Examples with Variable cbit.vcell.math.Variable used on opensource projects

Example 66 with Variable

use of cbit.vcell.math.Variable in project vcell by virtualcell.

the class InitialConditionsPanel method jMenuItemPaste_ActionPerformed.

/**
 * Comment
 */
private void jMenuItemPaste_ActionPerformed(final java.awt.event.ActionEvent actionEvent) {
    final Vector<String> pasteDescriptionsV = new Vector<String>();
    final Vector<Expression> newExpressionsV = new Vector<Expression>();
    final Vector<SpeciesContextSpec.SpeciesContextSpecParameter> changedParametersV = new Vector<SpeciesContextSpec.SpeciesContextSpecParameter>();
    AsynchClientTask task1 = new AsynchClientTask("validating", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            if (actionEvent.getSource() == getJMenuItemPaste() || actionEvent.getSource() == getJMenuItemPasteAll()) {
                Object pasteThis = VCellTransferable.getFromClipboard(VCellTransferable.OBJECT_FLAVOR);
                MathSymbolMapping msm = null;
                Exception mathMappingException = null;
                try {
                    MathMapping mm = null;
                    mm = getSimulationContext().createNewMathMapping();
                    msm = mm.getMathSymbolMapping();
                } catch (Exception e) {
                    mathMappingException = e;
                    e.printStackTrace(System.out);
                }
                int[] rows = null;
                if (actionEvent.getSource() == getJMenuItemPasteAll()) {
                    rows = new int[getScrollPaneTable().getRowCount()];
                    for (int i = 0; i < rows.length; i += 1) {
                        rows[i] = i;
                    }
                } else {
                    rows = getScrollPaneTable().getSelectedRows();
                }
                // 
                // Check paste
                // 
                StringBuffer errors = null;
                for (int i = 0; i < rows.length; i += 1) {
                    SpeciesContextSpec scs = tableModel.getValueAt(rows[i]);
                    try {
                        if (pasteThis instanceof VCellTransferable.ResolvedValuesSelection) {
                            VCellTransferable.ResolvedValuesSelection rvs = (VCellTransferable.ResolvedValuesSelection) pasteThis;
                            for (int j = 0; j < rvs.getPrimarySymbolTableEntries().length; j += 1) {
                                SpeciesContextSpec.SpeciesContextSpecParameter pasteDestination = null;
                                SpeciesContextSpec.SpeciesContextSpecParameter clipboardBiologicalParameter = null;
                                if (rvs.getPrimarySymbolTableEntries()[j] instanceof SpeciesContextSpec.SpeciesContextSpecParameter) {
                                    clipboardBiologicalParameter = (SpeciesContextSpec.SpeciesContextSpecParameter) rvs.getPrimarySymbolTableEntries()[j];
                                } else if (rvs.getAlternateSymbolTableEntries() != null && rvs.getAlternateSymbolTableEntries()[j] instanceof SpeciesContextSpec.SpeciesContextSpecParameter) {
                                    clipboardBiologicalParameter = (SpeciesContextSpec.SpeciesContextSpecParameter) rvs.getAlternateSymbolTableEntries()[j];
                                }
                                if (clipboardBiologicalParameter == null) {
                                    Variable pastedMathVariable = null;
                                    if (rvs.getPrimarySymbolTableEntries()[j] instanceof Variable) {
                                        pastedMathVariable = (Variable) rvs.getPrimarySymbolTableEntries()[j];
                                    } else if (rvs.getAlternateSymbolTableEntries() != null && rvs.getAlternateSymbolTableEntries()[j] instanceof Variable) {
                                        pastedMathVariable = (Variable) rvs.getAlternateSymbolTableEntries()[j];
                                    }
                                    if (pastedMathVariable != null) {
                                        if (msm == null) {
                                            throw mathMappingException;
                                        }
                                        Variable localMathVariable = msm.findVariableByName(pastedMathVariable.getName());
                                        if (localMathVariable == null) {
                                            // try if localMathVariable is a speciesContext init parameter
                                            String initSuffix = DiffEquMathMapping.MATH_FUNC_SUFFIX_SPECIES_INIT_CONC_UNIT_PREFIX + TokenMangler.fixTokenStrict(scs.getInitialConcentrationParameter().getUnitDefinition().getSymbol());
                                            localMathVariable = msm.findVariableByName(pastedMathVariable.getName() + initSuffix);
                                        }
                                        if (localMathVariable != null) {
                                            SymbolTableEntry[] localBiologicalSymbolArr = msm.getBiologicalSymbol(localMathVariable);
                                            for (int k = 0; k < localBiologicalSymbolArr.length; k += 1) {
                                                if (localBiologicalSymbolArr[k] instanceof SpeciesContext && scs.getSpeciesContext() == localBiologicalSymbolArr[k]) {
                                                    // need to change
                                                    pasteDestination = scs.getInitialConditionParameter();
                                                } else if (localBiologicalSymbolArr[k] instanceof SpeciesContextSpec.SpeciesContextSpecParameter) {
                                                    for (int l = 0; l < scs.getParameters().length; l += 1) {
                                                        if (scs.getParameters()[l] == localBiologicalSymbolArr[k]) {
                                                            pasteDestination = (SpeciesContextSpec.SpeciesContextSpecParameter) localBiologicalSymbolArr[k];
                                                            break;
                                                        }
                                                    }
                                                }
                                                if (pasteDestination != null) {
                                                    break;
                                                }
                                            }
                                        }
                                    }
                                } else {
                                    for (int k = 0; k < scs.getParameters().length; k += 1) {
                                        SpeciesContextSpec.SpeciesContextSpecParameter scsp = (SpeciesContextSpec.SpeciesContextSpecParameter) scs.getParameters()[k];
                                        if (scsp.getRole() == clipboardBiologicalParameter.getRole() && scs.getSpeciesContext().compareEqual(((SpeciesContextSpec) clipboardBiologicalParameter.getNameScope().getScopedSymbolTable()).getSpeciesContext())) {
                                            pasteDestination = (SpeciesContextSpec.SpeciesContextSpecParameter) scsp;
                                        }
                                    }
                                }
                                if (pasteDestination != null) {
                                    changedParametersV.add(pasteDestination);
                                    newExpressionsV.add(rvs.getExpressionValues()[j]);
                                    pasteDescriptionsV.add(VCellCopyPasteHelper.formatPasteList(scs.getSpeciesContext().getName(), pasteDestination.getName(), pasteDestination.getExpression().infix(), rvs.getExpressionValues()[j].infix()));
                                }
                            }
                        }
                    } catch (Throwable e) {
                        if (errors == null) {
                            errors = new StringBuffer();
                        }
                        errors.append(scs.getSpeciesContext().getName() + " (" + e.getClass().getName() + ") " + e.getMessage() + "\n\n");
                    }
                }
                if (errors != null) {
                    throw new Exception(errors.toString());
                }
            }
        }
    };
    AsynchClientTask task2 = new AsynchClientTask("pasting", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            // Do paste
            if (pasteDescriptionsV.size() > 0) {
                String[] pasteDescriptionArr = new String[pasteDescriptionsV.size()];
                pasteDescriptionsV.copyInto(pasteDescriptionArr);
                SpeciesContextSpec.SpeciesContextSpecParameter[] changedParametersArr = new SpeciesContextSpec.SpeciesContextSpecParameter[changedParametersV.size()];
                changedParametersV.copyInto(changedParametersArr);
                Expression[] newExpressionsArr = new Expression[newExpressionsV.size()];
                newExpressionsV.copyInto(newExpressionsArr);
                VCellCopyPasteHelper.chooseApplyPaste(InitialConditionsPanel.this, pasteDescriptionArr, changedParametersArr, newExpressionsArr);
            } else {
                PopupGenerator.showInfoDialog(InitialConditionsPanel.this, "No paste items match the destination (no changes made).");
            }
        }
    };
    ClientTaskDispatcher.dispatch(this, new Hashtable<String, Object>(), new AsynchClientTask[] { task1, task2 });
}

Example 67 with Variable

use of cbit.vcell.math.Variable 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 68 with Variable

use of cbit.vcell.math.Variable in project vcell by virtualcell.

the class FastSystemAnalyzer method refreshSubstitutedRateExps.

/**
 */
private void refreshSubstitutedRateExps() throws MathException, ExpressionException {
    // 
    // refresh PseudoConstants (temp constants involved with fastInvariants)
    // 
    pseudoConstantList.removeAllElements();
    Enumeration<FastInvariant> enum_fi = fastSystem.getFastInvariants();
    while (enum_fi.hasMoreElements()) {
        FastInvariant fi = enum_fi.nextElement();
        fi.getFunction().bindExpression(this);
        PseudoConstant pc = new PseudoConstant(getAvailablePseudoConstantName(), fi.getFunction(), MathMapping_4_8.nullDomain);
        pseudoConstantList.addElement(pc);
    // System.out.println("FastSystem.refreshSubstitutedRateExps() __C"+i+" = "+fi.getFunction());
    }
    // 
    // build expressions for dependent variables in terms of independent vars
    // and pseudoConstants
    // 
    dependencyExpList.removeAllElements();
    for (int row = 0; row < dependentVarList.size(); row++) {
        Expression exp = new Expression("0.0;");
        // 
        for (int col = 0; col < independentVarList.size(); col++) {
            Variable indepVar = (Variable) independentVarList.elementAt(col);
            RationalExp coefExp = dependencyMatrix.get(row, col).simplify();
            if (!coefExp.isZero()) {
                exp = Expression.add(exp, new Expression(coefExp.infixString() + "*" + indepVar.getName()));
            }
        }
        // 
        for (int col = independentVarList.size(); col < dependencyMatrix.getNumCols(); col++) {
            PseudoConstant pc = (PseudoConstant) pseudoConstantList.elementAt(col - independentVarList.size());
            RationalExp coefExp = dependencyMatrix.get(row, col);
            if (!coefExp.isZero()) {
                exp = Expression.add(exp, new Expression(coefExp.infixString() + "*" + pc.getName()));
            }
        }
        exp.bindExpression(null);
        exp = exp.flatten();
        exp.bindExpression(this);
        // System.out.println("FastSystem.refreshSubstitutedRateExps() "+((Variable)dependentVarList.elementAt(row)).getName()+" = "+exp.toString()+";");
        dependencyExpList.addElement(exp);
    }
    // 
    // flatten functions, then substitute expressions for dependent vars into rate expressions
    // 
    fastRateExpList.removeAllElements();
    // VariableSymbolTable combinedSymbolTable = getCombinedSymbolTable();
    Enumeration<FastRate> enum_fr = fastSystem.getFastRates();
    while (enum_fr.hasMoreElements()) {
        FastRate fr = enum_fr.nextElement();
        Expression exp = new Expression(MathUtilities.substituteFunctions(new Expression(fr.getFunction()), this));
        // System.out.println("FastSystem.refreshSubstitutedRateExps() fast rate before substitution = "+exp.toString());
        for (int j = 0; j < dependentVarList.size(); j++) {
            Variable depVar = (Variable) dependentVarList.elementAt(j);
            Expression subExp = new Expression((Expression) dependencyExpList.elementAt(j));
            exp.substituteInPlace(new Expression(depVar.getName()), subExp);
        }
        exp.bindExpression(null);
        exp = exp.flatten();
        // System.out.println("FastSystem.refreshSubstitutedRateExps() fast rate after substitution  = "+exp.toString());
        exp.bindExpression(this);
        fastRateExpList.addElement(exp);
    }
}

Example 69 with Variable

use of cbit.vcell.math.Variable in project vcell by virtualcell.

the class FastSystemAnalyzer method refreshFastVarList.

/**
 * @return java.util.Vector
 */
private void refreshFastVarList() throws MathException, ExpressionException {
    fastVarList.clear();
    // 
    // get list of unique (VolVariables and MemVariables) in fastRate expressions
    // 
    Enumeration<FastRate> fastRatesEnum = fastSystem.getFastRates();
    while (fastRatesEnum.hasMoreElements()) {
        FastRate fr = fastRatesEnum.nextElement();
        Expression exp = fr.getFunction();
        Enumeration<Variable> enum1 = MathUtilities.getRequiredVariables(exp, this);
        while (enum1.hasMoreElements()) {
            Variable var = enum1.nextElement();
            if (var instanceof VolVariable || var instanceof MemVariable) {
                if (!fastVarList.contains(var)) {
                    fastVarList.addElement(var);
                // System.out.println("FastSystemImplicit.refreshFastVarList(), FAST RATE VARIABLE: "+var.getName());
                }
            }
        }
    }
    // 
    // get list of all variables used in invariant expressions that are not used in fast rates
    // 
    Enumeration<FastInvariant> fastInvariantsEnum = fastSystem.getFastInvariants();
    while (fastInvariantsEnum.hasMoreElements()) {
        FastInvariant fi = (FastInvariant) fastInvariantsEnum.nextElement();
        Expression exp = fi.getFunction();
        // System.out.println("FastSystemImplicit.refreshFastVarList(), ORIGINAL FAST INVARIANT: "+exp);
        Enumeration<Variable> enum1 = MathUtilities.getRequiredVariables(exp, this);
        while (enum1.hasMoreElements()) {
            Variable var = enum1.nextElement();
            if (var instanceof VolVariable || var instanceof MemVariable) {
                if (!fastVarList.contains(var)) {
                    fastVarList.addElement(var);
                }
            }
        }
    }
    // 
    // verify that there are N equations (rates+invariants) and N unknowns (fastVariables)
    // 
    int numBoundFunctions = fastSystem.getNumFastInvariants() + fastSystem.getNumFastRates();
    if (fastVarList.size() != numBoundFunctions) {
        throw new MathException("FastSystem.checkDimension(), there are " + fastVarList.size() + " variables and " + numBoundFunctions + " FastInvariant's & FastRates");
    }
}

Example 70 with Variable

use of cbit.vcell.math.Variable in project vcell by virtualcell.

the class MathMapping_4_8 method getResolvedVolVariable.

/**
 * Find the defined variable (VolVariable) for the resolved compartments.
 * This method is used to assure only one variable is created.
 * @return cbit.vcell.math.VolVariable
 * @param species cbit.vcell.model.Species
 */
private VolVariable getResolvedVolVariable(Species species) {
    Enumeration<SpeciesContextMapping> enum1 = getSpeciesContextMappings();
    while (enum1.hasMoreElements()) {
        SpeciesContextMapping scm = enum1.nextElement();
        if (scm.getSpeciesContext().getSpecies() == species) {
            Variable var = scm.getVariable();
            if (var instanceof VolVariable) {
                Structure structure = scm.getSpeciesContext().getStructure();
                StructureMapping sm = simContext.getGeometryContext().getStructureMapping(structure);
                if (structure instanceof Feature && getResolved(sm)) {
                    return (VolVariable) var;
                }
            }
        }
    }
    return new VolVariable(TokenMangler.fixTokenStrict(species.getCommonName()), nullDomain);
}