Zeiss CZI: fix dimension calculations when expected planes are missing (rebased onto dev_5_0)

[melissalinkert]

This is the same as gh-1386 but rebased onto dev_5_0.

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This should fix http://trac.openmicroscopy.org.uk/ome/ticket/12556. The dimensions for the files in QA 9521 and 10301 should now match the expected dimensions listed in the ticket and QA issues. I would not expect this to cause any test failures.

/cc @emilroz

[melissalinkert]

--rebased-from #1386

[dominikl]

Checked with image from ticket 12556, looks fine:

Filename = /Users/dlindner/Desktop/c3_z11_t1.czi
Series count = 1
Series #0 :
    Image count = 33
    RGB = false (1) 
    Interleaved = false
    Indexed = true (false color, 16-bit LUT: 3 x 65536)
    Width = 512
    Height = 512
    SizeZ = 11
    SizeT = 1
    SizeC = 3

Unfortunately I couldn't figure out, what the expected result for the QA 10301 files should look like, handing over to someone else to review

[dominikl]

The showinf results for 141016_OP43adult_Worm3_DAPI_head.czi (QA 10301) match the results from the original PR's review, so I think, it's good to merge!
Just noticed that the last file mentioned in QA 10301, couldn't be read (but probably nothing to do with this PR):

Checking file format [Zeiss CZI]
Initializing reader
ZeissCZIReader initializing /Users/dlindner/Desktop/10301/FixDoubleIlluMax.czi
Unknown segment type: //dir = "/Volum
Exception in thread "main" java.lang.IndexOutOfBoundsException: Index: 0, Size: 0
    at java.util.ArrayList.rangeCheck(ArrayList.java:635)
    at java.util.ArrayList.get(ArrayList.java:411)
    at loci.formats.in.ZeissCZIReader.initFile(ZeissCZIReader.java:541)
    at loci.formats.FormatReader.setId(FormatReader.java:1317)
    at loci.formats.ImageReader.setId(ImageReader.java:753)
    at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:569)
    at loci.formats.tools.ImageInfo.testRead(ImageInfo.java:992)
    at loci.formats.tools.ImageInfo.main(ImageInfo.java:1074)

[emilroz]

It doesn't look like FixDoubleIlluMax.czi is a part of the original QA 10301. It is also very small (5 KB) so we should probably get rid of it. Unless someone knows what is that file good for.

[melissalinkert]

I can't remove FixDoubleIluMax.czi from /ome/apache_repo/10301, but it is removed from /ome/data_repo/from_skyking/zeiss-czi/10301 (which is what is being tested automatically).

[emilroz]

From QA post: FixDoubleIlluMax.czi is not a .czi, it's a Fiji Macro.