Examples with VisMesh org.vcell.vis.vismesh.thrift.VisMesh used on opensource projects

Example 1 with VisMesh

use of org.vcell.vis.vismesh.thrift.VisMesh in project vcell by virtualcell.

the class ComsolMeshReader method main.

public static void main(String[] args) {
    try {
        System.getProperties().setProperty(PropertyLoader.installationRoot, "d:\\developer\\eclipse\\workspace_refactor\\VCell_6.1_userdata");
        File comsolFile = new File("simoutput_multitime.txt");
        VisMesh visMesh = new VisMesh();
        read(visMesh, comsolFile);
        System.out.println("done");
    } catch (Exception e) {
        e.printStackTrace();
    }
}

Example 2 with VisMesh

use of org.vcell.vis.vismesh.thrift.VisMesh in project vcell by virtualcell.

the class ComsolSolver method startSolver.

@Override
public void startSolver() {
    try {
        setSolverStatus(new SolverStatus(SolverStatus.SOLVER_STARTING, SimulationMessage.MESSAGE_SOLVER_STARTING_INIT));
        initialize();
        setSolverStatus(new SolverStatus(SolverStatus.SOLVER_RUNNING, SimulationMessage.MESSAGE_SOLVER_RUNNING_START));
        fireSolverStarting(SimulationMessage.MESSAGE_SOLVEREVENT_STARTING);
        String filePrefix = simTask.getSimulationJob().getSimulationJobID();
        try {
            comsolService.connectComsol();
            File reportFile = new File(getSaveDirectory(), filePrefix + ".comsoldat");
            File javaFile = new File(getSaveDirectory(), filePrefix + ".java");
            File mphFile = new File(getSaveDirectory(), filePrefix + ".mph");
            comsolService.solve(this.vccModel, reportFile, javaFile, mphFile);
        } finally {
            comsolService.disconnectComsol();
        }
        File logFile = new File(getSaveDirectory(), filePrefix + ".log");
        FileUtils.writeStringToFile(logFile, createLogFileContents(simTask.getSimulation().getSolverTaskDescription()));
        VisMesh visMesh = new VisMesh();
        File reportFile = new File(getSaveDirectory(), filePrefix + ".comsoldat");
        ComsolMeshReader.read(visMesh, reportFile);
        time = simTask.getSimulation().getSolverTaskDescription().getTimeBounds().getEndingTime();
        progress = 1.0;
        fireSolverPrinted(time);
        fireSolverProgress(progress);
        setSolverStatus(new SolverStatus(SolverStatus.SOLVER_FINISHED, SimulationMessage.MESSAGE_SOLVER_FINISHED));
        fireSolverFinished();
    } catch (Exception e) {
        e.printStackTrace(System.out);
        setSolverStatus(new SolverStatus(SolverStatus.SOLVER_ABORTED, SimulationMessage.solverAborted(e.getMessage())));
        fireSolverAborted(SimulationMessage.solverAborted(e.getMessage()));
    }
}

Example 3 with VisMesh

use of org.vcell.vis.vismesh.thrift.VisMesh in project vcell by virtualcell.

the class MovingBoundaryVtkFileWriter method writeEmptyMeshFiles.

public File[] writeEmptyMeshFiles(MovingBoundarySimFiles movingBoundaryFiles, int timeIndex, File destinationDirectory, ProgressListener progressListener) throws IOException, MathException, DataAccessException {
    HashMap<String, VisMesh> domainMeshMap = new HashMap<String, VisMesh>();
    ArrayList<String> allDomainNames = new ArrayList<String>();
    File hdf5OutputFile = movingBoundaryFiles.hdf5OutputFile;
    MovingBoundaryReader reader = new MovingBoundaryReader(hdf5OutputFile.getAbsolutePath());
    // 
    // for inside volume domain in mesh, extract the associated VisMesh
    // 
    {
        String insideDomainName = reader.getFakeInsideDomainName();
        MovingBoundaryMeshMapping insideMeshMapping = new MovingBoundaryMeshMapping();
        VisMesh insideVisMesh = insideMeshMapping.fromReader(reader, DomainType.INSIDE, timeIndex);
        domainMeshMap.put(insideDomainName, insideVisMesh);
        allDomainNames.add(insideDomainName);
    }
    // {
    // String outsideDomainName = reader.getFakeOutsideDomainName();
    // MovingBoundaryMeshMapping outsideMeshMapping = new MovingBoundaryMeshMapping();
    // VisMesh outsideVisMesh = outsideMeshMapping.fromReader(reader, DomainType.OUTSIDE, timeIndex);
    // domainMeshMap.put(outsideDomainName, outsideVisMesh);
    // allDomainNames.add(outsideDomainName);
    // }
    // {
    // String membraneDomainName = reader.getFakeMembraneDomainName();
    // MovingBoundaryMeshMapping membraneMeshMapping = new MovingBoundaryMeshMapping();
    // VisMesh membraneVisMesh = membraneMeshMapping.fromReader(reader, DomainType.MEMBRANE, timeIndex);
    // domainMeshMap.put(membraneDomainName, membraneVisMesh);
    // allDomainNames.add(membraneDomainName);
    // }
    int numFiles = allDomainNames.size();
    ArrayList<File> files = new ArrayList<File>();
    int filesProcessed = 0;
    for (final String domainName : allDomainNames) {
        // 
        // find the globalIndexes for each domain element - use this to extract the domain-only data.
        // 
        VisMesh visMesh = domainMeshMap.get(domainName);
        File vtuFile = getVtuMeshFileName(destinationDirectory, movingBoundaryFiles, domainName, timeIndex);
        File mbIndexDataFileName = getMovingBoundaryIndexDataFileName(movingBoundaryFiles, domainName, timeIndex);
        VtkService.getInstance().writeMovingBoundaryVtkGridAndIndexData(visMesh, domainName, vtuFile, mbIndexDataFileName);
        files.add(vtuFile);
        filesProcessed++;
        if (progressListener != null) {
            progressListener.progress(((double) filesProcessed) / numFiles);
        }
    }
    return files.toArray(new File[0]);
}

Example 4 with VisMesh

use of org.vcell.vis.vismesh.thrift.VisMesh in project vcell by virtualcell.

the class CartesianMeshMapping method fromMesh3DMembrane.

private VisMesh fromMesh3DMembrane(CartesianMesh cartesianMesh, String domainName) {
    ISize size = cartesianMesh.getSize();
    int numX = size.getX();
    int numY = size.getY();
    int dimension = 3;
    Vect3D origin = new Vect3D(cartesianMesh.getOrigin().x, cartesianMesh.getOrigin().y, cartesianMesh.getOrigin().z);
    Vect3D extent = new Vect3D(cartesianMesh.getExtent().x, cartesianMesh.getExtent().y, cartesianMesh.getExtent().z);
    // invoke VisMesh() constructor
    VisMesh visMesh = new VisMesh(dimension, origin, extent);
    int currPointIndex = 0;
    HashMap<String, Integer> pointDict = new HashMap<String, Integer>();
    List<MembraneElement> membraneElements = cartesianMesh.getMembraneElements(domainName);
    for (MembraneElement membraneElement : membraneElements) {
        // inside
        int insideVolumeIndex = membraneElement.getInsideVolumeIndex();
        int insideI = insideVolumeIndex % numX;
        int insideJ = (insideVolumeIndex % (numX * numY)) / numX;
        int insideK = insideVolumeIndex / (numX * numY);
        Box3D insideBox = cartesianMesh.getVolumeElementBox(insideI, insideJ, insideK);
        // outside
        int outsideVolumeIndex = membraneElement.getOutsideVolumeIndex();
        int outsideI = outsideVolumeIndex % numX;
        int outsideJ = (outsideVolumeIndex % (numX * numY)) / numX;
        int outsideK = outsideVolumeIndex / (numX * numY);
        VisPoint p1Coord;
        VisPoint p2Coord;
        VisPoint p3Coord;
        VisPoint p4Coord;
        if (insideI == outsideI + 1) {
            // x-   z cross y
            double x = insideBox.x_lo;
            p1Coord = new VisPoint(x, insideBox.y_lo, insideBox.z_lo);
            p2Coord = new VisPoint(x, insideBox.y_lo, insideBox.z_hi);
            p3Coord = new VisPoint(x, insideBox.y_hi, insideBox.z_hi);
            p4Coord = new VisPoint(x, insideBox.y_hi, insideBox.z_lo);
        } else if (outsideI == insideI + 1) {
            // x+   y cross z
            double x = insideBox.x_hi;
            p1Coord = new VisPoint(x, insideBox.y_lo, insideBox.z_lo);
            p2Coord = new VisPoint(x, insideBox.y_hi, insideBox.z_lo);
            p3Coord = new VisPoint(x, insideBox.y_hi, insideBox.z_hi);
            p4Coord = new VisPoint(x, insideBox.y_lo, insideBox.z_hi);
        } else if (insideJ == outsideJ + 1) {
            // y-   x cross z
            double y = insideBox.y_lo;
            p1Coord = new VisPoint(insideBox.x_lo, y, insideBox.z_lo);
            p2Coord = new VisPoint(insideBox.x_hi, y, insideBox.z_lo);
            p3Coord = new VisPoint(insideBox.x_hi, y, insideBox.z_hi);
            p4Coord = new VisPoint(insideBox.x_lo, y, insideBox.z_hi);
        } else if (outsideJ == insideJ + 1) {
            // y+   z cross x
            double y = insideBox.y_hi;
            p1Coord = new VisPoint(insideBox.x_lo, y, insideBox.z_lo);
            p2Coord = new VisPoint(insideBox.x_lo, y, insideBox.z_hi);
            p3Coord = new VisPoint(insideBox.x_hi, y, insideBox.z_hi);
            p4Coord = new VisPoint(insideBox.x_hi, y, insideBox.z_lo);
        } else if (insideK == outsideK + 1) {
            // z-   y cross x
            double z = insideBox.z_lo;
            p1Coord = new VisPoint(insideBox.x_lo, insideBox.y_lo, z);
            p2Coord = new VisPoint(insideBox.x_lo, insideBox.y_hi, z);
            p3Coord = new VisPoint(insideBox.x_hi, insideBox.y_hi, z);
            p4Coord = new VisPoint(insideBox.x_hi, insideBox.y_lo, z);
        } else if (outsideK == insideK + 1) {
            // z+   x cross y
            double z = insideBox.z_hi;
            p1Coord = new VisPoint(insideBox.x_lo, insideBox.y_lo, z);
            p2Coord = new VisPoint(insideBox.x_hi, insideBox.y_lo, z);
            p3Coord = new VisPoint(insideBox.x_hi, insideBox.y_hi, z);
            p4Coord = new VisPoint(insideBox.x_lo, insideBox.y_hi, z);
        } else {
            throw new RuntimeException("inside/outside volume indices not reconciled in membraneElement " + membraneElement.getMembraneIndex() + " in domain " + domainName);
        }
        // 
        // make sure vertices are added to model without duplicates and get the assigned identifier.
        // 
        String p1Key = toStringKey(p1Coord);
        Integer i1 = pointDict.get(p1Key);
        if (i1 == null) {
            pointDict.put(p1Key, currPointIndex);
            i1 = currPointIndex;
            visMesh.addToPoints(p1Coord);
            currPointIndex++;
        }
        String p2Key = toStringKey(p2Coord);
        Integer i2 = pointDict.get(p2Key);
        if (i2 == null) {
            pointDict.put(p2Key, currPointIndex);
            i2 = currPointIndex;
            visMesh.addToPoints(p2Coord);
            currPointIndex++;
        }
        String p3Key = toStringKey(p3Coord);
        Integer i3 = pointDict.get(p3Key);
        if (i3 == null) {
            pointDict.put(p3Key, currPointIndex);
            i3 = currPointIndex;
            visMesh.addToPoints(p3Coord);
            currPointIndex++;
        }
        String p4Key = toStringKey(p4Coord);
        Integer i4 = pointDict.get(p4Key);
        if (i4 == null) {
            pointDict.put(p4Key, currPointIndex);
            i4 = currPointIndex;
            visMesh.addToPoints(p4Coord);
            currPointIndex++;
        }
        VisPolygon quad = new VisPolygon(Arrays.asList(new Integer[] { i1, i2, i3, i4 }));
        quad.setFiniteVolumeIndex(new FiniteVolumeIndex(membraneElement.getMembraneIndex(), cartesianMesh.getMembraneRegionIndex(membraneElement.getMembraneIndex())));
        // print('adding a cell at level '+str(currLevel.getLevel())+" from "+str(p1Coord)+" to "+str(p3Coord))
        visMesh.addToPolygons(quad);
    }
    return visMesh;
}

Example 5 with VisMesh

use of org.vcell.vis.vismesh.thrift.VisMesh in project vcell by virtualcell.

the class ChomboMeshMapping method fromMeshData2D.

private VisMesh fromMeshData2D(ChomboMeshData chomboMeshData) {
    ChomboMesh chomboMesh = chomboMeshData.getMesh();
    ChomboLevel finestLevel = chomboMesh.getLevel(chomboMesh.getNumLevels() - 1);
    int finestAbsRefinement = finestLevel.getAbsoluteRefinement();
    ISize size = finestLevel.getSize();
    int numX = size.getX();
    int numY = size.getY();
    int numZ = size.getZ();
    int dimension = chomboMeshData.getMesh().getDimension();
    int z = 0;
    // invoke VisMesh() constructor
    VisMesh visMesh = new VisMesh(chomboMesh.getDimension(), toThrift(chomboMesh.getOrigin()), toThrift(chomboMesh.getExtent()));
    int currPointIndex = 0;
    HashMap<String, Integer> pointDict = new HashMap<String, Integer>();
    double originX = chomboMesh.getOrigin().x;
    double originY = chomboMesh.getOrigin().y;
    double originZ = chomboMesh.getOrigin().z;
    double extentX = chomboMesh.getExtent().x;
    double extentY = chomboMesh.getExtent().y;
    double extentZ = chomboMesh.getExtent().z;
    ChomboBoundaries chomboBoundaries = chomboMesh.getBoundaries();
    for (ChomboBoundaries.Point chomboPoint : chomboBoundaries.getPoints()) {
        double px = chomboPoint.x;
        double py = chomboPoint.y;
        double pz = z;
        px = (px - originX) * (numX) / extentX * 2 - 1;
        py = (py - originY) * (numY) / extentY * 2 - 1;
        pz = (pz - originZ) * (numZ) / extentZ * 2 - 1;
        if (dimension == 2) {
            pz = z;
        }
        VisPoint newVisPoint = new VisPoint(px, py, pz);
        String coordKey = toStringKey(newVisPoint);
        pointDict.put(coordKey, currPointIndex);
        visMesh.addToPoints(newVisPoint);
        visMesh.addToSurfacePoints(newVisPoint);
        currPointIndex += 1;
    }
    for (ChomboBoundaries.Segment segment : chomboBoundaries.getSegments()) {
        VisLine newVisLine = new VisLine(segment.getP1(), segment.getP2());
        newVisLine.setChomboSurfaceIndex(new ChomboSurfaceIndex(segment.getChomboIndex()));
        visMesh.addToVisLines(newVisLine);
    }
    for (int levelIndex = 0; levelIndex < chomboMesh.getNumLevels(); levelIndex++) {
        ChomboLevelData chomboLevelData = chomboMeshData.getLevelData(levelIndex);
        ChomboLevel currLevel = chomboMesh.getLevel(levelIndex);
        int currAbsRefinement = currLevel.getAbsoluteRefinement();
        Covering covering = currLevel.getCovering();
        int[] levelMap = covering.getLevelMap();
        int[] boxNumberMap = covering.getBoxNumberMap();
        int[] boxIndexMap = covering.getBoxIndexMap();
        int levelNumX = currLevel.getSize().getX();
        int levelNumY = currLevel.getSize().getY();
        for (int x = 0; x < levelNumX; x++) {
            for (int y = 0; y < levelNumY; y++) {
                int mapIndex = x + y * levelNumX;
                if (levelMap[mapIndex] == levelIndex) {
                    // 
                    // if fraction (volume fraction of element in box) is 0 ... then skip this element
                    // 
                    int boxNumber = boxNumberMap[mapIndex];
                    int boxIndex = boxIndexMap[mapIndex];
                    double fraction = chomboLevelData.getCellFraction(currLevel, boxNumber, boxIndex);
                    if (fraction > 0) {
                        // 
                        // add cell
                        // 
                        ChomboBox chomboBox = new ChomboBox(currLevel, x, x, y, y, z, z, dimension).getProjectedBox(currAbsRefinement, finestAbsRefinement);
                        double minX = 2 * chomboBox.getMinX() - 1;
                        double maxX = 2 * chomboBox.getMaxX() + 1;
                        double minY = 2 * chomboBox.getMinY() - 1;
                        double maxY = 2 * chomboBox.getMaxY() + 1;
                        // 
                        // counter clockwise points for a VisPolygon ... initially a quad ... then may be
                        // 
                        // minX,minY
                        // minX,maxY
                        // maxX,maxY
                        // maxX,minY
                        // 
                        VisPoint p1Coord = new VisPoint(minX, minY, z);
                        String p1Key = toStringKey(p1Coord);
                        Integer i1 = pointDict.get(p1Key);
                        if (i1 == null) {
                            pointDict.put(p1Key, currPointIndex);
                            i1 = currPointIndex;
                            visMesh.addToPoints(p1Coord);
                            currPointIndex++;
                        }
                        VisPoint p2Coord = new VisPoint(minX, maxY, z);
                        String p2Key = toStringKey(p2Coord);
                        Integer i2 = pointDict.get(p2Key);
                        if (i2 == null) {
                            pointDict.put(p2Key, currPointIndex);
                            i2 = currPointIndex;
                            visMesh.addToPoints(p2Coord);
                            currPointIndex++;
                        }
                        VisPoint p3Coord = new VisPoint(maxX, maxY, z);
                        String p3Key = toStringKey(p3Coord);
                        Integer i3 = pointDict.get(p3Key);
                        if (i3 == null) {
                            pointDict.put(p3Key, currPointIndex);
                            i3 = currPointIndex;
                            visMesh.addToPoints(p3Coord);
                            currPointIndex++;
                        }
                        VisPoint p4Coord = new VisPoint(maxX, minY, z);
                        String p4Key = toStringKey(p4Coord);
                        Integer i4 = pointDict.get(p4Key);
                        if (i4 == null) {
                            pointDict.put(p4Key, currPointIndex);
                            i4 = currPointIndex;
                            visMesh.addToPoints(p4Coord);
                            currPointIndex++;
                        }
                        VisPolygon quad = new VisPolygon(Arrays.asList(new Integer[] { i1, i2, i3, i4 }));
                        quad.setChomboVolumeIndex(new ChomboVolumeIndex(levelIndex, boxNumber, boxIndex, fraction));
                        // print('adding a cell at level '+str(currLevel.getLevel())+" from "+str(p1Coord)+" to "+str(p3Coord))
                        visMesh.addToPolygons(quad);
                    }
                }
            }
        }
    }
    cropQuads(visMesh);
    return visMesh;
}