Package edu.claflin.finder.algo.clustering.struct.leading_eigenvector_struct

Class Matrix

java.lang.Object
edu.claflin.finder.algo.clustering.struct.leading_eigenvector_struct.Matrix
All Implemented Interfaces:
Serializable, Cloneable
public class Matrix extends Object implements Cloneable, Serializable
Jama = Java Matrix class. This is a reduced version of JAMA, a public domain linear algebra package for Java. I trimmed it to only keep EigenvalueDecomposition since that's all I needed for the leading eigenvector algorithm. I added the source files instead of using the .jar due to issues registering dependencies with Ant. For the full source code, jar, documentation, examples, etc. visit: https://math.nist.gov/javanumerics/jama/
Version:
5 August 1998
Author:
The MathWorks, Inc. and the National Institute of Standards and Technology.
See Also:

  • Field Details

    • A

      private double[][] A
      Array for internal storage of elements.

    • m

      private int m
      Row and column dimensions.

    • n

      private int n
      Row and column dimensions.

    • serialVersionUID

      private static final long serialVersionUID
      See Also:

  • Constructor Details

    • Matrix

      public Matrix(int m, int n)
      Construct an m-by-n matrix of zeros.
      Parameters:
      m - Number of rows.
      n - Number of colums.

    • Matrix

      public Matrix(int m, int n, double s)
      Construct an m-by-n constant matrix.
      Parameters:
      m - Number of rows.
      n - Number of colums.
      s - Fill the matrix with this scalar value.

    • Matrix

      public Matrix(double[][] A)
      Construct a matrix from a 2-D array.
      Parameters:
      A - Two-dimensional array of doubles.
      Throws:
      IllegalArgumentException - All rows must have the same length
      See Also:

    • Matrix

      public Matrix(double[][] A, int m, int n)
      Construct a matrix quickly without checking arguments.
      Parameters:
      A - Two-dimensional array of doubles.
      m - Number of rows.
      n - Number of colums.

    • Matrix

      public Matrix(double[] vals, int m)
      Construct a matrix from a one-dimensional packed array
      Parameters:
      vals - One-dimensional array of doubles, packed by columns (ala Fortran).
      m - Number of rows.
      Throws:
      IllegalArgumentException - Array length must be a multiple of m.

  • Method Details

    • constructWithCopy

      public static Matrix constructWithCopy(double[][] A)
      Construct a matrix from a copy of a 2-D array.
      Parameters:
      A - Two-dimensional array of doubles.
      Throws:
      IllegalArgumentException - All rows must have the same length

    • copy

      public Matrix copy()
      Make a deep copy of a matrix

    • clone

      public Object clone()
      Clone the Matrix object.
      Overrides:
      clone in class Object

    • getArray

      public double[][] getArray()
      Access the internal two-dimensional array.
      Returns:
      Pointer to the two-dimensional array of matrix elements.

    • getArrayCopy

      public double[][] getArrayCopy()
      Copy the internal two-dimensional array.
      Returns:
      Two-dimensional array copy of matrix elements.

    • getColumnPackedCopy

      public double[] getColumnPackedCopy()
      Make a one-dimensional column packed copy of the internal array.
      Returns:
      Matrix elements packed in a one-dimensional array by columns.

    • getRowPackedCopy

      public double[] getRowPackedCopy()
      Make a one-dimensional row packed copy of the internal array.
      Returns:
      Matrix elements packed in a one-dimensional array by rows.

    • getRowDimension

      public int getRowDimension()
      Get row dimension.
      Returns:
      m, the number of rows.

    • getColumnDimension

      public int getColumnDimension()
      Get column dimension.
      Returns:
      n, the number of columns.

    • get

      public double get(int i, int j)
      Get a single element.
      Parameters:
      i - Row index.
      j - Column index.
      Returns:
      A(i,j)
      Throws:
      ArrayIndexOutOfBoundsException

    • getMatrix

      public Matrix getMatrix(int i0, int i1, int j0, int j1)
      Get a submatrix.
      Parameters:
      i0 - Initial row index
      i1 - Final row index
      j0 - Initial column index
      j1 - Final column index
      Returns:
      A(i0:i1,j0:j1)
      Throws:
      ArrayIndexOutOfBoundsException - Submatrix indices

    • getMatrix

      public Matrix getMatrix(int[] r, int[] c)
      Get a submatrix.
      Parameters:
      r - Array of row indices.
      c - Array of column indices.
      Returns:
      A(r(:),c(:))
      Throws:
      ArrayIndexOutOfBoundsException - Submatrix indices

    • getMatrix

      public Matrix getMatrix(int i0, int i1, int[] c)
      Get a submatrix.
      Parameters:
      i0 - Initial row index
      i1 - Final row index
      c - Array of column indices.
      Returns:
      A(i0:i1,c(:))
      Throws:
      ArrayIndexOutOfBoundsException - Submatrix indices

    • getMatrix

      public Matrix getMatrix(int[] r, int j0, int j1)
      Get a submatrix.
      Parameters:
      r - Array of row indices.
      j0 - Initial column index
      j1 - Final column index
      Returns:
      A(r(:),j0:j1)
      Throws:
      ArrayIndexOutOfBoundsException - Submatrix indices

    • set

      public void set(int i, int j, double s)
      Set a single element.
      Parameters:
      i - Row index.
      j - Column index.
      s - A(i,j).
      Throws:
      ArrayIndexOutOfBoundsException

    • setMatrix

      public void setMatrix(int i0, int i1, int j0, int j1, Matrix X)
      Set a submatrix.
      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(int[] r, int[] c, Matrix X)
      Set a submatrix.
      Parameters:
      r - Array of row indices.
      c - Array of column indices.
      X - A(r(:),c(:))
      Throws:
      ArrayIndexOutOfBoundsException - Submatrix indices

    • setMatrix

      public void setMatrix(int[] r, int j0, int j1, Matrix X)
      Set a submatrix.
      Parameters:
      r - Array of row indices.
      j0 - Initial column index
      j1 - Final column index
      X - A(r(:),j0:j1)
      Throws:
      ArrayIndexOutOfBoundsException - Submatrix indices

    • setMatrix

      public void setMatrix(int i0, int i1, int[] c, Matrix X)
      Set a submatrix.
      Parameters:
      i0 - Initial row index
      i1 - Final row index
      c - Array of column indices.
      X - A(i0:i1,c(:))
      Throws:
      ArrayIndexOutOfBoundsException - Submatrix indices

    • transpose

      public Matrix transpose()
      Matrix transpose.
      Returns:
      A'

    • norm1

      public double norm1()
      One norm
      Returns:
      maximum column sum.

    • normInf

      public double normInf()
      Infinity norm
      Returns:
      maximum row sum.

    • normF

      public double normF()
      Frobenius norm
      Returns:
      sqrt of sum of squares of all elements.

    • uminus

      public Matrix uminus()
      Unary minus
      Returns:
      -A

    • plus

      public Matrix plus(Matrix B)
      C = A + B
      Parameters:
      B - another matrix
      Returns:
      A + B

    • plusEquals

      public Matrix plusEquals(Matrix B)
      A = A + B
      Parameters:
      B - another matrix
      Returns:
      A + B

    • minus

      public Matrix minus(Matrix B)
      C = A - B
      Parameters:
      B - another matrix
      Returns:
      A - B

    • minusEquals

      public Matrix minusEquals(Matrix B)
      A = A - B
      Parameters:
      B - another matrix
      Returns:
      A - B

    • arrayTimes

      public Matrix arrayTimes(Matrix B)
      Element-by-element multiplication, C = A.*B
      Parameters:
      B - another matrix
      Returns:
      A.*B

    • arrayTimesEquals

      public Matrix arrayTimesEquals(Matrix B)
      Element-by-element multiplication in place, A = A.*B
      Parameters:
      B - another matrix
      Returns:
      A.*B

    • arrayRightDivide

      public Matrix arrayRightDivide(Matrix B)
      Element-by-element right division, C = A./B
      Parameters:
      B - another matrix
      Returns:
      A./B

    • arrayRightDivideEquals

      public Matrix arrayRightDivideEquals(Matrix B)
      Element-by-element right division in place, A = A./B
      Parameters:
      B - another matrix
      Returns:
      A./B

    • arrayLeftDivide

      public Matrix arrayLeftDivide(Matrix B)
      Element-by-element left division, C = A.\B
      Parameters:
      B - another matrix
      Returns:
      A.\B

    • arrayLeftDivideEquals

      public Matrix arrayLeftDivideEquals(Matrix B)
      Element-by-element left division in place, A = A.\B
      Parameters:
      B - another matrix
      Returns:
      A.\B

    • times

      public Matrix times(double s)
      Multiply a matrix by a scalar, C = s*A
      Parameters:
      s - scalar
      Returns:
      s*A

    • timesEquals

      public Matrix timesEquals(double s)
      Multiply a matrix by a scalar in place, A = s*A
      Parameters:
      s - scalar
      Returns:
      replace A by s*A

    • times

      public Matrix times(Matrix B)
      Linear algebraic matrix multiplication, A * B
      Parameters:
      B - another matrix
      Returns:
      Matrix product, A * B
      Throws:
      IllegalArgumentException - Matrix inner dimensions must agree.

    • trace

      public double trace()
      Matrix trace.
      Returns:
      sum of the diagonal elements.

    • random

      public static Matrix random(int m, int n)
      Generate matrix with random elements
      Parameters:
      m - Number of rows.
      n - Number of colums.
      Returns:
      An m-by-n matrix with uniformly distributed random elements.

    • identity

      public static Matrix identity(int m, int n)
      Generate identity matrix
      Parameters:
      m - Number of rows.
      n - Number of colums.
      Returns:
      An m-by-n matrix with ones on the diagonal and zeros elsewhere.

    • print

      public void print(int w, int d)
      Print the matrix to stdout. Line the elements up in columns with a Fortran-like 'Fw.d' style format.
      Parameters:
      w - Column width.
      d - Number of digits after the decimal.

    • print

      public void print(PrintWriter output, int w, int d)
      Print the matrix to the output stream. Line the elements up in columns with a Fortran-like 'Fw.d' style format.
      Parameters:
      output - Output stream.
      w - Column width.
      d - Number of digits after the decimal.

    • print

      public void print(NumberFormat format, int width)
      Print the matrix to stdout. Line the elements up in columns. Use the format object, and right justify within columns of width characters. Note that is the matrix is to be read back in, you probably will want to use a NumberFormat that is set to US Locale.
      Parameters:
      format - A Formatting object for individual elements.
      width - Field width for each column.
      See Also:

    • print

      public void print(PrintWriter output, NumberFormat format, int width)
      Print the matrix to the output stream. Line the elements up in columns. Use the format object, and right justify within columns of width characters. Note that is the matrix is to be read back in, you probably will want to use a NumberFormat that is set to US Locale.
      Parameters:
      output - the output stream.
      format - A formatting object to format the matrix elements
      width - Column width.
      See Also:

    • read

      public static Matrix read(BufferedReader input) throws IOException
      Read a matrix from a stream. The format is the same the print method, so printed matrices can be read back in (provided they were printed using US Locale). Elements are separated by whitespace, all the elements for each row appear on a single line, the last row is followed by a blank line.
      Parameters:
      input - the input stream.
      Throws:
      IOException

    • checkMatrixDimensions

      private void checkMatrixDimensions(Matrix B)
      Check if size(A) == size(B)