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

Example 16 with CompartmentSubDomain

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

the class MathTestingUtilities method comparePDEResultsWithExact.

/**
 * Insert the method's description here.
 * Creation date: (8/20/2003 12:58:10 PM)
 */
public static SimulationComparisonSummary comparePDEResultsWithExact(SimulationSymbolTable simSymbolTable, PDEDataManager dataManager, String type, double absErrorThreshold, double relErrorThreshold) throws DataAccessException, ExpressionException {
    java.util.Hashtable<String, DataErrorSummary> tempVarHash = new java.util.Hashtable<String, DataErrorSummary>();
    double[] timeArray = dataManager.getDataSetTimes();
    Variable[] vars = simSymbolTable.getVariables();
    CartesianMesh mesh = dataManager.getMesh();
    MathDescription mathDesc = simSymbolTable.getSimulation().getMathDescription();
    // Get volumeSubdomains from mathDesc/mesh and store in lookupTable
    int numVol = mesh.getSizeX() * mesh.getSizeY() * mesh.getSizeZ();
    CompartmentSubDomain[] volSubDomainLookup = new CompartmentSubDomain[numVol];
    for (int i = 0; i < numVol; i++) {
        int subVolumeIndex = mesh.getSubVolumeFromVolumeIndex(i);
        SubVolume subVolume = mathDesc.getGeometry().getGeometrySpec().getSubVolume(subVolumeIndex);
        CompartmentSubDomain compSubDomain = mathDesc.getCompartmentSubDomain(subVolume.getName());
        volSubDomainLookup[i] = compSubDomain;
    }
    // Get membraneSubdomains from mathDesc/mesh and store in lookupTable
    int numMem = mesh.getMembraneElements().length;
    MembraneSubDomain[] memSubDomainLookup = new MembraneSubDomain[numMem];
    for (int i = 0; i < numMem; i++) {
        int insideVolIndex = mesh.getMembraneElements()[i].getInsideVolumeIndex();
        int outsideVolIndex = mesh.getMembraneElements()[i].getOutsideVolumeIndex();
        MembraneSubDomain memSubDomain = mathDesc.getMembraneSubDomain(volSubDomainLookup[insideVolIndex], volSubDomainLookup[outsideVolIndex]);
        memSubDomainLookup[i] = memSubDomain;
    }
    double[] valueArray = new double[4];
    SimpleSymbolTable symbolTable = new SimpleSymbolTable(new String[] { "t", "x", "y", "z" });
    int tIndex = symbolTable.getEntry("t").getIndex();
    int xIndex = symbolTable.getEntry("x").getIndex();
    int yIndex = symbolTable.getEntry("y").getIndex();
    int zIndex = symbolTable.getEntry("z").getIndex();
    SimulationComparisonSummary simComparisonSummary = new SimulationComparisonSummary();
    String hashKey = new String("");
    long dataLength = 0;
    // for each var, do the following :
    for (int i = 0; i < vars.length; i++) {
        if (vars[i] instanceof VolVariable || vars[i] instanceof MemVariable || vars[i] instanceof FilamentVariable || vars[i] instanceof VolumeRegionVariable || vars[i] instanceof MembraneRegionVariable || vars[i] instanceof FilamentRegionVariable) {
            // for each time in timeArray,
            for (int j = 0; j < timeArray.length; j++) {
                if (type.equals(TestCaseNew.EXACT_STEADY)) {
                    if (j != (timeArray.length - 1)) {
                        continue;
                    }
                }
                // get data block from varName, data from datablock
                SimDataBlock simDataBlock = dataManager.getSimDataBlock(vars[i].getName(), timeArray[j]);
                double[] data = simDataBlock.getData();
                dataLength = data.length;
                SubDomain subDomain = null;
                Coordinate subDomainCoord = null;
                // for each point in data block ...
                for (int k = 0; k < dataLength; k++) {
                    // Get subdomain from mesh (from the lookupTable), get coordinates (x,y,z) from mesh, evaluate EXACT SOLN at that coord
                    if (vars[i] instanceof VolVariable) {
                        subDomain = volSubDomainLookup[k];
                        subDomainCoord = mesh.getCoordinateFromVolumeIndex(k);
                    } else if (vars[i] instanceof MemVariable) {
                        subDomain = memSubDomainLookup[k];
                        subDomainCoord = mesh.getCoordinateFromMembraneIndex(k);
                    } else {
                        throw new RuntimeException("Var " + vars[i].getName() + " not supported yet!");
                    }
                    hashKey = vars[i].getName() + ":" + subDomain.getName();
                    DataErrorSummary tempVar = (DataErrorSummary) tempVarHash.get(hashKey);
                    if (tempVar == null) {
                        Expression exp = new Expression(subDomain.getEquation(vars[i]).getExactSolution());
                        exp.bindExpression(simSymbolTable);
                        exp = MathUtilities.substituteFunctions(exp, simSymbolTable);
                        exp = exp.flatten();
                        exp.bindExpression(symbolTable);
                        tempVar = new DataErrorSummary(exp);
                        tempVarHash.put(hashKey, tempVar);
                    }
                    // time
                    valueArray[tIndex] = timeArray[j];
                    // x
                    valueArray[xIndex] = subDomainCoord.getX();
                    // y
                    valueArray[yIndex] = subDomainCoord.getY();
                    // z
                    valueArray[zIndex] = subDomainCoord.getZ();
                    // EXACT soln at coord subDomainCoord
                    double value = tempVar.getExactExp().evaluateVector(valueArray);
                    tempVar.addDataValues(value, data[k], timeArray[j], k, absErrorThreshold, relErrorThreshold);
                }
            // end for (k)
            }
        // end for (j)
        }
    // end - if (var)
    }
    // end for (i)
    Enumeration<String> enumKeys = tempVarHash.keys();
    while (enumKeys.hasMoreElements()) {
        String key = enumKeys.nextElement();
        DataErrorSummary tempVarSummary = tempVarHash.get(key);
        simComparisonSummary.addVariableComparisonSummary(new VariableComparisonSummary(key, tempVarSummary.getMinRef(), tempVarSummary.getMaxRef(), tempVarSummary.getMaxAbsoluteError(), tempVarSummary.getMaxRelativeError(), tempVarSummary.getL2Norm(), tempVarSummary.getTimeAtMaxAbsoluteError(), tempVarSummary.getIndexAtMaxAbsoluteError(), tempVarSummary.getTimeAtMaxRelativeError(), tempVarSummary.getIndexAtMaxRelativeError()));
    }
    return simComparisonSummary;
}

Example 17 with CompartmentSubDomain

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

the class FiniteVolumeFileWriter method writeChomboSpec.

private void writeChomboSpec() throws ExpressionException, SolverException, PropertyVetoException, ClassNotFoundException, IOException, GeometryException, ImageException {
    if (!bChomboSolver) {
        return;
    }
    GeometrySpec geometrySpec = resampledGeometry.getGeometrySpec();
    int dimension = geometrySpec.getDimension();
    if (dimension == 1) {
        throw new SolverException(simTask.getSimulation().getSolverTaskDescription().getSolverDescription().getDisplayLabel() + " is only supported for simulations with 2D or 3D geometry.");
    }
    Simulation simulation = getSimulationTask().getSimulation();
    SolverTaskDescription solverTaskDescription = simulation.getSolverTaskDescription();
    ChomboSolverSpec chomboSolverSpec = solverTaskDescription.getChomboSolverSpec();
    printWriter.println(FVInputFileKeyword.CHOMBO_SPEC_BEGIN);
    printWriter.println(FVInputFileKeyword.DIMENSION + " " + geometrySpec.getDimension());
    Extent extent = geometrySpec.getExtent();
    Origin origin = geometrySpec.getOrigin();
    ISize isize = simulation.getMeshSpecification().getSamplingSize();
    switch(geometrySpec.getDimension()) {
        case 2:
            printWriter.println(FVInputFileKeyword.MESH_SIZE + " " + isize.getX() + " " + isize.getY());
            printWriter.println(FVInputFileKeyword.DOMAIN_SIZE + " " + extent.getX() + " " + extent.getY());
            printWriter.println(FVInputFileKeyword.DOMAIN_ORIGIN + " " + origin.getX() + " " + origin.getY());
            break;
        case 3:
            printWriter.println(FVInputFileKeyword.MESH_SIZE + " " + isize.getX() + " " + isize.getY() + " " + isize.getZ());
            printWriter.println(FVInputFileKeyword.DOMAIN_SIZE + " " + extent.getX() + " " + extent.getY() + " " + extent.getZ());
            printWriter.println(FVInputFileKeyword.DOMAIN_ORIGIN + " " + origin.getX() + " " + origin.getY() + " " + origin.getZ());
            break;
    }
    List<CompartmentSubDomain> featureList = new ArrayList<CompartmentSubDomain>();
    Enumeration<SubDomain> enum1 = simulation.getMathDescription().getSubDomains();
    while (enum1.hasMoreElements()) {
        SubDomain sd = enum1.nextElement();
        if (sd instanceof CompartmentSubDomain) {
            featureList.add((CompartmentSubDomain) sd);
        }
    }
    int numFeatures = featureList.size();
    CompartmentSubDomain[] features = featureList.toArray(new CompartmentSubDomain[0]);
    int[] phases = new int[numFeatures];
    Arrays.fill(phases, -1);
    phases[numFeatures - 1] = 0;
    int[] numAssigned = new int[] { 1 };
    assignPhases(features, numFeatures - 1, phases, numAssigned);
    Map<String, Integer> subDomainPhaseMap = new HashMap<String, Integer>();
    for (int i = 0; i < phases.length; ++i) {
        if (phases[i] == -1) {
            throw new SolverException("Failed to assign a phase to CompartmentSubdomain '" + features[i].getName() + "'. It might be caused by too coarsh a mesh.");
        }
        subDomainPhaseMap.put(features[i].getName(), phases[i]);
    }
    SubVolume[] subVolumes = geometrySpec.getSubVolumes();
    if (geometrySpec.hasImage()) {
        Geometry geometry = (Geometry) BeanUtils.cloneSerializable(simulation.getMathDescription().getGeometry());
        Geometry simGeometry = geometry;
        VCImage img = geometry.getGeometrySpec().getImage();
        int factor = Math.max(Math.max(img.getNumX(), img.getNumY()), img.getNumZ()) < 512 ? 2 : 1;
        ISize distanceMapMeshSize = new ISize(img.getNumX() * factor, img.getNumY() * factor, img.getNumZ() * factor);
        Vect3d deltaX = null;
        boolean bCellCentered = false;
        double dx = 0.5;
        double dy = 0.5;
        double dz = 0.5;
        int Nx = distanceMapMeshSize.getX();
        int Ny = distanceMapMeshSize.getY();
        int Nz = distanceMapMeshSize.getZ();
        if (dimension == 2) {
            // pad the 2D image with itself in order to obtain a 3D image used to compute the distance map
            // because the distance map algorithm is 3D only (using distance to triangles)
            byte[] oldPixels = img.getPixels();
            byte[] newPixels = new byte[oldPixels.length * 3];
            System.arraycopy(oldPixels, 0, newPixels, 0, oldPixels.length);
            System.arraycopy(oldPixels, 0, newPixels, oldPixels.length, oldPixels.length);
            System.arraycopy(oldPixels, 0, newPixels, oldPixels.length * 2, oldPixels.length);
            double distX = geometry.getExtent().getX() / img.getNumX();
            double distY = geometry.getExtent().getY() / img.getNumY();
            // we set the distance on the z axis to something that makes sense
            double distZ = Math.max(distX, distY);
            Extent newExtent = new Extent(geometry.getExtent().getX(), geometry.getExtent().getY(), distZ * 3);
            VCImage newImage = new VCImageUncompressed(null, newPixels, newExtent, img.getNumX(), img.getNumY(), 3);
            // copy the pixel classes too
            ArrayList<VCPixelClass> newPixelClasses = new ArrayList<VCPixelClass>();
            for (VCPixelClass origPixelClass : geometry.getGeometrySpec().getImage().getPixelClasses()) {
                SubVolume origSubvolume = geometry.getGeometrySpec().getImageSubVolumeFromPixelValue(origPixelClass.getPixel());
                newPixelClasses.add(new VCPixelClass(null, origSubvolume.getName(), origPixelClass.getPixel()));
            }
            newImage.setPixelClasses(newPixelClasses.toArray(new VCPixelClass[newPixelClasses.size()]));
            simGeometry = new Geometry(geometry, newImage);
            Nz = 3;
        }
        GeometrySpec simGeometrySpec = simGeometry.getGeometrySpec();
        Extent simExtent = simGeometrySpec.getExtent();
        dx = simExtent.getX() / (Nx - 1);
        dy = simExtent.getY() / (Ny - 1);
        dz = simExtent.getZ() / (Nz - 1);
        if (Math.abs(dx - dy) > 0.1 * Math.max(dx, dy)) {
            dx = Math.min(dx, dy);
            dy = dx;
            Nx = (int) (simExtent.getX() / dx + 1);
            Ny = (int) (simExtent.getY() / dx + 1);
            if (dimension == 3) {
                dz = dx;
                Nz = (int) (simExtent.getZ() / dx + 1);
            }
        }
        deltaX = new Vect3d(dx, dy, dz);
        // one more point in each direction
        distanceMapMeshSize = new ISize(Nx + 1, Ny + 1, Nz + 1);
        Extent distanceMapExtent = new Extent(simExtent.getX() + dx, simExtent.getY() + dy, simExtent.getZ() + dz);
        simGeometrySpec.setExtent(distanceMapExtent);
        GeometrySurfaceDescription geoSurfaceDesc = simGeometry.getGeometrySurfaceDescription();
        geoSurfaceDesc.setVolumeSampleSize(distanceMapMeshSize);
        geoSurfaceDesc.updateAll();
        VCImage vcImage = RayCaster.sampleGeometry(simGeometry, distanceMapMeshSize, bCellCentered);
        SubvolumeSignedDistanceMap[] distanceMaps = DistanceMapGenerator.computeDistanceMaps(simGeometry, vcImage, bCellCentered);
        if (dimension == 2) {
            distanceMaps = DistanceMapGenerator.extractMiddleSlice(distanceMaps);
        }
        printWriter.println(FVInputFileKeyword.SUBDOMAINS + " " + simGeometrySpec.getNumSubVolumes() + " " + FVInputFileKeyword.DISTANCE_MAP);
        for (int i = 0; i < subVolumes.length; i++) {
            File distanceMapFile = new File(workingDirectory, getSimulationTask().getSimulationJobID() + "_" + subVolumes[i].getName() + DISTANCE_MAP_FILE_EXTENSION);
            writeDistanceMapFile(deltaX, distanceMaps[i], distanceMapFile);
            int phase = subDomainPhaseMap.get(subVolumes[i].getName());
            printWriter.println(subVolumes[i].getName() + " " + phase + " " + distanceMapFile.getAbsolutePath());
        }
    } else {
        printWriter.println(FVInputFileKeyword.SUBDOMAINS + " " + geometrySpec.getNumSubVolumes());
        Expression[] rvachevExps = convertAnalyticGeometryToRvachevFunction(geometrySpec);
        for (int i = 0; i < subVolumes.length; i++) {
            if (subVolumes[i] instanceof AnalyticSubVolume) {
                String name = subVolumes[i].getName();
                int phase = subDomainPhaseMap.get(name);
                printWriter.println(name + " " + phase + " ");
                printWriter.println(FVInputFileKeyword.IF + " " + rvachevExps[i].infix() + ";");
                printWriter.println(FVInputFileKeyword.USER + " " + ((AnalyticSubVolume) subVolumes[i]).getExpression().infix() + ";");
            }
        }
    }
    printWriter.println(FVInputFileKeyword.MAX_BOX_SIZE + " " + chomboSolverSpec.getMaxBoxSize());
    printWriter.println(FVInputFileKeyword.FILL_RATIO + " " + chomboSolverSpec.getFillRatio());
    printWriter.println(FVInputFileKeyword.RELATIVE_TOLERANCE + " " + simulation.getSolverTaskDescription().getErrorTolerance().getRelativeErrorTolerance());
    printWriter.println(FVInputFileKeyword.SAVE_VCELL_OUTPUT + " " + chomboSolverSpec.isSaveVCellOutput());
    printWriter.println(FVInputFileKeyword.SAVE_CHOMBO_OUTPUT + " " + chomboSolverSpec.isSaveChomboOutput());
    printWriter.println(FVInputFileKeyword.ACTIVATE_FEATURE_UNDER_DEVELOPMENT + " " + chomboSolverSpec.isActivateFeatureUnderDevelopment());
    printWriter.println(FVInputFileKeyword.SMALL_VOLFRAC_THRESHOLD + " " + chomboSolverSpec.getSmallVolfracThreshold());
    printWriter.println(FVInputFileKeyword.BLOCK_FACTOR + " " + chomboSolverSpec.getBlockFactor());
    printWriter.println(FVInputFileKeyword.TAGS_GROW + " " + chomboSolverSpec.getTagsGrow());
    // Refinement
    int numLevels = chomboSolverSpec.getNumRefinementLevels();
    // Refinements #Levels ratio 1, ratio 2, etc
    printWriter.print(FVInputFileKeyword.REFINEMENTS + " " + (numLevels + 1));
    List<Integer> ratios = chomboSolverSpec.getRefineRatioList();
    for (int i : ratios) {
        printWriter.print(" " + i);
    }
    // write last refinement ratio, fake
    printWriter.println(" 2");
    // membrane rois
    List<RefinementRoi> memRios = chomboSolverSpec.getMembraneRefinementRois();
    printWriter.println(FVInputFileKeyword.REFINEMENT_ROIS + " " + RoiType.Membrane + " " + memRios.size());
    for (RefinementRoi roi : memRios) {
        if (roi.getRoiExpression() == null) {
            throw new SolverException("ROI expression cannot be null");
        }
        // level tagsGrow ROIexpression
        printWriter.println(roi.getLevel() + " " + roi.getRoiExpression().infix() + ";");
    }
    List<RefinementRoi> volRios = chomboSolverSpec.getVolumeRefinementRois();
    printWriter.println(FVInputFileKeyword.REFINEMENT_ROIS + " " + RoiType.Volume + " " + volRios.size());
    for (RefinementRoi roi : volRios) {
        if (roi.getRoiExpression() == null) {
            throw new SolverException("ROI expression cannot be null");
        }
        printWriter.println(roi.getLevel() + " " + roi.getRoiExpression().infix() + ";");
    }
    printWriter.println(FVInputFileKeyword.VIEW_LEVEL + " " + chomboSolverSpec.getViewLevel());
    printWriter.println(FVInputFileKeyword.CHOMBO_SPEC_END);
    printWriter.println();
}

Example 18 with CompartmentSubDomain

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

the class FiniteVolumeFileWriter method writeCompartments.

/**
 *COMPARTMENT_BEGIN nucleus
 *
 *BOUNDARY_CONDITIONS value value value value
 *
 *EQUATION_BEGIN rfB
 *INITIAL _VCell_FieldData_0;
 *RATE ( - (50.0 * rfB * ((x > -5.0) && (x < 5.0) && (y > -5.0) && (y < 5.0))) + (0.02 * ( - rB - rfB + (20.0 * ((x > -3.0) && (x < 3.0) && (y > -5.0) && (y < 5.0))) + _VCell_FieldData_0) * rf) - (0.1 * rfB));
 *EQUATION_END
 *
 *EQUATION_BEGIN r
 *INITIAL 5.0;
 *RATE ( - ((0.02 * r * ( - rB - rfB + (20.0 * ((x > -3.0) && (x < 3.0) && (y > -5.0) && (y < 5.0))) + _VCell_FieldData_0)) - (0.1 * rB)) + (50.0 * rf * ((x > -5.0) && (x < 5.0) && (y > -5.0) && (y < 5.0))));
 *DIFFUSION 10.0;
 *BOUNDARY_XM 5.0;
 *BOUNDARY_XP 5.0;
 *BOUNDARY_YM 5.0;
 *BOUNDARY_YP 5.0;
 *EQUATION_END
 *
 *COMPARTMENT_END
 * @throws ExpressionException
 * @throws MathException
 */
private void writeCompartments() throws ExpressionException, MathException {
    Simulation simulation = simTask.getSimulation();
    MathDescription mathDesc = simulation.getMathDescription();
    Enumeration<SubDomain> enum1 = mathDesc.getSubDomains();
    while (enum1.hasMoreElements()) {
        SubDomain sd = enum1.nextElement();
        if (sd instanceof CompartmentSubDomain) {
            CompartmentSubDomain csd = (CompartmentSubDomain) sd;
            printWriter.println("COMPARTMENT_BEGIN " + csd.getName());
            printWriter.println();
            writeCompartment_VarContext(csd);
            writeFastSystem(csd);
            printWriter.println("COMPARTMENT_END");
            printWriter.println();
        }
    }
    printWriter.println();
}

Example 19 with CompartmentSubDomain

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

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

the class ITextWriter method writeSubDomainsEquationsAsText.

protected void writeSubDomainsEquationsAsText(Section mathDescSection, MathDescription mathDesc) throws DocumentException {
    Enumeration<SubDomain> subDomains = mathDesc.getSubDomains();
    Section volDomains = mathDescSection.addSection("Volume Domains", mathDescSection.depth() + 1);
    Section memDomains = mathDescSection.addSection("Membrane Domains", mathDescSection.depth() + 1);
    Section filDomains = mathDescSection.addSection("Filament Domains", mathDescSection.depth() + 1);
    while (subDomains.hasMoreElements()) {
        Section tempSection = null;
        SubDomain subDomain = subDomains.nextElement();
        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);
        } else if (subDomain instanceof FilamentSubDomain) {
            tempSection = filDomains.addSection(subDomain.getName(), filDomains.depth() + 1);
        }
        Enumeration<Equation> equationsList = subDomain.getEquations();
        while (equationsList.hasMoreElements()) {
            Equation equ = equationsList.nextElement();
            writeEquation(tempSection, equ);
        }
        if (subDomain.getFastSystem() != null) {
            writeFastSystem(tempSection, subDomain.getFastSystem());
        }
        if (subDomain instanceof MembraneSubDomain) {
            Enumeration<JumpCondition> jcList = ((MembraneSubDomain) subDomain).getJumpConditions();
            while (jcList.hasMoreElements()) {
                JumpCondition jc = jcList.nextElement();
                writeJumpCondition(tempSection, jc);
            }
        }
    }
    if (volDomains.isEmpty()) {
        mathDescSection.remove(volDomains);
    }
    if (memDomains.isEmpty()) {
        mathDescSection.remove(memDomains);
    }
    if (filDomains.isEmpty()) {
        mathDescSection.remove(filDomains);
    }
}