[ome-users] Bio-formats - Bug when recycling TiffDelegateReader

[Stephane Dallongeville]

Hi Sebastien,

Thanks for taking the time to investigate the question !

 > Looking at the data, I think the issue is a related to the unwrapping 
of the ImageReader using thegetReader() API
 > while the two files are actually different formats from the 
Bio-Formats standpoint:
 >  - 3dtestbigger.tif is a TIFF file generated by ImageJ. As you 
mentioned, the ImageReader will delegate to
 >    the TiffDelegateReader and parse the image dimensions from the 
content of the ImageDescription tag (`slices=40`)
 >  - rotated.tif is a TIFF file with an OME-XML string in its 
ImageDescription tag. An ImageReader will detect
 >    such a file as an OME-TIFF and read its dimensions using the OME 
metadata.
 >    The TiffReader will also read this file but detect it a regular 
multi-page TIFF and aggregate all the planes alongside the T dimension.
 > ....
 > All understood. As mentioned above, the code snippet above also 
includes the assumption that the initial format
 > reader can be used for all the files. I assume this might be a 
constraint in addition to the reader recycling.
 > Otherwise, it should be possible to recycle the generic ImageReader.

Ok, i totally understand, i though file where both generated by ImageJ 
so i used that example but in fact my code snippet was incomplete (to 
make it simpler), what we really do is we first check if we can re-use 
the reader by using this code in between file opening :

if (!reader.isThisType(path, false) && !reader.isThisType(path, true))
       reader = mainReader.getReader(path);

As you can see we first want to check without opening the file (again 
because it's faster) and i though it was the issue as the reader 
probably used the file extension to assume it can open it properly so i 
changed the code to

if (!reader.isThisType(path, true))
       reader = mainReader.getReader(path);

But the result is the same, the TiffDelegateReader return 'true' for 
reader.isThisType('rotated.tif', true).
Looking at the mainReader.getReader(path) implementation it uses the 
same method internally to determine which reader to return.
The only difference is that mainReader (ImageReader) is always scanning 
readers from its list instead of trying to recycle the last used one... 
that means that OME Tiff Reader probably appears before in the list than 
TiffDelegateReader ending to that difference.

Best,

-- 
Stephane Dallongeville
Unité d'Analyse d'Images Biologiques
CNRS UMR 3691
Institut Pasteur
25 rue du Dr. Roux
75724 Paris cedex 15 (FRANCE)

Tel: +33 (0)1 45 68 87 01
Fax: +33 (0)1 40 61 33 30

http://www.bioimageanalysis.org/