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import imagej
from pathlib import Path
from PIL import Image
import scyjava
import logging

# Enable debug logging for scyjava
logging.basicConfig(level=logging.DEBUG)

# Ensure JVM is started
scyjava.start_jvm()

# Attempt to import the Java class
try:
    Accesses = scyjava.jimport("net.imglib2.img.basictypeaccess.Accesses")
    print("Successfully imported Accesses class")
except Exception as e:
    print("Error importing Accesses class:", e)


def load_leica_image_to_imagej(imagej, image_path):
    # Load image into ImageJ
    imagej.ui().show(image_path)
    imagej.ui().waitForUI()
    imagej.ui().getWindow().pack()
    imagej.ui().getWindow().toFront()
    
def export_image_sequence(imagej, output_folder, image_name_prefix):
    # Iterate through all open images in ImageJ
    for idx, image_id in enumerate(imagej.ui().getImageIDs()):
        # Activate each image
        imagej.ui().getImagePlus().setID(image_id)
        imagej.ui().getImagePlus().setSlice(1)
        
        # Get image data
        image_title = imagej.ui().getImagePlus().getTitle()
        img = imagej.ui().getImagePlus().getProcessor().getBufferedImage()
        
        # Save as JPEG with specified naming convention
        output_filename = f"{image_name_prefix}_{idx+1:05d}.jpg"
        output_path = output_folder / output_filename
        img_rgb = Image.fromarray(img)
        img_rgb.save(output_path)
        print(f"Saved {output_filename}")

def main():
    # Initialize ImageJ
    ij = imagej.init('net.imagej:imagej-legacy:0.37.1')
    
    # Path to the Leica image file
    leica_image_path = '/Volumes/Elements/WO153_pep22_16p25_240607.lif'
    
    # Load Leica image into ImageJ
    load_leica_image_to_imagej(ij, leica_image_path)
    
    # Export images as JPEG sequence
    output_folder = Path('/Volumes/Elements/results')
    image_name_prefix = 'WO153_pep22_16p25_240607'
    export_image_sequence(ij, output_folder, image_name_prefix)

if __name__ == "__main__":
    main()