Examples with RTrees org.bytedeco.opencv.opencv_ml.RTrees used on opensource projects

Example 1 with RTrees

use of org.bytedeco.opencv.opencv_ml.RTrees in project qupath by qupath.

the class RTreesClassifier method createClassifier.

@Override
protected RTrees createClassifier() {
    RTrees trees = RTrees.create();
    ParameterList params = getParameterList();
    if (params != null) {
        int maxDepth = params.getIntParameterValue("maxDepth");
        int minSamples = params.getIntParameterValue("minSamples");
        boolean use1SE = params.getBooleanParameterValue("use1SE");
        trees.setMaxDepth(maxDepth == 0 ? Integer.MAX_VALUE : maxDepth);
        trees.setMinSampleCount(minSamples);
        trees.setUse1SERule(use1SE);
        // setUseSurrogates should help with missing data... but it appears not actually to be implemented
        // System.out.println("DEFAULT SURROGATES: " + trees.getUseSurrogates());
        // trees.setUseSurrogates(true);
        // Set termination criteria
        int termCritMaxTrees = params.getIntParameterValue("termCritMaxTrees");
        double termCritEPS = params.getDoubleParameterValue("termCritEPS");
        termCriteria = createTerminationCriteria(termCritMaxTrees, termCritEPS);
        if (termCriteria != null)
            trees.setTermCriteria(termCriteria);
        else
            termCriteria = trees.getTermCriteria();
        logger.info("RTrees classifier termination criteria: {}", termCriteria);
    }
    return trees;
}

Example 2 with RTrees

use of org.bytedeco.opencv.opencv_ml.RTrees in project qupath by qupath.

the class PixelClassifierPane method initialize.

private void initialize() {
    var imageData = qupath.getImageData();
    int row = 0;
    // Classifier
    pane = new GridPane();
    var labelClassifier = new Label("Classifier");
    var comboClassifier = new ComboBox<OpenCVStatModel>();
    labelClassifier.setLabelFor(comboClassifier);
    selectedClassifier = comboClassifier.getSelectionModel().selectedItemProperty();
    selectedClassifier.addListener((v, o, n) -> updateClassifier());
    var btnEditClassifier = new Button("Edit");
    btnEditClassifier.setOnAction(e -> editClassifierParameters());
    btnEditClassifier.disableProperty().bind(selectedClassifier.isNull());
    PaneTools.addGridRow(pane, row++, 0, "Choose classifier type (RTrees or ANN_MLP are generally good choices)", labelClassifier, comboClassifier, comboClassifier, btnEditClassifier);
    // Image resolution
    var labelResolution = new Label("Resolution");
    labelResolution.setLabelFor(comboResolutions);
    var btnResolution = new Button("Add");
    btnResolution.setOnAction(e -> addResolution());
    selectedResolution = comboResolutions.getSelectionModel().selectedItemProperty();
    PaneTools.addGridRow(pane, row++, 0, "Choose the base image resolution based upon required detail in the classification (see preview on the right)", labelResolution, comboResolutions, comboResolutions, btnResolution);
    // Features
    var labelFeatures = new Label("Features");
    var comboFeatures = new ComboBox<ImageDataTransformerBuilder>();
    comboFeatures.getItems().add(new ImageDataTransformerBuilder.DefaultFeatureCalculatorBuilder(imageData));
    // comboFeatures.getItems().add(new FeatureCalculatorBuilder.ExtractNeighborsFeatureCalculatorBuilder(viewer.getImageData()));
    labelFeatures.setLabelFor(comboFeatures);
    selectedFeatureCalculatorBuilder = comboFeatures.getSelectionModel().selectedItemProperty();
    // var labelFeaturesSummary = new Label("No features selected");
    var btnShowFeatures = new Button("Show");
    btnShowFeatures.setOnAction(e -> showFeatures());
    var btnCustomizeFeatures = new Button("Edit");
    btnCustomizeFeatures.disableProperty().bind(Bindings.createBooleanBinding(() -> {
        var calc = selectedFeatureCalculatorBuilder.get();
        return calc == null || !calc.canCustomize(imageData);
    }, selectedFeatureCalculatorBuilder));
    btnCustomizeFeatures.setOnAction(e -> {
        if (selectedFeatureCalculatorBuilder.get().doCustomize(imageData)) {
            updateFeatureCalculator();
        }
    });
    comboFeatures.getItems().addAll(defaultFeatureCalculatorBuilders);
    comboFeatures.getSelectionModel().select(0);
    comboFeatures.getSelectionModel().selectedItemProperty().addListener((v, o, n) -> updateFeatureCalculator());
    // btnCustomizeFeatures.setOnAction(e -> showFeatures());
    PaneTools.addGridRow(pane, row++, 0, "Select features for the classifier", labelFeatures, comboFeatures, btnCustomizeFeatures, btnShowFeatures);
    // Output
    var labelOutput = new Label("Output");
    var comboOutput = new ComboBox<ImageServerMetadata.ChannelType>();
    comboOutput.getItems().addAll(ImageServerMetadata.ChannelType.CLASSIFICATION, ImageServerMetadata.ChannelType.PROBABILITY);
    selectedOutputType = comboOutput.getSelectionModel().selectedItemProperty();
    selectedOutputType.addListener((v, o, n) -> {
        updateClassifier();
    });
    comboOutput.getSelectionModel().clearAndSelect(0);
    var btnShowOutput = new Button("Show");
    btnShowOutput.setOnAction(e -> showOutput());
    PaneTools.addGridRow(pane, row++, 0, "Choose whether to output classifications only, or estimated probabilities per class (not all classifiers support probabilities, which also require more memory)", labelOutput, comboOutput, comboOutput, btnShowOutput);
    // Region
    var labelRegion = new Label("Region");
    var comboRegionFilter = PixelClassifierUI.createRegionFilterCombo(qupath.getOverlayOptions());
    // var nodeLimit = PixelClassifierTools.createLimitToAnnotationsControl(qupath.getOverlayOptions());
    PaneTools.addGridRow(pane, row++, 0, "Control where the pixel classification is applied during preview", labelRegion, comboRegionFilter, comboRegionFilter, comboRegionFilter);
    // Live predict
    var btnAdvancedOptions = new Button("Advanced options");
    btnAdvancedOptions.setTooltip(new Tooltip("Advanced options to customize preprocessing and classifier behavior"));
    btnAdvancedOptions.setOnAction(e -> {
        if (showAdvancedOptions())
            updateClassifier();
    });
    // Live predict
    var btnProject = new Button("Load training");
    btnProject.setTooltip(new Tooltip("Train using annotations from more images in the current project"));
    btnProject.setOnAction(e -> {
        if (promptToLoadTrainingImages()) {
            updateClassifier();
            int n = trainingEntries.size();
            if (n > 0)
                btnProject.setText("Load training (" + n + ")");
            else
                btnProject.setText("Load training");
        }
    });
    btnProject.disableProperty().bind(qupath.projectProperty().isNull());
    var btnLive = new ToggleButton("Live prediction");
    btnLive.selectedProperty().bindBidirectional(livePrediction);
    btnLive.setTooltip(new Tooltip("Toggle whether to calculate classification 'live' while viewing the image"));
    livePrediction.addListener((v, o, n) -> {
        if (overlay == null) {
            if (n) {
                updateClassifier(n);
                return;
            }
        } else {
            overlay.setLivePrediction(n);
        }
        if (featureOverlay != null)
            featureOverlay.setLivePrediction(n);
    });
    var panePredict = PaneTools.createColumnGridControls(btnProject, btnAdvancedOptions);
    pane.add(panePredict, 0, row++, pane.getColumnCount(), 1);
    // addGridRow(pane, row++, 0, btnPredict, btnPredict, btnPredict);
    // var btnUpdate = new Button("Update classifier");
    // btnUpdate.setMaxWidth(Double.MAX_VALUE);
    // btnUpdate.setOnAction(e -> updateClassifier(true));
    // btnUpdate.disableProperty().bind(qupath.imageDataProperty().isNull().or(btnLive.selectedProperty()));
    pane.add(btnLive, 0, row++, pane.getColumnCount(), 1);
    pieChart = new PieChart();
    // var hierarchy = viewer.getHierarchy();
    // Map<PathClass, List<PathObject>> map = hierarchy == null ? Collections.emptyMap() : PathClassificationLabellingHelper.getClassificationMap(hierarchy, false);
    pieChart.setLabelsVisible(false);
    pieChart.setLegendVisible(true);
    pieChart.setMinSize(40, 40);
    pieChart.setPrefSize(120, 120);
    // pieChart.setMaxSize(Double.MAX_VALUE, Double.MAX_VALUE);
    pieChart.setLegendSide(Side.RIGHT);
    // GridPane.setVgrow(pieChart, Priority.ALWAYS);
    // Tooltip.install(pieChart, new Tooltip("View training classes by proportion"));
    var paneChart = new BorderPane(pieChart);
    // paneChart.setMaxSize(Double.MAX_VALUE, Double.MAX_VALUE);
    // PaneTools.addGridRow(pane, row++, 0,
    // //				null,
    // "View information about the current classifier training",
    // paneChart, paneChart, paneChart);
    PaneTools.setFillWidth(Boolean.TRUE, paneChart);
    PaneTools.setFillHeight(Boolean.TRUE, paneChart);
    PaneTools.setVGrowPriority(Priority.ALWAYS, paneChart);
    PaneTools.setHGrowPriority(Priority.ALWAYS, paneChart);
    pane.add(paneChart, 0, row++, pane.getColumnCount(), 1);
    // Label showing cursor location
    var labelCursor = new Label();
    labelCursor.textProperty().bindBidirectional(cursorLocation);
    labelCursor.setAlignment(Pos.CENTER);
    labelCursor.setTextAlignment(TextAlignment.CENTER);
    labelCursor.setContentDisplay(ContentDisplay.CENTER);
    labelCursor.setWrapText(true);
    labelCursor.setMaxHeight(Double.MAX_VALUE);
    labelCursor.setMinWidth(100);
    labelCursor.setPrefWidth(390);
    labelCursor.setMaxWidth(390);
    labelCursor.setTooltip(new Tooltip("Prediction for current cursor location"));
    paneChart.setBottom(labelCursor);
    // This tends to make it harder to read the proportions as tooltips when putting the mouse over the pie chart
    // Tooltip.install(paneChart, new Tooltip("Relative proportion of training samples"));
    paneChart.setMaxWidth(400);
    // PaneTools.addGridRow(pane, row++, 0,
    // "Prediction for current cursor location",
    // labelCursor, labelCursor, labelCursor);
    comboClassifier.getItems().addAll(OpenCVClassifiers.createStatModel(RTrees.class), OpenCVClassifiers.createStatModel(ANN_MLP.class), OpenCVClassifiers.createStatModel(LogisticRegression.class), OpenCVClassifiers.createStatModel(KNearest.class));
    comboClassifier.getSelectionModel().clearAndSelect(1);
    PaneTools.setHGrowPriority(Priority.ALWAYS, comboResolutions, comboClassifier, comboFeatures);
    PaneTools.setFillWidth(Boolean.TRUE, comboResolutions, comboClassifier, comboFeatures);
    miniViewer = new MiniViewers.MiniViewerManager(qupath.getViewer(), 0);
    var viewerPane = miniViewer.getPane();
    Tooltip.install(viewerPane, new Tooltip("View image at classification resolution"));
    updateAvailableResolutions(imageData);
    selectedResolution.addListener((v, o, n) -> {
        updateResolution(n);
        updateClassifier();
        ensureOverlaySet();
    });
    if (!comboResolutions.getItems().isEmpty())
        comboResolutions.getSelectionModel().clearAndSelect(resolutions.size() / 2);
    pane.setHgap(5);
    pane.setVgap(6);
    var classifierName = new SimpleStringProperty(null);
    var panePostProcess = PaneTools.createRowGrid(PixelClassifierUI.createSavePixelClassifierPane(qupath.projectProperty(), currentClassifier, classifierName), PixelClassifierUI.createPixelClassifierButtons(qupath.imageDataProperty(), currentClassifier, classifierName));
    panePostProcess.setVgap(5);
    // var panePostProcess = PixelClassifierUI.createPixelClassifierButtons(qupath.imageDataProperty(), currentClassifier);
    pane.add(panePostProcess, 0, row++, pane.getColumnCount(), 1);
    PaneTools.setMaxWidth(Double.MAX_VALUE, pane.getChildren().stream().filter(p -> p instanceof Region).toArray(Region[]::new));
    var viewerBorderPane = new BorderPane(viewerPane);
    comboDisplayFeatures.getSelectionModel().selectedItemProperty().addListener((v, o, n) -> ensureOverlaySet());
    comboDisplayFeatures.setMaxWidth(Double.MAX_VALUE);
    spinFeatureMin.setPrefWidth(100);
    spinFeatureMax.setPrefWidth(100);
    spinFeatureMin.valueProperty().addListener((v, o, n) -> updateFeatureDisplayRange());
    spinFeatureMax.valueProperty().addListener((v, o, n) -> updateFeatureDisplayRange());
    sliderFeatureOpacity.valueProperty().addListener((v, o, n) -> {
        if (featureOverlay != null) {
            featureOverlay.setOpacity(n.doubleValue());
        }
        if (overlay != null)
            overlay.setOpacity(n.doubleValue());
        qupath.repaintViewers();
    });
    var btnFeatureAuto = new Button("Auto");
    btnFeatureAuto.setOnAction(e -> autoFeatureContrast());
    comboDisplayFeatures.getItems().setAll(DEFAULT_CLASSIFICATION_OVERLAY);
    comboDisplayFeatures.getSelectionModel().select(DEFAULT_CLASSIFICATION_OVERLAY);
    var featureDisableBinding = comboDisplayFeatures.valueProperty().isEqualTo(DEFAULT_CLASSIFICATION_OVERLAY).or(comboDisplayFeatures.valueProperty().isNull());
    btnFeatureAuto.disableProperty().bind(featureDisableBinding);
    btnFeatureAuto.setMaxHeight(Double.MAX_VALUE);
    spinFeatureMin.disableProperty().bind(featureDisableBinding);
    spinFeatureMin.setEditable(true);
    GuiTools.restrictTextFieldInputToNumber(spinFeatureMin.getEditor(), true);
    spinFeatureMax.disableProperty().bind(featureDisableBinding);
    spinFeatureMax.setEditable(true);
    GuiTools.restrictTextFieldInputToNumber(spinFeatureMax.getEditor(), true);
    var paneFeatures = new GridPane();
    comboDisplayFeatures.setTooltip(new Tooltip("Choose classification result or feature overlay to display (Warning: This requires a lot of memory & computation!)"));
    spinFeatureMin.setTooltip(new Tooltip("Min display value for feature overlay"));
    spinFeatureMax.setTooltip(new Tooltip("Max display value for feature overlay"));
    sliderFeatureOpacity.setTooltip(new Tooltip("Adjust classification/feature overlay opacity"));
    PaneTools.addGridRow(paneFeatures, 0, 0, null, comboDisplayFeatures, comboDisplayFeatures, comboDisplayFeatures, comboDisplayFeatures);
    PaneTools.addGridRow(paneFeatures, 1, 0, null, sliderFeatureOpacity, spinFeatureMin, spinFeatureMax, btnFeatureAuto);
    var factory = new Callback<ListView<String>, ListCell<String>>() {

        @Override
        public ListCell<String> call(ListView<String> param) {
            var listCell = new ListCell<String>() {

                @Override
                public void updateItem(String value, boolean empty) {
                    super.updateItem(value, empty);
                    if (value == null || empty)
                        setText(null);
                    else
                        setText(value);
                }
            };
            listCell.setTextOverrun(OverrunStyle.ELLIPSIS);
            return listCell;
        }
    };
    comboDisplayFeatures.setCellFactory(factory);
    comboDisplayFeatures.setButtonCell(factory.call(null));
    PaneTools.setMaxWidth(Double.MAX_VALUE, comboDisplayFeatures, sliderFeatureOpacity);
    PaneTools.setFillWidth(Boolean.TRUE, comboDisplayFeatures, sliderFeatureOpacity);
    PaneTools.setHGrowPriority(Priority.ALWAYS, comboDisplayFeatures, sliderFeatureOpacity);
    paneFeatures.setHgap(5);
    paneFeatures.setVgap(5);
    paneFeatures.setPadding(new Insets(5));
    paneFeatures.prefWidthProperty().bind(viewerBorderPane.prefWidthProperty());
    viewerBorderPane.setBottom(paneFeatures);
    var splitPane = new BorderPane(viewerBorderPane);
    splitPane.setLeft(pane);
    pane.setMinWidth(400);
    // pane.setPrefWidth(400);
    // pane.setMaxWidth(400);
    // new StackPane(splitPane);
    var fullPane = splitPane;
    pane.setPadding(new Insets(5));
    stage = new Stage();
    stage.setScene(new Scene(fullPane));
    stage.setMinHeight(400);
    stage.setMinWidth(600);
    stage.sizeToScene();
    stage.initOwner(QuPathGUI.getInstance().getStage());
    // stage.getScene().getRoot().disableProperty().bind(
    // QuPathGUI.getInstance().viewerProperty().isNotEqualTo(viewer)
    // );
    updateTitle();
    updateFeatureCalculator();
    PaneTools.setMinWidth(Region.USE_PREF_SIZE, PaneTools.getContentsOfType(stage.getScene().getRoot(), Region.class, true).toArray(Region[]::new));
    stage.show();
    stage.setOnCloseRequest(e -> destroy());
    qupath.getStage().addEventFilter(MouseEvent.MOUSE_MOVED, mouseListener);
    qupath.imageDataProperty().addListener(imageDataListener);
    if (qupath.getImageData() != null)
        qupath.getImageData().getHierarchy().addPathObjectListener(hierarchyListener);
    stage.focusedProperty().addListener((v, o, n) -> {
        if (n) {
            for (var viewer : qupath.getViewers()) {
                var currentOverlay = viewer.getCustomPixelLayerOverlay();
                if (currentOverlay != this.featureOverlay && currentOverlay != this.overlay) {
                    ensureOverlaySet();
                    break;
                }
            }
        }
    });
    nThreads.addListener((v, o, n) -> {
        if (n == null)
            return;
        if (overlay != null)
            overlay.setMaxThreads(n.intValue());
        if (featureOverlay != null)
            featureOverlay.setMaxThreads(n.intValue());
    });
}