java.lang.Object
- gov.nih.mipav.view.renderer.WildMagic.AAM.CVisDMatrix
- - gov.nih.mipav.view.renderer.WildMagic.AAM.CDMatrix

```
public class CDMatrix
extends CVisDMatrix
```
This is the Java modified version of C++ active appearance model API (AAM_API). It is modified with a subset of required functions for automatic MRI prostate segmentation. AAM-API LICENSE - file: license.txt This software is freely available for non-commercial use such as research and education. Please see the full disclaimer below. All publications describing work using this software should cite the reference given below. Copyright (c) 2000-2003 Mikkel B. Stegmann, mbs@imm.dtu.dk IMM, Informatics & Mathematical Modelling DTU, Technical University of Denmark Richard Petersens Plads, Building 321 DK-2800 Lyngby, Denmark http://www.imm.dtu.dk/~aam/ REFERENCES Please use the reference below, when writing articles, reports etc. where the AAM-API has been used. A draft version the article is available from the homepage. I will be happy to receive pre- or reprints of such articles. /Mikkel ------------- M. B. Stegmann, B. K. Ersboll, R. Larsen, "FAME -- A Flexible Appearance Modelling Environment", IEEE Transactions on Medical Imaging, IEEE, 2003 (to appear) ------------- 3RD PART SOFTWARE The software is partly based on the following libraries: - The Microsoft(tm) Vision Software Developers Kit, VisSDK - LAPACK DISCLAIMER This software is provided 'as-is', without any express or implied warranty. In no event will the author be held liable for any damages arising from the use of this software. Permission is granted to anyone to use this software for any non-commercial purpose, and to alter it, subject to the following restrictions: 1. The origin of this software must not be misrepresented; you must not claim that you wrote the original software. 2. Altered source versions must be plainly marked as such, and must not be misrepresented as being the original software. 3. This notice may not be removed or altered from any source distribution. -- No guarantees of performance accompany this software, nor is any responsibility assumed on the part of the author or IMM. This software is provided by Mikkel B. Stegmann and IMM ``as is'' and any express or implied warranties, including, but not limited to, the implied warranties of merchantability and fitness for a particular purpose are disclaimed. In no event shall IMM or Mikkel B. Stegmann be liable for any direct, indirect, incidental, special, exemplary, or consequential damages (including, but not limited to, procurement of substitute goods or services; loss of use, data, or profits; or business interruption) however caused and on any theory of liability, whether in contract, strict liability, or tort (including negligence or otherwise) arising in any way out of the use of this software, even if advised of the possibility of such damage. $Revision: 1.4 $ $Date: 2003/04/23 14:49:15 $ Base matrix operations within AAM model.

Author:

Ruida Cheng

Field Summary

Fields
Modifier and Type Field Description

static int RAND_MAX
- Fields inherited from class gov.nih.mipav.view.renderer.WildMagic.AAM.CVisDMatrix
  eftData, eftDims, eftEnd, eftName, FieldType, m_data, m_fExternalStorage, m_nCols, m_nRows, s_fVerboseOutput

Constructor Summary

Constructors
Constructor	Description
`CDMatrix()`	Constructors
`CDMatrix(int rows, int cols)`
`CDMatrix(int rows, int cols, double[][] storage)`
`CDMatrix(CDMatrix mat)`
`CDMatrix(CVisDMatrix mat)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`CDMatrix`	`assign(double value)`	Assignment operator (double).
`CDMatrix`	`assign(double[][] value)`	Assignment operator
`CDMatrix`	`assign(CDMatrix mat)`	Assignment operator (CDMatrix).
`CDMatrix`	`assign(CVisDMatrix mat)`	Assignment operator (CVisDMatrix).
`void`	`Col(int i, CDVector vCol)`	Return the i-th column of the matrix.
`void`	`CombVert(CVisDMatrix Top, CVisDMatrix Bottom)`	Composes the matrix of Top and Bottom (on top of each other).
`double`	`Det()`	Calculates the determinant of a square matrix up to the 3rd order.
`void`	`Diag(CDVector vec)`	Make the matrix a diagonal matrix containing 'vec'.
`void`	`ElementDivide(CDMatrix matrix)`	Element-wise matrix division.
`void`	`ElementMultiply(CDMatrix matrix)`	Element-wise matrix multiply.
`void`	`Eq(double B, CDMatrix C)`	Element wise equal to.
`void`	`Eq(CDMatrix B, CDMatrix C)`	Element wise equal to.
`void`	`Eye()`	Converts the matrix in the identity matrix - i.e. zeros all-over except the ones in the diagonal.
`void`	`FlipLR()`	FlipLR modifies the matrix with row preserved and columns flipped in the left/right direction.
`void`	`FlipUD()`	Flip matrix in up/down direction.
`void`	`FromFile(java.io.DataInputStream fh)`	Reads a matrix from disk in binary format (from the current position of the file pointer), as written from ToFile().
`void`	`FromFile(java.lang.String sFilename)`	Reads a matrix from disk in binary format, as written from ToFile().
`void`	`Ge(double B, CDMatrix C)`	Element wise greater than or equal.
`void`	`Ge(CDMatrix B, CDMatrix C)`	Element wise greater than or equal.
`void`	`Gt(double B, CDMatrix C)`	Element wise greater than.
`void`	`Gt(CDMatrix B, CDMatrix C)`	Element wise greater than.
`void`	`Kron(CDMatrix mX, CDMatrix mY)`	Forms the Kronecker tensor product of two matrices.
`void`	`Le(double B, CDMatrix C)`	Element wise less than or equal.
`void`	`Le(CDMatrix B, CDMatrix C)`	Element wise less than or equal.
`void`	`Log()`	Takes the natural logarithm (base e=2.71..) of each matrix element.
`void`	`Lt(double B, CDMatrix C)`	Element wise less than.
`void`	`Lt(CDMatrix B, CDMatrix C)`	Element wise less than.
`double`	`Mean()`	Calcs the mean value of the matrix.
`void`	`MeanCol(CDVector vMean)`	Calc the mean of each column into a vector.
`void`	`Ne(double B, CDMatrix C)`	Element wise not equal to.
`void`	`Ne(CDMatrix B, CDMatrix C)`	Element wise not equal to.
`void`	`OneWayANOVA(double[] dZ, int[] nDFModel, int[] nDFError)`	One-way analysis of variance (ANOVA).
`void`	`OuterProduct(CDVector v1, CDVector v2)`	Forms the outer product of two vectors and store the result in this.
`void`	`Rand()`	Uniformly distributed random numbers.
`void`	`Row(int i, CDVector vRow)`	Return the i-th row of the matrix.
`void`	`Sqr()`	Takes the power of two of each element.
`void`	`Sqrt()`	Takes the square root of each element.
`double`	`Std()`	Calc the standard diviation of the matrix.
`void`	`StdCol(CDVector vStd)`	Calc the standard deviation of each column into a vector.
`double`	`Sum()`	Calc the total sum of the matrix.
`void`	`SumCol(CDVector vSum)`	Calc the sum of each column into a vector.
`void`	`ToFile(java.io.DataOutputStream fh)`	Writes the matrix to disk in binary format.
`void`	`ToFile(java.lang.String sFilename)`	Writes the matrix to disk in binary format.
`void`	`ToMatlab(java.lang.String sFilename, java.lang.String sName, java.lang.String sComment, boolean fAppend)`	Writes the matrix to disk in MatLab (.m) format.
`java.lang.String`	`ToString()`	Returns a string representing the matrix.
`void`	`ToVector(CDVector v, boolean rowWise)`	Converts this matrix to a vector, either by row (default) or column.
`double`	`Trace()`	Calculates the trace - i.e. the sum of diagonal elements.
`void`	`TriL(CDMatrix matrix, int K)`	Extract lower triangular part of matrix.
`void`	`TriU(CDMatrix matrix, int K)`	Extract upper triangular part of matrix.
`void`	`TTest(int iCol1, int iCol2, double[] dZ, int[] nDF)`	Student's T-test.
`double`	`Var()`	Calc the variance of the matrix.
`void`	`VarCol(CDVector vVar)`	Calc the variance of each column into a vector.

Methods inherited from class gov.nih.mipav.view.renderer.WildMagic.AAM.CVisDMatrix
add, add_into, Column, Determinant, Determinant, Dgelss, Dgesv, Dgesvd, Dgetrf, dispose, div, div_into, Dposv, Dsyev, EqDiff, EqProd, EqSum, equals, FreeBuffer, Invert, Inverted, IsSymmetric, lessThan, mult, mult, mult, mult_into, mult_into, NCols, neg, not_equals, NRows, Resize, Resize, Row, SetColumn, SetRow, SetSize, SetSize, sub, sub_into, Submatrix, Submatrix, Submatrix, Transpose, Transposed, VisCrossProduct, VisCrossProduct, VisDMatrixLeastSquares, VisDMatrixLeastSquares, VisDMatrixLeastSquares, VisDMatrixLeastSquares, VisDMatrixLLS, VisDMatrixSolve, VisDMatrixSolve, VisDMatrixSolveSPD, VisDMatrixSolveSPD, VisDMatrixSqrtInverse, VisDMatrixSqrtInverse, VisDMatrixSVD, VisDMatrixSVD, VisDMatrixSymmetricEigen, VisGaussJordanSolveDMatrix, VisOuterProduct

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

- Field Detail
  - RAND_MAX
```
public static int RAND_MAX
```
- Constructor Detail
  - CDMatrix
```
public CDMatrix()
```
    Constructors
  - CDMatrix
```
public CDMatrix(int rows,
                int cols)
```
  - CDMatrix
```
public CDMatrix(int rows,
                int cols,
                double[][] storage)
```
  - CDMatrix
```
public CDMatrix(CDMatrix mat)
```
  - CDMatrix
```
public CDMatrix(CVisDMatrix mat)
```
- Method Detail
  - assign
```
public CDMatrix assign(CVisDMatrix mat)
```
    Assignment operator (CVisDMatrix).
    
    Overrides:
    
    assign in class CVisDMatrix
    
    Parameters:
    
    mat - Input matrix.
    
    Returns:
    
    This.
  - assign
```
public CDMatrix assign(CDMatrix mat)
```
    Assignment operator (CDMatrix).
    
    Parameters:
    
    mat - Input matrix.
    
    Returns:
    
    This.
  - assign
```
public CDMatrix assign(double value)
```
    Assignment operator (double). Set all values equal to 'value'.
    
    Overrides:
    
    assign in class CVisDMatrix
    
    Parameters:
    
    value - Input double.
    
    Returns:
    
    This.
  - assign
```
public CDMatrix assign(double[][] value)
```
    Assignment operator
    
    Parameters:
    
    value - double matrix
    
    Returns:
    
    this.
  - SumCol
```
public void SumCol(CDVector vSum)
```
    Calc the sum of each column into a vector. The vector will be resized if it doesn't have the right length.
    
    Parameters:
    
    vSum - Output vector.
  - MeanCol
```
public void MeanCol(CDVector vMean)
```
    Calc the mean of each column into a vector. The vector will be resized if it doesn't have the right length.
    
    Parameters:
    
    vMean - Output vector.
  - VarCol
```
public void VarCol(CDVector vVar)
```
    Calc the variance of each column into a vector. The vector will be resized if it doesn't have the right length.
    
    Parameters:
    
    vVar - Output vector.
  - StdCol
```
public void StdCol(CDVector vStd)
```
    Calc the standard deviation of each column into a vector. The vector will be resized if it doesn't have the right length.
    
    Parameters:
    
    vStd - Output vector.
  - Sum
```
public double Sum()
```
    Calc the total sum of the matrix.
    
    Returns:
    
    The sum.
  - Mean
```
public double Mean()
```
    Calcs the mean value of the matrix.
    
    Returns:
    
    The mean value.
  - Var
```
public double Var()
```
    Calc the variance of the matrix.
    
    Returns:
    
    The variance value.
  - Std
```
public double Std()
```
    Calc the standard diviation of the matrix.
    
    Returns:
    
    The standard diviation value.
  - OneWayANOVA
```
public void OneWayANOVA(double[] dZ,
                        int[] nDFModel,
                        int[] nDFError)
```
    One-way analysis of variance (ANOVA). Determination of the fluctuations observed in a sample, and their dependencies in the form of a one-way analysis of variance (ANOVA).
    
    Parameters:
    
    dZ -
    
    nDFModel -
    
    nDFError -
  - TTest
```
public void TTest(int iCol1,
                  int iCol2,
                  double[] dZ,
                  int[] nDF)
```
    Student's T-test.
    
    Parameters:
    
    iCol1 -
    
    iCol2 -
    
    dZ -
    
    nDF -
  - Row
```
public void Row(int i,
                CDVector vRow)
```
    Return the i-th row of the matrix. The vector will be resized if it doesn't have the right length. Notice that due to the row major nature of matrices, row read/writes are *much* faster than col read/writes. Alternatively, one could use the more costly CVisDVector CVisDMatrix::Row(int r) method. To set the i-th row use: void CVisDMatrix::SetRow(int r, const CVisDVector &v)
    
    Parameters:
    
    i - The row number.
    
    vRow - Output vector;
  - Col
```
public void Col(int i,
                CDVector vCol)
```
    Return the i-th column of the matrix. The vector will be resized if it doesn't have the right length.
    
    Parameters:
    
    i - The column number.
    
    vCol - Output vector;
  - Diag
```
public void Diag(CDVector vec)
```
    Make the matrix a diagonal matrix containing 'vec'. This function transforms the matrix into a diagonal matrix, with the values of 'vec' in the diagonal.
    
    Parameters:
    
    vec - Vector to place in the diagonal.
  - ToString
```
public java.lang.String ToString()
```
    Returns a string representing the matrix.
    
    Returns:
    
    A string.
  - CombVert
```
public void CombVert(CVisDMatrix Top,
                     CVisDMatrix Bottom)
```
    Composes the matrix of Top and Bottom (on top of each other).
    
    Parameters:
    
    Top - Matrix to be placed in the top of this matrix.
    
    Bottom - Matrix to be placed in the bottom of this matrix.
  - ToMatlab
```
public void ToMatlab(java.lang.String sFilename,
                     java.lang.String sName,
                     java.lang.String sComment,
                     boolean fAppend)
```
    Writes the matrix to disk in MatLab (.m) format. To read the matrix into MatLab write e.g. 'my_matrix.m' at the MatLab prompt. Notice that this should be used for storage a (really) large matrices, due to the computational and i/o overhead induced by the simple MatLab text format. Also, remember that MatLab can't read (.m) files with lines longer than 4096 bytes. If no communication with MatLab is needed, but merely to/from disk functionality within a DIVA program, it is suggested to use the fast binary i/o methods ToFile() and FromFile().
    
    Parameters:
    
    sFilename - Output file name. Should have the extension '.m'.
    
    sName - Name of destination matlab variable.
    
    sComment - Optional comment inside the file.
    
    fAppend - If true, the vector is appended to the file 'sFilename'.
  - Sqrt
```
public void Sqrt()
```
    Takes the square root of each element.
  - Sqr
```
public void Sqr()
```
    Takes the power of two of each element.
  - ElementMultiply
```
public void ElementMultiply(CDMatrix matrix)
```
    Element-wise matrix multiply. Multiply each element in the matrix with the corresponding element of the input matrix.
  - ElementDivide
```
public void ElementDivide(CDMatrix matrix)
```
    Element-wise matrix division. Divide each element in the matrix with the corresponding element of the input matrix.
  - ToFile
```
public void ToFile(java.lang.String sFilename)
```
    Writes the matrix to disk in binary format. The dimensions are saved as two doubles (!!?) (rows,cols) in the start.
    
    Parameters:
    
    sFilename - Input file name.
  - ToFile
```
public void ToFile(java.io.DataOutputStream fh)
```
    Writes the matrix to disk in binary format. The dimensions are saved as two doubles (!!?) (rows,cols) in the start. The matrix is written to the binary file 'fh' at the current position of the file pointer.
    
    Parameters:
    
    fh - Open file handle.
  - FromFile
```
public void FromFile(java.lang.String sFilename)
```
    Reads a matrix from disk in binary format, as written from ToFile(). The matrix is resizew if it doesn't fit the disk matrix.
    
    Parameters:
    
    sFilename - Input file name.
  - FromFile
```
public void FromFile(java.io.DataInputStream fh)
```
    Reads a matrix from disk in binary format (from the current position of the file pointer), as written from ToFile(). The matrix is resized if it doesn't fit the disk matrix.
    
    Parameters:
    
    fh - Open file handle.
  - Kron
```
public void Kron(CDMatrix mX,
                 CDMatrix mY)
```
    Forms the Kronecker tensor product of two matrices. The result is placed in this.
  - Eye
```
public void Eye()
```
    Converts the matrix in the identity matrix - i.e. zeros all-over except the ones in the diagonal.
  - TriU
```
public void TriU(CDMatrix matrix,
                 int K)
```
    Extract upper triangular part of matrix. Extracts the elements on and above the K-th diagonal. K = 0 is the main diagonal, K > 0 is above the main diagonal and K
    
    TriL
    
    public void TriL(CDMatrix matrix, int K)
    
    Extract lower triangular part of matrix. Extracts the elements on and below the K-th diagonal. K = 0 is the main diagonal, K > 0 is above the main diagonal and K
    
    Eq
    
    public void Eq(double B, CDMatrix C)
    
    Element wise equal to. Comparison of a matrix and a double. Compares each element in this matrix (A) with double B. Result matrix C has elements with values 1 or 0. C(i,j) = 1 if A(i,j) == B C(i,j) = 0 else
    
    Eq
    
    public void Eq(CDMatrix B, CDMatrix C)
    
    Element wise equal to. Comparison of two matrices. Compares each element in this matrix (A) with corresponding element in B. Result matrix C has elements with values 1 or 0. C(i,j) = 1 if A(i,j) == B(i,j) C(i,j) = 0 else
    
    Ne
    
    public void Ne(double B, CDMatrix C)
    
    Element wise not equal to. Comparison of a matrix and a double. Compares each element in this matrix (A) with double B. Result matrix C has elements with values 1 or 0. C(i,j) = 1 if A(i,j) != B C(i,j) = 0 else
    
    Ne
    
    public void Ne(CDMatrix B, CDMatrix C)
    
    Element wise not equal to. Comparison of two matrices. Compares each element in this matrix (A) with corresponding element in B. Result matrix C has elements with values 1 or 0. C(i,j) = 1 if A(i,j) != B(i,j) C(i,j) = 0 else
    
    Lt
    
    public void Lt(double B, CDMatrix C)
    
    Element wise less than. Comparison of a matrix and a double. Compares each element in this matrix (A) with double B. Result matrix C has elements with values 1 or 0. C(i,j) = 1 if A(i,j)
    
    Lt
    
    public void Lt(CDMatrix B, CDMatrix C)
    
    Element wise less than. Comparison of two matrices. Compares each element in this matrix (A) with corresponding element in B. Result matrix C has elements with values 1 or 0. C(i,j) = 1 if A(i,j)
    
    Le
    
    public void Le(double B, CDMatrix C)
    
    Element wise less than or equal. Comparison of a matrix and a double. Compares each element in this matrix (A) with double B. Result matrix C has elements with values 1 or 0. C(i,j) = 1 if A(i,j)
    
    Le
    
    public void Le(CDMatrix B, CDMatrix C)
    
    Element wise less than or equal. Comparison of two matrices. Compares each element in this matrix (A) with corresponding element in B. Result matrix C has elements with values 1 or 0. C(i,j) = 1 if A(i,j)
    
    Gt
    
    public void Gt(double B, CDMatrix C)
    
    Element wise greater than. Comparison of a matrix and a double. Compares each element in this matrix (A) with double B. Result matrix C has elements with values 1 or 0. C(i,j) = 1 if A(i,j) > B C(i,j) = 0 else
    
    Gt
    
    public void Gt(CDMatrix B, CDMatrix C)
    
    Element wise greater than. Comparison of two matrices. Compares each element in this matrix (A) with corresponding element in B. Result matrix C has elements with values 1 or 0. C(i,j) = 1 if A(i,j) > B(i,j) C(i,j) = 0 else
    
    Ge
    
    public void Ge(double B, CDMatrix C)
    
    Element wise greater than or equal. Comparison of a matrix and a double. Compares each element in this matrix (A) with double B. Result matrix C has elements with values 1 or 0. C(i,j) = 1 if A(i,j) >= B C(i,j) = 0 else
    
    Ge
    
    public void Ge(CDMatrix B, CDMatrix C)
    
    Element wise greater than or equal. Comparison of two matrices. Compares each element in this matrix (A) with corresponding element in B. Result matrix C has elements with values 1 or 0. C(i,j) = 1 if A(i,j)
    
    Log
    
    public void Log()
    
    Takes the natural logarithm (base e=2.71..) of each matrix element.
    
    FlipLR
    
    public void FlipLR()
    
    FlipLR modifies the matrix with row preserved and columns flipped in the left/right direction.
    
    FlipUD
    
    public void FlipUD()
    
    Flip matrix in up/down direction. FlipUD(X) modifies the matrix with columns preserved and rows flipped in the up/down direction.
    
    Rand
    
    public void Rand()
    
    Uniformly distributed random numbers. Inserts uniformly distributed random numbers in the range [0;1].
    
    OuterProduct
    
    public void OuterProduct(CDVector v1, CDVector v2)
    
    Forms the outer product of two vectors and store the result in this. If the matrix does have the correct size, it will be resized.
    
    Parameters:
    
    v1 - Input vector.
    
    v2 - Input vector.
    
    Det
    
    public double Det()
    
    Calculates the determinant of a square matrix up to the 3rd order.
    
    Returns:
    
    The determinant.
    
    Trace
    
    public double Trace()
    
    Calculates the trace - i.e. the sum of diagonal elements.
    
    Returns:
    
    The trace.
    
    ToVector
    
    public void ToVector(CDVector v, boolean rowWise)
    
    Converts this matrix to a vector, either by row (default) or column.
    
    Parameters:
    
    v - Output vector
    
    rowWise - If true (default) matrix data is extracted row-wise. If false matrix data is extracted column-wise.
    
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Class CDMatrix

Field Summary

Fields inherited from class gov.nih.mipav.view.renderer.WildMagic.AAM.CVisDMatrix

Constructor Summary

Method Summary

Methods inherited from class gov.nih.mipav.view.renderer.WildMagic.AAM.CVisDMatrix

Methods inherited from class java.lang.Object

Field Detail

RAND_MAX

Constructor Detail

CDMatrix

CDMatrix

CDMatrix

CDMatrix

CDMatrix

Method Detail

assign

assign

assign

assign

SumCol

MeanCol

VarCol

StdCol

Sum

Mean

Var

Std

OneWayANOVA

TTest

Row

Col

Diag

ToString

CombVert

ToMatlab

Sqrt

Sqr

ElementMultiply

ElementDivide

ToFile

ToFile

FromFile

FromFile

Kron

Eye

TriU

TriL

Eq

Eq

Ne

Ne

Lt

Lt

Le

Le

Gt

Gt

Ge

Ge

Log

FlipLR

FlipUD

Rand

OuterProduct

Det

Trace

ToVector