code: /* This file is part of the jgpml Project.
   * http://github.com/renzodenardi/jgpml
   *
   * Copyright (c) 2011 Renzo De Nardi and Hugo Gravato-Marques
   *
   * Permission is hereby granted, free of charge, to any person
   * obtaining a copy of this software and associated documentation
   * files (the "Software"), to deal in the Software without
   * restriction, including without limitation the rights to use,
   * copy, modify, merge, publish, distribute, sublicense, and/or sell
   * copies of the Software, and to permit persons to whom the
   * Software is furnished to do so, subject to the following
   * conditions:
   *
   * The above copyright notice and this permission notice shall be
   * included in all copies or substantial portions of the Software.
   *
   * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
   * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
   * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
   * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
   * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
   * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
   * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
   * OTHER DEALINGS IN THE SOFTWARE.
   */
  
  package jgpml.covariancefunctions;
  
  import Jama.Matrix;
  
  /**
   * Some useful operations defined over Matrices
   */
  public class MatrixOperations {
  
  
      /**
       * Computes the exponential of the input <code>Matrix</code>
       * @param A  input <code>Matrix</code>
       * @return exp(A) result
       */
      public static Matrix exp(Matrix A){
  
          Matrix out = new Matrix(A.getRowDimension(),A.getColumnDimension());
          for(int i=0; i<A.getRowDimension(); i++)
              for(int j=0; j<A.getColumnDimension(); j++)
                  out.set(i,j,Math.exp(A.get(i,j)));
  
          return out;
      }
  
      /**
       * Sums across the rows of the <code>Matrix</code> and return the result as a single column <code>MAtrix</code>
       * @param A  input <code>Matrix</code>
       * @return result
       */
  
      public static Matrix sumRows(Matrix A){
          Matrix sum = new Matrix(A.getRowDimension(),1);
          for(int i=0; i<A.getColumnDimension(); i++)
              sum.plusEquals(A.getMatrix(0,A.getRowDimension()-1,i,i));
          return sum;
      }
  
  
      /**
       * Adds a value to each elemnts of the <code>Matrix</code>
       * @param A  <code>Matrix</code>
       * @param val  value to be added
       * @return  result
       */
      public static Matrix addValue(Matrix A,double val){
          for(int i=0; i<A.getRowDimension(); i++)
              for(int j=0; j<A.getColumnDimension(); j++)
                  A.set(i,j,A.get(i,j)+val);
  
          return A;
      }
  
      /**
       * Computes the arcsin of the input <code>Matrix</code> (element by element)
       * @param A input <code>Matrix</code>
       * @return asin(A)  result
       */
      public static Matrix asin(Matrix A){
  
          Matrix out = new Matrix(A.getRowDimension(),A.getColumnDimension());
          for(int i=0; i<A.getRowDimension(); i++)
              for(int j=0; j<A.getColumnDimension(); j++)
                  out.set(i,j,Math.asin(A.get(i,j)));
  
          return out;
      }
  
      /**
       * Computes the square root of the input <code>Matrix</code> (element by element)
       * @param A input <code>Matrix</code>
       * @return sqrt(A)  result
       */
      public static Matrix sqrt(Matrix A){
  
          Matrix out = new Matrix(A.getRowDimension(),A.getColumnDimension());
          for(int i=0; i<A.getRowDimension(); i++)
              for(int j=0; j<A.getColumnDimension(); j++)
                  out.set(i,j,Math.sqrt(A.get(i,j)));
  
          return out;
      }
  
      /**
       * If the argument is a row or column <code>Matrix</code> it returns a new diagonal <code>Matrix</code>
       * with the input as diagonal elements.
       * If the argument is a <code>Matrix</code> it returns the diagonal elements as a single column <code>Matrix</code>
       * Is a clone of the Matlab's function diag(A)
       * @param A input <code>Matrix</code>
       * @return diag(A) result
       */
      public static Matrix diag(Matrix A){
          Matrix diag =null;
          if(A.getColumnDimension()==1 || A.getRowDimension()==1){
              if(A.getColumnDimension()==1) {
                  diag = new Matrix(A.getRowDimension(),A.getRowDimension());
                  for(int i=0; i<diag.getColumnDimension(); i++)
                      diag.set(i,i,A.get(i,0));
              } else {
                  diag = new Matrix(A.getColumnDimension(),A.getColumnDimension());
                  for(int i=0; i<diag.getRowDimension(); i++)
                      diag.set(i,i,A.get(0,i));
              }
          } else {
  
              diag = new Matrix(A.getRowDimension(),1);
              for(int i=0; i<diag.getRowDimension(); i++)
                  diag.set(i,0,A.get(i,i));
          }
  
          return diag;
      }
  
  
      public static Matrix mean(Matrix A){
  
          if(A.getRowDimension()==1) {
              double m = 0;
              for(int i=0; i<A.getColumnDimension(); i++) m+=A.get(0,i);
  
              Matrix M = new Matrix(1,1);
              M.set(0,0,m/A.getColumnDimension());
              return M;
          } else {
              Matrix M = new Matrix(1,A.getColumnDimension());
              for(int i=0; i<A.getColumnDimension(); i++){
                  double m=0;
                  for(int j=0; j<A.getRowDimension(); j++){
                      m+=A.get(j,i);
                  }
                  M.set(0,i,m/A.getRowDimension());
              }
              return M;
          }
      }
  
      public static Matrix std(Matrix A){
  
            if(A.getRowDimension()==1) {
                double m = 0; double var=0;
                for(int i=0; i<A.getColumnDimension(); i++){
                    m = (m*(i-1) + A.get(0,i))/i;
                    var = var*(i-1)/i + ((A.get(0,i)-m)*(A.get(0,i)-m))/(i-1);
                }
                Matrix M = new Matrix(1,1);
                M.set(0,0,Math.sqrt(var));
                return M;
            } else {
                Matrix M = new Matrix(1,A.getColumnDimension());
                for(int i=0; i<A.getColumnDimension(); i++){
                    double m=0; double var=0;
                    for(int j=0; j<A.getRowDimension(); j++){
                        m = (m*(j-1) + A.get(j,i))/j;
                        var = var*(j-1)/j + ((A.get(j,i)-m)*(A.get(j,i)-m))/(j-1);
                    }
                    M.set(0,i,Math.sqrt(var));
                }
                return M;
            }
        }
  
  
  
  }
  
  