Examples with PathClass qupath.lib.objects.classes.PathClass used on opensource projects

Example 26 with PathClass

use of qupath.lib.objects.classes.PathClass in project qupath by qupath.

the class RetainedTrainingObjects method put.

Map<PathClass, List<PathObject>> put(final String key, final Map<PathClass, List<PathObject>> value) {
    if (key == null)
        throw new IllegalArgumentException("Cannot retain objects without a key! Do you have a project open?");
    // Also, we create a new map to ensure it's sorted
    Map<PathClass, List<PathObject>> newMap = new TreeMap<>();
    for (PathClass pathClass : value.keySet()) {
        List<PathObject> originalList = value.get(pathClass);
        List<PathObject> newList = originalList.stream().map(p -> {
            if (p.isDetection())
                return PathObjects.createDetectionObject(p.getROI(), p.getPathClass(), p.getMeasurementList());
            else {
                logger.debug("Adding non-detection object to retained map: {}", p);
                return p;
            }
        }).collect(Collectors.toList());
        newMap.put(pathClass, newList);
        value.put(pathClass, newList);
    }
    return retainedObjectsMap.put(key, value);
}

Example 27 with PathClass

use of qupath.lib.objects.classes.PathClass in project qupath by qupath.

the class PathIntensityClassifierPane method getIntensityClassifier.

/**
 * Returns a PathIntensityClassifier, or null if none was requested by the user's interactions with this JPanel.
 * @return
 */
public PathObjectClassifier getIntensityClassifier() {
    String intensityMeasurement = comboIntensities.getSelectionModel().getSelectedItem();
    PathObjectClassifier intensityClassifier = null;
    if (intensityMeasurement != null && !intensityMeasurement.equals("None")) {
        boolean singleThreshold = paramsIntensity.getBooleanParameterValue("single_threshold");
        double t1 = paramsIntensity.getDoubleParameterValue("threshold_1");
        // PathClass baseClass = PathClassFactory.getDefaultPathClass(PathClassFactory.PathClasses.TUMOR);
        PathClass baseClass = null;
        if (singleThreshold) {
            intensityClassifier = PathClassifierTools.createIntensityClassifier(baseClass, intensityMeasurement, t1);
        } else {
            double t2 = Math.max(t1, paramsIntensity.getDoubleParameterValue("threshold_2"));
            double t3 = Math.max(t2, paramsIntensity.getDoubleParameterValue("threshold_3"));
            intensityClassifier = PathClassifierTools.createIntensityClassifier(baseClass, intensityMeasurement, t1, t2, t3);
        }
    }
    return intensityClassifier;
}

Example 28 with PathClass

use of qupath.lib.objects.classes.PathClass in project qupath by qupath.

the class TestPixelClassifierTools method checkCreateObjects.

private void checkCreateObjects(ImageServer<BufferedImage> server, int[] hist, Map<PathClass, Integer> classificationLabelsReverse) throws IOException {
    var hierarchy = new PathObjectHierarchy();
    boolean success = PixelClassifierTools.createObjectsFromPredictions(server, hierarchy, Collections.singleton(hierarchy.getRootObject()), r -> PathObjects.createAnnotationObject(r), 0, 0);
    assertTrue(success);
    // Recall that we have an object for zero as well
    var annotations = new ArrayList<>(hierarchy.getAnnotationObjects());
    assertEquals(hist.length, annotations.size());
    // Check areas for all our annotations
    Collections.sort(annotations, Comparator.comparingInt(a -> classificationLabelsReverse.get(a.getPathClass())));
    for (var annotation : annotations) {
        int label = classificationLabelsReverse.get(annotation.getPathClass());
        var roi = annotation.getROI();
        double area = roi.getArea();
        if (printAreas)
            logger.debug(hist[label] + ": \t" + area);
        assertEquals(hist[label], area);
        var geom = roi.getGeometry();
        if (alwaysCheckValidity || geom.getNumPoints() < MAX_POINTS_FOR_VALIDITY) {
            var error = new IsValidOp(geom).getValidationError();
            if (error != null)
                logger.warn("{}", error);
            assertNull(error);
        }
        assertEquals(hist[label], geom.getArea());
    }
}

Example 29 with PathClass

use of qupath.lib.objects.classes.PathClass in project qupath by qupath.

the class DistanceTools method detectionCentroidDistances.

/**
 * Compute the distance for all detection object centroids to the closest annotation with each valid, not-ignored classification and add
 * the result to the detection measurement list.
 * @param imageData
 * @param splitClassNames if true, split the classification name. For example, if an image contains classifications for both "CD3: CD4" and "CD3: CD8",
 *                        distances will be calculated for all components (e.g. "CD3", "CD4" and "CD8").
 */
public static void detectionCentroidDistances(ImageData<?> imageData, boolean splitClassNames) {
    var server = imageData.getServer();
    var hierarchy = imageData.getHierarchy();
    var detections = hierarchy.getCellObjects();
    if (detections.isEmpty())
        detections = hierarchy.getDetectionObjects();
    // TODO: Support TMA cores
    if (hierarchy.getTMAGrid() != null)
        logger.warn("Detection centroid distances command currently ignores TMA grid information!");
    var pathClasses = detections.stream().map(p -> p.getPathClass()).filter(p -> p != null && p.isValid() && !PathClassTools.isIgnoredClass(p)).collect(Collectors.toSet());
    var cal = server.getPixelCalibration();
    String xUnit = cal.getPixelWidthUnit();
    String yUnit = cal.getPixelHeightUnit();
    double pixelWidth = cal.getPixelWidth().doubleValue();
    double pixelHeight = cal.getPixelHeight().doubleValue();
    if (!xUnit.equals(yUnit))
        throw new IllegalArgumentException("Pixel width & height units do not match! Width " + xUnit + ", height " + yUnit);
    String unit = xUnit;
    for (PathClass pathClass : pathClasses) {
        if (splitClassNames) {
            var names = PathClassTools.splitNames(pathClass);
            for (var name : names) {
                logger.debug("Computing distances for {}", pathClass);
                var filteredDetections = detections.stream().filter(a -> PathClassTools.containsName(a.getPathClass(), name)).collect(Collectors.toList());
                if (!filteredDetections.isEmpty()) {
                    String measurementName = "Distance to detection with " + name + " " + unit;
                    centroidToCentroidDistance2D(detections, filteredDetections, pixelWidth, pixelHeight, measurementName);
                }
            }
        } else {
            logger.debug("Computing distances for {}", pathClass);
            var filteredDetections = detections.stream().filter(a -> a.getPathClass() == pathClass).collect(Collectors.toList());
            if (!filteredDetections.isEmpty()) {
                String name = "Distance to detection " + pathClass + " " + unit;
                centroidToCentroidDistance2D(detections, filteredDetections, pixelWidth, pixelHeight, name);
            }
        }
    }
    hierarchy.fireObjectMeasurementsChangedEvent(DistanceTools.class, detections);
}

Example 30 with PathClass

use of qupath.lib.objects.classes.PathClass in project qupath by qupath.

the class ClassifierBuilderPane method exportTrainingFeatures.

private boolean exportTrainingFeatures(final File file) {
    // First, add existing objects to map
    ImageData<?> imageData = getImageData();
    // Get the features to export
    List<String> features = featurePanel.getSelectedFeatures();
    // Write the header
    PrintWriter writer;
    try {
        writer = new PrintWriter(file);
    } catch (FileNotFoundException e) {
        e.printStackTrace();
        return false;
    }
    boolean includePath = !retainedObjectsMap.isEmpty();
    // String delim = "\t";
    String delim = ",";
    if (includePath) {
        writer.print("Image");
        writer.print(delim);
    }
    writer.print("Class");
    for (String feature : features) {
        writer.print(delim);
        // Make sure we replace the delimiter so we don't have trouble
        writer.print(feature.replace(delim, "-"));
    }
    writer.println();
    // Write the current objects
    String currentPath = null;
    if (imageData != null) {
        currentPath = imageData.getServerPath();
        Map<PathClass, List<PathObject>> map = getTrainingMap();
        for (Entry<PathClass, List<PathObject>> entry : map.entrySet()) {
            for (PathObject pathObject : entry.getValue()) {
                if (includePath) {
                    writer.print(currentPath);
                    writer.print(delim);
                }
                writer.print(entry.getKey().getName());
                writer.print(delim);
                for (String name : features) {
                    writer.print(Double.toString(pathObject.getMeasurementList().getMeasurementValue(name)));
                    writer.print(delim);
                }
                writer.println();
            }
        }
    }
    writer.close();
    return true;
}