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

Example 1 with PixelCalibration

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

the class DelaunayClusteringPlugin method addRunnableTasks.

@Override
protected void addRunnableTasks(ImageData<T> imageData, PathObject parentObject, List<Runnable> tasks) {
    // Get pixel sizes, if possible
    ImageServer<?> server = imageData.getServer();
    double pixelWidth = 1, pixelHeight = 1;
    PixelCalibration cal = server.getPixelCalibration();
    boolean hasMicrons = server != null && cal.hasPixelSizeMicrons();
    if (hasMicrons) {
        pixelWidth = cal.getPixelWidthMicrons();
        pixelHeight = cal.getPixelHeightMicrons();
    }
    double distanceThresholdPixels;
    if (cal.hasPixelSizeMicrons())
        distanceThresholdPixels = params.getDoubleParameterValue("distanceThresholdMicrons") / cal.getAveragedPixelSizeMicrons();
    else
        distanceThresholdPixels = params.getDoubleParameterValue("distanceThreshold");
    tasks.add(new DelaunayRunnable(imageData, parentObject, params.getBooleanParameterValue("addClusterMeasurements"), pixelWidth, pixelHeight, distanceThresholdPixels, params.getBooleanParameterValue("limitByClass")));
}

Example 2 with PixelCalibration

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

the class SpecifyAnnotationCommand method init.

private void init() {
    pane = new GridPane();
    int row = 0;
    var cbMicrons = new CheckBox("Use " + GeneralTools.micrometerSymbol());
    var units = Bindings.createStringBinding(() -> {
        if (cbMicrons.isSelected())
            return GeneralTools.micrometerSymbol();
        return "px";
    }, cbMicrons.selectedProperty());
    var comboType = new ComboBox<ROI_TYPE>(FXCollections.observableArrayList(ROI_TYPE.values()));
    comboType.setMaxWidth(Double.MAX_VALUE);
    comboType.getSelectionModel().select(ROI_TYPE.RECTANGLE);
    PaneTools.addGridRow(pane, row++, 0, "Type of ROI to create", createLabelFor(comboType, "Type"), comboType, comboType);
    var comboClassification = new ComboBox<>(qupath.getAvailablePathClasses());
    comboClassification.setMaxWidth(Double.MAX_VALUE);
    comboClassification.setCellFactory(o -> {
        return new ClassificationCell();
    });
    // comboClassification.cell;
    PaneTools.addGridRow(pane, row++, 0, "Classification for the annotation (may be empty if annotation should be unclassified)", createLabelFor(comboClassification, "Classification"), comboClassification, comboClassification);
    var tfX = new TextField("");
    var tfY = new TextField("");
    var tfWidth = new TextField("1000");
    var tfHeight = new TextField("1000");
    tfX.setPrefColumnCount(10);
    tfY.setPrefColumnCount(10);
    tfWidth.setPrefColumnCount(10);
    tfHeight.setPrefColumnCount(10);
    PaneTools.addGridRow(pane, row++, 0, "X-coordinate of top left of annotation bounding box (if missing or < 0, annotation will be centered in current viewer)", createLabelFor(tfX, "X origin"), tfX, createBoundLabel(units));
    PaneTools.addGridRow(pane, row++, 0, "Y-coordinate of top left of annotation bounding box (if missing or < 0, annotation will be centered in current viewer)", createLabelFor(tfY, "Y origin"), tfY, createBoundLabel(units));
    PaneTools.addGridRow(pane, row++, 0, "Width of annotation bounding box (must be > 0)", createLabelFor(tfWidth, "Width"), tfWidth, createBoundLabel(units));
    PaneTools.addGridRow(pane, row++, 0, "Height of annotation bounding box (must be > 0)", createLabelFor(tfHeight, "Height"), tfHeight, createBoundLabel(units));
    cbMicrons.setMaxWidth(Double.MAX_VALUE);
    PaneTools.addGridRow(pane, row++, 0, "Specify coordinates in " + GeneralTools.micrometerSymbol() + " - pixel calibration information must be available", cbMicrons, cbMicrons, cbMicrons);
    var cbLock = new CheckBox("Set locked");
    cbLock.setMaxWidth(Double.MAX_VALUE);
    PaneTools.addGridRow(pane, row++, 0, "Set annotation as locked, so that it can't be immediately edited", cbLock, cbLock, cbLock);
    var tfName = new TextField("");
    PaneTools.addGridRow(pane, row++, 0, "Name of annotation (can be empty)", createLabelFor(tfName, "Name"), tfName, tfName);
    var btnAdd = new Button("Add annotation");
    btnAdd.setOnAction(e -> {
        var viewer = qupath.getViewer();
        var imageData = viewer == null ? null : viewer.getImageData();
        if (imageData == null) {
            Dialogs.showNoImageError("Create annotation");
            return;
        }
        var server = imageData.getServer();
        var hierarchy = imageData.getHierarchy();
        double xScale = 1;
        double yScale = 1;
        PixelCalibration cal = server.getPixelCalibration();
        if (cbMicrons.isSelected()) {
            if (!cal.hasPixelSizeMicrons()) {
                Dialogs.showErrorMessage("Create annotation", "No pixel size information available! Try again using pixel units.");
                return;
            }
            xScale = 1.0 / cal.getPixelWidthMicrons();
            yScale = 1.0 / cal.getPixelHeightMicrons();
        }
        var xOrig = tryToParse(tfX.getText());
        var yOrig = tryToParse(tfY.getText());
        var width = tryToParse(tfWidth.getText());
        var height = tryToParse(tfHeight.getText());
        if (width == null || width.doubleValue() <= 0 || height == null || height.doubleValue() <= 0) {
            Dialogs.showErrorMessage("Create annotation", "Width and height must be specified, and > 0!");
            return;
        }
        double w = width.doubleValue() * xScale;
        double h = height.doubleValue() * yScale;
        // It helps to start at integer pixels, since otherwise the width can be surprising when exporting regions
        // (since when requesting ROIs, Math.ceil is currently applied to ensure that the full ROI is included).
        double x;
        if (xOrig == null || xOrig.doubleValue() < 0)
            x = (int) Math.max(0, viewer.getCenterPixelX() - w / 2.0);
        else
            x = xOrig.doubleValue() * xScale;
        double y;
        if (yOrig == null || yOrig.doubleValue() < 0)
            y = (int) Math.max(viewer.getCenterPixelY() - h / 2.0, 0);
        else
            y = yOrig.doubleValue() * yScale;
        if (x + w > server.getWidth() || y + h > server.getHeight()) {
            Dialogs.showErrorMessage("Create annotation", "Specified annotation is too large for the image bounds!");
            return;
        }
        int z = viewer.getZPosition();
        int t = viewer.getTPosition();
        ROI roi = null;
        switch(comboType.getSelectionModel().getSelectedItem()) {
            case ELLIPSE:
                roi = ROIs.createEllipseROI(x, y, w, h, ImagePlane.getPlane(z, t));
                break;
            case RECTANGLE:
                roi = ROIs.createRectangleROI(x, y, w, h, ImagePlane.getPlane(z, t));
                break;
            default:
                Dialogs.showErrorMessage("Create annotation", "No ROI type selected!");
                return;
        }
        var pathClass = comboClassification.getSelectionModel().getSelectedItem();
        if (pathClass != null && !pathClass.isValid())
            pathClass = null;
        var annotation = PathObjects.createAnnotationObject(roi, pathClass);
        // Set name, if necessary
        var name = tfName.getText();
        if (name != null && !name.isEmpty())
            annotation.setName(name);
        if (cbLock.isSelected())
            ((PathAnnotationObject) annotation).setLocked(true);
        hierarchy.addPathObject(annotation);
    });
    btnAdd.setMaxWidth(Double.MAX_VALUE);
    PaneTools.addGridRow(pane, row++, 0, "Create annotation with specified options & add to object hierarchy", btnAdd, btnAdd, btnAdd);
    PaneTools.setFillWidth(Boolean.TRUE, tfX, tfY, tfWidth, tfHeight, btnAdd, comboType);
    PaneTools.setHGrowPriority(Priority.ALWAYS, tfX, tfY, tfWidth, tfHeight, btnAdd, comboType);
    pane.setHgap(5);
    pane.setVgap(5);
    pane.setPadding(new Insets(10));
}

Example 3 with PixelCalibration

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

the class QuPathViewer method getImageLocationString.

/**
 * Get a string representing the image coordinates for a particular x & y location.
 * @param xx x-coordinate in the image space (not the component/viewer space)
 * @param yy y-coordinate in the image space (not the component/viewer space)
 * @param useCalibratedUnits
 * @return
 */
private String getImageLocationString(double xx, double yy, boolean useCalibratedUnits) {
    ImageServer<BufferedImage> server = getServer();
    if (server == null)
        return "";
    String units;
    if (xx < 0 || yy < 0 || xx > server.getWidth() - 1 || yy > server.getHeight() - 1)
        return "";
    double xDisplay = xx;
    double yDisplay = yy;
    PixelCalibration cal = server.getPixelCalibration();
    if (useCalibratedUnits && cal.hasPixelSizeMicrons()) {
        units = GeneralTools.micrometerSymbol();
        xDisplay *= cal.getPixelWidthMicrons();
        yDisplay *= cal.getPixelHeightMicrons();
    } else {
        units = "px";
    }
    // See if we're on top of a TMA core
    String prefix = "";
    TMAGrid tmaGrid = getHierarchy().getTMAGrid();
    if (tmaGrid != null) {
        TMACoreObject core = PathObjectTools.getTMACoreForPixel(tmaGrid, xx, yy);
        if (core != null && core.getName() != null)
            prefix = "Core: " + core.getName() + "\n";
    }
    String s = null;
    RegionRequest request = ImageRegionStoreHelpers.getTileRequest(server, xx, yy, downsampleFactor.get(), getZPosition(), getTPosition());
    if (request != null) {
        BufferedImage img = regionStore.getCachedTile(server, request);
        int xi = 0, yi = 0;
        if (img == null) {
            // Try getting a value from the thumbnail for the whole image
            BufferedImage imgThumbnail = regionStore.getCachedThumbnail(server, getZPosition(), getTPosition());
            if (imgThumbnail != null) {
                img = imgThumbnail;
                double downsample = (double) server.getWidth() / imgThumbnail.getWidth();
                xi = (int) (xx / downsample + .5);
                yi = (int) (yy / downsample + .5);
            }
        } else {
            xi = (int) ((xx - request.getX()) / request.getDownsample());
            yi = (int) ((yy - request.getY()) / request.getDownsample());
        }
        if (img != null) {
            // Make sure we are within range
            xi = Math.min(xi, img.getWidth() - 1);
            yi = Math.min(yi, img.getHeight() - 1);
            // Get the value, having applied any required color transforms
            if (imageDisplay != null)
                s = imageDisplay.getTransformedValueAsString(img, xi, yi);
        }
    }
    // Append z, t position if required
    String zString = null;
    if (server.nZSlices() > 1) {
        double zSpacing = server.getPixelCalibration().getZSpacingMicrons();
        if (!useCalibratedUnits || Double.isNaN(zSpacing))
            zString = "z = " + getZPosition();
        else
            zString = String.format("z = %.2f %s", getZPosition() * zSpacing, GeneralTools.micrometerSymbol());
    }
    String tString = null;
    if (server.nTimepoints() > 1) {
        // TODO: Consider use of TimeUnit
        // TimeUnit timeUnit = server.getTimeUnit();
        // if (!useMicrons || timeUnit == null)
        tString = "t = " + getTPosition();
    // else
    // tString = String.format("z = %.2f %s", getTPosition(), timeUnit.toString());
    }
    String dimensionString;
    if (tString == null && zString == null)
        dimensionString = "";
    else {
        dimensionString = "\n";
        if (zString != null) {
            dimensionString += zString;
            if (tString != null)
                dimensionString += ", " + tString;
        } else
            dimensionString += tString;
    }
    if (s != null)
        return String.format("%s%.2f, %.2f %s\n%s%s", prefix, xDisplay, yDisplay, units, s, dimensionString);
    else
        return String.format("%s%.2f, %.2f %s%s", prefix, xDisplay, yDisplay, units, dimensionString);
// if (s != null)
// return String.format("<html><center>%.2f, %.2f %s<br>%s", xDisplay, yDisplay, units, s);
// else
// return String.format("<html><center>%.2f, %.2f %s", xDisplay, yDisplay, units);
}

Example 4 with PixelCalibration

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

the class DoGSuperpixelsPlugin method getPreferredPixelSizeMicrons.

@Override
protected double getPreferredPixelSizeMicrons(final ImageData<BufferedImage> imageData, final ParameterList params) {
    double pixelSize = params.getDoubleParameterValue("downsampleFactor");
    PixelCalibration cal = imageData.getServer().getPixelCalibration();
    if (imageData != null && cal.hasPixelSizeMicrons())
        pixelSize *= cal.getAveragedPixelSizeMicrons();
    return pixelSize;
}

Example 5 with PixelCalibration

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

the class IJTools method calibrateImagePlus.

/**
 * Set an ImagePlus's Calibration and FileInfo properties based on a RegionRequest and PathImageServer.
 * It is assumed at the image contained in the ImagePlus has been correctly read from the server.
 *
 * @param imp
 * @param request
 * @param server
 */
public static void calibrateImagePlus(final ImagePlus imp, final RegionRequest request, final ImageServer<BufferedImage> server) {
    // Set the file info & calibration appropriately
    // TODO: Check if this is correct!  And consider storing more info regarding actual server...
    Calibration cal = new Calibration();
    double downsampleFactor = request.getDownsample();
    PixelCalibration pixelCalibration = server.getPixelCalibration();
    double pixelWidth = pixelCalibration.getPixelWidthMicrons();
    double pixelHeight = pixelCalibration.getPixelHeightMicrons();
    if (!Double.isNaN(pixelWidth + pixelHeight)) {
        cal.pixelWidth = pixelWidth * downsampleFactor;
        cal.pixelHeight = pixelHeight * downsampleFactor;
        cal.pixelDepth = pixelCalibration.getZSpacingMicrons();
        if (server.nTimepoints() > 1) {
            cal.frameInterval = server.getMetadata().getTimepoint(1);
            if (server.getMetadata().getTimeUnit() != null)
                cal.setTimeUnit(server.getMetadata().getTimeUnit().toString());
        }
        cal.setUnit("um");
    }
    // Set the origin
    cal.xOrigin = -request.getX() / downsampleFactor;
    cal.yOrigin = -request.getY() / downsampleFactor;
    // Need to set calibration afterwards, as it will be copied
    imp.setCalibration(cal);
    FileInfo fi = imp.getFileInfo();
    File file = new File(server.getPath());
    fi.directory = file.getParent() + File.separator;
    fi.fileName = file.getName();
    String path = server.getPath();
    if (path != null && path.toLowerCase().startsWith("http"))
        fi.url = path;
    imp.setFileInfo(fi);
    imp.setProperty("Info", "location=" + server.getPath());
}