Bug: CZI Reader fails with invalid T index

[rleigh]

Using /ome/data_repo/from_skyking/zeiss-czi/stephane/AO5.czi
Exception seen with dev_4_4, dev_5_0 and develop.

% LOCI_DEVEL=1 SCIFIO_DEVEL=1 CLASSPATH=./artifacts/loci_tools.jar ./tools/showinf ./AO5.czi
Checking file format [Zeiss CZI]
Initializing reader
ZeissCZIReader initializing ./AO5.czi
Unknown IlluminationType value 'Fluorescence' will be stored as "Other"
Unknown IlluminationType value 'Fluorescence' will be stored as "Other"
Unknown Immersion value 'Unknown' will be stored as "Other"
Unknown Immersion value 'Unknown' will be stored as "Other"
Exception in thread "main" java.lang.IllegalArgumentException: Invalid T index: 1/1
        at loci.formats.FormatTools.getIndex(FormatTools.java:383)
        at loci.formats.FormatTools.getIndex(FormatTools.java:328)
        at loci.formats.FormatReader.getIndex(FormatReader.java:1071)
        at loci.formats.in.ZeissCZIReader.assignPlaneIndices(ZeissCZIReader.java:1017)
        at loci.formats.in.ZeissCZIReader.initFile(ZeissCZIReader.java:612)
        at loci.formats.FormatReader.setId(FormatReader.java:1360)
        at loci.formats.ImageReader.setId(ImageReader.java:781)
        at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:576)
        at loci.formats.tools.ImageInfo.testRead(ImageInfo.java:993)
        at loci.formats.tools.ImageInfo.main(ImageInfo.java:1075)

[rleigh]

Using Zen Blue, it looks like the dimensionality is 1388x1040 (xy) with 1C (14bit) and 120T. However, the timepoints are split into two blocks of size 60, and it looks like the two blocks are discontinuous. Block 1 is from 0:0.0 to 0:5.852 (relative) and Block 2 is from 02:01.526 to 03:00.380. The acquition rate is about 1s with a 1 minute gap between the two blocks. Maybe we're not coping with this properly?

While the model can store this directly, it would be nice to be able to be able to partition into blocks as here to make the separation between the two sets clear. Modulo could work here, but only because the sets are of the same size; it wouldn't work well if they were of differing sizes, or of different acquisition rates with different units.

[mlinkert]

See also data_repo/from_*-Round_2/007+.czi (dimensions are incorrectly reported; one series is missing).

[mlinkert]

Fixed with ​https://github.com/openmicroscopy/bioformats/pull/1078; email forthcoming on ome-users/ome-devel with details of how to try this out prior to 5.0.2.

[rleigh]

A05.czi looks fine now, thanks.