{"action":"created","issue":{"url":"https://api.github.com/repos/openmicroscopy/bioformats/issues/1969","labels_url":"https://api.github.com/repos/openmicroscopy/bioformats/issues/1969/labels{/name}","comments_url":"https://api.github.com/repos/openmicroscopy/bioformats/issues/1969/comments","events_url":"https://api.github.com/repos/openmicroscopy/bioformats/issues/1969/events","html_url":"https://github.com/openmicroscopy/bioformats/pull/1969","id":105728702,"number":1969,"title":"ScreenReader: the next generation","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":13,"created_at":"2015-09-10T04:14:17Z","updated_at":"2015-10-01T10:10:57Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/openmicroscopy/bioformats/pulls/1969","html_url":"https://github.com/openmicroscopy/bioformats/pull/1969","diff_url":"https://github.com/openmicroscopy/bioformats/pull/1969.diff","patch_url":"https://github.com/openmicroscopy/bioformats/pull/1969.patch"},"body":"Rewrite of ScreenReader to only accept a *.screen file, which describes how the plate/well/field-to-file mapping works.  ScreenReader will no longer attempt to guess the plate layout based upon the data file names, and so is now always included.\r\n\r\nExamples of what a ```.screen``` file should look like are in /ome/team/mlinkert/idr_screen_files; happy to make other more generally useful examples and docs once we know that those actually work as desired.\r\n\r\nI have not yet tested this in OMERO, so there may yet be one or two small issues (possibly related to memoization).\r\n\r\nSee https://trello.com/c/vpc8NKAC/286-metamorph-stk-per-channel, https://trello.com/c/3D964ahX/299-plate-grouping-of-zeiss-axiovision-zvi-files."},"comment":{"url":"https://api.github.com/repos/openmicroscopy/bioformats/issues/comments/144686302","html_url":"https://github.com/openmicroscopy/bioformats/pull/1969#issuecomment-144686302","issue_url":"https://api.github.com/repos/openmicroscopy/bioformats/issues/1969","id":144686302,"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":"2015-10-01T10:10:56Z","updated_at":"2015-10-01T10:10:56Z","body":"Aroo?\r\n```\r\n2015-10-01 10:08:06,054 1216041    [      main] ERROR     ome.formats.importer.cli.ErrorHandler - FILE_EXCEPTION: /idr/versions/demo/metadata/idr0015-UNKNOWN-taraoceans/screenA/patterns/TARA_HCS1_H5_G100001988_G100001989--2013_09_23_19_42_50_chamber--U00--V01.screen\r\njava.lang.ArrayIndexOutOfBoundsException: 5\r\n        at loci.formats.in.DeltavisionReader.initExtraMetadata(DeltavisionReader.java:768) ~[formats-gpl.jar:5.1.3-SNAPSHOT]\r\n        at loci.formats.in.DeltavisionReader.initFile(DeltavisionReader.java:280) ~[formats-gpl.jar:5.1.3-SNAPSHOT]\r\n        at loci.formats.FormatReader.setId(FormatReader.java:1426) ~[formats-api.jar:5.1.3-SNAPSHOT]\r\n        at loci.formats.ImageReader.setId(ImageReader.java:835) ~[formats-api.jar:5.1.3-SNAPSHOT]\r\n        at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:651) ~[formats-api.jar:5.1.3-SNAPSHOT]\r\n        at loci.formats.DimensionSwapper.setId(DimensionSwapper.java:293) ~[formats-bsd.jar:5.1.3-SNAPSHOT]\r\n        at loci.formats.FileStitcher$ExternalSeries.<init>(FileStitcher.java:1269) ~[formats-bsd.jar:5.1.3-SNAPSHOT]\r\n        at loci.formats.FileStitcher.initFile(FileStitcher.java:927) ~[formats-bsd.jar:5.1.3-SNAPSHOT]\r\n        at loci.formats.FileStitcher.setId(FileStitcher.java:878) ~[formats-bsd.jar:5.1.3-SNAPSHOT]\r\n        at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:651) ~[formats-api.jar:5.1.3-SNAPSHOT]\r\n        at loci.formats.DimensionSwapper.setId(DimensionSwapper.java:293) ~[formats-bsd.jar:5.1.3-SNAPSHOT]\r\n        at loci.formats.in.ScreenReader.initFile(ScreenReader.java:338) ~[formats-gpl.jar:5.1.3-SNAPSHOT]\r\n        at loci.formats.FormatReader.setId(FormatReader.java:1426) ~[formats-api.jar:5.1.3-SNAPSHOT]\r\n        at loci.formats.ImageReader.setId(ImageReader.java:835) ~[formats-api.jar:5.1.3-SNAPSHOT]\r\n        at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:651) ~[formats-api.jar:5.1.3-SNAPSHOT]\r\n        at loci.formats.ChannelFiller.setId(ChannelFiller.java:223) ~[formats-bsd.jar:5.1.3-SNAPSHOT]\r\n        at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:651) ~[formats-api.jar:5.1.3-SNAPSHOT]\r\n        at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:289) ~[formats-bsd.jar:5.1.3-SNAPSHOT]\r\n        at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:651) ~[formats-api.jar:5.1.3-SNAPSHOT]\r\n        at loci.formats.Memoizer.setId(Memoizer.java:650) ~[formats-bsd.jar:5.1.3-SNAPSHOT]\r\n        at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:651) ~[formats-api.jar:5.1.3-SNAPSHOT]\r\n        at ome.formats.importer.ImportCandidates.singleFile(ImportCandidates.java:414) [blitz.jar:na]\r\n        at ome.formats.importer.ImportCandidates.handleFile(ImportCandidates.java:570) [blitz.jar:na]\r\n        at ome.formats.importer.ImportCandidates.execute(ImportCandidates.java:371) [blitz.jar:na]\r\n        at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:229) [blitz.jar:na]\r\n        at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:180) [blitz.jar:na]\r\n```"}}