generate_mask_from_annotation.grovvy

import qupath.lib.images.servers.LabeledImageServer
import qupath.lib.objects.PathObjects
import qupath.lib.regions.RegionRequest
import qupath.lib.images.writers.ImageWriterTools
import java.awt.image.BufferedImage
import java.awt.Graphics2D

def imageData = getCurrentImageData()
def server = imageData.getServer()
def hierarchy = imageData.getHierarchy()

// Filter for tumor annotations
def tumorAnnotations = hierarchy.getAnnotationObjects().findAll {it.getPathClass() == getPathClass("Tumor")}

if (tumorAnnotations.isEmpty()) {
    print "No tumor annotations found. Please ensure you have a tumor annotation in your image."
    return
}

// Define output path
def outputPath = "C:\\Users\\rakti\\Downloads\\qupath\\tumor_mask.tif"

// Get the full image bounds
def bounds = RegionRequest.createInstance(server.getPath(), 1, 0, 0, server.getWidth(), server.getHeight())

// Create a blank binary image
def img = new BufferedImage(server.getWidth(), server.getHeight(), BufferedImage.TYPE_BYTE_GRAY)
def g2d = img.createGraphics()
g2d.setColor(java.awt.Color.WHITE)

// Draw each tumor annotation
tumorAnnotations.each { annotation ->
    def roi = annotation.getROI()
    def shape = roi.getShape()
    g2d.fill(shape)
}

g2d.dispose()

// Write the binary mask
ImageWriterTools.writeImage(img, outputPath)

print "Tumor mask saved to: " + outputPath