{"action":"created","issue":{"url":"https://api.github.com/repos/openmicroscopy/bioformats/issues/2151","labels_url":"https://api.github.com/repos/openmicroscopy/bioformats/issues/2151/labels{/name}","comments_url":"https://api.github.com/repos/openmicroscopy/bioformats/issues/2151/comments","events_url":"https://api.github.com/repos/openmicroscopy/bioformats/issues/2151/events","html_url":"https://github.com/openmicroscopy/bioformats/pull/2151","id":121057558,"number":2151,"title":"Updates for Metamorph plates with one file per channel","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/metadata","name":"metadata","color":"069856"}],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":5,"created_at":"2015-12-08T17:29:40Z","updated_at":"2015-12-09T22:27:07Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/openmicroscopy/bioformats/pulls/2151","html_url":"https://github.com/openmicroscopy/bioformats/pull/2151","diff_url":"https://github.com/openmicroscopy/bioformats/pull/2151.diff","patch_url":"https://github.com/openmicroscopy/bioformats/pull/2151.patch"},"body":"See https://trello.com/c/vpc8NKAC/163-idr-metamorph-stk-per-channel.\r\n\r\nThe Metamorph changes use stage labels starting with ```Scan ``` to detect when a whole plate is saved in a single .stk file.  That doesn't allow for Z stacks/time series as well as a plate being stored, but I imagine we could extend it if/when we have an example.\r\n\r\nThe AxisGuesser changes allow a pattern block such as ```<53bp1,dapi>``` to be automatically detected as 2 channels, instead of 2 Z sections"},"comment":{"url":"https://api.github.com/repos/openmicroscopy/bioformats/issues/comments/163420014","html_url":"https://github.com/openmicroscopy/bioformats/pull/2151#issuecomment-163420014","issue_url":"https://api.github.com/repos/openmicroscopy/bioformats/issues/2151","id":163420014,"user":{"login":"joshmoore","id":88113,"avatar_url":"https://avatars.githubusercontent.com/u/88113?v=3","gravatar_id":"","url":"https://api.github.com/users/joshmoore","html_url":"https://github.com/joshmoore","followers_url":"https://api.github.com/users/joshmoore/followers","following_url":"https://api.github.com/users/joshmoore/following{/other_user}","gists_url":"https://api.github.com/users/joshmoore/gists{/gist_id}","starred_url":"https://api.github.com/users/joshmoore/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/joshmoore/subscriptions","organizations_url":"https://api.github.com/users/joshmoore/orgs","repos_url":"https://api.github.com/users/joshmoore/repos","events_url":"https://api.github.com/users/joshmoore/events{/privacy}","received_events_url":"https://api.github.com/users/joshmoore/received_events","type":"User","site_admin":false},"created_at":"2015-12-09T22:27:07Z","updated_at":"2015-12-09T22:27:07Z","body":"Old datasets are now again readable; currently re-trying the dna damage import. Currently much further along!\r\n\r\n```\r\n2015-12-09 21:13:48,744 6552       [      main] INFO   ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\r\n2015-12-09 21:13:48,856 6664       [      main] INFO   ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 5224482\r\n2015-12-09 21:14:14,504 32312      [l.Client-0] INFO   ormats.importer.cli.LoggingImportMonitor - METADATA_IMPORTED Step: 1 of 5  Logfile: 5224482\r\n```\r\n\r\nJust waiting on the likes of:\r\n\r\n```\r\n        at java.util.regex.Pattern$Start.match(Pattern.java:3408)\r\n        at java.util.regex.Matcher.search(Matcher.java:1199)\r\n        at java.util.regex.Matcher.find(Matcher.java:592)\r\n        at java.util.regex.Matcher.replaceAll(Matcher.java:907)\r\n        at java.lang.String.replaceAll(String.java:2162)\r\n        at loci.formats.tiff.IFD.getIFDTextValue(IFD.java:378)\r\n        at loci.formats.tiff.IFD.getComment(IFD.java:490)\r\n        at loci.formats.in.MetamorphReader.getComment(MetamorphReader.java:1450)\r\n        at loci.formats.in.MetamorphReader.getFirstComment(MetamorphReader.java:1439)\r\n        at loci.formats.in.MetamorphReader.initFile(MetamorphReader.java:809)\r\n        at loci.formats.FormatReader.setId(FormatReader.java:1426)\r\n        at loci.formats.ImageReader.setId(ImageReader.java:844)\r\n        at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:651)\r\n        at loci.formats.DimensionSwapper.setId(DimensionSwapper.java:293)\r\n        at loci.formats.FileStitcher.initReader(FileStitcher.java:1238)\r\n        at loci.formats.FileStitcher.getReader(FileStitcher.java:189)\r\n        at loci.formats.FileStitcher.isLittleEndian(FileStitcher.java:408)\r\n        at loci.formats.in.FilePatternReader.isLittleEndian(FilePatternReader.java:196)\r\n        at loci.formats.ImageReader.isLittleEndian(ImageReader.java:402)\r\n        at loci.formats.ReaderWrapper.isLittleEndian(ReaderWrapper.java:298)\r\n        at loci.formats.ReaderWrapper.isLittleEndian(ReaderWrapper.java:298)\r\n        at loci.formats.ReaderWrapper.isLittleEndian(ReaderWrapper.java:298)\r\n        at loci.formats.ReaderWrapper.isLittleEndian(ReaderWrapper.java:298)\r\n        at loci.formats.MinMaxCalculator.updateMinMax(MinMaxCalculator.java:321)\r\n        at ome.formats.importer.OMEROWrapper.updateMinMax(OMEROWrapper.java:247)\r\n```\r\n\r\nIt might be that more sub-Memoization is needed."}}