[ome-users] ND2 issue

[Sebastien Besson (Staff)]

Hi Casper,

thanks for contacting and providing the file allowing to reproduce the
bug which we can certainly reproduce using the versions mentioned
below.

As you reported this bug via a GitHub issue [1] as well as this thread,
we can use the former to continue the technical discussion on the issue
and how best to resolve it.

Best,
Sebastien

[1] https://github.com/openmicroscopy/bioformats/issues/2955

On 5 Sep 2017, at 17:21, Wel C. van der <wel at Physics.LeidenUniv.nl<mailto:wel at Physics.LeidenUniv.nl>> wrote:

Dear bioformats developers,

I am maintaining a package that wraps a Python interface around Bioformats (part of PIMS, see https://github.com/soft-matter/pims). Some unittests continuously test the correct functioning of the wrapper (and indirectly also of Bioformats). For some time now, Bioformats is failing on a small multidimensional (X, Y, Z, C, T) ND2 file that we use for testing.

There are no issues using Bioformats 5.3.4.

Starting from Bioformats 5.4.0, the following exception is displayed when calling setId(): java.lang.IndexOutOfBoundsException: Index: 0, Size: 0

For the newest version (5.7.0) there is no exception at setId(), but getSizeZ() and getSizeT() both return 1 while the should return 10 and 3 respectively.

A link to the file: https://github.com/soft-matter/pims/blob/master/pims/tests/data/bioformats/cluster.nd2
See here for the relevant issue at PIMS: https://github.com/soft-matte
r/pims/pull/266

I hope you can reproduce this issue and that it can be solved in a future version of Bioformats. Thanks for the  work on this great project!

Best regards,
Casper van der Wel
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