Examples with ExpressionException cbit.vcell.parser.ExpressionException used on opensource projects

Example 61 with ExpressionException

use of cbit.vcell.parser.ExpressionException in project vcell by virtualcell.

the class FiniteVolumeFileWriter method generateRandomNumbers.

private double[] generateRandomNumbers(RandomVariable rv, int numRandomNumbers) throws ExpressionException {
    VariableDomain variableDomain = (rv instanceof VolumeRandomVariable) ? VariableDomain.VARIABLEDOMAIN_VOLUME : VariableDomain.VARIABLEDOMAIN_MEMBRANE;
    Expression seedExpr = subsituteExpression(rv.getSeed(), variableDomain);
    if (!seedExpr.isNumeric()) {
        throw new ExpressionException("Seed for RandomVariable '" + rv.getName() + " is not Constant!");
    }
    int seed = (int) rv.getSeed().evaluateConstant();
    Distribution distribution = rv.getDistribution();
    double[] randomNumbers = new double[numRandomNumbers];
    Random random = new Random(seed);
    if (distribution instanceof UniformDistribution) {
        UniformDistribution ud = (UniformDistribution) distribution;
        Expression minFlattened = subsituteExpression(ud.getMinimum(), variableDomain);
        Expression maxFlattened = subsituteExpression(ud.getMaximum(), variableDomain);
        if (!minFlattened.isNumeric()) {
            throw new ExpressionException("For RandomVariable '" + rv.getName() + "', minimum for UniformDistribution is not Constant!");
        }
        if (!maxFlattened.isNumeric()) {
            throw new ExpressionException("For RandomVariable '" + rv.getName() + "', maximum for UniformDistribution is not Constant!");
        }
        double minVal = minFlattened.evaluateConstant();
        double maxVal = maxFlattened.evaluateConstant();
        for (int i = 0; i < numRandomNumbers; i++) {
            double r = random.nextDouble();
            randomNumbers[i] = (maxVal - minVal) * r + minVal;
        }
    } else if (distribution instanceof GaussianDistribution) {
        GaussianDistribution gd = (GaussianDistribution) distribution;
        Expression meanFlattened = subsituteExpression(gd.getMean(), variableDomain);
        Expression sdFlattened = subsituteExpression(gd.getStandardDeviation(), variableDomain);
        if (!meanFlattened.isNumeric()) {
            throw new ExpressionException("For RandomVariable '" + rv.getName() + "', mean for GaussianDistribution is not Constant!");
        }
        if (!sdFlattened.isNumeric()) {
            throw new ExpressionException("For RandomVariable '" + rv.getName() + "', standard deviation for GaussianDistribution is not Constant!");
        }
        double muVal = meanFlattened.evaluateConstant();
        double sigmaVal = sdFlattened.evaluateConstant();
        for (int i = 0; i < numRandomNumbers; i++) {
            double r = random.nextGaussian();
            randomNumbers[i] = sigmaVal * r + muVal;
        }
    }
    return randomNumbers;
}

Example 62 with ExpressionException

use of cbit.vcell.parser.ExpressionException in project vcell by virtualcell.

the class FiniteVolumeFileWriter method convertAnalyticGeometryToRvachevFunction.

public static Expression[] convertAnalyticGeometryToRvachevFunction(GeometrySpec geoSpec) throws ExpressionException {
    SubVolume[] subVolumes = geoSpec.getSubVolumes();
    int numSubVolumes = subVolumes.length;
    Expression[] newExps = new Expression[numSubVolumes];
    if (numSubVolumes == 1) {
        newExps[0] = new Expression(-1.0);
    } else {
        for (int i = 0; i < numSubVolumes - 1; i++) {
            if (!(subVolumes[i] instanceof AnalyticSubVolume)) {
                throw new RuntimeException("Subdomain " + i + " is not a analytic subdomain.");
            }
            AnalyticSubVolume subvolume = (AnalyticSubVolume) subVolumes[i];
            try {
                newExps[i] = RvachevFunctionUtils.convertToRvachevFunction(subvolume.getExpression());
                if (newExps[numSubVolumes - 1] == null) {
                    newExps[numSubVolumes - 1] = Expression.negate(newExps[i]);
                } else {
                    newExps[numSubVolumes - 1] = Expression.max(newExps[numSubVolumes - 1], Expression.negate(newExps[i]));
                }
            } catch (ExpressionException ex) {
                throw new ExpressionException("Domain " + subvolume.getName() + ": " + ex.getMessage());
            }
        }
        for (int i = 1; i < numSubVolumes - 1; i++) {
            for (int j = 0; j < i; j++) {
                newExps[i] = Expression.max(newExps[i], Expression.negate(newExps[j]));
            }
        }
    }
    return newExps;
}

Example 63 with ExpressionException

use of cbit.vcell.parser.ExpressionException in project vcell by virtualcell.

the class DataSetControllerImpl method getSimDataBlock.

/**
 * This method was created by a SmartGuide.
 * @return double[]
 * @param varName java.lang.String
 * @param time double
 */
public SimDataBlock getSimDataBlock(OutputContext outputContext, VCDataIdentifier vcdID, String varName, double time) throws DataAccessException {
    VCMongoMessage.sendTrace("DataSetControllerImpl.getSimDataBlock(" + varName + ", " + time + ")  <<ENTER>>");
    try {
        // 
        // check if already cached for non-function variables
        // 
        VCData simData = getVCData(vcdID);
        VCMongoMessage.sendTrace("DataSetControllerImpl.getSimDataBlock(" + varName + ", " + time + ") got VCData");
        long dataBlockTimeStamp = simData.getDataBlockTimeStamp(PDE_DATA, time);
        VCMongoMessage.sendTrace("DataSetControllerImpl.getSimDataBlock(" + varName + ", " + time + ") got dataBlockTimeStamp");
        PDEDataInfo pdeDataInfo = new PDEDataInfo(vcdID.getOwner(), vcdID.getID(), varName, time, dataBlockTimeStamp);
        SimDataBlock simDataBlock = null;
        AnnotatedFunction function = getFunction(outputContext, vcdID, varName);
        VCMongoMessage.sendTrace("DataSetControllerImpl.getSimDataBlock(" + varName + ", " + time + ") got function");
        if (function == null) {
            simDataBlock = (cacheTable0 != null ? cacheTable0.get(pdeDataInfo) : null);
            if (simDataBlock == null) {
                simDataBlock = simData.getSimDataBlock(outputContext, varName, time);
                if (simDataBlock != null && dataCachingEnabled) {
                    // cacheTable.put(pdeDataInfo,simDataBlock);
                    if (cacheTable0 != null) {
                        try {
                            cacheTable0.put(pdeDataInfo, simDataBlock);
                        } catch (CacheException e) {
                            // if can't cache the data, it is ok
                            e.printStackTrace();
                        }
                    }
                }
            }
        } else {
            if (simData instanceof SimulationData) {
                function = ((SimulationData) simData).simplifyFunction(function);
            }
            VCMongoMessage.sendTrace("DataSetControllerImpl.getSimDataBlock(" + varName + ", " + time + ") evaluating function");
            simDataBlock = evaluateFunction(outputContext, vcdID, simData, function, time);
        }
        CartesianMesh mesh = getMesh(vcdID);
        if (mesh != null && mesh.isChomboMesh()) {
            for (int i = 0; i < simDataBlock.getData().length; i++) {
                if (simDataBlock.getData()[i] == 1.23456789e300) {
                    simDataBlock.getData()[i] = Double.NaN;
                }
            }
        }
        if (simDataBlock != null) {
            VCMongoMessage.sendTrace("DataSetControllerImpl.getSimDataBlock(" + varName + ", " + time + ")  <<EXIT-simDataBlock not null>>");
            return simDataBlock;
        } else {
            String msg = "failure reading " + varName + " at t=" + time + " for " + vcdID.getOwner().getName() + "'s " + vcdID.getID();
            if (lg.isWarnEnabled())
                lg.warn("DataSetControllerImpl.getDataBlockValues(): " + msg);
            VCMongoMessage.sendTrace("DataSetControllerImpl.getSimDataBlock(" + varName + ", " + time + ")  <<EXIT-Exception>>");
            throw new DataAccessException(msg);
        }
    } catch (MathException e) {
        lg.error(e.getMessage(), e);
        VCMongoMessage.sendTrace("DataSetControllerImpl.getSimDataBlock(" + varName + ", " + time + ")  <<EXIT-Exception>>");
        throw new DataAccessException(e.getMessage());
    } catch (IOException e) {
        lg.error(e.getMessage(), e);
        VCMongoMessage.sendTrace("DataSetControllerImpl.getSimDataBlock(" + varName + ", " + time + ")  <<EXIT-Exception>>");
        throw new DataAccessException(e.getMessage());
    } catch (ExpressionException e) {
        lg.error(e.getMessage(), e);
        VCMongoMessage.sendTrace("DataSetControllerImpl.getSimDataBlock(" + varName + ", " + time + ")  <<EXIT-Exception>>");
        throw new DataAccessException(e.getMessage());
    }
}

Example 64 with ExpressionException

use of cbit.vcell.parser.ExpressionException in project vcell by virtualcell.

the class ITextWriter method writeSubDomainsEquationsAsImages.

// currently not used.
protected void writeSubDomainsEquationsAsImages(Section mathDescSection, MathDescription mathDesc) {
    Enumeration<SubDomain> subDomains = mathDesc.getSubDomains();
    Expression[] expArray;
    Section volDomains = mathDescSection.addSection("Volume Domains", mathDescSection.depth() + 1);
    Section memDomains = mathDescSection.addSection("Membrane Domains", mathDescSection.depth() + 1);
    // arbitrary
    int scale = 1, height = 200;
    int viewableWidth = (int) (document.getPageSize().width() - document.leftMargin() - document.rightMargin());
    BufferedImage dummy = new BufferedImage(viewableWidth, height, BufferedImage.TYPE_3BYTE_BGR);
    while (subDomains.hasMoreElements()) {
        SubDomain subDomain = subDomains.nextElement();
        Enumeration<Equation> equationsList = subDomain.getEquations();
        ArrayList<Expression> expList = new ArrayList<Expression>();
        while (equationsList.hasMoreElements()) {
            Equation equ = equationsList.nextElement();
            try {
                Enumeration<Expression> enum_equ = equ.getTotalExpressions();
                while (enum_equ.hasMoreElements()) {
                    Expression exp = new Expression(enum_equ.nextElement());
                    expList.add(exp.flatten());
                }
            } catch (ExpressionException ee) {
                System.err.println("Unable to process the equation for subdomain: " + subDomain.getName());
                ee.printStackTrace();
                continue;
            }
        }
        expArray = (Expression[]) expList.toArray(new Expression[expList.size()]);
        Section tempSection = null;
        if (subDomain instanceof CompartmentSubDomain) {
            tempSection = volDomains.addSection(subDomain.getName(), volDomains.depth() + 1);
        } else if (subDomain instanceof MembraneSubDomain) {
            tempSection = memDomains.addSection(subDomain.getName(), memDomains.depth() + 1);
        }
        try {
            Dimension dim = ExpressionCanvas.getExpressionImageSize(expArray, (Graphics2D) dummy.getGraphics());
            System.out.println("Image dim: " + dim.width + " " + dim.height);
            BufferedImage bufferedImage = new BufferedImage((int) dim.getWidth() * scale, (int) dim.getHeight() * scale, BufferedImage.TYPE_3BYTE_BGR);
            ExpressionCanvas.getExpressionAsImage(expArray, bufferedImage, scale);
            // Table imageTable = null;;
            com.lowagie.text.Image expImage = com.lowagie.text.Image.getInstance(bufferedImage, null);
            expImage.setAlignment(com.lowagie.text.Image.LEFT);
            if (viewableWidth < expImage.scaledWidth()) {
                expImage.scaleToFit(viewableWidth, expImage.height());
                System.out.println("SubDomain expresions After scaling: " + expImage.scaledWidth());
            }
            /*Cell imageCell = new Cell();
				imageCell.add(expImage);
				if (imageTable == null) {
					imageTable = getTable(1, 100, 1, 1, 0);
				}
				imageTable.setTableFitsPage(false);
 				imageTable.setCellsFitPage(false);
				imageTable.addCell(imageCell);
				imageTable.setWidth(100);
				tempSection.add(imageTable);*/
            tempSection.add(expImage);
        } catch (Exception e) {
            System.err.println("Unable to add subdomain equation image to report.");
            e.printStackTrace();
        }
    }
    if (volDomains.isEmpty()) {
        mathDescSection.remove(volDomains);
    }
    if (memDomains.isEmpty()) {
        mathDescSection.remove(memDomains);
    }
}

Example 65 with ExpressionException

use of cbit.vcell.parser.ExpressionException 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);
}