Examples with PixelCalibration qupath.lib.images.servers.PixelCalibration used on opensource projects

Example 6 with PixelCalibration

use of qupath.lib.images.servers.PixelCalibration in project qupath by qupath.

the class PathImagePlus method getPixelCalibration.

@Override
public PixelCalibration getPixelCalibration() {
    if (calibration == null) {
        var builder = new PixelCalibration.Builder();
        Calibration cal = getImage().getCalibration();
        if (isMicrons(cal.getXUnit()) && isMicrons(cal.getYUnit())) {
            builder.pixelSizeMicrons(cal.pixelWidth, cal.pixelHeight);
        }
        if (isMicrons(cal.getZUnit())) {
            builder.zSpacingMicrons(cal.pixelDepth);
        }
        calibration = builder.build();
    }
    return calibration;
}

Example 7 with PixelCalibration

use of qupath.lib.images.servers.PixelCalibration in project qupath by qupath.

the class HaralickFeaturesPlugin method getPreferredTileSizePixels.

static ImmutableDimension getPreferredTileSizePixels(final ImageServer<BufferedImage> server, final ParameterList params) {
    // Determine tile size
    int tileWidth, tileHeight;
    PixelCalibration cal = server.getPixelCalibration();
    if (cal.hasPixelSizeMicrons()) {
        double tileSize = params.getDoubleParameterValue("tileSizeMicrons");
        tileWidth = (int) (tileSize / cal.getPixelWidthMicrons() + .5);
        tileHeight = (int) (tileSize / cal.getPixelHeightMicrons() + .5);
    } else {
        tileWidth = (int) (params.getDoubleParameterValue("tileSizePx") + .5);
        tileHeight = tileWidth;
    }
    return ImmutableDimension.getInstance(tileWidth, tileHeight);
}

Example 8 with PixelCalibration

use of qupath.lib.images.servers.PixelCalibration in project qupath by qupath.

the class ObjectMeasurements method addShapeMeasurements.

/**
 * Add shape measurements for multiple objects. If any of these objects is a cell, measurements will be made for both the
 * nucleus and cell boundary where possible.
 *
 * @param pathObjects the objects for which measurements should be added
 * @param cal pixel calibration, used to determine units and scaling
 * @param features specific features to add; if empty, all available shape features will be added
 */
public static void addShapeMeasurements(Collection<? extends PathObject> pathObjects, PixelCalibration cal, ShapeFeatures... features) {
    PixelCalibration calibration = cal == null || !cal.unitsMatch2D() ? PixelCalibration.getDefaultInstance() : cal;
    Collection<ShapeFeatures> featureCollection = features.length == 0 ? ALL_SHAPE_FEATURES : Arrays.asList(features);
    pathObjects.parallelStream().filter(p -> p.hasROI()).forEach(pathObject -> {
        if (pathObject instanceof PathCellObject) {
            addCellShapeMeasurements((PathCellObject) pathObject, calibration, featureCollection);
        } else {
            try (var ml = pathObject.getMeasurementList()) {
                addShapeMeasurements(ml, pathObject.getROI(), calibration, "", featureCollection);
            }
        }
    });
}

Example 9 with PixelCalibration

use of qupath.lib.images.servers.PixelCalibration in project qupath by qupath.

the class IntensityFeaturesPlugin method processObject.

static boolean processObject(final PathObject pathObject, final ParameterList params, final ImageData<BufferedImage> imageData) throws IOException {
    // Determine amount to downsample
    var server = imageData.getServer();
    var stains = imageData.getColorDeconvolutionStains();
    PixelCalibration cal = server.getPixelCalibration();
    double downsample = calculateDownsample(cal, params);
    if (downsample <= 0) {
        logger.warn("Effective downsample must be > 0 (requested value {})", downsample);
    }
    // Determine region shape
    RegionType regionType = (RegionType) params.getChoiceParameterValue("region");
    // Try to get ROI
    boolean useROI = regionType == RegionType.ROI || regionType == RegionType.NUCLEUS;
    ROI roi = null;
    if (regionType == RegionType.NUCLEUS) {
        if (pathObject instanceof PathCellObject)
            roi = ((PathCellObject) pathObject).getNucleusROI();
    } else
        roi = pathObject.getROI();
    // pathROI = ((PathCellObject)pathObject).getNucleusROI();
    if (roi == null)
        return false;
    // Create a map - this is useful for occasions when tiling is needed
    Map<FeatureColorTransform, List<FeatureComputer>> map = new LinkedHashMap<>();
    if (server.isRGB()) {
        for (FeatureColorTransform transform : FeatureColorTransformEnum.values()) {
            List<FeatureComputer> list = new ArrayList<>();
            map.put(transform, list);
            for (FeatureComputerBuilder builder : builders) {
                list.add(builder.build());
            }
        }
    } else {
        for (FeatureColorTransform transform : getBasicChannelTransforms(server.nChannels())) {
            List<FeatureComputer> list = new ArrayList<>();
            map.put(transform, list);
            for (FeatureComputerBuilder builder : builders) {
                list.add(builder.build());
            }
        }
    }
    String prefix = getDiameterString(server, params);
    // Create tiled ROIs, if required
    ImmutableDimension sizePreferred = ImmutableDimension.getInstance((int) (2000 * downsample), (int) (2000 * downsample));
    // ImmutableDimension sizePreferred = new ImmutableDimension((int)(200*downsample), (int)(200*downsample));
    Collection<? extends ROI> rois = RoiTools.computeTiledROIs(roi, sizePreferred, sizePreferred, false, 0);
    if (rois.size() > 1)
        logger.info("Splitting {} into {} tiles for intensity measurements", roi, rois.size());
    for (ROI pathROI : rois) {
        if (Thread.currentThread().isInterrupted()) {
            logger.warn("Measurement skipped - thread interrupted!");
            return false;
        }
        // Get bounds
        RegionRequest region;
        if (useROI) {
            region = RegionRequest.createInstance(server.getPath(), downsample, pathROI);
        } else {
            ImmutableDimension size = getPreferredTileSizePixels(server, params);
            // 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) (Math.round(pathROI.getCentroidX() / downsample) * downsample) - size.width / 2;
            int yStart = (int) (Math.round(pathROI.getCentroidY() / downsample) * 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 < 1 || region.getHeight() / downsample < 1) {
        // logger.trace("Requested region is too small! {}", region);
        // 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 intensity features for {}", pathObject);
            return false;
        }
        // Create mask ROI if necessary
        // If we just have 1 pixel, we want to use it so that the mean/min/max measurements are valid (even if nothing else is)
        byte[] maskBytes = null;
        if (useROI && img.getWidth() * img.getHeight() > 1) {
            BufferedImage imgMask = BufferedImageTools.createROIMask(img.getWidth(), img.getHeight(), pathROI, region);
            maskBytes = ((DataBufferByte) imgMask.getRaster().getDataBuffer()).getData();
        }
        boolean isRGB = server.isRGB();
        List<FeatureColorTransform> transforms;
        if (isRGB)
            transforms = Arrays.asList(FeatureColorTransformEnum.values());
        else
            transforms = getBasicChannelTransforms(server.nChannels());
        int w = img.getWidth();
        int h = img.getHeight();
        int[] rgbBuffer = isRGB ? img.getRGB(0, 0, w, h, null, 0, w) : null;
        float[] pixels = null;
        for (FeatureColorTransform transform : transforms) {
            // Check if the color transform is requested
            if (params.containsKey(transform.getKey()) && Boolean.TRUE.equals(params.getBooleanParameterValue(transform.getKey()))) {
                // Transform the pixels
                pixels = transform.getTransformedPixels(img, rgbBuffer, stains, pixels);
                // Create the simple image
                SimpleModifiableImage pixelImage = SimpleImages.createFloatImage(pixels, w, h);
                // Apply any arbitrary mask
                if (maskBytes != null) {
                    for (int i = 0; i < pixels.length; i++) {
                        if (maskBytes[i] == (byte) 0)
                            pixelImage.setValue(i % w, i / w, Float.NaN);
                    }
                } else if (regionType == RegionType.CIRCLE) {
                    // Apply circular tile mask
                    double cx = (w - 1) / 2;
                    double cy = (h - 1) / 2;
                    double radius = Math.max(w, h) * .5;
                    double distThreshold = radius * radius;
                    for (int y = 0; y < h; y++) {
                        for (int x = 0; x < w; x++) {
                            if ((cx - x) * (cx - x) + (cy - y) * (cy - y) > distThreshold)
                                pixelImage.setValue(x, y, Float.NaN);
                        }
                    }
                }
                // Do the computations
                for (FeatureComputer computer : map.get(transform)) {
                    computer.updateFeatures(pixelImage, transform, params);
                }
            }
        }
    }
    // Add measurements to the parent object
    for (Entry<FeatureColorTransform, List<FeatureComputer>> entry : map.entrySet()) {
        String name = prefix + ": " + entry.getKey().getName(imageData, false) + ":";
        for (FeatureComputer computer : entry.getValue()) computer.addMeasurements(pathObject, name, params);
    }
    pathObject.getMeasurementList().close();
    // Lock any measurements that require it
    if (pathObject instanceof PathAnnotationObject)
        ((PathAnnotationObject) pathObject).setLocked(true);
    else if (pathObject instanceof TMACoreObject)
        ((TMACoreObject) pathObject).setLocked(true);
    return true;
}

Example 10 with PixelCalibration

use of qupath.lib.images.servers.PixelCalibration in project qupath by qupath.

the class IntensityFeaturesPlugin method addRunnableTasks.

@Override
protected void addRunnableTasks(final ImageData<BufferedImage> imageData, final PathObject parentObject, List<Runnable> tasks) {
    final ParameterList params = getParameterList(imageData);
    final ImageServer<BufferedImage> server = imageData.getServer();
    // Don't add any tasks if the downsample isn't value
    PixelCalibration cal = server.getPixelCalibration();
    double downsample = calculateDownsample(cal, params);
    if (downsample <= 0) {
        throw new IllegalArgumentException("Effective downsample must be > 0 (requested value " + GeneralTools.formatNumber(downsample, 1) + ")");
    }
    tasks.add(new IntensityFeatureRunnable(imageData, parentObject, params));
}