Examples with MembraneElement org.vcell.vis.vcell.MembraneElement used on opensource projects

Example 1 with MembraneElement

use of org.vcell.vis.vcell.MembraneElement in project vcell by virtualcell.

the class CartesianMeshFileReader method readCartesianMesh.

private CartesianMesh readCartesianMesh(CommentStringTokenizer tokens, final MembraneMeshMetrics membraneMeshMetrics, final SubdomainInfo subdomainInfo) throws MathException {
    // 
    // clear previous contents
    // 
    MembraneElement[] membraneElements = null;
    String version = null;
    MeshRegionInfo meshRegionInfo = null;
    ISize size = null;
    Vect3D extent = null;
    Vect3D origin = null;
    ContourElement[] contourElements = null;
    // 
    // read new stuff
    // 
    String token = null;
    token = tokens.nextToken();
    if (token.equalsIgnoreCase(VCML.Version)) {
        // 
        // read version number
        // 
        token = tokens.nextToken();
        version = token;
        token = tokens.nextToken();
    }
    if (token.equalsIgnoreCase(VCML.CartesianMesh)) {
        token = tokens.nextToken();
    } else {
        throw new MathFormatException("unexpected token " + token + " expecting " + VCML.CartesianMesh);
    }
    // 
    // only Version 1.1 and later supports membrane connectivity  (as of 8/30/2000)
    // 
    boolean bConnectivity = false;
    if (version.equals(VERSION_1_1) || version.equals(VERSION_1_2)) {
        bConnectivity = true;
    }
    // 
    // only Version 1.2 and later supports Regions
    // 
    boolean bRegions = false;
    if (version.equals(VERSION_1_2)) {
        bRegions = true;
        meshRegionInfo = new MeshRegionInfo();
    }
    if (!token.equalsIgnoreCase(VCML.BeginBlock)) {
        throw new MathFormatException("unexpected token " + token + " expecting " + VCML.BeginBlock);
    }
    while (tokens.hasMoreTokens()) {
        token = tokens.nextToken();
        if (token.equalsIgnoreCase(VCML.EndBlock)) {
            break;
        }
        if (token.equalsIgnoreCase(VCML.Size)) {
            int sx, sy, sz;
            try {
                token = tokens.nextToken();
                sx = Integer.valueOf(token).intValue();
                token = tokens.nextToken();
                sy = Integer.valueOf(token).intValue();
                token = tokens.nextToken();
                sz = Integer.valueOf(token).intValue();
            } catch (NumberFormatException e) {
                throw new MathFormatException("expected:  " + VCML.Size + " # # #");
            }
            size = new ISize(sx, sy, sz);
            continue;
        }
        if (token.equalsIgnoreCase(VCML.Extent)) {
            double ex, ey, ez;
            try {
                token = tokens.nextToken();
                ex = Double.valueOf(token).doubleValue();
                token = tokens.nextToken();
                ey = Double.valueOf(token).doubleValue();
                token = tokens.nextToken();
                ez = Double.valueOf(token).doubleValue();
            } catch (NumberFormatException e) {
                throw new MathFormatException("expected:  " + VCML.Extent + " # # #");
            }
            extent = new Vect3D(ex, ey, ez);
            continue;
        }
        if (token.equalsIgnoreCase(VCML.Origin)) {
            double ox, oy, oz;
            try {
                token = tokens.nextToken();
                ox = Double.valueOf(token).doubleValue();
                token = tokens.nextToken();
                oy = Double.valueOf(token).doubleValue();
                token = tokens.nextToken();
                oz = Double.valueOf(token).doubleValue();
            } catch (NumberFormatException e) {
                throw new MathFormatException("expected:  " + VCML.Origin + " # # #");
            }
            origin = new Vect3D(ox, oy, oz);
            continue;
        }
        // 
        if (token.equalsIgnoreCase(VCML.VolumeRegionsMapSubvolume)) {
            token = tokens.nextToken();
            if (!token.equalsIgnoreCase(VCML.BeginBlock)) {
                throw new MathFormatException("unexpected token " + token + " expecting " + VCML.BeginBlock);
            }
            token = tokens.nextToken();
            int numVolumeRegions = 0;
            try {
                numVolumeRegions = Integer.valueOf(token).intValue();
            } catch (NumberFormatException e) {
                throw new MathFormatException("unexpected token " + token + " expecting the VolumeRegionsMapSubvolume list length");
            }
            int checkCount = 0;
            while (tokens.hasMoreTokens()) {
                token = tokens.nextToken();
                if (token.equalsIgnoreCase(VCML.EndBlock)) {
                    break;
                }
                try {
                    int volRegionID = Integer.valueOf(token).intValue();
                    token = tokens.nextToken();
                    int subvolumeID = Integer.valueOf(token).intValue();
                    token = tokens.nextToken();
                    double volume = Double.valueOf(token).doubleValue();
                    String subdomainName = null;
                    if (subdomainInfo != null) {
                        subdomainName = subdomainInfo.getCompartmentSubdomainName(subvolumeID);
                    }
                    meshRegionInfo.mapVolumeRegionToSubvolume(volRegionID, subvolumeID, volume, subdomainName);
                } catch (NumberFormatException e) {
                    throw new MathFormatException("expected:  # # #");
                }
                checkCount += 1;
            }
            if (checkCount != numVolumeRegions) {
                throw new MathFormatException("CartesianMesh.read->VolumeRegionsMapSubvolume: read " + checkCount + " VolRegions but was expecting " + numVolumeRegions);
            }
            continue;
        }
        if (token.equalsIgnoreCase(VCML.MembraneRegionsMapVolumeRegion)) {
            token = tokens.nextToken();
            if (!token.equalsIgnoreCase(VCML.BeginBlock)) {
                throw new MathFormatException("unexpected token " + token + " expecting " + VCML.BeginBlock);
            }
            token = tokens.nextToken();
            int numMembraneRegions = 0;
            try {
                numMembraneRegions = Integer.valueOf(token).intValue();
            } catch (NumberFormatException e) {
                throw new MathFormatException("unexpected token " + token + " expecting the MembraneRegionsMapVolumeRegion list length");
            }
            int checkCount = 0;
            while (tokens.hasMoreTokens()) {
                token = tokens.nextToken();
                if (token.equalsIgnoreCase(VCML.EndBlock)) {
                    break;
                }
                try {
                    int memRegionID = Integer.valueOf(token).intValue();
                    token = tokens.nextToken();
                    int volRegionIn = Integer.valueOf(token).intValue();
                    token = tokens.nextToken();
                    int volRegionOut = Integer.valueOf(token).intValue();
                    token = tokens.nextToken();
                    double surface = Double.valueOf(token).doubleValue();
                    meshRegionInfo.mapMembraneRegionToVolumeRegion(memRegionID, volRegionIn, volRegionOut, surface);
                } catch (NumberFormatException e) {
                    throw new MathFormatException("expected:  # # #");
                }
                checkCount += 1;
            }
            if (checkCount != numMembraneRegions) {
                throw new MathFormatException("CartesianMesh.read->MembraneRegionsMapVolumeRegion: read " + checkCount + " MembraneRegions but was expecting " + numMembraneRegions);
            }
            continue;
        }
        if (token.equalsIgnoreCase(VCML.VolumeElementsMapVolumeRegion)) {
            token = tokens.nextToken();
            if (!token.equalsIgnoreCase(VCML.BeginBlock)) {
                throw new MathFormatException("unexpected token " + token + " expecting " + VCML.BeginBlock);
            }
            token = tokens.nextToken();
            int numVolumeElements = 0;
            try {
                numVolumeElements = Integer.valueOf(token).intValue();
            } catch (NumberFormatException e) {
                throw new MathFormatException("unexpected token " + token + " expecting the VolumeElementsMapVolumeRegion list length");
            }
            token = tokens.nextToken();
            boolean bCompressed = token.equalsIgnoreCase("Compressed");
            if (!bCompressed) {
                if (!token.equalsIgnoreCase("UnCompressed")) {
                    throw new MathFormatException("unexpected token " + token + " expecting Compress or UnCompress");
                }
            }
            byte[] volumeElementMap = new byte[numVolumeElements];
            int checkCount = 0;
            if (bCompressed) {
                // Get HEX encoded bytes of the compressed VolumeElements-RegionID Map
                StringBuffer hexOfCompressed = new StringBuffer();
                while (tokens.hasMoreTokens()) {
                    token = tokens.nextToken();
                    if (token.equalsIgnoreCase(VCML.EndBlock)) {
                        break;
                    }
                    hexOfCompressed.append(token);
                }
                // Un-HEX the compressed data
                byte[] compressedData = Hex.toBytes(hexOfCompressed.toString());
                try {
                    meshRegionInfo.setCompressedVolumeElementMapVolumeRegion(compressedData, numVolumeElements);
                } catch (IOException e) {
                    throw new MathFormatException("CartesianMesh.read->VolumeElementsMapVolumeRegion " + e.toString());
                }
                checkCount = meshRegionInfo.getUncompressedVolumeElementMapVolumeRegionLength();
            } else {
                while (tokens.hasMoreTokens()) {
                    token = tokens.nextToken();
                    if (token.equalsIgnoreCase(VCML.EndBlock)) {
                        break;
                    }
                    try {
                        int volumeRegionID = Integer.valueOf(token).intValue();
                        volumeElementMap[checkCount] = (byte) volumeRegionID;
                    } catch (NumberFormatException e) {
                        throw new MathFormatException("expected:  # # #");
                    }
                    checkCount += 1;
                }
            }
            if (checkCount != numVolumeElements && checkCount != 2 * numVolumeElements) {
                throw new MathFormatException("CartesianMesh.read->VolumeElementsMapVolumeRegion: read " + checkCount + " VolumeElements but was expecting " + numVolumeElements);
            }
            continue;
        }
        // 
        // 
        // 
        HashMap<Integer, Integer> volumeRegionMapSubvolume = getVolumeRegionMapSubvolume(meshRegionInfo);
        if (token.equalsIgnoreCase(VCML.MembraneElements)) {
            // 
            // read '{'
            // 
            token = tokens.nextToken();
            if (!token.equalsIgnoreCase(VCML.BeginBlock)) {
                throw new MathFormatException("unexpected token " + token + " expecting " + VCML.BeginBlock);
            }
            token = tokens.nextToken();
            int numMemElements = 0;
            try {
                numMemElements = Integer.valueOf(token).intValue();
            } catch (NumberFormatException e) {
                throw new MathFormatException("unexpected token " + token + " expecting the membraneElement list length");
            }
            // 
            // read list of the following format:
            // 
            // memIndex insideVolIndex outsideVolIndex
            // 
            membraneElements = new MembraneElement[numMemElements];
            int index = 0;
            int[] membraneElementMapMembraneRegion = null;
            if (bRegions) {
                membraneElementMapMembraneRegion = new int[numMemElements];
                meshRegionInfo.mapMembraneElementsToMembraneRegions(membraneElementMapMembraneRegion);
            }
            // 
            while (tokens.hasMoreTokens()) {
                token = tokens.nextToken();
                if (token.equalsIgnoreCase(VCML.EndBlock)) {
                    break;
                }
                int memIndex = -1;
                int insideIndex = -1;
                int outsideIndex = -1;
                try {
                    // 
                    // read first three tokens of a membrane element
                    // 
                    // membraneIndex   insideIndex    outsideIndex
                    // 
                    memIndex = Integer.valueOf(token).intValue();
                    token = tokens.nextToken();
                    insideIndex = Integer.valueOf(token).intValue();
                    token = tokens.nextToken();
                    outsideIndex = Integer.valueOf(token).intValue();
                    if (subdomainInfo != null) {
                        int insideRegionIndex = meshRegionInfo.getVolumeElementMapVolumeRegion(insideIndex);
                        int outsideRegionIndex = meshRegionInfo.getVolumeElementMapVolumeRegion(outsideIndex);
                        int insideSubVolumeHandle = volumeRegionMapSubvolume.get(insideRegionIndex);
                        int outsideSubVolumeHandle = volumeRegionMapSubvolume.get(outsideRegionIndex);
                        int realInsideSubVolumeHandle = subdomainInfo.getInside(insideSubVolumeHandle, outsideSubVolumeHandle);
                        if (realInsideSubVolumeHandle != insideSubVolumeHandle) {
                            int temp = insideIndex;
                            insideIndex = outsideIndex;
                            outsideIndex = temp;
                        }
                    }
                } catch (NumberFormatException e) {
                    throw new MathFormatException("expected:  # # #");
                }
                MembraneElement me = null;
                // 
                if (bConnectivity) {
                    try {
                        token = tokens.nextToken();
                        int neighbor1 = Integer.valueOf(token).intValue();
                        token = tokens.nextToken();
                        int neighbor2 = Integer.valueOf(token).intValue();
                        token = tokens.nextToken();
                        int neighbor3 = Integer.valueOf(token).intValue();
                        token = tokens.nextToken();
                        int neighbor4 = Integer.valueOf(token).intValue();
                        // 
                        if (bRegions) {
                            token = tokens.nextToken();
                            int regionID = Integer.valueOf(token).intValue();
                            membraneElementMapMembraneRegion[memIndex] = regionID;
                        }
                        if (membraneMeshMetrics == null) {
                            me = new MembraneElement(memIndex, insideIndex, outsideIndex, neighbor1, neighbor2, neighbor3, neighbor4, MembraneElement.AREA_UNDEFINED, 0, 0, 0, 0, 0, 0);
                        } else {
                            me = new MembraneElement(memIndex, insideIndex, outsideIndex, neighbor1, neighbor2, neighbor3, neighbor4, membraneMeshMetrics.areas[memIndex], membraneMeshMetrics.normals[memIndex][0], membraneMeshMetrics.normals[memIndex][1], membraneMeshMetrics.normals[memIndex][2], membraneMeshMetrics.centroids[memIndex][0], membraneMeshMetrics.centroids[memIndex][1], membraneMeshMetrics.centroids[memIndex][2]);
                        }
                    } catch (NumberFormatException e) {
                        throw new MathFormatException("expected:  # # # # # # #");
                    }
                } else {
                    me = new MembraneElement(memIndex, insideIndex, outsideIndex);
                }
                membraneElements[index] = me;
                index++;
            }
            continue;
        }
        if (token.equalsIgnoreCase(VCML.ContourElements)) {
            // 
            // read '{'
            // 
            token = tokens.nextToken();
            if (!token.equalsIgnoreCase(VCML.BeginBlock)) {
                throw new MathFormatException("unexpected token " + token + " expecting " + VCML.BeginBlock);
            }
            token = tokens.nextToken();
            int numContourElements = 0;
            try {
                numContourElements = Integer.valueOf(token).intValue();
            } catch (NumberFormatException e) {
                throw new MathFormatException("unexpected token " + token + " expecting the contourElement list length");
            }
            // 
            // read list of the following format:
            // 
            // contourIndex volumeIndex beginCoord endCoord prevIndex nextIndex
            // 
            contourElements = new ContourElement[numContourElements];
            int index = 0;
            // 
            while (tokens.hasMoreTokens()) {
                token = tokens.nextToken();
                if (token.equalsIgnoreCase(VCML.EndBlock)) {
                    break;
                }
                ContourElement ce = null;
                try {
                    // 
                    // read first two tokens of a contour element
                    // 
                    // contourIndex volumeIndex
                    // 
                    int contourIndex = Integer.valueOf(token).intValue();
                    token = tokens.nextToken();
                    int volumeIndex = Integer.valueOf(token).intValue();
                    token = tokens.nextToken();
                    // 
                    // read beginCoord endCoord
                    // 
                    double beginX = Double.valueOf(token).doubleValue();
                    token = tokens.nextToken();
                    double beginY = Double.valueOf(token).doubleValue();
                    token = tokens.nextToken();
                    double beginZ = Double.valueOf(token).doubleValue();
                    token = tokens.nextToken();
                    double endX = Double.valueOf(token).doubleValue();
                    token = tokens.nextToken();
                    double endY = Double.valueOf(token).doubleValue();
                    token = tokens.nextToken();
                    double endZ = Double.valueOf(token).doubleValue();
                    token = tokens.nextToken();
                    Coordinate begin = new Coordinate(beginX, beginY, beginZ);
                    Coordinate end = new Coordinate(endX, endY, endZ);
                    // 
                    // read last two tokens of a contour element
                    // 
                    // prevContourIndex nextContourIndex
                    // 
                    int prevContourIndex = Integer.valueOf(token).intValue();
                    token = tokens.nextToken();
                    int nextContourIndex = Integer.valueOf(token).intValue();
                    ce = new ContourElement(contourIndex, volumeIndex, begin, end, prevContourIndex, nextContourIndex);
                } catch (NumberFormatException e) {
                    throw new MathFormatException("expected:  %d %d   %f %f %f    %f %f %f   %d %d");
                }
                contourElements[index] = ce;
                index++;
            }
            continue;
        }
        throw new MathFormatException("unexpected identifier " + token);
    }
    int dimension = getGeometryDimension(size);
    switch(dimension) {
        case 1:
            {
                if (extent.y != 1 || extent.z != 1) {
                    System.out.println("Extent " + extent.toString() + " for a 1-D mesh truncated to 1 for y and z");
                    extent = new Vect3D(extent.x, 1.0, 1.0);
                }
                break;
            }
        case 2:
            {
                if (extent.z != 1) {
                    System.out.println("Extent " + extent.toString() + " for a 2-D mesh truncated to 1 for z");
                    extent = new Vect3D(extent.x, extent.y, 1.0);
                }
                break;
            }
    }
    CartesianMesh mesh = new CartesianMesh(version, subdomainInfo, membraneElements, contourElements, meshRegionInfo, size, extent, origin, dimension);
    return mesh;
}

Example 2 with MembraneElement

use of org.vcell.vis.vcell.MembraneElement 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;
}