Examples with PathDetectionObject qupath.lib.objects.PathDetectionObject used on opensource projects

Example 1 with PathDetectionObject

use of qupath.lib.objects.PathDetectionObject in project qupath by qupath.

the class PathHierarchyPaintingHelper method paintObject.

/**
 * Paint an object (or, more precisely, its ROI), optionally along with the ROIs of any child objects.
 *
 * This is subject to the OverlayOptions, and therefore may not actually end up painting anything
 * (if the settings are such that objects of the class provided are not to be displayed)
 *
 * @param pathObject
 * @param paintChildren
 * @param g
 * @param boundsDisplayed
 * @param overlayOptions
 * @param selectionModel
 * @param downsample
 * @return true if anything was painted, false otherwise
 */
public static boolean paintObject(PathObject pathObject, boolean paintChildren, Graphics2D g, Rectangle boundsDisplayed, OverlayOptions overlayOptions, PathObjectSelectionModel selectionModel, double downsample) {
    if (pathObject == null)
        return false;
    // g.setRenderingHint(RenderingHints.KEY_ALPHA_INTERPOLATION, RenderingHints.VALUE_ALPHA_INTERPOLATION_SPEED);
    // g.setRenderingHint(RenderingHints.KEY_ALPHA_INTERPOLATION, RenderingHints.VALUE_ALPHA_INTERPOLATION_QUALITY);
    // Always paint the selected object
    // Note: this makes the assumption that child ROIs are completely contained within their parents;
    // this probably should be the case, but isn't guaranteed
    boolean isSelected = (selectionModel != null && selectionModel.isSelected(pathObject)) && (PathPrefs.useSelectedColorProperty().get() || !PathObjectTools.hasPointROI(pathObject));
    boolean isDetectedObject = pathObject.isDetection() || (pathObject.isTile() && pathObject.hasMeasurements());
    // Check if the PathClass isn't being shown
    PathClass pathClass = pathObject.getPathClass();
    if (!isSelected && overlayOptions != null && overlayOptions.isPathClassHidden(pathClass))
        return false;
    boolean painted = false;
    // See if we need to check the children
    ROI pathROI = pathObject.getROI();
    if (pathROI != null) {
        double roiBoundsX = pathROI.getBoundsX();
        double roiBoundsY = pathROI.getBoundsY();
        double roiBoundsWidth = pathROI.getBoundsWidth();
        double roiBoundsHeight = pathROI.getBoundsHeight();
        if (PathObjectTools.hasPointROI(pathObject) || boundsDisplayed == null || pathROI instanceof LineROI || boundsDisplayed.intersects(roiBoundsX, roiBoundsY, Math.max(roiBoundsWidth, 1), Math.max(roiBoundsHeight, 1))) {
            // Paint the ROI, if necessary
            if (isSelected || (overlayOptions.getShowDetections() && isDetectedObject) || (overlayOptions.getShowAnnotations() && pathObject.isAnnotation()) || (overlayOptions.getShowTMAGrid() && pathObject.isTMACore())) {
                boolean doFill = overlayOptions.getFillDetections() || pathObject instanceof ParallelTileObject;
                boolean doOutline = true;
                Color color = null;
                boolean useMapper = false;
                double fillOpacity = .75;
                if (isSelected && PathPrefs.useSelectedColorProperty().get() && PathPrefs.colorSelectedObjectProperty().getValue() != null)
                    color = ColorToolsAwt.getCachedColor(PathPrefs.colorSelectedObjectProperty().get());
                else {
                    MeasurementMapper mapper = overlayOptions.getMeasurementMapper();
                    useMapper = mapper != null && mapper.isValid() && pathObject.isDetection();
                    if (useMapper) {
                        if (pathObject.hasMeasurements()) {
                            Integer rgb = mapper.getColorForObject(pathObject);
                            // If the mapper returns null, the object shouldn't be painted
                            if (rgb == null)
                                return false;
                            // , mapper.getColorMapper().hasAlpha());
                            color = ColorToolsAwt.getCachedColor(rgb);
                        } else
                            color = null;
                        // System.out.println(color + " - " + pathObject.getMeasurementList().getMeasurementValue(mapper.));
                        fillOpacity = 1.0;
                        // Outlines are not so helpful with the measurement mapper
                        if (doFill)
                            doOutline = doOutline && !pathObject.isTile();
                    } else {
                        Integer rgb = ColorToolsFX.getDisplayedColorARGB(pathObject);
                        color = ColorToolsAwt.getCachedColor(rgb);
                    }
                // color = PathObjectHelpers.getDisplayedColor(pathObject);
                }
                // Check if we have only one or two pixels to draw - if so, we can be done quickly
                if (isDetectedObject && downsample > 4 && roiBoundsWidth / downsample < 3 && roiBoundsHeight / downsample < 3) {
                    int x = (int) roiBoundsX;
                    int y = (int) roiBoundsY;
                    // Prefer rounding up, lest we lose a lot of regions unnecessarily
                    int w = (int) (roiBoundsWidth + .9);
                    int h = (int) (roiBoundsHeight + .9);
                    if (w > 0 && h > 0) {
                        g.setColor(color);
                        // g.setColor(DisplayHelpers.getMoreTranslucentColor(color));
                        // g.setStroke(getCachedStroke(overlayOptions.strokeThinThicknessProperty().get()));
                        g.fillRect(x, y, w, h);
                    }
                    painted = true;
                } else {
                    Stroke stroke = null;
                    // Decide whether to fill or not
                    Color colorFill = doFill && (isDetectedObject || PathObjectTools.hasPointROI(pathObject)) ? color : null;
                    if (colorFill != null && fillOpacity != 1) {
                        if (pathObject instanceof ParallelTileObject)
                            colorFill = ColorToolsAwt.getMoreTranslucentColor(colorFill);
                        else if (pathObject instanceof PathCellObject && overlayOptions.getShowCellBoundaries() && overlayOptions.getShowCellNuclei()) {
                            // if (isSelected)
                            // colorFill = ColorToolsAwt.getTranslucentColor(colorFill);
                            // else
                            colorFill = ColorToolsAwt.getMoreTranslucentColor(colorFill);
                        } else if (pathObject.getParent() instanceof PathDetectionObject) {
                            colorFill = ColorToolsAwt.getTranslucentColor(colorFill);
                        } else if (pathObject instanceof PathTileObject && pathClass == null && color != null && color.getRGB() == PathPrefs.colorTileProperty().get()) {
                            // Don't fill in empty, unclassified tiles
                            // DisplayHelpers.getMoreTranslucentColor(colorFill);
                            colorFill = null;
                        }
                    }
                    // Color colorStroke = doOutline ? (colorFill == null ? color : (downsample > overlayOptions.strokeThinThicknessProperty().get() ? null : DisplayHelpers.darkenColor(color))) : null;
                    Color colorStroke = doOutline ? (colorFill == null ? color : ColorToolsAwt.darkenColor(color)) : null;
                    // For thick lines, antialiasing is very noticeable... less so for thin lines (of which there may be a huge number)
                    if (isDetectedObject) {
                        // Detections inside detections get half the line width
                        if (pathObject.getParent() instanceof PathDetectionObject)
                            stroke = getCachedStroke(PathPrefs.detectionStrokeThicknessProperty().get() / 2.0);
                        else
                            stroke = getCachedStroke(PathPrefs.detectionStrokeThicknessProperty().get());
                    } else {
                        double thicknessScale = downsample * (isSelected && !PathPrefs.useSelectedColorProperty().get() ? 1.6 : 1);
                        float thickness = (float) (PathPrefs.annotationStrokeThicknessProperty().get() * thicknessScale);
                        if (isSelected && pathObject.getParent() == null && PathPrefs.selectionModeProperty().get()) {
                            stroke = getCachedStrokeDashed(thickness);
                        } else {
                            stroke = getCachedStroke(thickness);
                        }
                    }
                    g.setStroke(stroke);
                    boolean paintSymbols = overlayOptions.getDetectionDisplayMode() == DetectionDisplayMode.CENTROIDS && pathObject.isDetection() && !pathObject.isTile();
                    if (paintSymbols) {
                        pathROI = PathObjectTools.getROI(pathObject, true);
                        double x = pathROI.getCentroidX();
                        double y = pathROI.getCentroidY();
                        double radius = PathPrefs.detectionStrokeThicknessProperty().get() * 2.0;
                        if (pathObject.getParent() instanceof PathDetectionObject)
                            radius /= 2.0;
                        Shape shape;
                        int nSubclasses = 0;
                        if (pathClass != null) {
                            nSubclasses = PathClassTools.splitNames(pathClass).size();
                        }
                        switch(nSubclasses) {
                            case 0:
                                var ellipse = localEllipse2D.get();
                                ellipse.setFrame(x - radius, y - radius, radius * 2, radius * 2);
                                shape = ellipse;
                                break;
                            case 1:
                                var rect = localRect2D.get();
                                rect.setFrame(x - radius, y - radius, radius * 2, radius * 2);
                                shape = rect;
                                break;
                            case 2:
                                var triangle = localPath2D.get();
                                double sqrt3 = Math.sqrt(3.0);
                                triangle.reset();
                                triangle.moveTo(x, y - radius * 2.0 / sqrt3);
                                triangle.lineTo(x - radius, y + radius / sqrt3);
                                triangle.lineTo(x + radius, y + radius / sqrt3);
                                triangle.closePath();
                                shape = triangle;
                                break;
                            case 3:
                                var plus = localPath2D.get();
                                plus.reset();
                                plus.moveTo(x, y - radius);
                                plus.lineTo(x, y + radius);
                                plus.moveTo(x - radius, y);
                                plus.lineTo(x + radius, y);
                                shape = plus;
                                break;
                            default:
                                var cross = localPath2D.get();
                                cross.reset();
                                radius /= Math.sqrt(2);
                                cross.moveTo(x - radius, y - radius);
                                cross.lineTo(x + radius, y + radius);
                                cross.moveTo(x + radius, y - radius);
                                cross.lineTo(x - radius, y + radius);
                                shape = cross;
                                break;
                        }
                        paintShape(shape, g, colorStroke, stroke, colorFill);
                    } else if (pathObject instanceof PathCellObject) {
                        PathCellObject cell = (PathCellObject) pathObject;
                        if (overlayOptions.getShowCellBoundaries())
                            paintROI(pathROI, g, colorStroke, stroke, colorFill, downsample);
                        if (overlayOptions.getShowCellNuclei())
                            paintROI(cell.getNucleusROI(), g, colorStroke, stroke, colorFill, downsample);
                        painted = true;
                    } else {
                        if ((overlayOptions.getFillAnnotations() && pathObject.isAnnotation() && pathObject.getPathClass() != PathClassFactory.getPathClass(StandardPathClasses.REGION) && (pathObject.getPathClass() != null || !pathObject.hasChildren())) || (pathObject.isTMACore() && overlayOptions.getShowTMACoreLabels()))
                            paintROI(pathROI, g, colorStroke, stroke, ColorToolsAwt.getMoreTranslucentColor(colorStroke), downsample);
                        else
                            paintROI(pathROI, g, colorStroke, stroke, colorFill, downsample);
                        painted = true;
                    }
                }
            }
        }
    }
    // Paint the children, if necessary
    if (paintChildren) {
        for (PathObject childObject : pathObject.getChildObjectsAsArray()) {
            // Only call the painting method if required
            ROI childROI = childObject.getROI();
            if ((childROI != null && boundsDisplayed.intersects(childROI.getBoundsX(), childROI.getBoundsY(), childROI.getBoundsWidth(), childROI.getBoundsHeight())) || childObject.hasChildren())
                painted = paintObject(childObject, paintChildren, g, boundsDisplayed, overlayOptions, selectionModel, downsample) | painted;
        }
    }
    return painted;
}

Example 2 with PathDetectionObject

use of qupath.lib.objects.PathDetectionObject in project qupath by qupath.

the class IJExtension method extractOverlay.

/**
 * Extract an ImageJ overlay for the specified region.
 * @param hierarchy
 * @param request
 * @param options options to control which objects are being displayed
 * @param filter optional additional filter used to determine which objects will be included (may be used in combination with options)
 * @return
 */
public static Overlay extractOverlay(PathObjectHierarchy hierarchy, RegionRequest request, OverlayOptions options, Predicate<PathObject> filter) {
    Overlay overlay = new Overlay();
    double downsample = request.getDownsample();
    double xOrigin = -request.getX() / downsample;
    double yOrigin = -request.getY() / downsample;
    // TODO: Permit filling/unfilling ROIs
    for (PathObject child : hierarchy.getObjectsForRegion(PathObject.class, request, null)) {
        if (filter != null && !filter.test(child))
            continue;
        if (child.hasROI()) {
            // Check if this is displayed - skip it not
            if (options != null && ((child instanceof PathDetectionObject && !options.getShowDetections()) || (child instanceof PathAnnotationObject && !options.getShowAnnotations()) || (child instanceof TMACoreObject && !options.getShowTMAGrid())))
                continue;
            boolean isCell = child instanceof PathCellObject;
            Color color = ColorToolsAwt.getCachedColor(ColorToolsFX.getDisplayedColorARGB(child));
            if (!(isCell && (options == null || !options.getShowCellBoundaries()))) {
                Roi roi = IJTools.convertToIJRoi(child.getROI(), xOrigin, yOrigin, downsample);
                roi.setStrokeColor(color);
                roi.setName(child.getDisplayedName());
                // roi.setStrokeWidth(2);
                overlay.add(roi);
            }
            if (isCell && (options == null || options.getShowCellNuclei())) {
                ROI nucleus = ((PathCellObject) child).getNucleusROI();
                if (nucleus == null)
                    continue;
                Roi roi = IJTools.convertToIJRoi(((PathCellObject) child).getNucleusROI(), xOrigin, yOrigin, downsample);
                roi.setStrokeColor(color);
                roi.setName(child.getDisplayedName() + " - nucleus");
                overlay.add(roi);
            }
        }
    }
    return overlay;
}

Example 3 with PathDetectionObject

use of qupath.lib.objects.PathDetectionObject in project qupath by qupath.

the class SmoothFeaturesPlugin method smoothMeasurements.

/**
 * Using the centroids of the ROIs within PathObjects, 'smooth' measurements by summing up the corresponding measurements of
 * nearby objects, weighted by centroid distance.
 *
 * @param pathObjects
 * @param measurements
 * @param fwhmPixels
 * @param fwhmString
 * @param withinClass
 * @param useLegacyNames
 */
// public static Set<String> smoothMeasurements(List<PathObject> pathObjects, List<String> measurements, double fwhmPixels) {
public static void smoothMeasurements(List<PathObject> pathObjects, List<String> measurements, double fwhmPixels, String fwhmString, boolean withinClass, boolean useLegacyNames) {
    if (measurements.isEmpty() || pathObjects.size() <= 1)
        // Collections.emptySet();
        return;
    if (fwhmString == null)
        fwhmString = String.format("%.2f px", fwhmPixels);
    double fwhmPixels2 = fwhmPixels * fwhmPixels;
    double sigmaPixels = fwhmPixels / Math.sqrt(8 * Math.log(2));
    double sigma2 = 2 * sigmaPixels * sigmaPixels;
    double maxDist = sigmaPixels * 3;
    // Maximum separation
    double maxDistSq = maxDist * maxDist;
    int nObjects = pathObjects.size();
    // int counter = 0;
    // Sort by x-coordinate - this gives us a method of breaking early
    Collections.sort(pathObjects, new Comparator<PathObject>() {

        @Override
        public int compare(PathObject o1, PathObject o2) {
            double x1 = o1.getROI().getCentroidX();
            double x2 = o2.getROI().getCentroidX();
            // System.out.println(String.format("(%.2f, %.2f) vs (%.2f, %.2f)", o1.getROI().getCentroidX(), o1.getROI().getCentroidY(), o2.getROI().getCentroidX(), o2.getROI().getCentroidY()));				}
            return Double.compare(x1, x2);
        // if (x1 > x2)
        // return 1;
        // if (x2 < x1)
        // return -1;
        // System.out.println(x1 + " vs. " + x2);
        // System.out.println(String.format("(%.2f, %.2f) vs (%.2f, %.2f)", o1.getROI().getCentroidX(), o1.getROI().getCentroidY(), o2.getROI().getCentroidX(), o2.getROI().getCentroidY()));
        // return 0;
        // return (int)Math.signum(o1.getROI().getCentroidX() - o2.getROI().getCentroidX());
        }
    });
    // Create a LUT for distances - calculating exp every time is expensive
    double[] distanceWeights = new double[(int) (maxDist + .5) + 1];
    for (int i = 0; i < distanceWeights.length; i++) {
        distanceWeights[i] = Math.exp(-(i * i) / sigma2);
    }
    System.currentTimeMillis();
    float[] xCentroids = new float[nObjects];
    float[] yCentroids = new float[nObjects];
    PathClass[] pathClasses = new PathClass[nObjects];
    int[] nearbyDetectionCounts = new int[nObjects];
    float[][] measurementsWeighted = new float[nObjects][measurements.size()];
    float[][] measurementDenominators = new float[nObjects][measurements.size()];
    float[][] measurementValues = new float[nObjects][measurements.size()];
    for (int i = 0; i < nObjects; i++) {
        PathObject pathObject = pathObjects.get(i);
        if (withinClass)
            pathClasses[i] = pathObject.getPathClass() == null ? null : pathObject.getPathClass().getBaseClass();
        ROI roi = pathObject.getROI();
        xCentroids[i] = (float) roi.getCentroidX();
        yCentroids[i] = (float) roi.getCentroidY();
        MeasurementList measurementList = pathObject.getMeasurementList();
        int ind = 0;
        for (String name : measurements) {
            float value = (float) measurementList.getMeasurementValue(name);
            // Used to cache values
            measurementValues[i][ind] = value;
            // Based on distances and measurements
            measurementsWeighted[i][ind] = value;
            // Based on distances along
            measurementDenominators[i][ind] = 1;
            ind++;
        }
    }
    String prefix, postfix, denomName, countsName;
    // Use previous syntax for naming smoothed measurements
    if (useLegacyNames) {
        prefix = "";
        postfix = String.format(" - Smoothed (FWHM %s)", fwhmString);
        denomName = String.format("Smoothed denominator (local density, FWHM %s)", fwhmString);
        countsName = String.format("Nearby detection counts (radius %s)", fwhmString);
    } else {
        prefix = String.format("Smoothed: %s: ", fwhmString);
        postfix = "";
        // prefix + "Weighted density";
        denomName = null;
        countsName = prefix + "Nearby detection counts";
    // denomName = prefix + "Denominator (local density)";
    // countsName = prefix + "Nearby detection counts";
    }
    // Loop through objects, computing predominant class based on distance weighting
    for (int i = 0; i < nObjects; i++) {
        // Extract the current class index
        PathObject pathObject = pathObjects.get(i);
        PathClass pathClass = pathClasses[i];
        MeasurementList measurementList = pathObject.getMeasurementList();
        float[] mValues = measurementValues[i];
        float[] mWeighted = measurementsWeighted[i];
        float[] mDenominator = measurementDenominators[i];
        // Compute centroid distances
        double xi = xCentroids[i];
        double yi = yCentroids[i];
        for (int j = i + 1; j < nObjects; j++) {
            double xj = xCentroids[j];
            double yj = yCentroids[j];
            // Break early if we are already too far away
            if (Math.abs(xj - xi) > maxDist) {
                break;
            }
            double distSq = (xj - xi) * (xj - xi) + (yj - yi) * (yj - yi);
            // // Check if we are close enough to have an influence
            if (distSq > maxDistSq || Double.isNaN(distSq))
                continue;
            // Check if the class is ok, if check needed
            if (withinClass && pathClass != pathClasses[j])
                continue;
            // Update the counts, if close enough
            if (distSq < fwhmPixels2) {
                nearbyDetectionCounts[i]++;
                nearbyDetectionCounts[j]++;
            }
            // Update the class weights for both objects currently being tested
            // Compute weight based on centroid distances
            // double weight = Math.exp(-distSq/sigma2);
            // * pathObjects.get(j).getClassProbability();
            double weight = distanceWeights[(int) (Math.sqrt(distSq) + .5)];
            float[] temp = measurementValues[j];
            float[] tempWeighted = measurementsWeighted[j];
            float[] tempDenominator = measurementDenominators[j];
            for (int ind = 0; ind < measurements.size(); ind++) {
                float tempVal = temp[ind];
                if (Float.isNaN(tempVal))
                    continue;
                mWeighted[ind] += tempVal * weight;
                mDenominator[ind] += weight;
                float tempVal2 = mValues[ind];
                if (Float.isNaN(tempVal2))
                    continue;
                tempWeighted[ind] += tempVal2 * weight;
                tempDenominator[ind] += weight;
            }
        }
        // Store the measurements
        int ind = 0;
        float maxDenominator = Float.NEGATIVE_INFINITY;
        for (String name : measurements) {
            // if (name.contains(" - Smoothed (FWHM ") || name.startsWith("Smoothed denominator (local density, ") || name.startsWith("Nearby detection counts"))
            // continue;
            float denominator = mDenominator[ind];
            if (denominator > maxDenominator)
                maxDenominator = denominator;
            String nameToAdd = prefix + name + postfix;
            measurementList.putMeasurement(nameToAdd, mWeighted[ind] / denominator);
            // measurementsAdded.add(nameToAdd);
            // measurementList.putMeasurement(name + " - weighted sum", mWeighted[ind]); // TODO: Support optionally providing weighted sums
            // measurementList.addMeasurement(name + " - smoothed", mWeighted[ind] / mDenominator[ind]);
            ind++;
        }
        if (pathObject instanceof PathDetectionObject && denomName != null) {
            measurementList.putMeasurement(denomName, maxDenominator);
        // measurementsAdded.add(denomName);
        }
        if (pathObject instanceof PathDetectionObject && countsName != null) {
            measurementList.putMeasurement(countsName, nearbyDetectionCounts[i]);
        // measurementsAdded.add(countsName);
        }
        measurementList.close();
    }
    System.currentTimeMillis();
// return measurementsAdded;
}

Example 4 with PathDetectionObject

use of qupath.lib.objects.PathDetectionObject in project qupath by qupath.

the class ObservableMeasurementTableData method updateMeasurementList.

/**
 * Update the entire measurement list for the current objects.
 * @see #setImageData(ImageData, Collection)
 */
public synchronized void updateMeasurementList() {
    // PathPrefs.setAllredMinPercentagePositive(0);
    builderMap.clear();
    // Add the image name
    if (!PathPrefs.maskImageNamesProperty().get())
        builderMap.put("Image", new ImageNameMeasurementBuilder(imageData));
    // Check if we have any annotations / TMA cores
    boolean containsDetections = false;
    boolean containsAnnotations = false;
    // boolean containsParentAnnotations = false;
    boolean containsTMACores = false;
    boolean containsRoot = false;
    List<PathObject> pathObjectListCopy = new ArrayList<>(list);
    for (PathObject temp : pathObjectListCopy) {
        if (temp instanceof PathAnnotationObject) {
            // if (temp.hasChildren())
            // containsParentAnnotations = true;
            containsAnnotations = true;
        } else if (temp instanceof TMACoreObject) {
            containsTMACores = true;
        } else if (temp instanceof PathDetectionObject) {
            containsDetections = true;
        } else if (temp.isRootObject())
            containsRoot = true;
    }
    boolean detectionsAnywhere = imageData == null ? containsDetections : !imageData.getHierarchy().getDetectionObjects().isEmpty();
    // Include the object displayed name
    // if (containsDetections || containsAnnotations || containsTMACores)
    builderMap.put("Name", new ObjectNameMeasurementBuilder());
    // Include the class
    if (containsAnnotations || containsDetections) {
        builderMap.put("Class", new PathClassMeasurementBuilder());
        // Get the name of the containing TMA core if we have anything other than cores
        if (imageData != null && imageData.getHierarchy().getTMAGrid() != null) {
            builderMap.put("TMA core", new TMACoreNameMeasurementBuilder());
        }
        // Get the name of the first parent object
        builderMap.put("Parent", new ParentNameMeasurementBuilder());
    }
    // Include the TMA missing status, if appropriate
    if (containsTMACores) {
        builderMap.put("Missing", new MissingTMACoreMeasurementBuilder());
    }
    if (containsAnnotations || containsDetections) {
        builderMap.put("ROI", new ROINameMeasurementBuilder());
    }
    // Add centroids
    if (containsAnnotations || containsDetections || containsTMACores) {
        // ROICentroidMeasurementBuilder builder = new ROICentroidMeasurementBuilder(imageData, CentroidType.X);
        // builderMap.put("Centroid X", builder);
        // builder = new ROICentroidMeasurementBuilder(imageData, CentroidType.Y);
        // builderMap.put("Centroid Y", builder);
        ROICentroidMeasurementBuilder builder = new ROICentroidMeasurementBuilder(imageData, CentroidType.X);
        builderMap.put(builder.getName(), builder);
        builder = new ROICentroidMeasurementBuilder(imageData, CentroidType.Y);
        builderMap.put(builder.getName(), builder);
    }
    // If we have metadata, store it
    Set<String> metadataNames = new LinkedHashSet<>();
    metadataNames.addAll(builderMap.keySet());
    for (PathObject pathObject : pathObjectListCopy) {
        if (pathObject instanceof MetadataStore) {
            metadataNames.addAll(((MetadataStore) pathObject).getMetadataKeys());
        }
    }
    // Ensure we have suitable builders
    for (String name : metadataNames) {
        if (!builderMap.containsKey(name))
            builderMap.put(name, new StringMetadataMeasurementBuilder(name));
    }
    // Get all the 'built-in' feature measurements, stored in the measurement list
    Collection<String> features = PathClassifierTools.getAvailableFeatures(pathObjectListCopy);
    // Add derived measurements if we don't have only detections
    if (containsAnnotations || containsTMACores || containsRoot) {
        if (detectionsAnywhere) {
            var builder = new ObjectTypeCountMeasurementBuilder(PathDetectionObject.class);
            builderMap.put(builder.getName(), builder);
            features.add(builder.getName());
        }
        // Here, we allow TMA cores to act like annotations
        manager = new DerivedMeasurementManager(getImageData(), containsAnnotations || containsTMACores);
        for (MeasurementBuilder<?> builder2 : manager.getMeasurementBuilders()) {
            builderMap.put(builder2.getName(), builder2);
            features.add(builder2.getName());
        }
    }
    // If we have an annotation, add shape features
    if (containsAnnotations) {
        boolean anyPoints = false;
        boolean anyAreas = false;
        boolean anyLines = false;
        @SuppressWarnings("unused") boolean anyPolygons = false;
        for (PathObject pathObject : pathObjectListCopy) {
            if (!pathObject.isAnnotation())
                continue;
            ROI roi = pathObject.getROI();
            if (roi == null)
                continue;
            if (roi.isPoint())
                anyPoints = true;
            if (roi.isArea())
                anyAreas = true;
            if (roi.isLine())
                anyLines = true;
            if (pathObject.getROI() instanceof PolygonROI)
                anyPolygons = true;
        }
        // Add point count, if needed
        if (anyPoints) {
            MeasurementBuilder<?> builder = new NumPointsMeasurementBuilder();
            builderMap.put(builder.getName(), builder);
            features.add(builder.getName());
        }
        // Add spatial measurements, if needed
        if (anyAreas) {
            MeasurementBuilder<?> builder = new AreaMeasurementBuilder(imageData);
            builderMap.put(builder.getName(), builder);
            features.add(builder.getName());
            builder = new PerimeterMeasurementBuilder(imageData);
            builderMap.put(builder.getName(), builder);
            features.add(builder.getName());
        }
        if (anyLines) {
            MeasurementBuilder<?> builder = new LineLengthMeasurementBuilder(imageData);
            builderMap.put(builder.getName(), builder);
            features.add(builder.getName());
        }
    // if (anyPolygons) {
    // MeasurementBuilder<?> builder = new MaxDiameterMeasurementBuilder(imageData);
    // builderMap.put(builder.getName(), builder);
    // features.add(builder.getName());
    // 
    // builder = new MinDiameterMeasurementBuilder(imageData);
    // builderMap.put(builder.getName(), builder);
    // features.add(builder.getName());
    // }
    }
    if (containsAnnotations || containsTMACores || containsRoot) {
        var pixelClassifier = getPixelLayer(imageData);
        if (pixelClassifier instanceof ImageServer<?>) {
            ImageServer<BufferedImage> server = (ImageServer<BufferedImage>) pixelClassifier;
            if (server.getMetadata().getChannelType() == ImageServerMetadata.ChannelType.CLASSIFICATION || server.getMetadata().getChannelType() == ImageServerMetadata.ChannelType.PROBABILITY) {
                var pixelManager = new PixelClassificationMeasurementManager(server);
                for (String name : pixelManager.getMeasurementNames()) {
                    // String nameLive = name + " (live)";
                    String nameLive = "(Live) " + name;
                    builderMap.put(nameLive, new PixelClassifierMeasurementBuilder(pixelManager, name));
                    features.add(nameLive);
                }
            }
        }
    }
    // Update all the lists, if necessary
    boolean changes = false;
    if (metadataNames.size() != metadataList.size() || !metadataNames.containsAll(metadataList)) {
        changes = metadataList.setAll(metadataNames);
    }
    if (features.size() != measurementList.size() || !features.containsAll(measurementList))
        changes = measurementList.setAll(features);
    if (changes) {
        if (metadataList.isEmpty())
            fullList.setAll(measurementList);
        else {
            fullList.setAll(metadataList);
            fullList.addAll(measurementList);
        }
    }
}

Example 5 with PathDetectionObject

use of qupath.lib.objects.PathDetectionObject in project qupath by qupath.

the class SmoothFeaturesPlugin method addRunnableTasks.

@Override
protected void addRunnableTasks(final ImageData<T> imageData, final PathObject parentObject, List<Runnable> tasks) {
    double fwhm;
    ImageServer<T> server = imageData.getServer();
    String fwhmStringTemp;
    PixelCalibration cal = server == null ? null : server.getPixelCalibration();
    if (cal != null && cal.hasPixelSizeMicrons()) {
        fwhm = getParameterList(imageData).getDoubleParameterValue("fwhmMicrons");
        fwhmStringTemp = GeneralTools.createFormatter(2).format(fwhm) + " " + GeneralTools.micrometerSymbol();
        fwhm /= cal.getAveragedPixelSizeMicrons();
    // params.addDoubleParameter("fwhmPixels", "Radius (FWHM)", fwhm, "pixels"); // Set the FWHM in pixels too
    } else {
        fwhm = getParameterList(imageData).getDoubleParameterValue("fwhmPixels");
        fwhmStringTemp = GeneralTools.createFormatter(2).format(fwhm) + " px";
    }
    // sigma = 50;
    final String fwhmString = fwhmStringTemp;
    final double fwhmPixels = fwhm;
    final boolean withinClass = params.getBooleanParameterValue("smoothWithinClasses");
    final boolean useLegacyNames = params.containsKey("useLegacyNames") && Boolean.TRUE.equals(params.getBooleanParameterValue("useLegacyNames"));
    tasks.add(new Runnable() {

        @Override
        public void run() {
            try {
                if (!parentObject.hasChildren())
                    return;
                // System.out.println("Smoothing with FWHM " +fwhmPixels);
                // TODO: MAKE A MORE ELEGANT LIST!!!!
                List<PathObject> pathObjects = PathObjectTools.getFlattenedObjectList(parentObject, null, false);
                Iterator<PathObject> iterObjects = pathObjects.iterator();
                while (iterObjects.hasNext()) {
                    PathObject temp = iterObjects.next();
                    if (!(temp instanceof PathDetectionObject || temp instanceof PathTileObject))
                        iterObjects.remove();
                }
                if (pathObjects.isEmpty())
                    return;
                // TODO: ACCESS & USE THE CLASSIFIER DATA!!!!
                List<String> measurements = new ArrayList<>(PathClassifierTools.getAvailableFeatures(pathObjects));
                Iterator<String> iter = measurements.iterator();
                while (iter.hasNext()) {
                    String name = iter.next().toLowerCase();
                    if (name.endsWith("smoothed") || name.startsWith("smoothed") || name.contains(" - smoothed (fwhm ") || name.startsWith("smoothed denominator (local density, ") || name.startsWith("nearby detection counts"))
                        iter.remove();
                }
                logger.debug(String.format("Smooth features: %s (FWHM: %.2f px)", parentObject.getDisplayedName(), fwhmPixels));
                smoothMeasurements(pathObjects, measurements, fwhmPixels, fwhmString, withinClass, useLegacyNames);
            // // REMOVE - the purpose was to test a 'difference of Gaussians' type of thing
            // List<String> namesAdded1 = new ArrayList<>(smoothMeasurements(pathObjects, measurements, fwhmPixels));
            // List<String> namesAdded2 = new ArrayList<>(smoothMeasurements(pathObjects, measurements, fwhmPixels * 2));
            // for (PathObject pathObject : pathObjects) {
            // MeasurementList ml = pathObject.getMeasurementList();
            // ml.ensureListOpen();
            // for (int i = 0; i < namesAdded1.size(); i++) {
            // String name1 = namesAdded1.get(i);
            // String name2 = namesAdded2.get(i);
            // double m1 = ml.getMeasurementValue(name1);
            // double m2 = ml.getMeasurementValue(name2);
            // ml.addMeasurement(name1 + " - " + name2, m1 - m2);
            // }
            // ml.closeList();
            // }
            } catch (Exception e) {
                e.printStackTrace();
                throw (e);
            }
        }
    });
}