Examples with ObservableMeasurementTableData qupath.lib.gui.measure.ObservableMeasurementTableData used on opensource projects

Example 1 with ObservableMeasurementTableData

use of qupath.lib.gui.measure.ObservableMeasurementTableData 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();
        }
    }
}

Example 2 with ObservableMeasurementTableData

use of qupath.lib.gui.measure.ObservableMeasurementTableData in project qupath by qupath.

the class QPEx method saveMeasurements.

/**
 * Save measurements for the specified image for objects of a fixed type.
 * @param imageData the image data
 * @param type the type of objects to measure
 * @param path file path describing where to write the results
 * @param includeColumns specific columns to include, or empty to indicate that all measurements should be exported
 */
public static void saveMeasurements(final ImageData<?> imageData, final Class<? extends PathObject> type, final String path, final String... includeColumns) {
    File fileOutput = new File(resolvePath(path));
    if (fileOutput.isDirectory()) {
        String ext = ",".equals(PathPrefs.tableDelimiterProperty().get()) ? ".csv" : ".txt";
        fileOutput = new File(fileOutput, ServerTools.getDisplayableImageName(imageData.getServer()) + " " + PathObjectTools.getSuitableName(type, true) + ext);
    }
    ObservableMeasurementTableData model = new ObservableMeasurementTableData();
    model.setImageData(imageData, imageData == null ? Collections.emptyList() : imageData.getHierarchy().getObjects(null, type));
    try (PrintWriter writer = new PrintWriter(fileOutput, StandardCharsets.UTF_8)) {
        Collection<String> excludeColumns;
        if (includeColumns.length == 0) {
            excludeColumns = Collections.emptyList();
        } else {
            excludeColumns = new LinkedHashSet<>(model.getAllNames());
            excludeColumns.removeAll(Arrays.asList(includeColumns));
        }
        for (String row : SummaryMeasurementTableCommand.getTableModelStrings(model, PathPrefs.tableDelimiterProperty().get(), excludeColumns)) writer.println(row);
        writer.close();
    } catch (IOException e) {
        logger.error("Error writing file to " + fileOutput, e);
    }
}

Example 3 with ObservableMeasurementTableData

use of qupath.lib.gui.measure.ObservableMeasurementTableData in project qupath by qupath.

the class TMASummaryViewer method getEntriesForTMAData.

private static List<TMAEntry> getEntriesForTMAData(final ImageData<BufferedImage> imageData) {
    List<TMAEntry> entriesNew = new ArrayList<>();
    if (imageData.getHierarchy().getTMAGrid() == null)
        return entriesNew;
    ObservableMeasurementTableData data = new ObservableMeasurementTableData();
    data.setImageData(imageData, imageData.getHierarchy().getTMAGrid().getTMACoreList());
    for (TMACoreObject core : imageData.getHierarchy().getTMAGrid().getTMACoreList()) {
        entriesNew.add(TMAEntries.createTMAObjectEntry(imageData, data, core));
    }
    return entriesNew;
}

Example 4 with ObservableMeasurementTableData

use of qupath.lib.gui.measure.ObservableMeasurementTableData 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 5 with ObservableMeasurementTableData

use of qupath.lib.gui.measure.ObservableMeasurementTableData 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);
    }
}