00:51 Changeset [3860] by curtis
Move list of libraries into external configuration file.


19:16 Changeset [3859] by curtis
* Respect enabled status of each format when importing. * Really add …
18:58 Changeset [3858] by curtis
Save enabled status of each reader into IJ preferences.
18:33 Changeset [3857] by curtis
* Hook up Flex configuration with LuraWave license code logic. * Add …
15:39 Changeset [3856] by curtis
First cut at interface for individual formats' custom widgets.
13:45 Changeset [3855] by curtis
Fill in a few TODO blocks.
13:32 Ticket #138 (Document details of supported formats) closed by melissa
13:32 Changeset [3854] by melissa
* Eliminated remainder of string logic for parsing XML. * Added a few more …
13:29 Changeset [3853] by melissa
Make sure temporary RandomAccessStreams get closed.
09:33 Changeset [3852] by curtis
Move QTJava version detection into tools class.


21:54 Changeset [3851] by melissa
* Added utility methods to unpack short and long values into a byte array. …
16:18 Changeset [3850] by curtis
Initial version of Bio-Formats configuration dialog. Not finished yet.
11:13 Changeset [3849] by melissa
Removed string logic for parsing XML.


14:13 Changeset [3848] by melissa
Big-endian Slidebook files are now supported.


14:56 Changeset [3847] by melissa
Changed comments/format name to reflect correct version (Imaris 3).
14:36 Ticket #67 (Finish OME-TIFF and Bio-Formats section of FAQ web page) closed by curtis
fixed: Fleshed out FAQ and Manifesto pages.
11:56 Changeset [3846] by melissa
Preliminary support for checking UUIDs.
10:06 Changeset [3845] by melissa
Added warning comment to beginning of OME-XML block.


14:37 Ticket #208 (Add information about format versions to web site) closed by melissa
10:00 Changeset [3844] by melissa
Fixed bug with certain multi-series files.
07:34 Ticket #68 (Test all format readers with omebf) closed by melissa
fixed: As of r3843, all formats have been tested, and all but one are working - …
07:33 Ticket #266 (L2D datasets cannot be imported using omebf) created by melissa
When files are uploaded using omebf, the 'name' attribute is set to the …
07:29 Changeset [3843] by melissa
Yet another file mapping fix.


14:56 Changeset [3842] by melissa
Fixed a bunch of file mapping problems.
09:28 Ticket #242 (Turn off NetCDF debugging output) closed by melissa
fixed: r3841. Solution was to write a PrintStream implementation that filters …
09:27 Changeset [3841] by melissa
"WARN" messages are now filtered from Imaris HDF output.


17:00 Changeset [3840] by curtis
Fix some problems with OME-XML metadata store logic.
10:25 Changeset [3839] by melissa
Fixed close/reopen logic so that it no longer breaks with files …


15:20 Ticket #265 (Separate widget for each sub-C dimension) created by curtis
Right now the Data Browser provides a single C widget (either a checkbox …
15:18 Ticket #264 (Better ImageJ open/save integration) created by curtis
ImageJ's HandleExtraFileTypes logic currently calls Bio-Formats last, …
15:08 Ticket #173 (Standard way to "fail through" to another reader) closed by curtis
wontfix: We have moved away from using "multi-format" readers in favor of embedding …
14:56 Ticket #19 (File pattern detection sometimes depends on the file chosen as the basis) closed by curtis
fixed: Fixed in r3838. For now we just redetect the pattern from the first file …
14:54 Changeset [3838] by curtis
Hack to prevent file pattern detection from depending on choice of base …
14:11 Ticket #263 (Bio-Formats configuration dialog) created by curtis
The Bio-Formats-related plugins have many options with enough complexity …
14:02 Ticket #262 (Readd configurable caching support to Data Browser using Bio-Formats ...) created by curtis
The old version of the Data Browser had flexible caching support with an …
12:47 Changeset [3837] by melissa
Test/import files in the same order as was specified on the command line.
12:41 Changeset [3836] by melissa
Fixed a few file name mapping bugs.


17:59 Changeset [3835] by curtis
Fix up ReflectedUniverse javadoc.
15:42 Changeset [3834] by curtis
Add support for nulls.
15:09 Ticket #4 (Bio-Formats native solution) closed by curtis
fixed: Ansari and I have created a library called …
14:23 Changeset [3833] by curtis
* Fix problem with arrays larger than 64K. * More robust client-side …
14:16 Changeset [3832] by melissa
Recompiled with 1.4 (instead of 1.6).
13:40 Ticket #260 (omeul doesn't upload original file(s)) closed by melissa
fixed: r3831
13:36 Changeset [3831] by melissa
omeul now uploads the original file(s).
12:51 Changeset [3830] by curtis
Fix bugs with single booleans, and arrays of strings.
12:44 Changeset [3829] by melissa
More bugfixes.
10:57 Changeset [3828] by melissa
Don't fail if recorded pixel type is int16 and BufferedImage pixel type is …
10:56 Changeset [3827] by melissa
* Fixed "too many open files" bug. * Fixed problem with stitching files …


18:48 Changeset [3826] by curtis
* Run some tests only on the first few image planes, for speed. * …
18:44 Changeset [3825] by curtis
Fix bug with arrays of shorts.
17:37 Changeset [3824] by curtis
* Fix server shutdown race condition. * Turn off verbose debug output on …
16:59 Changeset [3823] by curtis
Arrays work now, including arrays of strings.
14:39 Changeset [3822] by curtis
Reenable Metadata button -- displays syntax highlighted XML tree for now.
13:28 Changeset [3821] by curtis
Fix up Notes a little.
13:15 Changeset [3820] by curtis
JTree cell renderer for displaying syntax highlighted XML.
07:33 Changeset [3819] by melissa
Fixed bug with scaling 8-bit indexed color images.


20:20 Changeset [3818] by melissa
* Removed duplicate logic from OMEWriter and added support for writing …
17:21 Changeset [3817] by melissa
Fixed an NPE and removed obsolete pixel type hack.
17:15 Changeset [3816] by melissa
Set creation date to current time if a creation date is not stored in the …
16:03 Changeset [3815] by curtis
Tweak LOCI plugins about dialog and copyright notice.
16:02 Changeset [3814] by curtis
Little tweaks.
14:44 Changeset [3813] by curtis
Default to 2007-06, not 2003 (FC), for OME-XML output.
14:34 Changeset [3812] by curtis
Fix typo.
14:33 Changeset [3811] by curtis
Fix jikes warning.
14:31 Changeset [3810] by curtis
Remove obsolete channel min/max stuff, and fix some NPEs.
11:28 Changeset [3809] by curtis
Don't convert to string before doing the metadata conversion.
09:21 Ticket #193 (Test omeul with OME 2.6.1) closed by melissa
fixed: Replacing with tickets #260, #261.
09:20 Ticket #261 (omeul should upload OME-XML metadata) created by melissa
Right now, omeul only uploads core pixels metadata. It should be …
09:02 Ticket #260 (omeul doesn't upload original file(s)) created by melissa
omeul should upload the original files to OMEIS and appropriately link …


16:01 Changeset [3808] by curtis
Add timestamps to test output.
15:53 Changeset [3807] by curtis
Subtract Unix epoch (even though it's pointless).
12:12 Changeset [3806] by melissa
Fixed bug with files that have an extra "garbage" plane.
09:59 Changeset [3805] by melissa
Improved initialization time.


17:18 Changeset [3804] by melissa
Minor bugfixes.
12:37 Changeset [3803] by melissa
Use absolute path to LEI file.
09:56 Changeset [3802] by melissa
Propagate lurawave.license property when running the test suite.


14:38 Changeset [3801] by melissa
Fixed several bugs exposed by the test suite.
10:09 Changeset [3800] by melissa
Added JBoss JAR (required for OMERO connectivity).


14:09 Changeset [3799] by melissa
Fixed compile error.
13:29 Ticket #240 (Update OMEROReader to work with 2.3 server) closed by melissa
fixed: r3797. Actually didn't need to change the OME plugin or OMEROReader at …
13:22 Changeset [3798] by melissa
Added debugging messages to OME plugin and updated OME plugin menu entry.
13:13 Changeset [3797] by melissa
Added spring.jar (required for OMERO 2.3 server connectivity) and updated …


23:22 Ticket #228 (Add support for writing BigTIFF files) closed by melissa
fixed: r3796. TiffWriter has new method called setBigTiff(boolean) that toggles …
23:19 Changeset [3796] by melissa
Added support for exporting to BigTIFF. You can test this from the …
11:01 Ticket #259 (Add support for JPEG2000-compressed SVS files) created by melissa
Many SVS files are compressed using JPEG2000, which we do not currently …
10:35 Changeset [3795] by melissa
Fixed NPE when trying to download from OME.


14:09 Changeset [3794] by melissa
FileStitcher's initFile now checks the value of fileGroupOption(id) - if …
11:42 Changeset [3793] by curtis
Fix threading issue with Data Browser.
11:33 Changeset [3792] by curtis
Speed up QuickTime initialization on Windows.
11:05 Changeset [3791] by curtis
Speed up checkEfficiency on Windows.
08:25 Changeset [3790] by melissa
Better isThisType implementations for TIFF-based readers.


20:29 Changeset [3789] by melissa
Fixed image count calculation.
17:02 Changeset [3788] by curtis
Update to final version of ImageJ v1.39.
16:51 Changeset [3787] by curtis
Uncomment array tests, and use new setVar signatures for arrays (but the …
16:45 Changeset [3786] by curtis
Up TestNG memory even more, to 1024 MB, which seems to work. (Actually, …
15:59 Changeset [3785] by curtis
Speed up IFD parsing for lists of unsigned bytes.
15:39 Changeset [3784] by curtis
Up TestNG memory to 512MB; tweak output.
15:28 Changeset [3783] by curtis
Remove debug statement.
15:13 Changeset [3782] by melissa
IPWReader now extends FormatReader, instead of BaseTiffReader.
15:10 Changeset [3781] by curtis
Add checkSuffix utility method that properly checks for compressed …
14:27 Ticket #258 (Move Zip detection logic to ZipReader) created by melissa
We need to add a new format reader (ZipReader) to handle Zip files. It …
14:27 Changeset [3780] by curtis
Fix compile error.
14:24 Changeset [3779] by curtis
Put legal compressed file suffixes into their own constant.
14:23 Ticket #257 (Improve RAUrl) created by melissa
RAUrl currently uses marks the entire input stream, to make random access …
14:18 Ticket #256 (Add new isThisType signature) created by melissa
Add "boolean isThisType(RandomAccessStream)" to IFormatReader API. …
14:01 Changeset [3778] by curtis
Faster zip file parsing.
12:52 Changeset [3777] by curtis
Print more timing results.
12:39 Changeset [3776] by curtis
Add timing tester for reading compressed image files with Bio-Formats.
11:01 Changeset [3775] by curtis
Fix some scanning bugs.
10:26 Changeset [3774] by curtis
Fix Leica TCS type detection.
10:01 Changeset [3773] by curtis
Do not use file existence tests or other file system operations when …
09:52 Changeset [3772] by curtis
Cleanup and TODO notes for TIFF-based isThisType(byte[]) implementations.
09:40 Changeset [3771] by curtis
Add comment with some results.
09:27 Changeset [3770] by curtis
Add simple utility for testing performance of file system operations.
09:01 Ticket #255 (ICS reader performs poorly with highly multichannel ICS datasets) closed by melissa
fixed: r3769. ICS files with SizeC > 4 now take 30-60 ms per plane, at the price …
08:54 Changeset [3769] by melissa
Improved plane access time.
07:07 Changeset [3768] by curtis
Update path to online sample data.


15:14 Changeset [3767] by curtis
Combine memory and access time tests into one test, for efficiency.
14:21 Changeset [3766] by ansari
added setVar array signatures
13:50 Ticket #255 (ICS reader performs poorly with highly multichannel ICS datasets) created by curtis
For datasets with SizeC > 4, ICSReader takes multiple seconds per plane to …
13:22 Changeset [3765] by curtis
Output timing results for initial file scan.
10:59 Changeset [3764] by curtis
Update TIFF reader documentation.
10:32 Changeset [3763] by melissa
Added Li-Cor L2D reader.


14:55 Ticket #254 (FV1000 reader doesn't support lookup tables) closed by melissa
fixed: r3762
14:55 Changeset [3762] by melissa
Added LUT support to FV1000Reader.
14:04 Ticket #253 (BioRad reader doesn't support lookup tables) closed by melissa
fixed: r3761
14:04 Changeset [3761] by melissa
Added LUT support and fixed SizeC calculation.
13:12 Ticket #229 (Support multi-series OME-TIFF export) closed by melissa
fixed: r3760
13:12 Changeset [3760] by melissa
Added support for writing multi-series OME-TIFF files.
12:57 Changeset [3759] by curtis
* Fix class loader problem with ImageJ versions prior to 1.38. * Add …


16:54 Changeset [3758] by curtis
Fix setVar(JVMLinkObject*) to work on non-array primitives, and change …
14:23 Changeset [3757] by melissa
Fixed plane height and offset calculations.
13:55 Changeset [3756] by curtis
Send strings prefixed by length, rather than terminated with newlines …
13:30 Changeset [3755] by curtis
Fix large longs; fix warnings.
12:58 Changeset [3754] by curtis
No need for this file in the repository.
12:57 Changeset [3753] by curtis
* Encapsulate endianness concerns. * Add a command to switch server's …
10:35 Ticket #254 (FV1000 reader doesn't support lookup tables) created by melissa
LUTs can be present in FV1000 OIB/OIF datasets - we should check if a LUT …
10:33 Ticket #253 (BioRad reader doesn't support lookup tables) created by melissa
Lookup tables can be present in BioRad files; we should detect when LUTs …
10:15 Ticket #252 (Bio-Rad reader does not include data.raw files on its used files list) closed by melissa
fixed: r3752
10:14 Changeset [3752] by melissa
data.raw file is now added to BioRad used file list.
10:12 Changeset [3751] by melissa
Cleaned up isThisType implementations - Location.list() is no longer …
09:44 Changeset [3750] by curtis
Fix SAX parsing exception caused by earlier hack/fix.
08:41 Changeset [3749] by curtis
Ignore comments in .bioformats files.
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