Examples with ROI qupath.lib.roi.interfaces.ROI used on opensource projects

Example 61 with ROI

use of qupath.lib.roi.interfaces.ROI in project qupath by qupath.

the class Commands method createFullImageAnnotation.

/**
 * Create a full image annotation for the image in the specified viewer.
 * The z and t positions of the viewer will be used.
 * @param viewer the viewer containing the image to be processed
 */
public static void createFullImageAnnotation(QuPathViewer viewer) {
    if (viewer == null)
        return;
    ImageData<?> imageData = viewer.getImageData();
    if (imageData == null)
        return;
    PathObjectHierarchy hierarchy = imageData.getHierarchy();
    // Check if we already have a comparable annotation
    int z = viewer.getZPosition();
    int t = viewer.getTPosition();
    ImageRegion bounds = viewer.getServerBounds();
    ROI roi = ROIs.createRectangleROI(bounds.getX(), bounds.getY(), bounds.getWidth(), bounds.getHeight(), ImagePlane.getPlane(z, t));
    for (PathObject pathObject : hierarchy.getAnnotationObjects()) {
        ROI r2 = pathObject.getROI();
        if (r2 instanceof RectangleROI && roi.getBoundsX() == r2.getBoundsX() && roi.getBoundsY() == r2.getBoundsY() && roi.getBoundsWidth() == r2.getBoundsWidth() && roi.getBoundsHeight() == r2.getBoundsHeight() && roi.getImagePlane().equals(r2.getImagePlane())) {
            logger.info("Full image annotation already exists! {}", pathObject);
            viewer.setSelectedObject(pathObject);
            return;
        }
    }
    PathObject pathObject = PathObjects.createAnnotationObject(roi);
    hierarchy.addPathObject(pathObject);
    viewer.setSelectedObject(pathObject);
    // Log in the history
    if (z == 0 && t == 0)
        imageData.getHistoryWorkflow().addStep(new DefaultScriptableWorkflowStep("Create full image annotation", "createSelectAllObject(true);"));
    else
        imageData.getHistoryWorkflow().addStep(new DefaultScriptableWorkflowStep("Create full image annotation", String.format("createSelectAllObject(true, %d, %d);", z, t)));
}

Example 62 with ROI

use of qupath.lib.roi.interfaces.ROI in project qupath by qupath.

the class Commands method combineAnnotations.

/**
 * Combine all the annotations that overlap with a selected object.
 * <p>
 * The selected object should itself be an annotation.
 *
 * @param hierarchy
 * @param pathObjects
 * @param op
 * @return true if any changes were made, false otherwise
 */
static boolean combineAnnotations(PathObjectHierarchy hierarchy, List<PathObject> pathObjects, RoiTools.CombineOp op) {
    if (hierarchy == null || hierarchy.isEmpty() || pathObjects.isEmpty()) {
        logger.warn("Combine annotations: Cannot combine - no annotations found");
        return false;
    }
    pathObjects = new ArrayList<>(pathObjects);
    PathObject pathObject = pathObjects.get(0);
    if (!pathObject.isAnnotation()) {
        // || !RoiTools.isShapeROI(pathObject.getROI())) {
        logger.warn("Combine annotations: No annotation with ROI selected");
        return false;
    }
    var plane = pathObject.getROI().getImagePlane();
    // pathObjects.removeIf(p -> !RoiTools.isShapeROI(p.getROI())); // Remove any null or point ROIs, TODO: Consider supporting points
    // Remove any null or point ROIs, TODO: Consider supporting points
    pathObjects.removeIf(p -> !p.hasROI() || !p.getROI().getImagePlane().equals(plane));
    if (pathObjects.isEmpty()) {
        logger.warn("Cannot combine annotations - only one suitable annotation found");
        return false;
    }
    var allROIs = pathObjects.stream().map(p -> p.getROI()).collect(Collectors.toCollection(() -> new ArrayList<>()));
    ROI newROI;
    switch(op) {
        case ADD:
            newROI = RoiTools.union(allROIs);
            break;
        case INTERSECT:
            newROI = RoiTools.intersection(allROIs);
            break;
        case SUBTRACT:
            var first = allROIs.remove(0);
            newROI = RoiTools.combineROIs(first, RoiTools.union(allROIs), op);
            break;
        default:
            throw new IllegalArgumentException("Unknown combine op " + op);
    }
    if (newROI == null) {
        logger.debug("No changes were made");
        return false;
    }
    PathObject newObject = null;
    if (!newROI.isEmpty()) {
        newObject = PathObjects.createAnnotationObject(newROI, pathObject.getPathClass());
        newObject.setName(pathObject.getName());
        newObject.setColorRGB(pathObject.getColorRGB());
    }
    // Remove previous objects
    hierarchy.removeObjects(pathObjects, true);
    if (newObject != null)
        hierarchy.addPathObject(newObject);
    return true;
}

Example 63 with ROI

use of qupath.lib.roi.interfaces.ROI in project qupath by qupath.

the class HaralickFeaturesPlugin method processObject.

static boolean processObject(final PathObject pathObject, final ParameterList params, final ImageServer<BufferedImage> server, final ColorDeconvolutionStains stains) throws IOException {
    String stainsName = (String) params.getChoiceParameterValue("stainChoice");
    double mag = params.getDoubleParameterValue("magnification");
    int d = params.getIntParameterValue("haralickDistance");
    int nBins = params.getIntParameterValue("haralickBins");
    boolean includeStats = params.getBooleanParameterValue("includeStats");
    boolean doCircular = params.getBooleanParameterValue("doCircular");
    double downsample;
    boolean hasMagnification = !Double.isNaN(server.getMetadata().getMagnification());
    PixelCalibration cal = server.getPixelCalibration();
    if (hasMagnification)
        downsample = server.getMetadata().getMagnification() / mag;
    else if (cal.hasPixelSizeMicrons()) {
        downsample = params.getDoubleParameterValue("pixelSizeMicrons") / cal.getAveragedPixelSizeMicrons();
    } else
        downsample = params.getDoubleParameterValue("downsample");
    // double downsample = server.getMagnification() / mag;
    // Try to get ROI
    ROI pathROI = null;
    if (pathObject instanceof PathCellObject && Boolean.TRUE.equals(params.getBooleanParameterValue("useNucleusROIs")))
        pathROI = ((PathCellObject) pathObject).getNucleusROI();
    else
        pathROI = pathObject.getROI();
    if (pathROI == null)
        return false;
    // Get bounds
    ImmutableDimension size = getPreferredTileSizePixels(server, params);
    RegionRequest region;
    boolean createMaskROI = false;
    if (size.getWidth() <= 0 || size.getHeight() <= 0) {
        region = RegionRequest.createInstance(server.getPath(), downsample, pathObject.getROI());
        createMaskROI = true;
        doCircular = false;
    } else if (size.getWidth() / downsample < 1 || size.getHeight() / downsample < 1)
        // Positive size, but insufficient to make measurements
        return false;
    else {
        // RegionRequest region = RegionRequest.createInstance(server.getPath(), downsample, (int)(pathROI.getCentroidX() + .5) - size.width/2, (int)(pathROI.getCentroidY() + .5) - size.height/2, size.width, size.height, pathROI.getT(), pathROI.getZ());
        // Try to align with pixel boundaries according to the downsample being used - otherwise, interpolation can cause some strange, pattern artefacts
        int xStart = (int) ((int) (pathROI.getCentroidX() / downsample + .5) * downsample) - size.width / 2;
        int yStart = (int) ((int) (pathROI.getCentroidY() / downsample + .5) * downsample) - size.height / 2;
        int width = Math.min(server.getWidth(), xStart + size.width) - xStart;
        int height = Math.min(server.getHeight(), yStart + size.height) - yStart;
        region = RegionRequest.createInstance(server.getPath(), downsample, xStart, yStart, width, height, pathROI.getT(), pathROI.getZ());
    }
    // Check image large enough to do *anything* of value
    if (region.getWidth() / downsample < 3 || region.getHeight() / downsample < 3)
        return false;
    // System.out.println(bounds);
    // System.out.println("Size: " + size);
    BufferedImage img = server.readBufferedImage(region);
    if (img == null) {
        logger.error("Could not read image - unable to compute Haralick features for {}", pathObject);
        return false;
    }
    // Create mask ROI if necessary
    byte[] maskBytes = null;
    if (createMaskROI) {
        ROI roi = pathObject.getROI();
        // if (pathObject instanceof PathCellObject && ((PathCellObject)pathObject).getNucleusROI() != null)
        // roi = ((PathCellObject)pathObject).getNucleusROI();
        BufferedImage imgMask = BufferedImageTools.createROIMask(img.getWidth(), img.getHeight(), roi, region);
        maskBytes = ((DataBufferByte) imgMask.getRaster().getDataBuffer()).getData();
    }
    double minValue = Double.NaN;
    double maxValue = Double.NaN;
    // Get a buffer containing the image pixels
    int w = img.getWidth();
    int h = img.getHeight();
    int[] buf = img.getRGB(0, 0, w, h, null, 0, w);
    // Create a color transformer to get the images we need
    float[] pixels = new float[buf.length];
    SimpleModifiableImage pxImg = SimpleImages.createFloatImage(pixels, w, h);
    MeasurementList measurementList = pathObject.getMeasurementList();
    String postfix = maskBytes == null ? " (" + getDiameterString(server, params) + ")" : "";
    if (stainsName.equals("H-DAB")) {
        minValue = 0;
        maxValue = 2.0;
        processTransformedImage(pxImg, buf, pixels, measurementList, "Hematoxylin" + postfix, ColorTransformer.ColorTransformMethod.Hematoxylin_H_DAB, minValue, maxValue, d, nBins, stains, maskBytes, includeStats, doCircular);
        processTransformedImage(pxImg, buf, pixels, measurementList, "DAB" + postfix, ColorTransformer.ColorTransformMethod.DAB_H_DAB, minValue, maxValue, d, nBins, stains, maskBytes, includeStats, doCircular);
    } else if (stainsName.equals("H&E")) {
        minValue = 0;
        maxValue = 2;
        processTransformedImage(pxImg, buf, pixels, measurementList, "Hematoxylin" + postfix, ColorTransformer.ColorTransformMethod.Hematoxylin_H_E, minValue, maxValue, d, nBins, stains, maskBytes, includeStats, doCircular);
        processTransformedImage(pxImg, buf, pixels, measurementList, "Eosin" + postfix, ColorTransformer.ColorTransformMethod.Eosin_H_E, minValue, maxValue, d, nBins, stains, maskBytes, includeStats, doCircular);
    } else if (stainsName.equals("H-DAB (8-bit)")) {
        minValue = 0;
        maxValue = 255;
        processTransformedImage(pxImg, buf, pixels, measurementList, "Hematoxylin 8-bit" + postfix, ColorTransformer.ColorTransformMethod.Hematoxylin_H_DAB_8_bit, minValue, maxValue, d, nBins, stains, maskBytes, includeStats, doCircular);
        processTransformedImage(pxImg, buf, pixels, measurementList, "DAB 8-bit" + postfix, ColorTransformer.ColorTransformMethod.DAB_H_DAB_8_bit, minValue, maxValue, d, nBins, stains, maskBytes, includeStats, doCircular);
    } else if (stainsName.equals("H&E (8-bit)")) {
        minValue = 0;
        maxValue = 255;
        processTransformedImage(pxImg, buf, pixels, measurementList, "Hematoxylin 8-bit" + postfix, ColorTransformer.ColorTransformMethod.Hematoxylin_H_E_8_bit, minValue, maxValue, d, nBins, stains, maskBytes, includeStats, doCircular);
        processTransformedImage(pxImg, buf, pixels, measurementList, "Eosin 8-bit" + postfix, ColorTransformer.ColorTransformMethod.Eosin_H_E_8_bit, minValue, maxValue, d, nBins, stains, maskBytes, includeStats, doCircular);
    } else if (stainsName.equals("Optical density")) {
        minValue = 0;
        maxValue = 2.5;
        processTransformedImage(pxImg, buf, pixels, measurementList, "OD sum" + postfix, ColorTransformer.ColorTransformMethod.Optical_density_sum, minValue, maxValue, d, nBins, stains, maskBytes, includeStats, doCircular);
    } else if (stainsName.equals("RGB")) {
        minValue = 0;
        maxValue = 255;
        processTransformedImage(pxImg, buf, pixels, measurementList, "Red" + postfix, ColorTransformer.ColorTransformMethod.Red, minValue, maxValue, d, nBins, stains, maskBytes, includeStats, doCircular);
        processTransformedImage(pxImg, buf, pixels, measurementList, "Green" + postfix, ColorTransformer.ColorTransformMethod.Green, minValue, maxValue, d, nBins, stains, maskBytes, includeStats, doCircular);
        processTransformedImage(pxImg, buf, pixels, measurementList, "Blue" + postfix, ColorTransformer.ColorTransformMethod.Blue, minValue, maxValue, d, nBins, stains, maskBytes, includeStats, doCircular);
    } else if (stainsName.equals("RGB OD")) {
        minValue = 0;
        // Actual possible max is around 2.4 for 8-bit input... but this gives a lot of bins for (almost) saturated pixels
        maxValue = 1.5;
        processTransformedImage(pxImg, buf, pixels, measurementList, "Red OD" + postfix, ColorTransformer.ColorTransformMethod.Red_OD, minValue, maxValue, d, nBins, stains, maskBytes, includeStats, doCircular);
        processTransformedImage(pxImg, buf, pixels, measurementList, "Green OD" + postfix, ColorTransformer.ColorTransformMethod.Green_OD, minValue, maxValue, d, nBins, stains, maskBytes, includeStats, doCircular);
        processTransformedImage(pxImg, buf, pixels, measurementList, "Blue OD" + postfix, ColorTransformer.ColorTransformMethod.Blue_OD, minValue, maxValue, d, nBins, stains, maskBytes, includeStats, doCircular);
    } else if (stainsName.equals("Grayscale")) {
        minValue = 0;
        maxValue = 255;
        processTransformedImage(pxImg, buf, pixels, measurementList, "Grayscale" + postfix, ColorTransformer.ColorTransformMethod.RGB_mean, minValue, maxValue, d, nBins, stains, maskBytes, includeStats, doCircular);
    } else if (stainsName.equals("HSB")) {
        minValue = 0;
        maxValue = 1;
        float[] hsb = null;
        double sinX = 0;
        double cosX = 0;
        float[] pixelsBrightness = new float[pixels.length];
        float[] pixelsSaturation = new float[pixels.length];
        for (int i = 0; i < buf.length; i++) {
            if (maskBytes != null && maskBytes[i] == (byte) 0)
                continue;
            int val = buf[i];
            hsb = Color.RGBtoHSB(ColorTools.red(val), ColorTools.green(val), ColorTools.blue(val), hsb);
            pixelsSaturation[i] = hsb[1];
            pixelsBrightness[i] = hsb[2];
            double alpha = hsb[0] * 2 * Math.PI;
            sinX += Math.sin(alpha);
            cosX += Math.cos(alpha);
        }
        measurementList.putMeasurement("Mean hue", Math.atan2(sinX, cosX) / (2 * Math.PI) + 0.5);
        // measurementList.putMeasurement("Mean saturation", hsb[1]);
        // measurementList.putMeasurement("Mean brightness", hsb[2]);
        processTransformedImage(SimpleImages.createFloatImage(pixelsSaturation, w, h), buf, pixelsSaturation, measurementList, "Saturation" + postfix, null, minValue, maxValue, d, nBins, stains, maskBytes, includeStats, doCircular);
        processTransformedImage(SimpleImages.createFloatImage(pixelsBrightness, w, h), buf, pixelsBrightness, measurementList, "Brightness" + postfix, null, minValue, maxValue, d, nBins, stains, maskBytes, includeStats, doCircular);
    }
    measurementList.close();
    return true;
}

Example 64 with ROI

use of qupath.lib.roi.interfaces.ROI in project qupath by qupath.

the class CoherenceFeaturePlugin method processObject.

static boolean processObject(final PathObject pathObject, final ParameterList params, final ImageServer<BufferedImage> server, final ColorDeconvolutionStains stains) throws InterruptedException, IOException {
    String stainsName = (String) params.getChoiceParameterValue("stainChoice");
    double mag = params.getDoubleParameterValue("magnification");
    boolean includeStats = params.getBooleanParameterValue("includeStats");
    boolean doCircular = params.getBooleanParameterValue("doCircular");
    double downsample = server.getMetadata().getMagnification() / mag;
    ROI pathROI = pathObject.getROI();
    if (pathROI == null)
        return false;
    // Get bounds
    ImmutableDimension size = getPreferredTileSizePixels(server, params);
    if (size.getWidth() / downsample < 1 || size.getHeight() / downsample < 1)
        return false;
    // RegionRequest region = RegionRequest.createInstance(server.getPath(), downsample, (int)(pathROI.getCentroidX() + .5) - size.width/2, (int)(pathROI.getCentroidY() + .5) - size.height/2, size.width, size.height, pathROI.getT(), pathROI.getZ());
    // Try to align with pixel boundaries according to the downsample being used - otherwise, interpolation can cause some strange, pattern artefacts
    int xStart = (int) ((int) (pathROI.getCentroidX() / downsample + .5) * downsample) - size.width / 2;
    int yStart = (int) ((int) (pathROI.getCentroidY() / downsample + .5) * downsample) - size.height / 2;
    int width = Math.min(server.getWidth(), xStart + size.width) - xStart;
    int height = Math.min(server.getHeight(), yStart + size.height) - yStart;
    RegionRequest region = RegionRequest.createInstance(server.getPath(), downsample, xStart, yStart, width, height, pathROI.getT(), pathROI.getZ());
    // System.out.println(bounds);
    // System.out.println("Size: " + size);
    BufferedImage img = server.readBufferedImage(region);
    // Get a buffer containing the image pixels
    int w = img.getWidth();
    int h = img.getHeight();
    int[] buf = img.getRGB(0, 0, w, h, null, 0, w);
    // Create a color transformer to get the images we need
    float[] pixels = new float[buf.length];
    SimpleModifiableImage pxImg = SimpleImages.createFloatImage(pixels, w, h);
    MeasurementList measurementList = pathObject.getMeasurementList();
    String postfix = " (" + getDiameterString(server, params) + ")";
    if (stainsName.equals("H-DAB")) {
        processTransformedImage(pxImg, buf, pixels, measurementList, "Hematoxylin" + postfix, ColorTransformer.ColorTransformMethod.Hematoxylin_H_DAB, stains, includeStats, doCircular);
        processTransformedImage(pxImg, buf, pixels, measurementList, "DAB" + postfix, ColorTransformer.ColorTransformMethod.DAB_H_DAB, stains, includeStats, doCircular);
    } else if (stainsName.equals("H&E")) {
        processTransformedImage(pxImg, buf, pixels, measurementList, "Hematoxylin" + postfix, ColorTransformer.ColorTransformMethod.Hematoxylin_H_E, stains, includeStats, doCircular);
        processTransformedImage(pxImg, buf, pixels, measurementList, "Eosin" + postfix, ColorTransformer.ColorTransformMethod.Eosin_H_E, stains, includeStats, doCircular);
    } else if (stainsName.equals("H-DAB (8-bit)")) {
        processTransformedImage(pxImg, buf, pixels, measurementList, "Hematoxylin 8-bit" + postfix, ColorTransformer.ColorTransformMethod.Hematoxylin_H_DAB_8_bit, stains, includeStats, doCircular);
        processTransformedImage(pxImg, buf, pixels, measurementList, "DAB 8-bit" + postfix, ColorTransformer.ColorTransformMethod.DAB_H_DAB_8_bit, stains, includeStats, doCircular);
    } else if (stainsName.equals("H&E (8-bit)")) {
        processTransformedImage(pxImg, buf, pixels, measurementList, "Hematoxylin 8-bit" + postfix, ColorTransformer.ColorTransformMethod.Hematoxylin_H_E_8_bit, stains, includeStats, doCircular);
        processTransformedImage(pxImg, buf, pixels, measurementList, "Eosin 8-bit" + postfix, ColorTransformer.ColorTransformMethod.Eosin_H_E_8_bit, stains, includeStats, doCircular);
    } else if (stainsName.equals("Optical density")) {
        processTransformedImage(pxImg, buf, pixels, measurementList, "OD sum" + postfix, ColorTransformer.ColorTransformMethod.Optical_density_sum, stains, includeStats, doCircular);
    } else if (stainsName.equals("RGB")) {
        processTransformedImage(pxImg, buf, pixels, measurementList, "Red" + postfix, ColorTransformer.ColorTransformMethod.Red, stains, includeStats, doCircular);
        processTransformedImage(pxImg, buf, pixels, measurementList, "Green" + postfix, ColorTransformer.ColorTransformMethod.Green, stains, includeStats, doCircular);
        processTransformedImage(pxImg, buf, pixels, measurementList, "Blue" + postfix, ColorTransformer.ColorTransformMethod.Blue, stains, includeStats, doCircular);
    } else if (stainsName.equals("Grayscale")) {
        processTransformedImage(pxImg, buf, pixels, measurementList, "Grayscale" + postfix, ColorTransformer.ColorTransformMethod.RGB_mean, stains, includeStats, doCircular);
    }
    measurementList.close();
    return true;
}

Example 65 with ROI

use of qupath.lib.roi.interfaces.ROI in project qupath by qupath.

the class IJTools method convertToPathObject.

/**
 * Create a {@link PathObject} for a specific ImageJ Roi.
 *
 * @param roi the ImageJ ROI
 * @param xOrigin the x-origin to translate the Roi; should be {@link Calibration#xOrigin} if available, or 0 otherwise
 * @param yOrigin the y-origin to translate the Roi; should be {@link Calibration#yOrigin} if available, or 0 otherwise
 * @param downsampleFactor the downsample factor used for rescaling (or 1.0 for no rescaling)
 * @param creator a function
 * @param plane the specific plane to use for the QuPath ROI; if null, the ImageJ Roi position properties will be used instead, where possible
 * @return a {@link PathObject} or null if no object could be created (e.g. the ImageJ roi is null or incompatible)
 *
 * @see #convertToPathObject(Roi, double, Function, ImagePlus)
 * @since v0.4.0
 */
public static PathObject convertToPathObject(Roi roi, double xOrigin, double yOrigin, double downsampleFactor, Function<ROI, PathObject> creator, ImagePlane plane) {
    ROI pathROI = IJTools.convertToROI(roi, xOrigin, yOrigin, downsampleFactor, plane);
    if (pathROI == null)
        return null;
    PathObject pathObject = creator.apply(pathROI);
    calibrateObject(pathObject, roi);
    return pathObject;
}