{"push_id":661867860,"size":152,"distinct_size":2,"ref":"refs/heads/tables","head":"d1f9dcd71038f83119adb753e666d88df9cfe38e","before":"4d904352eaf97e56097f91f3961969d8e3976a1b","commits":[{"sha":"efb6801af709b841adb1ec4b604a781b1f23cc0e","author":{"email":"531f60ec930dbf1e884c7d868e0fb95608efaff8@wisc.edu","name":"Curtis Rueden"},"message":"Add SCIFIO format for OMERO-backed images\n\nThis is similar to Bio-Formats 4's OmeroReader (and OmeroWriter, which\nwas never finished), for storing and retrieving pixels and metadata to\nand from an OMERO database.\n\nIt is implemented as a SCIFIO format, making it compatible with ImageJ2.\nMore specifically, a SCIFIOCellImg can be used to wrap the SCIFIO-backed\ndata, providing the data as an ImgLib2 Img object, including cached\nread-write capabilities on the local machine.\n\nWith this format implementation, SCIFIO's ImgOpener class can be used to\n\"open\" (i.e., download on demand) an ImgLib2 ImgPlus directly from an\nOMERO server. The ImgPlus will be a SCIFIOImgPlus, which is backed by a\nSCIFIOCellImg, which is backed by an OMEROFormat.Reader, which is backed\nby an omero.client connection.\n\nThe ImgPlus can then be wrapped as an ImageJ2 Dataset, enabling ImageJ2\ncommands to operate upon it directly.\n\nWhen changes are made to the local ImgPlus's pixels, those changes\nhappen in memory, to the Img's \"cells\"; i.e., paged blocks. As new cells\nare requested which push memory consumption beyond desired limits, old\ndirty cells are cached out to disk. These cached cells, when present,\nare used in preference to data from the original source. In this way, it\nis possible to iterate over a massive remote dataset and apply image\nprocessing filters, with all changes recorded to the disk cache, as long\nas there is sufficient disk space.\n\nFinally, once processing is complete, SCIFIO's ImgSaver class can be\nused to \"save\" (i.e., upload) the ImgPlus back to OMERO as a new pixels\nobject.\n\nThis first implementation handles only the Reader side of the equation.\nThe Writer side will be needed to conveniently write ImgLib2 data back\nto OMERO using SCIFIO's ImgSaver.","distinct":false,"url":"https://api.github.com/repos/imagej/imagej-omero/commits/efb6801af709b841adb1ec4b604a781b1f23cc0e"},{"sha":"0545fde4f8ab58d045934d2b0457636455c13928","author":{"email":"531f60ec930dbf1e884c7d868e0fb95608efaff8@wisc.edu","name":"Curtis Rueden"},"message":"Add some omero-client POMs\n\nThese describe two different versions of omero_client.jar that I\ndownloaded on Aug 30 based on recommendations from the OMERO team:\n\nhttp://cvs.openmicroscopy.org.uk/snapshots/omero/4.4.8p1/OMERO.clients-4.4.8p1-ice33-b304.linux.zip\nhttp://hudson.openmicroscopy.org.uk/view/2.%20Stable/job/OMERO-stable-ice34/lastSuccessfulBuild/artifact/src/target/OMERO.java-4.4.8-452-cbe42bc-ice34-b326.zip\n\nOf course, the Jenkins build will change over time.\n\nFor now, I have made them available from our Maven repository at:\n\nhttp://maven.imagej.net/content/repositories/thirdparty/ome/omero-client/\n\nContributing to the project will become much easier once the\nOMERO project provides its components in a properly managed way.","distinct":false,"url":"https://api.github.com/repos/imagej/imagej-omero/commits/0545fde4f8ab58d045934d2b0457636455c13928"},{"sha":"961326b468d63f07e1aaf98c8cb20fd3100285fa","author":{"email":"531f60ec930dbf1e884c7d868e0fb95608efaff8@wisc.edu","name":"Curtis Rueden"},"message":"OMEROFormat: remove unused import","distinct":false,"url":"https://api.github.com/repos/imagej/imagej-omero/commits/961326b468d63f07e1aaf98c8cb20fd3100285fa"},{"sha":"8655b09a826e1316ad83e0338231a68865b218ed","author":{"email":"531f60ec930dbf1e884c7d868e0fb95608efaff8@wisc.edu","name":"Curtis Rueden"},"message":"OMEROFormat: use more direct tile extraction API","distinct":false,"url":"https://api.github.com/repos/imagej/imagej-omero/commits/8655b09a826e1316ad83e0338231a68865b218ed"},{"sha":"9cce8fd537314b9cf9f1bd494b64dd0683c15876","author":{"email":"531f60ec930dbf1e884c7d868e0fb95608efaff8@wisc.edu","name":"Curtis Rueden"},"message":"Add a helper class for managing OMERO sessions\n\nThis class encapsulates session-specific state, so that the\nOMEROFormat.Metadata does not have to do so.\n\nI.e., it is wrong for the Metadata to have sensitive transient state.\nRather, it is the job of the Parser to initialize a session based on the\ncredentials, then populate the metadata with format-specific information\nobtained from the session at parse time. Then the Metadata's\npopulateImagMetadata can translate that format-specific information into\nImageMetadata without needing access to the OMERO session.","distinct":false,"url":"https://api.github.com/repos/imagej/imagej-omero/commits/9cce8fd537314b9cf9f1bd494b64dd0683c15876"},{"sha":"0af9624dbdf692d3048e29ad048b7044069c8082","author":{"email":"531f60ec930dbf1e884c7d868e0fb95608efaff8@wisc.edu","name":"Curtis Rueden"},"message":"OMEROFormat: set default port to 4664","distinct":false,"url":"https://api.github.com/repos/imagej/imagej-omero/commits/0af9624dbdf692d3048e29ad048b7044069c8082"},{"sha":"290812863d57ff395e2412ab4fe0ed402a34e06f","author":{"email":"531f60ec930dbf1e884c7d868e0fb95608efaff8@wisc.edu","name":"Curtis Rueden"},"message":"OMEROFormat: add missing accessors","distinct":false,"url":"https://api.github.com/repos/imagej/imagej-omero/commits/290812863d57ff395e2412ab4fe0ed402a34e06f"},{"sha":"6c9a1ba5349d879b7e6bf888944307035d3685c4","author":{"email":"531f60ec930dbf1e884c7d868e0fb95608efaff8@wisc.edu","name":"Curtis Rueden"},"message":"OMEROFormat: add more format-specific fields\n\nThe idea is for these fields to be populated at parse time, so that the\nMetadata does not need to keep an OMERO session as internal state.","distinct":false,"url":"https://api.github.com/repos/imagej/imagej-omero/commits/6c9a1ba5349d879b7e6bf888944307035d3685c4"},{"sha":"82dba0c066b839fdebd8b9abf1d062fbbb613f6b","author":{"email":"531f60ec930dbf1e884c7d868e0fb95608efaff8@wisc.edu","name":"Curtis Rueden"},"message":"OMEROFormat: get metadata from OMERO while parsing\n\nThe previous implementation created an OMERO session and parsed the\nmetadata within the Metadata itself, which is a violation of SCIFIO\nprinciples. Now the metadata parsing actually happens during parsing,\nand the OMERO session is no longer stored in the Metadata itself.","distinct":false,"url":"https://api.github.com/repos/imagej/imagej-omero/commits/82dba0c066b839fdebd8b9abf1d062fbbb613f6b"},{"sha":"c395c6630424b1b3b486f69e41376787f34bd99c","author":{"email":"531f60ec930dbf1e884c7d868e0fb95608efaff8@wisc.edu","name":"Curtis Rueden"},"message":"OMEROSession: make pixels access higher level\n\nThere is now an openPixels() method which returns the raw pixels store\nto use for reading the pixels. This simplifies OMEROFormat's Reader.","distinct":false,"url":"https://api.github.com/repos/imagej/imagej-omero/commits/c395c6630424b1b3b486f69e41376787f34bd99c"},{"sha":"a57def61d464638284941234bd57ab4f81864450","author":{"email":"531f60ec930dbf1e884c7d868e0fb95608efaff8@wisc.edu","name":"Curtis Rueden"},"message":"OMEROSession: add createPixels method for writing\n\nThis method configures a raw pixels store for writing to the pixels\nof a newly created Image, and will be instrumental in implementing\nthe OMEROFormat's Writer.","distinct":false,"url":"https://api.github.com/repos/imagej/imagej-omero/commits/a57def61d464638284941234bd57ab4f81864450"},{"sha":"2a77864bf00b63f62d86785ccce460487ae11dcd","author":{"email":"531f60ec930dbf1e884c7d868e0fb95608efaff8@wisc.edu","name":"Curtis Rueden"},"message":"OMEROFormat: add first Writer implementation","distinct":false,"url":"https://api.github.com/repos/imagej/imagej-omero/commits/2a77864bf00b63f62d86785ccce460487ae11dcd"},{"sha":"e1945516d12b697d5799827ed23b8801e1a713ef","author":{"email":"531f60ec930dbf1e884c7d868e0fb95608efaff8@wisc.edu","name":"Curtis Rueden"},"message":"OMEROFormat: close Writer session when finished","distinct":false,"url":"https://api.github.com/repos/imagej/imagej-omero/commits/e1945516d12b697d5799827ed23b8801e1a713ef"},{"sha":"24af1ac6f17ef34e92f71a6a34d5fc23cb773857","author":{"email":"531f60ec930dbf1e884c7d868e0fb95608efaff8@wisc.edu","name":"Curtis Rueden"},"message":"OMEROFormat: add a couple of comments","distinct":false,"url":"https://api.github.com/repos/imagej/imagej-omero/commits/24af1ac6f17ef34e92f71a6a34d5fc23cb773857"},{"sha":"c208d281d8c1cd931fdd69b48f5ef48599f9d909","author":{"email":"531f60ec930dbf1e884c7d868e0fb95608efaff8@wisc.edu","name":"Curtis Rueden"},"message":"OMEROFormat: unify error handling a bit","distinct":false,"url":"https://api.github.com/repos/imagej/imagej-omero/commits/c208d281d8c1cd931fdd69b48f5ef48599f9d909"},{"sha":"ad82f0660bfdf7e5e7c50f0250233ba4f71f77d4","author":{"email":"531f60ec930dbf1e884c7d868e0fb95608efaff8@wisc.edu","name":"Curtis Rueden"},"message":"OMEROSession: remove erroneous @Plugin annotation","distinct":false,"url":"https://api.github.com/repos/imagej/imagej-omero/commits/ad82f0660bfdf7e5e7c50f0250233ba4f71f77d4"},{"sha":"b883b3a585386fabbc555b395391440500e9bc03","author":{"email":"531f60ec930dbf1e884c7d868e0fb95608efaff8@wisc.edu","name":"Curtis Rueden"},"message":"OMEROFormat: populate Metadata's pixelType field","distinct":false,"url":"https://api.github.com/repos/imagej/imagej-omero/commits/b883b3a585386fabbc555b395391440500e9bc03"},{"sha":"860cab0f60c24d1a8ad901e48188e92f58c3f2e9","author":{"email":"531f60ec930dbf1e884c7d868e0fb95608efaff8@wisc.edu","name":"Curtis Rueden"},"message":"Add POM for omero-client develop build","distinct":false,"url":"https://api.github.com/repos/imagej/imagej-omero/commits/860cab0f60c24d1a8ad901e48188e92f58c3f2e9"},{"sha":"1543bbd1deaa619f72fa32b251d61351378f8e78","author":{"email":"531f60ec930dbf1e884c7d868e0fb95608efaff8@wisc.edu","name":"Curtis Rueden"},"message":"Depend on snapshot build of OMERO develop branch\n\nThe server-side ImageJ support requires the develop branch of OMERO.\nSo it makes sense to depend on develop across the board here.\n\nThe API appears to be unchanged, so it may even be binary compatible\nwith 4.4.x still...","distinct":false,"url":"https://api.github.com/repos/imagej/imagej-omero/commits/1543bbd1deaa619f72fa32b251d61351378f8e78"},{"sha":"940b6524a59e7eabdc21bd4c48018b843317c1d2","author":{"email":"531f60ec930dbf1e884c7d868e0fb95608efaff8@wisc.edu","name":"Curtis Rueden"},"message":"Bump to next development cycle\n\nSigned-off-by: Curtis Rueden <ctrueden@wisc.edu>","distinct":false,"url":"https://api.github.com/repos/imagej/imagej-omero/commits/940b6524a59e7eabdc21bd4c48018b843317c1d2"}]}