openmicroscopy/bioformats — pull request #75 by rleigh-dundee (2012-05-28 18:27:06+00:00)
Title: Support for Zeiss AxioVision TIFF

Hi,

This pull request is for the merging of the Zeiss AxioVision TIFF format. This also includes refactoring of the Zeiss ZVI reader, due to the two formats being essentially the same. It's also anticipated that more code may be shared between the two in the future as the ROI support in the ZVI reader is enhanced to support all the features of the TIFF reader now the structures have been mostly deciphered. The common code is factored out of the ZVI reader into a new base class containing all the code shared by both readers. Due to the very finicky ordering requirements of the metadata population, this is split out into a number of "passes" which permit the setting of the metadata in the correct order, and for the common parts of this to be put into the base class. This should be possible to clean up further with additional refactoring of the ZVI code, which will relax the ordering requirements somewhat.

The TIFF Reader is at this point mostly functional. Initial testing with the newly-created zeiss-tiff test dataset suggests that some corner-cases exist which will need further investigation, such as the ROI attributes block having a different size to that declared for a very small number of images, and also some odd colour issues with 48-bit RGB images which are not seen in AxioVision (not yet clear if this is a bug or not). I'll get a better handle on this once I've done a full run of the testsuite and compared all the metadata with the ZVI equivalents. By and large, however, it's all working as expected.

I'm just running a final commit test of the zeiss-zvi images to make sure there are no regressions introduced since last week. This should be finished by tomorrow morning.

Thanks,
Roger