WildMagic.LibFoundation.Mathematics.Matrix4f

gov.nih.mipav.model.structures.TransMatrix

All Implemented Interfaces:: 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:

Nested Class Summary

Nested Classes

Modifier and Type

Class

Description

private static enum

TransMatrix.DataFileV2Keys
Field Summary

Fields

Modifier and Type

Field

Description

static final 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 final String

MIPAV_DATA_FILE_V2_HEADER

static final int

RADIANS

used for setting rotation

private static final long

serialVersionUID

Use serialVersionUID for interoperability.

static final int

TRANSFORM_ANOTHER_DATASET

Another Dataset transform ID.

static final int

TRANSFORM_COMPOSITE

Composite, dynamically generated matrix type

private static final String[]

TRANSFORM_ID_STR

Array of transform ID strings.

static final int

TRANSFORM_MNI_152

MNI 152 transform ID.

static final int

TRANSFORM_NIFTI_SCANNER_ANATOMICAL

Scanner anatomical matrix associated with NIFTI type

static final int

TRANSFORM_SCANNER_ANATOMICAL

Scanner Anatomical transform ID.

static final int

TRANSFORM_TALAIRACH_TOURNOUX

Talairach Tournoux transform ID.

static final 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

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(ArrayList<Float> d)

private void

decodeLine(RandomAccessFile raFile, int row, WildMagic.LibFoundation.Mathematics.Matrix4f matrix)

Decodes the line in the matrix file.

private static void

decodeLine(RandomAccessFile raFile, int row, WildMagic.LibFoundation.Mathematics.Matrix4f matrix, int dim)

Reads a row of the matrix from file

private void

decodeLine(String str, int row, WildMagic.LibFoundation.Mathematics.Matrix4f matrix)

Decodes the line in the matrix file.

void

decodeMatrixString(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)*ShearXY*ShearXZ*ShearYZ* RotateX*RotateY*RotateZ*Translate(tx, ty, tz) ( *Perspective(Px, Py, Pz, Pw), no longer supported)

private boolean

getBooleanProperty(Properties props, 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(Properties props, String key)

private int

getIntProperty(Properties props, String key)

private String

getProperty(Properties props, String key)

final int

getTransformID()

Returns the transform ID associated with the matrix.

static int

getTransformIDFromStr(String s)

Returns the transform ID associated with a string.

static String[]

getTransformIDStr()

Return the list of transform ID strings (for edit attributes combo box.

static 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(File f)

String

matrixToString(int w, int d)

Produces a string of the matrix values.

static TransMatrix

readAfniMatrix(RandomAccessFile raFile)

Reads AFNI-style matrix and does processing to generate TransMatrix result

private void

readLegacyFileParameters(RandomAccessFile raFile, int[] interp, float[] oXres, float[] oYres, float[] oZres, int[] oXdim, int[] oYdim, int[] oZdim, boolean[] tVOI, boolean[] clip, boolean[] pad)

void

readMatrix(RandomAccessFile raFile, boolean composite)

Reads transformation matrix to a text file.

boolean

readMatrix(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(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(RandomAccessFile raFile)

Reads a file containing a list of multiple TransMatrix values.

void

saveMatrix(RandomAccessFile raFile)

Saves transformation matrix to a text file MIPAV format.

void

saveMatrix(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, String message)

Saves transformation matrix to a text file MIPAV format.

void

saveMatrix(RandomAccessFile raFile, int interp, float oXres, float oYres, float oZres, int oXdim, int oYdim, int oZdim, boolean tVOI, boolean clip, boolean pad, String message)

Saves transformation matrix to a text file MIPAV format

void

saveMatrix(RandomAccessFile raFile, String message)

Saves transformation matrix to a text file MIPAV format.

void

saveMatrix(String fileName)

Saves transformation matrix to a text file MIPAV format

void

saveMatrix(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, String message)

void

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

void

saveMatrix(String fileName, String message)

Saves transformation matrix to a text file MIPAV format

void

saveXFMMatrix(RandomAccessFile raFile)

Saves transformation matrix to McGill XFM format

TransMatrix

set(int r, int c, double val)

private void

setBooleanProperty(Properties props, String key, boolean val)

private void

setFloatProperty(Properties props, String key, float val)

private void

setIntProperty(Properties props, 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.

String

toDialogString()

Produces a string of the matrix values, rows separated by tabs.

String

toString()

ToString method that includes the matrix printout as well as the transform ID of the transmatrix

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.

final void

transform(double x, double y, double[] tPt)

Takes double components of a 2D point and premultiplies it by the 2d transformation matrix.

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.

final void

transform(float[] pt, float[] tPt)

Takes a 3D point, as a float array, and premultiplies it by the 3D transformation matrix.

final void

transform(float x, float y, float[] tPt)

Takes float components of a 2D point and premultiplies it by the 2d transformation matrix.

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.

final Polygon

transform(Polygon gon)

Tranforms a Polygon (2D).

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.

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.

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.

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.

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 Details
- 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 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 String MIPAV_DATA_FILE_V2_HEADER
  See Also:
  
  Constant Field Values
Constructor Details
- 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 Details
- 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 Object
  
  Returns:
  
  deep copy of this.
- Copy
  
  public void Copy(TransMatrix rkTM)
  
  copy, overwrite this.
  
  Parameters:
  
  rkTM - matrix to copy
- decodeMatrixString
  
  public void decodeMatrixString(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(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(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(RandomAccessFile raFile, int[] interp, float[] oXres, float[] oYres, float[] oZres, int[] oXdim, int[] oYdim, int[] oZdim, boolean[] tVOI, boolean[] clip, boolean[] pad) throws IOException
  
  Throws:
  
  IOException
- readMatrix
  
  public boolean readMatrix(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(File f)
- getProperty
  
  private String getProperty(Properties props, String key) throws Exception
  
  Throws:
  
  Exception
- getIntProperty
  
  private int getIntProperty(Properties props, String key) throws Exception
  
  Throws:
  
  Exception
- getFloatProperty
  
  private float getFloatProperty(Properties props, String key) throws Exception
  
  Throws:
  
  Exception
- getBooleanProperty
  
  private boolean getBooleanProperty(Properties props, String key) throws Exception
  
  Throws:
  
  Exception
- setIntProperty
  
  private void setIntProperty(Properties props, String key, int val)
- setFloatProperty
  
  private void setFloatProperty(Properties props, String key, float val)
- setBooleanProperty
  
  private void setBooleanProperty(Properties props, String key, boolean val)
- readMultiMatrix
  
  public static TransMatrix[] readMultiMatrix(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(RandomAccessFile raFile)
  
  Reads AFNI-style matrix and does processing to generate TransMatrix result
- createMatrixFromAfni
  
  private static TransMatrix createMatrixFromAfni(ArrayList<Float> d)
- saveMatrix
  
  public void saveMatrix(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(String fileName, 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(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(RandomAccessFile raFile, 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(String fileName, int interp, float oXres, float oYres, float oZres, int oXdim, int oYdim, int oZdim, boolean tVOI, boolean clip, boolean pad, String message)
- saveMatrix
  
  public void saveMatrix(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, String message)
- saveMatrix
  
  public void saveMatrix(RandomAccessFile raFile, int interp, float oXres, float oYres, float oZres, int oXdim, int oYdim, int oZdim, boolean tVOI, boolean clip, boolean pad, 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(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, 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(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:
  
  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:
  
  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 String toDialogString()
  
  Produces a string of the matrix values, rows separated by tabs.
  
  Returns:
  
  formatted string
- transform
  
  public final Polygon transform(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(String s)
  
  Returns the transform ID associated with a string.
  
  Parameters:
  
  s - String to test
  
  Returns:
  
  data type
- getTransformIDStr
  
  public static String[] getTransformIDStr()
  
  Return the list of transform ID strings (for edit attributes combo box.
  
  Returns:
  
  string [] of transform ID
- getTransformIDStr
  
  public static 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 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(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(String str, int row, WildMagic.LibFoundation.Mathematics.Matrix4f matrix)
  
  Decodes the line in the matrix file.
  
  Parameters:
  
  row - row reference to store transformation matrix
  
  matrix - the matrix where the data is to be stored
  
  raFile - file pointer
- decodeLine
  
  private static void decodeLine(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 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 Details

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 Details

TransMatrix

TransMatrix

TransMatrix

TransMatrix

Method Details

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