source: trunk/loci/formats/in @ 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) @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) @4083   12 years melissa Use JPEG2000Codec instead of manually calling the JAI library. Somehow …
(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) @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) @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) @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) @4048   12 years curtis Licensing and packaging changes. * Change Bio-Formats and SLIM Plotter …
(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) @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) @4018   12 years melissa Removed setId(String, boolean).
(edit) @4003   12 years melissa Fixed compile error.
(edit) @4002   12 years melissa Fixed timestamp parsing bug.
(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) @3979   12 years melissa Fixed bug in metadata block detection logic.
(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) @3965   12 years melissa Moved image count correction logic for line scan images.
(edit) @3963   12 years melissa Cleaned up image name parsing.
(edit) @3954   12 years melissa Treat XZ and XT scans like regular XY images.
(edit) @3952   12 years melissa Updated plane width/height calculation based on new files.
(edit) @3950   12 years melissa Fixed ArrayIndexOutOfBounds; one more getUsedFiles fix.
(edit) @3949   12 years melissa Fixed getUsedFiles to return all of the files in the dataset.
(edit) @3948   12 years melissa When applying scaling factors, don't assume that the source image is …
(edit) @3936   12 years melissa Fixed ArrayIndexOutOfBounds.
(edit) @3935   12 years melissa If an XML TIFF comment is found, do not place it in the metadata …
(edit) @3929   12 years melissa Minor tweaks to timestamp parsing logic; place timestamps in OME-XML.
(edit) @3928   12 years curtis Code from Tom Caswell to parse timestamp for each image plane.
(edit) @3925   12 years melissa Remainder of ND2 bug fixes.
(edit) @3921   12 years melissa Fixed series splitting again.
(edit) @3920   12 years melissa More bug fixes.
(edit) @3919   12 years melissa Fixed RGB/indexed values for single-image series.
(edit) @3918   12 years melissa * Fixed PerkinElmer file ordering bug. * Fixed LSM image count calculation …
(edit) @3915   12 years melissa * Fixed calculation of fake strip byte counts. * PrairieReader should …
(edit) @3911   12 years melissa Fixed series-splitting bug - if all of the image planes were stored before …
(edit) @3909   12 years melissa Finally fixed the remaining plane size detection bugs.
(edit) @3906   12 years curtis Fix jikes warnings.
(edit) @3904   12 years melissa Removed swapIfRequired - because of recent fixes to TiffTools, it's no …
(edit) @3903   12 years melissa Fixed endian problem.
(edit) @3902   12 years melissa Tweaked series detection logic so that images with different numbers of …
(edit) @3901   12 years melissa Added isThisType(RandomAccessStream) and updated other isThisType methods …
(edit) @3900   12 years melissa Fixed a bunch of TIFF problems. Some stuff is still broken - namely 2, 4, …
(edit) @3893   12 years melissa Use multiple series to handle MNG stacks with varying pixel types.
(edit) @3891   12 years curtis * Set L2DReader grouping policy to MUST_GROUP. * Fix some documentation …
(edit) @3886   12 years melissa Added support for square root scaling.
(edit) @3883   12 years melissa Fixed pixel offset calculation.
(edit) @3881   12 years melissa Fixed TIFF pixel size calculations.
(edit) @3880   12 years melissa Fixed endian bug and removed debugging statement.
(edit) @3879   12 years melissa Fixed OOMEs when reading XML string.
(edit) @3876   12 years curtis * Use exception chaining when no ND2 plugin found. * Tweak PICT reader.
(edit) @3875   12 years melissa * Added setLegacy methods to ND2Reader and PictReader and updated …
(edit) @3874   12 years melissa Swapped Z and T sizes.
(edit) @3869   12 years melissa Parse series names.
(edit) @3867   12 years curtis Remove obsolete intensity system property check.
(edit) @3865   12 years melissa Fixed some endianness and pixel offset calculation problems.
(edit) @3863   12 years curtis Check for out-of-bounds IFDs.
(edit) @3862   12 years curtis Minor tweaks.
(edit) @3861   12 years curtis * Add debug statements for Gatan DM3 tag parsing. * Fix bug with …
(edit) @3854   12 years melissa * Eliminated remainder of string logic for parsing XML. * Added a few more …
(edit) @3849   12 years melissa Removed string logic for parsing XML.
(edit) @3848   12 years melissa Big-endian Slidebook files are now supported.
(edit) @3847   12 years melissa Changed comments/format name to reflect correct version (Imaris 3).
(edit) @3846   12 years melissa Preliminary support for checking UUIDs.
(edit) @3844   12 years melissa Fixed bug with certain multi-series files.
(edit) @3843   12 years melissa Yet another file mapping fix.
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