Examples with PixelImageIJ qupath.imagej.tools.PixelImageIJ used on opensource projects

Example 1 with PixelImageIJ

use of qupath.imagej.tools.PixelImageIJ in project qupath by qupath.

the class ObjectMeasurements method addIntensityMeasurements.

/**
 * Measure all channels of an image for one individual object or cell.
 * All compartments are measured where possible (nucleus, cytoplasm, membrane and full cell).
 * <p>
 * Note: This implementation is likely to change in the future, to enable neighboring cells to be
 * measured more efficiently.
 *
 * @param server the server containing the pixels (and channels) to be measured
 * @param pathObject the cell to measure (the {@link MeasurementList} will be updated)
 * @param downsample resolution at which to request pixels
 * @param measurements requested measurements to make
 * @param compartments the cell compartments to measure; ignored if the object is not a cell
 * @throws IOException
 */
public static void addIntensityMeasurements(ImageServer<BufferedImage> server, PathObject pathObject, double downsample, Collection<Measurements> measurements, Collection<Compartments> compartments) throws IOException {
    var roi = pathObject.getROI();
    int pad = (int) Math.ceil(downsample * 2);
    var request = RegionRequest.createInstance(server.getPath(), downsample, roi).pad2D(pad, pad).intersect2D(0, 0, server.getWidth(), server.getHeight());
    var pathImage = IJTools.convertToImagePlus(server, request);
    var imp = pathImage.getImage();
    Map<String, ImageProcessor> channels = new LinkedHashMap<>();
    var serverChannels = server.getMetadata().getChannels();
    if (server.isRGB() && imp.getStackSize() == 1 && imp.getProcessor() instanceof ColorProcessor) {
        ColorProcessor cp = (ColorProcessor) imp.getProcessor();
        for (int i = 0; i < serverChannels.size(); i++) {
            channels.put(serverChannels.get(i).getName(), cp.getChannel(i + 1, null));
        }
    } else {
        assert imp.getStackSize() == serverChannels.size();
        for (int i = 0; i < imp.getStackSize(); i++) {
            channels.put(serverChannels.get(i).getName(), imp.getStack().getProcessor(i + 1));
        }
    }
    ByteProcessor bpCell = new ByteProcessor(imp.getWidth(), imp.getHeight());
    bpCell.setValue(1.0);
    var roiIJ = IJTools.convertToIJRoi(roi, pathImage);
    bpCell.fill(roiIJ);
    if (pathObject instanceof PathCellObject) {
        var cell = (PathCellObject) pathObject;
        ByteProcessor bpNucleus = new ByteProcessor(imp.getWidth(), imp.getHeight());
        if (cell.getNucleusROI() != null) {
            bpNucleus.setValue(1.0);
            var roiNucleusIJ = IJTools.convertToIJRoi(cell.getNucleusROI(), pathImage);
            bpNucleus.fill(roiNucleusIJ);
        }
        measureCells(bpNucleus, bpCell, Map.of(1.0, cell), channels, compartments, measurements);
    } else {
        var imgLabels = new PixelImageIJ(bpCell);
        for (var entry : channels.entrySet()) {
            var img = new PixelImageIJ(entry.getValue());
            measureObjects(img, imgLabels, new PathObject[] { pathObject }, entry.getKey(), measurements);
        }
    }
}

Example 2 with PixelImageIJ

use of qupath.imagej.tools.PixelImageIJ in project qupath by qupath.

the class ObjectMeasurements method measureCells.

/**
 * Make cell measurements based on labelled images.
 * All compartments are measured where possible (nucleus, cytoplasm, membrane and full cell).
 *
 * @param ipNuclei labelled image representing nuclei
 * @param ipCells labelled image representing cells
 * @param pathObjects cell objects mapped to integer values in the labelled images
 * @param channels channels to measure, mapped to the name to incorporate into the measurements for that channel
 * @param compartments the cell compartments to measure
 * @param measurements requested measurements to make
 */
private static void measureCells(ImageProcessor ipNuclei, ImageProcessor ipCells, Map<? extends Number, ? extends PathObject> pathObjects, Map<String, ImageProcessor> channels, Collection<Compartments> compartments, Collection<Measurements> measurements) {
    var array = mapToArray(pathObjects);
    // PathObjectTools.constrainCellByScaledNucleus(cell, nucleusScaleFactor, keepMeasurements)
    int width = ipNuclei.getWidth();
    int height = ipNuclei.getHeight();
    ImageProcessor ipMembrane = new FloatProcessor(width, height);
    ImageProcessor ipCytoplasm = ipCells.duplicate();
    for (int y = 0; y < height; y++) {
        for (int x = 0; x < width; x++) {
            float cell = ipCells.getf(x, y);
            float nuc = ipNuclei.getf(x, y);
            if (nuc != 0f)
                ipCytoplasm.setf(x, y, 0f);
            if (cell == 0f)
                continue;
            // Check 4-neighbours to decide if we're at the membrane
            if ((y >= 1 && ipCells.getf(x, y - 1) != cell) || (y < height - 1 && ipCells.getf(x, y + 1) != cell) || (x >= 1 && ipCells.getf(x - 1, y) != cell) || (x < width - 1 && ipCells.getf(x + 1, y) != cell))
                ipMembrane.setf(x, y, cell);
        }
    }
    var imgNuclei = new PixelImageIJ(ipNuclei);
    var imgCells = new PixelImageIJ(ipCells);
    var imgCytoplasm = new PixelImageIJ(ipCytoplasm);
    var imgMembrane = new PixelImageIJ(ipMembrane);
    for (var entry : channels.entrySet()) {
        var img = new PixelImageIJ(entry.getValue());
        if (compartments.contains(Compartments.NUCLEUS))
            measureObjects(img, imgNuclei, array, entry.getKey().trim() + ": " + "Nucleus", measurements);
        if (compartments.contains(Compartments.CYTOPLASM))
            measureObjects(img, imgCytoplasm, array, entry.getKey().trim() + ": " + "Cytoplasm", measurements);
        if (compartments.contains(Compartments.MEMBRANE))
            measureObjects(img, imgMembrane, array, entry.getKey().trim() + ": " + "Membrane", measurements);
        if (compartments.contains(Compartments.CELL))
            measureObjects(img, imgCells, array, entry.getKey().trim() + ": " + "Cell", measurements);
    }
}