Examples with TMAEntry qupath.lib.gui.tma.TMAEntries.TMAEntry used on opensource projects

Example 1 with TMAEntry

use of qupath.lib.gui.tma.TMAEntries.TMAEntry 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 2 with TMAEntry

use of qupath.lib.gui.tma.TMAEntries.TMAEntry in project qupath by qupath.

the class TMASummaryViewer method setTMAEntries.

void setTMAEntries(final Collection<TMAEntry> newEntries) {
    // Turn off use-selected - can be crashy when replacing entries
    if (!newEntries.equals(entriesBase)) {
        useSelectedProperty.set(false);
        // Reset the cache
        imageCache.clear();
        // Try to load small images in a background thread
        List<TMAEntry> duplicateEntries = new ArrayList<>(newEntries);
        ExecutorService service = Executors.newSingleThreadExecutor();
        service.submit(() -> {
            duplicateEntries.parallelStream().forEach(entry -> {
                imageCache.getImage(entry, maxSmallWidth.get());
                imageCache.getOverlay(entry, maxSmallWidth.get());
            });
        });
        service.shutdown();
    }
    this.entriesBase.setAll(newEntries);
    // Store the names of any currently hidden columns
    lastHiddenColumns = table.getColumns().stream().filter(c -> !c.isVisible()).map(c -> c.getText()).collect(Collectors.toSet());
    // this.table.getColumns().clear();
    // // Useful for a paper, but not generally...
    // int count = 0;
    // int nCells = 0;
    // int nTumor = 0;
    // for (TMAEntry entry : entriesBase) {
    // if (!entry.isMissing() && (predicate.get() == null || predicate.get().test(entry))) {
    // count++;
    // nCells += (int)(entry.getMeasurement("Num Tumor").doubleValue() + entry.getMeasurement("Num Stroma").doubleValue());
    // nTumor += (int)(entry.getMeasurement("Num Tumor").doubleValue());
    // }
    // }
    // System.err.println(String.format("Num entries:\t%d\tNum tumor:\t%d\tNum cells:\t%d", count, nTumor, nCells));
    // Update measurement names
    Set<String> namesMeasurements = new LinkedHashSet<>();
    Set<String> namesMetadata = new LinkedHashSet<>();
    // boolean containsSummaries = false;
    for (TMAEntry entry : newEntries) {
        namesMeasurements.addAll(entry.getMeasurementNames());
        namesMetadata.addAll(entry.getMetadataNames());
    // containsSummaries = containsSummaries || entry instanceof TMASummaryEntry;
    }
    // Get the available survival columns
    String currentSurvival = getSurvivalColumn();
    survivalColumns.clear();
    if (namesMeasurements.contains(TMACoreObject.KEY_OVERALL_SURVIVAL))
        survivalColumns.add(TMACoreObject.KEY_OVERALL_SURVIVAL);
    if (namesMeasurements.contains(TMACoreObject.KEY_RECURRENCE_FREE_SURVIVAL))
        survivalColumns.add(TMACoreObject.KEY_RECURRENCE_FREE_SURVIVAL);
    if (currentSurvival != null && survivalColumns.contains(currentSurvival))
        comboSurvival.getSelectionModel().select(currentSurvival);
    else if (!survivalColumns.isEmpty())
        comboSurvival.getSelectionModel().select(survivalColumns.get(0));
    // // Add the count of non-missing cores if we are working with summaries
    // if (containsSummaries)
    namesMeasurements.add("Available cores");
    // Make sure there are no nulls or other unusable values
    namesMeasurements.remove(null);
    namesMeasurements.remove("");
    // measurementNames.clear();
    String selectedMainMeasurement = comboMainMeasurement.getSelectionModel().getSelectedItem();
    measurementNames.setAll(namesMeasurements);
    if (namesMeasurements.contains(selectedMainMeasurement))
        comboMainMeasurement.getSelectionModel().select(selectedMainMeasurement);
    else {
        namesMeasurements.remove(TMACoreObject.KEY_UNIQUE_ID);
        namesMeasurements.remove(TMACoreObject.KEY_OVERALL_SURVIVAL);
        namesMeasurements.remove(TMACoreObject.KEY_RECURRENCE_FREE_SURVIVAL);
        namesMeasurements.remove(TMACoreObject.KEY_OS_CENSORED);
        namesMeasurements.remove(TMACoreObject.KEY_RFS_CENSORED);
        // For historical reasons when there was only one censored column supported...
        namesMeasurements.remove("Censored");
        if (!namesMeasurements.isEmpty())
            comboMainMeasurement.getSelectionModel().select(0);
    }
    metadataNames.clear();
    metadataNames.addAll(namesMetadata);
    refreshTableData();
    // The next time the table is empty, show a different placeholder
    // from the original (which is for loading/import)
    table.setPlaceholder(new Text("No data"));
}

Example 3 with TMAEntry

use of qupath.lib.gui.tma.TMAEntries.TMAEntry in project qupath by qupath.

the class TMASummaryViewer method parseInputFile.

private void parseInputFile(File file, List<TMAEntry> entries) {
    int nEntries = entries.size();
    String serverPath = null;
    try {
        Scanner scanner = new Scanner(file);
        serverPath = scanner.nextLine().trim();
        scanner.close();
    } catch (Exception e) {
        logger.error("Error parsing input file", e);
    }
    if (serverPath == null) {
        // || !(new File(serverPath).exists())) {
        logger.error("Unable to find a server with path " + serverPath + " - cannot parse " + file.getAbsolutePath());
        return;
    }
    File dirData = new File(file.getAbsolutePath() + ".data");
    try {
        File fileResults = getTMAResultsFile(dirData);
        if (fileResults == null) {
            logger.error("No results file found for {}", dirData.getAbsolutePath());
            return;
        }
        Map<String, List<String>> csvData = TMAScoreImporter.readCSV(fileResults);
        if (csvData.isEmpty()) {
            logger.warn("Results file empty: {}", fileResults.getAbsolutePath());
            return;
        }
        // Identify metadata and numeric columns
        Map<String, List<String>> metadataColumns = new LinkedHashMap<>();
        Map<String, double[]> measurementColumns = new LinkedHashMap<>();
        List<String> idColumn = csvData.remove(TMACoreObject.KEY_UNIQUE_ID);
        if (idColumn != null) {
            metadataColumns.put(TMACoreObject.KEY_UNIQUE_ID, idColumn);
            // Make sure IDs are trimmed
            if (trimUniqueIDs) {
                for (int i = 0; i < idColumn.size(); i++) idColumn.set(i, idColumn.get(i) == null ? null : idColumn.get(i).trim());
            }
        }
        List<String> nameColumn = csvData.remove("Name");
        if (nameColumn == null)
            nameColumn = csvData.remove("Object");
        // Handle 'missing-ness' separately from general metadata
        List<String> missingColumn = csvData.remove(MISSING_COLUMN);
        // csvData.values().iterator().next().size();
        int n = idColumn == null ? 0 : idColumn.size();
        for (Entry<String, List<String>> entry : csvData.entrySet()) {
            List<String> list = entry.getValue();
            n = list.size();
            double[] values = TMAScoreImporter.parseNumeric(list, true);
            if (values == null || GeneralTools.numNaNs(values) == list.size())
                metadataColumns.put(entry.getKey(), list);
            else
                measurementColumns.put(entry.getKey(), values);
        }
        for (int i = 0; i < n; i++) {
            // Don't permit 'NaN' as an ID
            if (idColumn != null && "NaN".equals(idColumn.get(i)))
                continue;
            String name = nameColumn == null ? idColumn.get(i) : nameColumn.get(i);
            boolean missing = missingColumn != null && "True".equals(missingColumn.get(i));
            File fileImage = new File(dirData, name + ".jpg");
            File fileOverlayImage = new File(dirData, name + "-overlay.jpg");
            if (!fileOverlayImage.exists())
                fileOverlayImage = new File(dirData, name + "-overlay.png");
            TMAEntry entry = TMAEntries.createDefaultTMAEntry(serverPath, fileImage.getAbsolutePath(), fileOverlayImage.getAbsolutePath(), name, missing);
            for (Entry<String, List<String>> temp : metadataColumns.entrySet()) {
                entry.putMetadata(temp.getKey(), temp.getValue().get(i));
            }
            for (Entry<String, double[]> temp : measurementColumns.entrySet()) {
                entry.putMeasurement(temp.getKey(), temp.getValue()[i]);
            }
            entries.add(entry);
        }
    } catch (Exception e) {
        logger.error("Error parsing input file " + file, e);
    }
    logger.info("Parsed " + (entries.size() - nEntries) + " from " + file.getName() + " (" + entries.size() + " total)");
}

Example 4 with TMAEntry

use of qupath.lib.gui.tma.TMAEntries.TMAEntry in project qupath by qupath.

the class TMASummaryViewer method initialize.

private void initialize() {
    model = new TMATableModel();
    groupByIDProperty.addListener((v, o, n) -> refreshTableData());
    MenuBar menuBar = new MenuBar();
    Menu menuFile = new Menu("File");
    MenuItem miOpen = new MenuItem("Open...");
    miOpen.setAccelerator(new KeyCodeCombination(KeyCode.O, KeyCombination.SHORTCUT_DOWN));
    miOpen.setOnAction(e -> {
        File file = Dialogs.getChooser(stage).promptForFile(null, null, "TMA data files", new String[] { "qptma" });
        if (file == null)
            return;
        setInputFile(file);
    });
    MenuItem miSave = new MenuItem("Save As...");
    miSave.setAccelerator(new KeyCodeCombination(KeyCode.S, KeyCombination.SHORTCUT_DOWN, KeyCombination.SHIFT_DOWN));
    miSave.setOnAction(e -> SummaryMeasurementTableCommand.saveTableModel(model, null, Collections.emptyList()));
    MenuItem miImportFromImage = new MenuItem("Import from current image...");
    miImportFromImage.setAccelerator(new KeyCodeCombination(KeyCode.I, KeyCombination.SHORTCUT_DOWN, KeyCombination.SHIFT_DOWN));
    miImportFromImage.setOnAction(e -> setTMAEntriesFromOpenImage());
    MenuItem miImportFromProject = new MenuItem("Import from current project... (experimental)");
    miImportFromProject.setAccelerator(new KeyCodeCombination(KeyCode.P, KeyCombination.SHORTCUT_DOWN, KeyCombination.SHIFT_DOWN));
    miImportFromProject.setOnAction(e -> setTMAEntriesFromOpenProject());
    MenuItem miImportClipboard = new MenuItem("Import from clipboard...");
    miImportClipboard.setOnAction(e -> {
        String text = Clipboard.getSystemClipboard().getString();
        if (text == null) {
            Dialogs.showErrorMessage("Import scores", "Clipboard is empty!");
            return;
        }
        int n = importScores(text);
        if (n > 0) {
            setTMAEntries(new ArrayList<>(entriesBase));
        }
        Dialogs.showMessageDialog("Import scores", "Number of scores imported: " + n);
    });
    Menu menuEdit = new Menu("Edit");
    MenuItem miCopy = new MenuItem("Copy table to clipboard");
    miCopy.setOnAction(e -> {
        SummaryMeasurementTableCommand.copyTableContentsToClipboard(model, Collections.emptyList());
    });
    combinedPredicate.addListener((v, o, n) -> {
        // We want any other changes triggered by this to have happened,
        // so that the data has already been updated
        Platform.runLater(() -> handleTableContentChange());
    });
    // Reset the scores for missing cores - this ensures they will be NaN and not influence subsequent results
    MenuItem miResetMissingScores = new MenuItem("Reset scores for missing cores");
    miResetMissingScores.setOnAction(e -> {
        int changes = 0;
        for (TMAEntry entry : entriesBase) {
            if (!entry.isMissing())
                continue;
            boolean changed = false;
            for (String m : entry.getMeasurementNames().toArray(new String[0])) {
                if (!TMASummaryEntry.isSurvivalColumn(m) && !Double.isNaN(entry.getMeasurementAsDouble(m))) {
                    entry.putMeasurement(m, null);
                    changed = true;
                }
            }
            if (changed)
                changes++;
        }
        if (changes == 0) {
            logger.info("No changes made when resetting scores for missing cores!");
            return;
        }
        logger.info("{} change(s) made when resetting scores for missing cores!", changes);
        table.refresh();
        updateSurvivalCurves();
        if (scatterPane != null)
            scatterPane.updateChart();
        if (histogramDisplay != null)
            histogramDisplay.refreshHistogram();
    });
    menuEdit.getItems().add(miResetMissingScores);
    MenuTools.addMenuItems(menuFile, miOpen, miSave, null, miImportClipboard, null, miImportFromImage, miImportFromProject);
    menuBar.getMenus().add(menuFile);
    menuEdit.getItems().add(miCopy);
    menuBar.getMenus().add(menuEdit);
    menuFile.setOnShowing(e -> {
        boolean imageDataAvailable = QuPathGUI.getInstance() != null && QuPathGUI.getInstance().getImageData() != null && QuPathGUI.getInstance().getImageData().getHierarchy().getTMAGrid() != null;
        miImportFromImage.setDisable(!imageDataAvailable);
        boolean projectAvailable = QuPathGUI.getInstance() != null && QuPathGUI.getInstance().getProject() != null && !QuPathGUI.getInstance().getProject().getImageList().isEmpty();
        miImportFromProject.setDisable(!projectAvailable);
    });
    // Double-clicking previously used for comments... but conflicts with tree table expansion
    // table.setOnMouseClicked(e -> {
    // if (!e.isPopupTrigger() && e.getClickCount() > 1)
    // promptForComment();
    // });
    table.setPlaceholder(new Text("Drag TMA data folder onto window, or choose File -> Open"));
    table.getSelectionModel().setSelectionMode(SelectionMode.MULTIPLE);
    BorderPane pane = new BorderPane();
    pane.setTop(menuBar);
    menuBar.useSystemMenuBarProperty().bindBidirectional(PathPrefs.useSystemMenubarProperty());
    // menuBar.setUseSystemMenuBar(true);
    // Create options
    ToolBar toolbar = new ToolBar();
    Label labelMeasurementMethod = new Label("Combination method");
    labelMeasurementMethod.setLabelFor(comboMeasurementMethod);
    labelMeasurementMethod.setTooltip(new Tooltip("Method whereby measurements for multiple cores with the same " + TMACoreObject.KEY_UNIQUE_ID + " will be combined"));
    CheckBox cbHidePane = new CheckBox("Hide pane");
    cbHidePane.setSelected(hidePaneProperty.get());
    cbHidePane.selectedProperty().bindBidirectional(hidePaneProperty);
    CheckBox cbGroupByID = new CheckBox("Group by ID");
    entriesBase.addListener((Change<? extends TMAEntry> event) -> {
        if (!event.getList().stream().anyMatch(e -> e.getMetadataValue(TMACoreObject.KEY_UNIQUE_ID) != null)) {
            cbGroupByID.setSelected(false);
            cbGroupByID.setDisable(true);
        } else {
            cbGroupByID.setDisable(false);
        }
    });
    cbGroupByID.setSelected(groupByIDProperty.get());
    cbGroupByID.selectedProperty().bindBidirectional(groupByIDProperty);
    CheckBox cbUseSelected = new CheckBox("Use selection only");
    cbUseSelected.selectedProperty().bindBidirectional(useSelectedProperty);
    CheckBox cbSkipMissing = new CheckBox("Hide missing cores");
    cbSkipMissing.selectedProperty().bindBidirectional(skipMissingCoresProperty);
    skipMissingCoresProperty.addListener((v, o, n) -> {
        table.refresh();
        updateSurvivalCurves();
        if (histogramDisplay != null)
            histogramDisplay.refreshHistogram();
        updateSurvivalCurves();
        if (scatterPane != null)
            scatterPane.updateChart();
    });
    toolbar.getItems().addAll(labelMeasurementMethod, comboMeasurementMethod, new Separator(Orientation.VERTICAL), cbHidePane, new Separator(Orientation.VERTICAL), cbGroupByID, new Separator(Orientation.VERTICAL), cbUseSelected, new Separator(Orientation.VERTICAL), cbSkipMissing);
    comboMeasurementMethod.getItems().addAll(TMAEntries.MeasurementCombinationMethod.values());
    comboMeasurementMethod.getSelectionModel().select(TMAEntries.MeasurementCombinationMethod.MEDIAN);
    selectedMeasurementCombinationProperty.addListener((v, o, n) -> table.refresh());
    ContextMenu popup = new ContextMenu();
    MenuItem miSetMissing = new MenuItem("Set missing");
    miSetMissing.setOnAction(e -> setSelectedMissingStatus(true));
    MenuItem miSetAvailable = new MenuItem("Set available");
    miSetAvailable.setOnAction(e -> setSelectedMissingStatus(false));
    MenuItem miExpand = new MenuItem("Expand all");
    miExpand.setOnAction(e -> {
        if (table.getRoot() == null)
            return;
        for (TreeItem<?> item : table.getRoot().getChildren()) {
            item.setExpanded(true);
        }
    });
    MenuItem miCollapse = new MenuItem("Collapse all");
    miCollapse.setOnAction(e -> {
        if (table.getRoot() == null)
            return;
        for (TreeItem<?> item : table.getRoot().getChildren()) {
            item.setExpanded(false);
        }
    });
    popup.getItems().addAll(miSetMissing, miSetAvailable, new SeparatorMenuItem(), miExpand, miCollapse);
    table.setContextMenu(popup);
    table.setRowFactory(e -> {
        TreeTableRow<TMAEntry> row = new TreeTableRow<>();
        // // Make rows invisible if they don't pass the predicate
        // row.visibleProperty().bind(Bindings.createBooleanBinding(() -> {
        // TMAEntry entry = row.getItem();
        // if (entry == null || (entry.isMissing() && skipMissingCoresProperty.get()))
        // return false;
        // return entries.getPredicate() == null || entries.getPredicate().test(entry);
        // },
        // skipMissingCoresProperty,
        // entries.predicateProperty()));
        // Style rows according to what they contain
        row.styleProperty().bind(Bindings.createStringBinding(() -> {
            if (row.isSelected())
                return "";
            TMAEntry entry = row.getItem();
            if (entry == null || entry instanceof TMASummaryEntry)
                return "";
            else if (entry.isMissing())
                return "-fx-background-color:rgb(225,225,232)";
            else
                return "-fx-background-color:rgb(240,240,245)";
        }, row.itemProperty(), row.selectedProperty()));
        // });
        return row;
    });
    BorderPane paneTable = new BorderPane();
    paneTable.setTop(toolbar);
    paneTable.setCenter(table);
    MasterDetailPane mdTablePane = new MasterDetailPane(Side.RIGHT, paneTable, createSidePane(), true);
    mdTablePane.showDetailNodeProperty().bind(Bindings.createBooleanBinding(() -> !hidePaneProperty.get() && !entriesBase.isEmpty(), hidePaneProperty, entriesBase));
    mdTablePane.setDividerPosition(2.0 / 3.0);
    pane.setCenter(mdTablePane);
    model.getItems().addListener(new ListChangeListener<TMAEntry>() {

        @Override
        public void onChanged(ListChangeListener.Change<? extends TMAEntry> c) {
            if (histogramDisplay != null)
                histogramDisplay.refreshHistogram();
            updateSurvivalCurves();
            if (scatterPane != null)
                scatterPane.updateChart();
        }
    });
    Label labelPredicate = new Label();
    labelPredicate.setPadding(new Insets(5, 5, 5, 5));
    labelPredicate.setAlignment(Pos.CENTER);
    // labelPredicate.setStyle("-fx-background-color: rgba(20, 120, 20, 0.15);");
    labelPredicate.setStyle("-fx-background-color: rgba(120, 20, 20, 0.15);");
    labelPredicate.textProperty().addListener((v, o, n) -> {
        if (n.trim().length() > 0)
            pane.setBottom(labelPredicate);
        else
            pane.setBottom(null);
    });
    labelPredicate.setMaxWidth(Double.MAX_VALUE);
    labelPredicate.setMaxHeight(labelPredicate.getPrefHeight());
    labelPredicate.setTextAlignment(TextAlignment.CENTER);
    predicateMeasurements.addListener((v, o, n) -> {
        if (n == null)
            labelPredicate.setText("");
        else if (n instanceof TablePredicate) {
            TablePredicate tp = (TablePredicate) n;
            if (tp.getOriginalCommand().trim().isEmpty())
                labelPredicate.setText("");
            else
                labelPredicate.setText("Predicate: " + tp.getOriginalCommand());
        } else
            labelPredicate.setText("Predicate: " + n.toString());
    });
    // predicate.set(new TablePredicate("\"Tumor\" > 100"));
    scene = new Scene(pane);
    scene.addEventHandler(KeyEvent.KEY_PRESSED, e -> {
        KeyCode code = e.getCode();
        if ((code == KeyCode.SPACE || code == KeyCode.ENTER) && entrySelected != null) {
            promptForComment();
            return;
        }
    });
}

Example 5 with TMAEntry

use of qupath.lib.gui.tma.TMAEntries.TMAEntry in project qupath by qupath.

the class TMAImageCache method getLargeCachedImage.

private Image getLargeCachedImage(final TMAEntry entry, final boolean isOverlay) {
    Map<TMAEntry, SoftReference<Image>> cache = isOverlay ? overlayLarge : imageLarge;
    SoftReference<Image> ref = cache.get(entry);
    Image img = ref == null ? null : ref.get();
    if (img == null) {
        img = isOverlay ? entry.getOverlay(-1) : entry.getImage(-1);
        if (img != null) {
            cache.put(entry, new SoftReference<>(img));
        }
    }
    return img;
}