Examples with PixelCalibration qupath.lib.images.servers.PixelCalibration used on opensource projects

Example 26 with PixelCalibration

use of qupath.lib.images.servers.PixelCalibration in project qupath by qupath.

the class ImageDetailsPane method promptToSetPixelSize.

static boolean promptToSetPixelSize(ImageData<BufferedImage> imageData, boolean requestZSpacing) {
    var server = imageData.getServer();
    var hierarchy = imageData.getHierarchy();
    var selected = hierarchy.getSelectionModel().getSelectedObject();
    var roi = selected == null ? null : selected.getROI();
    PixelCalibration cal = server.getPixelCalibration();
    double pixelWidthMicrons = cal.getPixelWidthMicrons();
    double pixelHeightMicrons = cal.getPixelHeightMicrons();
    double zSpacingMicrons = cal.getZSpacingMicrons();
    // Use line or area ROI if possible
    if (!requestZSpacing && roi != null && !roi.isEmpty() && (roi.isArea() || roi.isLine())) {
        boolean setPixelHeight = true;
        boolean setPixelWidth = true;
        String message;
        String units = GeneralTools.micrometerSymbol();
        double pixelWidth = cal.getPixelWidthMicrons();
        double pixelHeight = cal.getPixelHeightMicrons();
        if (!Double.isFinite(pixelWidth))
            pixelWidth = 1;
        if (!Double.isFinite(pixelHeight))
            pixelHeight = 1;
        Double defaultValue = null;
        if (roi.isLine()) {
            setPixelHeight = roi.getBoundsHeight() != 0;
            setPixelWidth = roi.getBoundsWidth() != 0;
            message = "Enter selected line length";
            defaultValue = roi.getScaledLength(pixelWidth, pixelHeight);
        } else {
            message = "Enter selected ROI area";
            units = units + "^2";
            defaultValue = roi.getScaledArea(pixelWidth, pixelHeight);
        }
        // }
        if (Double.isNaN(defaultValue))
            defaultValue = 1.0;
        var params = new ParameterList().addDoubleParameter("inputValue", message, defaultValue, units, "Enter calibrated value in " + units + " for the selected ROI to calculate the pixel size").addBooleanParameter("squarePixels", "Assume square pixels", true, "Set the pixel width to match the pixel height");
        params.setHiddenParameters(setPixelHeight && setPixelWidth, "squarePixels");
        if (!Dialogs.showParameterDialog("Set pixel size", params))
            return false;
        Double result = params.getDoubleParameterValue("inputValue");
        setPixelHeight = setPixelHeight || params.getBooleanParameterValue("squarePixels");
        setPixelWidth = setPixelWidth || params.getBooleanParameterValue("squarePixels");
        // Double result = Dialogs.showInputDialog("Set pixel size", message, defaultValue);
        // if (result == null)
        // return false;
        double sizeMicrons;
        if (roi.isLine())
            sizeMicrons = result.doubleValue() / roi.getLength();
        else
            sizeMicrons = Math.sqrt(result.doubleValue() / roi.getArea());
        if (setPixelHeight)
            pixelHeightMicrons = sizeMicrons;
        if (setPixelWidth)
            pixelWidthMicrons = sizeMicrons;
    } else {
        // Prompt for all required values
        ParameterList params = new ParameterList().addDoubleParameter("pixelWidth", "Pixel width", pixelWidthMicrons, GeneralTools.micrometerSymbol(), "Enter the pixel width").addDoubleParameter("pixelHeight", "Pixel height", pixelHeightMicrons, GeneralTools.micrometerSymbol(), "Entry the pixel height").addDoubleParameter("zSpacing", "Z-spacing", zSpacingMicrons, GeneralTools.micrometerSymbol(), "Enter the spacing between slices of a z-stack");
        params.setHiddenParameters(server.nZSlices() == 1, "zSpacing");
        if (!Dialogs.showParameterDialog("Set pixel size", params))
            return false;
        if (server.nZSlices() != 1) {
            zSpacingMicrons = params.getDoubleParameterValue("zSpacing");
        }
        pixelWidthMicrons = params.getDoubleParameterValue("pixelWidth");
        pixelHeightMicrons = params.getDoubleParameterValue("pixelHeight");
    }
    if ((pixelWidthMicrons <= 0 || pixelHeightMicrons <= 0) || (server.nZSlices() > 1 && zSpacingMicrons <= 0)) {
        if (!Dialogs.showConfirmDialog("Set pixel size", "You entered values <= 0, do you really want to remove this pixel calibration information?")) {
            return false;
        }
        zSpacingMicrons = server.nZSlices() > 1 && zSpacingMicrons > 0 ? zSpacingMicrons : Double.NaN;
        if (pixelWidthMicrons <= 0 || pixelHeightMicrons <= 0) {
            pixelWidthMicrons = Double.NaN;
            pixelHeightMicrons = Double.NaN;
        }
    }
    if (QP.setPixelSizeMicrons(imageData, pixelWidthMicrons, pixelHeightMicrons, zSpacingMicrons)) {
        // Log for scripts
        WorkflowStep step;
        if (server.nZSlices() == 1) {
            var map = Map.of("pixelWidthMicrons", pixelWidthMicrons, "pixelHeightMicrons", pixelHeightMicrons);
            String script = String.format("setPixelSizeMicrons(%f, %f)", pixelWidthMicrons, pixelHeightMicrons);
            step = new DefaultScriptableWorkflowStep("Set pixel size " + GeneralTools.micrometerSymbol(), map, script);
        } else {
            var map = Map.of("pixelWidthMicrons", pixelWidthMicrons, "pixelHeightMicrons", pixelHeightMicrons, "zSpacingMicrons", zSpacingMicrons);
            String script = String.format("setPixelSizeMicrons(%f, %f, %f)", pixelWidthMicrons, pixelHeightMicrons, zSpacingMicrons);
            step = new DefaultScriptableWorkflowStep("Set pixel size " + GeneralTools.micrometerSymbol(), map, script);
        }
        imageData.getHistoryWorkflow().addStep(step);
        return true;
    } else
        return false;
}

Example 27 with PixelCalibration

use of qupath.lib.images.servers.PixelCalibration in project qupath by qupath.

the class ImageDetailsPane method getValue.

private Object getValue(ImageDetailRow rowType) {
    if (imageData == null)
        return null;
    ImageServer<BufferedImage> server = imageData.getServer();
    PixelCalibration cal = server.getPixelCalibration();
    switch(rowType) {
        case NAME:
            var project = QuPathGUI.getInstance().getProject();
            var entry = project == null ? null : project.getEntry(imageData);
            if (entry == null)
                return ServerTools.getDisplayableImageName(server);
            else
                return entry.getImageName();
        case URI:
            Collection<URI> uris = server.getURIs();
            if (uris.isEmpty())
                return "Not available";
            if (uris.size() == 1)
                return decodeURI(uris.iterator().next());
            return "[" + String.join(", ", uris.stream().map(ImageDetailsPane::decodeURI).collect(Collectors.toList())) + "]";
        case IMAGE_TYPE:
            return imageData.getImageType();
        case METADATA_CHANGED:
            return hasOriginalMetadata(imageData.getServer()) ? "No" : "Yes";
        case PIXEL_TYPE:
            String type = server.getPixelType().toString().toLowerCase();
            if (server.isRGB())
                type += " (rgb)";
            return type;
        case MAGNIFICATION:
            double mag = server.getMetadata().getMagnification();
            if (Double.isNaN(mag))
                return "Unknown";
            return mag;
        case WIDTH:
            if (cal.hasPixelSizeMicrons())
                return String.format("%s px (%.2f %s)", server.getWidth(), server.getWidth() * cal.getPixelWidthMicrons(), GeneralTools.micrometerSymbol());
            else
                return String.format("%s px", server.getWidth());
        case HEIGHT:
            if (cal.hasPixelSizeMicrons())
                return String.format("%s px (%.2f %s)", server.getHeight(), server.getHeight() * cal.getPixelHeightMicrons(), GeneralTools.micrometerSymbol());
            else
                return String.format("%s px", server.getHeight());
        case DIMENSIONS:
            return String.format("%d x %d x %d", server.nChannels(), server.nZSlices(), server.nTimepoints());
        case PIXEL_WIDTH:
            if (cal.hasPixelSizeMicrons())
                return String.format("%.4f %s", cal.getPixelWidthMicrons(), GeneralTools.micrometerSymbol());
            else
                return "Unknown";
        case PIXEL_HEIGHT:
            if (cal.hasPixelSizeMicrons())
                return String.format("%.4f %s", cal.getPixelHeightMicrons(), GeneralTools.micrometerSymbol());
            else
                return "Unknown";
        case Z_SPACING:
            if (cal.hasZSpacingMicrons())
                return String.format("%.4f %s", cal.getZSpacingMicrons(), GeneralTools.micrometerSymbol());
            else
                return "Unknown";
        case UNCOMPRESSED_SIZE:
            double size = server.getWidth() / 1024.0 * server.getHeight() / 1024.0 * server.getPixelType().getBytesPerPixel() * server.nChannels() * server.nZSlices() * server.nTimepoints();
            String units = " MB";
            if (size > 1000) {
                size /= 1024.0;
                units = " GB";
            }
            return GeneralTools.formatNumber(size, 1) + units;
        case SERVER_TYPE:
            return server.getServerType();
        case PYRAMID:
            if (server.nResolutions() == 1)
                return "No";
            return GeneralTools.arrayToString(Locale.getDefault(Locale.Category.FORMAT), server.getPreferredDownsamples(), 1);
        case STAIN_1:
            return imageData.getColorDeconvolutionStains().getStain(1);
        case STAIN_2:
            return imageData.getColorDeconvolutionStains().getStain(2);
        case STAIN_3:
            return imageData.getColorDeconvolutionStains().getStain(3);
        case BACKGROUND:
            ColorDeconvolutionStains stains = imageData.getColorDeconvolutionStains();
            double[] whitespace = new double[] { stains.getMaxRed(), stains.getMaxGreen(), stains.getMaxBlue() };
            return whitespace;
        default:
            return null;
    }
}

Example 28 with PixelCalibration

use of qupath.lib.images.servers.PixelCalibration in project qupath by qupath.

the class DilateAnnotationPlugin method getTasks.

@Override
protected Collection<Runnable> getTasks(final PluginRunner<T> runner) {
    Collection<? extends PathObject> parentObjects = getParentObjects(runner);
    if (parentObjects == null || parentObjects.isEmpty())
        return Collections.emptyList();
    // Add a single task, to avoid multithreading - which may complicate setting parents
    List<Runnable> tasks = new ArrayList<>(parentObjects.size());
    ImageServer<T> server = getServer(runner);
    Rectangle bounds = new Rectangle(0, 0, server.getWidth(), server.getHeight());
    PathObjectHierarchy hierarchy = getHierarchy(runner);
    double radiusPixels;
    PixelCalibration cal = server.getPixelCalibration();
    if (cal.hasPixelSizeMicrons())
        radiusPixels = params.getDoubleParameterValue("radiusMicrons") / cal.getAveragedPixelSizeMicrons();
    else
        radiusPixels = params.getDoubleParameterValue("radiusPixels");
    boolean constrainToParent = params.getBooleanParameterValue("constrainToParent");
    boolean removeInterior = params.getBooleanParameterValue("removeInterior");
    LineCap cap = params.containsKey("lineCap") ? (LineCap) params.getChoiceParameterValue("lineCap") : LineCap.ROUND;
    // Want to reset selection
    PathObject selected = hierarchy.getSelectionModel().getSelectedObject();
    Collection<PathObject> previousSelection = new ArrayList<>(hierarchy.getSelectionModel().getSelectedObjects());
    tasks.add(() -> {
        for (PathObject pathObject : parentObjects) {
            addExpandedAnnotation(bounds, hierarchy, pathObject, radiusPixels, constrainToParent, removeInterior, cap);
        }
        hierarchy.getSelectionModel().selectObjects(previousSelection);
        hierarchy.getSelectionModel().setSelectedObject(selected, true);
    });
    return tasks;
}

Example 29 with PixelCalibration

use of qupath.lib.images.servers.PixelCalibration 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 30 with PixelCalibration

use of qupath.lib.images.servers.PixelCalibration 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);
            }
        }
    });
}