Examples with ParameterPanelFX qupath.lib.gui.dialogs.ParameterPanelFX used on opensource projects

Example 1 with ParameterPanelFX

use of qupath.lib.gui.dialogs.ParameterPanelFX in project qupath by qupath.

the class EstimateStainVectorsCommand method showStainEditor.

@SuppressWarnings("unchecked")
public static ColorDeconvolutionStains showStainEditor(final BufferedImage img, final ColorDeconvolutionStains stains) {
    // 
    int[] buf = img.getRGB(0, 0, img.getWidth(), img.getHeight(), null, 0, img.getWidth());
    // int[] rgb = buf;
    int[] rgb = EstimateStainVectors.subsample(buf, 10000);
    float[] red = ColorDeconvolutionHelper.getRedOpticalDensities(rgb, stains.getMaxRed(), null);
    float[] green = ColorDeconvolutionHelper.getGreenOpticalDensities(rgb, stains.getMaxGreen(), null);
    float[] blue = ColorDeconvolutionHelper.getBlueOpticalDensities(rgb, stains.getMaxBlue(), null);
    // panelPlots.setBorder(BorderFactory.createTitledBorder(null, "Stain vector scatterplots", TitledBorder.CENTER, TitledBorder.TOP));
    StainsWrapper stainsWrapper = new StainsWrapper(stains);
    Node panelRedGreen = createScatterPanel(new ScatterPlot(red, green, null, rgb), stainsWrapper, AxisColor.RED, AxisColor.GREEN);
    Node panelRedBlue = createScatterPanel(new ScatterPlot(red, blue, null, rgb), stainsWrapper, AxisColor.RED, AxisColor.BLUE);
    Node panelGreenBlue = createScatterPanel(new ScatterPlot(green, blue, null, rgb), stainsWrapper, AxisColor.GREEN, AxisColor.BLUE);
    // GridPane panelPlots = PanelToolsFX.createColumnGrid(panelRedGreen, panelRedBlue, panelGreenBlue);
    GridPane panelPlots = new GridPane();
    panelPlots.setHgap(10);
    panelPlots.add(panelRedGreen, 0, 0);
    panelPlots.add(panelRedBlue, 1, 0);
    panelPlots.add(panelGreenBlue, 2, 0);
    // panelPlots.getChildren().addAll(panelRedGreen, panelRedBlue, panelGreenBlue);
    panelPlots.setPadding(new Insets(0, 0, 10, 0));
    BorderPane panelSouth = new BorderPane();
    TableView<Integer> table = new TableView<>();
    table.getItems().setAll(1, 2, 3);
    stainsWrapper.addStainListener(new StainChangeListener() {

        @Override
        public void stainChanged(StainsWrapper stainsWrapper) {
            table.refresh();
        }
    });
    TableColumn<Integer, String> colName = new TableColumn<>("Name");
    colName.setCellValueFactory(v -> new SimpleStringProperty(stainsWrapper.getStains().getStain(v.getValue()).getName()));
    TableColumn<Integer, String> colOrig = new TableColumn<>("Original");
    colOrig.setCellValueFactory(v -> new SimpleStringProperty(stainArrayAsString(Locale.getDefault(Category.FORMAT), stainsWrapper.getOriginalStains().getStain(v.getValue()), " | ", 3)));
    TableColumn<Integer, String> colCurrent = new TableColumn<>("Current");
    colCurrent.setCellValueFactory(v -> new SimpleStringProperty(stainArrayAsString(Locale.getDefault(Category.FORMAT), stainsWrapper.getStains().getStain(v.getValue()), " | ", 3)));
    TableColumn<Integer, String> colAngle = new TableColumn<>("Angle");
    colAngle.setCellValueFactory(v -> {
        return new SimpleStringProperty(GeneralTools.formatNumber(StainVector.computeAngle(stainsWrapper.getOriginalStains().getStain(v.getValue()), stainsWrapper.getStains().getStain(v.getValue())), 2));
    });
    // new SimpleStringProperty(stainsWrapper.getStains().getStain(v.getValue()).arrayAsString(", ", 3)));
    table.getColumns().addAll(colName, colOrig, colCurrent, colAngle);
    table.setColumnResizePolicy(TableView.UNCONSTRAINED_RESIZE_POLICY);
    table.setPrefHeight(120);
    // // Fix first & preferred column sizes
    // int widthName = 0, widthStain = 0;
    // for (int row = 0; row < table.getRowCount(); row++) {
    // TableCellRenderer renderer = table.getCellRenderer(row, 0);
    // Component comp = table.prepareRenderer(renderer, row, 0);
    // widthName = Math.max(comp.getPreferredSize().width, widthName);
    // 
    // renderer = table.getCellRenderer(row, 1);
    // comp = table.prepareRenderer(renderer, row, 1);
    // widthStain = Math.max(comp.getPreferredSize().width, widthStain);
    // renderer = table.getCellRenderer(row, 2);
    // comp = table.prepareRenderer(renderer, row, 2);
    // widthStain = Math.max(comp.getPreferredSize().width, widthStain);
    // }
    // table.getColumnModel().getColumn(0).setMaxWidth(widthName + 10);
    // table.getColumnModel().getColumn(0).setPreferredWidth(widthName + 10);
    // table.getColumnModel().getColumn(1).setPreferredWidth(widthStain + 20);
    // table.getColumnModel().getColumn(2).setPreferredWidth(widthStain + 20);
    // Create auto detection parameters
    ParameterList params = new ParameterList().addDoubleParameter("minStainOD", "Min channel OD", 0.05, "", "Minimum staining OD - pixels with a lower OD in any channel (RGB) are ignored (default = 0.05)").addDoubleParameter("maxStainOD", "Max total OD", 1., "", "Maximum staining OD - more densely stained pixels are ignored (default = 1)").addDoubleParameter("ignorePercentage", "Ignore extrema", 1., "%", "Percentage of extreme pixels to ignore, to improve robustness in the presence of noise/other artefacts (default = 1)").addBooleanParameter("checkColors", "Exclude unrecognised colors (H&E only)", false, "Exclude unexpected colors (e.g. green) that are likely to be caused by artefacts and not true staining");
    // .addDoubleParameter("ignorePercentage", "Ignore extrema", 1., "%", 0, 20, "Percentage of extreme pixels to ignore, to improve robustness in the presence of noise/other artefacts");
    Button btnAuto = new Button("Auto");
    btnAuto.setOnAction(e -> {
        double minOD = params.getDoubleParameterValue("minStainOD");
        double maxOD = params.getDoubleParameterValue("maxStainOD");
        double ignore = params.getDoubleParameterValue("ignorePercentage");
        // Only accept if H&E
        boolean checkColors = params.getBooleanParameterValue("checkColors") && stainsWrapper.getOriginalStains().isH_E();
        ignore = Math.max(0, Math.min(ignore, 100));
        // ColorDeconvolutionStains stains = estimateStains(imgFinal, stainsWrapper.getStains(), minOD, maxOD, ignore);
        try {
            ColorDeconvolutionStains stainsNew = EstimateStainVectors.estimateStains(img, stainsWrapper.getStains(), minOD, maxOD, ignore, checkColors);
            stainsWrapper.setStains(stainsNew);
        } catch (Exception e2) {
            Dialogs.showErrorMessage("Estimate stain vectors", e2);
        }
    });
    ParameterPanelFX panelParams = new ParameterPanelFX(params);
    // panelParams.setBorder(BorderFactory.createEmptyBorder(5, 5, 5, 5));
    BorderPane panelAuto = new BorderPane();
    // panelAuto.setBorder(BorderFactory.createTitledBorder("Auto detect"));
    panelAuto.setCenter(panelParams.getPane());
    panelAuto.setBottom(btnAuto);
    // JScrollPane scrollPane = new JScrollPane(table);
    // JPanel panelTable = new JPanel(new BorderLayout());
    // panelTable.add(scrollPane, BorderLayout.CENTER);
    // //		JTextArea textInstructions = new JTextArea();
    // //		textInstructions.setWrapStyleWord(true);
    // //		textInstructions.setLineWrap(true);
    // //		textInstructions.setText(
    // //				"Viewer for manually and automatically adjusting stain vectors used for stain separation.\n\n" +
    // //				"Each stain vector is 3 values describing the red, green and blue components that define the colour of each " +
    // //				"stain (e.g. hematoxylin, DAB, eosin).  The scatterplots show how these relate to pixel colours for each " +
    // //				"combination of red, green and blue.\n\n" +
    // //				"'Good' stain vectors should point along the edges of the scattered points, ignoring any artefacts resulting from " +
    // //				"pixels that don't belong to normal staining patterns."
    // //				);
    // //		panelTable.add(new JScrollPane(textInstructions), BorderLayout.SOUTH);
    // panelTable.setBorder(BorderFactory.createTitledBorder("Stain vectors"));
    panelSouth.setCenter(new TitledPane("Stain vectors", table));
    panelSouth.setBottom(new TitledPane("Auto detect", panelAuto));
    BorderPane panelMain = new BorderPane();
    panelMain.setCenter(panelPlots);
    panelMain.setBottom(panelSouth);
    if (Dialogs.showConfirmDialog("Visual Stain Editor", panelMain)) {
        return stainsWrapper.getStains();
    } else {
        stainsWrapper.resetStains();
        return stainsWrapper.getStains();
    }
}

Example 2 with ParameterPanelFX

use of qupath.lib.gui.dialogs.ParameterPanelFX in project qupath by qupath.

the class KaplanMeierDisplay method generatePlot.

@SuppressWarnings("unchecked")
private void generatePlot() {
    KaplanMeierDisplay.ScoreData newScoreData = scoreData;
    // If we have a hierarchy, update the scores with the most recent data
    if (hierarchy != null) {
        List<TMACoreObject> cores = PathObjectTools.getTMACoreObjects(hierarchy, false);
        double[] survival = new double[cores.size()];
        boolean[] censored = new boolean[cores.size()];
        double[] scores = new double[cores.size()];
        // scoreColumn = "RoughScore";
        for (int i = 0; i < cores.size(); i++) {
            TMACoreObject core = cores.get(i);
            MeasurementList ml = core.getMeasurementList();
            survival[i] = core.getMeasurementList().getMeasurementValue(survivalColumn);
            double censoredValue = core.getMeasurementList().getMeasurementValue(censoredColumn);
            boolean hasCensoredValue = !Double.isNaN(censoredValue) && (censoredValue == 0 || censoredValue == 1);
            censored[i] = censoredValue != 0;
            if (!hasCensoredValue) {
                // If we don't have a censored value, ensure we mask out everything else
                scores[i] = Double.NaN;
                survival[i] = Double.NaN;
            } else if (ml.containsNamedMeasurement(scoreColumn))
                // Get the score if we can
                scores[i] = ml.getMeasurementValue(scoreColumn);
            else {
                // // Try to compute score if we need to
                // Map<String, Number> map = ROIMeaningfulMeasurements.getPathClassSummaryMeasurements(core.getChildObjects(), true);
                // Number value = map.get(scoreColumn);
                // if (value == null)
                scores[i] = Double.NaN;
            // else
            // scores[i] = value.doubleValue();
            }
        }
        // Mask out any scores that don't have associated survival data
        for (int i = 0; i < survival.length; i++) {
            if (Double.isNaN(survival[i]))
                scores[i] = Double.NaN;
        }
        newScoreData = new ScoreData(scores, survival, censored);
    }
    if (newScoreData == null || newScoreData.scores.length == 0)
        return;
    // KaplanMeier kmHigh = new KaplanMeier("Above threshold");
    // KaplanMeier kmLow = new KaplanMeier("Below threshold");
    double[] quartiles = StatisticsHelper.getQuartiles(newScoreData.scores);
    double q1 = quartiles[0];
    double median = quartiles[1];
    double q3 = quartiles[2];
    double[] thresholds;
    if (params != null) {
        Object thresholdMethod = params.getChoiceParameterValue("scoreThresholdMethod");
        if (thresholdMethod.equals("Median")) {
            // panelParams.setNumericParameterValue("scoreThreshold", median);
            // ((DoubleParameter)params.getParameters().get("scoreThreshold")).setValue(median); // TODO: UPDATE DIALOG!
            thresholds = new double[] { median };
        } else if (thresholdMethod.equals("Tertiles")) {
            // ((DoubleParameter)params.getParameters().get("scoreThreshold")).setValue(median); // TODO: UPDATE DIALOG!
            thresholds = StatisticsHelper.getTertiles(newScoreData.scores);
        } else if (thresholdMethod.equals("Quartiles")) {
            // ((DoubleParameter)params.getParameters().get("scoreThreshold")).setValue(median); // TODO: UPDATE DIALOG!
            thresholds = new double[] { q1, median, q3 };
        } else if (thresholdMethod.equals("Manual (1)")) {
            thresholds = new double[] { params.getDoubleParameterValue("threshold1") };
        } else if (thresholdMethod.equals("Manual (2)")) {
            thresholds = new double[] { params.getDoubleParameterValue("threshold1"), params.getDoubleParameterValue("threshold2") };
        } else
            // if (thresholdMethod.equals("Manual (3)")) {
            thresholds = new double[] { params.getDoubleParameterValue("threshold1"), params.getDoubleParameterValue("threshold2"), params.getDoubleParameterValue("threshold3") };
    } else
        thresholds = new double[] { median };
    double minVal = Double.POSITIVE_INFINITY;
    double maxVal = Double.NEGATIVE_INFINITY;
    int numNonNaN = 0;
    for (double d : newScoreData.scores) {
        if (Double.isNaN(d))
            continue;
        if (d < minVal)
            minVal = d;
        if (d > maxVal)
            maxVal = d;
        numNonNaN++;
    }
    // If not this, we don't have valid scores that we can work with
    boolean scoresValid = maxVal > minVal;
    double maxTimePoint = 0;
    for (double d : newScoreData.survival) {
        if (Double.isNaN(d))
            continue;
        if (d > maxTimePoint)
            maxTimePoint = d;
    }
    if (panelParams != null && maxTimePoint > ((IntParameter) params.getParameters().get("censorTimePoints")).getUpperBound()) {
        panelParams.setNumericParameterValueRange("censorTimePoints", 0, Math.ceil(maxTimePoint));
    }
    // Optionally censor at specified time
    double censorThreshold = params == null ? maxTimePoint : params.getIntParameterValue("censorTimePoints");
    // Compute log-rank p-values for *all* possible thresholds
    // Simultaneously determine the threshold that yields the lowest p-value,
    // resolving ties in favour of a more even split between high/low numbers of events
    boolean pValuesChanged = false;
    if (calculateAllPValues) {
        if (!(pValues != null && pValueThresholds != null && newScoreData.equals(scoreData) && censorThreshold == lastPValueCensorThreshold)) {
            Map<Double, Double> mapLogRank = new TreeMap<>();
            Set<Double> setObserved = new HashSet<>();
            for (int i = 0; i < newScoreData.scores.length; i++) {
                Double d = newScoreData.scores[i];
                boolean observed = !newScoreData.censored[i] && newScoreData.survival[i] < censorThreshold;
                if (observed)
                    setObserved.add(d);
                if (mapLogRank.containsKey(d))
                    continue;
                List<KaplanMeierData> kmsTemp = splitByThresholds(newScoreData, new double[] { d }, censorThreshold, false);
                // if (kmsTemp.get(1).nObserved() == 0 || kmsTemp.get(1).nObserved() == 0)
                // continue;
                LogRankResult test = LogRankTest.computeLogRankTest(kmsTemp.get(0), kmsTemp.get(1));
                double pValue = test.getPValue();
                // double pValue = test.hazardRatio < 1 ? test.hazardRatio : 1.0/test.hazardRatio; // Checking usefulness of Hazard ratios...
                if (!Double.isFinite(pValue))
                    continue;
                // if (!Double.isFinite(test.getHazardRatio())) {
                // //						continue;
                // pValue = Double.NaN;
                // }
                mapLogRank.put(d, pValue);
            }
            pValueThresholds = new double[mapLogRank.size()];
            pValues = new double[mapLogRank.size()];
            pValueThresholdsObserved = new boolean[mapLogRank.size()];
            int count = 0;
            for (Entry<Double, Double> entry : mapLogRank.entrySet()) {
                pValueThresholds[count] = entry.getKey();
                pValues[count] = entry.getValue();
                if (setObserved.contains(entry.getKey()))
                    pValueThresholdsObserved[count] = true;
                count++;
            }
            // Find the longest 'significant' stretch
            int maxSigCount = 0;
            int maxSigInd = -1;
            int sigCurrent = 0;
            int[] sigCount = new int[pValues.length];
            for (int i = 0; i < pValues.length; i++) {
                if (pValues[i] < 0.05) {
                    sigCurrent++;
                    sigCount[i] = sigCurrent;
                    if (sigCurrent > maxSigCount) {
                        maxSigCount = sigCurrent;
                        maxSigInd = i;
                    }
                } else
                    sigCurrent = 0;
            }
            if (maxSigCount == 0) {
                logger.info("No p-values < 0.05");
            } else {
                double minThresh = maxSigInd - maxSigCount < 0 ? pValueThresholds[0] - 0.0000001 : pValueThresholds[maxSigInd - maxSigCount];
                double maxThresh = pValueThresholds[maxSigInd];
                int nBetween = 0;
                int nBetweenObserved = 0;
                for (int i = 0; i < newScoreData.scores.length; i++) {
                    if (newScoreData.scores[i] > minThresh && newScoreData.scores[i] <= maxThresh) {
                        nBetween++;
                        if (newScoreData.survival[i] < censorThreshold && !newScoreData.censored[i])
                            nBetweenObserved++;
                    }
                }
                logger.info("Longest stretch of p-values < 0.05: {} - {} ({} entries, {} observed)", minThresh, maxThresh, nBetween, nBetweenObserved);
            }
            pValuesSmoothed = new double[pValues.length];
            Arrays.fill(pValuesSmoothed, Double.NaN);
            int n = (pValues.length / 20) * 2 + 1;
            logger.info("Smoothing log-rank test p-values by " + n);
            for (int i = n / 2; i < pValues.length - n / 2; i++) {
                double sum = 0;
                for (int k = i - n / 2; k < i - n / 2 + n; k++) {
                    sum += pValues[k];
                }
                pValuesSmoothed[i] = sum / n;
            }
            // for (int i = 0; i < pValues.length; i++) {
            // double sum = 0;
            // for (int k = Math.max(0, i-n/2); k < Math.min(pValues.length, i-n/2+n); k++) {
            // sum += pValues[k];
            // }
            // pValuesSmoothed[i] = sum/n;
            // }
            // pValues = pValuesSmoothed;
            lastPValueCensorThreshold = censorThreshold;
            pValuesChanged = true;
        }
    } else {
        lastPValueCensorThreshold = Double.NaN;
        pValueThresholds = null;
        pValues = null;
    }
    // if (params != null && !Double.isNaN(bestThreshold) && (params.getChoiceParameterValue("scoreThresholdMethod").equals("Lowest p-value")))
    if (params != null && (params.getChoiceParameterValue("scoreThresholdMethod").equals("Lowest p-value"))) {
        int bestIdx = -1;
        double bestPValue = Double.POSITIVE_INFINITY;
        for (int i = pValueThresholds.length / 10; i < pValueThresholds.length * 9 / 10; i++) {
            if (pValues[i] < bestPValue) {
                bestIdx = i;
                bestPValue = pValues[i];
            }
        }
        thresholds = bestIdx >= 0 ? new double[] { pValueThresholds[bestIdx] } : new double[0];
    } else if (params != null && (params.getChoiceParameterValue("scoreThresholdMethod").equals("Lowest smoothed p-value"))) {
        int bestIdx = -1;
        double bestPValue = Double.POSITIVE_INFINITY;
        for (int i = pValueThresholds.length / 10; i < pValueThresholds.length * 9 / 10; i++) {
            if (pValuesSmoothed[i] < bestPValue) {
                bestIdx = i;
                bestPValue = pValuesSmoothed[i];
            }
        }
        thresholds = bestIdx >= 0 ? new double[] { pValueThresholds[bestIdx] } : new double[0];
    }
    // Split into different curves using the provided thresholds
    List<KaplanMeierData> kms = splitByThresholds(newScoreData, thresholds, censorThreshold, params != null && "Quartiles".equals(params.getChoiceParameterValue("scoreThresholdMethod")));
    if (plotter == null) {
        plotter = new KaplanMeierChartWrapper(survivalColumn + " time");
    // plotter.setBorder(BorderFactory.createTitledBorder("Survival plot"));
    // plotter.getCanvas().setWidth(300);
    // plotter.getCanvas().setHeight(300);
    }
    KaplanMeierData[] kmArray = new KaplanMeierData[kms.size()];
    plotter.setKaplanMeierCurves(survivalColumn + " time", kms.toArray(kmArray));
    tableModel.setSurvivalCurves(thresholds, params != null && params.getChoiceParameterValue("scoreThresholdMethod").equals("Lowest p-value"), kmArray);
    // Bar width determined using 'Freedman and Diaconis' rule' (but overridden if this gives < 16 bins...)
    double barWidth = (2 * q3 - q1) * Math.pow(numNonNaN, -1.0 / 3.0);
    int nBins = 100;
    if (!Double.isNaN(barWidth))
        barWidth = (int) Math.max(16, Math.ceil((maxVal - minVal) / barWidth));
    Histogram histogram = scoresValid ? new Histogram(newScoreData.scores, nBins) : null;
    if (histogramPanel == null) {
        GridPane paneHistogram = new GridPane();
        histogramPanel = new HistogramPanelFX();
        histogramPanel.getChart().setAnimated(false);
        histogramWrapper = new ThresholdedChartWrapper(histogramPanel.getChart());
        for (ObservableNumberValue val : threshProperties) histogramWrapper.addThreshold(val, ColorToolsFX.getCachedColor(240, 0, 0, 128));
        histogramWrapper.getPane().setPrefHeight(150);
        paneHistogram.add(histogramWrapper.getPane(), 0, 0);
        Tooltip.install(histogramPanel.getChart(), new Tooltip("Distribution of scores"));
        GridPane.setHgrow(histogramWrapper.getPane(), Priority.ALWAYS);
        GridPane.setVgrow(histogramWrapper.getPane(), Priority.ALWAYS);
        NumberAxis xAxis = new NumberAxis();
        xAxis.setLabel("Score threshold");
        NumberAxis yAxis = new NumberAxis();
        yAxis.setLowerBound(0);
        yAxis.setUpperBound(1);
        yAxis.setTickUnit(0.1);
        yAxis.setAutoRanging(false);
        yAxis.setLabel("P-value");
        chartPValues = new LineChart<>(xAxis, yAxis);
        chartPValues.setAnimated(false);
        chartPValues.setLegendVisible(false);
        // Make chart so it can be navigated
        ChartTools.makeChartInteractive(chartPValues, xAxis, yAxis);
        pValuesChanged = true;
        Tooltip.install(chartPValues, new Tooltip("Distribution of p-values (log-rank test) comparing low vs. high for all possible score thresholds"));
        // chartPValues.getYAxis().setAutoRanging(false);
        pValuesWrapper = new ThresholdedChartWrapper(chartPValues);
        for (ObservableNumberValue val : threshProperties) pValuesWrapper.addThreshold(val, ColorToolsFX.getCachedColor(240, 0, 0, 128));
        pValuesWrapper.getPane().setPrefHeight(150);
        paneHistogram.add(pValuesWrapper.getPane(), 0, 1);
        GridPane.setHgrow(pValuesWrapper.getPane(), Priority.ALWAYS);
        GridPane.setVgrow(pValuesWrapper.getPane(), Priority.ALWAYS);
        ContextMenu popup = new ContextMenu();
        ChartTools.addChartExportMenu(chartPValues, popup);
        RadioMenuItem miZoomY1 = new RadioMenuItem("0-1");
        miZoomY1.setOnAction(e -> {
            yAxis.setAutoRanging(false);
            yAxis.setUpperBound(1);
            yAxis.setTickUnit(0.2);
        });
        RadioMenuItem miZoomY05 = new RadioMenuItem("0-0.5");
        miZoomY05.setOnAction(e -> {
            yAxis.setAutoRanging(false);
            yAxis.setUpperBound(0.5);
            yAxis.setTickUnit(0.1);
        });
        RadioMenuItem miZoomY02 = new RadioMenuItem("0-0.2");
        miZoomY02.setOnAction(e -> {
            yAxis.setAutoRanging(false);
            yAxis.setUpperBound(0.2);
            yAxis.setTickUnit(0.05);
        });
        RadioMenuItem miZoomY01 = new RadioMenuItem("0-0.1");
        miZoomY01.setOnAction(e -> {
            yAxis.setAutoRanging(false);
            yAxis.setUpperBound(0.1);
            yAxis.setTickUnit(0.05);
        });
        RadioMenuItem miZoomY005 = new RadioMenuItem("0-0.05");
        miZoomY005.setOnAction(e -> {
            yAxis.setAutoRanging(false);
            yAxis.setUpperBound(0.05);
            yAxis.setTickUnit(0.01);
        });
        RadioMenuItem miZoomY001 = new RadioMenuItem("0-0.01");
        miZoomY001.setOnAction(e -> {
            yAxis.setAutoRanging(false);
            yAxis.setUpperBound(0.01);
            yAxis.setTickUnit(0.005);
        });
        ToggleGroup tgZoom = new ToggleGroup();
        miZoomY1.setToggleGroup(tgZoom);
        miZoomY05.setToggleGroup(tgZoom);
        miZoomY02.setToggleGroup(tgZoom);
        miZoomY01.setToggleGroup(tgZoom);
        miZoomY005.setToggleGroup(tgZoom);
        miZoomY001.setToggleGroup(tgZoom);
        Menu menuZoomY = new Menu("Set y-axis range");
        menuZoomY.getItems().addAll(miZoomY1, miZoomY05, miZoomY02, miZoomY01, miZoomY005, miZoomY001);
        MenuItem miCopyData = new MenuItem("Copy chart data");
        miCopyData.setOnAction(e -> {
            String dataString = ChartTools.getChartDataAsString(chartPValues);
            ClipboardContent content = new ClipboardContent();
            content.putString(dataString);
            Clipboard.getSystemClipboard().setContent(content);
        });
        popup.getItems().addAll(miCopyData, menuZoomY);
        chartPValues.setOnContextMenuRequested(e -> {
            popup.show(chartPValues, e.getScreenX(), e.getScreenY());
        });
        for (int col = 0; col < tableModel.getColumnCount(); col++) {
            TableColumn<Integer, String> column = new TableColumn<>(tableModel.getColumnName(col));
            int colNumber = col;
            column.setCellValueFactory(new Callback<CellDataFeatures<Integer, String>, ObservableValue<String>>() {

                @Override
                public ObservableValue<String> call(CellDataFeatures<Integer, String> p) {
                    return new SimpleStringProperty((String) tableModel.getValueAt(p.getValue(), colNumber));
                }
            });
            column.setCellFactory(new Callback<TableColumn<Integer, String>, TableCell<Integer, String>>() {

                @Override
                public TableCell<Integer, String> call(TableColumn<Integer, String> param) {
                    TableCell<Integer, String> cell = new TableCell<Integer, String>() {

                        @Override
                        protected void updateItem(String item, boolean empty) {
                            super.updateItem(item, empty);
                            setText(item);
                            setTooltip(new Tooltip(item));
                        }
                    };
                    return cell;
                }
            });
            table.getColumns().add(column);
        }
        table.setPrefHeight(250);
        table.setColumnResizePolicy(TableView.CONSTRAINED_RESIZE_POLICY);
        table.maxHeightProperty().bind(table.prefHeightProperty());
        params = new ParameterList();
        // maxTimePoint = 0;
        // for (TMACoreObject core : hierarchy.getTMAGrid().getTMACoreList()) {
        // double os = core.getMeasurementList().getMeasurementValue(TMACoreObject.KEY_OVERALL_SURVIVAL);
        // double rfs = core.getMeasurementList().getMeasurementValue(TMACoreObject.KEY_RECURRENCE_FREE_SURVIVAL);
        // if (os > maxTimePoint)
        // maxTimePoint = os;
        // if (rfs > maxTimePoint)
        // maxTimePoint = rfs;
        // }
        params.addIntParameter("censorTimePoints", "Max censored time", (int) (censorThreshold + 0.5), null, 0, (int) Math.ceil(maxTimePoint), "Latest time point beyond which data will be censored");
        // params.addChoiceParameter("scoreThresholdMethod", "Threshold method", "Manual", Arrays.asList("Manual", "Median", "Log-rank test"));
        if (calculateAllPValues)
            // Don't include "Lowest smoothed p-value" - it's not an established method and open to misinterpretation...
            params.addChoiceParameter("scoreThresholdMethod", "Threshold method", "Median", Arrays.asList("Manual (1)", "Manual (2)", "Manual (3)", "Median", "Tertiles", "Quartiles", "Lowest p-value"));
        else
            // params.addChoiceParameter("scoreThresholdMethod", "Threshold method", "Median", Arrays.asList("Manual (1)", "Manual (2)", "Manual (3)", "Median", "Tertiles", "Quartiles", "Lowest p-value", "Lowest smoothed p-value"));
            params.addChoiceParameter("scoreThresholdMethod", "Threshold method", "Median", Arrays.asList("Manual (1)", "Manual (2)", "Manual (3)", "Median", "Tertiles", "Quartiles"));
        params.addDoubleParameter("threshold1", "Threshold 1", thresholds.length > 0 ? thresholds[0] : (minVal + maxVal) / 2, null, "Threshold to distinguish between patient groups");
        params.addDoubleParameter("threshold2", "Threshold 2", thresholds.length > 1 ? thresholds[1] : (minVal + maxVal) / 2, null, "Threshold to distinguish between patient groups");
        params.addDoubleParameter("threshold3", "Threshold 3", thresholds.length > 2 ? thresholds[2] : (minVal + maxVal) / 2, null, "Threshold to distinguish between patient groups");
        params.addBooleanParameter("showAtRisk", "Show at risk", plotter.getShowAtRisk(), "Show number of patients at risk below the plot");
        params.addBooleanParameter("showTicks", "Show censored ticks", plotter.getShowCensoredTicks(), "Show ticks to indicate censored data");
        params.addBooleanParameter("showKey", "Show key", plotter.getShowKey(), "Show key indicating display of each curve");
        // Hide threshold parameters if threshold can't be used
        if (!scoresValid) {
            // params.setHiddenParameters(true, "scoreThresholdMethod", "scoreThreshold");
            histogramPanel.getChart().setVisible(false);
        }
        panelParams = new ParameterPanelFX(params);
        panelParams.addParameterChangeListener(this);
        updateThresholdsEnabled();
        for (int i = 0; i < threshProperties.length; i++) {
            String p = "threshold" + (i + 1);
            threshProperties[i].addListener((v, o, n) -> {
                if (interactiveThresholds()) {
                    // Need to do a decent double check with tolerance to text field value changing while typing
                    if (!GeneralTools.almostTheSame(params.getDoubleParameterValue(p), n.doubleValue(), 0.0001))
                        panelParams.setNumericParameterValue(p, n);
                }
            });
        }
        BorderPane paneBottom = new BorderPane();
        TitledPane paneOptions = new TitledPane("Options", panelParams.getPane());
        // paneOptions.setCollapsible(false);
        Pane paneCanvas = new StackPane();
        paneCanvas.getChildren().add(plotter.getCanvas());
        GridPane paneLeft = new GridPane();
        paneLeft.add(paneOptions, 0, 0);
        paneLeft.add(table, 0, 1);
        GridPane.setHgrow(paneOptions, Priority.ALWAYS);
        GridPane.setHgrow(table, Priority.ALWAYS);
        paneBottom.setLeft(paneLeft);
        paneBottom.setCenter(paneHistogram);
        paneMain.setCenter(paneCanvas);
        paneMain.setBottom(paneBottom);
        paneMain.setPadding(new Insets(10, 10, 10, 10));
    } else if (thresholds.length > 0) {
        // Ensure the sliders/text fields are set sensibly
        if (!GeneralTools.almostTheSame(thresholds[0], params.getDoubleParameterValue("threshold1"), 0.0001)) {
            panelParams.setNumericParameterValue("threshold1", thresholds[0]);
        }
        if (thresholds.length > 1 && !GeneralTools.almostTheSame(thresholds[1], params.getDoubleParameterValue("threshold2"), 0.0001)) {
            panelParams.setNumericParameterValue("threshold2", thresholds[1]);
        }
        if (thresholds.length > 2 && !GeneralTools.almostTheSame(thresholds[2], params.getDoubleParameterValue("threshold3"), 0.0001)) {
            panelParams.setNumericParameterValue("threshold3", thresholds[2]);
        }
    }
    if (histogram != null) {
        histogramPanel.getHistogramData().setAll(HistogramPanelFX.createHistogramData(histogram, false, (Color) null));
        histogramPanel.getChart().getXAxis().setLabel(scoreColumn);
        histogramPanel.getChart().getYAxis().setLabel("Count");
        ChartTools.addChartExportMenu(histogramPanel.getChart(), null);
    // histogramWrapper.setVerticalLines(thresholds, ColorToolsFX.getCachedColor(240, 0, 0, 128));
    // Deal with threshold adjustment
    // histogramWrapper.getThresholds().addListener((Observable o) -> generatePlot());
    }
    if (pValues != null) {
        // TODO: Raise earlier where p-value calculation is
        if (pValuesChanged) {
            ObservableList<XYChart.Data<Number, Number>> data = FXCollections.observableArrayList();
            for (int i = 0; i < pValueThresholds.length; i++) {
                double pValue = pValues[i];
                if (Double.isNaN(pValue))
                    continue;
                data.add(new XYChart.Data<>(pValueThresholds[i], pValue, pValueThresholdsObserved[i]));
            }
            ObservableList<XYChart.Data<Number, Number>> dataSmoothed = null;
            if (pValuesSmoothed != null) {
                dataSmoothed = FXCollections.observableArrayList();
                for (int i = 0; i < pValueThresholds.length; i++) {
                    double pValueSmoothed = pValuesSmoothed[i];
                    if (Double.isNaN(pValueSmoothed))
                        continue;
                    dataSmoothed.add(new XYChart.Data<>(pValueThresholds[i], pValueSmoothed));
                }
            }
            // Don't bother showing the smoothed data... it tends to get in the way...
            // if (dataSmoothed != null)
            // chartPValues.getData().setAll(new XYChart.Series<>("P-values", data), new XYChart.Series<>("Smoothed P-values", dataSmoothed));
            // else
            chartPValues.getData().setAll(new XYChart.Series<>("P-values", data));
            // Add line to show 0.05 significance threshold
            if (pValueThresholds.length > 1) {
                Data<Number, Number> sigData1 = new Data<>(pValueThresholds[0], 0.05);
                Data<Number, Number> sigData2 = new Data<>(pValueThresholds[pValueThresholds.length - 1], 0.05);
                XYChart.Series<Number, Number> dataSignificant = new XYChart.Series<>("Significance 0.05", FXCollections.observableArrayList(sigData1, sigData2));
                chartPValues.getData().add(dataSignificant);
                sigData1.getNode().setVisible(false);
                sigData2.getNode().setVisible(false);
            }
            // pValuesWrapper.clearThresholds();
            for (XYChart.Data<Number, Number> dataPoint : data) {
                if (!Boolean.TRUE.equals(dataPoint.getExtraValue()))
                    dataPoint.getNode().setVisible(false);
            }
        // if (dataSmoothed != null) {
        // for (XYChart.Data<Number, Number> dataPoint : dataSmoothed) {
        // dataPoint.getNode().setVisible(false);
        // }
        // chartPValues.getData().get(1).getNode().setOpacity(0.5);
        // }
        // int count = 0;
        // for (int i = 0; i < pValueThresholds.length; i++) {
        // double pValue = pValues[i];
        // if (Double.isNaN(pValue))
        // continue;
        // boolean observed = pValueThresholdsObserved[i];
        // //						if (observed)
        // //							pValuesWrapper.addThreshold(new ReadOnlyDoubleWrapper(pValueThresholds[i]), Color.rgb(0, 0, 0, 0.05));
        // 
        // if (!observed) {
        // //							StackPane pane = (StackPane)data.get(count).getNode();
        // //							pane.setEffect(new DropShadow());
        // data.get(count).getNode().setVisible(false);
        // }
        // count++;
        // }
        }
        for (int i = 0; i < threshProperties.length; i++) {
            if (i < thresholds.length)
                threshProperties[i].set(thresholds[i]);
            else
                threshProperties[i].set(Double.NaN);
        }
        boolean isInteractive = interactiveThresholds();
        histogramWrapper.setIsInteractive(isInteractive);
        pValuesWrapper.setIsInteractive(isInteractive);
        chartPValues.setVisible(true);
    }
    // else
    // chartPValues.setVisible(false);
    // Store values for next time
    scoreData = newScoreData;
}

Example 3 with ParameterPanelFX

use of qupath.lib.gui.dialogs.ParameterPanelFX 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;
}

Example 4 with ParameterPanelFX

use of qupath.lib.gui.dialogs.ParameterPanelFX in project qupath by qupath.

the class ImageDetailsPane method editStainVector.

void editStainVector(Object value) {
    if (!(value instanceof StainVector || value instanceof double[]))
        return;
    // JOptionPane.showMessageDialog(null, "Modifying stain vectors not yet implemented...");
    ImageData<BufferedImage> imageData = qupath.getImageData();
    if (imageData == null)
        return;
    ColorDeconvolutionStains stains = imageData.getColorDeconvolutionStains();
    // Default to background values
    int num = -1;
    String name = null;
    String message = null;
    if (value instanceof StainVector) {
        StainVector stainVector = (StainVector) value;
        if (stainVector.isResidual() && imageData.getImageType() != ImageType.BRIGHTFIELD_OTHER) {
            logger.warn("Cannot set residual stain vector - this is computed from the known vectors");
            return;
        }
        num = stains.getStainNumber(stainVector);
        if (num <= 0) {
            logger.error("Could not identify stain vector " + stainVector + " inside " + stains);
            return;
        }
        name = stainVector.getName();
        message = "Set stain vector from ROI?";
    } else
        message = "Set color deconvolution background values from ROI?";
    ROI pathROI = imageData.getHierarchy().getSelectionModel().getSelectedROI();
    boolean wasChanged = false;
    String warningMessage = null;
    boolean editableName = imageData.getImageType() == ImageType.BRIGHTFIELD_OTHER;
    if (pathROI != null) {
        if ((pathROI instanceof RectangleROI) && !pathROI.isEmpty() && ((RectangleROI) pathROI).getArea() < 500 * 500) {
            if (Dialogs.showYesNoDialog("Color deconvolution stains", message)) {
                ImageServer<BufferedImage> server = imageData.getServer();
                BufferedImage img = null;
                try {
                    img = server.readBufferedImage(RegionRequest.createInstance(server.getPath(), 1, pathROI));
                } catch (IOException e) {
                    Dialogs.showErrorMessage("Set stain vector", "Unable to read image region");
                    logger.error("Unable to read region", e);
                }
                int rgb = ColorDeconvolutionHelper.getMedianRGB(img.getRGB(0, 0, img.getWidth(), img.getHeight(), null, 0, img.getWidth()));
                if (num >= 0) {
                    StainVector vectorValue = ColorDeconvolutionHelper.generateMedianStainVectorFromPixels(name, img.getRGB(0, 0, img.getWidth(), img.getHeight(), null, 0, img.getWidth()), stains.getMaxRed(), stains.getMaxGreen(), stains.getMaxBlue());
                    if (!Double.isFinite(vectorValue.getRed() + vectorValue.getGreen() + vectorValue.getBlue())) {
                        Dialogs.showErrorMessage("Set stain vector", "Cannot set stains for the current ROI!\n" + "It might be too close to the background color.");
                        return;
                    }
                    value = vectorValue;
                } else {
                    // Update the background
                    value = new double[] { ColorTools.red(rgb), ColorTools.green(rgb), ColorTools.blue(rgb) };
                }
                wasChanged = true;
            }
        } else {
            warningMessage = "Note: To set stain values from an image region, draw a small, rectangular ROI first";
        }
    }
    // Prompt to set the name / verify stains
    ParameterList params = new ParameterList();
    String title;
    String nameBefore = null;
    String valuesBefore = null;
    String collectiveNameBefore = stains.getName();
    String suggestedName;
    if (collectiveNameBefore.endsWith("default"))
        suggestedName = collectiveNameBefore.substring(0, collectiveNameBefore.lastIndexOf("default")) + "modified";
    else
        suggestedName = collectiveNameBefore;
    params.addStringParameter("collectiveName", "Collective name", suggestedName, "Enter collective name for all 3 stains (e.g. H-DAB Scanner A, H&E Scanner B)");
    if (value instanceof StainVector) {
        nameBefore = ((StainVector) value).getName();
        valuesBefore = ((StainVector) value).arrayAsString(Locale.getDefault(Category.FORMAT));
        params.addStringParameter("name", "Name", nameBefore, "Enter stain name").addStringParameter("values", "Values", valuesBefore, "Enter 3 values (red, green, blue) defining color deconvolution stain vector, separated by spaces");
        title = "Set stain vector";
    } else {
        nameBefore = "Background";
        valuesBefore = GeneralTools.arrayToString(Locale.getDefault(Category.FORMAT), (double[]) value, 2);
        params.addStringParameter("name", "Stain name", nameBefore);
        params.addStringParameter("values", "Stain values", valuesBefore, "Enter 3 values (red, green, blue) defining background, separated by spaces");
        params.setHiddenParameters(true, "name");
        title = "Set background";
    }
    if (warningMessage != null)
        params.addEmptyParameter(warningMessage);
    // Disable editing the name if it should be fixed
    ParameterPanelFX parameterPanel = new ParameterPanelFX(params);
    parameterPanel.setParameterEnabled("name", editableName);
    ;
    if (!Dialogs.showConfirmDialog(title, parameterPanel.getPane()))
        return;
    // Check if anything changed
    String collectiveName = params.getStringParameterValue("collectiveName");
    String nameAfter = params.getStringParameterValue("name");
    String valuesAfter = params.getStringParameterValue("values");
    if (collectiveName.equals(collectiveNameBefore) && nameAfter.equals(nameBefore) && valuesAfter.equals(valuesBefore) && !wasChanged)
        return;
    double[] valuesParsed = ColorDeconvolutionStains.parseStainValues(Locale.getDefault(Category.FORMAT), valuesAfter);
    if (valuesParsed == null) {
        logger.error("Input for setting color deconvolution information invalid! Cannot parse 3 numbers from {}", valuesAfter);
        return;
    }
    if (num >= 0) {
        try {
            stains = stains.changeStain(StainVector.createStainVector(nameAfter, valuesParsed[0], valuesParsed[1], valuesParsed[2]), num);
        } catch (Exception e) {
            logger.error("Error setting stain vectors", e);
            Dialogs.showErrorMessage("Set stain vectors", "Requested stain vectors are not valid!\nAre two stains equal?");
        }
    } else {
        // Update the background
        stains = stains.changeMaxValues(valuesParsed[0], valuesParsed[1], valuesParsed[2]);
    }
    // Set the collective name
    stains = stains.changeName(collectiveName);
    imageData.setColorDeconvolutionStains(stains);
    qupath.getViewer().repaintEntireImage();
}

Example 5 with ParameterPanelFX

use of qupath.lib.gui.dialogs.ParameterPanelFX in project qupath by qupath.

the class ParameterDialogWrapper method createDialog.

private Stage createDialog(final PathInteractivePlugin<T> plugin, final ParameterList params, final PluginRunner<T> pluginRunner) {
    panel = new ParameterPanelFX(params);
    panel.getPane().setPadding(new Insets(5, 5, 5, 5));
    // panel.addParameterChangeListener(new ParameterChangeListener() {
    // 
    // @Override
    // public void parameterChanged(ParameterList parameterList, String key, boolean isAdjusting) {
    // 
    // if (!plugin.requestLiveUpdate())
    // return;
    // 
    // PathObjectHierarchy hierarchy = pluginRunner.getHierarchy();
    // if (hierarchy == null)
    // return;
    // 
    // Collection<Class<? extends PathObject>> supportedParents = plugin.getSupportedParentObjectClasses();
    // 
    // PathObject selectedObject = pluginRunner.getSelectedObject();
    // if (selectedObject == null) {
    // if (supportedParents.contains(PathRootObject.class))
    // Collections.singleton(hierarchy.getRootObject());
    // } else if (supportedParents.contains(selectedObject.getClass()))
    // Collections.singleton(selectedObject);
    // }
    // 
    // });
    // final Button btnRun = new Button("Run " + plugin.getName());
    final Button btnRun = new Button("Run");
    btnRun.textProperty().bind(Bindings.createStringBinding(() -> {
        if (btnRun.isDisabled())
            return "Please wait...";
        else
            return "Run";
    }, btnRun.disabledProperty()));
    final Stage dialog = new Stage();
    QuPathGUI qupath = QuPathGUI.getInstance();
    if (qupath != null)
        dialog.initOwner(qupath.getStage());
    dialog.setTitle(plugin.getName());
    final String emptyLabel = " \n";
    final Label label = new Label(emptyLabel);
    label.setStyle("-fx-font-weight: bold;");
    label.setPadding(new Insets(5, 5, 5, 5));
    label.setAlignment(Pos.CENTER);
    label.setTextAlignment(TextAlignment.CENTER);
    btnRun.setOnAction(e -> {
        // Check if we have the parent objects available to make this worthwhile
        if (plugin instanceof PathInteractivePlugin) {
            // // Strip off any of our extra parameters
            // params.removeParameter(KEY_REGIONS);
            boolean alwaysPrompt = plugin.alwaysPromptForObjects();
            ImageData<?> imageData = pluginRunner.getImageData();
            Collection<PathObject> selected = imageData == null ? Collections.emptyList() : imageData.getHierarchy().getSelectionModel().getSelectedObjects();
            Collection<? extends PathObject> parents = PathObjectTools.getSupportedObjects(selected, plugin.getSupportedParentObjectClasses());
            if (alwaysPrompt || parents == null || parents.isEmpty()) {
                if (!ParameterDialogWrapper.promptForParentObjects(pluginRunner, plugin, alwaysPrompt && !parents.isEmpty()))
                    return;
            }
        // promptForParentObjects
        }
        dialog.getScene().setCursor(Cursor.WAIT);
        btnRun.setDisable(true);
        Runnable runnable = new Runnable() {

            @Override
            public void run() {
                try {
                    WorkflowStep lastStep = pluginRunner.getImageData().getHistoryWorkflow().getLastStep();
                    boolean success = plugin.runPlugin(pluginRunner, ParameterList.getParameterListJSON(params, "  "));
                    WorkflowStep lastStepNew = pluginRunner.getImageData().getHistoryWorkflow().getLastStep();
                    if (success && lastStep != lastStepNew)
                        lastWorkflowStep = lastStepNew;
                    else
                        lastWorkflowStep = null;
                } catch (Exception e) {
                    Dialogs.showErrorMessage("Plugin error", e);
                } catch (OutOfMemoryError e) {
                    // This doesn't actually work...
                    Dialogs.showErrorMessage("Out of memory error", "Out of memory - try to close other applications, or decrease the number of parallel processors in the QuPath preferences");
                } finally {
                    Platform.runLater(() -> {
                        QuPathGUI.getInstance().pluginRunningProperty().set(false);
                        dialog.getScene().setCursor(Cursor.DEFAULT);
                        label.setText(plugin.getLastResultsDescription());
                        btnRun.setDisable(false);
                    });
                }
            }
        };
        Thread t = new Thread(runnable, "Plugin thread");
        QuPathGUI.getInstance().pluginRunningProperty().set(true);
        t.start();
    });
    BorderPane pane = new BorderPane();
    ScrollPane scrollPane = new ScrollPane();
    label.setMaxWidth(Double.MAX_VALUE);
    scrollPane.setContent(panel.getPane());
    scrollPane.setFitToWidth(true);
    pane.setCenter(scrollPane);
    btnRun.setMaxWidth(Double.MAX_VALUE);
    btnRun.setPadding(new Insets(5, 5, 5, 5));
    pane.setBottom(btnRun);
    Scene scene = new Scene(pane);
    dialog.setScene(scene);
    // Request focus, to make it easier to run from the keyboard
    btnRun.requestFocus();
    dialog.sizeToScene();
    return dialog;
}