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Hi Casper,
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<div class="">thanks for contacting and providing the file allowing to reproduce the</div>
<div class="">bug which we can certainly reproduce using the versions mentioned</div>
<div class="">below.</div>
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<div class="">As you reported this bug via a GitHub issue [1] as well as this thread,</div>
<div class="">we can use the former to continue the technical discussion on the issue</div>
<div class="">and how best to resolve it.</div>
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<div class="">Best,</div>
<div class="">Sebastien</div>
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<div class="">[1] <a href="https://github.com/openmicroscopy/bioformats/issues/2955" class="">https://github.com/openmicroscopy/bioformats/issues/2955</a> </div>
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<div class="">On 5 Sep 2017, at 17:21, Wel C. van der <<a href="mailto:wel@Physics.LeidenUniv.nl" class="">wel@Physics.LeidenUniv.nl</a>> wrote:</div>
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<div class="">Dear bioformats developers,<br class="">
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I am maintaining a package that wraps a Python interface around Bioformats (part of PIMS, see
<a href="https://github.com/soft-matter/pims" class="">https://github.com/soft-matter/pims</a>). 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.<br class="">
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There are no issues using Bioformats 5.3.4.<br class="">
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Starting from Bioformats 5.4.0, the following exception is displayed when calling setId(): java.lang.IndexOutOfBoundsException: Index: 0, Size: 0<br class="">
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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.<br class="">
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A link to the file: <a href="https://github.com/soft-matter/pims/blob/master/pims/tests/data/bioformats/cluster.nd2" class="">
https://github.com/soft-matter/pims/blob/master/pims/tests/data/bioformats/cluster.nd2</a><br class="">
See here for the relevant issue at PIMS: <a href="https://github.com/soft-matte" class="">
https://github.com/soft-matte</a><br class="">
r/pims/pull/266<br class="">
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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!<br class="">
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Best regards,<br class="">
Casper van der Wel<br class="">
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