Examples with MeasurementList qupath.lib.measurements.MeasurementList used on opensource projects

Example 21 with MeasurementList

use of qupath.lib.measurements.MeasurementList in project qupath by qupath.

the class ShapeFeaturesPlugin method addRunnableTasks.

@Override
protected void addRunnableTasks(final ImageData<T> imageData, final PathObject parentObject, List<Runnable> tasks) {
    PixelCalibration cal = imageData == null ? null : imageData.getServer().getPixelCalibration();
    boolean useMicrons = params.getBooleanParameterValue("useMicrons") && cal != null && cal.hasPixelSizeMicrons();
    double pixelWidth = useMicrons ? cal.getPixelWidthMicrons() : 1;
    double pixelHeight = useMicrons ? cal.getPixelHeightMicrons() : 1;
    String unit = useMicrons ? GeneralTools.micrometerSymbol() : "px";
    boolean doArea = params.getBooleanParameterValue("area");
    boolean doPerimeter = params.getBooleanParameterValue("perimeter");
    boolean doCircularity = params.getBooleanParameterValue("circularity");
    ROI roi = (parentObject.hasROI() && parentObject.getROI().isArea()) ? parentObject.getROI() : null;
    if (roi != null) {
        tasks.add(new Runnable() {

            @Override
            public void run() {
                try {
                    MeasurementList measurementList = parentObject.getMeasurementList();
                    ROI roi;
                    if (parentObject instanceof PathCellObject) {
                        roi = ((PathCellObject) parentObject).getNucleusROI();
                        if (roi != null && roi.isArea())
                            addMeasurements(measurementList, roi, "Nucleus Shape: ", pixelWidth, pixelHeight, unit, doArea, doPerimeter, doCircularity);
                        roi = parentObject.getROI();
                        if (roi != null && roi.isArea())
                            addMeasurements(measurementList, roi, "Cell Shape: ", pixelWidth, pixelHeight, unit, doArea, doPerimeter, doCircularity);
                    } else {
                        roi = parentObject.getROI();
                        if (roi != null && roi.isArea())
                            addMeasurements(measurementList, roi, "ROI Shape: ", pixelWidth, pixelHeight, unit, doArea, doPerimeter, doCircularity);
                    }
                    measurementList.close();
                } catch (Exception e) {
                    e.printStackTrace();
                    throw (e);
                }
            }
        });
    }
}

Example 22 with MeasurementList

use of qupath.lib.measurements.MeasurementList in project qupath by qupath.

the class SmoothFeaturesPlugin method addRunnableTasks.

@Override
protected void addRunnableTasks(final ImageData<T> imageData, final PathObject parentObject, List<Runnable> tasks) {
    double fwhm;
    ImageServer<T> server = imageData.getServer();
    String fwhmStringTemp;
    PixelCalibration cal = server == null ? null : server.getPixelCalibration();
    if (cal != null && cal.hasPixelSizeMicrons()) {
        fwhm = getParameterList(imageData).getDoubleParameterValue("fwhmMicrons");
        fwhmStringTemp = GeneralTools.createFormatter(2).format(fwhm) + " " + GeneralTools.micrometerSymbol();
        fwhm /= cal.getAveragedPixelSizeMicrons();
    // params.addDoubleParameter("fwhmPixels", "Radius (FWHM)", fwhm, "pixels"); // Set the FWHM in pixels too
    } else {
        fwhm = getParameterList(imageData).getDoubleParameterValue("fwhmPixels");
        fwhmStringTemp = GeneralTools.createFormatter(2).format(fwhm) + " px";
    }
    // sigma = 50;
    final String fwhmString = fwhmStringTemp;
    final double fwhmPixels = fwhm;
    final boolean withinClass = params.getBooleanParameterValue("smoothWithinClasses");
    final boolean useLegacyNames = params.containsKey("useLegacyNames") && Boolean.TRUE.equals(params.getBooleanParameterValue("useLegacyNames"));
    tasks.add(new Runnable() {

        @Override
        public void run() {
            try {
                if (!parentObject.hasChildren())
                    return;
                // System.out.println("Smoothing with FWHM " +fwhmPixels);
                // TODO: MAKE A MORE ELEGANT LIST!!!!
                List<PathObject> pathObjects = PathObjectTools.getFlattenedObjectList(parentObject, null, false);
                Iterator<PathObject> iterObjects = pathObjects.iterator();
                while (iterObjects.hasNext()) {
                    PathObject temp = iterObjects.next();
                    if (!(temp instanceof PathDetectionObject || temp instanceof PathTileObject))
                        iterObjects.remove();
                }
                if (pathObjects.isEmpty())
                    return;
                // TODO: ACCESS & USE THE CLASSIFIER DATA!!!!
                List<String> measurements = new ArrayList<>(PathClassifierTools.getAvailableFeatures(pathObjects));
                Iterator<String> iter = measurements.iterator();
                while (iter.hasNext()) {
                    String name = iter.next().toLowerCase();
                    if (name.endsWith("smoothed") || name.startsWith("smoothed") || name.contains(" - smoothed (fwhm ") || name.startsWith("smoothed denominator (local density, ") || name.startsWith("nearby detection counts"))
                        iter.remove();
                }
                logger.debug(String.format("Smooth features: %s (FWHM: %.2f px)", parentObject.getDisplayedName(), fwhmPixels));
                smoothMeasurements(pathObjects, measurements, fwhmPixels, fwhmString, withinClass, useLegacyNames);
            // // REMOVE - the purpose was to test a 'difference of Gaussians' type of thing
            // List<String> namesAdded1 = new ArrayList<>(smoothMeasurements(pathObjects, measurements, fwhmPixels));
            // List<String> namesAdded2 = new ArrayList<>(smoothMeasurements(pathObjects, measurements, fwhmPixels * 2));
            // for (PathObject pathObject : pathObjects) {
            // MeasurementList ml = pathObject.getMeasurementList();
            // ml.ensureListOpen();
            // for (int i = 0; i < namesAdded1.size(); i++) {
            // String name1 = namesAdded1.get(i);
            // String name2 = namesAdded2.get(i);
            // double m1 = ml.getMeasurementValue(name1);
            // double m2 = ml.getMeasurementValue(name2);
            // ml.addMeasurement(name1 + " - " + name2, m1 - m2);
            // }
            // ml.closeList();
            // }
            } catch (Exception e) {
                e.printStackTrace();
                throw (e);
            }
        }
    });
}

Example 23 with MeasurementList

use of qupath.lib.measurements.MeasurementList in project qupath by qupath.

the class LocalBinaryPatternsPlugin method processObject.

static boolean processObject(final PathObject pathObject, final ParameterList params, final ImageServer<BufferedImage> server, final ColorDeconvolutionStains stains) throws InterruptedException, IOException {
    String stainsName = (String) params.getChoiceParameterValue("stainChoice");
    double mag = params.getDoubleParameterValue("magnification");
    // int d = params.getIntParameterValue("haralickDistance");
    boolean includeStats = params.getBooleanParameterValue("includeStats");
    boolean doCircular = params.getBooleanParameterValue("doCircular");
    double downsample = server.getMetadata().getMagnification() / mag;
    ROI pathROI = pathObject.getROI();
    if (pathROI == null)
        return false;
    // Get bounds
    ImmutableDimension size = getPreferredTileSizePixels(server, params);
    if (size.getWidth() / downsample < 1 || size.getHeight() / downsample < 1)
        return false;
    RegionRequest region = RegionRequest.createInstance(server.getPath(), downsample, (int) (pathROI.getCentroidX() + .5) - size.width / 2, (int) (pathROI.getCentroidY() + .5) - size.height / 2, size.width, size.height, pathROI.getT(), pathROI.getZ());
    // System.out.println(bounds);
    // System.out.println("Size: " + size);
    BufferedImage img = server.readBufferedImage(region);
    // System.out.println("Image size: " + img.getWidth() + " x " + img.getHeight() + " pixels");
    // Get a buffer containing the image pixels
    int w = img.getWidth();
    int h = img.getHeight();
    int[] buf = img.getRGB(0, 0, w, h, null, 0, w);
    // Create a color transformer to get the images we need
    float[] pixels = new float[buf.length];
    SimpleModifiableImage pxImg = SimpleImages.createFloatImage(pixels, w, h);
    MeasurementList measurementList = pathObject.getMeasurementList();
    String postfix = " (" + getDiameterString(server, params) + ")";
    if (stainsName.equals("H-DAB")) {
        processTransformedImage(pxImg, buf, pixels, measurementList, "Hematoxylin" + postfix, ColorTransformer.ColorTransformMethod.Hematoxylin_H_DAB, stains, includeStats, doCircular);
        processTransformedImage(pxImg, buf, pixels, measurementList, "DAB" + postfix, ColorTransformer.ColorTransformMethod.DAB_H_DAB, stains, includeStats, doCircular);
    } else if (stainsName.equals("H&E")) {
        processTransformedImage(pxImg, buf, pixels, measurementList, "Hematoxylin" + postfix, ColorTransformer.ColorTransformMethod.Hematoxylin_H_E, stains, includeStats, doCircular);
        processTransformedImage(pxImg, buf, pixels, measurementList, "Eosin" + postfix, ColorTransformer.ColorTransformMethod.Eosin_H_E, stains, includeStats, doCircular);
    } else if (stainsName.equals("H-DAB (8-bit)")) {
        processTransformedImage(pxImg, buf, pixels, measurementList, "Hematoxylin 8-bit" + postfix, ColorTransformer.ColorTransformMethod.Hematoxylin_H_DAB_8_bit, stains, includeStats, doCircular);
        processTransformedImage(pxImg, buf, pixels, measurementList, "DAB 8-bit" + postfix, ColorTransformer.ColorTransformMethod.DAB_H_DAB_8_bit, stains, includeStats, doCircular);
    } else if (stainsName.equals("H&E (8-bit)")) {
        processTransformedImage(pxImg, buf, pixels, measurementList, "Hematoxylin 8-bit" + postfix, ColorTransformer.ColorTransformMethod.Hematoxylin_H_E_8_bit, stains, includeStats, doCircular);
        processTransformedImage(pxImg, buf, pixels, measurementList, "Eosin 8-bit" + postfix, ColorTransformer.ColorTransformMethod.Eosin_H_E_8_bit, stains, includeStats, doCircular);
    } else if (stainsName.equals("Optical density")) {
        processTransformedImage(pxImg, buf, pixels, measurementList, "OD sum" + postfix, ColorTransformer.ColorTransformMethod.Optical_density_sum, stains, includeStats, doCircular);
    } else if (stainsName.equals("RGB")) {
        processTransformedImage(pxImg, buf, pixels, measurementList, "Red" + postfix, ColorTransformer.ColorTransformMethod.Red, stains, includeStats, doCircular);
        processTransformedImage(pxImg, buf, pixels, measurementList, "Green" + postfix, ColorTransformer.ColorTransformMethod.Green, stains, includeStats, doCircular);
        processTransformedImage(pxImg, buf, pixels, measurementList, "Blue" + postfix, ColorTransformer.ColorTransformMethod.Blue, stains, includeStats, doCircular);
    } else if (stainsName.equals("Grayscale")) {
        processTransformedImage(pxImg, buf, pixels, measurementList, "Grayscale" + postfix, ColorTransformer.ColorTransformMethod.RGB_mean, stains, includeStats, doCircular);
    }
    measurementList.close();
    return true;
}

Example 24 with MeasurementList

use of qupath.lib.measurements.MeasurementList in project qupath by qupath.

the class TMAExplorer method createAndShowStage.

private void createAndShowStage() {
    Project<BufferedImage> project = qupath.getProject();
    entries.clear();
    if (project != null) {
        // Create an output directory for the images
        File dirBaseImageOutput = Projects.getBaseDirectory(project);
        dirBaseImageOutput = new File(dirBaseImageOutput, "TMA");
        dirBaseImageOutput = new File(dirBaseImageOutput, "images");
        if (!dirBaseImageOutput.exists())
            dirBaseImageOutput.mkdirs();
        Map<String, RunningStatistics> statsMap = new HashMap<>();
        for (ProjectImageEntry<BufferedImage> imageEntry : project.getImageList()) {
            // Look for data file
            if (!imageEntry.hasImageData())
                continue;
            File dirImageOutput = new File(dirBaseImageOutput, imageEntry.getImageName());
            if (!dirImageOutput.exists())
                dirImageOutput.mkdirs();
            // Read data
            ImageData<BufferedImage> imageData;
            try {
                imageData = imageEntry.readImageData();
            } catch (IOException e) {
                logger.error("Error reading ImageData for " + imageEntry.getImageName(), e);
                continue;
            }
            TMAGrid tmaGrid = imageData.getHierarchy().getTMAGrid();
            if (tmaGrid == null) {
                logger.warn("No TMA data for {}", imageEntry.getImageName());
                continue;
            }
            // Figure out downsample value
            ImageServer<BufferedImage> server = imageData.getServer();
            double downsample = Math.round(5 / server.getPixelCalibration().getAveragedPixelSizeMicrons());
            // Read the TMA entries
            int counter = 0;
            for (TMACoreObject core : tmaGrid.getTMACoreList()) {
                counter++;
                String name = core.getName();
                if (name == null)
                    name = Integer.toString(counter);
                File fileOutput = new File(dirImageOutput, name + ".jpg");
                if (!fileOutput.exists()) {
                    try {
                        RegionRequest request = RegionRequest.createInstance(server.getPath(), downsample, core.getROI());
                        BufferedImage img = server.readBufferedImage(request);
                        ImageIO.write(img, "jpg", fileOutput);
                    } catch (Exception e) {
                        logger.error("Unable to write {}", fileOutput.getAbsolutePath());
                    }
                }
                var entry = TMAEntries.createDefaultTMAEntry(imageEntry.getImageName(), fileOutput.getAbsolutePath(), null, core.getName(), core.isMissing());
                MeasurementList ml = core.getMeasurementList();
                for (int i = 0; i < ml.size(); i++) {
                    String measurement = ml.getMeasurementName(i);
                    double val = ml.getMeasurementValue(i);
                    entry.putMeasurement(measurement, val);
                    if (!Double.isNaN(val)) {
                        RunningStatistics stats = statsMap.get(measurement);
                        if (stats == null) {
                            stats = new RunningStatistics();
                            statsMap.put(measurement, stats);
                        }
                        stats.addValue(val);
                    }
                }
                entries.add(entry);
            }
            try {
                server.close();
            } catch (Exception e) {
                logger.warn("Problem closing server", e);
            }
        }
        // Loop through all entries and perform outlier count
        double k = 3;
        for (TMAEntry entry : entries) {
            int outlierCount = 0;
            for (Entry<String, RunningStatistics> statsEntry : statsMap.entrySet()) {
                RunningStatistics stats = statsEntry.getValue();
                double val = entry.getMeasurementAsDouble(statsEntry.getKey());
                if (!(val >= stats.getMean() - stats.getStdDev() * k && val <= stats.getMean() + stats.getStdDev() * k))
                    outlierCount++;
            }
            entry.putMeasurement("Outlier count", outlierCount);
        }
    }
    Stage stage = new Stage();
    stage.initOwner(qupath.getStage());
    TMASummaryViewer summaryViewer = new TMASummaryViewer(stage);
    summaryViewer.setTMAEntries(entries);
    summaryViewer.getStage().show();
}