import java.io.*;
import loci.common.ByteArrayHandle;
import loci.common.Location;
import loci.common.services.DependencyException;
import loci.common.services.ServiceException;
import loci.common.services.ServiceFactory;
import loci.formats.*;
import loci.formats.meta.IMetadata;
import loci.formats.services.OMEXMLService;
import loci.formats.in.NDPIReader;
import loci.formats.gui.BufferedImageReader;
import java.awt.image.BufferedImage;

public class testfile {
  public static void main(String[] args) {
    try {
        String fn = "test3-DAPI 2 (387) .ndpi";

        // read in entire file
        System.out.println("Reading file from disk...");

        NDPIReader reader = new NDPIReader();
        reader.setFlattenedResolutions(true);
        reader.setId(fn);
        System.out.println("size reader: "+reader.getSizeX()+" x"
+reader.getSizeY()); // works
        try {
            BufferedImageReader bir = new BufferedImageReader(reader);
            BufferedImage bi = bir.openImage(0, 0, 0, 100, 100);   // IndexOutOfBoundsException !!!
            System.out.println("size image: " + bi.getWidth() + " x " +
bi.getHeight());
        } finally {
            reader.close();
        }

    }
    catch (Exception e)
      {
        System.err.println("Exception: " + e);
        e.printStackTrace();
      }
  }
}