matrix.h

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/***************************************************************************
                          matrix.h  -  description
                             -------------------
    email                : georg.martius@web.de
***************************************************************************/
// provides Matrix class with convinient operators
//  and fast inversion for nonzero square matrixes
//
// $Log: matrix.h,v $
// Revision 1.24  2008/06/18 13:46:20  martius
// beside and toBeside added
// addColumns and addRows is now based on toAbove and toBeside
// bug fix in removeColumns
//
// Revision 1.23  2008/05/30 11:58:08  martius
// equals method and cmath
//
// Revision 1.22  2008/05/07 16:45:52  martius
// code cosmetics and documentation
//
// Revision 1.21  2008/05/02 17:20:04  martius
// *** empty log message ***
//
// Revision 1.20  2008/04/30 14:54:14  guettler
// -indextype of matrices is now unsigned int (bigger matrices than
//  256x256 can be used now, if not AVR defined)
// -code cleaned up
//
// Revision 1.19  2008/04/29 11:04:44  guettler
// forgot to deactivate += operator
//
// Revision 1.18  2008/04/29 11:01:32  guettler
// -added toMap2 and toMap2P
// -removed operator + for scalar (use add or toSum instead)
//
// Revision 1.17  2008/04/28 15:24:14  guettler
// -added deleteRows and deleteColumns
// -fixed memory leak in addColumns
//
// Revision 1.16  2008/04/28 10:33:05  guettler
// -added operator + and += for adding a scalar to each element of the matrix
// -added add function and toSum for adding a scalar to each element
// -added addRows and addColumns for adding new rows or colums to the matrix
//
// Revision 1.15  2008/03/01 01:33:30  martius
// size added
//
// Revision 1.14  2007/08/22 08:28:07  martius
// contrains for reshape relaxed
//
// Revision 1.13  2007/06/21 16:29:18  martius
// added map2P
// map2 into cpp
//
// Revision 1.12  2007/06/08 15:50:29  martius
// added unsafeGetData
//
// Revision 1.11  2007/05/22 13:52:36  martius
// inplace operators return *this which makes them more useable for temporary matrices
//
// Revision 1.10  2007/04/03 09:58:20  martius
// memory management done with free and malloc
//
// Revision 1.9  2007/04/03 07:13:32  der
// plus lambdaI
//
// Revision 1.8  2007/02/05 12:31:21  martius
// reshape
//
// Revision 1.7  2006/11/29 16:22:43  martius
// name is a variable of configurable and is used as such
//
// Revision 1.6  2006/08/04 15:16:13  martius
// documentation
//
// Revision 1.5  2006/07/20 17:14:35  martius
// removed std namespace from matrix.h
// storable interface
// abstract model and invertablemodel as superclasses for networks
//
// Revision 1.4  2006/07/19 09:26:37  martius
// namespace std removed from header
// store and restore
// read and write
// columns accessor
//
// Revision 1.3  2006/07/18 14:13:09  martius
// crucial bug fixing in *= operator!
//
// Revision 1.2  2006/07/14 12:24:01  martius
// selforg becomes HEAD
//
// Revision 1.1.2.2  2006/07/14 08:56:53  der
// New function NullTimesNull
//
// Revision 1.1.2.1  2006/07/10 12:01:02  martius
// Matrixlib moved to selforg
//
// Revision 1.20.6.4  2006/03/30 23:08:53  martius
// comments
//
// Revision 1.20.6.3  2006/03/30 12:34:45  martius
// documentation updated
//
// Revision 1.20.6.2  2006/03/29 15:12:46  martius
// column accessor function added
//
// Revision 1.20.6.1  2005/12/06 17:38:10  martius
// *** empty log message ***
//
// Revision 1.20  2005/10/21 11:58:25  martius
// map2 (similar to map but for 2 matrices)
// changed naming of functions to be more consistent.
//  Functions with "to" in front indicate the change of this. (Still not consistent with add, mult ...)
//
// Revision 1.19  2005/10/06 17:10:06  martius
// convertToList
// above and toAbove
//
// Revision 1.18  2005/09/21 08:43:01  martius
// convertToBuffer is const
//
// Revision 1.17  2005/08/06 20:47:36  martius
// Commented
//
// Revision 1.16  2005/07/21 15:13:36  martius
// mapP addid (mapping with additional parameter)
//
// Revision 1.15  2005/06/21 15:35:21  martius
// hide invert3x3 and invert_nonzero for AVR to minimize binary size
//
// Revision 1.14  2005/06/17 15:19:03  martius
// version workes with avr
//
// Revision 1.13  2005/06/10 08:23:15  martius
// mult???wise are copy operations now!
// toMult???wise are the inplace variant.
//
// Revision 1.11  2005/06/09 11:52:03  martius
// multMT (M * M^T) and multTM (M^T * M)
//
// Revision 1.10  2005/06/02 22:48:54  martius
// copy is inline and works correct now
//
// Revision 1.9  2005/06/02 08:48:31  martius
// mult_row/column_wise
// convertToBuffer
//
// Revision 1.8  2005/05/30 22:40:56  martius
// map becomes toMap and the new map returns a new matrix
// exp becomes toExp
//
// Revision 1.7  2005/05/30 21:46:54  martius
// *** empty log message ***
//
// Revision 1.6  2005/05/30 17:21:26  martius
// added zero
// set() and constructor(m,n,0) initialise with zero
// id returns void (more consistent)
//
// Revision 1.5  2005/05/30 16:42:56  martius
// map function included (component-wise function application)
//
// Revision 1.4  2005/05/30 11:28:09  martius
// marked "row" as untested
//
// Revision 1.3  2005/05/30 10:14:54  martius
// 3x3 explicit matrix inversion
//
// Revision 1.2  2005/05/30 09:45:46  martius
// Working. Interface not tested in pratice
//
// Revision 1.1  2005/05/29 22:43:08  martius
// proper Makefile with dependencies and tag generator
//
/***************************************************************************/

#ifndef MATRIX_H
#define MATRIX_H

#include <string.h>
#include <assert.h>
#include <list>

#ifndef AVR
#include <iostream>
#endif

#include "storeable.h"

// TODO: add doxygen section

/**
 * namespace for matrix library
 *@author Georg Martius
 */
namespace matrix{

  /// integer constant for use with exp function and (^) operator to transpose the matrix
  extern const int T;

#ifndef AVR
/// type for matrix indices
  typedef unsigned int I;
  /// type for matrix elements
  typedef double D;
#else
/// type for matrix indices, if AVR
/// NOTE: You cannot use matrices bigger than m*n>255 if AVR!
  typedef unsigned short I;
  /// type for matrix elements
  typedef float D;
#endif


#define D_Zero 0
#define D_One 1
  /** Matrix type. Type D is datatype of matrix elements,
   * which is fixed to double.
   * Type I is the indextype of matrix elements,
   * which is fixed to unsigned int, if AVR is not defined.
   * There are basicly two different types of operation:
   * Inplace operations and copy operations.
   * Please use the latter ones unless you know what you are doing.
   * Just in case of critical performance optimisation use the inplace
   * operations.
   * The most convinient way is to use the overloaded operators
   * (like + * ...).
   * All constructed matrices are initialised with zero elements
   * (unless data is given).
   * All functions perform range checks if in debug mode
   * (NDEBUG is not defined).
   * Please use debug the version (default) for testing
   * @see examples/matrix/matrixexample.cpp
   *
   * @author Georg Martius
   */
  class Matrix : public Storeable {
  public:
    /// default constructor: zero matrix (0x0)
    Matrix()
      : m(0), n(0), buffersize(0), data(0) {};
    /** constucts a matrix with the given size.
        If _data is null then the matrix is filled with zeros.
        otherwise matrix will be filled with _data in a row-wise manner.
        In this case _data must be at least _m*_n elements long
    */
    Matrix(I _m, I _n, const D* _data=0);
    /** constucts a matrix with the given size and fills it with the default value
    */
    Matrix(I _m, I _n, D def);
    /// constucts a instance on the base of a deep copy of the given matrix
    Matrix (const Matrix& c);
    ~Matrix() { if(data) free(data); };

  public:
    //  /////////////////// Accessors ///////////////////////////////
    /** @return number of rows */
    I getM() const { return m; };
    /** @return number of columns */
    I getN() const { return n; };
    /// @return number number elements in the matrix (getM()*getN())
    I size() const { return n*m; };


    /** @return element at position i,j (row, column index) */
    inline D val(I i, I j) const {
      assert( i<m && j<n);
      return data[i*n+j];
    };
    /** @return reference to element at position i,j
        (can be used as left side value) */
    inline D& val(I i, I j) {
      assert( i<m && j<n);
      return data[i*n+j];
    };

    /** @return element at position i,j (row, column index) and 0 if out of bounds */
    inline D valDef0(I i, I j) const {
      if(0<=i && i<m && 0<=j && j<n)
        return data[i*n+j];
      else return 0;
    };

    /** sets the size of the matrix and maybe the data if given (row-wise).
        If data=null then the matrix is set to zero
        @see toZero()
        @see constructor Matrix(m,n,data)
    */
    void set(I _m, I _n, const D* _data=0);
    /** sets the data (row-wise).
        @param _data if null then matrix elements are set to zero
        otherwise the field MUST have the length should be getM()*getN()*/
    void set(const D* _data);
    /** @return row-vector(as 1xN matrix) containing the index'th row */
    Matrix row(I index) const;
    /** @returns submatrix (as KxN matrix)
        containing row from startindex to endindex inclusively (K=stopindex-endindex)
        indices can be out of bounds, they are clipped in any case
    */
    Matrix rows(I startindex, I endindex) const;
    /** @returns column-vector(as Nx1 matrix) containing the index'th column */
    Matrix column(I index) const;
    /** @returns submatrix (as NxK matrix) 
        containing column from startindex to endindex inclusively (K=endindex-startindex) 
        indices can be out of bounds, they are clipped in any case
    */
    Matrix columns(I startindex, I endindex) const;


    /** stores the content of the matrix (row-wise) in the given buffer
        @param buffer Buffer for storing the elements (should have the length given by len)
        @param len Length of the provided buffer.
               In any case only min(len, getM()*getN()) elements are copied.
        @return number of actually written elements
     */
    int convertToBuffer(D* buffer, I len) const;

    /** @return a list of the content of the matrix (row-wise)
     */
    std::list<D> convertToList() const;

    /// returns a pointer to the data. UNSAFE!!!
    const double* unsafeGetData() const{return data;}

    /*       STOREABLE       */
    /** stores the Matrix into the given file stream (binary)
     */
    bool store(FILE* f) const;

    /** reads a Matrix from the given file stream (binary)
     */
    bool restore(FILE* f);

    /** writes the Matrix into the given file stream (ascii)
     */
    bool write(FILE* f) const;

    /** reads a Matrix from the given file stream (ascii)
     */
    bool read(FILE* f);


  public:
    // ////////////////////////////////////////////////////////////////////
    // /////////////  operations  /////////////////////////////
    //  (the result of the operation is not stored in one of the operands)
    void add(const Matrix& a, const Matrix& b); ///< addition:    this = a + b
    void add(const Matrix& a, const D& summand); /// add scalar to each element
    void sub(const Matrix& a, const Matrix& b); ///< subtraction: this = a - b
    void mult(const Matrix& a, const Matrix& b);///< multiplication: this = a * b
    void mult(const Matrix& a, const D& fac);///< scaling: this = a * fac

    /// returns true if matrix is a 0x0 matrix
    bool isNulltimesNull() const;

    /** bytewise comparison (compares data buffer bytewise, which implies that
        n1*m1 == n2*m2 but not necessarily n1==n2) */
    bool equals(const Matrix& a) const;


    /**  maps the matrix to a new matrix
         with all elements mapped with the given function
    */
    Matrix map(D (*fun)(D)) const;
    /**  like map but with additional parameter for the mapping function
    */
    Matrix mapP(void* param, D (*fun)(void*, D)) const;

    // Exotic operations ///////////
    /** binary map operator for matrices.
       The resulting matrix consists of the function values applied to the elements of a and b.
       In haskell this would something like: map (uncurry . fun) $ zip a b
    */
    static Matrix map2( D (*fun)(D,D), const Matrix& a, const Matrix& b);

    /** binary map operator for matrices with parameter.
       The resulting matrix consists of the function values applied to the elements of a and b.
       In haskell this would something like: map (uncurry . (fun p)) $ zip a b
    */
    static Matrix map2P( void* param, D (*fun)(void*, D,D), const Matrix& a, const Matrix& b);

    /** row-wise multiplication
        @param factors column vector (Mx1) of factors, one for each row
    */
    Matrix multrowwise(const Matrix& factors) const;
    /** column-wise multiplication
        @param factors column vector (Mx1) of factors, one for each column
    */
    Matrix multcolwise(const Matrix& factors) const;

    /// optimised multiplication of Matrix with its transposed: M * M^T
    Matrix multMT() const;
    /// optimised multiplication of transpsoed of Matrix with itself: M^T * M
    Matrix multTM() const;

    /// returns the product of all elements (\f$ \Pi_{ij} m_{ij} \f$)
    D elementProduct() const;
    /// returns the sum of all elements (\f$ \sum_{ij} m_{ij} \f$)
    D elementSum() const;

    /// returns a matrix that consists of this matrix above A (number of rows is getM + a.getM())
    Matrix above(const Matrix& a) const ;
    /// returns a matrix that consists of this left beside A  (number of columns is getN + a.getN())
    Matrix beside(const Matrix& a) const ;

  public:   /// normal binary Operators
    /// deep copy
    Matrix& operator = (const Matrix& c) { copy(c); return *this; }
    Matrix operator +  (const Matrix& sum) const;
    //    Matrix operator +  (const D& sum) const; /// new operator (guettler)
    Matrix operator -  (const Matrix& sum) const;
    /** matrix product*/
    Matrix operator *  (const Matrix& fac) const;
    /** product with scalar (D) */
    Matrix operator *  (const D& fac) const;
    /** special matrix potence:
        @param exponent -1 -> inverse;
                       0 -> Identity Matrix;
                    1 -> itself;
                    T -> Transpose
    */
    Matrix operator ^ (int exponent) const;
    /// performant combined assigment operators
    Matrix& operator += (const Matrix& c) {toSum(c);   return *this; }
    Matrix& operator -= (const Matrix& c) {toDiff(c);  return *this; }
    Matrix& operator *= (const Matrix& c) {
      Matrix result;
      result.mult(*this, c);
      this->copy(result);
      return *this;
    }
    Matrix& operator *= (const D& fac) {toMult(fac); return *this; }

#ifndef AVR
    /// comparison operator (compares elements with tolerance distance of COMPARE_EPS)
    bool operator == (const Matrix& c) const;
    /** printing operator:
        output format: mxn (\n row0\n..rown \n) where rowX is tab seperated list of values
    */
    friend std::ostream& operator<<(std::ostream& , const Matrix&);
#endif

  public:
    // /////////////////// inplace Operators ///////////////////////////////
    /** performs a deep copy of the given matrix */
    void copy(const Matrix& c){ // Deep copy
      m=c.m; n=c.n;
      allocate();
      memcpy(data,c.data,m*n*sizeof(D));
    }

    Matrix& toTranspose();  ///< inplace transpose
    Matrix& toZero();       ///< inplace converts matrix to zero matrix
    Matrix& toId();         ///< inplace converts matrix to identity (use ^0 to get a copy version of it)
    /// inplace addition: this = this + a
    Matrix& toSum(const Matrix& a) {
      assert(a.m==m && a.n==n);
      for(I i=0; i<m*n; i++){
        data[i]+=a.data[i];
      }
      return *this;
    }

    /// inplace addition: this = this + a, where a is a scalar
    Matrix& toSum(const D& sum) {
      for(I i=0; i<m*n; i++){
        data[i]+=sum;
      }
      return *this;
    }

    /// inplace subtraction: this = this - a
    Matrix& toDiff(const Matrix& a){
      assert(a.m==m && a.n==n);
      for(I i=0; i<m*n; i++){
        data[i]-=a.data[i];
      }
      return *this;
    }

    /// inplace multiplication with scalar: this = this*fac
    Matrix& toMult(const D& fac);

    /** special inplace matrix potence:
        @param exponent -1 -> inverse; (matrix MUST be SQUARE and NONZERO)
                    0 -> Identity Matrix;
                    1 -> itself;
                    T -> Transpose
    */
    Matrix& toExp(int exponent);
    /**  inplace mapping of matrix elements (element-wise application) */
    Matrix& toMap(D (*fun)(D));
    /**  like toMap, but with an extra parameter for the mapping function. */
    Matrix& toMapP(void* param, D (*fun)(void*, D));

    /**  like toMap, but with 2 arguments for the mapping function. */
    Matrix& toMap2(D (*fun)(D,D), const Matrix& b);

    Matrix& toMap2P( void* param, D (*fun)(void*, D,D), const Matrix& b);

    // Exotic operations
    /** Inplace row-wise multiplication
        @param factors column vector of factors, one for each row
    */
    Matrix& toMultrowwise(const Matrix& factors);
    /** Inplace column-wise multiplication
        @param factors column vector of factors, one for each column
    */
    Matrix& toMultcolwise(const Matrix& factors);

    /// sets the matrix a below this matrix
    Matrix& toAbove(const Matrix& a);
    /// sets the matrix a right beside this matrix
    Matrix& toBeside(const Matrix& a);

    /// sorts the matrix (rowwise)
    Matrix& toSort();

    /** reshapes the matrix without destroying the data. 
        Remember: The data is stored rowwise.

        Only shrinking is allowed i.e. m*n must be lower or equal to getM()*getN()
    */
    Matrix& reshape(I m, I n);

    /// adds the given value to the diagonal
    Matrix& pluslambdaI(double lambda);

    /** adds one or more rows to the existing matrix and fills it with the given data
     * 
     * same as toAbove(Matrix(numberRows,getN(),data))
     * @param numberRows number of rows to add (this extends m)
     * @param _data data to add
     * @return the address of the matrix itself
     */
    Matrix& addRows(I numberRows, const D* _data=0);

    /**
     * same as toAbove(dataMatrix)
     * @param numberRows number of rows to add (unused)
     * @param dataMatrix matrix which contains the data of the new rows
     * @return the address of the matrix itself
     */
    Matrix& addRows(I numberRows, const Matrix& dataMatrix);

    /** adds one or more columns to the existing matrix
     * same as toBeside(Matrix(getM, numberColumns, _data))
     * @see toBeside()
     * @param numberColumns number of columns to add (this extends n)
     * @param _data data to add
     * @return the address of the matrix itself
     */
     Matrix& addColumns(I numberColumns, const D* _data=0);

    /**
     * same as toBeside(dataMatrix)
     * @see toBeside()
     * @param numberColumns number of columns to add (unused)
     * @param dataMatrix matrix which contains the data of the new rows
     * @return the address of the matrix itself
     */
    Matrix& addColumns(I numberColumns, const Matrix& dataMatrix);

    
    /** removes one or more rows of the existing matrix, 
        same as reshape(getM()-numberRows, getN());
     * @param numberRows number of rows to remove (this reduces m)
     * @return the address of the matrix itself
     */
    Matrix& removeRows(I numberRows);

    /** removes one or more columns of the existing matrix
     * resets the size of the matrix and deletes the appropiate data.
     * @param numberColumns number of columns to remove (this reduces n)
     * @return the address of the matrix itself
     */
    Matrix& removeColumns(I numberColumns);

  private:
    // NOTE: buffersize determines available memory storage.
    // m and n define the actual size
    I m, n;
    I buffersize;  // max number if elements
    D* data;      // where the data contents of the matrix are stored


  private: // internals
    void allocate();  //internal allocation
    /*inplace matrix invertation:
        Matrix must be SQARE, in addition, all DIAGONAL ELEMENTS MUST BE NONZERO
        (positive definite)
    */

#ifndef AVR
    void invertnonzero();
    void invert3x3();
#endif
    void invert2x2();
  };

} // namespace matrix
#endif

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