Examples with MeasurementList qupath.lib.measurements.MeasurementList used on opensource projects

Example 16 with MeasurementList

use of qupath.lib.measurements.MeasurementList in project qupath by qupath.

the class DelaunayTriangulation method addNodeMeasurements.

/**
 * Add Delaunay measurements to each pathObject.
 */
public void addNodeMeasurements() {
    if (nodeMap == null)
        return;
    // If 0, no averaging is performed
    // If 1, the averages of each object's measurements & those of its immediate neighbors are added
    // If 2, the neighbors of the neighbors are included as well
    // If 3, the neighbors or the neighbors of the neighbors are included... and so on...
    int averagingSeparation = 0;
    String[] measurementNames = new String[0];
    double[] averagedMeasurements = new double[0];
    Set<PathObject> neighborSet = new HashSet<>();
    for (Entry<PathObject, DelaunayNode> entry : nodeMap.entrySet()) {
        MeasurementList measurementList = entry.getKey().getMeasurementList();
        DelaunayNode node = entry.getValue();
        // Create a set of neighbors
        if (averagingSeparation > 0) {
            neighborSet.clear();
            node.addNeighborsToSet(neighborSet, averagingSeparation);
            // Get the smoothed measurements now, since access is likely to be much faster we start modifying it
            measurementNames = measurementList.getMeasurementNames().toArray(measurementNames);
            if (averagedMeasurements.length < measurementNames.length)
                averagedMeasurements = new double[measurementNames.length];
            for (int i = 0; i < measurementNames.length; i++) {
                String name = measurementNames[i];
                if (name == null || name.startsWith("Delaunay"))
                    continue;
                double sum = 0;
                int n = 0;
                for (PathObject tempObject : neighborSet) {
                    double value = tempObject.getMeasurementList().getMeasurementValue(name);
                    if (Double.isNaN(value))
                        continue;
                    sum += value;
                    n++;
                }
                averagedMeasurements[i] = n > 0 ? sum / n : Double.NaN;
            }
        }
        // TODO: PUT MEASUREMENTS IN UNITS OTHER THAN PIXELS????
        measurementList.putMeasurement("Delaunay: Num neighbors", node.nNeighbors());
        measurementList.putMeasurement("Delaunay: Mean distance", node.meanDistance());
        measurementList.putMeasurement("Delaunay: Median distance", node.medianDistance());
        measurementList.putMeasurement("Delaunay: Max distance", node.maxDistance());
        measurementList.putMeasurement("Delaunay: Min distance", node.minDistance());
        // measurementList.putMeasurement("Delaunay: Displacement sum mag", node.magDisplacementSum());
        measurementList.putMeasurement("Delaunay: Mean triangle area", node.getMeanTriangleArea());
        measurementList.putMeasurement("Delaunay: Max triangle area", node.getMaxTriangleArea());
        // Put in averaged measurements using immediate neighbours
        if (averagingSeparation > 0) {
            for (int i = 0; i < measurementNames.length; i++) {
                String name = measurementNames[i];
                if (name == null || name.startsWith("Delaunay"))
                    continue;
                measurementList.putMeasurement("Delaunay averaged (" + averagingSeparation + "): " + name, averagedMeasurements[i]);
            }
        }
        measurementList.close();
    }
}

Example 17 with MeasurementList

use of qupath.lib.measurements.MeasurementList in project qupath by qupath.

the class PathObjectTools method transformObject.

/**
 * Create a(n optionally) transformed version of a {@link PathObject}.
 * <p>
 * Note: only detections (including tiles and cells) and annotations are fully supported by this method.
 * Root objects are duplicated.
 * TMA core objects are transformed only if the resulting transform creates an ellipse ROI, since this is
 * currently the only ROI type supported for a TMA core (this behavior may change).
 * Any other object types result in an {@link UnsupportedOperationException} being thrown.
 *
 * @param pathObject the object to transform; this will be unchanged
 * @param transform optional affine transform; if {@code null}, this effectively acts to duplicate the object
 * @param copyMeasurements if true, the measurement list of the new object will be populated with the measurements of pathObject
 *
 * @return a duplicate of pathObject, with affine transform applied to the object's ROI(s) if required
 */
public static PathObject transformObject(PathObject pathObject, AffineTransform transform, boolean copyMeasurements) {
    ROI roi = maybeTransformROI(pathObject.getROI(), transform);
    PathClass pathClass = pathObject.getPathClass();
    PathObject newObject;
    if (pathObject instanceof PathCellObject) {
        ROI roiNucleus = maybeTransformROI(((PathCellObject) pathObject).getNucleusROI(), transform);
        newObject = PathObjects.createCellObject(roi, roiNucleus, pathClass, null);
    } else if (pathObject instanceof PathTileObject) {
        newObject = PathObjects.createTileObject(roi, pathClass, null);
    } else if (pathObject instanceof PathDetectionObject) {
        newObject = PathObjects.createDetectionObject(roi, pathClass, null);
    } else if (pathObject instanceof PathAnnotationObject) {
        newObject = PathObjects.createAnnotationObject(roi, pathClass, null);
    } else if (pathObject instanceof PathRootObject) {
        newObject = new PathRootObject();
    } else if (pathObject instanceof TMACoreObject && roi instanceof EllipseROI) {
        var core = (TMACoreObject) pathObject;
        newObject = PathObjects.createTMACoreObject(roi.getBoundsX(), roi.getBoundsY(), roi.getBoundsWidth(), roi.getBoundsHeight(), core.isMissing());
    } else
        throw new UnsupportedOperationException("Unable to transform object " + pathObject);
    if (copyMeasurements && !pathObject.getMeasurementList().isEmpty()) {
        MeasurementList measurements = pathObject.getMeasurementList();
        for (int i = 0; i < measurements.size(); i++) {
            String name = measurements.getMeasurementName(i);
            double value = measurements.getMeasurementValue(i);
            newObject.getMeasurementList().addMeasurement(name, value);
        }
        newObject.getMeasurementList().close();
    }
    return newObject;
}

Example 18 with MeasurementList

use of qupath.lib.measurements.MeasurementList 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 19 with MeasurementList

use of qupath.lib.measurements.MeasurementList 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 20 with MeasurementList

use of qupath.lib.measurements.MeasurementList in project qupath by qupath.

the class PathObjectTestWrapper method test_getMeasurementList.

// @Test
public void test_getMeasurementList(PathObject myPO) {
    MeasurementList myPOML = myPO.getMeasurementList();
    assertTrue(myPOML instanceof MeasurementList);
}