Timeline


and

03/20/08:

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 …

03/19/08:

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.

03/17/08:

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 …

03/14/08:

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.

03/13/08:

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 …

03/12/08:

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.

03/11/08:

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.

03/10/08:

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).

03/09/08:

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 …

03/08/08:

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.

03/06/08:

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.

03/05/08:

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.

03/04/08:

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.

03/03/08:

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 …

02/29/08:

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.

02/28/08:

16:36 Changeset [3748] by curtis
Rewrite configuration manager class to use a tree structure.
16:20 Ticket #252 (Bio-Rad reader does not include data.raw files on its used files list) created by curtis
[…] For consistency, the data.raw companion file should always be …
15:21 Changeset [3747] by curtis
These readers should also not indiscriminately green-light TIFFs.
15:06 Changeset [3746] by curtis
Leica reader should not green-light TIFFs unless it knows they are Leica.
14:25 Changeset [3745] by curtis
More efficient isThisType(String) for ImageReader.
12:52 Ticket #250 (Bio-Rad reader throws StringIndexOutOfBoundsException with some XML ...) closed by melissa
fixed: r3744
12:52 Ticket #251 (Bio-Rad reader sometimes looks for an incorrectly named PIC file) closed by melissa
fixed: r3744
12:51 Changeset [3744] by melissa
Various fixes to BioRad reader.
12:24 Changeset [3743] by curtis
Minor tweaks.

02/27/08:

18:58 Changeset [3742] by ansari
fixed double, float, long, short
17:40 Changeset [3741] by curtis
Fix used files list for PerkinElmer.
17:30 Changeset [3740] by curtis
Increase TestNG memory limit to avoid memory error during results …
17:27 Ticket #251 (Bio-Rad reader sometimes looks for an incorrectly named PIC file) created by curtis
When opening a Bio-Rad PIC file via its companion lse.xml or data.raw …
17:25 Ticket #250 (Bio-Rad reader throws StringIndexOutOfBoundsException with some XML ...) created by curtis
BioRadReader currently uses error-prone string parsing to extract …
17:08 Changeset [3739] by curtis
Allow TIFF reader to redundantly green-light files, since many specific …
16:47 Changeset [3738] by curtis
Remove debugging output.
16:44 Changeset [3737] by curtis
* ImageReader.isThisType(String) no longer needs to default to open=false. …
15:45 Changeset [3736] by curtis
Add a test to exercise isThisType more thoroughly.
15:19 Changeset [3735] by curtis
Do not call super.isThisType unless absolutely necessary.
14:58 Changeset [3734] by melissa
Fixed isThisType problem.
14:50 Changeset [3733] by curtis
BufferedReader does not work; revert to previous revision for now.
14:50 Changeset [3732] by melissa
Miscellaneous bug fixes.
14:46 Changeset [3731] by curtis
Use reader instead of input stream for readLine calls.

02/26/08:

19:21 Changeset [3730] by curtis
Copy resources into classes directory up front, rather than within jar …
13:51 Changeset [3729] by curtis
Skip inapplicable tests rather than trivially passing.

02/25/08:

10:58 Changeset [3728] by melissa
Make sure the MetadataStore is updated to reflect the chosen stack order.
10:23 Changeset [3727] by melissa
* Slight improvements to some isThisType implementations. * Added reader …

02/21/08:

16:27 Changeset [3726] by curtis
Add more tests and fix some bugs.
14:56 Changeset [3725] by curtis
Lots of cleanup and tweaks to JVMLink.
13:17 Changeset [3724] by melissa
Fixed RGB channel swapping.
13:02 Changeset [3723] by melissa
Strip offsets need to be treated as unsigned integers, to handle files …
11:10 Changeset [3722] by melissa
Fixed channel count check in testThumbnailImageDimensions.
10:16 Changeset [3721] by melissa
Populate image creation date in the MetadataStore.
08:50 Changeset [3720] by curtis
Add failure message for testByteArrayDimensions.
07:48 Ticket #249 (Sequential setId calls with BioRadReader do not fully reset state) closed by melissa
fixed: r3719
07:48 Ticket #247 (Sequential setId calls with SVSReader can throw an exception) closed by melissa
fixed: r3719
07:48 Changeset [3719] by melissa
Make sure that the state is fully reset when close() is called.
07:34 Ticket #248 (MetamorphTiffReader.isThisType throws NullPointerException on some files) closed by melissa
fixed: r3718
07:34 Changeset [3718] by melissa
isThisType now returns false if the first IFD's comment is null, instead …

02/20/08:

17:17 Changeset [3717] by curtis
Use factory instead of data provider to generate list of tests.
16:33 Ticket #249 (Sequential setId calls with BioRadReader do not fully reset state) created by curtis
The value of SizeZ differs when initializing a file with a fresh reader …
16:09 Ticket #248 (MetamorphTiffReader.isThisType throws NullPointerException on some files) created by curtis
[…]
15:38 Ticket #247 (Sequential setId calls with SVSReader can throw an exception) created by curtis
When calling setId iteratively on multiple SVS files, an …
13:56 Changeset [3716] by curtis
Fix class name.
13:53 Changeset [3715] by curtis
Progress on TestNG suite.
13:21 Ticket #243 (Thumbnail pixel values are incorrect) closed by melissa
fixed: r3714
13:21 Changeset [3714] by melissa
Fixed thumbnail generation problems.
09:44 Ticket #238 (Exception is thrown when multiple BioRad datasets are in the same ...) closed by melissa
fixed: r3713
09:44 Ticket #246 (Bio-Rad data.raw files are not recognized) closed by melissa
fixed: r3713
09:43 Changeset [3713] by melissa
Improved file grouping and type checking logic.
08:25 Ticket #245 (FV1000 reader dies when analyzing Bio-Rad ROIs) closed by melissa
fixed: r3712
08:16 Changeset [3712] by melissa
Better isThisType(byte[]) implementation; fixed bug with datasets whose …

02/19/08:

19:16 Ticket #244 (NullPointerException in GatanReader) closed by melissa
fixed: r3711
19:16 Changeset [3711] by melissa
Fixed NPE when instrument data is missing.
16:08 Changeset [3710] by curtis
Progress on testing framework.
15:34 Ticket #246 (Bio-Rad data.raw files are not recognized) created by curtis
Though they are returned as part of the used files list for Bio-Rad …
15:33 Ticket #245 (FV1000 reader dies when analyzing Bio-Rad ROIs) created by curtis
[…]
15:30 Ticket #244 (NullPointerException in GatanReader) created by curtis
[…] Other files in the folder have the same issue.
15:27 Changeset [3709] by melissa
Fixed BufferedImage -> byte array conversion for grayscale JPEG planes.
14:15 Changeset [3708] by melissa
More robust wavelength population.
13:52 Changeset [3707] by curtis
Use HTML for slightly nicer About dialog.
13:23 Changeset [3706] by melissa
Removed legacy ZVI reader.
13:18 Ticket #243 (Thumbnail pixel values are incorrect) created by melissa
For certain datasets (e.g. zeiss-zvi/cecilia/Day\ 1\ Naked\ NB\ positive\ …
12:51 Changeset [3705] by melissa
Moved common POI logic to utility class.
09:09 Ticket #242 (Turn off NetCDF debugging output) created by melissa
When reading Imaris HDF files, the message "WARN: Variable data has a …
09:03 Changeset [3704] by melissa
Cleaned up PrairieReader's isThisType.
08:50 Ticket #241 (More robust channel assignment) created by melissa
We naively assign channel 0 to red, channel 1 to green, channel 2 to blue, …
08:41 Ticket #240 (Update OMEROReader to work with 2.3 server) created by melissa
Currently, the OMERO reader (and corresponding ImageJ plugin) only works …
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