Fix disabled file grouping for Micro-Manager and OME-TIFF

[melissalinkert]

For both formats, if a TIFF file is chosen and file grouping is
disabled, then the file will be treated as a regular TIFF.
Some metadata will be unavailable (as is expected when file grouping is
disabled), but the images will be more quickly accessible.

See http://lists.openmicroscopy.org.uk/pipermail/ome-users/2015-March/005124.html.

I was testing with micromanager/scott/MM_1.4/Pos1 as it's the largest Micro-Manager dataset we have; showinf -nopix -nogroup on one of the TIFF files with this PR should be significantly faster with this PR, and result in only the chosen file being read.

[ghost]

Missing debug message?

[ghost]

The source changes looks OK, I'll test them shortly.

Does the corresponding change want making to the C++ OME-TIFF reader?

[melissalinkert]

Eventually, yes, but it doesn't necessarily need to happen before 5.1.0.

[ghost]

Looks fine for both micromanager and OME-TIFF. Should they be falling back to the regular TIFF reader? I see it using the micromanager/OME-TIFF reader with grouping disabled in both cases. I thought isThisType would be returning false here and it would fall back to TiffReader.

[melissalinkert]

Yes, it should be using the regular TIFF reader if grouping is disabled. Can you paste the exact command you're using?

[ghost]

It's using TiffDelegateReader underneath so maybe it's OK. I thought the "Checking file format [...]" would have changed as well though if isThisType was false?

./tools/showinf -nogroup -nopix /ome/data_repo/from_skyking/ome-tiff/ruben/Test_Ruben_001/W0001/P002/Test_Ruben_001--W0001--P002--Z001--C01--T00003.ome.tif 
Checking file format [OME-TIFF]
Initializing reader
TiffDelegateReader initializing /ome/data_repo/from_skyking/ome-tiff/ruben/Test_Ruben_001/W0001/P002/Test_Ruben_001--W0001--P002--Z001--C01--T00003.ome.tif
Reading IFDs
Populating metadata
Checking comment style
Populating OME metadata
Initialization took 1.381s

Reading core metadata
Filename = /ome/data_repo/from_skyking/ome-tiff/ruben/Test_Ruben_001/W0001/P002/Test_Ruben_001--W0001--P002--Z001--C01--T00003.ome.tif
Series count = 1
Series #0 :
        Image count = 1
        RGB = false (1) 
        Interleaved = false
        Indexed = false (false color)
        Width = 1344
        Height = 1024
        SizeZ = 1
        SizeT = 1
        SizeC = 1
        Thumbnail size = 128 x 97
        Endianness = intel (little)
        Dimension order = XYCZT (certain)
        Pixel type = uint16
        Valid bits per pixel = 16
        Metadata complete = true
        Thumbnail series = false
        -----
        Plane #0 <=> Z 0, C 0, T 0


Reading global metadata
BitsPerSample: 16
Compression: LZW
ImageLength: 1024
ImageWidth: 1344
MetaDataPhotometricInterpretation: Monochrome
MetaMorph: no
NumberOfChannels: 1
PhotometricInterpretation: BlackIsZero
Predictor: No prediction scheme
ResolutionUnit: None
SamplesPerPixel: 1
Software: LOCI Bio-Formats
XResolution: 1
YResolution: 1

% ./tools/showinf -nogroup -nopix /ome/data_repo/from_skyking/micromanager/scott/MM_1.4/Pos1/img_000000000_491_000.tif                                
Checking file format [Micro-Manager]
Initializing reader
TiffDelegateReader initializing /ome/data_repo/from_skyking/micromanager/scott/MM_1.4/Pos1/img_000000000_491_000.tif
Reading IFDs
Populating metadata
Checking comment style
Populating OME metadata
Initialization took 1.5s

Reading core metadata
Filename = /ome/data_repo/from_skyking/micromanager/scott/MM_1.4/Pos1/img_000000000_491_000.tif
Series count = 1
Series #0 :
        Image count = 1
        RGB = false (1) 
        Interleaved = false
        Indexed = false (false color)
        Width = 512
        Height = 512
        SizeZ = 1
        SizeT = 1
        SizeC = 1
        Thumbnail size = 128 x 128
        Endianness = motorola (big)
        Dimension order = XYCZT (certain)
        Pixel type = uint16
        Valid bits per pixel = 16
        Metadata complete = true
        Thumbnail series = false
        -----
        Plane #0 <=> Z 0, C 0, T 0


Reading global metadata
BitsPerSample: 16
Compression: Uncompressed
ImageJ: 1.44n
ImageLength: 512
ImageWidth: 512
MetaDataPhotometricInterpretation: Monochrome
MetaMorph: no
NewSubfileType: 0
NumberOfChannels: 1
PhotometricInterpretation: BlackIsZero
SamplesPerPixel: 1
max: 820.0
min: 554.0

[melissalinkert]

OK, that's expected then. The Checking file format line is printed before any of the arguments are applied; in this case, before setGroupFiles(false) is called. The important part is that only one file and plane are present in both cases.

[ghost]

@melissalinkert OK, in that case it's looking fine and good to merge.

[melissalinkert]

--no-rebase