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

Example 16 with TMACoreObject

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

the class QuPathViewer method getTooltipText.

private String getTooltipText(final double x, final double y) {
    // Try to show which TMA core is selected - if we have a TMA image
    PathObjectHierarchy hierarchy = getHierarchy();
    TMAGrid tmaGrid = hierarchy == null ? null : hierarchy.getTMAGrid();
    if (tmaGrid != null) {
        Point2D p = componentPointToImagePoint(x, y, null, false);
        TMACoreObject core = PathObjectTools.getTMACoreForPixel(tmaGrid, p.getX(), p.getY());
        if (core != null) {
            if (core.isMissing())
                return String.format("TMA Core %s\n(missing)", core.getName());
            else
                return String.format("TMA Core %s", core.getName());
        }
    }
    return null;
}

Example 17 with TMACoreObject

use of qupath.lib.objects.TMACoreObject 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 18 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 19 with TMACoreObject

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

the class PathClassifierTools method runClassifier.

/**
 * Apply a classifier to the detection objects in a hierarchy.
 * @param hierarchy
 * @param classifier
 */
public static void runClassifier(final PathObjectHierarchy hierarchy, final PathObjectClassifier classifier) {
    // Apply classifier to everything
    // If we have a TMA grid, do one core at a time
    long startTime = System.currentTimeMillis();
    TMAGrid tmaGrid = hierarchy.getTMAGrid();
    Collection<PathObject> pathObjects = new ArrayList<>();
    int nClassified = 0;
    // tmaGrid = null;
    if (tmaGrid != null) {
        for (TMACoreObject core : tmaGrid.getTMACoreList()) {
            pathObjects = PathObjectTools.getDescendantObjects(core, pathObjects, PathDetectionObject.class);
            nClassified += classifier.classifyPathObjects(pathObjects);
            pathObjects.clear();
        }
    } else {
        hierarchy.getObjects(pathObjects, PathDetectionObject.class);
        nClassified = classifier.classifyPathObjects(pathObjects);
    }
    long endTime = System.currentTimeMillis();
    logger.info(String.format("Classification time: %.2f seconds", (endTime - startTime) / 1000.));
    // Fire a change event for all detection objects
    if (nClassified > 0)
        hierarchy.fireObjectClassificationsChangedEvent(classifier, hierarchy.getObjects(null, PathDetectionObject.class));
    else
        logger.warn("No objects classified!");
}

Example 20 with TMACoreObject

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

the class ImageJMacroRunner method runPlugin.

@Override
public boolean runPlugin(final PluginRunner<BufferedImage> runner, final String arg) {
    if (!parseArgument(runner.getImageData(), arg))
        return false;
    if (dialog == null) {
        dialog = new Stage();
        dialog.initOwner(qupath.getStage());
        dialog.setTitle("ImageJ macro runner");
        BorderPane pane = new BorderPane();
        if (arg != null)
            macroText = arg;
        // Create text area
        final TextArea textArea = new TextArea();
        textArea.setPrefRowCount(12);
        textArea.setPrefSize(400, 400);
        textArea.setWrapText(true);
        textArea.setFont(Font.font("Courier"));
        if (macroText != null)
            textArea.setText(macroText);
        BorderPane panelMacro = new BorderPane();
        // panelMacro.setBorder(BorderFactory.createTitledBorder("Macro"));
        panelMacro.setCenter(textArea);
        ParameterPanelFX parameterPanel = new ParameterPanelFX(getParameterList(runner.getImageData()));
        panelMacro.setBottom(parameterPanel.getPane());
        // Create button panel
        Button btnRun = new Button("Run");
        btnRun.setOnAction(e -> {
            macroText = textArea.getText().trim();
            if (macroText.length() == 0)
                return;
            PathObjectHierarchy hierarchy = getHierarchy(runner);
            PathObject pathObject = hierarchy.getSelectionModel().singleSelection() ? hierarchy.getSelectionModel().getSelectedObject() : null;
            if (pathObject instanceof PathAnnotationObject || pathObject instanceof TMACoreObject) {
                SwingUtilities.invokeLater(() -> {
                    runMacro(params, qupath.getViewer().getImageData(), qupath.getViewer().getImageDisplay(), pathObject, macroText);
                });
            } else {
                // DisplayHelpers.showErrorMessage(getClass().getSimpleName(), "Sorry, ImageJ macros can only be run for single selected images");
                // logger.warn("ImageJ macro being run in current thread");
                // runPlugin(runner, arg); // TODO: Consider running in a background thread?
                // Run in a background thread
                Collection<? extends PathObject> parents = getParentObjects(runner);
                if (parents.isEmpty()) {
                    Dialogs.showErrorMessage("ImageJ macro runner", "No annotation or TMA core objects selected!");
                    return;
                }
                List<Runnable> tasks = new ArrayList<>();
                for (PathObject parent : parents) addRunnableTasks(qupath.getViewer().getImageData(), parent, tasks);
                qupath.submitShortTask(() -> runner.runTasks(tasks, true));
            // runner.runTasks(tasks);
            // Runnable r = new Runnable() {
            // public void run() {
            // runPlugin(runner, arg);
            // }
            // };
            // new Thread(r).start();
            }
        });
        Button btnClose = new Button("Close");
        btnClose.setOnAction(e -> dialog.hide());
        GridPane panelButtons = PaneTools.createRowGridControls(btnRun, btnClose);
        pane.setCenter(panelMacro);
        pane.setBottom(panelButtons);
        panelButtons.setPadding(new Insets(5, 0, 0, 0));
        pane.setPadding(new Insets(10, 10, 10, 10));
        dialog.setScene(new Scene(pane));
    }
    dialog.show();
    return true;
}