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

        // read in entire file
        System.out.println("Reading file into memory from disk...");
        File inputFile = new File(fn);
        int fileSize = (int) inputFile.length();
        DataInputStream in = new DataInputStream(new
FileInputStream(inputFile));
        byte[] inBytes = new byte[fileSize];
        in.readFully(inBytes);
        System.out.println(fileSize + " bytes read.");
        in.close();

        String fileName = inputFile.getName();
        int dot = fileName.lastIndexOf(".");
        String suffix = dot < 0 ? "" : fileName.substring(dot);

        // map input id string to input byte array
        final String inId = "inBytes" + suffix;
        Location.mapFile(inId, new ByteArrayHandle(inBytes));

        NDPIReader reader = new NDPIReader();
        reader.setFlattenedResolutions(true);
        reader.setId(inId);
        System.out.println("size reader: "+reader.getSizeX()+" x"
+reader.getSizeY()); // works
        byte[] bytes =  reader.openBytes(0, 0, 0, 100, 100);   // IndexOutOfBoundsException !!!
            reader.close();

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