Examples with VCImage cbit.image.VCImage used on opensource projects

Example 11 with VCImage

use of cbit.image.VCImage in project vcell by virtualcell.

the class GeometrySpec method vetoableChange.

/**
 * Insert the method's description here.
 * Creation date: (6/3/00 9:58:08 AM)
 * @param event java.beans.PropertyChangeEvent
 */
public void vetoableChange(java.beans.PropertyChangeEvent event) throws PropertyVetoException {
    if (event.getSource() == this && event.getPropertyName().equals("image")) {
        if (event.getNewValue() != null) {
            VCImage newVCImage = (VCImage) event.getNewValue();
            if (newVCImage.getNumXYZ() > IMAGE_SIZE_LIMIT) {
                // throw new PropertyVetoException("image size "+newVCImage.getNumXYZ()+" pixels exceeded limit of "+IMAGE_SIZE_LIMIT,event);
                if (lg.isEnabledFor(Level.WARN)) {
                    lg.warn("WARNING: image size " + newVCImage.getNumXYZ() + " pixels exceeded limit of " + IMAGE_SIZE_LIMIT);
                }
            }
        }
    }
    if (event.getSource() == this && event.getPropertyName().equals("subVolumes")) {
        SubVolume[] subVolumes = (SubVolume[]) event.getNewValue();
        // 
        // add subvolumes
        // (handles must be unique and non-negative, and analytic subvolumes must be first in array)
        // 
        boolean bFoundImageSubVolume = false;
        for (int i = 0; i < subVolumes.length; i++) {
            SubVolume sv = subVolumes[i];
            // 
            if (sv.getHandle() < 0) {
                throw new PropertyVetoException("subdomain handle=" + sv.getHandle() + " must be non-negative", event);
            }
            if (sv.getName() == null || sv.getName().length() < 1) {
                throw new PropertyVetoException("Subdomain name cannot be null or blank : ", event);
            }
            // 
            for (int j = i + 1; j < subVolumes.length; j++) {
                if (subVolumes[j].getHandle() == subVolumes[i].getHandle()) {
                    throw new PropertyVetoException("subdomain handle=" + sv.getHandle() + " has already been used in geometry", event);
                }
                if (subVolumes[j].getName().equals(subVolumes[i].getName())) {
                    throw new PropertyVetoException("subdomain name=" + sv.getName() + " has already been used in geometry", event);
                }
            }
            // 
            if (sv instanceof ImageSubVolume) {
                bFoundImageSubVolume = true;
            } else if (sv instanceof AnalyticSubVolume) {
                if (bFoundImageSubVolume) {
                    throw new PropertyVetoException("subdomains are out of order, all analytic subdomains must preceed all image subdomains", event);
                }
            }
        }
        // 
        for (int i = 0; i < subVolumes.length; i++) {
            if (subVolumes[i] instanceof ImageSubVolume) {
                if (vcImage == null) {
                    throw new PropertyVetoException("adding image subdomain, an image must be set first", event);
                }
            }
        }
    // 
    // check for uniqueness of name and handles
    // check for handle values of (0..N-1)
    // 
    } else if (event.getSource() == this && event.getPropertyName().equals("extent")) {
        Extent newExtent = (Extent) event.getNewValue();
        if (newExtent == null) {
            throw new PropertyVetoException("extent cannot be null", event);
        }
        if (newExtent.getX() <= 0 || newExtent.getY() <= 0.0 || newExtent.getZ() <= 0) {
            throw new PropertyVetoException("extent must be positive in X,Y,Z", event);
        }
    } else if (event.getSource() instanceof SubVolume && event.getPropertyName().equals("name")) {
        String newName = (String) event.getNewValue();
        if (newName == null || newName.length() < 1) {
            throw new PropertyVetoException("subdomain name must be at least one character", event);
        }
        // 
        // check if name already used
        // 
        SubVolume sv = getSubVolume(newName);
        if (sv != null && sv != event.getSource()) {
            throw new PropertyVetoException("A subdomain with name '" + newName + "' already exists.", event);
        }
    }
}

Example 12 with VCImage

use of cbit.image.VCImage in project vcell by virtualcell.

the class GeometrySpec method gatherIssues.

public void gatherIssues(IssueContext issueContext, Geometry geometry, List<Issue> issueVector) {
    // 
    if (getDimension() > 0) {
        VCImage argSampledImage = getSampledImage().getCurrentValue();
        if (argSampledImage == null) {
            return;
        }
        try {
            // 
            // make sure that each sample was assigned to a SubVolume
            // 
            int count = 0;
            byte[] samples = argSampledImage.getPixels();
            for (int i = 0; i < samples.length; i++) {
                if (samples[i] == -1) {
                    count++;
                }
            }
            if (count > 0) {
                String errorMessage = "Invalid Geometry - " + count + " of " + samples.length + " samples of geometry domain didn't map to any subdomain";
                Issue issue = new Issue(geometry, issueContext, IssueCategory.SubVolumeVerificationError, errorMessage, Issue.SEVERITY_ERROR);
                issueVector.add(issue);
            }
            // 
            // make sure that each subvolume is resolved in the geometry
            // 
            ArrayList<SubVolume> missingSubVolumeList = new ArrayList<SubVolume>();
            SubVolume[] subVolumes = getSubVolumes();
            for (int i = 0; i < subVolumes.length; i++) {
                if (argSampledImage.getPixelClassFromPixelValue(subVolumes[i].getHandle()) == null) {
                    missingSubVolumeList.add(subVolumes[i]);
                }
            }
            if (missingSubVolumeList.size() > 0) {
                for (int i = 0; i < missingSubVolumeList.size(); i++) {
                    String errorMessage = "Subdomain '" + missingSubVolumeList.get(i).getName() + "' is not resolved in geometry domain";
                    Issue issue = new Issue(geometry, issueContext, IssueCategory.SubVolumeVerificationError, errorMessage, Issue.SEVERITY_ERROR);
                    issueVector.add(issue);
                }
            }
        } catch (Exception ex) {
            Issue issue = new Issue(geometry, issueContext, IssueCategory.SubVolumeVerificationError, ex.getMessage(), Issue.SEVERITY_ERROR);
            issueVector.add(issue);
        }
    }
}

Example 13 with VCImage

use of cbit.image.VCImage 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 14 with VCImage

use of cbit.image.VCImage in project vcell by virtualcell.

the class ITextWriter method generateGeometryImage.

// pretty similar to its static counterpart
/*
	protected ByteArrayOutputStream generateDocStructureImage(Model model, String resolution) throws Exception {

		if (model == null || !isValidResolutionSetting(resolution)) {
	    	throw new IllegalArgumentException("Invalid parameters for generating structure image for model:" + model.getName());
        }
		ByteArrayOutputStream bos;

		// Create a new model and clone the structures only
		// Getting rid of species so that the image created will not have a problem being added to the document
		// when there are more than 15 species in the model.
		Model sparseModel = new Model(model.getName());
		Structure[] oldStructures = (Structure[])BeanUtils.cloneSerializable(model.getStructures());
		sparseModel.setStructures(oldStructures);
		 
		StructureCartoon scartoon = new StructureCartoon();
		scartoon.setModel(sparseModel);
		scartoon.refreshAll();
		//scartoon.setZoomPercent(scartoon.getZoomPercent()*3);
		BufferedImage dummyBufferedImage = new BufferedImage(DEF_IMAGE_WIDTH, DEF_IMAGE_HEIGHT, BufferedImage.TYPE_3BYTE_BGR);
		Graphics2D dummyGraphics = (Graphics2D)dummyBufferedImage.getGraphics();
		Dimension prefDim = scartoon.getPreferedCanvasSize(dummyGraphics);
		
		int width = (int)prefDim.getWidth()*110/100;
		int height = (int)prefDim.getHeight()*110/100;
		if (width < ITextWriter.DEF_IMAGE_WIDTH) {
			width = ITextWriter.DEF_IMAGE_WIDTH;
		}
		if (height < ITextWriter.DEF_IMAGE_HEIGHT) {
			height = ITextWriter.DEF_IMAGE_HEIGHT;
		}

		BufferedImage bufferedImage = new BufferedImage(width, height, BufferedImage.TYPE_3BYTE_BGR);
		Graphics2D g = (Graphics2D)bufferedImage.getGraphics();
		g.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON);
		while (true) {
			GraphContainerLayout containerLayout = new GraphContainerLayoutVCellClassical();
			containerLayout.layout(scartoon, g, new Dimension(width,height));
			break;
		}
		scartoon.paint(g, null);
		bos = encodeJPEG(bufferedImage);
		return bos;
	}
*/
protected ByteArrayOutputStream generateGeometryImage(Geometry geom) throws Exception {
    GeometrySpec geomSpec = geom.getGeometrySpec();
    IndexColorModel icm = DisplayAdapterService.getHandleColorMap();
    geom.precomputeAll(new GeometryThumbnailImageFactoryAWT());
    VCImage geomImage = geomSpec.getSampledImage().getCurrentValue();
    if (geomImage == null) {
        throw new Exception("generateGeometryImage error : No Image");
    }
    int x = geomImage.getNumX();
    int y = geomImage.getNumY();
    int z = geomImage.getNumZ();
    BufferedImage bufferedImage = null;
    WritableRaster pixelWR = null;
    Image adjImage = null;
    BufferedImage newBufferedImage = null;
    if (geom.getDimension() > 0 && geom.getDimension() < 3) {
        bufferedImage = new BufferedImage(x, y, BufferedImage.TYPE_BYTE_INDEXED, icm);
        pixelWR = bufferedImage.getRaster();
        for (int i = 0; i < x; i++) {
            for (int j = 0; j < y; j++) {
                pixelWR.setSample(i, j, 0, geomImage.getPixel(i, j, 0));
            }
        }
        // Adjust the image width and height
        // retaining the aspect ratio. Start by adjusting the height, then adjust width to maintain aspect ratio.
        double scaleFactor = 1.0;
        if (x * scaleFactor > DEF_GEOM_WIDTH) {
            scaleFactor = ((double) DEF_GEOM_WIDTH) / x;
        }
        if (y * scaleFactor > DEF_GEOM_HEIGHT) {
            scaleFactor = ((double) DEF_GEOM_HEIGHT) / y;
        }
        int adjX = (int) Math.ceil(x * scaleFactor);
        int adjY = (int) Math.ceil(y * scaleFactor);
        adjImage = bufferedImage.getScaledInstance(adjX, adjY, BufferedImage.SCALE_REPLICATE);
        newBufferedImage = new BufferedImage(adjX, adjY, BufferedImage.TYPE_BYTE_INDEXED, icm);
        newBufferedImage.getGraphics().drawImage(adjImage, 0, 0, null);
    } else if (geom.getDimension() == 3) {
        WritableRaster smallPixelWR = null;
        int[] cmap = new int[256];
        final int DISPLAY_DIM_MAX = 256;
        try {
            // Reset colormap (grayscale)
            for (int i = 0; i < cmap.length; i += 1) {
                int iv = (int) (0x000000FF & i);
                cmap[i] = 0xFF << 24 | iv << 16 | iv << 8 | i;
            }
            // stretch cmap grays
            if (geomImage != null && geomImage.getPixelClasses().length < 32) {
                for (int i = 0; i < geomImage.getPixelClasses().length; i += 1) {
                    int stretchIndex = (int) (0xFF & geomImage.getPixelClasses()[i].getPixel());
                    int newI = 32 + (i * ((256 - 32) / geomImage.getPixelClasses().length));
                    cmap[stretchIndex] = 0xFF << 24 | newI << 16 | newI << 8 | newI;
                }
            }
            // Set grid color
            // white
            cmap[cmap.length - 1] = 0xFFFFFFFF;
            // Initialize image data
            int xSide = 0;
            int ySide = 0;
            if (pixelWR == null) {
                VCImage sampledImage = geomImage;
                double side = Math.sqrt(x * y * z);
                xSide = (int) Math.round(side / (double) x);
                if (xSide == 0) {
                    xSide = 1;
                }
                if (xSide > z) {
                    xSide = z;
                }
                ySide = (int) Math.ceil((double) z / (double) xSide);
                if (ySide == 0) {
                    ySide = 1;
                }
                if (ySide > z) {
                    ySide = z;
                }
                pixelWR = icm.createCompatibleWritableRaster(xSide * x, ySide * y);
                byte[] sib = sampledImage.getPixels();
                // write the image to buffer
                int ystride = x;
                int zstride = x * y;
                for (int row = 0; row < ySide; row += 1) {
                    for (int col = 0; col < xSide; col += 1) {
                        int xoffset = col * x;
                        int yoffset = (row * y);
                        int zoffset = (col + (row * xSide)) * zstride;
                        if (zoffset >= sib.length) {
                            for (int xi = 0; xi < x; xi += 1) {
                                for (int yi = 0; yi < y; yi += 1) {
                                    pixelWR.setSample(xi + xoffset, yi + yoffset, 0, cmap.length - 1);
                                }
                            }
                        } else {
                            for (int xi = 0; xi < x; xi += 1) {
                                for (int yi = 0; yi < y; yi += 1) {
                                    pixelWR.setSample(xi + xoffset, yi + yoffset, 0, (int) (0xFF & sib[xi + (ystride * yi) + zoffset]));
                                }
                            }
                        }
                    }
                }
                // scale if necessary
                double displayScale = 1.0;
                if (pixelWR.getWidth() < DISPLAY_DIM_MAX || pixelWR.getHeight() < DISPLAY_DIM_MAX) {
                    displayScale = (int) Math.min((DISPLAY_DIM_MAX / pixelWR.getWidth()), (DISPLAY_DIM_MAX / pixelWR.getHeight()));
                    if (displayScale == 0) {
                        displayScale = 1;
                    }
                }
                if ((displayScale == 1) && (pixelWR.getWidth() > DISPLAY_DIM_MAX || pixelWR.getHeight() > DISPLAY_DIM_MAX)) {
                    displayScale = Math.max((pixelWR.getWidth() / DISPLAY_DIM_MAX), (pixelWR.getHeight() / DISPLAY_DIM_MAX));
                    // displayScale = Math.min(((double)DISPLAY_DIM_MAX/(double)pixelWR.getWidth()),((double)DISPLAY_DIM_MAX/(double)pixelWR.getHeight()));
                    if (displayScale == 0) {
                        displayScale = 1;
                    }
                    displayScale = 1.0 / displayScale;
                }
                if (displayScale != 1) {
                    java.awt.geom.AffineTransform at = new java.awt.geom.AffineTransform();
                    at.setToScale(displayScale, displayScale);
                    java.awt.image.AffineTransformOp ato = new java.awt.image.AffineTransformOp(at, java.awt.image.AffineTransformOp.TYPE_NEAREST_NEIGHBOR);
                    smallPixelWR = ato.createCompatibleDestRaster(pixelWR);
                    ato.filter(pixelWR, smallPixelWR);
                }
            }
            // draw labels and grid
            if (pixelWR != null) {
                bufferedImage = new java.awt.image.BufferedImage(icm, smallPixelWR, false, null);
                if (xSide > 0 || ySide > 0) {
                    float gridXBlockLen = ((float) (bufferedImage.getWidth()) / xSide);
                    float gridYBlockLen = ((float) (bufferedImage.getHeight()) / ySide);
                    java.awt.Graphics g = bufferedImage.getGraphics();
                    g.setColor(java.awt.Color.white);
                    // horiz lines
                    for (int row = 0; row < ySide; row += 1) {
                        if (row > 0) {
                            g.drawLine(0, (int) (row * gridYBlockLen), bufferedImage.getWidth(), (int) (row * gridYBlockLen));
                        }
                    }
                    // vert lines
                    for (int col = 0; col < xSide; col += 1) {
                        if (col > 0) {
                            g.drawLine((int) (col * gridXBlockLen), 0, (int) (col * gridXBlockLen), bufferedImage.getHeight());
                        }
                    }
                    // z markers
                    if (xSide > 1 || ySide > 1) {
                        for (int row = 0; row < xSide; row += 1) {
                            for (int col = 0; col < ySide; col += 1) {
                                g.drawString("" + (1 + row + (col * xSide)), (int) (row * gridXBlockLen) + 3, (int) (col * gridYBlockLen) + 12);
                            }
                        }
                    }
                }
            }
        } catch (Throwable e) {
            throw new Exception("CreateGeometryImageIcon error\n" + (e.getMessage() != null ? e.getMessage() : e.getClass().getName()));
        }
        // Adjust the image width and height
        adjImage = bufferedImage.getScaledInstance(smallPixelWR.getWidth(), smallPixelWR.getHeight(), BufferedImage.SCALE_REPLICATE);
        newBufferedImage = new BufferedImage(smallPixelWR.getWidth(), smallPixelWR.getHeight(), BufferedImage.TYPE_BYTE_INDEXED, icm);
        newBufferedImage.getGraphics().drawImage(adjImage, 0, 0, null);
    }
    ByteArrayOutputStream bos = null;
    bos = encodeJPEG(newBufferedImage);
    return bos;
}

Example 15 with VCImage

use of cbit.image.VCImage in project vcell by virtualcell.

the class XmlHelper method XMLToImage.

static VCImage XMLToImage(String xmlString, boolean printKeys) throws XmlParseException {
    Namespace ns = Namespace.getNamespace(XMLTags.VCML_NS);
    if (xmlString == null || xmlString.length() == 0) {
        throw new XmlParseException("Invalid xml for Image: " + xmlString);
    }
    // default parser and no validation
    Element root = (XmlUtil.stringToXML(xmlString, null)).getRootElement();
    Element extentElement = root.getChild(XMLTags.ExtentTag, ns);
    Element imageElement = root.getChild(XMLTags.ImageTag, ns);
    // Element extentElement = root.getChild(XMLTags.ExtentTag);
    // Element imageElement = root.getChild(XMLTags.ImageTag);
    XmlReader reader = new XmlReader(printKeys, ns);
    Extent extent = reader.getExtent(extentElement);
    VCImage vcImage = reader.getVCImage(imageElement, extent);
    vcImage.refreshDependencies();
    return vcImage;
}