:

java.lang.ArrayIndexOutOfBoundsException - Submatrix indices

setMatrix
```
public void setMatrix(double[][] X)
```
Set a submatrix. Borrowed from Jama, useful for copying a Jama matrix M by passing in M.getArray() for param X

Parameters:

X - A(i0:i1,j0:j1)

Throws:

java.lang.ArrayIndexOutOfBoundsException - Submatrix indices

setRotate
```
public void setRotate(double theta)
```
Sets the rotation (2D) of transformation matrix.

Parameters:

theta - angle of rotation, in degrees

setRotate

public void setRotate(WildMagic.LibFoundation.Mathematics.Vector3f alpha,
                      WildMagic.LibFoundation.Mathematics.Vector3f beta,
                      WildMagic.LibFoundation.Mathematics.Vector3f gamma)

Sets rotation (3D) of transformation matrix.

Parameters:: alpha - row0; beta - row1; gamma - row2

setRotate
```
public void setRotate(double thetaX,
                      double thetaY,
                      double thetaZ,
                      int degreeORradian)
```
Sets rotation (3D) of transformation matrix.

Parameters:

thetaX - angle (degrees or radians) of rotation about the X axis;

thetaY - angle (degrees or radians) of rotation about the Y axis;

thetaZ - angle (degrees or radians) of rotation about the Z axis;

degreeORradian - DEGREES or RADIANS

setSkew
```
public void setSkew(double x,
                    double y)
```
Sets skew part of 2D matrix.

Parameters:

x - Skew x parameter.

y - Skew y parameter.

setSkew

public void setSkew(double x,
                    double y,
                    double z)

Sets the skew parts of 3D matrix (4D Homogenous).

Parameters:: x - x skew; y - y skew; z - z skew

setTransform
```
public void setTransform(double tX,
                         double tY,
                         double r)
```
Sets 2D transformation matrix.

Parameters:

tX - x translation

tY - y translation

r - rotation angle in degrees, about unseen z axis

setTransform

public void setTransform(double tX,
                         double tY,
                         double tZ,
                         double rX,
                         double rY,
                         double rZ)

Sets the 3D transformation matrix [4x4].

Parameters:: tX - x translation; tY - y translation; tZ - z translation; rX - x rotation angle in degrees; rY - y rotation angle in degrees; rZ - z rotation angle in degrees

setTransform

public void setTransform(double tX,
                         double tY,
                         double tZ,
                         double rX,
                         double rY,
                         double rZ,
                         double sX,
                         double sY,
                         double sZ,
                         double skX,
                         double skY,
                         double skZ)

Sets the 3D transformation matrix [4x4].

Parameters:: tX - x translation; tY - y translation; tZ - z translation; rX - x rotation angle in degrees; rY - y rotation angle in degrees; rZ - z rotation angle in degrees; sX - x scale; sY - y scale; sZ - z scale; skX - x skew; skY - y skew; skZ - z skew

setTranslate
```
public void setTranslate(double x,
                         double y)
```
Sets translation parts of 2D matrix.

Parameters:

x - x translation

y - y translation

setTranslate
```
public void setTranslate(double x,
                         double y,
                         double z)
```
Sets the translation parts of 3D matrix (4D Homogenous).

Parameters:

x - x translation

y - y translation

z - z translation

setZoom
```
public void setZoom(double sx,
                    double sy)
```
Sets the zoom parts of 2D matrix.

Parameters:

sx - zoom in the x coordinate

sy - zoom in the y coordinate

setZoom
```
public void setZoom(double sx,
                    double sy,
                    double sz)
```
Sets the zoom parts of 3D matrix.

Parameters:

sx - zoom in the x coordinate

sy - zoom in the y coordinate

sz - zoom in the z coordinate

toDialogString
```
public java.lang.String toDialogString()
```
Produces a string of the matrix values, rows separated by tabs.

Returns:

formatted string

transform
```
public final java.awt.Polygon transform(java.awt.Polygon gon)
```
Tranforms a Polygon (2D).

Parameters:

gon - input polygon

Returns:

returns new transformed Polygon

transformAsPoint2Df

public final void transformAsPoint2Df(WildMagic.LibFoundation.Mathematics.Vector2f[] vects,
                                      WildMagic.LibFoundation.Mathematics.Vector2f[] tVects)

Takes an array of Point2Df 2D vectors and multiplies them with the 2d transformation matrix.

Parameters:: vects - float vectors to be transformed; tVects - transformed vectors

transformAsVector3Df

public final void transformAsVector3Df(WildMagic.LibFoundation.Mathematics.Vector3f[] vects,
                                       WildMagic.LibFoundation.Mathematics.Vector3f[] tVects)

Takes an array of Vector3Df 2D vectors and multiplies them with the 2d transformation matrix.

Parameters:: vects - float vectors to be transformed; tVects - transformed vectors

transformAsVector3Df
```
public final void transformAsVector3Df(VOIBase vects,
                                       WildMagic.LibFoundation.Mathematics.Vector3f[] tVects)
```
Takes an array of Vector3Df 2D vectors and multiplies them with the 2d transformation matrix.

Parameters:

vects - float vectors to be transformed

tVects - transformed vectors

transform
```
public final void transform(double[] pt,
                            double[] tPt)
```
Takes a 3D or 2D point (as a double array) and premultiplies it by the 3D transformation matrix.

Parameters:

pt - coordinate to be transformed

tPt - transformed point

transform
```
public final void transform(float[] pt,
                            float[] tPt)
```
Takes a 3D point, as a float array, and premultiplies it by the 3D transformation matrix.

Parameters:

pt - coordinate to be transformed

tPt - the transformed point

transformAsPoint3Df

public final void transformAsPoint3Df(WildMagic.LibFoundation.Mathematics.Vector3f pt,
                                      WildMagic.LibFoundation.Mathematics.Vector3f tPt)

Takes a Point3Df 3D point and multiplies it by the 3D transformation matrix.

Parameters:: pt - 3D float point to be transformed; tPt - transformed point

transform
```
public final void transform(double x,
                            double y,
                            double[] tPt)
```
Takes double components of a 2D point and premultiplies it by the 2d transformation matrix.

Parameters:

x - x coordinate to be transformd

y - y coordinate to be transformd

tPt - transformed point

transform
```
public final void transform(float x,
                            float y,
                            float[] tPt)
```
Takes float components of a 2D point and premultiplies it by the 2d transformation matrix.

Parameters:

x - x coordinate to be transformed

y - y coordinate to be transformed

tPt - transformed point

transform
```
public final void transform(double x,
                            double y,
                            double z,
                            double[] tPt)
```
Takes the double components of a 3D point and premultiplies it by the 3D transformation matrix.

Parameters:

x - x coordinate to be transformed

y - y coordinate to be transformed

z - z coordinate to be transformed

tPt - transformed point

transform
```
public final void transform(float x,
                            float y,
                            float z,
                            float[] tPt)
```
Takes the float components of a 3D point and premultiplies it by the 3D transformation matrix.

Parameters:

x - x coordinate to be transformed

y - y coordinate to be transformed

z - z coordinate to be transformed

tPt - the transformed point

getTransformID
```
public final int getTransformID()
```
Returns the transform ID associated with the matrix.

Returns:

int transform ID

getTransformIDFromStr
```
public static int getTransformIDFromStr(java.lang.String s)
```
Returns the transform ID associated with a string.

Parameters:

s - String to test

Returns:

data type

getTransformIDStr
```
public static java.lang.String[] getTransformIDStr()
```
Return the list of transform ID strings (for edit attributes combo box.

Returns:

string [] of transform ID

getTransformIDStr
```
public static java.lang.String getTransformIDStr(int m)
```
Return the string associated with the matrix transform ID.

Parameters:

m - transform ID

Returns:

the string associated with the transform ID

setTransformID
```
public void setTransformID(int t_id)
```
Sets the transform ID for the matrix.

Parameters:

t_id - transform ID

toString
```
public java.lang.String toString()
```
ToString method that includes the matrix printout as well as the transform ID of the transmatrix

Overrides:

toString in class WildMagic.LibFoundation.Mathematics.Matrix4f

Returns:

printout

decodeLine
```
private void decodeLine(java.io.RandomAccessFile raFile,
                        int row,
                        WildMagic.LibFoundation.Mathematics.Matrix4f matrix)
```
Decodes the line in the matrix file.

Parameters:

raFile - file pointer

row - row reference to store transformation matrix

matrix - the matrix where the data is to be stored

decodeLine
```
private void decodeLine(java.lang.String str,
                        int row,
                        WildMagic.LibFoundation.Mathematics.Matrix4f matrix)
```
Decodes the line in the matrix file.

Parameters:

raFile - file pointer

row - row reference to store transformation matrix

matrix - the matrix where the data is to be stored

decodeLine

private static void decodeLine(java.io.RandomAccessFile raFile,
                               int row,
                               WildMagic.LibFoundation.Mathematics.Matrix4f matrix,
                               int dim)

Reads a row of the matrix from file

Parameters:: raFile - file containing matrix data; row - row; matrix - matrix; dim - column dimension

Inverse
```
public void Inverse()
```
Matrix inversion that replaces this objects matrix with an inverted matrix. Special handling for 2D vs 3D cases.

matrixToString
```
public java.lang.String matrixToString(int w,
                                       int d)
```
Produces a string of the matrix values.

Parameters:

w - Column width.

d - Number of digits after the decimal.

Returns:

String containing the values from the matrix.

Class TransMatrix

Nested Class Summary

Field Summary

Fields inherited from class WildMagic.LibFoundation.Mathematics.Matrix4f

Constructor Summary

Method Summary

Methods inherited from class WildMagic.LibFoundation.Mathematics.Matrix4f

Methods inherited from class java.lang.Object

Field Detail

serialVersionUID

TRANSFORM_UNKNOWN

TRANSFORM_SCANNER_ANATOMICAL

TRANSFORM_ANOTHER_DATASET

TRANSFORM_TALAIRACH_TOURNOUX

TRANSFORM_MNI_152

TRANSFORM_COMPOSITE

TRANSFORM_NIFTI_SCANNER_ANATOMICAL

TRANSFORM_ID_STR

DEGREES

RADIANS

m_TransformID

m_IsNIFTI

m_IsQform

m_Is2D

MIPAV_DATA_FILE_V2_HEADER

Constructor Detail

TransMatrix

TransMatrix

TransMatrix

TransMatrix

Method Detail

getDim

clone

Copy

decodeMatrixString

decomposeMatrix

isIdentity

isNIFTI

setIsNIFTI

isQform

setIsQform

readMatrix

readMatrix

readLegacyFileParameters

readMatrix

isV2MatrixDataFile

getProperty

getIntProperty

getFloatProperty

getBooleanProperty

setIntProperty

setFloatProperty

setBooleanProperty

readMultiMatrix

readAfniMatrix

createMatrixFromAfni

saveMatrix

saveMatrix

saveMatrix

saveMatrix

saveMatrix

saveMatrix

saveMatrix

saveMatrix

saveXFMMatrix

copyMatrix

getColumn

set

setMatrix

setMatrix

setRotate

setRotate

setRotate

setSkew

setSkew

setTransform

setTransform

setTransform

setTranslate

setTranslate