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

Example 21 with TMACoreObject

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

the class QP method clearTMAGrid.

/**
 * Remove the TMA grid from the current {@code PathObjectHierarchy}.
 *
 * @see #getCurrentHierarchy
 */
public static void clearTMAGrid() {
    PathObjectHierarchy hierarchy = getCurrentHierarchy();
    if (hierarchy == null)
        return;
    hierarchy.setTMAGrid(null);
    PathObject selected = hierarchy.getSelectionModel().getSelectedObject();
    if (selected instanceof TMACoreObject)
        hierarchy.getSelectionModel().setSelectedObject(null);
}

Example 22 with TMACoreObject

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

the class SmoothFeaturesPlugin method getParentObjects.

@Override
protected Collection<PathObject> getParentObjects(final PluginRunner<T> runner) {
    PathObjectHierarchy hierarchy = runner.getImageData().getHierarchy();
    List<PathObject> parents = new ArrayList<>();
    if (hierarchy.getTMAGrid() != null) {
        logger.info("Smoothing using TMA cores");
        for (TMACoreObject core : hierarchy.getTMAGrid().getTMACoreList()) {
            if (core.hasChildren())
                parents.add(core);
        }
    } else {
        for (PathObject pathObject : hierarchy.getSelectionModel().getSelectedObjects()) {
            if (pathObject.isAnnotation() && pathObject.hasChildren())
                parents.add(pathObject);
        }
        if (!parents.isEmpty())
            logger.warn("Smoothing using annotations");
    }
    return parents;
}

Example 23 with TMACoreObject

use of qupath.lib.objects.TMACoreObject 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 24 with TMACoreObject

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

the class MoveTool method mouseReleased.

@Override
public void mouseReleased(MouseEvent e) {
    super.mouseReleased(e);
    if (e.isConsumed())
        return;
    var viewer = getViewer();
    RoiEditor editor = viewer.getROIEditor();
    if (editor != null && (editor.hasActiveHandle() || editor.isTranslating())) {
        boolean roiChanged = (editor.isTranslating() && editor.finishTranslation()) || editor.hasActiveHandle();
        editor.resetActiveHandle();
        // if (editor.isTranslating())
        // editor.finishTranslation();
        e.consume();
        PathObject pathObject = viewer.getSelectedObject();
        if (requestParentClipping(e) && pathObject instanceof PathAnnotationObject) {
            ROI roiNew = refineROIByParent(pathObject.getROI());
            ((PathAnnotationObject) pathObject).setROI(roiNew);
        }
        if (pathObject != null && pathObject.hasROI() && pathObject.getROI().isEmpty()) {
            if (pathObject.getParent() != null)
                viewer.getHierarchy().removeObject(pathObject, true);
            viewer.setSelectedObject(null);
        } else {
            PathObjectHierarchy hierarchy = viewer.getHierarchy();
            if (pathObject instanceof TMACoreObject) {
                hierarchy.fireHierarchyChangedEvent(pathObject);
            } else if (pathObject != null) {
                // Handle ROI changes only if required
                if (roiChanged) {
                    var updatedROI = editor.getROI();
                    if (pathObject.getROI() != updatedROI && pathObject instanceof PathROIObject)
                        ((PathROIObject) pathObject).setROI(updatedROI);
                    // PathObject parentPrevious = pathObject.getParent();
                    hierarchy.removeObjectWithoutUpdate(pathObject, true);
                    if (getCurrentParent() == null || !PathPrefs.clipROIsForHierarchyProperty().get() || e.isShiftDown())
                        hierarchy.addPathObject(pathObject);
                    else
                        hierarchy.addPathObjectBelowParent(getCurrentParent(), pathObject, true);
                // PathObject parentNew = pathObject.getParent();
                // if (parentPrevious == parentNew)
                // hierarchy.fireHierarchyChangedEvent(this, parentPrevious);
                // else
                // hierarchy.fireHierarchyChangedEvent(this);
                }
            }
            viewer.setSelectedObject(pathObject);
        }
    }
    // Optionally continue a dragging movement until the canvas comes to a standstill
    if (pDragging != null && requestDynamicDragging && System.currentTimeMillis() - lastDragTimestamp < 100 && (dx * dx + dy * dy > viewer.getDownsampleFactor())) {
        mover = new ViewerMover(viewer);
        mover.startMoving(dx, dy, false);
    } else
        viewer.setDoFasterRepaint(false);
    // Make sure we don't have a previous point (to prevent weird dragging artefacts)
    pDragging = null;
// // If we were translating, stop
// if (editor.isTranslating()) {
// editor.finishTranslation();
// // TODO: Make this more efficient!
// viewer.getPathObjectHierarchy().fireHierarchyChangedEvent();
// return;
// }
}

Example 25 with TMACoreObject

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

the class QP method clearSelectedObjects.

/**
 * Delete the selected objects from the current hierarchy, optionally keeping their child (descendant) objects.
 *
 * @param keepChildren
 */
public static void clearSelectedObjects(boolean keepChildren) {
    PathObjectHierarchy hierarchy = getCurrentHierarchy();
    if (hierarchy == null)
        return;
    Collection<PathObject> selectedRaw = hierarchy.getSelectionModel().getSelectedObjects();
    List<PathObject> selected = selectedRaw.stream().filter(p -> !(p instanceof TMACoreObject)).collect(Collectors.toList());
    hierarchy.removeObjects(selected, keepChildren);
    hierarchy.getSelectionModel().clearSelection();
}