{"action":"created","issue":{"url":"https://api.github.com/repos/openmicroscopy/bioformats/issues/1687","labels_url":"https://api.github.com/repos/openmicroscopy/bioformats/issues/1687/labels{/name}","comments_url":"https://api.github.com/repos/openmicroscopy/bioformats/issues/1687/comments","events_url":"https://api.github.com/repos/openmicroscopy/bioformats/issues/1687/events","html_url":"https://github.com/openmicroscopy/bioformats/pull/1687","id":63858564,"number":1687,"title":"Fix disabled file grouping for Micro-Manager and OME-TIFF","user":{"login":"melissalinkert","id":109998,"avatar_url":"https://avatars.githubusercontent.com/u/109998?v=3","gravatar_id":"","url":"https://api.github.com/users/melissalinkert","html_url":"https://github.com/melissalinkert","followers_url":"https://api.github.com/users/melissalinkert/followers","following_url":"https://api.github.com/users/melissalinkert/following{/other_user}","gists_url":"https://api.github.com/users/melissalinkert/gists{/gist_id}","starred_url":"https://api.github.com/users/melissalinkert/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/melissalinkert/subscriptions","organizations_url":"https://api.github.com/users/melissalinkert/orgs","repos_url":"https://api.github.com/users/melissalinkert/repos","events_url":"https://api.github.com/users/melissalinkert/events{/privacy}","received_events_url":"https://api.github.com/users/melissalinkert/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/openmicroscopy/bioformats/labels/develop","name":"develop","color":"02e10c"}],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":5,"created_at":"2015-03-23T23:40:01Z","updated_at":"2015-03-26T16:48:05Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/openmicroscopy/bioformats/pulls/1687","html_url":"https://github.com/openmicroscopy/bioformats/pull/1687","diff_url":"https://github.com/openmicroscopy/bioformats/pull/1687.diff","patch_url":"https://github.com/openmicroscopy/bioformats/pull/1687.patch"},"body":"For both formats, if a TIFF file is chosen and file grouping is\r\ndisabled, then the file will be treated as a regular TIFF.\r\nSome metadata will be unavailable (as is expected when file grouping is\r\ndisabled), but the images will be more quickly accessible.\r\n\r\nSee http://lists.openmicroscopy.org.uk/pipermail/ome-users/2015-March/005124.html.\r\n\r\nI 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."},"comment":{"url":"https://api.github.com/repos/openmicroscopy/bioformats/issues/comments/86617824","html_url":"https://github.com/openmicroscopy/bioformats/pull/1687#issuecomment-86617824","issue_url":"https://api.github.com/repos/openmicroscopy/bioformats/issues/1687","id":86617824,"user":{"login":"rleigh-dundee","id":1528953,"avatar_url":"https://avatars.githubusercontent.com/u/1528953?v=3","gravatar_id":"","url":"https://api.github.com/users/rleigh-dundee","html_url":"https://github.com/rleigh-dundee","followers_url":"https://api.github.com/users/rleigh-dundee/followers","following_url":"https://api.github.com/users/rleigh-dundee/following{/other_user}","gists_url":"https://api.github.com/users/rleigh-dundee/gists{/gist_id}","starred_url":"https://api.github.com/users/rleigh-dundee/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/rleigh-dundee/subscriptions","organizations_url":"https://api.github.com/users/rleigh-dundee/orgs","repos_url":"https://api.github.com/users/rleigh-dundee/repos","events_url":"https://api.github.com/users/rleigh-dundee/events{/privacy}","received_events_url":"https://api.github.com/users/rleigh-dundee/received_events","type":"User","site_admin":false},"created_at":"2015-03-26T16:48:05Z","updated_at":"2015-03-26T16:48:05Z","body":"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?\r\n\r\n```\r\n./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 \r\nChecking file format [OME-TIFF]\r\nInitializing reader\r\nTiffDelegateReader initializing /ome/data_repo/from_skyking/ome-tiff/ruben/Test_Ruben_001/W0001/P002/Test_Ruben_001--W0001--P002--Z001--C01--T00003.ome.tif\r\nReading IFDs\r\nPopulating metadata\r\nChecking comment style\r\nPopulating OME metadata\r\nInitialization took 1.381s\r\n\r\nReading core metadata\r\nFilename = /ome/data_repo/from_skyking/ome-tiff/ruben/Test_Ruben_001/W0001/P002/Test_Ruben_001--W0001--P002--Z001--C01--T00003.ome.tif\r\nSeries count = 1\r\nSeries #0 :\r\n        Image count = 1\r\n        RGB = false (1) \r\n        Interleaved = false\r\n        Indexed = false (false color)\r\n        Width = 1344\r\n        Height = 1024\r\n        SizeZ = 1\r\n        SizeT = 1\r\n        SizeC = 1\r\n        Thumbnail size = 128 x 97\r\n        Endianness = intel (little)\r\n        Dimension order = XYCZT (certain)\r\n        Pixel type = uint16\r\n        Valid bits per pixel = 16\r\n        Metadata complete = true\r\n        Thumbnail series = false\r\n        -----\r\n        Plane #0 <=> Z 0, C 0, T 0\r\n\r\n\r\nReading global metadata\r\nBitsPerSample: 16\r\nCompression: LZW\r\nImageLength: 1024\r\nImageWidth: 1344\r\nMetaDataPhotometricInterpretation: Monochrome\r\nMetaMorph: no\r\nNumberOfChannels: 1\r\nPhotometricInterpretation: BlackIsZero\r\nPredictor: No prediction scheme\r\nResolutionUnit: None\r\nSamplesPerPixel: 1\r\nSoftware: LOCI Bio-Formats\r\nXResolution: 1\r\nYResolution: 1\r\n```\r\n\r\n```\r\n% ./tools/showinf -nogroup -nopix /ome/data_repo/from_skyking/micromanager/scott/MM_1.4/Pos1/img_000000000_491_000.tif                                \r\nChecking file format [Micro-Manager]\r\nInitializing reader\r\nTiffDelegateReader initializing /ome/data_repo/from_skyking/micromanager/scott/MM_1.4/Pos1/img_000000000_491_000.tif\r\nReading IFDs\r\nPopulating metadata\r\nChecking comment style\r\nPopulating OME metadata\r\nInitialization took 1.5s\r\n\r\nReading core metadata\r\nFilename = /ome/data_repo/from_skyking/micromanager/scott/MM_1.4/Pos1/img_000000000_491_000.tif\r\nSeries count = 1\r\nSeries #0 :\r\n        Image count = 1\r\n        RGB = false (1) \r\n        Interleaved = false\r\n        Indexed = false (false color)\r\n        Width = 512\r\n        Height = 512\r\n        SizeZ = 1\r\n        SizeT = 1\r\n        SizeC = 1\r\n        Thumbnail size = 128 x 128\r\n        Endianness = motorola (big)\r\n        Dimension order = XYCZT (certain)\r\n        Pixel type = uint16\r\n        Valid bits per pixel = 16\r\n        Metadata complete = true\r\n        Thumbnail series = false\r\n        -----\r\n        Plane #0 <=> Z 0, C 0, T 0\r\n\r\n\r\nReading global metadata\r\nBitsPerSample: 16\r\nCompression: Uncompressed\r\nImageJ: 1.44n\r\nImageLength: 512\r\nImageWidth: 512\r\nMetaDataPhotometricInterpretation: Monochrome\r\nMetaMorph: no\r\nNewSubfileType: 0\r\nNumberOfChannels: 1\r\nPhotometricInterpretation: BlackIsZero\r\nSamplesPerPixel: 1\r\nmax: 820.0\r\nmin: 554.0\r\n```"}}