[ome-users] Bug in Deltavision file reader.

[Roger Leigh]

On 17/12/13 22:29, Ian Dobbie wrote:
> Hi Everyone,
>
> I have discovered a slight bug in the delatvision file reader. It is to
> do with reading data that is 64 bit complex. The reason this comes up is
> trying to read OMX .otf files.
>
> I believe the bug is in the code below. The code correctly identifies
> the image type as complex in the getPixelString call but then doesn't do
> anything with the information and just returns the a type FLOAT (which I
> assume is a 32 bit number) in the getPixelType call. The 64 bit complex
> data is actually a pair of floats for real and imaginary parts and I
> guess to read it properly you need to create an image twice as large, or
> more likely two images, one for real component and one for the imaginary
> part. I suspect that this might be complicated!

Dear Ian,

Thanks for the investigation here.  I think the underlying issue here is
that bioformats itself currently lacks support for complex pixel formats
internally, which will need to be addressed to allow the deltavision
reader to fully support complex deltavision images.  There may be ways
of working around the limitation in the interim though.  I have opened a
few tickets to track various aspects of this:

http://trac.openmicroscopy.org.uk/ome/ticket/11860
http://trac.openmicroscopy.org.uk/ome/ticket/11861
http://trac.openmicroscopy.org.uk/ome/ticket/11862

Would it be possible to upload some example deltavision images which are
using complex numbers (using
http://qa.openmicroscopy.org.uk/qa/upload/)?  Having some reference
images which we can use for further investigation and testing would be
very helpful.  Do you also have any images using the 16-bit complex type?


Many thanks,
Roger

--
Dr Roger Leigh -- Open Microscopy Environment
Wellcome Trust Centre for Gene Regulation and Expression,
College of Life Sciences, University of Dundee, Dow Street,
Dundee DD1 5EH Scotland UK   Tel: (01382) 386364

The University of Dundee is a registered Scottish Charity, No: SC015096