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

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.
`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
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
`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)
`void`	`getColumn(int r, double[] column)`	Copy our data into the provided double array
`int`	`getDim()`	Return dimension passed to constructor.
`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
`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
`void`	`readMatrix(java.io.RandomAccessFile raFile, 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)`	Reads transformation matrix to a text file.
`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 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 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.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)`
`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, Adjoint, copy, Copy, determinant, Determinant, equals, get, Get, getColumnMajor, GetColumnMajor, getData, GetData, identity, inverse, inverse, Inverse, MakeIdentity, makeObliqueProjection, MakeObliqueProjection, makePerspectiveProjection, MakePerspectiveProjection, makeReflection, MakeReflection, makeZero, MakeZero, mult, mult, mult, mult, Mult, Mult, Mult, multLeft, multLeft, multLeft, MultLeft, MultLeft, multRight, multRight, MultRight, qForm, QForm, set, set, Set, Set, timesTranspose, TimesTranspose, transpose, transpose, Transpose, Transpose, transposeTimes, transposeTimes, 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
- 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)
```
    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.
  - 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.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)
```
    Saves transformation matrix to a text file MIPAV format
    
    Parameters:
    
    fileName - - file name, including the path
    
    interp -
    
    oXres -
    
    oYres -
    
    oZres -
    
    oXdim -
    
    oYdim -
    
    oZdim -
    
    tVOI -
    
    clip -
    
    pad -
    
    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
    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
    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.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.
  - 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 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.
    
    Overrides:
    
    Inverse in class WildMagic.LibFoundation.Mathematics.Matrix4f
  - 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

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

Constructor Detail

TransMatrix

TransMatrix

TransMatrix

TransMatrix

Method Detail

getDim

clone

Copy

decodeMatrixString

decomposeMatrix

isIdentity

isNIFTI

setIsNIFTI

isQform

setIsQform

readMatrix

readMatrix

readMultiMatrix

readAfniMatrix

createMatrixFromAfni

saveMatrix

saveMatrix

saveMatrix

saveMatrix

saveMatrix

saveMatrix

saveXFMMatrix

copyMatrix

getColumn

set

setMatrix

setMatrix

setRotate

setRotate

setRotate

setSkew

setSkew

setTransform

setTransform

setTransform

setTranslate

setTranslate

setZoom

setZoom

toDialogString

transform

transformAsPoint2Df

transformAsVector3Df

transformAsVector3Df

transform

transform

transformAsPoint3Df

transform

transform

transform

transform