source: trunk/loci/formats @ 4092

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Diff Rev Age Author Log Message
(edit) @4092   12 years curtis Clean up TIFF-based isThisType implementations: * Fixes miscellaneous …
(edit) @4090   12 years curtis Close only the active reader or writer, rather than all readers and …
(edit) @4089   12 years curtis Rewritten OME-TIFF reader: * Works with the latest OME-TIFF …
(edit) @4086   12 years melissa Improved OME-XML population for InCell 1000.
(edit) @4085   12 years curtis Enable Correction and Immersion for 2008-02 schema.
(edit) @4084   12 years curtis Enable Correction and Immersion for 2008-02 schema.
(edit) @4083   12 years melissa Use JPEG2000Codec instead of manually calling the JAI library. Somehow …
(edit) @4079   12 years curtis Make metadata converter only call property setters for non-null …
(edit) @4076   12 years melissa * Removed a bunch of duplicate code from PictReader * Fixed OpenlabReader …
(edit) @4074   12 years melissa Fixed C size calculation bug - closes #300.
(edit) @4073   12 years melissa Preserve physical dimensions.
(edit) @4072   12 years melissa Place slice names in metadata hashtable.
(edit) @4071   12 years melissa Reverted pixel size scaling logic - it was correct in the first place.
(edit) @4070   12 years melissa Added ICS writer.
(edit) @4069   12 years melissa Fixed pixel size scaling bug.
(edit) @4068   12 years melissa Fixed NPEs.
(edit) @4067   12 years melissa Added timestamp parsing logic.
(edit) @4066   12 years curtis Add some "to do" notes.
(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) @4063   12 years curtis Better error message when plane number is out of bounds.
(edit) @4062   12 years curtis Fix line spacing.
(edit) @4061   12 years melissa Remainder of improvements to openBytes, so that full-size images are read …
(edit) @4060   12 years melissa Slightly improved plane access time.
(edit) @4059   12 years melissa Added reader for Aquacosmos files and switched FEIReader's license.
(edit) @4058   12 years melissa Initial version of ScreenPlateWell support. FlexReader is currently the …
(edit) @4057   12 years melissa Preliminary support for FEI format - closes ticket 279.
(edit) @4056   12 years melissa Fixed absolute path bug, and a couple problems with RGB files.
(edit) @4054   12 years melissa Fixed offset calculation.
(edit) @4052   12 years melissa Support for < 8 bit BMP images; minor LSM bug fix.
(edit) @4051   12 years curtis Update the license in a few more places.
(edit) @4050   12 years curtis Update license in OME metadata source code templates.
(edit) @4049   12 years curtis Update license document to GPL.
(edit) @4048   12 years curtis Licensing and packaging changes. * Change Bio-Formats and SLIM Plotter …
(edit) @4047   12 years curtis Add some implementation notes for tasks left to do in the OME-TIFF writer.
(edit) @4045   12 years curtis Remove standalone OutputFilter class in favor of anonymous inner class.
(edit) @4043   12 years melissa Improved init time for JP2K ND2 files - files that previously took 10+ …
(edit) @4042   12 years melissa Fixed bug when trying to read an OME-TIFF file in the same directory as a …
(edit) @4041   12 years melissa Fixed bug in parsing UUID filenames. UUIDs are still not fully supported, …
(edit) @4040   12 years melissa Make sure C is before Z and T in dimension order string if the stack is …
(edit) @4039   12 years melissa Some speed improvements.
(edit) @4037   12 years melissa Fixed lingering Zeiss LSM bugs, and a bug in RandomAccessStream's …
(edit) @4035   12 years melissa Fix for Zeiss LSM files with incorrect bits per sample and strip byte …
(edit) @4034   12 years melissa Corrected event count calculation.
(edit) @4033   12 years melissa Added logic to handle BGR images.
(edit) @4032   12 years melissa Fixed off-by-1 in DeltaT population; adjusted DeltaT values to start with …
(edit) @4031   12 years melissa * Removed some obsolete logic from LSM reader. * Improved …
(edit) @4030   12 years curtis Document preferred entity traversal order for property population.
(edit) @4029   12 years melissa Fixed bug in how double images are handled.
(edit) @4027   12 years melissa Bug fixes.
(edit) @4025   12 years melissa Fixed dimension order and swapped Z/T sizes.
(edit) @4024   12 years melissa Rewrote support for renamed/missing files - closes #295. There are still …
(edit) @4023   12 years curtis Fix some file stitching bugs, and remove some obsolete logic.
(edit) @4022   12 years curtis Fix setId bug introduced in r4018.
(edit) @4021   12 years curtis Tweak usage.
(edit) @4020   12 years curtis Remove unnecessary import.
(edit) @4019   12 years curtis Some cleanup to file stitcher. Still has problems.
(edit) @4018   12 years melissa Removed setId(String, boolean).
(edit) @4017   12 years curtis Clean up close methods.
(edit) @4015   12 years curtis Some improvements to the image viewer: * Display "no image plane" …
(edit) @4012   12 years curtis Fix ZVI bug on Windows caused by previous OIB fix.
(edit) @4008   12 years curtis Add certainty flag to main's test output.
(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) @4004   12 years curtis Fix bug that caused erroneous stitching by resetting the patternIds flag.
(edit) @4003   12 years melissa Fixed compile error.
(edit) @4002   12 years melissa Fixed timestamp parsing bug.
(edit) @4001   12 years melissa Speed improvements to channel splitting.
(edit) @4000   12 years curtis Speed up SDT reading.
(edit) @3999   12 years melissa Fixed ArrayIndexOutOfBounds exceptions and applied patch from John Hansen.
(edit) @3998   12 years melissa Added hack to correct for the fact that SVI writes ICS files upside-down.
(edit) @3997   12 years melissa Make sure the corresponding NetcdfFile gets closed.
(edit) @3996   12 years melissa Fixed image names, hopefully for the last time.
(edit) @3995   12 years melissa Don't assume that images are transparent.
(edit) @3994   12 years melissa Fixed bug where sizeC was set to 0.
(edit) @3993   12 years curtis Fix Windows file path bug.
(edit) @3988   12 years curtis Add TiffData entity and properties to MetadataStore.
(edit) @3987   12 years curtis Remove unnecessary variable.
(edit) @3986   12 years curtis Fix threading problem with POI formats.
(edit) @3983   12 years curtis Tweak documentation.
(edit) @3982   12 years curtis Fixed multi-schema OME-XML support, and added 2008-02 schema version.
(edit) @3981   12 years curtis Tweaks for 2008-02 schema version.
(edit) @3980   12 years curtis Fix node creation logic.
(edit) @3979   12 years melissa Fixed bug in metadata block detection logic.
(edit) @3978   12 years curtis Tweak some autogenerator output.
(edit) @3977   12 years curtis New autogenerator is done and produces compilable code! Time for testing.
(edit) @3976   12 years curtis Remove unnecessary reflection logic.
(edit) @3974   12 years melissa Removed calls to DataTools.sanitizeXML - for some reason, this breaks ND2.
(edit) @3973   12 years melissa Parse channel names.
(edit) @3972   12 years melissa Set physical X and Y sizes.
(edit) @3969   12 years melissa OMEWriter now uploads original metadata (if available). Also added a …
(edit) @3968   12 years melissa Fixed ArrayIndexOutOfBounds.
(edit) @3967   12 years melissa * Fixed NPE * FileStitcher now swaps dimensions if a Z (or T) axis is …
(edit) @3965   12 years melissa Moved image count correction logic for line scan images.
(edit) @3963   12 years melissa Cleaned up image name parsing.
(edit) @3961   12 years curtis Remove legacy case logic.
(edit) @3959   12 years curtis Progress on metadata store autogenerator. MetadataStore/MetadataRetrieve …
(edit) @3955   12 years curtis Fix some problems with Bio-Formats macro extensions, add a few missing …
(edit) @3954   12 years melissa Treat XZ and XT scans like regular XY images.
(edit) @3953   12 years melissa Adjust effective channel count if RGB planes were written.
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