Examples with RegionRequest qupath.lib.regions.RegionRequest used on opensource projects

Example 1 with RegionRequest

use of qupath.lib.regions.RegionRequest in project qupath by qupath.

the class Commands method promptToExportImageRegion.

/**
 * Prompt to export the current image region selected in the viewer.
 * @param viewer the viewer containing the image to export
 * @param renderedImage if true, export the rendered (RGB) image rather than original pixel values
 */
public static void promptToExportImageRegion(QuPathViewer viewer, boolean renderedImage) {
    if (viewer == null || viewer.getServer() == null) {
        Dialogs.showErrorMessage("Export image region", "No viewer & image selected!");
        return;
    }
    ImageServer<BufferedImage> server = viewer.getServer();
    if (renderedImage)
        server = RenderedImageServer.createRenderedServer(viewer);
    PathObject pathObject = viewer.getSelectedObject();
    ROI roi = pathObject == null ? null : pathObject.getROI();
    double regionWidth = roi == null ? server.getWidth() : roi.getBoundsWidth();
    double regionHeight = roi == null ? server.getHeight() : roi.getBoundsHeight();
    // Create a dialog
    GridPane pane = new GridPane();
    int row = 0;
    pane.add(new Label("Export format"), 0, row);
    ComboBox<ImageWriter<BufferedImage>> comboImageType = new ComboBox<>();
    Function<ImageWriter<BufferedImage>, String> fun = (ImageWriter<BufferedImage> writer) -> writer.getName();
    comboImageType.setCellFactory(p -> GuiTools.createCustomListCell(fun));
    comboImageType.setButtonCell(GuiTools.createCustomListCell(fun));
    var writers = ImageWriterTools.getCompatibleWriters(server, null);
    comboImageType.getItems().setAll(writers);
    comboImageType.setTooltip(new Tooltip("Choose export image format"));
    if (writers.contains(lastWriter))
        comboImageType.getSelectionModel().select(lastWriter);
    else
        comboImageType.getSelectionModel().selectFirst();
    comboImageType.setMaxWidth(Double.MAX_VALUE);
    GridPane.setHgrow(comboImageType, Priority.ALWAYS);
    pane.add(comboImageType, 1, row++);
    TextArea textArea = new TextArea();
    textArea.setPrefRowCount(2);
    textArea.setEditable(false);
    textArea.setWrapText(true);
    // textArea.setPadding(new Insets(15, 0, 0, 0));
    comboImageType.setOnAction(e -> textArea.setText(((ImageWriter<BufferedImage>) comboImageType.getValue()).getDetails()));
    textArea.setText(((ImageWriter<BufferedImage>) comboImageType.getValue()).getDetails());
    pane.add(textArea, 0, row++, 2, 1);
    var label = new Label("Downsample factor");
    pane.add(label, 0, row);
    TextField tfDownsample = new TextField();
    label.setLabelFor(tfDownsample);
    pane.add(tfDownsample, 1, row++);
    tfDownsample.setTooltip(new Tooltip("Amount to scale down image - choose 1 to export at full resolution (note: for large images this may not succeed for memory reasons)"));
    ObservableDoubleValue downsample = Bindings.createDoubleBinding(() -> {
        try {
            return Double.parseDouble(tfDownsample.getText());
        } catch (NumberFormatException e) {
            return Double.NaN;
        }
    }, tfDownsample.textProperty());
    // Define a sensible limit for non-pyramidal images
    long maxPixels = 10000 * 10000;
    Label labelSize = new Label();
    labelSize.setMinWidth(400);
    labelSize.setTextAlignment(TextAlignment.CENTER);
    labelSize.setContentDisplay(ContentDisplay.CENTER);
    labelSize.setAlignment(Pos.CENTER);
    labelSize.setMaxWidth(Double.MAX_VALUE);
    labelSize.setTooltip(new Tooltip("Estimated size of exported image"));
    pane.add(labelSize, 0, row++, 2, 1);
    labelSize.textProperty().bind(Bindings.createStringBinding(() -> {
        if (!Double.isFinite(downsample.get())) {
            labelSize.setStyle("-fx-text-fill: red;");
            return "Invalid downsample value!  Must be >= 1";
        } else {
            long w = (long) (regionWidth / downsample.get() + 0.5);
            long h = (long) (regionHeight / downsample.get() + 0.5);
            String warning = "";
            var writer = comboImageType.getSelectionModel().getSelectedItem();
            boolean supportsPyramid = writer == null ? false : writer.supportsPyramidal();
            if (!supportsPyramid && w * h > maxPixels) {
                labelSize.setStyle("-fx-text-fill: red;");
                warning = " (too big!)";
            } else if (w < 5 || h < 5) {
                labelSize.setStyle("-fx-text-fill: red;");
                warning = " (too small!)";
            } else
                labelSize.setStyle(null);
            return String.format("Output image size: %d x %d pixels%s", w, h, warning);
        }
    }, downsample, comboImageType.getSelectionModel().selectedIndexProperty()));
    tfDownsample.setText(Double.toString(exportDownsample.get()));
    PaneTools.setMaxWidth(Double.MAX_VALUE, labelSize, textArea, tfDownsample, comboImageType);
    PaneTools.setHGrowPriority(Priority.ALWAYS, labelSize, textArea, tfDownsample, comboImageType);
    pane.setVgap(5);
    pane.setHgap(5);
    if (!Dialogs.showConfirmDialog("Export image region", pane))
        return;
    var writer = comboImageType.getSelectionModel().getSelectedItem();
    boolean supportsPyramid = writer == null ? false : writer.supportsPyramidal();
    int w = (int) (regionWidth / downsample.get() + 0.5);
    int h = (int) (regionHeight / downsample.get() + 0.5);
    if (!supportsPyramid && w * h > maxPixels) {
        Dialogs.showErrorNotification("Export image region", "Requested export region too large - try selecting a smaller region, or applying a higher downsample factor");
        return;
    }
    if (downsample.get() < 1 || !Double.isFinite(downsample.get())) {
        Dialogs.showErrorMessage("Export image region", "Downsample factor must be >= 1!");
        return;
    }
    exportDownsample.set(downsample.get());
    // Now that we know the output, we can create a new server to ensure it is downsampled as the necessary resolution
    if (renderedImage && downsample.get() != server.getDownsampleForResolution(0))
        server = new RenderedImageServer.Builder(viewer).downsamples(downsample.get()).build();
    // selectedImageType.set(comboImageType.getSelectionModel().getSelectedItem());
    // Create RegionRequest
    RegionRequest request = null;
    if (pathObject != null && pathObject.hasROI())
        request = RegionRequest.createInstance(server.getPath(), exportDownsample.get(), roi);
    // Create a sensible default file name, and prompt for the actual name
    String ext = writer.getDefaultExtension();
    String writerName = writer.getName();
    String defaultName = GeneralTools.getNameWithoutExtension(new File(ServerTools.getDisplayableImageName(server)));
    if (roi != null) {
        defaultName = String.format("%s (%s, x=%d, y=%d, w=%d, h=%d)", defaultName, GeneralTools.formatNumber(request.getDownsample(), 2), request.getX(), request.getY(), request.getWidth(), request.getHeight());
    }
    File fileOutput = Dialogs.promptToSaveFile("Export image region", null, defaultName, writerName, ext);
    if (fileOutput == null)
        return;
    try {
        if (request == null) {
            if (exportDownsample.get() == 1.0)
                writer.writeImage(server, fileOutput.getAbsolutePath());
            else
                writer.writeImage(ImageServers.pyramidalize(server, exportDownsample.get()), fileOutput.getAbsolutePath());
        } else
            writer.writeImage(server, request, fileOutput.getAbsolutePath());
        lastWriter = writer;
    } catch (IOException e) {
        Dialogs.showErrorMessage("Export region", e);
    }
}

Example 2 with RegionRequest

use of qupath.lib.regions.RegionRequest in project qupath by qupath.

the class TMAGridView method initializeData.

private void initializeData(ImageData<BufferedImage> imageData) {
    if (this.imageData != imageData) {
        if (this.imageData != null)
            this.imageData.getHierarchy().removePathObjectListener(this);
        this.imageData = imageData;
        if (imageData != null) {
            imageData.getHierarchy().addPathObjectListener(this);
        }
    }
    if (imageData == null || imageData.getHierarchy().getTMAGrid() == null) {
        model.setImageData(null, Collections.emptyList());
        grid.getItems().clear();
        return;
    }
    // Request all core thumbnails now
    List<TMACoreObject> cores = imageData.getHierarchy().getTMAGrid().getTMACoreList();
    ImageServer<BufferedImage> server = imageData.getServer();
    CountDownLatch latch = new CountDownLatch(cores.size());
    for (TMACoreObject core : cores) {
        ROI roi = core.getROI();
        if (roi != null) {
            qupath.submitShortTask(() -> {
                RegionRequest request = createRegionRequest(core);
                if (cache.containsKey(request)) {
                    latch.countDown();
                    return;
                }
                BufferedImage img;
                try {
                    img = server.readBufferedImage(request);
                } catch (IOException e) {
                    logger.debug("Unable to get tile for " + request, e);
                    latch.countDown();
                    return;
                }
                Image imageNew = SwingFXUtils.toFXImage(img, null);
                if (imageNew != null) {
                    cache.put(request, imageNew);
                // Platform.runLater(() -> updateGridDisplay());
                }
                latch.countDown();
            });
        } else
            latch.countDown();
    }
    long startTime = System.currentTimeMillis();
    try {
        latch.await(10, TimeUnit.SECONDS);
    } catch (InterruptedException e1) {
        if (latch.getCount() > 0)
            logger.warn("Loaded {} cores in 10 seconds", cores.size() - latch.getCount());
    }
    logger.info("Countdown complete in {} seconds", (System.currentTimeMillis() - startTime) / 1000.0);
    model.setImageData(imageData, cores);
    backingList.setAll(cores);
    String m = measurement.getValue();
    sortCores(backingList, model, m, descending.get());
    filteredList.setPredicate(p -> {
        return !(p.isMissing() || Double.isNaN(model.getNumericValue(p, m)));
    });
    grid.getItems().setAll(filteredList);
}

Example 3 with RegionRequest

use of qupath.lib.regions.RegionRequest in project qupath by qupath.

the class ContourTracing method traceGeometries.

/**
 * Trace one or more geometries in an image.
 * @param server
 * @param regionRequest optional region defining the area within which geometries should be traced
 * @param clipArea optional clip region, intersected with the created geometries (may be null)
 * @param thresholds min/max thresholds (inclusive) to apply to each channel to generate objects
 * @return
 * @throws IOException
 */
public static Map<Integer, Geometry> traceGeometries(ImageServer<BufferedImage> server, RegionRequest regionRequest, Geometry clipArea, ChannelThreshold... thresholds) throws IOException {
    RegionRequest region = regionRequest;
    if (region == null) {
        if (clipArea == null) {
            region = RegionRequest.createInstance(server, server.getDownsampleForResolution(0));
        } else {
            var env = clipArea.getEnvelopeInternal();
            region = RegionRequest.createInstance(server.getPath(), server.getDownsampleForResolution(0), GeometryTools.envelopToRegion(env, 0, 0));
        }
    } else if (clipArea != null) {
        // Ensure we don't compute more than we need to
        var env = clipArea.getEnvelopeInternal();
        region = region.intersect2D(GeometryTools.envelopToRegion(env, region.getZ(), region.getT()));
    }
    Collection<TileRequest> tiles = server.getTileRequestManager().getTileRequests(region);
    if (thresholds.length == 0 || tiles.isEmpty())
        return Collections.emptyMap();
    // If the region downsample doesn't match the tile requests, the scaling may be off
    // One way to resolve that (without requiring the region to be read in one go) is to generate new tile requests for a pyramidalized server at the correct resolution
    double downsample = region.getDownsample();
    if (Math.abs(tiles.iterator().next().getDownsample() - downsample) > 1e-3) {
        server = ImageServers.pyramidalize(server, downsample);
        tiles = server.getTileRequestManager().getTileRequests(region);
    }
    return traceGeometriesImpl(server, tiles, clipArea, thresholds);
// TODO: Consider restricting parallelization
// int nThreads = Math.min(Math.max(1, Math.max(thresholds.length, tiles.size())), Runtime.getRuntime().availableProcessors());
// var pool = new ForkJoinPool(nThreads);
// var task = pool.submit(() -> traceGeometriesImpl(server, tiles, clipArea, thresholds));
// pool.shutdown();
// try {
// return task.get();
// } catch (InterruptedException e) {
// // TODO Auto-generated catch block
// e.printStackTrace();
// } catch (ExecutionException e) {
// // TODO Auto-generated catch block
// e.printStackTrace();
// }
}

Example 4 with RegionRequest

use of qupath.lib.regions.RegionRequest in project qupath by qupath.

the class EstimateStainVectorsCommand method promptToEstimateStainVectors.

public static void promptToEstimateStainVectors(ImageData<BufferedImage> imageData) {
    if (imageData == null) {
        Dialogs.showNoImageError(TITLE);
        return;
    }
    if (imageData == null || !imageData.isBrightfield() || imageData.getServer() == null || !imageData.getServer().isRGB()) {
        Dialogs.showErrorMessage(TITLE, "No brightfield, RGB image selected!");
        return;
    }
    ColorDeconvolutionStains stains = imageData.getColorDeconvolutionStains();
    if (stains == null || !stains.getStain(3).isResidual()) {
        Dialogs.showErrorMessage(TITLE, "Sorry, stain editing is only possible for brightfield, RGB images with 2 stains");
        return;
    }
    PathObject pathObject = imageData.getHierarchy().getSelectionModel().getSelectedObject();
    ROI roi = pathObject == null ? null : pathObject.getROI();
    if (roi == null)
        roi = ROIs.createRectangleROI(0, 0, imageData.getServer().getWidth(), imageData.getServer().getHeight(), ImagePlane.getDefaultPlane());
    double downsample = Math.max(1, Math.sqrt((roi.getBoundsWidth() * roi.getBoundsHeight()) / MAX_PIXELS));
    RegionRequest request = RegionRequest.createInstance(imageData.getServerPath(), downsample, roi);
    BufferedImage img = null;
    try {
        img = imageData.getServer().readBufferedImage(request);
    } catch (IOException e) {
        Dialogs.showErrorMessage("Estimate stain vectors", e);
        logger.error("Unable to obtain pixels for " + request.toString(), e);
    }
    // Apply small amount of smoothing to reduce compression artefacts
    img = EstimateStainVectors.smoothImage(img);
    // Check modes for background
    int[] rgb = img.getRGB(0, 0, img.getWidth(), img.getHeight(), null, 0, img.getWidth());
    int[] rgbMode = EstimateStainVectors.getModeRGB(rgb);
    int rMax = rgbMode[0];
    int gMax = rgbMode[1];
    int bMax = rgbMode[2];
    // Check if the background values may need to be changed
    if (rMax != stains.getMaxRed() || gMax != stains.getMaxGreen() || bMax != stains.getMaxBlue()) {
        DialogButton response = Dialogs.showYesNoCancelDialog(TITLE, String.format("Modal RGB values %d, %d, %d do not match current background values - do you want to use the modal values?", rMax, gMax, bMax));
        if (response == DialogButton.CANCEL)
            return;
        else if (response == DialogButton.YES) {
            stains = stains.changeMaxValues(rMax, gMax, bMax);
            imageData.setColorDeconvolutionStains(stains);
        }
    }
    ColorDeconvolutionStains stainsUpdated = null;
    logger.info("Requesting region for stain vector editing: ", request);
    try {
        stainsUpdated = showStainEditor(img, stains);
    } catch (Exception e) {
        Dialogs.showErrorMessage(TITLE, "Error with stain estimation: " + e.getLocalizedMessage());
        logger.error("{}", e.getLocalizedMessage(), e);
        // JOptionPane.showMessageDialog(qupath.getFrame(), "Error with stain estimation: " + e.getLocalizedMessage(), "Estimate stain vectors", JOptionPane.ERROR_MESSAGE, null);
        return;
    }
    if (!stains.equals(stainsUpdated)) {
        String suggestedName;
        String collectiveNameBefore = stainsUpdated.getName();
        if (collectiveNameBefore.endsWith("default"))
            suggestedName = collectiveNameBefore.substring(0, collectiveNameBefore.lastIndexOf("default")) + "estimated";
        else
            suggestedName = collectiveNameBefore;
        String newName = Dialogs.showInputDialog(TITLE, "Set name for stain vectors", suggestedName);
        if (newName == null)
            return;
        if (!newName.isBlank())
            stainsUpdated = stainsUpdated.changeName(newName);
        imageData.setColorDeconvolutionStains(stainsUpdated);
    }
}

Example 5 with RegionRequest

use of qupath.lib.regions.RegionRequest 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();
        }
    }
}