Examples with ISize org.vcell.util.ISize used on opensource projects

Example 91 with ISize

use of org.vcell.util.ISize in project vcell by virtualcell.

the class SmoldynFileWriter method writeInitialConcentration.

private int writeInitialConcentration(ParticleInitialConditionConcentration initialConcentration, SubDomain subDomain, Variable variable, String variableName, StringBuilder sb) throws ExpressionException, MathException {
    SimpleSymbolTable simpleSymbolTable = new SimpleSymbolTable(new String[] { ReservedVariable.X.getName(), ReservedVariable.Y.getName(), ReservedVariable.Z.getName() });
    Expression disExpression = new Expression(initialConcentration.getDistribution());
    disExpression.bindExpression(simulationSymbolTable);
    disExpression = simulationSymbolTable.substituteFunctions(disExpression).flatten();
    disExpression.bindExpression(simpleSymbolTable);
    double[] values = new double[3];
    if (dimension == 1) {
        if (disExpression.getSymbolBinding(ReservedVariable.Y.getName()) != null || disExpression.getSymbolBinding(ReservedVariable.Z.getName()) != null) {
            throw new MathException(VCellErrorMessages.getSmoldynWrongCoordinates("'y' or 'z'", dimension, variable, disExpression));
        }
    } else if (dimension == 2) {
        if (disExpression.getSymbolBinding(ReservedVariable.Z.getName()) != null) {
            throw new MathException(VCellErrorMessages.getSmoldynWrongCoordinates("'z'", dimension, variable, disExpression));
        }
    }
    int totalCount = 0;
    StringBuilder localsb = new StringBuilder();
    if (subDomain instanceof CompartmentSubDomain) {
        MeshSpecification meshSpecification = simulation.getMeshSpecification();
        ISize sampleSize = meshSpecification.getSamplingSize();
        int numX = sampleSize.getX();
        int numY = dimension < 2 ? 1 : sampleSize.getY();
        int numZ = dimension < 3 ? 1 : sampleSize.getZ();
        boolean bCellCentered = simulation.hasCellCenteredMesh();
        double dx = meshSpecification.getDx(bCellCentered);
        double dy = meshSpecification.getDy(bCellCentered);
        double dz = meshSpecification.getDz(bCellCentered);
        Origin origin = resampledGeometry.getGeometrySpec().getOrigin();
        double ox = origin.getX();
        double oy = origin.getY();
        double oz = origin.getZ();
        Extent extent = resampledGeometry.getExtent();
        double ex = extent.getX();
        double ey = extent.getY();
        double ez = extent.getZ();
        int offset = 0;
        for (int k = 0; k < numZ; k++) {
            double centerz = oz + k * dz;
            double loz = Math.max(oz, centerz - dz / 2);
            double hiz = Math.min(oz + ez, centerz + dz / 2);
            double lz = hiz - loz;
            values[2] = centerz;
            for (int j = 0; j < numY; j++) {
                double centery = oy + j * dy;
                double loy = Math.max(oy, centery - dy / 2);
                double hiy = Math.min(oy + ey, centery + dy / 2);
                values[1] = centery;
                double ly = hiy - loy;
                for (int i = 0; i < numX; i++) {
                    int regionIndex = resampledGeometry.getGeometrySurfaceDescription().getRegionImage().getRegionInfoFromOffset(offset).getRegionIndex();
                    offset++;
                    GeometricRegion region = resampledGeometry.getGeometrySurfaceDescription().getGeometricRegions(regionIndex);
                    if (region instanceof VolumeGeometricRegion) {
                        if (!((VolumeGeometricRegion) region).getSubVolume().getName().equals(subDomain.getName())) {
                            continue;
                        }
                    }
                    double centerx = ox + i * dx;
                    double lox = Math.max(ox, centerx - dx / 2);
                    double hix = Math.min(ox + ex, centerx + dx / 2);
                    double lx = hix - lox;
                    values[0] = centerx;
                    double volume = lx;
                    if (dimension > 1) {
                        volume *= ly;
                        if (dimension > 2) {
                            volume *= lz;
                        }
                    }
                    double expectedCount = disExpression.evaluateVector(values) * volume;
                    if (expectedCount <= 0) {
                        continue;
                    }
                    long count = dist.nextPoisson(expectedCount);
                    if (count <= 0) {
                        continue;
                    }
                    totalCount += count;
                    localsb.append(SmoldynVCellMapper.SmoldynKeyword.mol + " " + count + " " + variableName + " " + (float) lox + "-" + (float) hix);
                    if (lg.isDebugEnabled()) {
                        lg.debug("Component subdomain " + variableName + " count " + count);
                    }
                    if (dimension > 1) {
                        localsb.append(" " + loy + "-" + hiy);
                        if (dimension > 2) {
                            localsb.append(" " + loz + "-" + hiz);
                        }
                    }
                    localsb.append("\n");
                }
            }
        }
        // otherwise we append the distributed molecules in different small boxes
        try {
            subsituteFlattenToConstant(disExpression);
            sb.append(SmoldynVCellMapper.SmoldynKeyword.compartment_mol);
            sb.append(" " + totalCount + " " + variableName + " " + subDomain.getName() + "\n");
        } catch (// can not be evaluated to a constant
        Exception e) {
            sb.append(localsb);
        }
    } else if (subDomain instanceof MembraneSubDomain) {
        ArrayList<TrianglePanel> trianglePanelList = membraneSubdomainTriangleMap.get(subDomain);
        for (TrianglePanel trianglePanel : trianglePanelList) {
            Triangle triangle = trianglePanel.triangle;
            switch(dimension) {
                case 1:
                    values[0] = triangle.getNodes(0).getX();
                    break;
                case 2:
                    {
                        double centroidX = triangle.getNodes(0).getX();
                        double centroidY = triangle.getNodes(0).getY();
                        if (triangle.getNodes(0).getX() == triangle.getNodes(1).getX() && triangle.getNodes(0).getY() == triangle.getNodes(1).getY()) {
                            centroidX += triangle.getNodes(2).getX();
                            centroidY += triangle.getNodes(2).getY();
                        } else {
                            centroidX += triangle.getNodes(1).getX();
                            centroidY += triangle.getNodes(1).getY();
                        }
                        values[0] = centroidX / 2;
                        values[1] = centroidY / 2;
                        break;
                    }
                case 3:
                    {
                        double centroidX = triangle.getNodes(0).getX() + triangle.getNodes(1).getX() + triangle.getNodes(2).getX();
                        double centroidY = triangle.getNodes(0).getY() + triangle.getNodes(1).getY() + triangle.getNodes(2).getY();
                        double centroidZ = triangle.getNodes(0).getZ() + triangle.getNodes(1).getZ() + triangle.getNodes(2).getZ();
                        values[0] = centroidX / 3;
                        values[1] = centroidY / 3;
                        values[2] = centroidZ / 3;
                        break;
                    }
            }
            double expectedCount = disExpression.evaluateVector(values) * triangle.getArea();
            if (expectedCount <= 0) {
                continue;
            }
            long count = dist.nextPoisson(expectedCount);
            if (count <= 0) {
                continue;
            }
            totalCount += count;
            if (lg.isDebugEnabled()) {
                lg.debug("Membrane subdomain " + subDomain.getName() + ' ' + variableName + " count " + count);
            }
            localsb.append(SmoldynVCellMapper.SmoldynKeyword.surface_mol + " " + count + " " + variableName + " " + subDomain.getName() + " " + SmoldynVCellMapper.SmoldynKeyword.tri + " " + trianglePanel.name + "\n");
        }
        // otherwise we append the distributed molecules in different small boxes
        try {
            subsituteFlattenToConstant(disExpression);
            sb.append(SmoldynVCellMapper.SmoldynKeyword.surface_mol);
            sb.append(" " + totalCount + " " + variableName + " " + subDomain.getName() + " " + SmoldynVCellMapper.SmoldynKeyword.all + " " + SmoldynVCellMapper.SmoldynKeyword.all + "\n");
        } catch (// can not be evaluated to a constant
        Exception e) {
            sb.append(localsb);
        }
    }
    if (lg.isDebugEnabled()) {
        lg.debug("Subdomain " + subDomain.getName() + ' ' + variableName + " total count " + totalCount);
    }
    return totalCount;
}

Example 92 with ISize

use of org.vcell.util.ISize in project vcell by virtualcell.

the class SmoldynFileWriter method writeWallSurfaces.

private void writeWallSurfaces() throws SolverException {
    GeometrySurfaceDescription geometrySurfaceDescription = resampledGeometry.getGeometrySurfaceDescription();
    GeometrySpec geometrySpec = resampledGeometry.getGeometrySpec();
    SubVolume[] subVolumes = geometrySpec.getSubVolumes();
    printWriter.println("# boundaries");
    Origin origin = geometrySpec.getOrigin();
    Extent extent = geometrySpec.getExtent();
    Coordinate lowWall = new Coordinate(origin.getX(), origin.getY(), origin.getZ());
    Coordinate highWall = new Coordinate(origin.getX() + extent.getX(), origin.getY() + extent.getY(), origin.getZ() + extent.getZ());
    // potential artifact.
    if (bHasNoSurface) {
        SubDomain subDomain0 = mathDesc.getSubDomains().nextElement();
        CompartmentSubDomain compartSubDomain0 = null;
        compartSubDomain0 = (CompartmentSubDomain) subDomain0;
        // x
        if (compartSubDomain0.getBoundaryConditionXm().isPERIODIC()) {
            printWriter.println(SmoldynVCellMapper.SmoldynKeyword.boundaries + " 0 " + lowWall.getX() + " " + highWall.getX() + " " + SmoldynVCellMapper.SmoldynKeyword.p);
        } else {
            printWriter.println(SmoldynVCellMapper.SmoldynKeyword.low_wall + " 0 " + lowWall.getX() + " " + (compartSubDomain0.getBoundaryConditionXm().isNEUMANN() ? SmoldynVCellMapper.SmoldynKeyword.r : SmoldynVCellMapper.SmoldynKeyword.a));
            printWriter.println(SmoldynVCellMapper.SmoldynKeyword.high_wall + " 0 " + highWall.getX() + " " + (compartSubDomain0.getBoundaryConditionXp().isNEUMANN() ? SmoldynVCellMapper.SmoldynKeyword.r : SmoldynVCellMapper.SmoldynKeyword.a));
        }
        if (dimension > 1) {
            // y
            if (compartSubDomain0.getBoundaryConditionYm().isPERIODIC()) {
                printWriter.println(SmoldynVCellMapper.SmoldynKeyword.boundaries + " 1 " + lowWall.getY() + " " + highWall.getY() + " " + SmoldynVCellMapper.SmoldynKeyword.p);
            } else {
                printWriter.println(SmoldynVCellMapper.SmoldynKeyword.low_wall + " 1 " + lowWall.getY() + " " + (compartSubDomain0.getBoundaryConditionYm().isNEUMANN() ? SmoldynVCellMapper.SmoldynKeyword.r : SmoldynVCellMapper.SmoldynKeyword.a));
                printWriter.println(SmoldynVCellMapper.SmoldynKeyword.high_wall + " 1 " + highWall.getY() + " " + (compartSubDomain0.getBoundaryConditionYp().isNEUMANN() ? SmoldynVCellMapper.SmoldynKeyword.r : SmoldynVCellMapper.SmoldynKeyword.a));
            }
            if (dimension > 2) {
                // z
                if (compartSubDomain0.getBoundaryConditionZm().isPERIODIC()) {
                    printWriter.println(SmoldynVCellMapper.SmoldynKeyword.boundaries + " 2 " + lowWall.getZ() + " " + highWall.getZ() + " " + SmoldynVCellMapper.SmoldynKeyword.p);
                } else {
                    printWriter.println(SmoldynVCellMapper.SmoldynKeyword.low_wall + " 2 " + lowWall.getZ() + " " + (compartSubDomain0.getBoundaryConditionZm().isNEUMANN() ? SmoldynVCellMapper.SmoldynKeyword.r : SmoldynVCellMapper.SmoldynKeyword.a));
                    printWriter.println(SmoldynVCellMapper.SmoldynKeyword.high_wall + " 2 " + highWall.getZ() + " " + (compartSubDomain0.getBoundaryConditionZp().isNEUMANN() ? SmoldynVCellMapper.SmoldynKeyword.r : SmoldynVCellMapper.SmoldynKeyword.a));
                }
            }
        }
        printWriter.println();
    } else {
        // x
        printWriter.println(SmoldynVCellMapper.SmoldynKeyword.boundaries + " 0 " + lowWall.getX() + " " + highWall.getX());
        if (dimension > 1) {
            // y
            printWriter.println(SmoldynVCellMapper.SmoldynKeyword.boundaries + " 1 " + lowWall.getY() + " " + highWall.getY());
            if (dimension > 2) {
                // z
                printWriter.println(SmoldynVCellMapper.SmoldynKeyword.boundaries + " 2 " + lowWall.getZ() + " " + highWall.getZ());
            }
        }
        printWriter.println();
        // bounding walls as surfaces
        // have to find boundary condition type
        ISize sampleSize = simulation.getMeshSpecification().getSamplingSize();
        int numX = sampleSize.getX();
        int numY = dimension < 2 ? 1 : sampleSize.getY();
        int numZ = dimension < 3 ? 1 : sampleSize.getZ();
        if (dimension > 2) {
            int[] k_wall = new int[] { 0, numZ - 1 };
            for (int k = 0; k < k_wall.length; k++) {
                for (int j = 0; j < numY; j++) {
                    for (int i = 0; i < numX; i++) {
                        int volIndex = k_wall[k] * numX * numY + j * numX + i;
                        for (SubVolume sv : subVolumes) {
                            // gather all the points in all the regions
                            GeometricRegion[] geometricRegions = geometrySurfaceDescription.getGeometricRegions(sv);
                            RegionInfo[] regionInfos = geometrySurfaceDescription.getRegionImage().getRegionInfos();
                            for (GeometricRegion gr : geometricRegions) {
                                VolumeGeometricRegion vgr = (VolumeGeometricRegion) gr;
                                for (RegionInfo ri : regionInfos) {
                                    if (ri.getRegionIndex() == vgr.getRegionID() && ri.isIndexInRegion(volIndex)) {
                                        boundaryZSubVolumes.add(sv);
                                    }
                                }
                            }
                        }
                    }
                }
            }
        }
        if (dimension > 1) {
            int[] j_wall = new int[] { 0, numY - 1 };
            for (int k = 0; k < numZ; k++) {
                for (int j = 0; j < j_wall.length; j++) {
                    for (int i = 0; i < numX; i++) {
                        int volIndex = k * numX * numY + j_wall[j] * numX + i;
                        for (SubVolume sv : subVolumes) {
                            // gather all the points in all the regions
                            GeometricRegion[] geometricRegions = geometrySurfaceDescription.getGeometricRegions(sv);
                            RegionInfo[] regionInfos = geometrySurfaceDescription.getRegionImage().getRegionInfos();
                            for (GeometricRegion gr : geometricRegions) {
                                VolumeGeometricRegion vgr = (VolumeGeometricRegion) gr;
                                for (RegionInfo ri : regionInfos) {
                                    if (ri.getRegionIndex() == vgr.getRegionID() && ri.isIndexInRegion(volIndex)) {
                                        boundaryYSubVolumes.add(sv);
                                    }
                                }
                            }
                        }
                    }
                }
            }
        }
        int[] i_wall = new int[] { 0, numX - 1 };
        for (int k = 0; k < numZ; k++) {
            for (int j = 0; j < numY; j++) {
                for (int i = 0; i < i_wall.length; i++) {
                    int volIndex = k * numX * numY + j * numX + i_wall[i];
                    for (SubVolume sv : subVolumes) {
                        // gather all the points in all the regions
                        GeometricRegion[] geometricRegions = geometrySurfaceDescription.getGeometricRegions(sv);
                        RegionInfo[] regionInfos = geometrySurfaceDescription.getRegionImage().getRegionInfos();
                        for (GeometricRegion gr : geometricRegions) {
                            VolumeGeometricRegion vgr = (VolumeGeometricRegion) gr;
                            for (RegionInfo ri : regionInfos) {
                                if (ri.getRegionIndex() == vgr.getRegionID() && ri.isIndexInRegion(volIndex)) {
                                    boundaryXSubVolumes.add(sv);
                                }
                            }
                        }
                    }
                }
            }
        }
        Set<SubVolume> boundarySubVolumes = new HashSet<SubVolume>();
        boundarySubVolumes.addAll(boundaryXSubVolumes);
        boundarySubVolumes.addAll(boundaryYSubVolumes);
        boundarySubVolumes.addAll(boundaryZSubVolumes);
        BoundaryConditionType[] computedBct = new BoundaryConditionType[dimension * 2];
        String[] smoldynBct = new String[dimension * 2];
        String[] wallNames = new String[] { "Xm", "Xp", "Ym", "Yp", "Zm", "Zp" };
        if (boundarySubVolumes.size() >= 1) {
            for (SubVolume sv : boundarySubVolumes) {
                CompartmentSubDomain csd = (CompartmentSubDomain) mathDesc.getSubDomain(sv.getName());
                BoundaryConditionType[] bct = new BoundaryConditionType[] { csd.getBoundaryConditionXm(), csd.getBoundaryConditionXp(), csd.getBoundaryConditionYm(), csd.getBoundaryConditionYp(), csd.getBoundaryConditionZm(), csd.getBoundaryConditionZp() };
                if (computedBct[0] == null) {
                    System.arraycopy(bct, 0, computedBct, 0, dimension * 2);
                    for (int i = 0; i < dimension * 2; i++) {
                        if (computedBct[i].isPERIODIC()) {
                            throw new SolverException("Models with both surfaces and periodic boundary conditions are not supported yet.");
                        }
                        smoldynBct[i] = computedBct[i].isDIRICHLET() ? SmoldynVCellMapper.SmoldynKeyword.absorb.name() : SmoldynVCellMapper.SmoldynKeyword.reflect.name();
                    }
                } else {
                    for (int i = 0; i < dimension * 2; i++) {
                        if (!computedBct[i].compareEqual(bct[i])) {
                            throw new SolverException(wallNames[i] + " wall has different boundary conditions");
                        }
                    }
                }
            }
        }
        printWriter.println("# bounding wall surface");
        // X walls
        printWriter.println(SmoldynVCellMapper.SmoldynKeyword.start_surface + " " + VCellSmoldynKeyword.bounding_wall_surface_X);
        printWriter.println(SmoldynVCellMapper.SmoldynKeyword.action + " " + SmoldynVCellMapper.SmoldynKeyword.all + "(" + SmoldynVCellMapper.SmoldynKeyword.up + ") " + SmoldynVCellMapper.SmoldynKeyword.both + " " + SmoldynVCellMapper.SmoldynKeyword.reflect);
        printWriter.println(SmoldynVCellMapper.SmoldynKeyword.action + " " + SmoldynVCellMapper.SmoldynKeyword.all + " " + SmoldynVCellMapper.SmoldynKeyword.front + " " + smoldynBct[0]);
        printWriter.println(SmoldynVCellMapper.SmoldynKeyword.action + " " + SmoldynVCellMapper.SmoldynKeyword.all + " " + SmoldynVCellMapper.SmoldynKeyword.back + " " + smoldynBct[1]);
        printWriter.println(SmoldynVCellMapper.SmoldynKeyword.color + " " + SmoldynVCellMapper.SmoldynKeyword.both + " 1 1 1");
        printWriter.println(SmoldynVCellMapper.SmoldynKeyword.polygon + " " + SmoldynVCellMapper.SmoldynKeyword.both + " " + SmoldynVCellMapper.SmoldynKeyword.edge);
        printWriter.println(SmoldynVCellMapper.SmoldynKeyword.max_panels + " " + SmoldynVCellMapper.SmoldynKeyword.rect + " 2");
        // yz walls
        switch(dimension) {
            case 1:
                printWriter.println(SmoldynVCellMapper.SmoldynKeyword.panel + " " + SmoldynVCellMapper.SmoldynKeyword.rect + " +0 " + lowWall.getX());
                printWriter.println(SmoldynVCellMapper.SmoldynKeyword.panel + " " + SmoldynVCellMapper.SmoldynKeyword.rect + " -0 " + highWall.getX());
                break;
            case 2:
                printWriter.println(SmoldynVCellMapper.SmoldynKeyword.panel + " " + SmoldynVCellMapper.SmoldynKeyword.rect + " +0 " + lowWall.getX() + " " + lowWall.getY() + " " + extent.getY());
                printWriter.println(SmoldynVCellMapper.SmoldynKeyword.panel + " " + SmoldynVCellMapper.SmoldynKeyword.rect + " -0 " + highWall.getX() + " " + lowWall.getY() + " " + extent.getY());
                break;
            case 3:
                printWriter.println(SmoldynVCellMapper.SmoldynKeyword.panel + " " + SmoldynVCellMapper.SmoldynKeyword.rect + " +0 " + lowWall.getX() + " " + lowWall.getY() + " " + lowWall.getZ() + " " + extent.getY() + " " + extent.getZ());
                printWriter.println(SmoldynVCellMapper.SmoldynKeyword.panel + " " + SmoldynVCellMapper.SmoldynKeyword.rect + " -0 " + highWall.getX() + " " + lowWall.getY() + " " + lowWall.getZ() + " " + extent.getY() + " " + extent.getZ());
                break;
        }
        printWriter.println(SmoldynVCellMapper.SmoldynKeyword.end_surface);
        printWriter.println();
        if (dimension > 1) {
            // Y walls
            printWriter.println(SmoldynVCellMapper.SmoldynKeyword.start_surface + " " + VCellSmoldynKeyword.bounding_wall_surface_Y);
            printWriter.println(SmoldynVCellMapper.SmoldynKeyword.action + " " + SmoldynVCellMapper.SmoldynKeyword.all + "(" + SmoldynVCellMapper.SmoldynKeyword.up + ") " + SmoldynVCellMapper.SmoldynKeyword.both + " " + SmoldynVCellMapper.SmoldynKeyword.reflect);
            printWriter.println(SmoldynVCellMapper.SmoldynKeyword.action + " " + SmoldynVCellMapper.SmoldynKeyword.all + " " + SmoldynVCellMapper.SmoldynKeyword.front + " " + smoldynBct[2]);
            printWriter.println(SmoldynVCellMapper.SmoldynKeyword.action + " " + SmoldynVCellMapper.SmoldynKeyword.all + " " + SmoldynVCellMapper.SmoldynKeyword.back + " " + smoldynBct[3]);
            printWriter.println(SmoldynVCellMapper.SmoldynKeyword.color + " " + SmoldynVCellMapper.SmoldynKeyword.both + " 1 1 1");
            printWriter.println(SmoldynVCellMapper.SmoldynKeyword.polygon + " " + SmoldynVCellMapper.SmoldynKeyword.both + " " + SmoldynVCellMapper.SmoldynKeyword.edge);
            printWriter.println(SmoldynVCellMapper.SmoldynKeyword.max_panels + " " + SmoldynVCellMapper.SmoldynKeyword.rect + " 2");
            // xz walls
            switch(dimension) {
                case 2:
                    printWriter.println(SmoldynVCellMapper.SmoldynKeyword.panel + " " + SmoldynVCellMapper.SmoldynKeyword.rect + " +1 " + lowWall.getX() + " " + lowWall.getY() + " " + extent.getX());
                    printWriter.println(SmoldynVCellMapper.SmoldynKeyword.panel + " " + SmoldynVCellMapper.SmoldynKeyword.rect + " -1 " + lowWall.getX() + " " + highWall.getY() + " " + extent.getX());
                    break;
                case 3:
                    printWriter.println(SmoldynVCellMapper.SmoldynKeyword.panel + " " + SmoldynVCellMapper.SmoldynKeyword.rect + " +1 " + lowWall.getX() + " " + lowWall.getY() + " " + lowWall.getZ() + " " + extent.getX() + " " + extent.getZ());
                    printWriter.println(SmoldynVCellMapper.SmoldynKeyword.panel + " " + SmoldynVCellMapper.SmoldynKeyword.rect + " -1 " + lowWall.getX() + " " + highWall.getY() + " " + lowWall.getZ() + " " + extent.getX() + " " + extent.getZ());
                    break;
            }
            printWriter.println(SmoldynVCellMapper.SmoldynKeyword.end_surface);
            printWriter.println();
            if (dimension > 2) {
                // Z walls
                printWriter.println(SmoldynVCellMapper.SmoldynKeyword.start_surface + " " + VCellSmoldynKeyword.bounding_wall_surface_Z);
                printWriter.println(SmoldynVCellMapper.SmoldynKeyword.action + " " + SmoldynVCellMapper.SmoldynKeyword.all + "(" + SmoldynVCellMapper.SmoldynKeyword.up + ") " + SmoldynVCellMapper.SmoldynKeyword.both + " " + SmoldynVCellMapper.SmoldynKeyword.reflect);
                printWriter.println(SmoldynVCellMapper.SmoldynKeyword.action + " " + SmoldynVCellMapper.SmoldynKeyword.all + " " + SmoldynVCellMapper.SmoldynKeyword.front + " " + smoldynBct[4]);
                printWriter.println(SmoldynVCellMapper.SmoldynKeyword.action + " " + SmoldynVCellMapper.SmoldynKeyword.all + " " + SmoldynVCellMapper.SmoldynKeyword.back + " " + smoldynBct[5]);
                printWriter.println(SmoldynVCellMapper.SmoldynKeyword.color + " " + SmoldynVCellMapper.SmoldynKeyword.both + " 1 1 1");
                printWriter.println(SmoldynVCellMapper.SmoldynKeyword.polygon + " " + SmoldynVCellMapper.SmoldynKeyword.both + " " + SmoldynVCellMapper.SmoldynKeyword.edge);
                printWriter.println(SmoldynVCellMapper.SmoldynKeyword.max_panels + " " + SmoldynVCellMapper.SmoldynKeyword.rect + " 2");
                // xy walls
                printWriter.println(SmoldynVCellMapper.SmoldynKeyword.panel + " " + SmoldynVCellMapper.SmoldynKeyword.rect + " +2 " + lowWall.getX() + " " + lowWall.getY() + " " + lowWall.getZ() + " " + extent.getX() + " " + extent.getY());
                printWriter.println(SmoldynVCellMapper.SmoldynKeyword.panel + " " + SmoldynVCellMapper.SmoldynKeyword.rect + " -2 " + lowWall.getX() + " " + lowWall.getY() + " " + highWall.getZ() + " " + extent.getX() + " " + extent.getY());
                printWriter.println(SmoldynVCellMapper.SmoldynKeyword.end_surface);
                printWriter.println();
            }
        }
    }
}

Example 93 with ISize

use of org.vcell.util.ISize in project vcell by virtualcell.

the class SmoldynFileWriter method writeRuntimeCommands.

// uncomment for debug
/*private void writeGraphicsLegend() throws MathException{
	try {
		java.awt.image.BufferedImage cmapImage = new java.awt.image.BufferedImage(200, particleVariableList.size()*30,java.awt.image.BufferedImage.TYPE_INT_RGB);
		Graphics g = cmapImage.getGraphics();
		for (int i = 0; i < particleVariableList.size(); i ++) {
			Color c = colors[i];
			System.out.println("color for legend: " + "red--"+ c.getRed() + "  green--" + c.getGreen() + "  blue--" + c.getBlue());
			String variableName = getVariableName(particleVariableList.get(i),null);
			g.setColor(c);
			g.drawString(variableName, 5, 30*i + 20);
			g.fillRect(105, 30*i + 10, 20, 10);
		}
		g.dispose();
		File tmpFile = File.createTempFile("legend", ".jpg");

		FileOutputStream fios = null;
		try {
			printWriter.println("# legend file: " + tmpFile.getAbsolutePath());
			fios = new FileOutputStream(tmpFile);
			ImageIO.write(cmapImage,"jpg",fios);
		}  finally {
			if(fios != null) {fios.close();}
		}
	} catch (Exception e) {
		e.printStackTrace();
		throw new MathException(e.getMessage());
	}
}*/
private void writeRuntimeCommands() throws SolverException, DivideByZeroException, DataAccessException, IOException, MathException, ExpressionException {
    printWriter.println("# " + SmoldynVCellMapper.SmoldynKeyword.killmolincmpt + " runtime command to kill molecules misplaced during initial condtions");
    for (ParticleVariable pv : particleVariableList) {
        CompartmentSubDomain varDomain = mathDesc.getCompartmentSubDomain(pv.getDomain().getName());
        if (varDomain == null) {
            continue;
        }
        boolean bkillMol = false;
        ArrayList<ParticleInitialCondition> iniConditionList = varDomain.getParticleProperties(pv).getParticleInitialConditions();
        for (ParticleInitialCondition iniCon : iniConditionList) {
            if (iniCon instanceof ParticleInitialConditionConcentration) {
                try {
                    subsituteFlattenToConstant(((ParticleInitialConditionConcentration) iniCon).getDistribution());
                } catch (// can not be evaluated to a constant
                Exception e) {
                    bkillMol = true;
                    break;
                }
            }
        }
        if (bkillMol) {
            Enumeration<SubDomain> subDomainEnumeration = mathDesc.getSubDomains();
            while (subDomainEnumeration.hasMoreElements()) {
                SubDomain subDomain = subDomainEnumeration.nextElement();
                if (subDomain instanceof CompartmentSubDomain && varDomain != subDomain) {
                    printWriter.println(SmoldynVCellMapper.SmoldynKeyword.cmd + " " + SmoldynVCellMapper.SmoldynKeyword.B + " " + SmoldynVCellMapper.SmoldynKeyword.killmolincmpt + " " + pv.getName() + "(" + SmoldynVCellMapper.SmoldynKeyword.all + ") " + subDomain.getName());
                }
            }
        }
    }
    printWriter.println();
    // write command to kill molecules on membrane for adsortption to nothing
    printWriter.println("# kill membrane molecues that are absorbed (to nothing)");
    for (String killMolCmd : killMolCommands) {
        printWriter.println(killMolCmd);
    }
    printWriter.println();
    printWriter.println("# runtime command");
    printWriter.println(SmoldynVCellMapper.SmoldynKeyword.cmd + " " + SmoldynVCellMapper.SmoldynKeyword.E + " " + VCellSmoldynKeyword.vcellPrintProgress);
    if (outputFile != null && cartesianMesh != null) {
        OutputTimeSpec ots = simulation.getSolverTaskDescription().getOutputTimeSpec();
        if (ots.isUniform()) {
            printWriter.println(SmoldynVCellMapper.SmoldynKeyword.output_files + " " + outputFile.getName());
            ISize sampleSize = simulation.getMeshSpecification().getSamplingSize();
            TimeStep timeStep = simulation.getSolverTaskDescription().getTimeStep();
            int n = (int) Math.round(((UniformOutputTimeSpec) ots).getOutputTimeStep() / timeStep.getDefaultTimeStep());
            if (simulation.getSolverTaskDescription().getSmoldynSimulationOptions().isSaveParticleLocations()) {
                printWriter.println(SmoldynVCellMapper.SmoldynKeyword.cmd + " " + SmoldynVCellMapper.SmoldynKeyword.N + " " + n + " " + SmoldynVCellMapper.SmoldynKeyword.incrementfile + " " + outputFile.getName());
                printWriter.println(SmoldynVCellMapper.SmoldynKeyword.cmd + " " + SmoldynVCellMapper.SmoldynKeyword.N + " " + n + " " + SmoldynVCellMapper.SmoldynKeyword.listmols + " " + outputFile.getName());
            }
            // DON'T CHANGE THE ORDER HERE.
            // DataProcess must be before vcellWriteOutput
            writeDataProcessor();
            printWriter.println(SmoldynVCellMapper.SmoldynKeyword.cmd + " " + SmoldynVCellMapper.SmoldynKeyword.N + " " + n + " " + VCellSmoldynKeyword.vcellWriteOutput + " begin");
            printWriter.println(SmoldynVCellMapper.SmoldynKeyword.cmd + " " + SmoldynVCellMapper.SmoldynKeyword.N + " " + n + " " + VCellSmoldynKeyword.vcellWriteOutput + " " + VCellSmoldynKeyword.dimension + " " + dimension);
            printWriter.print(SmoldynVCellMapper.SmoldynKeyword.cmd + " " + SmoldynVCellMapper.SmoldynKeyword.N + " " + n + " " + VCellSmoldynKeyword.vcellWriteOutput + " " + VCellSmoldynKeyword.sampleSize + " " + sampleSize.getX());
            if (dimension > 1) {
                printWriter.print(" " + sampleSize.getY());
                if (dimension > 2) {
                    printWriter.print(" " + sampleSize.getZ());
                }
            }
            printWriter.println();
            printWriter.println(SmoldynVCellMapper.SmoldynKeyword.cmd + " " + SmoldynVCellMapper.SmoldynKeyword.N + " " + n + " " + VCellSmoldynKeyword.vcellWriteOutput + " " + VCellSmoldynKeyword.numMembraneElements + " " + cartesianMesh.getNumMembraneElements());
            for (ParticleVariable pv : particleVariableList) {
                String type = pv instanceof MembraneParticleVariable ? VCellSmoldynKeyword.membrane.name() : VCellSmoldynKeyword.volume.name();
                printWriter.println(SmoldynVCellMapper.SmoldynKeyword.cmd + " " + SmoldynVCellMapper.SmoldynKeyword.N + " " + n + " " + VCellSmoldynKeyword.vcellWriteOutput + " " + VCellSmoldynKeyword.variable + " " + pv.getName() + " " + type + " " + pv.getDomain().getName());
            }
            printWriter.println(SmoldynVCellMapper.SmoldynKeyword.cmd + " " + SmoldynVCellMapper.SmoldynKeyword.N + " " + n + " " + VCellSmoldynKeyword.vcellWriteOutput + " end");
        } else {
            throw new SolverException(SolverDescription.Smoldyn.getDisplayLabel() + " only supports uniform output.");
        }
    }
    printWriter.println();
}

Example 94 with ISize

use of org.vcell.util.ISize in project vcell by virtualcell.

the class SmoldynSurfaceTessellator method cloneAndResample.

protected void cloneAndResample(Geometry geometry) throws Exception {
    // clone and resample geometry
    resampledGeometry = (Geometry) BeanUtils.cloneSerializable(geometry);
    GeometrySurfaceDescription geoSurfaceDesc = resampledGeometry.getGeometrySurfaceDescription();
    ISize newSize = simulation.getMeshSpecification().getSamplingSize();
    geoSurfaceDesc.setVolumeSampleSize(newSize);
    geoSurfaceDesc.updateAll();
    bHasNoSurface = geoSurfaceDesc.getSurfaceClasses() == null || geoSurfaceDesc.getSurfaceClasses().length == 0;
}

Example 95 with ISize

use of org.vcell.util.ISize in project vcell by virtualcell.

the class ROIMultiPaintManager method highlightHistogramPixels.

private void highlightHistogramPixels(final DefaultListSelectionModel histSelection) {
    final String HISTO_HIGHLIGHT = "HISTO_HIGHLIGHT";
    AsynchClientTask histoROITask = new AsynchClientTask("Calculating histogram highlight...", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            ROI highlight = overlayEditorPanelJAI.getHighliteInfo();
            if (highlight == null) {
                highlight = createEmptyROI(new ISize(roiComposite[0].getWidth(), roiComposite[0].getHeight(), roiComposite.length));
            }
            for (int i = 0; i < highlight.getRoiImages().length; i++) {
                short[] pixels = highlight.getRoiImages()[i].getPixels();
                for (int j = 0; j < pixels.length; j++) {
                    int currPixelVal = getImageDataSetChannel().getAllImages()[i].getPixels()[j] & 0x0000FFFF;
                    if (histSelection != null && histSelection.isSelectedIndex(currPixelVal)) {
                        pixels[j] = (short) 0xFFFF;
                    } else {
                        pixels[j] = 0;
                    }
                }
            }
            hashTable.put(HISTO_HIGHLIGHT, highlight);
        }
    };
    AsynchClientTask updatedisplayTask = new AsynchClientTask("Updating display...", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            overlayEditorPanelJAI.setHighliteInfo((ROI) hashTable.get(HISTO_HIGHLIGHT), OverlayEditorPanelJAI.FRAP_DATA_HISTOUPDATEHIGHLIGHT_PROPERTY);
        }
    };
    ClientTaskDispatcher.dispatch(overlayEditorPanelJAI, new Hashtable<String, Object>(), new AsynchClientTask[] { histoROITask, updatedisplayTask });
}