[ome-devel] OMERO API - Loading an Image

[Vanni Galli]

Dear Jean-Marie Burel,
I’m not sure if you remember, but several months ago you helped me in loading images from OMERO using the API (in Java).

You provided me with a class in order to get the images planes, called Gateway. In particular I am now using a function called getPlane, in order to get pixels data from an OMERO image:

public synchronized byte[] getPlane(long pixelsID, int z, int t, int c) throws Exception
{
    RawPixelsStorePrx service = entryEncrypted.createRawPixelsStore();
    try
    {
        service.setPixelsId(pixelsID, false);
        return service.getPlane(z, c, t);
    }
    catch (Throwable e)
    {
        new Exception("cannot retrieve the plane " + "(z=" + z + ", t=" + t + ", c=" + c + ") for pixelsID:  " + pixelsID, e);
    }
    finally
    {
        service.close();
    }

    return null;
}

What I’m trying to do now is to extract from the image also a time-dimension information (e.g.: the delta-t between the various frames of an image).

The OME schema (http://www.openmicroscopy.org/Schemas/OME/2011-06/ome.xsd) says that there is a Plane object that “holds microscope stage and image timing data for a given channel/z-section/timepoint”. How can I access this information from the API? 
The code you provided me is getting a byte[] array containing the pixels data, but no time information.

Accordingly to the OME schema, there should be also a TimeIncrement attribute (when time series have a global timing specification). How can I extract this information?

Thank you very much for your help!

Best Regards,
Vanni Galli


On Feb 07, 2011, at 01:19 PM, jburel <j.burel at dundee.ac.uk> wrote:


  You need to add 
  /**
   * Returns the XY-plane identified by the passed z-section, time-point 
   * and wavelength.
   * 
   * @param pixelsID The id of pixels containing the requested plane.
   * @param zThe selected z-section.
   * @param tThe selected time-point.
   * @param cThe selected wavelength.
  * @return See above.
  */
   synchronized byte[] getPlane(long pixelsID, int z, int t, int c)
   throws Exception
   {
    RawPixelsStorePrx service = entryEncrypted.createRawPixelsStore();
    try {
    service.setPixelsId(pixelsID, false);
    return service.getPlane(z, c, t);
    } catch (Throwable e) {
       new Exception("Cannot retrieve the plane " +
  "(z="+z+", t="+t+", c="+c+") for pixelsID:  "+pixelsID, e);
    }
    return null;
  }
  to the gateway


  Then you will be able to do
  gateway.getPlane(id, 0, 0, 0) for example




  jmarie


-- 
Scuola Universitaria Professionale della Svizzera Italiana
Dipartimento Tecnologie Innovative
Istituto Sistemi Informativi e Networking

Vanni Galli
Ricercatore

Galleria 2
CH - 6928 Manno

T +41 (0)58 666 65 62
vanni.galli at supsi.ch
www.supsi.ch/dti
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