[ome-users] CZIReader bug

[David Gault (Staff)]

Hi Nicholas,

Many thanks for spotting this bug and taking the time to investigate and suggest a fix.

I have opened a PR for this bug fix which you can follow at https://github.com/openmicroscopy/bioformats/pull/2884
Once tested and included in a Bio-Formats release we will add your name to the list of contributing developers for the project.

If any developers have similar bug fixes or improvements they are always welcome to open a PR on GitHub and submit their code changes directly.
Our contributing developers documentation has more information on how to get involved for those interested: http://www.openmicroscopy.org/site/support/contributing/index.html

With Thanks,
David Gault

> On 29 Jun 2017, at 15:48, Nick Trahearn <nick.trahearn at icr.ac.uk> wrote:
>
> 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.
>
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