Examples with PathObjectHierarchy qupath.lib.objects.hierarchy.PathObjectHierarchy used on opensource projects

Example 11 with PathObjectHierarchy

use of qupath.lib.objects.hierarchy.PathObjectHierarchy 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 12 with PathObjectHierarchy

use of qupath.lib.objects.hierarchy.PathObjectHierarchy in project qupath by qupath.

the class PathIO method writeImageDataSerialized.

private static void writeImageDataSerialized(final OutputStream stream, final ImageData<?> imageData) throws IOException {
    try (OutputStream outputStream = new BufferedOutputStream(stream)) {
        long startTime = System.currentTimeMillis();
        ObjectOutputStream outStream = new ObjectOutputStream(outputStream);
        // Write the identifier
        outStream.writeUTF("Data file version " + DATA_FILE_VERSION);
        // Try to write a backwards-compatible image path
        var server = imageData.getServer();
        // var uris = server.getURIs();
        // String path;
        // if (uris.size() == 1) {
        // var uri = uris.iterator().next();
        // var serverPath = GeneralTools.toPath(uri);
        // if (serverPath != null && Files.exists(serverPath))
        // path = serverPath.toFile().getAbsolutePath();
        // else
        // path = uri.toString();
        // } else
        // path = server.getPath();
        // outStream.writeObject("Image path: " + path);
        // Write JSON object including QuPath version and ServerBuilder
        // Note that the builder may be null, in which case the server cannot be recreated
        var builder = server.getBuilder();
        if (builder == null)
            logger.warn("Server {} does not provide a builder - it will not be possible to recover the ImageServer from this data file", server);
        var wrapper = ServerBuilderWrapper.create(builder, server.getPath());
        String json = GsonTools.getInstance().toJson(wrapper);
        outStream.writeObject(json);
        // Write the current locale
        outStream.writeObject(Locale.getDefault(Category.FORMAT));
        // Write the rest of the main image metadata
        outStream.writeObject(imageData.getImageType());
        outStream.writeObject(imageData.getColorDeconvolutionStains());
        outStream.writeObject(imageData.getHistoryWorkflow());
        // Write the rest of the main image metadata
        PathObjectHierarchy hierarchy = imageData.getHierarchy();
        logger.info(String.format("Writing object hierarchy with %d object(s)...", hierarchy.nObjects()));
        outStream.writeObject(hierarchy);
        // Write any remaining (serializable) properties
        Map<String, Object> map = new HashMap<>();
        for (Entry<String, Object> entry : imageData.getProperties().entrySet()) {
            if (entry.getValue() instanceof Serializable)
                map.put(entry.getKey(), entry.getValue());
            else
                logger.error("Property not serializable and will not be saved!  Key: " + entry.getKey() + ", Value: " + entry.getValue());
        }
        if (map != null)
            outStream.writeObject(map);
        // Write EOF marker
        outStream.writeObject("EOF");
        long endTime = System.currentTimeMillis();
        logger.info(String.format("Image data written in %.2f seconds", (endTime - startTime) / 1000.));
    }
}

Example 13 with PathObjectHierarchy

use of qupath.lib.objects.hierarchy.PathObjectHierarchy in project qupath by qupath.

the class PathIO method readImageDataSerialized.

@SuppressWarnings("unchecked")
private static <T> ImageData<T> readImageDataSerialized(final InputStream stream, ImageData<T> imageData, ImageServer<T> server, Class<T> cls) throws IOException {
    long startTime = System.currentTimeMillis();
    Locale locale = Locale.getDefault(Category.FORMAT);
    boolean localeChanged = false;
    try (ObjectInputStream inStream = new ObjectInputStream(new BufferedInputStream(stream))) {
        ServerBuilder<T> serverBuilder = null;
        PathObjectHierarchy hierarchy = null;
        ImageData.ImageType imageType = null;
        ColorDeconvolutionStains stains = null;
        Workflow workflow = null;
        Map<String, Object> propertyMap = null;
        String firstLine = inStream.readUTF();
        // int versionNumber = -1;
        if (!firstLine.startsWith("Data file version")) {
            logger.error("Input stream does not contain valid QuPath data!");
        }
        // else {
        // // Could try to parse version number... although frankly, at this time, we don't really care...
        // try {
        // versionNumber = NumberFormat.getInstance(Locale.US).parse(firstLine.substring("Data file version".length()).trim()).intValue();
        // } catch (Exception e) {
        // logger.warn("Unable to parse version number from {}", firstLine);
        // }
        // }
        String serverString = (String) inStream.readObject();
        // Don't log warnings if we are provided with a server
        serverBuilder = extractServerBuilder(serverString, server == null);
        while (true) {
            // logger.debug("Starting read: " + inStream.available());
            try {
                // Try to read a relevant object from the stream
                Object input = inStream.readObject();
                logger.debug("Read: {}", input);
                // If we have a Locale, then set it
                if (input instanceof Locale) {
                    if (input != locale) {
                        Locale.setDefault(Category.FORMAT, (Locale) input);
                        localeChanged = true;
                    }
                } else if (input instanceof PathObjectHierarchy)
                    hierarchy = (PathObjectHierarchy) input;
                else if (input instanceof ImageData.ImageType)
                    imageType = (ImageData.ImageType) input;
                else if (input instanceof String && "EOF".equals(input)) {
                    // else if ("EOF".equals(input)) {
                    break;
                // }
                } else if (input instanceof ColorDeconvolutionStains)
                    stains = (ColorDeconvolutionStains) input;
                else if (input instanceof Workflow)
                    workflow = (Workflow) input;
                else if (input instanceof Map)
                    propertyMap = (Map<String, Object>) input;
                else if (input == null) {
                    logger.debug("Null object will be skipped");
                } else
                    logger.warn("Unsupported object of class {} will be skipped: {}", input.getClass().getName(), input);
            } catch (ClassNotFoundException e) {
                logger.error("Unable to find class: " + e.getLocalizedMessage(), e);
            } catch (EOFException e) {
                // Try to recover from EOFExceptions - we may already have enough info
                logger.error("Reached end of file...");
                if (hierarchy == null)
                    logger.error(e.getLocalizedMessage(), e);
                break;
            }
        }
        // Create an entirely new ImageData if necessary
        var existingBuilder = imageData == null || imageData.getServer() == null ? null : imageData.getServer().getBuilder();
        if (imageData == null || !Objects.equals(serverBuilder, existingBuilder)) {
            // Create a new server if we need to
            if (server == null) {
                try {
                    server = serverBuilder.build();
                } catch (Exception e) {
                    logger.error(e.getLocalizedMessage());
                }
                ;
                if (server == null) {
                    logger.error("Warning: Unable to build server with " + serverBuilder);
                // throw new RuntimeException("Warning: Unable to create server for path " + serverPath);
                }
            }
            // TODO: Make this less clumsy... but for now we need to ensure we have a fully-initialized hierarchy (which deserialization alone doesn't achieve)
            PathObjectHierarchy hierarchy2 = new PathObjectHierarchy();
            hierarchy2.setHierarchy(hierarchy);
            hierarchy = hierarchy2;
            imageData = new ImageData<>(server, hierarchy, imageType);
        } else {
            if (imageType != null)
                imageData.setImageType(imageType);
            // Set the new hierarchy
            if (hierarchy != null)
                imageData.getHierarchy().setHierarchy(hierarchy);
        }
        // Set the other properties we have just read
        if (workflow != null) {
            imageData.getHistoryWorkflow().clear();
            imageData.getHistoryWorkflow().addSteps(workflow.getSteps());
        }
        if (stains != null) {
            imageData.setColorDeconvolutionStains(stains);
        }
        if (propertyMap != null) {
            for (Entry<String, Object> entry : propertyMap.entrySet()) imageData.setProperty(entry.getKey(), entry.getValue());
        }
        long endTime = System.currentTimeMillis();
        // if (hierarchy == null) {
        // logger.error(String.format("%s does not contain a valid QUPath object hierarchy!", file.getAbsolutePath()));
        // return null;
        // }
        logger.debug(String.format("Hierarchy with %d object(s) read in %.2f seconds", hierarchy.nObjects(), (endTime - startTime) / 1000.));
    } catch (ClassNotFoundException e1) {
        logger.warn("Class not found reading image data", e1);
    } finally {
        if (localeChanged)
            Locale.setDefault(Category.FORMAT, locale);
    }
    return imageData;
}

Example 14 with PathObjectHierarchy

use of qupath.lib.objects.hierarchy.PathObjectHierarchy in project qupath by qupath.

the class GuiTools method promptToClearAllSelectedObjects.

/**
 * Prompt user to select all currently-selected objects (except TMA core objects).
 *
 * @param imageData
 * @return
 */
public static boolean promptToClearAllSelectedObjects(final ImageData<?> imageData) {
    // Get all non-TMA core objects
    PathObjectHierarchy hierarchy = imageData.getHierarchy();
    Collection<PathObject> selectedRaw = hierarchy.getSelectionModel().getSelectedObjects();
    List<PathObject> selected = selectedRaw.stream().filter(p -> !(p instanceof TMACoreObject)).collect(Collectors.toList());
    if (selected.isEmpty()) {
        if (selectedRaw.size() > selected.size())
            Dialogs.showErrorMessage("Delete selected objects", "No valid objects selected! \n\nNote: Individual TMA cores cannot be deleted with this method.");
        else
            Dialogs.showErrorMessage("Delete selected objects", "No objects selected!");
        return false;
    }
    int n = selected.size();
    String message;
    if (n == 1)
        message = "Delete selected object?";
    else
        message = "Delete " + n + " selected objects?";
    if (Dialogs.showYesNoDialog("Delete objects", message)) {
        // Check for descendants
        List<PathObject> children = new ArrayList<>();
        for (PathObject temp : selected) {
            children.addAll(temp.getChildObjects());
        }
        children.removeAll(selected);
        boolean keepChildren = true;
        if (!children.isEmpty()) {
            Dialogs.DialogButton response = Dialogs.showYesNoCancelDialog("Delete objects", "Keep descendant objects?");
            if (response == Dialogs.DialogButton.CANCEL)
                return false;
            keepChildren = response == Dialogs.DialogButton.YES;
        }
        hierarchy.removeObjects(selected, keepChildren);
        hierarchy.getSelectionModel().clearSelection();
        imageData.getHistoryWorkflow().addStep(new DefaultScriptableWorkflowStep("Delete selected objects", "clearSelectedObjects(" + keepChildren + ");"));
        if (keepChildren)
            logger.info(selected.size() + " object(s) deleted");
        else
            logger.info(selected.size() + " object(s) deleted with descendants");
        imageData.getHistoryWorkflow().addStep(new DefaultScriptableWorkflowStep("Delete selected objects", "clearSelectedObjects();"));
        logger.info(selected.size() + " object(s) deleted");
        return true;
    } else
        return false;
}

Example 15 with PathObjectHierarchy

use of qupath.lib.objects.hierarchy.PathObjectHierarchy in project qupath by qupath.

the class QuPathViewer method setImageData.

/**
 * Set the current image for this viewer.
 * @param imageDataNew
 */
public void setImageData(ImageData<BufferedImage> imageDataNew) {
    if (this.imageDataProperty.get() == imageDataNew)
        return;
    imageDataChanging.set(true);
    // Remove listeners for previous hierarchy
    ImageData<BufferedImage> imageDataOld = this.imageDataProperty.get();
    if (imageDataOld != null) {
        imageDataOld.getHierarchy().removePathObjectListener(this);
        imageDataOld.getHierarchy().getSelectionModel().removePathObjectSelectionListener(this);
    }
    // Determine if the server has remained the same, so we can avoid shifting the viewer
    boolean sameServer = false;
    if (imageDataOld != null && imageDataNew != null && imageDataOld.getServerPath().equals(imageDataNew.getServerPath()))
        sameServer = true;
    this.imageDataProperty.set(imageDataNew);
    ImageServer<BufferedImage> server = imageDataNew == null ? null : imageDataNew.getServer();
    PathObjectHierarchy hierarchy = imageDataNew == null ? null : imageDataNew.getHierarchy();
    long startTime = System.currentTimeMillis();
    if (imageDisplay != null) {
        boolean keepDisplay = PathPrefs.keepDisplaySettingsProperty().get();
        // This is a bit of a hack to avoid calling internal methods for ImageDisplay
        // See https://github.com/qupath/qupath/issues/601
        boolean displaySet = false;
        if (imageDataNew != null && keepDisplay) {
            if (imageDisplay.getImageData() != null && serversCompatible(imageDataNew.getServer(), imageDisplay.getImageData().getServer())) {
                imageDisplay.setImageData(imageDataNew, keepDisplay);
                displaySet = true;
            } else {
                for (var viewer : QuPathGUI.getInstance().getViewers()) {
                    if (this == viewer || viewer.getImageData() == null)
                        continue;
                    var tempServer = viewer.getServer();
                    var currentServer = imageDataNew.getServer();
                    if (serversCompatible(tempServer, currentServer)) {
                        var json = viewer.getImageDisplay().toJSON(false);
                        imageDataNew.setProperty(ImageDisplay.class.getName(), json);
                        imageDisplay.setImageData(imageDataNew, false);
                        displaySet = true;
                        break;
                    }
                }
            }
        }
        if (!displaySet)
            imageDisplay.setImageData(imageDataNew, keepDisplay);
        // See https://github.com/qupath/qupath/issues/843
        if (server != null && !server.isRGB()) {
            var colors = imageDisplay.availableChannels().stream().filter(c -> c instanceof DirectServerChannelInfo).map(c -> c.getColor()).collect(Collectors.toList());
            if (server.nChannels() == colors.size())
                updateServerChannels(server, colors);
        }
    }
    long endTime = System.currentTimeMillis();
    logger.debug("Setting ImageData time: {} ms", endTime - startTime);
    initializeForServer(server);
    if (!sameServer) {
        setDownsampleFactorImpl(getZoomToFitDownsampleFactor(), -1, -1);
        centerImage();
    }
    fireImageDataChanged(imageDataOld, imageDataNew);
    if (imageDataNew != null) {
        // hierarchyPainter = new PathHierarchyPainter(hierarchy);
        hierarchy.addPathObjectListener(this);
        hierarchy.getSelectionModel().addPathObjectSelectionListener(this);
    }
    setSelectedObject(null);
    // TODO: Consider shifting, fixing magnification, repainting etc.
    if (isShowing())
        repaint();
    logger.info("Image data set to {}", imageDataNew);
}