[ome-users] CZIReader bug

[Nick Trahearn]

Hi,

I'm not sure if this is the right place to report this, but I think I've identified a coding error in BioFormats which is preventing some blank series from being discarded. If this is the wrong place, then I apologise and I'd appreciate it if you can point me in the right direction.

For reference, the following is a version of the source code with the mistake:

https://github.com/openmicroscopy/bioformats/blob/develop/components/formats-gpl/src/loci/formats/in/ZeissCZIReader.java

Any line numbers I mention come from this version of the code.

On line 972 there's a loop where each series is checked to see if it is blank (meaning that no planes correspond to this series). If one is found then it is removed from the list of series. However, the index variable, r, is not updated after the removal. So when the loop starts its next iteration, and r is incremented, the following series gets skipped. If there are multiple blank series in a row then the ones that are skipped don't get removed.

This is simple to fix, simply add "r--;" on line 988.

All the best.
Nicholas Trahearn.

The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP.

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