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05/01/08:

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14:05 Ticket #156 (Investigate LOCI Java software development in Eclipse) closed by curtis
fixed: I added some Eclipse project files to the repository, so it is now …

04/29/08:

15:58 Ticket #290 (Util.openProcessor does not properly handle RGB data) created by curtis
We currently use ChannelSeparator to ensure that image planes are split …
15:51 Ticket #289 (Review and adjust ImageJ color-related options) created by curtis
The options available in the Bio-Formats Importer plugin for handling …
15:14 Ticket #288 (Animated GIF reader sometimes leaves "trails") created by curtis
Image frames do not always get cleared from the previous frame when they …
14:59 Ticket #287 (SimplePCI reader fails to parse dimensional parameters for some CXDs) created by curtis
Bio-Formats reports zero channels, which wreaks general havoc elsewhere. …
13:04 Changeset [3993] by curtis
Fix Windows file path bug.
12:54 Changeset [3992] by curtis
Fix jikes warnings, and ignore .class files.
12:03 Changeset [3991] by curtis
Utility for extracting raw values from SDT files.
11:38 Changeset [3990] by nor
Remove obsolete implementation.
11:32 Changeset [3989] by nor
Initial checkin of slim plotter curve fitting utilities, and associated …

04/28/08:

16:21 Changeset [3988] by curtis
Add TiffData entity and properties to MetadataStore.

04/25/08:

19:26 Ticket #286 (Investigate improving AVI support based on new AVI_Reader) created by curtis
Michael Schmid created an updated AVI_Reader for ImageJ that fixes a …
18:59 Changeset [3987] by curtis
Remove unnecessary variable.
18:59 Changeset [3986] by curtis
Fix threading problem with POI formats.
16:42 Changeset [3985] by curtis
Update OME uploader to work with new Dataset implementation.
16:07 Changeset [3984] by curtis
Update Dataset logic to harness Bio-Formats more effectively.
16:06 Changeset [3983] by curtis
Tweak documentation.
08:48 Ticket #282 (Slidebook image names are truncated) reopened by melissa

04/24/08:

22:29 Ticket #285 (LSM timestamps not reliably parsed) created by melissa
See zeiss-lsm/anuradha/test2.lsm, which has 75 timepoints.
16:42 Changeset [3982] by curtis
Fixed multi-schema OME-XML support, and added 2008-02 schema version.
16:42 Changeset [3981] by curtis
Tweaks for 2008-02 schema version.
16:41 Changeset [3980] by curtis
Fix node creation logic.
15:05 Changeset [3979] by melissa
Fixed bug in metadata block detection logic.
14:30 Changeset [3978] by curtis
Tweak some autogenerator output.
14:19 Changeset [3977] by curtis
New autogenerator is done and produces compilable code! Time for testing.
14:14 Changeset [3976] by curtis
Remove unnecessary reflection logic.
11:57 Changeset [3975] by allison
Revised saving options.
10:41 Changeset [3974] by melissa
Removed calls to DataTools.sanitizeXML - for some reason, this breaks ND2.
10:15 Ticket #282 (Slidebook image names are truncated) closed by melissa
fixed: r3973
10:15 Changeset [3973] by melissa
Parse channel names.
08:00 Changeset [3972] by melissa
Set physical X and Y sizes.

04/23/08:

11:09 Changeset [3971] by melissa
Commented out application of 16 bit LUTs, since ImageJ doesn't really …
10:19 Changeset [3970] by melissa
Cast to ReaderWrapper instead of ImageReader.
09:56 Ticket #261 (omeul should upload OME-XML metadata) closed by melissa
fixed: As of r3969, original metadata is uploaded.
09:55 Changeset [3969] by melissa
OMEWriter now uploads original metadata (if available). Also added a …
08:01 Changeset [3968] by melissa
Fixed ArrayIndexOutOfBounds.

04/22/08:

15:18 Changeset [3967] by melissa
* Fixed NPE * FileStitcher now swaps dimensions if a Z (or T) axis is …
12:35 Changeset [3966] by curtis
Must use Double rather than Integer.
12:05 Changeset [3965] by melissa
Moved image count correction logic for line scan images.
11:49 Changeset [3964] by allison
saveBytes method still does not work correctly.
10:44 Changeset [3963] by melissa
Cleaned up image name parsing.
10:38 Ticket #284 (ZVI reader ignores xy positions beyond the first) created by curtis
See data/zeiss-zvi/vladan/vladan.zvi for an example.

04/21/08:

20:32 Ticket #283 (OMERO download has strange CLASSPATH requirements) created by melissa
To successfully download from OMERO in ImageJ, one must have either …
10:34 Ticket #282 (Slidebook image names are truncated) created by melissa
See for instance slidebook/john/1.sld and slidebook/john/60x.sld. For …
07:56 Ticket #281 (Attempting to colorize single channel data throws an exception) closed by melissa
fixed: r3962
07:55 Changeset [3962] by melissa
Don't use CompositeImage to colorize single-channel stacks.

04/20/08:

19:40 Changeset [3961] by curtis
Remove legacy case logic.
14:17 Ticket #267 (Write ImageJ plugin to swap dimension labels) closed by melissa
fixed: r3960. Decided not to implement this as a separate plugin, since it's …
14:15 Changeset [3960] by melissa
Added option to swap dimension labels.

04/18/08:

18:00 Ticket #281 (Attempting to colorize single channel data throws an exception) created by curtis
For example, try the following macro command: […]
17:44 Changeset [3959] by curtis
Progress on metadata store autogenerator. MetadataStore/MetadataRetrieve …
17:42 Changeset [3958] by curtis
Initial version of direct 2003-FC schema hierarchy.
15:44 Changeset [3957] by curtis
Add missing getImageCount function.
15:22 Changeset [3956] by curtis
Align documentation text better.
15:14 Changeset [3955] by curtis
Fix some problems with Bio-Formats macro extensions, add a few missing …
14:55 Changeset [3954] by melissa
Treat XZ and XT scans like regular XY images.
14:45 Changeset [3953] by melissa
Adjust effective channel count if RGB planes were written.
13:46 Changeset [3952] by melissa
Updated plane width/height calculation based on new files.
12:59 Ticket #280 (Move ImageJ-specific logic out of OMEUtils) created by melissa
loci.formats.ome.OMEUtils contains a fair amount of code that is specific …
12:50 Changeset [3951] by melissa
Added utility methods for packing and swapping floats/doubles. Fixed how …
12:49 Changeset [3950] by melissa
Fixed ArrayIndexOutOfBounds; one more getUsedFiles fix.
12:47 Changeset [3949] by melissa
Fixed getUsedFiles to return all of the files in the dataset.
07:57 Ticket #279 (Add support for FEI SEM format) created by melissa
We have several files in the FEI SEM format (data/fei/, .img extension). …

04/17/08:

14:13 Ticket #278 (Move OME/OMERO plugins out of loci_tools.jar) created by melissa
To reduce complaints about the size of loci_tools.jar (currently > 16 MB), …
12:39 Changeset [3948] by melissa
When applying scaling factors, don't assume that the source image is …
10:16 Ticket #269 (OMEReader does not read all metadata) closed by melissa
fixed: Original metadata is retrieved as of r3947.
10:15 Changeset [3947] by melissa
OMEReader now extracts appropriate OriginalMetadata elements from the OME …
09:01 Changeset [3946] by allison
Login works now
07:34 Changeset [3945] by melissa
2008 Apr 17 release of LOCI Tools
07:34 Changeset [3944] by melissa
2008 Apr 17 release of LOCI Tools
07:34 Changeset [3943] by melissa
2008 Apr 17 release of LOCI Tools
07:34 Changeset [3942] by melissa
2008 Apr 17 release of LOCI Tools
07:34 Changeset [3941] by melissa
2008 Apr 17 release of LOCI Tools
07:34 Changeset [3940] by melissa
2008 Apr 17 release of LOCI Tools
07:34 Changeset [3939] by melissa
2008 Apr 17 release of LOCI Tools
07:34 Changeset [3938] by melissa
2008 Apr 17 release of LOCI Tools
07:30 Changeset [3937] by melissa
Added what's new for today's release.
07:29 Changeset [3936] by melissa
Fixed ArrayIndexOutOfBounds.

04/16/08:

21:48 Changeset [3935] by melissa
If an XML TIFF comment is found, do not place it in the metadata …
18:22 Changeset [3934] by curtis
Progress on metadata store autogenerator. Not ready yet.
17:37 Changeset [3933] by curtis
Temporarily comment out offending lines of metadata conversion logic.
17:37 Changeset [3932] by curtis
Fix NullPointerException.
17:34 Changeset [3931] by curtis
Allow construction of legacy OME-XML documents using OMEXMLFactory.
17:28 Changeset [3930] by melissa
Added bytesToDouble.
17:08 Changeset [3929] by melissa
Minor tweaks to timestamp parsing logic; place timestamps in OME-XML.
16:23 Ticket #277 (Bio-Formats drag and drop window) created by curtis
Wayne Rasband suggests: What I would like to see is a "Bio-Formats" …
15:37 Changeset [3928] by curtis
Code from Tom Caswell to parse timestamp for each image plane.
15:02 Changeset [3927] by melissa
Colorize channels by default.
14:48 Changeset [3926] by melissa
Moved CompositeImage coloring logic to the colorizer plugin; as a result, …
10:34 Changeset [3925] by melissa
Remainder of ND2 bug fixes.
08:49 Ticket #276 (Make ND2 reader faster) created by melissa
Initializing ND2 files is painfully slow, especially if the file is larger …

04/15/08:

16:39 Ticket #275 (Review importer options) created by curtis
It would be good to review all of the options in the Bio-Formats Importer …
16:25 Changeset [3924] by curtis
Fix from Wayne Rasband to use CompositeImage if available.
15:36 Changeset [3923] by melissa
Don't assume channels are interleaved when undifferencing.
12:10 Changeset [3922] by curtis
Fix dev-compile by adding an explicit list of source files that need Java …
09:47 Changeset [3921] by melissa
Fixed series splitting again.

04/14/08:

14:58 Changeset [3920] by melissa
More bug fixes.
12:24 Changeset [3919] by melissa
Fixed RGB/indexed values for single-image series.
08:35 Changeset [3918] by melissa
* Fixed PerkinElmer file ordering bug. * Fixed LSM image count calculation …
07:52 Ticket #274 (Add animate key to ImageViewer) created by melissa
Would be nice to have a keyboard shortcut to animate in an ImageViewer …

04/11/08:

15:56 Changeset [3917] by curtis
A bunch of work on the loci.formats.meta autogenerator. Not finished yet.
15:55 Changeset [3916] by curtis
Some minor tweaks to the TIFF writing code.
14:38 Changeset [3915] by melissa
* Fixed calculation of fake strip byte counts. * PrairieReader should …
10:38 Changeset [3914] by melissa
Removed special unpacking logic for PackBits-compressed planes. I have no …

04/10/08:

12:55 Changeset [3913] by allison
Added code to login. Login still does not connect correctly.
12:51 Changeset [3912] by melissa
Make sure that unpacked samples will fit in the output buffer.
12:42 Changeset [3911] by melissa
Fixed series-splitting bug - if all of the image planes were stored before …
12:05 Changeset [3910] by melissa
Eliminated EOFExceptions.
11:35 Changeset [3909] by melissa
Finally fixed the remaining plane size detection bugs.
08:54 Changeset [3908] by curtis
OMERO Writer branch using OMERO 3.0 beta 2.3 libraries. Necessary because …
08:54 Changeset [3907] by curtis
OMERO Writer branch using OMERO 3.0 beta 2.3 libraries. Necessary because …
07:52 Ticket #268 (OMEWriter does not save all metadata) closed by melissa
duplicate: duplicate of ticket #261

04/09/08:

14:21 Changeset [3906] by curtis
Fix jikes warnings.
14:19 Changeset [3905] by curtis
Remove unused import.
12:46 Changeset [3904] by melissa
Removed swapIfRequired - because of recent fixes to TiffTools, it's no …
09:28 Changeset [3903] by melissa
Fixed endian problem.

04/08/08:

16:08 Changeset [3902] by melissa
Tweaked series detection logic so that images with different numbers of …
15:38 Changeset [3901] by melissa
Added isThisType(RandomAccessStream) and updated other isThisType methods …
15:24 Changeset [3900] by melissa
Fixed a bunch of TIFF problems. Some stuff is still broken - namely 2, 4, …
15:22 Changeset [3899] by curtis
Use [] instead of test.
15:19 Changeset [3898] by curtis
Initial skeleton for LOCI Tools release procedure document. Not done yet.
15:04 Changeset [3897] by curtis
Remove "Install" tab until installer dialog is complete.
14:25 Changeset [3896] by curtis
Tweak readers list again. NRRD should be in the multi-extension format …
13:48 Changeset [3895] by curtis
Put NNRD reader before PIC reader, so NRRD reader has a chance to grab PIC …
13:48 Ticket #273 (Some readers do not have sane file type checking) created by curtis
Sane file type checking means that for a given dataset, each used file on …
13:24 Changeset [3894] by curtis
* Allow Bio-Rad reader to flag PIC files from NRRD datasets. * Detect …
11:26 Ticket #272 (Ability to explicitly disable file stitching for certain files) created by curtis
The test suite needs a way, probably in the .bioformats configuration …
09:08 Ticket #271 (Some MNG datasets have pixel type mismatch) closed by melissa
fixed: r3893
09:08 Ticket #270 (Thumbnail generation fails with some MNG files) closed by melissa
fixed: r3893
09:08 Changeset [3893] by melissa
Use multiple series to handle MNG stacks with varying pixel types.

04/07/08:

12:30 Changeset [3892] by curtis
Tweak documentation.
12:29 Changeset [3891] by curtis
* Set L2DReader grouping policy to MUST_GROUP. * Fix some documentation …
12:23 Changeset [3890] by curtis
Fix pass-through problem with testng.filename property.
12:10 Changeset [3889] by curtis
Fix NullPointerException in hypothetical code.
12:08 Changeset [3888] by curtis
Remove obsolete comments.
11:58 Ticket #271 (Some MNG datasets have pixel type mismatch) created by curtis
[…]
11:54 Changeset [3887] by curtis
Add ability to test single files with testng.filename property.
11:26 Changeset [3886] by melissa
Added support for square root scaling.
10:44 Changeset [3885] by melissa
Automatically select 'Split channels...' if 'Colorize channels' is …
10:38 Ticket #270 (Thumbnail generation fails with some MNG files) created by curtis
[…]
10:10 Ticket #269 (OMEReader does not read all metadata) created by melissa
OMEReader only retrieves core metadata. It should retrieve original …
10:09 Ticket #268 (OMEWriter does not save all metadata) created by melissa
Currently, only core metadata is saved. At a minimum, we want to save …

04/04/08:

17:15 Changeset [3884] by curtis
* First cut at detecting native JAI Image I/O Tools library (untested). …
14:20 Changeset [3883] by melissa
Fixed pixel offset calculation.
13:47 Changeset [3882] by curtis
Simple wget-style Java command line tool for downloading URLs.
08:24 Changeset [3881] by melissa
Fixed TIFF pixel size calculations.

04/03/08:

14:20 Changeset [3880] by melissa
Fixed endian bug and removed debugging statement.
13:54 Changeset [3879] by melissa
Fixed OOMEs when reading XML string.
12:44 Changeset [3878] by curtis
Fix annoying compile error (I can't have "\u" in a COMMENT? Seriously?).
11:49 Changeset [3877] by curtis
No need to setEnabled(true).
11:47 Changeset [3876] by curtis
* Use exception chaining when no ND2 plugin found. * Tweak PICT reader.

04/02/08:

21:44 Changeset [3875] by melissa
* Added setLegacy methods to ND2Reader and PictReader and updated …
14:16 Changeset [3874] by melissa
Swapped Z and T sizes.
14:12 Changeset [3873] by curtis
Eclipse project configuration files.
14:11 Changeset [3872] by curtis
Eliminate some unused variables.
14:06 Changeset [3871] by curtis
Restore usedFiles logic, but respect noStitch flag first.
13:50 Changeset [3870] by curtis
Fix Java 1.4 compile errors.
13:23 Changeset [3869] by melissa
Parse series names.
12:49 Changeset [3868] by curtis
Widen config window to better accommodate longest checkbox string.
12:37 Changeset [3867] by curtis
Remove obsolete intensity system property check.
12:36 Changeset [3866] by curtis
* Hook up format-specific checkboxes to reader logic. * Encapsulate …
12:16 Changeset [3865] by melissa
Fixed some endianness and pixel offset calculation problems.
11:46 Ticket #267 (Write ImageJ plugin to swap dimension labels) created by melissa
There is currently no efficient way of swapping dimension labels in ImageJ …
10:58 Changeset [3864] by curtis
Read formats and libraries info in a separate thread.

04/01/08:

16:32 Changeset [3863] by curtis
Check for out-of-bounds IFDs.
13:45 Changeset [3862] by curtis
Minor tweaks.
13:41 Changeset [3861] by curtis
* Add debug statements for Gatan DM3 tag parsing. * Fix bug with …
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