QuPath script to export annotation to GeoJSON using calibrated pixel sizes

QuPath-Export scaled annotations to GeoJSON.groovy

/**
 * Export QuPath annotations in GeoJSON using calibrated pixel sizes 
 * (rather than pixel units).
 *
 * Written for QuPath v0.3.2
 * 
 * @author Pete Bankhead
 */

// Define export directory (or null if we don't want to export, but just print the GeoJSON)
def basePath = buildFilePath(PROJECT_BASE_DIR, 'geojson')

// Get all annotations
def annotations = getAnnotationObjects()

// Optionally filter to keep only annotations with a specified class
// annotations = annotations.findAll(a -> a.getPathClass() == getPathClass('Tumor'))

// Get the pixel size
def server = getCurrentServer()
def cal = server.getPixelCalibration()

// Scale all the annotations by the pixel size
// Here, we don't check the units
def transform = java.awt.geom.AffineTransform.getScaleInstance(cal.pixelWidth, cal.pixelHeight)
def annotationsScaled = annotations.collect(a -> PathObjectTools.transformObject(a, transform, true))

// Convert to GeoJSON
def json = GsonTools.getInstance(true).toJson(annotationsScaled)

// Export to a file, or print if no path is specified
if (basePath) {
    mkdirs(basePath) // Ensure directory exists
    def name = GeneralTools.getNameWithoutExtension(getProjectEntry().getImageName()) + ".geojson"
    def file = new File(basePath, name)
    file.text = json
    println "${annotationsScaled.size()} annotation(s) export to ${file.getAbsolutePath()}"
} else
    println json