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OME-TIFF: make sure BinaryOnly files reference a valid MetadataFile (rebased onto dev_5_1) #2220

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bramalingam
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This is the same as gh-2215 but rebased onto dev_5_1.


See https://trello.com/c/mVFYhwcJ/87-qa16988

To test, use the file from QA 16990. Without this change, showinf on the file should throw an exception as indicated in the QA and above card. With this change, showinf should display the image without an error, but note that it will be detected as plain TIFF and not OME-TIFF.

No configuration yet as QA 16990/16991 should be detected as a Micromanager dataset, but that will require a separate more involved PR to fix MicromanagerReader.

@bramalingam
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--rebased-from #2215

@bramalingam
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Tested locally : works as expected: @sbesson , @melissalinkert : looks good to merge?

ls29010:tools bramalingam$ ./showinf /Users/bramalingam/Desktop/QA/16990/20150121_HEK_48h_D1-Site_0.ome.tif 
Checking file format [Tagged Image File Format]
Initializing reader
TiffDelegateReader initializing /Users/bramalingam/Desktop/QA/16990/20150121_HEK_48h_D1-Site_0.ome.tif
Reading IFDs
Populating metadata
Checking comment style
Populating OME metadata
Initialization took 0.125s

Reading core metadata
filename = /Users/bramalingam/Desktop/QA/16990/20150121_HEK_48h_D1-Site_0.ome.tif
Series count = 1
Series #0 :
    Image count = 2
    RGB = false (1) 
    Interleaved = false
    Indexed = false (false color)
    Width = 2560
    Height = 2160
    SizeZ = 1
    SizeT = 2
    SizeC = 1
    Thumbnail size = 128 x 108
    Endianness = intel (little)
    Dimension order = XYCZT (uncertain)
    Pixel type = uint16
    Valid bits per pixel = 16
    Metadata complete = true
    Thumbnail series = false
    -----
    Plane #0 <=> Z 0, C 0, T 0
    Plane #1 <=> Z 0, C 0, T 1


Reading pixel data (0-1)
    Read 2/2 planes (100%)
[done]
0.653s elapsed (326.5ms per plane)

Launching image viewer

Reading global metadata
BitsPerSample: 16
Compression: Uncompressed
ImageLength: 2160
ImageWidth: 2560
MetaDataPhotometricInterpretation: Monochrome
MetaMorph: no
NumberOfChannels: 1
PhotometricInterpretation: BlackIsZero
ResolutionUnit: Centimeter
SamplesPerPixel: 1
XResolution: 63492
YResolution: 63492

Reading metadata

sbesson added a commit that referenced this pull request Feb 1, 2016
…pe-checking

OME-TIFF: make sure BinaryOnly files reference a valid MetadataFile (rebased onto dev_5_1)
@sbesson sbesson merged commit f43b625 into ome:dev_5_1 Feb 1, 2016
@sbesson sbesson added this to the 5.1.8 milestone Feb 15, 2016
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3 participants