Examples with MatrixException cbit.vcell.matrix.MatrixException used on opensource projects

Example 6 with MatrixException

use of cbit.vcell.matrix.MatrixException in project vcell by virtualcell.

the class FastSystemAnalyzer method refreshInvarianceMatrix.

/**
 */
private void refreshInvarianceMatrix() throws MathException, ExpressionException {
    // 
    // the invariance's are expressed in matrix form
    // 
    // |a a a a a -1  0  0|   |x1|   |0|
    // |a a a a a  0 -1  0| * |x2| = |0|
    // |a a a a a  0  0 -1|   |x3|   |0|
    // |x4|
    // |x5|
    // |c1|
    // |c2|
    // |c3|
    // 
    Variable[] vars = new Variable[fastVarList.size()];
    fastVarList.copyInto(vars);
    int numVars = fastVarList.size();
    int rows = fastSystem.getNumFastInvariants();
    int cols = numVars + fastSystem.getNumFastInvariants();
    RationalExpMatrix matrix = new RationalExpMatrix(rows, cols);
    Enumeration<FastInvariant> fastInvariantsEnum = fastSystem.getFastInvariants();
    for (int i = 0; i < rows && fastInvariantsEnum.hasMoreElements(); i++) {
        FastInvariant fi = (FastInvariant) fastInvariantsEnum.nextElement();
        Expression function = fi.getFunction();
        for (int j = 0; j < numVars; j++) {
            Variable var = (Variable) fastVarList.elementAt(j);
            Expression exp = function.differentiate(var.getName());
            exp.bindExpression(null);
            exp = exp.flatten();
            RationalExp coeffRationalExp = RationalExpUtils.getRationalExp(exp);
            matrix.set_elem(i, j, coeffRationalExp);
        }
        matrix.set_elem(i, numVars + i, -1);
    }
    // Print
    System.out.println("origMatrix");
    matrix.show();
    // 
    // gaussian elimination on the matrix give the following representation
    // note that some column pivoting (variable re-ordering) is sometimes required to
    // determine N-r dependent vars
    // 
    // |10i0iccc|
    // |01i0iccc|  where (c)'s are the coefficients for constants of invariances
    // |00i1iccc|        (i)'s are the coefficients for dependent vars in terms of independent vars
    // 
    // Print
    System.out.println("reducedMatrix");
    if (rows > 0) {
        try {
            matrix.gaussianElimination(new RationalExpMatrix(rows, rows));
        } catch (MatrixException e) {
            e.printStackTrace(System.out);
            throw new MathException(e.getMessage());
        }
    }
    matrix.show();
    for (int i = 0; i < vars.length; i++) {
        System.out.print(vars[i].getName() + "  ");
    }
    System.out.println("");
    // 
    for (int i = 0; i < rows; i++) {
        for (int j = 0; j < rows; j++) {
            RationalExp rexp = matrix.get(i, j).simplify();
            matrix.set_elem(i, j, rexp);
        }
    }
    for (int i = 0; i < rows; i++) {
        // 
        if (!matrix.get(i, i).isConstant() || matrix.get(i, i).getConstant().doubleValue() != 1) {
            for (int j = i + 1; j < numVars; j++) {
                if (matrix.get(i, j).isConstant() && matrix.get(i, j).getConstant().doubleValue() == 1.0) {
                    for (int ii = 0; ii < rows; ii++) {
                        RationalExp temp = matrix.get(ii, i);
                        matrix.set_elem(ii, i, matrix.get(ii, j));
                        matrix.set_elem(ii, j, temp);
                    }
                    Variable tempVar = vars[i];
                    vars[i] = vars[j];
                    vars[j] = tempVar;
                    break;
                }
            }
        }
    }
    // Print
    for (int i = 0; i < vars.length; i++) {
        System.out.print(vars[i].getName() + "  ");
    }
    System.out.println("");
    matrix.show();
    // 
    // separate into dependent and indepent variables, and chop off identity matrix (left N-r columns)
    // 
    // T       |iiccc|                   T
    // [x1 x2 x4] = -1 * |iiccc| * [x3 x5 c1 c2 c3]
    // |iiccc|
    // 
    // 
    int numInvariants = fastSystem.getNumFastInvariants();
    dependentVarList.removeAllElements();
    for (int i = 0; i < numInvariants; i++) {
        dependentVarList.addElement(vars[i]);
    }
    independentVarList.removeAllElements();
    for (int i = numInvariants; i < vars.length; i++) {
        independentVarList.addElement(vars[i]);
    }
    int new_cols = independentVarList.size() + numInvariants;
    dependencyMatrix = new RationalExpMatrix(rows, new_cols);
    for (int i = 0; i < rows; i++) {
        for (int j = 0; j < new_cols; j++) {
            RationalExp rexp = matrix.get(i, j + dependentVarList.size()).simplify().minus();
            dependencyMatrix.set_elem(i, j, rexp);
        }
    }
    // Print
    System.out.println("\n\nDEPENDENCY MATRIX");
    dependencyMatrix.show();
    System.out.print("dependent vars: ");
    for (int i = 0; i < dependentVarList.size(); i++) {
        System.out.print(((Variable) dependentVarList.elementAt(i)).getName() + "  ");
    }
    System.out.println("");
    System.out.print("independent vars: ");
    for (int i = 0; i < independentVarList.size(); i++) {
        System.out.print(((Variable) independentVarList.elementAt(i)).getName() + "  ");
    }
    System.out.println("");
}

Example 7 with MatrixException

use of cbit.vcell.matrix.MatrixException in project vcell by virtualcell.

the class ModelOptimizationMapping method computeOptimizationSpec.

/**
 * Insert the method's description here.
 * Creation date: (8/22/2005 9:26:52 AM)
 * @return cbit.vcell.opt.OptimizationSpec
 * @param modelOptimizationSpec cbit.vcell.modelopt.ModelOptimizationSpec
 */
MathSymbolMapping computeOptimizationSpec() throws MathException, MappingException {
    if (getModelOptimizationSpec().getReferenceData() == null) {
        System.out.println("no referenced data defined");
        return null;
    }
    OptimizationSpec optSpec = new OptimizationSpec();
    optSpec.setComputeProfileDistributions(modelOptimizationSpec.isComputeProfileDistributions());
    parameterMappings = null;
    // 
    // get original MathDescription (later to be substituted for local/global parameters).
    // 
    SimulationContext simContext = modelOptimizationSpec.getSimulationContext();
    MathMapping mathMapping = simContext.createNewMathMapping();
    MathDescription origMathDesc = null;
    mathSymbolMapping = null;
    try {
        origMathDesc = mathMapping.getMathDescription();
        mathSymbolMapping = mathMapping.getMathSymbolMapping();
    } catch (MatrixException e) {
        e.printStackTrace(System.out);
        throw new MappingException(e.getMessage());
    } catch (ModelException e) {
        e.printStackTrace(System.out);
        throw new MappingException(e.getMessage());
    } catch (ExpressionException e) {
        e.printStackTrace(System.out);
        throw new MathException(e.getMessage());
    }
    // 
    // create objective function (mathDesc and data)
    // 
    ReferenceData referenceData = getRemappedReferenceData(mathMapping);
    if (referenceData == null) {
        throw new RuntimeException("no referenced data defined");
    }
    // 
    // get parameter mappings
    // 
    ParameterMappingSpec[] parameterMappingSpecs = modelOptimizationSpec.getParameterMappingSpecs();
    Vector<ParameterMapping> parameterMappingList = new Vector<ParameterMapping>();
    Variable[] allVars = (Variable[]) BeanUtils.getArray(origMathDesc.getVariables(), Variable.class);
    for (int i = 0; i < parameterMappingSpecs.length; i++) {
        cbit.vcell.model.Parameter modelParameter = parameterMappingSpecs[i].getModelParameter();
        String mathSymbol = null;
        Variable mathVariable = null;
        if (mathSymbolMapping != null) {
            Variable variable = mathSymbolMapping.getVariable(modelParameter);
            if (variable != null) {
                mathSymbol = variable.getName();
            }
            if (mathSymbol != null) {
                mathVariable = origMathDesc.getVariable(mathSymbol);
            }
        }
        if (mathVariable != null) {
            if (parameterMappingSpecs[i].isSelected()) {
                if (parameterMappingSpecs[i].getHigh() < parameterMappingSpecs[i].getLow()) {
                    throw new MathException("The lower bound for Parameter '" + parameterMappingSpecs[i].getModelParameter().getName() + "' is greater than its upper bound.");
                }
                if (parameterMappingSpecs[i].getCurrent() < parameterMappingSpecs[i].getLow()) {
                    throw new MathException("The initial guess of '" + parameterMappingSpecs[i].getModelParameter().getName() + "' is smaller than its lower bound.");
                }
                if (parameterMappingSpecs[i].getCurrent() > parameterMappingSpecs[i].getHigh()) {
                    throw new MathException("The initial guess of '" + parameterMappingSpecs[i].getModelParameter().getName() + "' is greater than its upper bound.");
                }
                if (parameterMappingSpecs[i].getLow() < 0) {
                    throw new MathException("The lower bound for Parameter '" + parameterMappingSpecs[i].getModelParameter().getName() + "' is negative. All lower bounds must not be negative.");
                }
                if (Double.isInfinite(parameterMappingSpecs[i].getLow())) {
                    throw new MathException("The lower bound for Parameter '" + parameterMappingSpecs[i].getModelParameter().getName() + "' is infinity. Lower bounds must not be infinity.");
                }
                if (parameterMappingSpecs[i].getHigh() <= 0) {
                    throw new MathException("The upper bound for Parameter '" + parameterMappingSpecs[i].getModelParameter().getName() + "' is negative. All upper bounds must be positive.");
                }
                if (Double.isInfinite(parameterMappingSpecs[i].getHigh())) {
                    throw new MathException("The upper bound for Parameter '" + parameterMappingSpecs[i].getModelParameter().getName() + "' is infinity. Upper bounds must not be infinity.");
                }
            }
            double low = parameterMappingSpecs[i].isSelected() && parameterMappingSpecs[i].getLow() == 0 ? 1e-8 : parameterMappingSpecs[i].getLow();
            double high = parameterMappingSpecs[i].getHigh();
            double scale = Math.abs(parameterMappingSpecs[i].getCurrent()) < 1.0E-10 ? 1.0 : Math.abs(parameterMappingSpecs[i].getCurrent());
            double current = parameterMappingSpecs[i].getCurrent();
            low = Math.min(low, current);
            high = Math.max(high, current);
            Parameter optParameter = new Parameter(mathSymbol, low, high, scale, current);
            ParameterMapping parameterMapping = new ParameterMapping(modelParameter, optParameter, mathVariable);
            // 
            if (mathVariable instanceof Constant) {
                Constant origConstant = (Constant) mathVariable;
                for (int j = 0; j < allVars.length; j++) {
                    if (allVars[j].equals(origConstant)) {
                        if (parameterMappingSpecs[i].isSelected()) {
                            allVars[j] = new ParameterVariable(origConstant.getName());
                        } else {
                            allVars[j] = new Constant(origConstant.getName(), new Expression(optParameter.getInitialGuess()));
                        }
                        break;
                    }
                }
            }
            // 
            if (parameterMappingSpecs[i].isSelected()) {
                parameterMappingList.add(parameterMapping);
            }
        }
    }
    parameterMappings = (ParameterMapping[]) BeanUtils.getArray(parameterMappingList, ParameterMapping.class);
    try {
        origMathDesc.setAllVariables(allVars);
    } catch (ExpressionBindingException e) {
        e.printStackTrace(System.out);
        throw new MathException(e.getMessage());
    }
    // 
    for (int i = 0; i < parameterMappings.length; i++) {
        optSpec.addParameter(parameterMappings[i].getOptParameter());
    }
    Vector<Issue> issueList = new Vector<Issue>();
    IssueContext issueContext = new IssueContext();
    optSpec.gatherIssues(issueContext, issueList);
    for (int i = 0; i < issueList.size(); i++) {
        Issue issue = issueList.elementAt(i);
        if (issue.getSeverity() == Issue.SEVERITY_ERROR) {
            throw new RuntimeException(issue.getMessage());
        }
    }
    // 
    // 
    // 
    optimizationSpec = optSpec;
    return mathSymbolMapping;
}