Examples of edu.gmu.seor.prognos.unbbayesplugin.cps.Jama.Matrix

Package edu.gmu.seor.prognos.unbbayesplugin.cps.Jama

Examples of edu.gmu.seor.prognos.unbbayesplugin.cps.Jama.Matrix

edu.gmu.seor.prognos.unbbayesplugin.cps.Jama.Matrix
Jama = Java Matrix class.
The Java Matrix Class provides the fundamental operations of numerical linear algebra. Various constructors create Matrices from two dimensional arrays of double precision floating point numbers. Various "gets" and "sets" provide access to submatrices and matrix elements. Several methods implement basic matrix arithmetic, including matrix addition and multiplication, matrix norms, and element-by-element array operations. Methods for reading and printing matrices are also included. All the operations in this version of the Matrix Class involve real matrices. Complex matrices may be handled in a future version.
Five fundamental matrix decompositions, which consist of pairs or triples of matrices, permutation vectors, and the like, produce results in five decomposition classes. These decompositions are accessed by the Matrix class to compute solutions of simultaneous linear equations, determinants, inverses and other matrix functions. The five decompositions are:
- Cholesky Decomposition of symmetric, positive definite matrices.
- LU Decomposition of rectangular matrices.
- QR Decomposition of rectangular matrices.
- Singular Value Decomposition of rectangular matrices.
- Eigenvalue Decomposition of both symmetric and nonsymmetric square matrices.
Example of use:
Solve a linear system A x = b and compute the residual norm, ||b - A x||.
```
 double[][] vals = {{1.,2.,3},{4.,5.,6.},{7.,8.,10.}}; Matrix A = new Matrix(vals); Matrix b = Matrix.random(3,1); Matrix x = A.solve(b); Matrix r = A.times(x).minus(b); double rnorm = r.normInf(); 
```
@author The MathWorks, Inc. and the National Institute of Standards and Technology. @version 5 August 1998




  private CoVarMatrix opCoVarMatComponents(CoVarMatrix coVarMatrix,
      CoVarMatrix coVarMatrix2, int Operator) {
    CoVarMatrix res = new CoVarMatrix();
    Matrix one = new Matrix(coVarMatrix.getCoVarMatrix());
    Matrix two = new Matrix(coVarMatrix2.getCoVarMatrix());
    if(Operator == PLUS_OPERATOR){
      res.setCoVarMatrix(one.plus(two).getArray());
    }else if(Operator == MINUS_OPERATOR){
      res.setCoVarMatrix(one.minus(two).getArray());
    }

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  }


  private MeanMatrix opMMComponents(MeanMatrix meanMatrix,
      MeanMatrix meanMatrix2, int Operator) {
    MeanMatrix res = new MeanMatrix();
    Matrix one = new Matrix(meanMatrix.getMeanMatrix());
    Matrix two = new Matrix(meanMatrix2.getMeanMatrix());
    if(Operator == PLUS_OPERATOR){
      res.setMeanMatrix(one.plus(two).getArray());
    }else if(Operator == MINUS_OPERATOR){
      res.setMeanMatrix(one.minus(two).getArray());
    }

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  }


  
  private double[][] getK21(double mat[][], GHKPotentialTable ghkPot) {
    double res[][] = new double[mat.length][mat[0].length];
    Matrix M = new Matrix(res);
    boolean valueSet[][] = new boolean[mat.length][mat[0].length];
    initBooleanToFalse(valueSet);
    for (Node n1 : y2) {
      for (Node n2 : y1) {
        M.set(ghkPot.getContinuousNodeList().indexOf(n1), ghkPot.getContinuousNodeList()
            .indexOf(n2), mat[ghkPot.getContinuousNodeList().indexOf(n1)][ghkPot
            .getContinuousNodeList().indexOf(n2)]);
        valueSet[ghkPot.getContinuousNodeList().indexOf(n1)][ghkPot.getContinuousNodeList().indexOf(n2)] = true;
        // res[ghk.getContinuousNodeList().indexOf(n1)][ghk.getContinuousNodeList().indexOf(n2)]
        // =
        // mat[ghk.getContinuousNodeList().indexOf(n1)][ghk.getContinuousNodeList().indexOf(n2)];
      }
    }
    res = reduceMatrix(valueSet,M.getArray());
    return res;
  }

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    return res;
  }


  private double[][] getH1(double mat[][], GHKPotentialTable ghkPot) {
    double res[][] = new double[mat.length][mat[0].length];
    Matrix M = new Matrix(res);
    boolean valueSet[][] = new boolean[mat.length][mat[0].length];
    initBooleanToFalse(valueSet);
    for (Node n1 : y1) {
      M.set(ghkPot.getContinuousNodeList().indexOf(n1), 0, mat[ghkPot.getContinuousNodeList()
          .indexOf(n1)][0]);
      valueSet[ghkPot.getContinuousNodeList().indexOf(n1)][0]=true;
    }
    System.out.println("Sending "); printMatrix(M.getArray());
    res = reduceMatrix(valueSet,M.getArray());
    return res;
  }

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    return res;
  }


  private double[][] getK11(double mat[][], GHKPotentialTable ghkPot) {
    double res[][] = new double[mat.length][mat[0].length];
    Matrix M = new Matrix(res);
    boolean valueSet[][] = new boolean[mat.length][mat[0].length];
    initBooleanToFalse(valueSet);
    for (Node n1 : y1) {
      for (Node n2 : y1) {
        M.set(ghkPot.getContinuousNodeList().indexOf(n1), ghkPot.getContinuousNodeList()
            .indexOf(n2), mat[ghkPot.getContinuousNodeList().indexOf(n1)][ghkPot
            .getContinuousNodeList().indexOf(n2)]);
        valueSet[ghkPot.getContinuousNodeList().indexOf(n1)][ghkPot.getContinuousNodeList().indexOf(n2)] = true;
        // res[ghk.getContinuousNodeList().indexOf(n1)][ghk.getContinuousNodeList().indexOf(n2)]
        // =
        // mat[ghk.getContinuousNodeList().indexOf(n1)][ghk.getContinuousNodeList().indexOf(n2)];
      }
    }
    res = reduceMatrix(valueSet,M.getArray());
    return res;
  }

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    return temp;
  }
    
    public Matrix matInverse(Matrix m){
      Matrix temp;
      try{
        temp = m.inverse();
      }catch(Exception e){
        temp = m;
      }

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    printGHK(ghk);
    
  }


  private void adjustValues(ContinuousNode continuousNode, double d,ContinuousNode currentNode) {
    Matrix hx = null,hy = null,kxx = null,kxy = null,kyy = null;
    double g;
    HComponent hc = new HComponent();
    KComponent kc = new KComponent();
    
    if(hasNoParents(continuousNode)){ // special case when it is a root node
      Matrix h = new Matrix(continuousNode.getGHK().getGhkPot().getH().gethMatrix());
      Matrix k = new Matrix(continuousNode.getGHK().getGhkPot().getK().getkMatrix());
      
      g = continuousNode.getGHK().getGhkPot().getG() + h.transpose().times(d).det() - (k.times(d).times(d).times(0.5)).det();
      continuousNode.getGHK().getGhkPot().setG(g);
      
      double[][] hMat = new double[1][1];
      hMat[0][0]=0;
      hc.sethMatrix(hMat);
      continuousNode.getGHK().getGhkPot().setH(hc);
      
      double[][] kMat = new double[1][1];
      kMat[0][0]=0;
      kc.setkMatrix(kMat);
      continuousNode.getGHK().getGhkPot().setK(kc);
      
      return;
    }
    
    if(continuousNode.getGHK().hasNoDescreteStates){
      GHKPotential ghk = new GHKPotential();


        hx = new Matrix(getHX(currentNode.getGHK().getGhkPot().getH().gethMatrix(),currentNode.getGHK(),continuousNode));
        hy = new Matrix(getHy(currentNode.getGHK().getGhkPot().getH().gethMatrix(),currentNode.getGHK(),continuousNode));
        kxx = new Matrix(getKXX(currentNode.getGHK().getGhkPot().getK().getkMatrix(),currentNode.getGHK(),continuousNode));
        kxy = new Matrix(getKXY(currentNode.getGHK().getGhkPot().getK().getkMatrix(),currentNode.getGHK(),continuousNode));
        kyy = new Matrix(getKYY(currentNode.getGHK().getGhkPot().getK().getkMatrix(),currentNode.getGHK(),continuousNode));
        
        g = currentNode.getGHK().getGhkPot().getG() + hy.transpose().times(d).det() - (kyy.times(Math.pow(d, 2)).times(0.5)).det();
        ghk.setG(g);
        
        hc = new HComponent();
        hc.sethMatrix(extendAndOPMatrices(hx.getArray(),kxy.times(d).getArray(), MINUS_OPERATOR));
        ghk.setH(hc);
        
        kc = new KComponent();
        kc.setkMatrix(kxx.getArray());
        ghk.setK(kc);
        
        currentNode.getGHK().setGhkPot(ghk);
      
    }else{
      
      for(int i=0;i<currentNode.getGHK().tableSize();i++){
        
        hc = new HComponent();
        kc = new KComponent();
        
          hx = new Matrix(getHX(currentNode.getGHK().getHValue(i).gethMatrix(),currentNode.getGHK(),continuousNode));
          hy = new Matrix(getHy(currentNode.getGHK().getHValue(i).gethMatrix(),currentNode.getGHK(),continuousNode));
          kxx = new Matrix(getKXX(currentNode.getGHK().getKValue(i).getkMatrix(),currentNode.getGHK(),continuousNode));
          kxy = new Matrix(getKXY(currentNode.getGHK().getKValue(i).getkMatrix(),currentNode.getGHK(),continuousNode));
          kyy = new Matrix(getKYY(currentNode.getGHK().getKValue(i).getkMatrix(),currentNode.getGHK(),continuousNode));      
        
        g = currentNode.getGHK().getGValue(i)+ hy.transpose().times(d).det() - (kyy.times(Math.pow(d, 2)).times(0.5)).det();
        currentNode.getGHK().setGValue(i, g);
        
        hc = new HComponent();

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    for(Node n:continuousNodes){
      if(n.getIndex()!=continuousNode.getIndex())
        restOfNodes.add(n);
    }
    double res[][] = new double[mat.length][mat[0].length];
    Matrix M = new Matrix(res);
    boolean valueSet[][] = new boolean[mat.length][mat[0].length];
    initBooleanToFalse(valueSet);
      for (Node n2 : restOfNodes) {
        M.set(continuousNodes.indexOf(continuousNode), continuousNodes
            .indexOf(n2), mat[continuousNodes.indexOf(continuousNode)][continuousNodes.indexOf(n2)]);
        valueSet[continuousNodes.indexOf(continuousNode)][continuousNodes.indexOf(n2)] = true;
        // res[ghk.getContinuousNodeList().indexOf(n1)][ghk.getContinuousNodeList().indexOf(n2)]
        // =
        // mat[ghk.getContinuousNodeList().indexOf(n1)][ghk.getContinuousNodeList().indexOf(n2)];
      }
    res = reduceMatrix(valueSet,M.getArray());
    return res;
  }

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  }


  private double[][] getK11X(double[][] mat, GHKPotentialTable ghkPot, ContinuousNode continuousNode) {
    ArrayList<Node> continuousNodes = removeDuplicates((ArrayList<Node>) ghkPot.getContinuousNodeList());
    double res[][] = new double[mat.length][mat[0].length];
    Matrix M = new Matrix(res);
    boolean valueSet[][] = new boolean[mat.length][mat[0].length];
    initBooleanToFalse(valueSet);
    M.set(continuousNodes.indexOf(continuousNode), continuousNodes.indexOf(continuousNode), mat[continuousNodes.indexOf(continuousNode)][continuousNodes.indexOf(continuousNode)]);
    valueSet[continuousNodes.indexOf(continuousNode)][continuousNodes.indexOf(continuousNode)] = true;
    res = reduceMatrix(valueSet,M.getArray());
    return res;
  }

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    for(Node n:continuousNodes){
      if(n.getIndex()!=continuousNode.getIndex())
        restOfNodes.add(n);
    }
    double res[][] = new double[mat.length][mat[0].length];
    Matrix M = new Matrix(res);
    boolean valueSet[][] = new boolean[mat.length][mat[0].length];
    initBooleanToFalse(valueSet);
    for (Node n1 : restOfNodes) {
        M.set(continuousNodes.indexOf(n1), continuousNodes
            .indexOf(continuousNode), mat[continuousNodes.indexOf(n1)][continuousNodes.indexOf(continuousNode)]);
        valueSet[continuousNodes.indexOf(n1)][continuousNodes.indexOf(continuousNode)] = true;
    }
    res = reduceMatrix(valueSet,M.getArray());
    return res;
  }

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