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

Example 6 with TMACoreObject

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

the class QuPathGUI method setupViewer.

void setupViewer(final QuPathViewerPlus viewer) {
    viewer.getView().setFocusTraversable(true);
    // Update active viewer as required
    viewer.getView().focusedProperty().addListener((e, f, nowFocussed) -> {
        if (nowFocussed) {
            viewerManager.setActiveViewer(viewer);
        }
    });
    viewer.getView().addEventFilter(MouseEvent.MOUSE_PRESSED, e -> viewer.getView().requestFocus());
    viewer.zoomToFitProperty().bind(zoomToFit);
    // Create popup menu
    setViewerPopupMenu(viewer);
    viewer.getView().widthProperty().addListener((e, f, g) -> {
        if (viewer.getZoomToFit())
            updateMagnificationString();
    });
    viewer.getView().heightProperty().addListener((e, f, g) -> {
        if (viewer.getZoomToFit())
            updateMagnificationString();
    });
    // Enable drag and drop
    dragAndDrop.setupTarget(viewer.getView());
    // Listen to the scroll wheel
    viewer.getView().setOnScroll(e -> {
        if (viewer == viewerManager.getActiveViewer() || !viewerManager.getSynchronizeViewers()) {
            double scrollUnits = e.getDeltaY() * PathPrefs.getScaledScrollSpeed();
            // Use shift down to adjust opacity
            if (e.isShortcutDown()) {
                OverlayOptions options = viewer.getOverlayOptions();
                options.setOpacity((float) (options.getOpacity() + scrollUnits * 0.001));
                return;
            }
            // Avoid zooming at the end of a gesture when using touchscreens
            if (e.isInertia())
                return;
            if (PathPrefs.invertScrollingProperty().get())
                scrollUnits = -scrollUnits;
            double newDownsampleFactor = viewer.getDownsampleFactor() * Math.pow(viewer.getDefaultZoomFactor(), scrollUnits);
            newDownsampleFactor = Math.min(viewer.getMaxDownsample(), Math.max(newDownsampleFactor, viewer.getMinDownsample()));
            viewer.setDownsampleFactor(newDownsampleFactor, e.getX(), e.getY());
        }
    });
    viewer.getView().addEventFilter(RotateEvent.ANY, e -> {
        if (!PathPrefs.useRotateGesturesProperty().get())
            return;
        // logger.debug("Rotating: " + e.getAngle());
        viewer.setRotation(viewer.getRotation() + Math.toRadians(e.getAngle()));
        e.consume();
    });
    viewer.getView().addEventFilter(ZoomEvent.ANY, e -> {
        if (!PathPrefs.useZoomGesturesProperty().get())
            return;
        double zoomFactor = e.getZoomFactor();
        if (Double.isNaN(zoomFactor))
            return;
        logger.debug("Zooming: " + e.getZoomFactor() + " (" + e.getTotalZoomFactor() + ")");
        viewer.setDownsampleFactor(viewer.getDownsampleFactor() / zoomFactor, e.getX(), e.getY());
        e.consume();
    });
    viewer.getView().addEventFilter(ScrollEvent.ANY, new ScrollEventPanningFilter(viewer));
    viewer.getView().addEventHandler(KeyEvent.KEY_PRESSED, e -> {
        PathObject pathObject = viewer.getSelectedObject();
        if (!e.isConsumed() && pathObject != null) {
            if (pathObject.isTMACore()) {
                TMACoreObject core = (TMACoreObject) pathObject;
                if (e.getCode() == KeyCode.ENTER) {
                    defaultActions.TMA_ADD_NOTE.handle(new ActionEvent(e.getSource(), e.getTarget()));
                    e.consume();
                } else if (e.getCode() == KeyCode.BACK_SPACE) {
                    core.setMissing(!core.isMissing());
                    viewer.getHierarchy().fireObjectsChangedEvent(this, Collections.singleton(core));
                    e.consume();
                }
            } else if (pathObject.isAnnotation()) {
                if (e.getCode() == KeyCode.ENTER) {
                    GuiTools.promptToSetActiveAnnotationProperties(viewer.getHierarchy());
                    e.consume();
                }
            }
        }
    });
}

Example 7 with TMACoreObject

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

the class DefaultTMAGrid method getCoreIndex.

int getCoreIndex(String coreName) {
    int ind = 0;
    for (TMACoreObject core : cores) {
        String name = core.getName();
        if (coreName == null) {
            if (name == null)
                return ind;
        } else if (coreName.equals(name))
            return ind;
        ind++;
    }
    return -1;
}

Example 8 with TMACoreObject

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

the class TMASummaryViewer method updateSurvivalCurves.

private void updateSurvivalCurves() {
    String colID = null;
    String colScore = null;
    colCensored = null;
    for (String nameOrig : model.getAllNames()) {
        if (nameOrig.equals(TMACoreObject.KEY_UNIQUE_ID))
            colID = nameOrig;
        else // else if (nameOrig.equals(TMACoreObject.KEY_CENSORED))
        // colCensored = nameOrig;
        // else if (!Number.class.isAssignableFrom())
        // continue;
        {
            if (nameOrig.trim().length() == 0 || !model.getMeasurementNames().contains(nameOrig))
                continue;
            String name = nameOrig.toLowerCase();
            if (name.equals("h-score"))
                colScore = nameOrig;
            else if (name.equals("positive %") && colScore == null)
                colScore = nameOrig;
        }
    }
    // Check for a column with the exact requested name
    String colCensoredRequested = null;
    String colSurvival = getSurvivalColumn();
    if (colSurvival != null) {
        colCensoredRequested = getRequestedSurvivalCensoredColumn(colSurvival);
        if (model.getAllNames().contains(colCensoredRequested))
            colCensored = colCensoredRequested;
        else // Check for a general 'censored' column... less secure since it doesn't specify OS or RFS (but helps with backwards-compatibility)
        if (model.getAllNames().contains("Censored")) {
            logger.warn("Correct censored column for \"{}\" unavailable - should be \"{}\", but using \"Censored\" column instead", colSurvival, colCensoredRequested);
            colCensored = "Censored";
        }
    }
    if (colCensored == null && colSurvival != null) {
        logger.warn("Unable to find censored column - survival data will be uncensored");
    } else
        logger.info("Survival column: {}, Censored column: {}", colSurvival, colCensored);
    colScore = comboMainMeasurement.getSelectionModel().getSelectedItem();
    if (colID == null || colSurvival == null || colCensored == null) {
        // Adjust priority depending on whether we have any data at all..
        if (!model.getItems().isEmpty())
            logger.warn("No survival data found!");
        else
            logger.trace("No entries or survival data available");
        return;
    }
    // Generate a pseudo TMA core hierarchy
    Map<String, List<TMAEntry>> scoreMap = createScoresMap(model.getItems(), colScore, colID);
    // System.err.println("Score map size: " + scoreMap.size() + "\tEntries: " + model.getEntries().size());
    List<TMACoreObject> cores = new ArrayList<>(scoreMap.size());
    double[] scores = new double[15];
    for (Entry<String, List<TMAEntry>> entry : scoreMap.entrySet()) {
        TMACoreObject core = new TMACoreObject();
        core.setName("ID: " + entry.getKey());
        MeasurementList ml = core.getMeasurementList();
        Arrays.fill(scores, Double.POSITIVE_INFINITY);
        List<TMAEntry> list = entry.getValue();
        // Increase array size, if needed
        if (list.size() > scores.length)
            scores = new double[list.size()];
        for (int i = 0; i < list.size(); i++) {
            scores[i] = model.getNumericValue(list.get(i), colScore);
        // scores[i] = list.get(i).getMeasurement(colScore).doubleValue();
        }
        Arrays.sort(scores);
        int n = list.size();
        double score;
        if (n % 2 == 1)
            score = scores[n / 2];
        else
            score = (scores[n / 2 - 1] + scores[n / 2]) / 2;
        core.putMetadataValue(TMACoreObject.KEY_UNIQUE_ID, entry.getKey());
        // System.err.println("Putting: " + list.get(0).getMeasurement(colSurvival).doubleValue() + " LIST: " + list.size());
        ml.putMeasurement(colSurvival, list.get(0).getMeasurementAsDouble(colSurvival));
        ml.putMeasurement(colCensoredRequested, list.get(0).getMeasurementAsDouble(colCensored));
        if (colScore != null)
            ml.putMeasurement(colScore, score);
        cores.add(core);
    // logger.info(entry.getKey() + "\t" + score);
    }
    TMAGrid grid = DefaultTMAGrid.create(cores, 1);
    PathObjectHierarchy hierarchy = new PathObjectHierarchy();
    hierarchy.setTMAGrid(grid);
    kmDisplay.setHierarchy(hierarchy, colSurvival, colCensoredRequested);
    kmDisplay.setScoreColumn(comboMainMeasurement.getSelectionModel().getSelectedItem());
// new KaplanMeierPlotTMA.KaplanMeierDisplay(hierarchy, colScore).show(frame, colScore);
}

Example 9 with TMACoreObject

use of qupath.lib.objects.TMACoreObject 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 10 with TMACoreObject

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

the class TMADataIO method writeTMAData.

/**
 * Write TMA data in a human-readable (and viewable) way, with JPEGs and TXT/CSV files.
 *
 * @param file
 * @param imageData
 * @param overlayOptions
 * @param downsampleFactor The downsample factor used for the TMA cores. If NaN, an automatic downsample value will be selected (>= 1).  If <= 0, no cores are exported.
 */
public static void writeTMAData(File file, final ImageData<BufferedImage> imageData, OverlayOptions overlayOptions, final double downsampleFactor) {
    if (imageData == null || imageData.getHierarchy() == null || imageData.getHierarchy().getTMAGrid() == null) {
        logger.error("No TMA data available to save!");
        return;
    }
    final ImageServer<BufferedImage> server = imageData.getServer();
    String coreExt = imageData.getServer().isRGB() ? ".jpg" : ".tif";
    if (file == null) {
        file = Dialogs.promptToSaveFile("Save TMA data", null, ServerTools.getDisplayableImageName(server), "TMA data", "qptma");
        if (file == null)
            return;
    } else if (file.isDirectory() || (!file.exists() && file.getAbsolutePath().endsWith(File.pathSeparator))) {
        // Put inside the specified directory
        file = new File(file, ServerTools.getDisplayableImageName(server) + TMA_DEARRAYING_DATA_EXTENSION);
        if (!file.getParentFile().exists())
            file.getParentFile().mkdirs();
    }
    final File dirData = new File(file + ".data");
    if (!dirData.exists())
        dirData.mkdir();
    // Write basic file info
    String delimiter = "\t";
    TMAGrid tmaGrid = imageData.getHierarchy().getTMAGrid();
    try {
        PrintWriter writer = new PrintWriter(file);
        writer.println(server.getPath());
        writer.println(ServerTools.getDisplayableImageName(server));
        writer.println();
        writer.println("TMA grid width: " + tmaGrid.getGridWidth());
        writer.println("TMA grid height: " + tmaGrid.getGridHeight());
        writer.println("Core name" + delimiter + "X" + delimiter + "Y" + delimiter + "Width" + delimiter + "Height" + delimiter + "Present" + delimiter + TMACoreObject.KEY_UNIQUE_ID);
        for (int row = 0; row < tmaGrid.getGridHeight(); row++) {
            for (int col = 0; col < tmaGrid.getGridWidth(); col++) {
                TMACoreObject core = tmaGrid.getTMACore(row, col);
                if (!core.hasROI()) {
                    writer.println(core.getName() + delimiter + delimiter + delimiter + delimiter);
                    continue;
                }
                ROI pathROI = core.getROI();
                int x = (int) pathROI.getBoundsX();
                int y = (int) pathROI.getBoundsY();
                int w = (int) Math.ceil(pathROI.getBoundsWidth());
                int h = (int) Math.ceil(pathROI.getBoundsHeight());
                String id = core.getUniqueID() == null ? "" : core.getUniqueID();
                writer.println(core.getName() + delimiter + x + delimiter + y + delimiter + w + delimiter + h + delimiter + !core.isMissing() + delimiter + id);
            }
        }
        writer.close();
    } catch (Exception e) {
        logger.error("Error writing TMA data: " + e.getLocalizedMessage(), e);
        return;
    }
    // Save the summary results
    ObservableMeasurementTableData tableData = new ObservableMeasurementTableData();
    tableData.setImageData(imageData, tmaGrid.getTMACoreList());
    SummaryMeasurementTableCommand.saveTableModel(tableData, new File(dirData, "TMA results - " + ServerTools.getDisplayableImageName(server) + ".txt"), Collections.emptyList());
    boolean outputCoreImages = Double.isNaN(downsampleFactor) || downsampleFactor > 0;
    if (outputCoreImages) {
        // Create new overlay options, if we don't have some already
        if (overlayOptions == null) {
            overlayOptions = new OverlayOptions();
            overlayOptions.setFillDetections(true);
        }
        final OverlayOptions options = overlayOptions;
        // Write an overall TMA map (for quickly checking if the dearraying is ok)
        File fileTMAMap = new File(dirData, "TMA map - " + ServerTools.getDisplayableImageName(server) + ".jpg");
        double downsampleThumbnail = Math.max(1, (double) Math.max(server.getWidth(), server.getHeight()) / 1024);
        RegionRequest request = RegionRequest.createInstance(server.getPath(), downsampleThumbnail, 0, 0, server.getWidth(), server.getHeight());
        OverlayOptions optionsThumbnail = new OverlayOptions();
        optionsThumbnail.setShowTMAGrid(true);
        optionsThumbnail.setShowGrid(false);
        optionsThumbnail.setShowAnnotations(false);
        optionsThumbnail.setShowDetections(false);
        try {
            var renderedServer = new RenderedImageServer.Builder(imageData).layers(new TMAGridOverlay(overlayOptions)).downsamples(downsampleThumbnail).build();
            ImageWriterTools.writeImageRegion(renderedServer, request, fileTMAMap.getAbsolutePath());
        // ImageWriters.writeImageRegionWithOverlay(imageData.getServer(), Collections.singletonList(new TMAGridOverlay(overlayOptions, imageData)), request, fileTMAMap.getAbsolutePath());
        } catch (IOException e) {
            logger.warn("Unable to write image overview: " + e.getLocalizedMessage(), e);
        }
        final double downsample = Double.isNaN(downsampleFactor) ? (server.getPixelCalibration().hasPixelSizeMicrons() ? ServerTools.getDownsampleFactor(server, preferredExportPixelSizeMicrons) : 1) : downsampleFactor;
        // Creating a plugin makes it possible to parallelize & show progress easily
        var renderedImageServer = new RenderedImageServer.Builder(imageData).layers(new HierarchyOverlay(null, options, imageData)).downsamples(downsample).build();
        ExportCoresPlugin plugin = new ExportCoresPlugin(dirData, renderedImageServer, downsample, coreExt);
        PluginRunner<BufferedImage> runner;
        var qupath = QuPathGUI.getInstance();
        if (qupath == null || qupath.getImageData() != imageData) {
            runner = new CommandLinePluginRunner<>(imageData);
            plugin.runPlugin(runner, null);
        } else {
            try {
                qupath.runPlugin(plugin, null, false);
            } catch (Exception e) {
                logger.error("Error writing TMA data: " + e.getLocalizedMessage(), e);
            }
        // new Thread(() -> qupath.runPlugin(plugin, null, false)).start();
        // runner = new PluginRunnerFX(QuPathGUI.getInstance());
        // new Thread(() -> plugin.runPlugin(runner, null)).start();
        }
    }
}