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

Example 16 with Function

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

the class MathTestingUtilities method getOutwardNormalFromInsideOutsideFunction.

/**
 * Insert the method's description here.
 * Creation date: (1/23/2003 10:30:23 PM)
 * @return cbit.vcell.parser.Expression
 * @param analyticSubDomainExp cbit.vcell.parser.Expression
 */
public static Function[] getOutwardNormalFromInsideOutsideFunction(Expression insideOutsideFunction, String baseName) throws ExpressionException, MappingException {
    java.util.Vector<Function> varList = new java.util.Vector<Function>();
    Expression F = new Expression(insideOutsideFunction);
    F.bindExpression(null);
    F = F.flatten();
    if (insideOutsideFunction.isRelational() || insideOutsideFunction.isLogical()) {
        throw new RuntimeException("expecting smooth function for analytic function");
    }
    String F_name = baseName + "_F";
    String F_dx_name = baseName + "_F_dx";
    Expression F_dx = F.differentiate("x").flatten();
    String F_dy_name = baseName + "_F_dy";
    Expression F_dy = F.differentiate("y").flatten();
    String F_dz_name = baseName + "_F_dz";
    Expression F_dz = F.differentiate("z").flatten();
    String normalLengthName = baseName + "_F_d_length";
    Expression normalLength = new Expression("sqrt(pow(" + F_dx_name + ",2)+pow(" + F_dy_name + ",2)+pow(" + F_dz_name + ",2))");
    String distanceToSurfaceName = baseName + "_distance";
    Expression distanceToSurface = new Expression("abs(" + F_name + ")/" + normalLengthName);
    String normalXName = baseName + "_Nx";
    Expression normalX = new Expression(F_dx_name + "/" + normalLengthName);
    String normalYName = baseName + "_Ny";
    Expression normalY = new Expression(F_dy_name + "/" + normalLengthName);
    String normalZName = baseName + "_Nz";
    Expression normalZ = new Expression(F_dz_name + "/" + normalLengthName);
    Domain domain = null;
    varList.add(new Function(F_name, F, domain));
    varList.add(new Function(F_dx_name, F_dx, domain));
    varList.add(new Function(F_dy_name, F_dy, domain));
    varList.add(new Function(F_dz_name, F_dz, domain));
    varList.add(new Function(normalLengthName, normalLength, domain));
    varList.add(new Function(normalXName, normalX, domain));
    varList.add(new Function(normalYName, normalY, domain));
    varList.add(new Function(normalZName, normalZ, domain));
    varList.add(new Function(distanceToSurfaceName, distanceToSurface, domain));
    return (Function[]) BeanUtils.getArray(varList, Function.class);
}

Example 17 with Function

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

the class ITextWriter method writeMathDescAsText.

// container can be a chapter or a section of a chapter.
// MathDescription.description ignored.
protected void writeMathDescAsText(Section container, MathDescription mathDesc) throws DocumentException {
    if (mathDesc == null) {
        return;
    }
    Section mathDescSection = container.addSection("Math Description: " + mathDesc.getName(), container.depth() + 1);
    Section mathDescSubSection = null;
    Table expTable = null;
    int[] widths = { 2, 8 };
    // add Constants
    Enumeration<Constant> constantsList = mathDesc.getConstants();
    while (constantsList.hasMoreElements()) {
        Constant constant = constantsList.nextElement();
        Expression exp = constant.getExpression();
        if (expTable == null) {
            expTable = getTable(2, 100, 1, 2, 2);
            expTable.addCell(createHeaderCell("Constant Name", getBold(), 1));
            expTable.addCell(createHeaderCell("Expression", getBold(), 1));
            expTable.setWidths(widths);
            expTable.endHeaders();
        }
        // widths[0] = Math.max(constant.getName().length(), widths[0]);
        // widths[1] = Math.max(exp.infix().length(), widths[1]);
        expTable.addCell(createCell(constant.getName(), getFont()));
        expTable.addCell(createCell(exp.infix(), getFont()));
    }
    // expTable.setWidths(widths);    breaks the contents of the cell, also, widths[1] = widths[1]/widths[0], widths[0] = 1
    if (expTable != null) {
        mathDescSubSection = mathDescSection.addSection("Constants", mathDescSection.depth() + 1);
        mathDescSubSection.add(expTable);
        expTable = null;
    }
    mathDescSubSection = null;
    // add functions
    Enumeration<Function> functionsList = mathDesc.getFunctions();
    while (functionsList.hasMoreElements()) {
        Function function = functionsList.nextElement();
        Expression exp = function.getExpression();
        if (expTable == null) {
            expTable = getTable(2, 100, 1, 2, 2);
            expTable.addCell(createHeaderCell("Function Name", getBold(), 1));
            expTable.addCell(createHeaderCell("Expression", getBold(), 1));
            expTable.endHeaders();
            expTable.setWidths(widths);
        }
        expTable.addCell(createCell(function.getName(), getFont()));
        expTable.addCell(createCell(exp.infix(), getFont()));
    }
    if (expTable != null) {
        mathDescSubSection = mathDescSection.addSection("Functions", mathDescSection.depth() + 1);
        mathDescSubSection.add(expTable);
    }
    writeSubDomainsEquationsAsText(mathDescSection, mathDesc);
}

Example 18 with Function

use of cbit.vcell.math.Function 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 19 with Function

use of cbit.vcell.math.Function 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 20 with Function

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

the class DefaultODESolver method createODESolverResultSet.

/**
 */
private ODESolverResultSet createODESolverResultSet() throws ExpressionException {
    SimulationSymbolTable simSymbolTable = simTask.getSimulationJob().getSimulationSymbolTable();
    // 
    // create symbol table for binding expression
    // 
    String[] symbols = new String[fieldIdentifiers.size()];
    for (int i = 0; i < symbols.length; i++) {
        symbols[i] = ((Variable) fieldIdentifiers.elementAt(i)).getName();
    }
    // Initialize the ResultSet...
    ODESolverResultSet odeSolverResultSet = new ODESolverResultSet();
    odeSolverResultSet.addDataColumn(new ODESolverResultSetColumnDescription(ReservedVariable.TIME.getName()));
    for (int i = 0; i < getStateVariableCount(); i++) {
        StateVariable stateVariable = getStateVariable(i);
        if (stateVariable instanceof SensStateVariable) {
            SensStateVariable sensStateVariable = (SensStateVariable) stateVariable;
            odeSolverResultSet.addDataColumn(new ODESolverResultSetColumnDescription(sensStateVariable.getVariable().getName(), sensStateVariable.getParameter().getName(), sensStateVariable.getVariable().getName()));
        } else {
            odeSolverResultSet.addDataColumn(new ODESolverResultSetColumnDescription(stateVariable.getVariable().getName()));
        }
    }
    Variable[] variables = simSymbolTable.getVariables();
    for (int i = 0; i < variables.length; i++) {
        if (variables[i] instanceof Function && SimulationSymbolTable.isFunctionSaved((Function) variables[i])) {
            Function function = (Function) variables[i];
            Expression exp1 = new Expression(function.getExpression());
            try {
                exp1 = simSymbolTable.substituteFunctions(exp1);
            } catch (MathException e) {
                e.printStackTrace(System.out);
                throw new RuntimeException("Substitute function failed on function " + function.getName() + " " + e.getMessage());
            }
            odeSolverResultSet.addFunctionColumn(new FunctionColumnDescription(exp1.flatten(), function.getName(), null, function.getName(), false));
        }
    }
    // 
    if (getSensitivityParameter() != null) {
        if (odeSolverResultSet.findColumn(getSensitivityParameter().getName()) == -1) {
            FunctionColumnDescription fcd = new FunctionColumnDescription(new Expression(getSensitivityParameter().getConstantValue()), getSensitivityParameter().getName(), null, getSensitivityParameter().getName(), false);
            odeSolverResultSet.addFunctionColumn(fcd);
        }
        StateVariable[] stateVars = (StateVariable[]) org.vcell.util.BeanUtils.getArray(fieldStateVariables, StateVariable.class);
        for (int i = 0; i < variables.length; i++) {
            if (variables[i] instanceof Function && SimulationSymbolTable.isFunctionSaved((Function) variables[i])) {
                Function depSensFunction = (Function) variables[i];
                Expression depSensFnExpr = new Expression(depSensFunction.getExpression());
                try {
                    depSensFnExpr = simSymbolTable.substituteFunctions(depSensFnExpr);
                } catch (MathException e) {
                    e.printStackTrace(System.out);
                    throw new RuntimeException("Substitute function failed on function " + depSensFunction.getName() + " " + e.getMessage());
                }
                depSensFnExpr = getFunctionSensitivity(depSensFnExpr, getSensitivityParameter(), stateVars);
                // depSensFnExpr = depSensFnExpr.flatten(); 	// already bound and flattened in getFunctionSensitivity, no need here ...
                String depSensFnName = new String("sens_" + depSensFunction.getName() + "_wrt_" + getSensitivityParameter().getName());
                if (depSensFunction != null) {
                    FunctionColumnDescription cd = new FunctionColumnDescription(depSensFnExpr.flatten(), depSensFnName, getSensitivityParameter().getName(), depSensFnName, false);
                    odeSolverResultSet.addFunctionColumn(cd);
                }
            }
        }
    }
    return (odeSolverResultSet);
}