Examples with PathObjectHierarchy qupath.lib.objects.hierarchy.PathObjectHierarchy used on opensource projects

Example 6 with PathObjectHierarchy

use of qupath.lib.objects.hierarchy.PathObjectHierarchy in project qupath by qupath.

the class TMACommands method promptToExportTMAData.

/**
 * Prompt to export summary TMA data for a specific image to a directory.
 * @param qupath
 * @param imageData
 */
public static void promptToExportTMAData(QuPathGUI qupath, ImageData<BufferedImage> imageData) {
    String title = "Export TMA data";
    if (imageData == null) {
        Dialogs.showNoImageError(title);
        return;
    }
    PathObjectHierarchy hierarchy = imageData == null ? null : imageData.getHierarchy();
    if (hierarchy == null || hierarchy.isEmpty() || hierarchy.getTMAGrid() == null || hierarchy.getTMAGrid().nCores() == 0) {
        Dialogs.showErrorMessage(title, "No TMA data available!");
        return;
    }
    var overlayOptions = qupath.getViewers().stream().filter(v -> v.getImageData() == imageData).map(v -> v.getOverlayOptions()).findFirst().orElse(qupath.getOverlayOptions());
    String defaultName = ServerTools.getDisplayableImageName(imageData.getServer());
    File file = Dialogs.promptToSaveFile(null, null, defaultName, "TMA data", ".qptma");
    if (file != null) {
        if (!file.getName().endsWith(".qptma"))
            file = new File(file.getParentFile(), file.getName() + ".qptma");
        double downsample = PathPrefs.tmaExportDownsampleProperty().get();
        TMADataIO.writeTMAData(file, imageData, overlayOptions, downsample);
        WorkflowStep step = new DefaultScriptableWorkflowStep("Export TMA data", "exportTMAData(\"" + GeneralTools.escapeFilePath(file.getParentFile().getAbsolutePath()) + "\", " + downsample + ")");
        imageData.getHistoryWorkflow().addStep(step);
    // PathAwtIO.writeTMAData(file, imageData, viewer.getOverlayOptions(), Double.NaN);
    }
}

Example 7 with PathObjectHierarchy

use of qupath.lib.objects.hierarchy.PathObjectHierarchy in project qupath by qupath.

the class TMACommands method promptToDeleteTMAGridRowOrColumn.

private static boolean promptToDeleteTMAGridRowOrColumn(ImageData<?> imageData, TMARemoveType type) {
    String typeString = type.toString();
    String title = "Delete TMA " + typeString;
    boolean removeRow = type == TMARemoveType.ROW;
    if (imageData == null) {
        Dialogs.showNoImageError(title);
        return false;
    }
    if (imageData.getHierarchy().getTMAGrid() == null) {
        Dialogs.showErrorMessage(title, "No image with dearrayed TMA cores selected!");
        return false;
    }
    PathObjectHierarchy hierarchy = imageData.getHierarchy();
    PathObject selected = hierarchy.getSelectionModel().getSelectedObject();
    TMACoreObject selectedCore = null;
    if (selected != null)
        selectedCore = PathObjectTools.getAncestorTMACore(selected);
    // Try to identify the row/column that we want
    TMAGrid grid = hierarchy.getTMAGrid();
    int row = -1;
    int col = -1;
    if (selectedCore != null) {
        for (int y = 0; y < grid.getGridHeight(); y++) {
            for (int x = 0; x < grid.getGridWidth(); x++) {
                if (grid.getTMACore(y, x) == selectedCore) {
                    row = y;
                    col = x;
                    break;
                }
            }
        }
    }
    // We need a selected core to know what to remove
    if (row < 0 || col < 0) {
        Dialogs.showErrorMessage(title, "Please select a TMA core to indicate which " + typeString + " to remove");
        return false;
    }
    // Check we have enough rows/columns - if not, this is just a clear operation
    if ((removeRow && grid.getGridHeight() <= 1) || (!removeRow && grid.getGridWidth() <= 1)) {
        if (Dialogs.showConfirmDialog(title, "Are you sure you want to delete the entire TMA grid?"))
            hierarchy.setTMAGrid(null);
        return false;
    }
    // Confirm the removal - add 1 due to 'base 0' probably not being expected by most users...
    int num = removeRow ? row : col;
    if (!Dialogs.showConfirmDialog(title, "Are you sure you want to delete " + typeString + " " + (num + 1) + " from TMA grid?"))
        return false;
    // Create a new grid
    List<TMACoreObject> coresNew = new ArrayList<>();
    for (int r = 0; r < grid.getGridHeight(); r++) {
        if (removeRow && row == r)
            continue;
        for (int c = 0; c < grid.getGridWidth(); c++) {
            if (!removeRow && col == c)
                continue;
            coresNew.add(grid.getTMACore(r, c));
        }
    }
    int newWidth = removeRow ? grid.getGridWidth() : grid.getGridWidth() - 1;
    TMAGrid gridNew = DefaultTMAGrid.create(coresNew, newWidth);
    hierarchy.setTMAGrid(gridNew);
    hierarchy.getSelectionModel().clearSelection();
    // Request new labels
    promptToRelabelTMAGrid(imageData);
    return true;
}

Example 8 with PathObjectHierarchy

use of qupath.lib.objects.hierarchy.PathObjectHierarchy in project qupath by qupath.

the class Commands method convertDetectionsToPoints.

/**
 * Convert detection objects to point annotations based upon their ROI centroids.
 * @param imageData the image data to process
 * @param preferNucleus if true, use a nucleus ROI for cell objects (if available
 */
public static void convertDetectionsToPoints(ImageData<?> imageData, boolean preferNucleus) {
    if (imageData == null) {
        Dialogs.showNoImageError("Convert detections to points");
        return;
    }
    PathObjectHierarchy hierarchy = imageData.getHierarchy();
    Collection<PathObject> pathObjects = hierarchy.getDetectionObjects();
    if (pathObjects.isEmpty()) {
        Dialogs.showErrorMessage("Detections to points", "No detections found!");
        return;
    }
    // Remove any detections that don't have a ROI - can't do much with them
    Iterator<PathObject> iter = pathObjects.iterator();
    while (iter.hasNext()) {
        if (!iter.next().hasROI())
            iter.remove();
    }
    if (pathObjects.isEmpty()) {
        logger.warn("No detections found with ROIs!");
        return;
    }
    // Check if existing objects should be deleted
    String message = pathObjects.size() == 1 ? "Delete detection after converting to a point?" : String.format("Delete %d detections after converting to points?", pathObjects.size());
    var button = Dialogs.showYesNoCancelDialog("Detections to points", message);
    if (button == Dialogs.DialogButton.CANCEL)
        return;
    boolean deleteDetections = button == Dialogs.DialogButton.YES;
    PathObjectTools.convertToPoints(hierarchy, pathObjects, preferNucleus, deleteDetections);
}

Example 9 with PathObjectHierarchy

use of qupath.lib.objects.hierarchy.PathObjectHierarchy in project qupath by qupath.

the class QuPathGUI method setViewerPopupMenu.

private void setViewerPopupMenu(final QuPathViewerPlus viewer) {
    final ContextMenu popup = new ContextMenu();
    MenuItem miAddRow = new MenuItem("Add row");
    miAddRow.setOnAction(e -> viewerManager.addRow(viewer));
    MenuItem miAddColumn = new MenuItem("Add column");
    miAddColumn.setOnAction(e -> viewerManager.addColumn(viewer));
    MenuItem miRemoveRow = new MenuItem("Remove row");
    miRemoveRow.setOnAction(e -> viewerManager.removeViewerRow(viewer));
    MenuItem miRemoveColumn = new MenuItem("Remove column");
    miRemoveColumn.setOnAction(e -> viewerManager.removeViewerColumn(viewer));
    MenuItem miCloseViewer = new MenuItem("Close viewer");
    miCloseViewer.setOnAction(e -> {
        viewerManager.closeViewer(viewer);
    // viewerManager.removeViewer(viewer);
    });
    MenuItem miResizeGrid = new MenuItem("Reset grid size");
    miResizeGrid.setOnAction(e -> {
        viewerManager.resetGridSize();
    });
    MenuItem miToggleSync = ActionTools.createCheckMenuItem(defaultActions.TOGGLE_SYNCHRONIZE_VIEWERS, null);
    MenuItem miMatchResolutions = ActionTools.createMenuItem(defaultActions.MATCH_VIEWER_RESOLUTIONS);
    Menu menuMultiview = MenuTools.createMenu("Multi-view", miToggleSync, miMatchResolutions, miCloseViewer, null, miResizeGrid, null, // null,
    miAddRow, miAddColumn, null, miRemoveRow, miRemoveColumn);
    Menu menuView = MenuTools.createMenu("Display", ActionTools.createCheckMenuItem(defaultActions.SHOW_ANALYSIS_PANE, null), defaultActions.BRIGHTNESS_CONTRAST, null, ActionTools.createAction(() -> Commands.setViewerDownsample(viewer, 0.25), "400%"), ActionTools.createAction(() -> Commands.setViewerDownsample(viewer, 1), "100%"), ActionTools.createAction(() -> Commands.setViewerDownsample(viewer, 2), "50%"), ActionTools.createAction(() -> Commands.setViewerDownsample(viewer, 10), "10%"), ActionTools.createAction(() -> Commands.setViewerDownsample(viewer, 100), "1%"));
    ToggleGroup groupTools = new ToggleGroup();
    Menu menuTools = MenuTools.createMenu("Set tool", ActionTools.createCheckMenuItem(defaultActions.MOVE_TOOL, groupTools), ActionTools.createCheckMenuItem(defaultActions.RECTANGLE_TOOL, groupTools), ActionTools.createCheckMenuItem(defaultActions.ELLIPSE_TOOL, groupTools), ActionTools.createCheckMenuItem(defaultActions.LINE_TOOL, groupTools), ActionTools.createCheckMenuItem(defaultActions.POLYGON_TOOL, groupTools), ActionTools.createCheckMenuItem(defaultActions.POLYLINE_TOOL, groupTools), ActionTools.createCheckMenuItem(defaultActions.BRUSH_TOOL, groupTools), ActionTools.createCheckMenuItem(defaultActions.POINTS_TOOL, groupTools), null, ActionTools.createCheckMenuItem(defaultActions.SELECTION_MODE));
    // Handle awkward 'TMA core missing' option
    CheckMenuItem miTMAValid = new CheckMenuItem("Set core valid");
    miTMAValid.setOnAction(e -> setTMACoreMissing(viewer.getHierarchy(), false));
    CheckMenuItem miTMAMissing = new CheckMenuItem("Set core missing");
    miTMAMissing.setOnAction(e -> setTMACoreMissing(viewer.getHierarchy(), true));
    Menu menuTMA = new Menu("TMA");
    MenuTools.addMenuItems(menuTMA, miTMAValid, miTMAMissing, null, defaultActions.TMA_ADD_NOTE, null, MenuTools.createMenu("Add", createImageDataAction(imageData -> TMACommands.promptToAddRowBeforeSelected(imageData), "Add TMA row before"), createImageDataAction(imageData -> TMACommands.promptToAddRowAfterSelected(imageData), "Add TMA row after"), createImageDataAction(imageData -> TMACommands.promptToAddColumnBeforeSelected(imageData), "Add TMA column before"), createImageDataAction(imageData -> TMACommands.promptToAddColumnAfterSelected(imageData), "Add TMA column after")), MenuTools.createMenu("Remove", createImageDataAction(imageData -> TMACommands.promptToDeleteTMAGridRow(imageData), "Remove TMA row"), createImageDataAction(imageData -> TMACommands.promptToDeleteTMAGridColumn(imageData), "column")));
    // Create an empty placeholder menu
    Menu menuSetClass = MenuTools.createMenu("Set class");
    // CheckMenuItem miTMAValid = new CheckMenuItem("Set core valid");
    // miTMAValid.setOnAction(e -> setTMACoreMissing(viewer.getHierarchy(), false));
    // CheckMenuItem miTMAMissing = new CheckMenuItem("Set core missing");
    // miTMAMissing.setOnAction(e -> setTMACoreMissing(viewer.getHierarchy(), true));
    Menu menuCells = MenuTools.createMenu("Cells", ActionTools.createCheckMenuItem(defaultActions.SHOW_CELL_BOUNDARIES_AND_NUCLEI, null), ActionTools.createCheckMenuItem(defaultActions.SHOW_CELL_NUCLEI, null), ActionTools.createCheckMenuItem(defaultActions.SHOW_CELL_BOUNDARIES, null), ActionTools.createCheckMenuItem(defaultActions.SHOW_CELL_CENTROIDS, null));
    MenuItem miClearSelectedObjects = new MenuItem("Delete object");
    miClearSelectedObjects.setOnAction(e -> {
        PathObjectHierarchy hierarchy = viewer.getHierarchy();
        if (hierarchy == null)
            return;
        if (hierarchy.getSelectionModel().singleSelection()) {
            GuiTools.promptToRemoveSelectedObject(hierarchy.getSelectionModel().getSelectedObject(), hierarchy);
        } else {
            GuiTools.promptToClearAllSelectedObjects(viewer.getImageData());
        }
    });
    // Create a standard annotations menu
    Menu menuAnnotations = GuiTools.populateAnnotationsMenu(this, new Menu("Annotations"));
    SeparatorMenuItem topSeparator = new SeparatorMenuItem();
    popup.setOnShowing(e -> {
        // Check if we have any cells
        ImageData<?> imageData = viewer.getImageData();
        if (imageData == null)
            menuCells.setVisible(false);
        else
            menuCells.setVisible(!imageData.getHierarchy().getDetectionObjects().isEmpty());
        // Check what to show for TMA cores or annotations
        Collection<PathObject> selectedObjects = viewer.getAllSelectedObjects();
        PathObject pathObject = viewer.getSelectedObject();
        menuTMA.setVisible(false);
        if (pathObject instanceof TMACoreObject) {
            boolean isMissing = ((TMACoreObject) pathObject).isMissing();
            miTMAValid.setSelected(!isMissing);
            miTMAMissing.setSelected(isMissing);
            menuTMA.setVisible(true);
        }
        // Add clear objects option if we have more than one non-TMA object
        if (imageData == null || imageData.getHierarchy().getSelectionModel().noSelection() || imageData.getHierarchy().getSelectionModel().getSelectedObject() instanceof TMACoreObject)
            miClearSelectedObjects.setVisible(false);
        else {
            if (imageData.getHierarchy().getSelectionModel().singleSelection()) {
                miClearSelectedObjects.setText("Delete object");
                miClearSelectedObjects.setVisible(true);
            } else {
                miClearSelectedObjects.setText("Delete objects");
                miClearSelectedObjects.setVisible(true);
            }
        }
        boolean hasAnnotations = pathObject instanceof PathAnnotationObject || (!selectedObjects.isEmpty() && selectedObjects.stream().allMatch(p -> p.isAnnotation()));
        updateSetAnnotationPathClassMenu(menuSetClass, viewer);
        menuAnnotations.setVisible(hasAnnotations);
        topSeparator.setVisible(hasAnnotations || pathObject instanceof TMACoreObject);
        // Occasionally, the newly-visible top part of a popup menu can have the wrong size?
        popup.setWidth(popup.getPrefWidth());
    });
    // popup.add(menuClassify);
    popup.getItems().addAll(miClearSelectedObjects, menuTMA, menuSetClass, menuAnnotations, topSeparator, menuMultiview, menuCells, menuView, menuTools);
    popup.setAutoHide(true);
    // Enable circle pop-up for quick classification on right-click
    CirclePopupMenu circlePopup = new CirclePopupMenu(viewer.getView(), null);
    viewer.getView().addEventHandler(MouseEvent.MOUSE_PRESSED, e -> {
        if ((e.isPopupTrigger() || e.isSecondaryButtonDown()) && e.isShiftDown() && !getAvailablePathClasses().isEmpty()) {
            circlePopup.setAnimationDuration(Duration.millis(200));
            updateSetAnnotationPathClassMenu(circlePopup, viewer);
            circlePopup.show(e.getScreenX(), e.getScreenY());
            e.consume();
            return;
        } else if (circlePopup.isShown())
            circlePopup.hide();
        if (e.isPopupTrigger() || e.isSecondaryButtonDown()) {
            popup.show(viewer.getView().getScene().getWindow(), e.getScreenX(), e.getScreenY());
            e.consume();
        }
    });
// // It's necessary to make the Window the owner, since otherwise the context menu does not disappear when clicking elsewhere on the viewer
// viewer.getView().setOnContextMenuRequested(e -> {
// popup.show(viewer.getView().getScene().getWindow(), e.getScreenX(), e.getScreenY());
// //			popup.show(viewer.getView(), e.getScreenX(), e.getScreenY());
// });
}

Example 10 with PathObjectHierarchy

use of qupath.lib.objects.hierarchy.PathObjectHierarchy in project qupath by qupath.

the class PathObjectTools method mergePointsForAllClasses.

/**
 * Merge point annotations sharing the same {@link PathClass} and {@link ImagePlane},
 * creating multi-point annotations for all matching points and removing the (previously-separated) annotations.
 *
 * @param hierarchy object hierarchy to modify
 * @return true if changes are made to the hierarchy, false otherwise
 */
public static boolean mergePointsForAllClasses(PathObjectHierarchy hierarchy) {
    if (hierarchy == null)
        return false;
    var pathClasses = hierarchy.getAnnotationObjects().stream().filter(p -> p.getROI().isPoint()).map(p -> p.getPathClass()).collect(Collectors.toSet());
    boolean changes = false;
    for (PathClass pathClass : pathClasses) changes = changes || mergePointsForClass(hierarchy, pathClass);
    return changes;
}