Examples with DialogButton qupath.lib.gui.dialogs.Dialogs.DialogButton used on opensource projects

Example 1 with DialogButton

use of qupath.lib.gui.dialogs.Dialogs.DialogButton in project qupath by qupath.

the class EstimateStainVectorsCommand method promptToEstimateStainVectors.

public static void promptToEstimateStainVectors(ImageData<BufferedImage> imageData) {
    if (imageData == null) {
        Dialogs.showNoImageError(TITLE);
        return;
    }
    if (imageData == null || !imageData.isBrightfield() || imageData.getServer() == null || !imageData.getServer().isRGB()) {
        Dialogs.showErrorMessage(TITLE, "No brightfield, RGB image selected!");
        return;
    }
    ColorDeconvolutionStains stains = imageData.getColorDeconvolutionStains();
    if (stains == null || !stains.getStain(3).isResidual()) {
        Dialogs.showErrorMessage(TITLE, "Sorry, stain editing is only possible for brightfield, RGB images with 2 stains");
        return;
    }
    PathObject pathObject = imageData.getHierarchy().getSelectionModel().getSelectedObject();
    ROI roi = pathObject == null ? null : pathObject.getROI();
    if (roi == null)
        roi = ROIs.createRectangleROI(0, 0, imageData.getServer().getWidth(), imageData.getServer().getHeight(), ImagePlane.getDefaultPlane());
    double downsample = Math.max(1, Math.sqrt((roi.getBoundsWidth() * roi.getBoundsHeight()) / MAX_PIXELS));
    RegionRequest request = RegionRequest.createInstance(imageData.getServerPath(), downsample, roi);
    BufferedImage img = null;
    try {
        img = imageData.getServer().readBufferedImage(request);
    } catch (IOException e) {
        Dialogs.showErrorMessage("Estimate stain vectors", e);
        logger.error("Unable to obtain pixels for " + request.toString(), e);
    }
    // Apply small amount of smoothing to reduce compression artefacts
    img = EstimateStainVectors.smoothImage(img);
    // Check modes for background
    int[] rgb = img.getRGB(0, 0, img.getWidth(), img.getHeight(), null, 0, img.getWidth());
    int[] rgbMode = EstimateStainVectors.getModeRGB(rgb);
    int rMax = rgbMode[0];
    int gMax = rgbMode[1];
    int bMax = rgbMode[2];
    // Check if the background values may need to be changed
    if (rMax != stains.getMaxRed() || gMax != stains.getMaxGreen() || bMax != stains.getMaxBlue()) {
        DialogButton response = Dialogs.showYesNoCancelDialog(TITLE, String.format("Modal RGB values %d, %d, %d do not match current background values - do you want to use the modal values?", rMax, gMax, bMax));
        if (response == DialogButton.CANCEL)
            return;
        else if (response == DialogButton.YES) {
            stains = stains.changeMaxValues(rMax, gMax, bMax);
            imageData.setColorDeconvolutionStains(stains);
        }
    }
    ColorDeconvolutionStains stainsUpdated = null;
    logger.info("Requesting region for stain vector editing: ", request);
    try {
        stainsUpdated = showStainEditor(img, stains);
    } catch (Exception e) {
        Dialogs.showErrorMessage(TITLE, "Error with stain estimation: " + e.getLocalizedMessage());
        logger.error("{}", e.getLocalizedMessage(), e);
        // JOptionPane.showMessageDialog(qupath.getFrame(), "Error with stain estimation: " + e.getLocalizedMessage(), "Estimate stain vectors", JOptionPane.ERROR_MESSAGE, null);
        return;
    }
    if (!stains.equals(stainsUpdated)) {
        String suggestedName;
        String collectiveNameBefore = stainsUpdated.getName();
        if (collectiveNameBefore.endsWith("default"))
            suggestedName = collectiveNameBefore.substring(0, collectiveNameBefore.lastIndexOf("default")) + "estimated";
        else
            suggestedName = collectiveNameBefore;
        String newName = Dialogs.showInputDialog(TITLE, "Set name for stain vectors", suggestedName);
        if (newName == null)
            return;
        if (!newName.isBlank())
            stainsUpdated = stainsUpdated.changeName(newName);
        imageData.setColorDeconvolutionStains(stainsUpdated);
    }
}

Example 2 with DialogButton

use of qupath.lib.gui.dialogs.Dialogs.DialogButton in project qupath by qupath.

the class LegacyDetectionClassifierCommand method run.

@Override
public void run() {
    if (dialog == null) {
        dialog = new Stage();
        if (qupath != null)
            dialog.initOwner(qupath.getStage());
        dialog.setTitle(name);
        BorderPane pane = new BorderPane();
        RTreesClassifier defaultClassifier = new RTreesClassifier();
        List<OpenCvClassifier<?>> classifierList = Arrays.asList(defaultClassifier, new DTreesClassifier(), new BoostClassifier(), new BayesClassifier(), new KNearestClassifier(), new SVMClassifier(), new NeuralNetworksClassifier());
        Collections.sort(classifierList, (c1, c2) -> c1.getName().compareTo(c2.getName()));
        panel = new ClassifierBuilderPane<>(qupath, classifierList, defaultClassifier);
        pane.setCenter(panel.getPane());
        ScrollPane scrollPane = new ScrollPane(pane);
        scrollPane.setFitToWidth(true);
        scrollPane.setFitToHeight(true);
        dialog.setScene(new Scene(scrollPane));
    }
    dialog.setOnCloseRequest(e -> {
        // If we don't have a classifier yet, just remove completely
        if (panel.getSelectedFeatures().isEmpty()) {
            resetPanel();
            return;
        }
        // If we have a classifier, give option to hide
        DialogButton button = Dialogs.showYesNoCancelDialog("Classifier builder", "Retain classifier for later use?");
        if (button == DialogButton.CANCEL)
            e.consume();
        else if (button == DialogButton.NO) {
            resetPanel();
        }
    });
    dialog.show();
    dialog.setMinWidth(dialog.getWidth());
    if (dialog.getHeight() < javafx.stage.Screen.getPrimary().getVisualBounds().getHeight()) {
        dialog.setMinHeight(dialog.getHeight() / 2);
    }
// if (dialog.getHeight() < javafx.stage.Screen.getPrimary().getVisualBounds().getHeight())
// dialog.setResizable(false);
}

Example 3 with DialogButton

use of qupath.lib.gui.dialogs.Dialogs.DialogButton in project qupath by qupath.

the class DefaultScriptEditor method promptToClose.

boolean promptToClose(final ScriptTab tab) {
    int ind = listScripts.getItems().indexOf(tab);
    if (ind < 0)
        return false;
    // Check if we need to save
    if (tab.isModifiedProperty().get() && tab.hasScript()) {
        // TODO: Consider that this previously had a different parent for the dialog... and probably should
        DialogButton option = Dialogs.showYesNoCancelDialog("Close " + tab.getName(), String.format("Save %s before closing?", tab.getName()));
        if (option == DialogButton.CANCEL)
            return false;
        if (option == DialogButton.YES) {
            if (!save(tab, false))
                return false;
        }
    }
    // Update selection, or close window if all scripts have been closed
    listScripts.getItems().remove(ind);
    if (ind >= listScripts.getItems().size())
        ind--;
    if (ind < 0) {
        dialog.close();
        dialog = null;
    } else
        listScripts.getSelectionModel().select(ind);
    return true;
}

Example 4 with DialogButton

use of qupath.lib.gui.dialogs.Dialogs.DialogButton in project qupath by qupath.

the class QuPathGUI method promptToSaveChangesOrCancel.

/**
 * Show a prompt to save changes for an ImageData.
 * <p>
 * Note the return value indicates whether the user cancelled or not, rather than whether the data
 * was saved or not.
 *
 * @param dialogTitle
 * @param imageData
 * @return true if the prompt 'succeeded' (i.e. user chose 'Yes' or 'No'), false if it was cancelled.
 */
private boolean promptToSaveChangesOrCancel(String dialogTitle, ImageData<BufferedImage> imageData) {
    var project = getProject();
    var entry = project == null ? null : project.getEntry(imageData);
    File filePrevious = null;
    if (entry == null) {
        String lastPath = imageData.getLastSavedPath();
        filePrevious = lastPath == null ? null : new File(lastPath);
    }
    DialogButton response = DialogButton.YES;
    if (imageData.isChanged()) {
        response = Dialogs.showYesNoCancelDialog(dialogTitle, "Save changes to " + ServerTools.getDisplayableImageName(imageData.getServer()) + "?");
    }
    if (response == DialogButton.CANCEL)
        return false;
    if (response == DialogButton.YES) {
        if (filePrevious == null && entry == null) {
            filePrevious = Dialogs.promptToSaveFile("Save image data", filePrevious, ServerTools.getDisplayableImageName(imageData.getServer()), "QuPath Serialized Data", PathPrefs.getSerializationExtension());
            if (filePrevious == null)
                return false;
        }
        try {
            if (entry != null) {
                entry.saveImageData(imageData);
                // Should make sure we save the project in case metadata has changed as well
                project.syncChanges();
            } else
                PathIO.writeImageData(filePrevious, imageData);
        } catch (IOException e) {
            Dialogs.showErrorMessage("Save ImageData", e);
        }
    }
    return true;
}

Example 5 with DialogButton

use of qupath.lib.gui.dialogs.Dialogs.DialogButton in project qupath by qupath.

the class RigidObjectEditorCommand method commitChanges.

private void commitChanges(final boolean ignoreChanges) {
    if (this.originalObject == null)
        return;
    // PathObject pathObject = null;
    if (!ignoreChanges) {
        DialogButton option = Dialogs.showYesNoCancelDialog("Affine object editing", "Confirm object changes?");
        if (option == DialogButton.CANCEL)
            return;
        if (option == DialogButton.NO) {
            for (Entry<PathObject, ROI> entry : originalObjectROIs.entrySet()) ((PathROIObject) entry.getKey()).setROI(entry.getValue());
        } else {
            var transform = transformer.transform;
            var values = transform.getMatrixEntries();
            logger.info("Applied ROI transform: {}", String.format("\n %f, %f, %f,\n%f, %f, %f", values[0], values[1], values[2], values[3], values[4], values[5]));
            // Apply clipping now
            for (Entry<PathObject, ROI> entry : originalObjectROIs.entrySet()) {
                ROI roiTransformed = transformer.getTransformedROI(entry.getValue(), true);
                ((PathROIObject) entry.getKey()).setROI(roiTransformed);
            }
            viewer.getHierarchy().fireHierarchyChangedEvent(this, originalObject);
        }
    }
    // Update the mode if the viewer is still active
    qupath.setToolSwitchingEnabled(true);
    if (viewer == qupath.getViewer())
        viewer.setActiveTool(qupath.getSelectedTool());
    viewer.getView().removeEventHandler(MouseEvent.ANY, mouseListener);
    viewer.getCustomOverlayLayers().remove(overlay);
    viewer.removeViewerListener(this);
    // if (pathObject != null)
    // viewer.getHierarchy().addPathObject(pathObject, true);
    // // Ensure the object is selected
    // viewer.setSelectedObject(pathObject);
    viewer = null;
    overlay = null;
    originalObjectROIs.clear();
    originalObject = null;
    transformer = null;
}