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

Example 21 with Constant

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

the class ITextWriter method writeSimulation.

// container can be a chapter or a section of a chapter.
protected void writeSimulation(Section container, Simulation sim) throws DocumentException {
    if (sim == null) {
        return;
    }
    Section simSection = container.addSection(sim.getName(), container.numberDepth() + 1);
    writeMetadata(simSection, sim.getName(), sim.getDescription(), null, "Simulation ");
    // add overriden params
    Table overParamTable = null;
    MathOverrides mo = sim.getMathOverrides();
    if (mo != null) {
        String[] constants = mo.getOverridenConstantNames();
        for (int i = 0; i < constants.length; i++) {
            String actualStr = "", defStr = "";
            Expression tempExp = mo.getDefaultExpression(constants[i]);
            if (tempExp != null) {
                defStr = tempExp.infix();
            }
            if (mo.isScan(constants[i])) {
                actualStr = mo.getConstantArraySpec(constants[i]).toString();
            } else {
                tempExp = mo.getActualExpression(constants[i], 0);
                if (tempExp != null) {
                    actualStr = tempExp.infix();
                }
            }
            if (overParamTable == null) {
                overParamTable = getTable(3, 75, 1, 3, 3);
                overParamTable.setAlignment(Table.ALIGN_LEFT);
                overParamTable.addCell(createCell("Overriden Parameters", getBold(DEF_HEADER_FONT_SIZE), 3, 1, Element.ALIGN_CENTER, true));
                overParamTable.addCell(createHeaderCell("Name", getBold(), 1));
                overParamTable.addCell(createHeaderCell("Actual Value", getBold(), 1));
                overParamTable.addCell(createHeaderCell("Default Value", getBold(), 1));
            }
            overParamTable.addCell(createCell(constants[i], getFont()));
            overParamTable.addCell(createCell(actualStr, getFont()));
            overParamTable.addCell(createCell(defStr, getFont()));
        }
    }
    if (overParamTable != null) {
        simSection.add(overParamTable);
    }
    // add spatial details
    // sim.isSpatial();
    Table meshTable = null;
    MeshSpecification mesh = sim.getMeshSpecification();
    if (mesh != null) {
        Geometry geom = mesh.getGeometry();
        Extent extent = geom.getExtent();
        String extentStr = "(" + extent.getX() + ", " + extent.getY() + ", " + extent.getZ() + ")";
        ISize meshSize = mesh.getSamplingSize();
        String meshSizeStr = "(" + meshSize.getX() + ", " + meshSize.getY() + ", " + meshSize.getZ() + ")";
        meshTable = getTable(2, 75, 1, 3, 3);
        meshTable.setAlignment(Table.ALIGN_LEFT);
        meshTable.addCell(createCell("Geometry Setting", getBold(DEF_HEADER_FONT_SIZE), 2, 1, Element.ALIGN_CENTER, true));
        meshTable.addCell(createCell("Geometry Size (um)", getFont()));
        meshTable.addCell(createCell(extentStr, getFont()));
        meshTable.addCell(createCell("Mesh Size (elements)", getFont()));
        meshTable.addCell(createCell(meshSizeStr, getFont()));
    }
    if (meshTable != null) {
        simSection.add(meshTable);
    }
    // write advanced sim settings
    Table simAdvTable = null;
    SolverTaskDescription solverDesc = sim.getSolverTaskDescription();
    if (solverDesc != null) {
        String solverName = solverDesc.getSolverDescription().getDisplayLabel();
        simAdvTable = getTable(2, 75, 1, 3, 3);
        simAdvTable.setAlignment(Table.ALIGN_LEFT);
        simAdvTable.addCell(createCell("Advanced Settings", getBold(DEF_HEADER_FONT_SIZE), 2, 1, Element.ALIGN_CENTER, true));
        simAdvTable.addCell(createCell("Solver Name", getFont()));
        simAdvTable.addCell(createCell(solverName, getFont()));
        simAdvTable.addCell(createCell("Time Bounds - Starting", getFont()));
        simAdvTable.addCell(createCell("" + solverDesc.getTimeBounds().getStartingTime(), getFont()));
        simAdvTable.addCell(createCell("Time Bounds - Ending", getFont()));
        simAdvTable.addCell(createCell("" + solverDesc.getTimeBounds().getEndingTime(), getFont()));
        simAdvTable.addCell(createCell("Time Step - Min", getFont()));
        simAdvTable.addCell(createCell("" + solverDesc.getTimeStep().getMinimumTimeStep(), getFont()));
        simAdvTable.addCell(createCell("Time Step - Default", getFont()));
        simAdvTable.addCell(createCell("" + solverDesc.getTimeStep().getDefaultTimeStep(), getFont()));
        simAdvTable.addCell(createCell("Time Step - Max", getFont()));
        simAdvTable.addCell(createCell("" + solverDesc.getTimeStep().getMaximumTimeStep(), getFont()));
        ErrorTolerance et = solverDesc.getErrorTolerance();
        if (et != null) {
            simAdvTable.addCell(createCell("Error Tolerance - Absolute", getFont()));
            simAdvTable.addCell(createCell("" + et.getAbsoluteErrorTolerance(), getFont()));
            simAdvTable.addCell(createCell("Error Tolerance - Relative", getFont()));
            simAdvTable.addCell(createCell("" + et.getRelativeErrorTolerance(), getFont()));
        }
        OutputTimeSpec ots = solverDesc.getOutputTimeSpec();
        if (ots.isDefault()) {
            simAdvTable.addCell(createCell("Keep Every", getFont()));
            simAdvTable.addCell(createCell("" + ((DefaultOutputTimeSpec) ots).getKeepEvery(), getFont()));
            simAdvTable.addCell(createCell("Keep At Most", getFont()));
            simAdvTable.addCell(createCell("" + ((DefaultOutputTimeSpec) ots).getKeepAtMost(), getFont()));
        } else if (ots.isUniform()) {
            simAdvTable.addCell(createCell("Output Time Step", getFont()));
            simAdvTable.addCell(createCell("" + ((UniformOutputTimeSpec) ots).getOutputTimeStep(), getFont()));
        } else if (ots.isExplicit()) {
            simAdvTable.addCell(createCell("Output Time Points", getFont()));
            simAdvTable.addCell(createCell("" + ((ExplicitOutputTimeSpec) ots).toCommaSeperatedOneLineOfString(), getFont()));
        }
        simAdvTable.addCell(createCell("Use Symbolic Jacobian (T/F)", getFont()));
        simAdvTable.addCell(createCell((solverDesc.getUseSymbolicJacobian() ? " T " : " F "), getFont()));
        Constant sp = solverDesc.getSensitivityParameter();
        if (sp != null) {
            simAdvTable.addCell(createCell("Sensitivity Analysis Param", getFont()));
            simAdvTable.addCell(createCell(sp.getName(), getFont()));
        }
    }
    if (simAdvTable != null) {
        simSection.add(simAdvTable);
    }
}

Example 22 with Constant

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

the class ITextWriter method writeMathDescAsImages.

// container can be a chapter or a section of a chapter.
// MathDescription.description ignored.
// currently not used.
protected void writeMathDescAsImages(Section container, MathDescription mathDesc) throws DocumentException {
    if (mathDesc == null) {
        return;
    }
    Section mathDescSection = container.addSection("Math Description: " + mathDesc.getName(), container.depth() + 1);
    Section mathDescSubSection = null;
    Expression[] expArray = null;
    BufferedImage dummy = new BufferedImage(500, 50, BufferedImage.TYPE_3BYTE_BGR);
    int scale = 1;
    int viewableWidth = (int) (document.getPageSize().width() - document.leftMargin() - document.rightMargin());
    // add Constants
    Enumeration<Constant> constantsList = mathDesc.getConstants();
    while (constantsList.hasMoreElements()) {
        Constant constant = constantsList.nextElement();
        Expression exp = constant.getExpression();
        try {
            expArray = new Expression[] { Expression.assign(new Expression(constant.getName()), exp.flatten()) };
        } catch (ExpressionException ee) {
            System.err.println("Unable to process constant " + constant.getName() + " for publishing");
            ee.printStackTrace();
            continue;
        }
        try {
            Dimension dim = ExpressionCanvas.getExpressionImageSize(expArray, (Graphics2D) dummy.getGraphics());
            BufferedImage bufferedImage = new BufferedImage((int) dim.getWidth() * scale, (int) dim.getHeight() * scale, BufferedImage.TYPE_3BYTE_BGR);
            ExpressionCanvas.getExpressionAsImage(expArray, bufferedImage, scale);
            com.lowagie.text.Image expImage = com.lowagie.text.Image.getInstance(bufferedImage, null);
            expImage.setAlignment(com.lowagie.text.Image.ALIGN_LEFT);
            if (mathDescSubSection == null) {
                mathDescSubSection = mathDescSection.addSection("Constants", mathDescSection.depth() + 1);
            }
            if (viewableWidth < Math.floor(expImage.scaledWidth())) {
                expImage.scaleToFit(viewableWidth, expImage.plainHeight());
                System.out.println("Constant After scaling: " + expImage.scaledWidth());
            }
            mathDescSubSection.add(expImage);
        } catch (Exception e) {
            System.err.println("Unable to add structure mapping image to report.");
            e.printStackTrace();
        }
    }
    mathDescSubSection = null;
    // add functions
    Enumeration<Function> functionsList = mathDesc.getFunctions();
    while (functionsList.hasMoreElements()) {
        Function function = functionsList.nextElement();
        Expression exp = function.getExpression();
        try {
            expArray = new Expression[] { Expression.assign(new Expression(function.getName()), exp.flatten()) };
        } catch (ExpressionException ee) {
            System.err.println("Unable to process function " + function.getName() + " for publishing");
            ee.printStackTrace();
            continue;
        }
        try {
            Dimension dim = ExpressionCanvas.getExpressionImageSize(expArray, (Graphics2D) dummy.getGraphics());
            BufferedImage bufferedImage = new BufferedImage((int) dim.getWidth() * scale, (int) dim.getHeight() * scale, BufferedImage.TYPE_3BYTE_BGR);
            ExpressionCanvas.getExpressionAsImage(expArray, bufferedImage, scale);
            com.lowagie.text.Image expImage = com.lowagie.text.Image.getInstance(bufferedImage, null);
            expImage.setAlignment(com.lowagie.text.Image.ALIGN_LEFT);
            if (mathDescSubSection == null) {
                mathDescSubSection = mathDescSection.addSection("Functions", mathDescSection.depth() + 1);
            }
            if (viewableWidth < Math.floor(expImage.scaledWidth())) {
                expImage.scaleToFit(viewableWidth, expImage.height());
                System.out.println("Function After scaling: " + expImage.scaledWidth());
            }
            mathDescSubSection.add(expImage);
        } catch (Exception e) {
            System.err.println("Unable to add structure mapping image to report.");
            e.printStackTrace();
        }
    }
    writeSubDomainsEquationsAsImages(mathDescSection, mathDesc);
}

Example 23 with Constant

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

the class SimulationSymbolTable method createAnnotatedFunctionsList.

public Vector<AnnotatedFunction> createAnnotatedFunctionsList(MathDescription mathDescription) throws InconsistentDomainException {
    // Get the list of (volVariables) in the simulation. Needed to determine 'type' of  functions
    boolean bSpatial = getSimulation().isSpatial();
    String[] variableNames = null;
    VariableType[] variableTypes = null;
    if (bSpatial) {
        Variable[] allVariables = getVariables();
        Vector<Variable> varVector = new Vector<Variable>();
        for (int i = 0; i < allVariables.length; i++) {
            if ((allVariables[i] instanceof VolVariable) || (allVariables[i] instanceof VolumeRegionVariable) || (allVariables[i] instanceof MemVariable) || (allVariables[i] instanceof MembraneRegionVariable) || (allVariables[i] instanceof FilamentVariable) || (allVariables[i] instanceof FilamentRegionVariable) || (allVariables[i] instanceof PointVariable) || (allVariables[i] instanceof ParticleVariable) || (allVariables[i] instanceof InsideVariable) || (allVariables[i] instanceof OutsideVariable)) {
                varVector.addElement(allVariables[i]);
            } else if (allVariables[i] instanceof Constant || (allVariables[i] instanceof Function)) {
            } else {
                System.err.println("SimulationSymbolTable.createAnnotatedFunctionsList() found unexpected variable type " + allVariables[i].getClass().getSimpleName() + " in spatial simulation");
            }
        }
        variableNames = new String[varVector.size()];
        for (int i = 0; i < variableNames.length; i++) {
            variableNames[i] = varVector.get(i).getName();
        }
        // Lookup table for variableType for each variable in 'variables' array.
        variableTypes = new VariableType[variableNames.length];
        for (int i = 0; i < variableNames.length; i++) {
            variableTypes[i] = VariableType.getVariableType(varVector.get(i));
        }
    }
    // 
    // Bind and substitute functions to simulation before storing them in the '.functions' file
    // 
    Function[] functions = getFunctions();
    Vector<AnnotatedFunction> annotatedFunctionVector = new Vector<AnnotatedFunction>();
    for (int i = 0; i < functions.length; i++) {
        if (isFunctionSaved(functions[i])) {
            String errString = "";
            VariableType funcType = null;
            try {
                Expression substitutedExp = substituteFunctions(functions[i].getExpression());
                substitutedExp.bindExpression(this);
                functions[i].setExpression(substitutedExp.flatten());
            } catch (MathException e) {
                e.printStackTrace(System.out);
                errString = errString + ", " + e.getMessage();
            // throw new RuntimeException(e.getMessage());
            } catch (ExpressionException e) {
                e.printStackTrace(System.out);
                errString = errString + ", " + e.getMessage();
            // throw new RuntimeException(e.getMessage());
            }
            // 
            // get function's data type from the types of it's identifiers
            // 
            funcType = bSpatial ? getFunctionVariableType(functions[i], mathDescription, variableNames, variableTypes, bSpatial) : VariableType.NONSPATIAL;
            AnnotatedFunction annotatedFunc = new AnnotatedFunction(functions[i].getName(), functions[i].getExpression(), functions[i].getDomain(), errString, funcType, FunctionCategory.PREDEFINED);
            annotatedFunctionVector.addElement(annotatedFunc);
        }
    }
    return annotatedFunctionVector;
}

Example 24 with Constant

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

the class SolverTaskDescription method setSensitivityParameter.

/**
 * Sets the sensitivityParameter property (cbit.vcell.math.Constant) value.
 * @param sensitivityParameter The new value for the property.
 * @see #getSensitivityParameter
 */
public void setSensitivityParameter(Constant sensitivityParameter) throws java.beans.PropertyVetoException {
    if (!Matchable.areEqual(fieldSensitivityParameter, sensitivityParameter)) {
        Constant oldValue = fieldSensitivityParameter;
        fireVetoableChange("sensitivityParameter", oldValue, sensitivityParameter);
        fieldSensitivityParameter = sensitivityParameter;
        firePropertyChange("sensitivityParameter", oldValue, sensitivityParameter);
    }
}

Example 25 with Constant

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

the class DefaultODESolver method initialize.

/**
 * This method was created by a SmartGuide.
 * @exception SolverException The exception description.
 */
protected void initialize() throws SolverException {
    SimulationSymbolTable simSymbolTable = simTask.getSimulationJob().getSimulationSymbolTable();
    Simulation sim = simSymbolTable.getSimulation();
    try {
        // create a fast system if necessary
        fieldFastAlgebraicSystem = null;
        if (getSubDomain().getFastSystem() != null) {
            fieldFastAlgebraicSystem = new FastAlgebraicSystem(new FastSystemAnalyzer(getSubDomain().getFastSystem(), simSymbolTable));
        }
        // refreshIdentifiers();
        fieldIdentifiers = createIdentifiers();
        fieldSensVariables = createSensitivityVariables();
        // refreshStateVariables();
        fieldStateVariables = createStateVariables();
        // 
        // allocate ValueVectors object
        fieldValueVectors = new ValueVectors(getValueVectorCount(), fieldIdentifiers.size());
        // initialize indexes of variables
        fieldVariableIndexes = new int[getStateVariableCount()];
        for (int i = 0; i < getStateVariableCount(); i++) {
            fieldVariableIndexes[i] = getStateVariable(i).getVariable().getIndex();
        }
        // initialize constants
        double[] initialValues = getValueVector(0);
        for (int i = 0; i < fieldIdentifiers.size(); i++) {
            if (fieldIdentifiers.elementAt(i) instanceof Constant) {
                Constant constant = (Constant) fieldIdentifiers.elementAt(i);
                constant.bind(simSymbolTable);
                if (constant.isConstant()) {
                    // constant.getValue();
                    initialValues[constant.getIndex()] = constant.getExpression().evaluateConstant();
                } else {
                    throw new SolverException("cannot evaluate constant '" + constant.getName() + "' = " + constant.getExpression());
                }
            }
        }
        // initialize variables
        for (int i = 0; i < getStateVariableCount(); i++) {
            initialValues[getVariableIndex(i)] = getStateVariable(i).evaluateIC(initialValues);
        }
        fieldODESolverResultSet = createODESolverResultSet();
        // reset - in the ** default ** solvers we don't pick up from where we left off, we can override that behaviour in integrate() if ever necessary
        fieldCurrentTime = sim.getSolverTaskDescription().getTimeBounds().getStartingTime();
    } catch (ExpressionException expressionException) {
        expressionException.printStackTrace(System.out);
        throw new SolverException(expressionException.getMessage());
    } catch (MathException mathException) {
        mathException.printStackTrace(System.out);
        throw new SolverException(mathException.getMessage());
    }
}