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

Example 16 with TMAEntry

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

the class TMASummaryViewer method createScoresMap.

private Map<String, List<TMAEntry>> createScoresMap(final List<TMAEntry> entries, final String colScore, final String colID) {
    // Create a map of entries
    Map<String, List<TMAEntry>> scoreMap = new HashMap<>();
    for (TMAEntry entry : entries) {
        Number score = model.getNumericValue(entry, colScore);
        String id = entry.getMetadataValue(colID);
        if (id == null && entry.getMeasurement(colID) != null)
            id = Double.toString(entry.getMeasurement(colID).doubleValue());
        if (id != null && score != null && !Double.isNaN(score.doubleValue())) {
            List<TMAEntry> list = scoreMap.get(id);
            if (list == null) {
                list = new ArrayList<>();
                scoreMap.put(id, list);
            }
            list.add(entry);
        }
    }
    return scoreMap;
}

Example 17 with TMAEntry

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

the class TMASummaryViewer method importScores.

private int importScores(final String text) {
    Map<String, List<String>> data = TMAScoreImporter.readCSV(text);
    List<String> idColumn = data.remove(TMACoreObject.KEY_UNIQUE_ID);
    if (idColumn == null) {
        Dialogs.showErrorMessage("Import TMA data", "No '" + TMACoreObject.KEY_UNIQUE_ID + "' column found!");
        return 0;
    }
    // Nothing left to import...
    if (data.isEmpty())
        return 0;
    // Get the numeric columns, if possible
    Map<String, double[]> dataNumeric = new HashMap<>();
    for (String key : data.keySet().toArray(new String[0])) {
        double[] vals = TMAScoreImporter.parseNumeric(data.get(key), true);
        if (vals != null && GeneralTools.numNaNs(vals) != vals.length) {
            dataNumeric.put(key, vals);
            data.remove(key);
        }
    }
    // Loop through IDs, adding values where needed
    int counter = 0;
    for (int i = 0; i < idColumn.size(); i++) {
        boolean matched = false;
        String id = idColumn.get(i);
        if (id == null) {
            logger.debug("Skipping missing ID");
            continue;
        }
        for (TMAEntry entry : entriesBase) {
            if (id.equals(entry.getMetadataValue(TMACoreObject.KEY_UNIQUE_ID))) {
                matched = true;
                for (Entry<String, double[]> dataEntry : dataNumeric.entrySet()) {
                    entry.putMeasurement(dataEntry.getKey(), dataEntry.getValue()[i]);
                }
                for (Entry<String, List<String>> dataEntry : data.entrySet()) {
                    entry.putMetadata(dataEntry.getKey(), dataEntry.getValue().get(i));
                }
                counter++;
            }
        }
        if (!matched)
            logger.warn("No match for ID: " + id);
    }
    Optional<TMAEntry> objectEntry = entriesBase.stream().filter(t -> t instanceof TMAObjectEntry).findAny();
    if (objectEntry.isPresent()) {
        Dialogs.showInfoNotification("TMA data update", "TMA cores updated!");
    }
    return counter;
}

Example 18 with TMAEntry

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

the class TMASummaryViewer method setInputFile.

/**
 * Set the input file for the summary viewer.
 * @param file
 */
public void setInputFile(File file) {
    if (file == null)
        return;
    if (file.getName().toLowerCase().endsWith(PathPrefs.getSerializationExtension())) {
        try {
            ImageData<BufferedImage> imageData = PathIO.readImageData(file, null, null, BufferedImage.class);
            setTMAEntriesFromImageData(imageData);
        } catch (IOException e) {
            logger.error("Error reading image data", e);
        }
        return;
    }
    List<TMAEntry> entriesTemp = new ArrayList<>();
    File dir = file.isDirectory() ? file : file.getParentFile();
    for (File fileInput : dir.listFiles()) {
        if (fileInput.isHidden() || fileInput.isDirectory() || !fileInput.getName().toLowerCase().endsWith(".qptma"))
            continue;
        parseInputFile(fileInput, entriesTemp);
    }
    if (entriesTemp.isEmpty()) {
        logger.error("No data found for " + file.getAbsolutePath());
        return;
    }
    setTMAEntries(entriesTemp);
    stage.setTitle("TMA Results View: " + dir.getName());
}

Example 19 with TMAEntry

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

the class TMASummaryViewer method createSummaryEntries.

// class SummaryTreeItem extends TreeItem<TMAEntry> implements ChangeListener<Predicate<? super TMAEntry>> {
// 
// private TMASummaryEntry entry;
// 
// SummaryTreeItem(final TMASummaryEntry entry) {
// super(entry);
// this.entry = entry;
// combinedPredicate.addListener(new WeakChangeListener<Predicate<? super TMAEntry>>(this));
// updateChildren();
// }
// 
// private void updateChildren() {
// ArrayList<TreeItem<TMAEntry>> children = new ArrayList<>();
// for (TMAEntry subEntry : entry.getEntries())
// children.add(new TreeItem<>(subEntry));
// super.getChildren().setAll(children);
// }
// 
// @Override
// public void changed(ObservableValue<? extends Predicate<? super TMAEntry>> observable,
// Predicate<? super TMAEntry> oldValue, Predicate<? super TMAEntry> newValue) {
// updateChildren();
// }
// 
// }
/**
 * Create summaries entries by grouping according to Unique ID.
 *
 * @param entries
 * @return
 */
private Collection<? extends TMAEntry> createSummaryEntries(final List<? extends TMAEntry> entries) {
    Map<String, TMASummaryEntry> summaryEntryMap = new TreeMap<>();
    int maxSummaryLength = 0;
    for (TMAEntry entry : entries) {
        String id = entry.getMetadataValue(TMACoreObject.KEY_UNIQUE_ID);
        if (id == null && entry.getMeasurement(TMACoreObject.KEY_UNIQUE_ID) != null)
            id = entry.getMeasurement(TMACoreObject.KEY_UNIQUE_ID).toString();
        if (id == null || id.trim().length() == 0) {
            if (!"True".equals(entry.getMetadataValue(MISSING_COLUMN)))
                logger.trace("No ID found for {}", entry);
            continue;
        }
        TMASummaryEntry summary = summaryEntryMap.get(id);
        if (summary == null) {
            summary = new TMASummaryEntry(selectedMeasurementCombinationProperty, skipMissingCoresProperty, combinedPredicate);
            summaryEntryMap.put(id, summary);
        }
        summary.addEntry(entry);
        maxSummaryLength = Math.max(maxSummaryLength, summary.getEntries().size());
    }
    // If we don't have any summaries, just return the original entries
    if (summaryEntryMap.isEmpty() || maxSummaryLength <= 1)
        return entries;
    return summaryEntryMap.values();
}

Example 20 with TMAEntry

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

the class TMASummaryViewer method createSidePane.

private Pane createSidePane() {
    BorderPane pane = new BorderPane();
    TabPane tabPane = new TabPane();
    kmDisplay = new KaplanMeierDisplay(null, null, null, null);
    BorderPane paneKaplanMeier = new BorderPane();
    paneKaplanMeier.setCenter(kmDisplay.getView());
    paneKaplanMeier.setPadding(new Insets(10, 10, 10, 10));
    // comboMainMeasurement.prefWidthProperty().bind(paneKaplanMeier.widthProperty());
    comboMainMeasurement.setMaxWidth(Double.MAX_VALUE);
    comboMainMeasurement.setTooltip(new Tooltip("Measurement thresholded to create survival curves etc."));
    GridPane kmTop = new GridPane();
    kmTop.add(new Label("Score"), 0, 0);
    kmTop.add(comboMainMeasurement, 1, 0);
    kmTop.add(new Label("Survival type"), 0, 1);
    kmTop.add(comboSurvival, 1, 1);
    comboSurvival.setTooltip(new Tooltip("Specify overall or recurrence-free survival (if applicable)"));
    comboSurvival.setMaxWidth(Double.MAX_VALUE);
    GridPane.setHgrow(comboMainMeasurement, Priority.ALWAYS);
    GridPane.setHgrow(comboSurvival, Priority.ALWAYS);
    kmTop.setHgap(5);
    paneKaplanMeier.setTop(kmTop);
    // kmDisplay.setOrientation(Orientation.VERTICAL);
    histogramDisplay = new HistogramDisplay(model, false);
    comboMainMeasurement.getSelectionModel().selectedItemProperty().addListener((v, o, n) -> {
        histogramDisplay.refreshCombo();
        histogramDisplay.showHistogram(n);
        updateSurvivalCurves();
    });
    comboMeasurementMethod.getSelectionModel().selectedItemProperty().addListener((v, o, n) -> {
        histogramDisplay.refreshHistogram();
        scatterPane.updateChart();
        updateSurvivalCurves();
    });
    comboSurvival.getSelectionModel().selectedItemProperty().addListener((v, o, n) -> {
        updateSurvivalCurves();
    });
    // Create a Tab for showing images
    BorderPane paneImages = new BorderPane();
    CheckBox cbShowOverlay = new CheckBox("Show overlay");
    imageAvailability.addListener((c, v, n) -> {
        if (n == ImageAvailability.OVERLAY_ONLY)
            cbShowOverlay.setSelected(true);
        else if (n == ImageAvailability.IMAGE_ONLY)
            cbShowOverlay.setSelected(false);
        cbShowOverlay.setDisable(n != ImageAvailability.BOTH);
    });
    ListView<TMAEntry> listImages = new ListView<>();
    listImages.setCellFactory(v -> new ImageListCell(cbShowOverlay.selectedProperty(), imageCache));
    listImages.widthProperty().addListener((v, o, n) -> listImages.refresh());
    listImages.setStyle("-fx-control-inner-background-alt: -fx-control-inner-background ;");
    table.getSelectionModel().getSelectedItems().addListener((Change<? extends TreeItem<TMAEntry>> e) -> {
        List<TMAEntry> entries = new ArrayList<>();
        for (TreeItem<TMAEntry> item : e.getList()) {
            if (item.getChildren().isEmpty()) {
                if (item.getValue().hasImage() || item.getValue().hasOverlay())
                    entries.add(item.getValue());
            } else {
                for (TreeItem<TMAEntry> item2 : item.getChildren()) {
                    if (item2.getValue().hasImage() || item2.getValue().hasOverlay())
                        entries.add(item2.getValue());
                }
            }
            listImages.getItems().setAll(entries);
        }
    });
    cbShowOverlay.setAlignment(Pos.CENTER);
    cbShowOverlay.setMaxWidth(Double.MAX_VALUE);
    cbShowOverlay.setPadding(new Insets(5, 5, 5, 5));
    cbShowOverlay.selectedProperty().addListener((v, o, n) -> listImages.refresh());
    paneImages.setCenter(listImages);
    paneImages.setTop(cbShowOverlay);
    // Determine visibility based upon whether there are any images to show
    // Tab tabImages = new Tab("Images", paneImages);
    ScrollPane scrollPane = new ScrollPane(paneKaplanMeier);
    scrollPane.setFitToWidth(true);
    scrollPane.setFitToHeight(true);
    scrollPane.setVbarPolicy(ScrollBarPolicy.AS_NEEDED);
    scrollPane.setHbarPolicy(ScrollBarPolicy.AS_NEEDED);
    Tab tabSurvival = new Tab("Survival", scrollPane);
    tabPane.getTabs().addAll(new Tab("Table", getCustomizeTablePane()), // tabImages,
    new Tab("Histogram", histogramDisplay.getPane()), new Tab("Scatterplot", scatterPane.getPane()), tabSurvival);
    tabPane.setTabClosingPolicy(TabClosingPolicy.UNAVAILABLE);
    // if (imageAvailability.get() != ImageAvailability.NONE)
    // tabPane.getTabs().add(1, tabImages);
    // 
    // imageAvailability.addListener((c, v, n) -> {
    // if (n == ImageAvailability.NONE)
    // tabPane.getTabs().remove(tabImages);
    // else if (!tabPane.getTabs().contains(tabImages))
    // tabPane.getTabs().add(1, tabImages);
    // });
    // tabSurvival.visibleProperty().bind(
    // Bindings.createBooleanBinding(() -> !survivalColumns.isEmpty(), survivalColumns)
    // );
    pane.setCenter(tabPane);
    pane.setMinWidth(350);
    return pane;
}