source: trunk/loci/formats/ome @ 4092

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Diff Rev Age Author Log Message
(edit) @4084   12 years curtis Enable Correction and Immersion for 2008-02 schema.
(edit) @4065   12 years curtis Update MetadataStore to handle SPW data model in ome.xml.r20xxxx.spw …
(edit) @4064   12 years curtis MetadataStore improvements paving the way for a better OME-TIFF reader: …
(edit) @4058   12 years melissa Initial version of ScreenPlateWell support. FlexReader is currently the …
(edit) @4048   12 years curtis Licensing and packaging changes. * Change Bio-Formats and SLIM Plotter …
(edit) @4006   12 years melissa Removed unnecessary import statements.
(edit) @4005   12 years melissa Moved ImageJ-specific stuff from OMEUtils to OMEPlugin. Also updated …
(edit) @4001   12 years melissa Speed improvements to channel splitting.
(edit) @3988   12 years curtis Add TiffData entity and properties to MetadataStore.
(edit) @3982   12 years curtis Fixed multi-schema OME-XML support, and added 2008-02 schema version.
(edit) @3969   12 years melissa OMEWriter now uploads original metadata (if available). Also added a …
(edit) @3947   12 years melissa OMEReader now extracts appropriate OriginalMetadata elements from the OME …
(edit) @3840   12 years curtis Fix some problems with OME-XML metadata store logic.
(edit) @3837   12 years melissa Test/import files in the same order as was specified on the command line.
(edit) @3831   12 years melissa omeul now uploads the original file(s).
(edit) @3818   12 years melissa * Removed duplicate logic from OMEWriter and added support for writing …
(edit) @3817   12 years melissa Fixed an NPE and removed obsolete pixel type hack.
(edit) @3816   12 years melissa Set creation date to current time if a creation date is not stored in the …
(edit) @3810   12 years curtis Remove obsolete channel min/max stuff, and fix some NPEs.
(edit) @3683   12 years curtis First cut at streamlining isThisType implementations.
(edit) @3624   12 years curtis * Move ImageProcessorSource to loci.plugins; use Util.openProcessor …
(edit) @3605   12 years curtis Initial version of metadata framework with working object references …
(edit) @3587   12 years melissa Make sure endianness is set correctly.
(edit) @3578   12 years curtis Initial version of autogenerated convertMetadata implementation.
(edit) @3576   12 years curtis Progress on OME-XML support. * Add entity counter methods. * Add …
(edit) @3569   12 years melissa * Progress on metadata population for ~10 formats. * Better …
(edit) @3567   12 years curtis * Lots of improvements and bugfixes to OME-XML MetadataTools methods. * …
(edit) @3565   12 years curtis Add entity retrieval methods that return Object for agnostic use with …
(edit) @3564   12 years curtis Whitespace.
(edit) @3555   12 years curtis Fix for omebf with indexed color images.
(edit) @3553   12 years curtis Fix problem with null Image element during OriginalMetadata population.
(edit) @3550   12 years curtis Create Image object through more "official" channels, so that CreationDate …
(edit) @3546   12 years curtis Turn off debugging flag.
(edit) @3541   12 years curtis * Fix bug in OriginalMetadata generation. * Assign unique ID to each …
(edit) @3524   12 years curtis Initial version of LOCI codebase with multi-version OME-XML support. This …
(edit) @3503   12 years melissa * Added image name filter. * OMEReader and OMEWriter now use …
(edit) @3495   12 years melissa Re-added search functionality to OME/OMERO downloader - allows searching …
(edit) @3487   12 years melissa Downloading from OMERO is now much faster. Also, ownership rules are now …
(edit) @3431   12 years melissa Updated all OME download logic to support downloading from OMERO.
(edit) @3430   12 years melissa Moving OMEUtils to loci.formats.ome.
(edit) @3429   12 years melissa Added reader to download images from an OMERO database.
(edit) @3326   12 years curtis No more need for omebf script.
(edit) @3200   13 years curtis Fix some problems with XML validation.
(edit) @3197   13 years melissa * Added isFalseColor() to IFormatReader API; updated ChannelFiller …
(edit) @3165   13 years curtis Update Javadocs.
(edit) @3130   13 years curtis Add -version command line flag.
(edit) @3108   13 years curtis 1. Cleaned up MetadataStore and MetadataRetrieve interface usage: * …
(edit) @3104   13 years curtis A bunch of miscellaneous bugfixes and tweaks: * Remove some faulty …
(edit) @3097   13 years curtis Whitespace.
(edit) @3074   13 years melissa Preserve user-specified file ordering.
(edit) @3023   13 years melissa Updated MetadataStore.setLogicalChannel to be more complete; updated …
(edit) @3018   13 years melissa Fixed NullPointerException.
(edit) @3015   13 years curtis Add source code links to the Javadoc for every class. I automated the …
(edit) @3013   13 years melissa Added OME-TIFF writer. Also added API for writing multi-series files, …
(edit) @3011   13 years curtis Apply workaround for the Apache Axis2 bug in more places.
(edit) @2977   13 years curtis Whitespace.
(edit) @2976   13 years curtis Whitespace.
(edit) @2957   13 years melissa Added setOriginalMetadataPopulated(boolean) and …
(edit) @2922   13 years melissa - Don't automatically populate OriginalMetadata nodes in …
(edit) @2867   13 years melissa Fixed how ImageTools.splitChannels(byte[], ...) handles multiple bytes per …
(edit) @2857   13 years curtis Fix up Bio-Formats logging to use a simple, common logging infrastructure.
(edit) @2838   13 years melissa Fixed serious bugs with uploading to/downloading from OME servers whose …
(edit) @2830   13 years melissa Speed up calls to setOriginalMetadata.
(edit) @2822   13 years melissa Save the first image's CustomAttributes when setOriginalMetadata is …
(edit) @2801   13 years curtis Style.
(edit) @2800   13 years curtis Whitespace.
(edit) @2791   13 years melissa Added main method to OMEWriter; updated omeul to use OMEWriter.
(edit) @2762   13 years melissa - Fixed used files list for NRRD files - Fixed multi-series issue with …
(edit) @2758   13 years melissa Fixed bug in custom semantic type definition.
(edit) @2740   13 years melissa Fixed possible NPE in OMEWriter; fixed OME upload plugin to respect …
(edit) @2712   13 years curtis Remove unnecessary deprecated method (old method was added since last …
(edit) @2693   13 years melissa Make better use of core metadata model.
(edit) @2687   13 years curtis * Switch IFormatWriter over to setId model * Switch SDTReader API …
(edit) @2682   13 years melissa * Converted OME uploader to use the IFormatWriter API; updated VisBio and …
(edit) @2673   13 years curtis Whitespace.
(edit) @2672   13 years curtis * Eliminate unnecessary exceptions from new method signatures * Update …
(edit) @2637   13 years melissa Place SemanticType node under SemanticTypeDefinitions.
(edit) @2631   13 years melissa Record values from the metadata hashtable in OME-XML using a custom ST …
(edit) @2601   13 years curtis Style fixes.
(edit) @2583   13 years melissa Deprecated all methods that take the 'id' parameter. The id should be st …
(edit) @2566   13 years melissa Fixed bug that caused an ArrayIndexOutOfBoundsException when populating …
(edit) @2557   13 years melissa Moved core metadata variables to loci.formats.CoreMetadata.
(edit) @2536   13 years melissa Removed calls to updateMinMax.
(edit) @2523   13 years curtis More work on support for multiple dimensions rasterized into C. * …
(edit) @2510   13 years curtis Eliminate needless warnings in setChannelGlobalMinMax.
(edit) @2457   13 years curtis Add status reporting to OME uploader. But uploader is broken right now.
(edit) @2455   13 years curtis Clean up comments, style and whitespace.
(edit) @2454   13 years curtis Add status update hooks to loci.formats.ome.Uploader logic.
(edit) @2445   13 years curtis Whitespace.
(edit) @2441   13 years curtis OMEUploader should work, though events still aren't worked out.
(edit) @2430   13 years curtis Move static FormatReader methods to new FormatTools class. The rationale …
(edit) @2422   13 years melissa Changed OMEXMLMetadataStore.setDimensions to populate PixelSizeX if it is …
(edit) @2418   13 years curtis Whitespace.
(edit) @2349   13 years curtis Update omebf script and move into ome subpackage.
(add) @2327   13 years curtis Rearrange Bio-Formats OME logic into loci.formats.ome package.
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