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

Example 31 with Constant

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

the class MathOverrides method isValid.

/**
 * Insert the method's description here.
 * Creation date: (5/4/01 11:44:22 AM)
 * @return boolean
 */
public boolean isValid(MathDescription mathDescription) {
    // 
    // returns true if MathOverrides has exactly the same list of Constants as MathDescription
    // 
    // 
    // look for Constants from MathDescription not present in Overrides
    // 
    Enumeration<Constant> enumeration = mathDescription.getConstants();
    java.util.HashSet<String> mathDescriptionHash = new java.util.HashSet<String>();
    while (enumeration.hasMoreElements()) {
        Constant constant = enumeration.nextElement();
        mathDescriptionHash.add(constant.getName());
        if (!getOverridesHash().containsKey(constant.getName())) {
            return false;
        }
    }
    // 
    // look for Constants from Overrides not present in MathDescription
    // 
    Enumeration<String> mathOverrideNamesEnum = getOverridesHash().keys();
    while (mathOverrideNamesEnum.hasMoreElements()) {
        String name = mathOverrideNamesEnum.nextElement();
        if (!mathDescriptionHash.contains(name)) {
            return false;
        }
    }
    return true;
}

Example 32 with Constant

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

the class OutputFunctionContext method getEntries.

// public abstract void validateNamingConflicts(String symbolDescription, Class<?> newSymbolClass, String newSymbolName, PropertyChangeEvent e)  throws PropertyVetoException ;
public void getEntries(Map<String, SymbolTableEntry> entryMap) {
    // add all valid entries (variables) from mathdescription
    MathDescription mathDescription = simulationOwner.getMathDescription();
    if (mathDescription != null) {
        Enumeration<Variable> varEnum = mathDescription.getVariables();
        while (varEnum.hasMoreElements()) {
            Variable var = varEnum.nextElement();
            if (!(var instanceof PseudoConstant) && !(var instanceof Constant)) {
                entryMap.put(var.getName(), var);
            }
        }
        for (DataGenerator dataGenerator : mathDescription.getPostProcessingBlock().getDataGeneratorList()) {
            entryMap.put(dataGenerator.getName(), dataGenerator);
        }
    }
    entryMap.put(ReservedVariable.TIME.getName(), ReservedVariable.TIME);
    int dimension = mathDescription.getGeometry().getDimension();
    if (dimension > 0) {
        entryMap.put(ReservedVariable.X.getName(), ReservedVariable.X);
        if (dimension > 1) {
            entryMap.put(ReservedVariable.Y.getName(), ReservedVariable.Y);
            if (dimension > 2) {
                entryMap.put(ReservedVariable.Z.getName(), ReservedVariable.Z);
            }
        }
    }
    // then add list of output functions.
    for (SymbolTableEntry ste : outputFunctionsList) {
        entryMap.put(ste.getName(), ste);
    }
}

Example 33 with Constant

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

the class MathTestingUtilities method constructOdesForSensitivity.

// 
// This method is used to solve for sensitivity of variables to a given parameter.
// The mathDescription and the sensitivity parameter are passed as arguments.
// New variables and ODEs are constructed according to the rule listed below and are added to the mathDescription.
// The method returns the modified mathDescription.
// 
public static MathDescription constructOdesForSensitivity(MathDescription mathDesc, Constant sensParam) throws ExpressionException, MathException, MappingException {
    // 
    // For each ODE :
    // 
    // dX/dt = F(X, P)
    // 
    // (where P is the sensitivity parameter)
    // 
    // we create two other ODEs :
    // 
    // dX_1/dt = F(X_1, P_1)    and
    // 
    // dX_2/dt = F(X_2, P_2)
    // 
    // where P_1 = P + epsilon, and
    // P_2 = P - epsilon.
    // 
    // We keep the initial conditions for both the new ODEs to be the same,
    // i.e., X_1_init = X_2_init.
    // 
    // Then, solving for X_1 & X_2, sensitivity of X wrt P can be computed as :
    // 
    // dX = (X_1 - X_2)
    // --	 -----------   .
    // dP	 (P_1 - P_2)
    // 
    // 
    // REMOVE PRINTS AFTER CHECKING !!!
    System.out.println(" \n\n------------  Old Math Description -----------------");
    System.out.println(mathDesc.getVCML_database());
    if (mathDesc.getGeometry().getDimension() > 0) {
        throw new RuntimeException("Suppport for Spatial systems not yet implemented.");
    }
    VariableHash varHash = new VariableHash();
    Enumeration<Variable> enumVar = mathDesc.getVariables();
    while (enumVar.hasMoreElements()) {
        varHash.addVariable(enumVar.nextElement());
    }
    // 
    // Get 2 values of senstivity parameter (P + epsilon) & (P - epsilon)
    // 
    Constant epsilon = new Constant("epsilon", new Expression(sensParam.getConstantValue() * 1e-3));
    Constant sensParam1 = new Constant(sensParam.getName() + "_1", new Expression(sensParam.getConstantValue() + epsilon.getConstantValue()));
    Constant sensParam2 = new Constant(sensParam.getName() + "_2", new Expression(sensParam.getConstantValue() - epsilon.getConstantValue()));
    // 
    // Iterate through each subdomain (only 1 in compartmental case), and each equation in the subdomain
    // 
    Enumeration<SubDomain> subDomainEnum = mathDesc.getSubDomains();
    // 
    // Create a vector of equations to store the 2 equations for each ODE variable in the subdomain.
    // Later, add it to the equations list in the subdomain.
    // 
    Vector<Equation> equnsVector = new Vector<Equation>();
    Vector<Variable> varsVector = new Vector<Variable>();
    Vector<Variable> var1s = new Vector<Variable>();
    Vector<Variable> var2s = new Vector<Variable>();
    while (subDomainEnum.hasMoreElements()) {
        SubDomain subDomain = subDomainEnum.nextElement();
        Enumeration<Equation> equationEnum = subDomain.getEquations();
        Domain domain = new Domain(subDomain);
        while (equationEnum.hasMoreElements()) {
            Equation equation = equationEnum.nextElement();
            if (equation instanceof OdeEquation) {
                OdeEquation odeEquation = (OdeEquation) equation;
                // Similar to substituteWithExactSolutions, to bind and substitute functions in the ODE
                Expression substitutedRateExp = substituteFunctions(odeEquation.getRateExpression(), mathDesc);
                String varName = odeEquation.getVariable().getName();
                VolVariable var = new VolVariable(varName, domain);
                varsVector.addElement(var);
                // 
                // Create the variable var1, and get the initExpr and rateExpr from the original ODE.
                // Substitute the new vars (var1 and param1) in the old initExpr and rateExpr and create a new ODE
                // 
                String varName1 = new String("__" + varName + "_1");
                Expression initExpr1 = odeEquation.getInitialExpression();
                Expression rateExpr1 = new Expression(substitutedRateExp);
                rateExpr1.substituteInPlace(new Expression(varName), new Expression(varName1));
                rateExpr1.substituteInPlace(new Expression(sensParam.getName()), new Expression(sensParam1.getName()));
                VolVariable var1 = new VolVariable(varName1, domain);
                var1s.addElement(var1);
                OdeEquation odeEqun1 = new OdeEquation(var1, initExpr1, rateExpr1);
                equnsVector.addElement(odeEqun1);
                // 
                // Create the variable var2, and get the initExpr and rateExpr from the original ODE.
                // Substitute the new vars (var2 and param2) in the old initExpr and rateExpr and create a new ODE
                // 
                String varName2 = new String("__" + varName + "_2");
                Expression initExpr2 = odeEquation.getInitialExpression();
                Expression rateExpr2 = new Expression(substitutedRateExp);
                rateExpr2.substituteInPlace(new Expression(varName), new Expression(varName2));
                rateExpr2.substituteInPlace(new Expression(sensParam.getName()), new Expression(sensParam2.getName()));
                VolVariable var2 = new VolVariable(varName2, domain);
                var2s.addElement(var2);
                OdeEquation odeEqun2 = new OdeEquation(var2, initExpr2, rateExpr2);
                equnsVector.addElement(odeEqun2);
                // 
                // Create a function for the sensitivity function expression (X1-X2)/(P1-P2), and save in varHash
                // 
                Expression diffVar = Expression.add(new Expression(var1.getName()), Expression.negate(new Expression(var2.getName())));
                Expression diffParam = Expression.add(new Expression(sensParam1.getName()), Expression.negate(new Expression(sensParam2.getName())));
                Expression sensitivityExpr = Expression.mult(diffVar, Expression.invert(diffParam));
                Function sens_Func = new Function("__sens" + varName + "_wrt_" + sensParam.getName(), sensitivityExpr, domain);
                varHash.addVariable(epsilon);
                varHash.addVariable(sensParam1);
                varHash.addVariable(sensParam2);
                varHash.addVariable(var1);
                varHash.addVariable(var2);
                varHash.addVariable(sens_Func);
            } else {
                // sensitivity not implemented for PDEs or other equation types.
                throw new RuntimeException("SolverTest.constructedExactMath(): equation type " + equation.getClass().getName() + " not yet implemented");
            }
        }
        // 
        // Need to substitute the new variables in the new ODEs.
        // i.e., if Rate Expr for ODE_1 for variable X_1 contains variable Y, variable Z, etc.
        // Rate Expr is already substituted with X_1, but it also needs substitute Y with Y_1, Z with Z_1, etc.
        // So get the volume variables, from the vectors for vars, var_1s and var_2s
        // Substitute the rate expressions for the newly added ODEs in equnsVector.
        // 
        Variable[] vars = (Variable[]) BeanUtils.getArray(varsVector, Variable.class);
        Variable[] var_1s = (Variable[]) BeanUtils.getArray(var1s, Variable.class);
        Variable[] var_2s = (Variable[]) BeanUtils.getArray(var2s, Variable.class);
        Vector<Equation> newEqunsVector = new Vector<Equation>();
        for (int i = 0; i < equnsVector.size(); i++) {
            Equation equn = equnsVector.elementAt(i);
            Expression initEx = equn.getInitialExpression();
            Expression rateEx = equn.getRateExpression();
            for (int j = 0; j < vars.length; j++) {
                if (equn.getVariable().getName().endsWith("_1")) {
                    rateEx.substituteInPlace(new Expression(vars[j].getName()), new Expression(var_1s[j].getName()));
                } else if (equn.getVariable().getName().endsWith("_2")) {
                    rateEx.substituteInPlace(new Expression(vars[j].getName()), new Expression(var_2s[j].getName()));
                }
            }
            OdeEquation odeEqun = new OdeEquation(equn.getVariable(), initEx, rateEx);
            newEqunsVector.addElement(odeEqun);
        }
        // 
        for (int i = 0; i < newEqunsVector.size(); i++) {
            mathDesc.getSubDomain(subDomain.getName()).addEquation((Equation) newEqunsVector.elementAt(i));
        }
        // 
        // FAST SYSTEM
        // If the subdomain has a fast system, create a new fast system by substituting the high-low variables/parameters
        // in the expressions for the fastInvariants and fastRates and adding them to the fast system.
        // 
        Vector<FastInvariant> invarsVector = new Vector<FastInvariant>();
        Vector<FastRate> ratesVector = new Vector<FastRate>();
        Enumeration<FastInvariant> fastInvarsEnum = null;
        Enumeration<FastRate> fastRatesEnum = null;
        // Get the fast invariants and fast rates in the system.
        FastSystem fastSystem = subDomain.getFastSystem();
        if (fastSystem != null) {
            fastInvarsEnum = fastSystem.getFastInvariants();
            fastRatesEnum = fastSystem.getFastRates();
            // 
            while (fastInvarsEnum.hasMoreElements()) {
                FastInvariant fastInvar = fastInvarsEnum.nextElement();
                Expression fastInvarExpr = fastInvar.getFunction();
                fastInvarExpr = MathUtilities.substituteFunctions(fastInvarExpr, mathDesc);
                Expression fastInvarExpr1 = new Expression(fastInvarExpr);
                Expression fastInvarExpr2 = new Expression(fastInvarExpr);
                for (int i = 0; i < vars.length; i++) {
                    fastInvarExpr1.substituteInPlace(new Expression(vars[i].getName()), new Expression(var_1s[i].getName()));
                    fastInvarExpr2.substituteInPlace(new Expression(vars[i].getName()), new Expression(var_2s[i].getName()));
                }
                fastInvarExpr1.substituteInPlace(new Expression(sensParam.getName()), new Expression(sensParam1.getName()));
                FastInvariant fastInvar1 = new FastInvariant(fastInvarExpr1);
                invarsVector.addElement(fastInvar1);
                fastInvarExpr2.substituteInPlace(new Expression(sensParam.getName()), new Expression(sensParam2.getName()));
                FastInvariant fastInvar2 = new FastInvariant(fastInvarExpr2);
                invarsVector.addElement(fastInvar2);
            }
            // Add the newly created fast invariants to the existing list of fast invariants in the fast system.
            for (int i = 0; i < invarsVector.size(); i++) {
                FastInvariant inVar = (FastInvariant) invarsVector.elementAt(i);
                fastSystem.addFastInvariant(inVar);
            }
            // 
            while (fastRatesEnum.hasMoreElements()) {
                FastRate fastRate = fastRatesEnum.nextElement();
                Expression fastRateExpr = fastRate.getFunction();
                fastRateExpr = MathUtilities.substituteFunctions(fastRateExpr, mathDesc);
                Expression fastRateExpr1 = new Expression(fastRateExpr);
                Expression fastRateExpr2 = new Expression(fastRateExpr);
                for (int i = 0; i < vars.length; i++) {
                    fastRateExpr1.substituteInPlace(new Expression(vars[i].getName()), new Expression(var_1s[i].getName()));
                    fastRateExpr2.substituteInPlace(new Expression(vars[i].getName()), new Expression(var_2s[i].getName()));
                }
                fastRateExpr1.substituteInPlace(new Expression(sensParam.getName()), new Expression(sensParam1.getName()));
                FastRate fastRate1 = new FastRate(fastRateExpr1);
                ratesVector.addElement(fastRate1);
                fastRateExpr2.substituteInPlace(new Expression(sensParam.getName()), new Expression(sensParam2.getName()));
                FastRate fastRate2 = new FastRate(fastRateExpr2);
                ratesVector.addElement(fastRate2);
            }
            // Add the newly created fast rates to the existing list of fast rates in the fast system.
            for (int i = 0; i < ratesVector.size(); i++) {
                FastRate rate = (FastRate) ratesVector.elementAt(i);
                fastSystem.addFastRate(rate);
            }
        }
    }
    // Reset all variables in mathDesc.
    mathDesc.setAllVariables(varHash.getAlphabeticallyOrderedVariables());
    // REMOVE PRINTS AFTER CHECKING
    System.out.println(" \n\n------------  New Math Description -----------------");
    System.out.println(mathDesc.getVCML_database());
    return mathDesc;
}

Example 34 with Constant

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

the class VCellCopyPasteHelper method chooseApplyPaste.

/**
 * Insert the method's description here.
 * Creation date: (7/10/2006 11:05:19 AM)
 */
public static void chooseApplyPaste(Component requester, String[] pasteDetails, MathOverrides mathOverrides, String[] changingMathOverridesNames, java.util.Vector<?> newMathOverridesValuesV) {
    if (pasteDetails.length != changingMathOverridesNames.length || changingMathOverridesNames.length != newMathOverridesValuesV.size()) {
        throw new IllegalArgumentException(VCellCopyPasteHelper.class.getName() + ".chooseApplyPaste(...) arguments must have unequal lengths");
    }
    // Only present things that will actually change
    boolean bAtLeatOneDifferent = false;
    boolean[] bEnableDisplay = new boolean[changingMathOverridesNames.length];
    for (int i = 0; i < changingMathOverridesNames.length; i += 1) {
        Object newValue = newMathOverridesValuesV.elementAt(i);
        if (newValue instanceof Expression) {
            bEnableDisplay[i] = !Compare.isEqualOrNull(mathOverrides.getActualExpression(changingMathOverridesNames[i], 0), ((Expression) newValue));
        } else if (newValue instanceof ConstantArraySpec) {
            bEnableDisplay[i] = !Compare.isEqualOrNull(mathOverrides.getConstantArraySpec(changingMathOverridesNames[i]), (ConstantArraySpec) newValue);
        } else {
            PopupGenerator.showErrorDialog(requester, "Unexpected MathOverride type=" + newValue.getClass().getName() + "\nPaste Failed, nothing changed.");
            return;
        }
        bAtLeatOneDifferent = bAtLeatOneDifferent || bEnableDisplay[i];
    }
    if (!bAtLeatOneDifferent) {
        PopupGenerator.showInfoDialog(requester, "All valid paste values are equal to the destination values.\nNo paste needed.");
        return;
    }
    boolean[] bChoices = showChoices(requester, pasteDetails, bEnableDisplay);
    if (bChoices != null) {
        StringBuffer statusMessages = new StringBuffer();
        boolean bFailure = false;
        for (int i = 0; i < changingMathOverridesNames.length; i += 1) {
            try {
                if (bChoices[i]) {
                    if (newMathOverridesValuesV.elementAt(i) instanceof Expression) {
                        mathOverrides.putConstant(new Constant(changingMathOverridesNames[i], (Expression) newMathOverridesValuesV.elementAt(i)));
                    } else if (newMathOverridesValuesV.elementAt(i) instanceof ConstantArraySpec) {
                        mathOverrides.putConstantArraySpec((ConstantArraySpec) newMathOverridesValuesV.elementAt(i));
                    }
                }
                statusMessages.append("(OK) " + pasteDetails + "\n");
            } catch (Exception e) {
                bFailure = true;
                statusMessages.append("(Failed) " + pasteDetails + " " + e.getMessage() + " " + e.getClass().getName() + "\n");
            }
        }
        if (bFailure) {
            PopupGenerator.showErrorDialog(requester, "Paste Results:\n" + statusMessages.toString());
        }
    }
}

Example 35 with Constant

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

the class SimResultsViewer method initialize.

/**
 * Insert the method's description here.
 * Creation date: (10/17/2005 11:37:52 PM)
 * @exception org.vcell.util.DataAccessException The exception description.
 */
private void initialize() throws DataAccessException {
    // create main viewer for jobIndex 0 and wire it up
    if (isODEData) {
        setMainViewer(createODEDataViewer());
    } else {
        setMainViewer(createPDEDataViewer());
    }
    java.beans.PropertyChangeListener pcl = new java.beans.PropertyChangeListener() {

        public void propertyChange(java.beans.PropertyChangeEvent evt) {
            if (evt.getSource() == SimResultsViewer.this && (evt.getPropertyName().equals("dataViewerManager"))) {
                try {
                    getMainViewer().setDataViewerManager(getDataViewerManager());
                } catch (java.beans.PropertyVetoException exc) {
                    exc.printStackTrace();
                }
            }
            if (evt.getSource() == SimResultsViewer.this && (evt.getPropertyName().equals("simulationModelInfo"))) {
                getMainViewer().setSimulationModelInfo(getSimulationModelInfo());
            }
        }
    };
    addPropertyChangeListener(pcl);
    // if necessarry, create parameter choices panel and wire it up
    if (getSimulation().getScanCount() > 1) {
        JPanel panel = new JPanel();
        panel.setLayout(new BorderLayout(5, 0));
        panel.setBorder(BorderFactory.createEtchedBorder());
        JLabel label = new JLabel("<html><b>Choose Parameter Values</b></html>");
        label.setHorizontalAlignment(SwingConstants.CENTER);
        label.setBorder(BorderFactory.createEmptyBorder(2, 2, 0, 2));
        panel.add(label, BorderLayout.NORTH);
        String[] scanParams = getSimulation().getMathOverrides().getScannedConstantNames();
        Arrays.sort(scanParams);
        JPanel tablePanel = new JPanel();
        tablePanel.setLayout(new BoxLayout(tablePanel, BoxLayout.X_AXIS));
        for (int i = 0; i < scanParams.length; i++) {
            Constant[] scanConstants = getSimulation().getMathOverrides().getConstantArraySpec(scanParams[i]).getConstants();
            String[][] values = new String[scanConstants.length][1];
            for (int j = 0; j < scanConstants.length; j++) {
                values[j][0] = scanConstants[j].getExpression().infix();
            }
            class ScanChoicesTableModel extends javax.swing.table.AbstractTableModel {

                String[] columnNames;

                Object[][] rowData;

                ScanChoicesTableModel(Object[][] argData, String[] argNames) {
                    columnNames = argNames;
                    rowData = argData;
                }

                public String getColumnName(int column) {
                    return columnNames[column].toString();
                }

                public int getRowCount() {
                    return rowData.length;
                }

                public int getColumnCount() {
                    return columnNames.length;
                }

                public Object getValueAt(int row, int col) {
                    return rowData[row][col];
                }

                public boolean isCellEditable(int row, int column) {
                    return false;
                }

                public void setValueAt(Object value, int row, int col) {
                    rowData[row][col] = value;
                    fireTableCellUpdated(row, col);
                }
            }
            ;
            ScanChoicesTableModel tm = new ScanChoicesTableModel(values, new String[] { scanParams[i] });
            final JTable table = new JTable(tm);
            choicesHash.put(scanParams[i], table);
            table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
            table.getSelectionModel().setSelectionInterval(0, 0);
            final ListSelectionListener[] nextListSelectionListener = new ListSelectionListener[1];
            nextListSelectionListener[0] = new javax.swing.event.ListSelectionListener() {

                public void valueChanged(javax.swing.event.ListSelectionEvent e) {
                    if (!e.getValueIsAdjusting()) {
                        DefaultListSelectionModel list = (DefaultListSelectionModel) e.getSource();
                        int selected = list.getAnchorSelectionIndex();
                        final int previous = (selected == e.getFirstIndex() ? e.getLastIndex() : e.getFirstIndex());
                        ListReset listReset = new ListReset() {

                            @Override
                            public void reset(VCDataIdentifier myVcDataIdentifier) {
                                if (myVcDataIdentifier instanceof VCSimulationDataIdentifier) {
                                    int paramScanIndex = ((VCSimulationDataIdentifier) myVcDataIdentifier).getJobIndex();
                                    table.getSelectionModel().removeListSelectionListener(nextListSelectionListener[0]);
                                    try {
                                        table.setRowSelectionInterval(paramScanIndex, paramScanIndex);
                                    } finally {
                                        table.getSelectionModel().addListSelectionListener(nextListSelectionListener[0]);
                                    }
                                } else {
                                    table.setRowSelectionInterval(previous, previous);
                                }
                            }
                        };
                        updateScanParamChoices("SimResultsViewer set paramScan index=" + getSelectedParamScanJobIndex(), listReset);
                    }
                }
            };
            table.getSelectionModel().addListSelectionListener(nextListSelectionListener[0]);
            JScrollPane scr = new JScrollPane(table);
            JPanel p = new JPanel();
            scr.setPreferredSize(new java.awt.Dimension(100, Math.min(150, table.getPreferredSize().height + table.getTableHeader().getPreferredSize().height + 5)));
            p.setLayout(new java.awt.BorderLayout());
            p.add(scr, java.awt.BorderLayout.CENTER);
            p.setBorder(BorderFactory.createEmptyBorder(4, 4, 4, 4));
            tablePanel.add(p);
        }
        panel.add(tablePanel, BorderLayout.CENTER);
        if (isODEData) {
            JPanel buttonPanel = new JPanel(new FlowLayout());
            JButton button = new JButton("Time Plot with Multiple Parameter Value Sets");
            buttonPanel.add(button);
            panel.add(buttonPanel, BorderLayout.SOUTH);
            button.addActionListener(new ActionListener() {

                public void actionPerformed(ActionEvent e) {
                    mainViewer.showTimePlotMultipleScans(dataManager);
                }
            });
        } else {
            pdeDataViewer.setSimNameSimDataID(new ExportSpecs.SimNameSimDataID(getSimulation().getName(), getSimulation().getSimulationInfo().getAuthoritativeVCSimulationIdentifier(), SimResultsViewer.getParamScanInfo(getSimulation(), getSelectedParamScanJobIndex())));
        }
        setParamChoicesPanel(panel);
    }
    // put things together
    setLayout(new java.awt.BorderLayout());
    add(getMainViewer(), java.awt.BorderLayout.CENTER);
    if (getSimulation().getScanCount() > 1) {
        add(getParamChoicesPanel(), java.awt.BorderLayout.SOUTH);
    }
}