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

Example 11 with PixelCalibration

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

the class RefineAnnotationsPlugin method getTasks.

@Override
protected Collection<Runnable> getTasks(final PluginRunner<T> runner) {
    Collection<? extends PathObject> parentObjects = getParentObjects(runner);
    if (parentObjects == null || parentObjects.isEmpty())
        return Collections.emptyList();
    // Add a single task, to avoid multithreading - which may complicate setting parents
    List<Runnable> tasks = new ArrayList<>(1);
    PathObjectHierarchy hierarchy = getHierarchy(runner);
    double minFragmentSize;
    double maxHoleSize, maxHoleSizeTemp;
    ImageServer<T> server = getServer(runner);
    PixelCalibration cal = server.getPixelCalibration();
    if (cal.hasPixelSizeMicrons()) {
        double pixelAreaMicrons = cal.getPixelWidthMicrons() * cal.getPixelHeightMicrons();
        minFragmentSize = params.getDoubleParameterValue("minFragmentSizeMicrons") / pixelAreaMicrons;
        maxHoleSizeTemp = params.getDoubleParameterValue("maxHoleSizeMicrons") / pixelAreaMicrons;
    } else {
        minFragmentSize = params.getDoubleParameterValue("minFragmentSizePixels");
        maxHoleSizeTemp = params.getDoubleParameterValue("maxHoleSizePixels");
    }
    // Handle negative values
    if (maxHoleSizeTemp < 0)
        maxHoleSize = Double.POSITIVE_INFINITY;
    else
        maxHoleSize = maxHoleSizeTemp;
    // Want to reset selection
    PathObject selected = hierarchy.getSelectionModel().getSelectedObject();
    Collection<PathObject> previousSelection = new ArrayList<>(hierarchy.getSelectionModel().getSelectedObjects());
    tasks.add(() -> {
        List<PathObject> toRemove = new ArrayList<>();
        Map<PathROIObject, ROI> toUpdate = new HashMap<>();
        for (PathObject pathObject : parentObjects) {
            ROI roiOrig = pathObject.getROI();
            if (roiOrig == null || !roiOrig.isArea())
                continue;
            ROI roiUpdated = RoiTools.removeSmallPieces(roiOrig, minFragmentSize, maxHoleSize);
            if (roiUpdated == null || roiUpdated.isEmpty())
                toRemove.add(pathObject);
            else if (roiOrig != roiUpdated && pathObject instanceof PathROIObject) {
                toUpdate.put((PathROIObject) pathObject, roiUpdated);
            }
        }
        if (toRemove.isEmpty() && toUpdate.isEmpty())
            return;
        hierarchy.getSelectionModel().clearSelection();
        if (!toRemove.isEmpty())
            hierarchy.removeObjects(toRemove, true);
        if (!toUpdate.isEmpty()) {
            hierarchy.removeObjects(toUpdate.keySet(), true);
            toUpdate.forEach((p, r) -> p.setROI(r));
            hierarchy.addPathObjects(toUpdate.keySet());
        }
        hierarchy.getSelectionModel().selectObjects(previousSelection);
        hierarchy.getSelectionModel().setSelectedObject(selected, true);
    });
    return tasks;
}

Example 12 with PixelCalibration

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

the class IntensityFeaturesPlugin method getPreferredTileSizePixels.

private 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) Math.round(tileSize / cal.getPixelWidthMicrons());
        tileHeight = (int) Math.round(tileSize / cal.getPixelHeightMicrons());
    } else {
        tileWidth = (int) Math.round(params.getDoubleParameterValue("tileSizePixels"));
        tileHeight = tileWidth;
    }
    return ImmutableDimension.getInstance(tileWidth, tileHeight);
}

Example 13 with PixelCalibration

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

the class DelaunayTools method createGeometryExtractor.

private static Function<PathObject, Collection<Coordinate>> createGeometryExtractor(PixelCalibration cal, boolean preferNucleus, double densifyFactor, double erosion) {
    PrecisionModel precision = calibrated(cal) ? null : GeometryTools.getDefaultFactory().getPrecisionModel();
    AffineTransformation transform = calibrated(cal) ? AffineTransformation.scaleInstance(cal.getPixelWidth().doubleValue(), cal.getPixelHeight().doubleValue()) : null;
    return p -> {
        var roi = PathObjectTools.getROI(p, preferNucleus);
        if (roi == null || roi.isEmpty())
            return Collections.emptyList();
        var geom = roi.getGeometry();
        if (transform != null)
            geom = transform.transform(geom);
        // Shared boundaries can be problematic, so try to buffer away from these
        double buffer = -Math.abs(erosion);
        if (buffer < 0 && geom instanceof Polygonal) {
            var geomBefore = geom;
            geom = GeometryTools.attemptOperation(geom, g -> g.buffer(buffer));
            // Do not permit Geometry to disappear
            if (geom.isEmpty()) {
                geom = geomBefore;
            }
        }
        // Therefore we take extra care in case empty geometries are being generated accidentally.
        if (precision != null) {
            var geom2 = GeometryTools.attemptOperation(geom, g -> GeometryPrecisionReducer.reduce(g, precision));
            if (!geom2.isEmpty())
                geom = geom2;
        }
        if (densifyFactor > 0) {
            var geom2 = GeometryTools.attemptOperation(geom, g -> Densifier.densify(g, densifyFactor));
            if (!geom2.isEmpty())
                geom = geom2;
        }
        // if (!(geom instanceof Polygon))
        // logger.warn("Unexpected Geometry: {}", geom);
        // Making precise is essential! Otherwise there can be small artifacts occurring
        var coords = geom.getCoordinates();
        var output = new LinkedHashSet<Coordinate>();
        var p2 = precision;
        Coordinate lastCoordinate = null;
        if (p2 == null)
            p2 = GeometryTools.getDefaultFactory().getPrecisionModel();
        // Add coordinates, unless they are extremely close to an existing coordinate
        int n = coords.length;
        if (n == 0) {
            logger.warn("Empty Geometry found for {}", p);
            return Collections.emptyList();
        }
        double minDistance = densifyFactor * 0.5;
        var firstCoordinate = coords[0];
        while (n > 2 && firstCoordinate.distance(coords[n - 1]) < minDistance) n--;
        for (int i = 0; i < n; i++) {
            var c = coords[i];
            p2.makePrecise(c);
            if (i == 0 || c.distance(lastCoordinate) > minDistance) {
                output.add(c);
                lastCoordinate = c;
            }
        }
        return output;
    };
}

Example 14 with PixelCalibration

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

the class ClassificationResolution method getDefaultResolutions.

/**
 * Get a list of default resolutions to show, derived from {@link PixelCalibration} objects.
 * @param imageData
 * @param selected
 * @return
 */
public static List<ClassificationResolution> getDefaultResolutions(ImageData<?> imageData, ClassificationResolution selected) {
    var temp = new ArrayList<ClassificationResolution>();
    PixelCalibration cal = imageData.getServer().getPixelCalibration();
    int scale = 1;
    for (String name : resolutionNames) {
        var newResolution = new ClassificationResolution(name, cal.createScaledInstance(scale, scale, 1));
        if (Objects.equals(selected, newResolution))
            temp.add(selected);
        else
            temp.add(newResolution);
        scale *= 2;
    }
    if (selected == null)
        selected = temp.get(0);
    else if (!temp.contains(selected))
        temp.add(selected);
    return temp;
}

Example 15 with PixelCalibration

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

the class PixelClassifierPane method addResolution.

private boolean addResolution() {
    var imageData = qupath.getImageData();
    ImageServer<BufferedImage> server = imageData == null ? null : imageData.getServer();
    if (server == null) {
        Dialogs.showNoImageError("Add resolution");
        return false;
    }
    String units = null;
    Double pixelSize = null;
    PixelCalibration cal = server.getPixelCalibration();
    if (cal.hasPixelSizeMicrons()) {
        pixelSize = Dialogs.showInputDialog("Add resolution", "Enter requested pixel size in " + GeneralTools.micrometerSymbol(), 1.0);
        units = PixelCalibration.MICROMETER;
    } else {
        pixelSize = Dialogs.showInputDialog("Add resolution", "Enter requested downsample factor", 1.0);
    }
    if (pixelSize == null)
        return false;
    ClassificationResolution res;
    if (PixelCalibration.MICROMETER.equals(units)) {
        double scale = pixelSize / cal.getAveragedPixelSizeMicrons();
        res = new ClassificationResolution("Custom", cal.createScaledInstance(scale, scale, 1));
    } else
        res = new ClassificationResolution("Custom", cal.createScaledInstance(pixelSize, pixelSize, 1));
    List<ClassificationResolution> temp = new ArrayList<>(resolutions);
    temp.add(res);
    Collections.sort(temp, Comparator.comparingDouble((ClassificationResolution w) -> w.cal.getAveragedPixelSize().doubleValue()));
    resolutions.setAll(temp);
    comboResolutions.getSelectionModel().select(res);
    return true;
}