Examples with ImageData qupath.lib.images.ImageData used on opensource projects

Example 6 with ImageData

use of qupath.lib.images.ImageData 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 7 with ImageData

use of qupath.lib.images.ImageData 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 8 with ImageData

use of qupath.lib.images.ImageData 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);
}

Example 9 with ImageData

use of qupath.lib.images.ImageData in project qupath by qupath.

the class MeasurementExporter method exportMeasurements.

/**
 * Exports the measurements of one or more entries in the project.
 * This function first opens all the images in the project to store
 * all the column names and values of the measurements.
 * Then, it loops through the maps containing the values to write
 * them to the given output stream.
 * @param stream
 */
public void exportMeasurements(OutputStream stream) {
    long startTime = System.currentTimeMillis();
    Map<ProjectImageEntry<?>, String[]> imageCols = new HashMap<>();
    Map<ProjectImageEntry<?>, Integer> nImageEntries = new HashMap<>();
    List<String> allColumns = new ArrayList<>();
    Multimap<String, String> valueMap = LinkedListMultimap.create();
    String pattern = "(?=(?:[^\"]*\"[^\"]*\")*[^\"]*$)";
    for (ProjectImageEntry<?> entry : imageList) {
        try {
            ImageData<?> imageData = entry.readImageData();
            ObservableMeasurementTableData model = new ObservableMeasurementTableData();
            Collection<PathObject> pathObjects = imageData == null ? Collections.emptyList() : imageData.getHierarchy().getObjects(null, type);
            if (filter != null)
                pathObjects = pathObjects.stream().filter(filter).collect(Collectors.toList());
            model.setImageData(imageData, pathObjects);
            List<String> data = SummaryMeasurementTableCommand.getTableModelStrings(model, separator, excludeColumns);
            // Get header
            String[] header;
            String headerString = data.get(0);
            if (headerString.chars().filter(e -> e == '"').count() > 1)
                header = headerString.split(separator.equals("\t") ? "\\" + separator : separator + pattern, -1);
            else
                header = headerString.split(separator);
            imageCols.put(entry, header);
            nImageEntries.put(entry, data.size() - 1);
            for (String col : header) {
                if (!allColumns.contains(col) && !excludeColumns.contains(col))
                    allColumns.add(col);
            }
            // To keep the same column order, just delete non-relevant columns
            if (!includeOnlyColumns.isEmpty())
                allColumns.removeIf(n -> !includeOnlyColumns.contains(n));
            for (int i = 1; i < data.size(); i++) {
                String[] row;
                String rowString = data.get(i);
                // Check if some values in the row are escaped
                if (rowString.chars().filter(e -> e == '"').count() > 1)
                    row = rowString.split(separator.equals("\t") ? "\\" + separator : separator + pattern, -1);
                else
                    row = rowString.split(separator);
                // Put value in map
                for (int elem = 0; elem < row.length; elem++) {
                    if (allColumns.contains(header[elem]))
                        valueMap.put(header[elem], row[elem]);
                }
            }
        } catch (Exception e) {
            logger.error(e.getLocalizedMessage(), e);
        }
    }
    try (PrintWriter writer = new PrintWriter(new OutputStreamWriter(stream, StandardCharsets.UTF_8))) {
        writer.write(String.join(separator, allColumns));
        writer.write(System.lineSeparator());
        Iterator[] its = new Iterator[allColumns.size()];
        for (int col = 0; col < allColumns.size(); col++) {
            its[col] = valueMap.get(allColumns.get(col)).iterator();
        }
        for (ProjectImageEntry<?> entry : imageList) {
            for (int nObject = 0; nObject < nImageEntries.get(entry); nObject++) {
                for (int nCol = 0; nCol < allColumns.size(); nCol++) {
                    if (Arrays.stream(imageCols.get(entry)).anyMatch(allColumns.get(nCol)::equals)) {
                        String val = (String) its[nCol].next();
                        // NaN values -> blank
                        if (val.equals("NaN"))
                            val = "";
                        writer.write(val);
                    }
                    if (nCol < allColumns.size() - 1)
                        writer.write(separator);
                }
                writer.write(System.lineSeparator());
            }
        }
    } catch (Exception e) {
        logger.error("Error writing to file: " + e.getLocalizedMessage(), e);
    }
    long endTime = System.currentTimeMillis();
    long timeMillis = endTime - startTime;
    String time = null;
    if (timeMillis > 1000 * 60)
        time = String.format("Total processing time: %.2f minutes", timeMillis / (1000.0 * 60.0));
    else if (timeMillis > 1000)
        time = String.format("Total processing time: %.2f seconds", timeMillis / (1000.0));
    else
        time = String.format("Total processing time: %d milliseconds", timeMillis);
    logger.info("Processed {} images", imageList.size());
    logger.info(time);
}

Example 10 with ImageData

use of qupath.lib.images.ImageData in project qupath by qupath.

the class ObservableMeasurementTableDataTest method test.

@SuppressWarnings("javadoc")
@Test
public void test() {
    // See https://github.com/locationtech/jts/issues/571
    for (int counter = 0; counter < 50; counter++) {
        ImageData<BufferedImage> imageData = new ImageData<>(null);
        PathClass tumorClass = PathClassFactory.getPathClass(StandardPathClasses.TUMOR);
        PathClass stromaClass = PathClassFactory.getPathClass(StandardPathClasses.STROMA);
        // PathClass otherClass = PathClassFactory.getDefaultPathClass(PathClasses.OTHER);
        PathClass artefactClass = PathClassFactory.getPathClass("Artefact");
        PathObjectHierarchy hierarchy = imageData.getHierarchy();
        // Add a parent annotation
        PathObject parent = PathObjects.createAnnotationObject(ROIs.createRectangleROI(500, 500, 1000, 1000, ImagePlane.getDefaultPlane()));
        // Create 100 tumor detections
        // ROI emptyROI = ROIs.createEmptyROI();
        ROI smallROI = ROIs.createRectangleROI(500, 500, 1, 1, ImagePlane.getDefaultPlane());
        for (int i = 0; i < 100; i++) {
            if (i < 25)
                parent.addPathObject(PathObjects.createDetectionObject(smallROI, PathClassFactory.getNegative(tumorClass)));
            else if (i < 50)
                parent.addPathObject(PathObjects.createDetectionObject(smallROI, PathClassFactory.getOnePlus(tumorClass)));
            else if (i < 75)
                parent.addPathObject(PathObjects.createDetectionObject(smallROI, PathClassFactory.getTwoPlus(tumorClass)));
            else if (i < 100)
                parent.addPathObject(PathObjects.createDetectionObject(smallROI, PathClassFactory.getThreePlus(tumorClass)));
        }
        // Create 100 stroma detections
        for (int i = 0; i < 100; i++) {
            if (i < 50)
                parent.addPathObject(PathObjects.createDetectionObject(smallROI, PathClassFactory.getNegative(stromaClass)));
            else if (i < 60)
                parent.addPathObject(PathObjects.createDetectionObject(smallROI, PathClassFactory.getOnePlus(stromaClass)));
            else if (i < 70)
                parent.addPathObject(PathObjects.createDetectionObject(smallROI, PathClassFactory.getTwoPlus(stromaClass)));
            else if (i < 100)
                parent.addPathObject(PathObjects.createDetectionObject(smallROI, PathClassFactory.getThreePlus(stromaClass)));
        }
        // Create 50 artefact detections
        for (int i = 0; i < 50; i++) {
            parent.addPathObject(PathObjects.createDetectionObject(smallROI, artefactClass));
        }
        hierarchy.addPathObject(parent);
        ObservableMeasurementTableData model = new ObservableMeasurementTableData();
        model.setImageData(imageData, Collections.singletonList(parent));
        // Check tumor counts
        assertEquals(100, model.getNumericValue(parent, "Num Tumor (base)"), EPSILON);
        assertEquals(25, model.getNumericValue(parent, "Num Tumor: Negative"), EPSILON);
        assertEquals(25, model.getNumericValue(parent, "Num Tumor: 1+"), EPSILON);
        assertEquals(25, model.getNumericValue(parent, "Num Tumor: 2+"), EPSILON);
        assertEquals(25, model.getNumericValue(parent, "Num Tumor: 3+"), EPSILON);
        assertTrue(Double.isNaN(model.getNumericValue(parent, "Num Tumor: 4+")));
        // Check tumor H-score, Allred score & positive %
        assertEquals(150, model.getNumericValue(parent, "Tumor: H-score"), EPSILON);
        assertEquals(75, model.getNumericValue(parent, "Tumor: Positive %"), EPSILON);
        assertEquals(2, model.getNumericValue(parent, "Tumor: Allred intensity"), EPSILON);
        assertEquals(5, model.getNumericValue(parent, "Tumor: Allred proportion"), EPSILON);
        assertEquals(7, model.getNumericValue(parent, "Tumor: Allred score"), EPSILON);
        // Check tumor H-score unaffected when tumor detections added without intensity classification
        for (int i = 0; i < 10; i++) parent.addPathObject(PathObjects.createDetectionObject(smallROI, tumorClass));
        hierarchy.fireHierarchyChangedEvent(this);
        model.refreshEntries();
        // model.setImageData(imageData, Collections.singletonList(parent));
        assertEquals(100, model.getNumericValue(parent, "Num Stroma (base)"), EPSILON);
        assertEquals(50, model.getNumericValue(parent, "Num Stroma: Negative"), EPSILON);
        assertEquals(150, model.getNumericValue(parent, "Tumor: H-score"), EPSILON);
        assertEquals(75, model.getNumericValue(parent, "Tumor: Positive %"), EPSILON);
        // Check stroma scores
        assertEquals(100, model.getNumericValue(parent, "Num Stroma (base)"), EPSILON);
        assertEquals(120, model.getNumericValue(parent, "Stroma: H-score"), EPSILON);
        // Check complete scores
        assertEquals(135, model.getNumericValue(parent, "Stroma + Tumor: H-score"), EPSILON);
        // Add a new parent that completely contains the current object, and confirm complete scores agree
        PathObject parentNew = PathObjects.createAnnotationObject(ROIs.createRectangleROI(0, 0, 2000, 2000, ImagePlane.getDefaultPlane()));
        hierarchy.addPathObject(parentNew);
        model.refreshEntries();
        assertEquals(135, model.getNumericValue(parent, "Stroma + Tumor: H-score"), EPSILON);
        assertEquals(135, model.getNumericValue(parentNew, "Stroma + Tumor: H-score"), EPSILON);
        // Create a new object and demonstrate Allred dependence on a single cell
        PathObject parentAllred = PathObjects.createAnnotationObject(ROIs.createRectangleROI(4000, 4000, 1000, 1000, ImagePlane.getDefaultPlane()));
        ROI newROI = ROIs.createEllipseROI(4500, 4500, 10, 10, ImagePlane.getDefaultPlane());
        for (int i = 0; i < 100; i++) parentAllred.addPathObject(PathObjects.createDetectionObject(newROI, PathClassFactory.getNegative(tumorClass)));
        hierarchy.addPathObject(parentAllred);
        model.refreshEntries();
        assertEquals(0, model.getNumericValue(parentAllred, "Tumor: Allred score"), EPSILON);
        parentAllred.addPathObject(PathObjects.createDetectionObject(newROI, PathClassFactory.getThreePlus(tumorClass)));
        hierarchy.fireHierarchyChangedEvent(parentAllred);
        model.refreshEntries();
        assertEquals(4, model.getNumericValue(parentAllred, "Tumor: Allred score"), EPSILON);
    }
}