[ome-devel] in-memory reading

[Manuel Stritt]

Dear all,

I'm trying to use the in-memory reading method as documented here:

https://docs.openmicroscopy.org/bio-formats/5.6.0/developers/in-memory.html

in combination with a NDPI reader + BufferedImageReader:


        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(false);
        reader.setId(inId);
        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();
        }

NDPI testfile from here:
http://downloads.openmicroscopy.org/images/Hamamatsu-NDPI/manuel/test3-DAPI%202%20(387)%20.ndpi

the line bir.openImage throws an IndexOutOfBoundsException - without the
memory mapping it works.
Any hints what I'm doing wrong?

Thanks a lot for your help!

Regards,
Manuel

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