Timeline


and

06/29/10:

16:18 Changeset [6603] by curtis
Cosmetic tweaks.
15:40 Changeset [6602] by melissa
Throw a nicer exception if LuraWaveServiceImpl is instantiated with …
15:07 Changeset [6601] by melissa
Added 'unknown' domain and updated various readers to use the unknown …
14:48 Changeset [6600] by melissa
Fixed and uncommented most of the AnnotationRef conversion logic (and a …
14:31 Changeset [6599] by curtis
Backport r6598 to 4.2 branch.
14:30 Ticket #495 (Lookup tables are not correctly applied if there is one LUT per channel) closed by curtis
fixed: (In [6598]) Preserve channel-specific LUTs. Fixes #495 (again).
14:30 Changeset [6598] by curtis
Preserve channel-specific LUTs. Fixes #495 (again).
12:29 Changeset [6597] by melissa
Better XZ/XT scan detection; see  omero:2321.
11:38 Changeset [6596] by curtis
Backport r6595 to 4.2 branch.
11:36 Changeset [6595] by curtis
Better error handling when reading thumbnails.
11:13 Changeset [6594] by bdezonia
put most all virtual subcases in place
10:46 Changeset [6593] by curtis
Backport r6592 to 4.2 branch.
10:46 Changeset [6592] by curtis
Update required ImageJ version to 1.42+, due to CompositeImage.setLUTs …
10:18 Changeset [6591] by bdezonia
more virtual test code
09:48 Changeset [6590] by bdezonia
Added some virtual testing methods
09:41 Changeset [6589] by curtis
Backport r6588 to 4.2 branch.
09:36 Changeset [6588] by curtis
Update copyright notice for LOCI plugins.
09:36 Changeset [6587] by bdezonia
modified comboConcatSplit methods to work with BF's latest changes
08:48 Changeset [6586] by curtis
Backport r6585 to 4.2 branch.
08:47 Changeset [6585] by curtis
Update component version numbers from 4.1.1 to 4.2-DEV.
08:43 Changeset [6584] by curtis
Backport recent bugfixes to 4.2 branch.
08:34 Changeset [6583] by curtis
Populate version information from Git, where applicable.
07:52 Changeset [6582] by callan
Re-run of code generation; fixes UUID population in OMEXMLMetadataImpl. …

06/28/10:

15:43 Changeset [6581] by curtis
Preserve dimensional extents on concatenation.
15:42 Changeset [6580] by curtis
Update color mode documentation a bit.
15:34 Changeset [6579] by bdezonia
more options.setVirtual() support
15:28 Changeset [6578] by bdezonia
started adding code to test everything with VirtualStacks also
14:58 Changeset [6577] by melissa
Merged r6576 to 4.2 branch.
13:46 Changeset [6576] by melissa
Added experimental support for an alternate JPEG-2000 compression code.
12:30 Changeset [6575] by curtis
Disable calibration function for INT32, since FloatProcessor is used. Also …
12:20 Changeset [6574] by bdezonia
minor edits. enabled openAllSeries with concatenate in the combo tests.
10:09 Changeset [6573] by melissa
Fixed GZIP pixel data detection for ICS files.

06/25/10:

18:15 Changeset [6572] by bdezonia
Fixed the two split timepoints tests to match against modified CZT order
16:27 Changeset [6571] by curtis
Fix indexing bug when reading only a subset of planes.
16:26 Changeset [6570] by curtis
Minor tweaks.
12:06 Changeset [6569] by melissa
Updated C++ headers to reflect changes to ome.xml.* in r6531.

06/24/10:

14:39 Ticket #492 (OME-TIFF reader does not support qualified namespaces) closed by melissa
fixed: (In [6568]) Various fixes to OME-XML/OME-TIFF handling, including support …
14:39 Changeset [6568] by melissa
Various fixes to OME-XML/OME-TIFF handling, including support for …
11:24 Ticket #495 (Lookup tables are not correctly applied if there is one LUT per channel) reopened by melissa
This bug was reintroduced in r6554 (trunk) and r6555 (4.2 branch).

06/23/10:

13:09 Changeset [6567] by melissa
Fixed how pixels files are found, so that having multiple *.vws files in …
12:13 Changeset [6566] by melissa
Tweaked pixel block detection to work with Slidebook 5.0.0.5 files.
10:22 Changeset [6565] by callan
Fixing constructor of OMEXMLMetadataImpl

06/22/10:

17:58 Changeset [6564] by curtis
Backport r6563 to 4.2 branch.
17:57 Changeset [6563] by curtis
Remove debugging statement.
17:54 Changeset [6562] by curtis
Backport indexed color fix to 4.2 branch.
17:53 Changeset [6561] by curtis
Do not fill indices for true color data if LUT is compatible with ImageJ.
17:38 Changeset [6560] by curtis
Add a TODO note about discontinuous 16-bit LUT resampling.
17:32 Changeset [6559] by curtis
Backport colorization fix for filled indices to 4.2 branch.
17:31 Changeset [6558] by curtis
Use composite mode by default for formerly-indexed images.
17:11 Changeset [6557] by curtis
Backport 16-bit LUT fix to 4.2 branch.
17:10 Ticket #507 (Exception importing 16-bit indexed color data) closed by curtis
fixed: Fixed in r6556.
17:10 Changeset [6556] by curtis
Fix problem with signed LUT indices.
16:59 Ticket #506 (Color mode settings do not work for single-channel images) closed by curtis
fixed: r6554 supports the various color modes as fully as possible for sizeC=1.
16:51 Changeset [6555] by curtis
Merge color mode progress to 4.2 branch.
16:50 Changeset [6554] by curtis
Progress on proper handling of color modes.
15:38 Changeset [6553] by melissa
Fixed a handful of core metadata and pixels offset bugs in Visitech …
13:48 Changeset [6552] by bdezonia
minor edits
07:40 Changeset [6551] by callan
Updating stylesheets. ( ome-xml:r640)
07:39 Changeset [6550] by callan
Fixing enumeration handler logging when the requested value is null.
07:39 Changeset [6549] by callan
More verbose tracing to track problems with stylesheet transforms.
03:38 Changeset [6548] by callan
Moving transformed XML logging dump to the TRACE level.
03:04 Changeset [6547] by callan
Make sure 2010-04-to-2010-06.xsl makes it into bio-formats.jar

06/21/10:

17:00 Changeset [6546] by melissa
Fixed compile errors introduced in r6531.
16:47 Changeset [6545] by curtis
For indexed color fake data, return a different LUT for each channel.
13:02 Changeset [6544] by melissa
Reverting r6536, as r6543 fixes the underlying problems in ListAnnotation.
12:25 Changeset [6543] by callan
Re-run of code generation; superclass reference support. Added test case …
12:24 Changeset [6542] by callan
Adding Xalan and its serializer dependency JAR to the Eclipse CLASSPATH.
12:15 Changeset [6541] by bdezonia
Improved falseColor support in getPixelValue().
10:57 Changeset [6540] by callan
Support for 2010-06 schema translation.
08:16 Changeset [6539] by callan
Fixing "External libraries" Eclipse project CLASSPATH.
08:00 Changeset [6538] by callan
Updating stylesheets from  ome-xml:r635.

06/18/10:

16:49 Changeset [6537] by bdezonia
minor changes
14:16 Changeset [6536] by melissa
Temporarily commented out ListAnnotationRef population.
13:40 Changeset [6535] by bdezonia
refactoring
13:18 Changeset [6534] by melissa
Fixed a few issues with 16-bit LUTs.

06/17/10:

17:33 Changeset [6533] by bdezonia
more refactoring
14:49 Changeset [6532] by bdezonia
mostly refactoring
07:13 Changeset [6531] by callan
Re-run of code generation; working copy schema. Huge merge. (See …

06/16/10:

05:24 Matlab edited by melissa
(diff)
05:08 Ticket #508 (Allow unit tests to be randomized) created by melissa
Right now unit tests are always run in the same order. We should allow …

06/15/10:

14:59 Changeset [6530] by bdezonia
Further support for indexed data

06/14/10:

16:58 Changeset [6529] by bdezonia
testColorCompositeSubcases() implemented for nonindexed data

06/11/10:

17:34 Changeset [6528] by bdezonia
started work on testCompositeSubcases(). Began refactor for general …
12:16 Changeset [6527] by melissa
Tweaked Metamorph reader's type detection so that TIFFs are not …
11:22 Changeset [6526] by melissa
Fixed Detector indices so that Detectors are properly populated and linked …
10:49 Changeset [6525] by melissa
Merged r6520 to 4.2.
10:43 Changeset [6524] by melissa
Merged r6521 and a bunch of ImageJ plugin changes to 4.2.

06/10/10:

23:13 Changeset [6523] by curtis
Backport Stack Slicer macro fix to 4.2 branch.
23:11 Changeset [6522] by curtis
Fix problem with Stack Slicer macro keys.
21:05 Changeset [6521] by curtis
Use explicit version number for JUnit JAR.
18:50 Changeset [6520] by curtis
Remove dependency on OME Notes, in favor of loci.formats.gui.XMLWindow. …
16:17 Changeset [6519] by bdezonia
minor refactorings
15:26 Changeset [6518] by bdezonia
further work on various methods
14:02 Changeset [6517] by melissa
Fixed scan-deps.pl warnings.
12:03 Changeset [6516] by melissa
Eliminated several deprecation warnings.
08:28 Changeset [6515] by melissa
Allow Metamorph reader to pick up TIFF files.

06/09/10:

16:35 Changeset [6514] by melissa
Javadoc tweaks.
16:30 Changeset [6513] by bdezonia
edits towards a general getColorTable() based testing method. Also enabled …
15:37 Changeset [6512] by melissa
Fixed a couple of minor channel bugs. testColorizeSubcases should pass …
15:05 Changeset [6511] by bdezonia
remove print statements to simplify debugging
14:59 Changeset [6510] by bdezonia
further work related to testColorizedSubcases()
13:10 Matlab edited by melissa
(diff)
12:20 Changeset [6509] by melissa
Adjust strip offsets if 32-bit signed values are being used in > 2 GB …
00:28 Ticket #289 (Review and adjust ImageJ color-related options) closed by curtis
fixed: As explained above, the color options have been reworked as per this …
00:25 Ticket #507 (Exception importing 16-bit indexed color data) created by curtis
E.g., with "index16&pixelType=uint16&indexed=true.fake": […]

06/08/10:

23:38 Ticket #506 (Color mode settings do not work for single-channel images) created by curtis
For datasets with sizeC=1, choosing a non-default color mode has no …
19:25 Matlab created by melissa
17:11 WikiStart edited by melissa
(diff)
16:55 Ticket #465 (Add tests for ImageJ plugin) closed by melissa
fixed: See tests in components/loci-plugins/test/.
16:51 Ticket #413 (Very large images cannot be saved) closed by melissa
fixed: Closing, as the API and several implementations are in place as of r6508. …
16:48 Export edited by melissa
(diff)
16:48 Ticket #505 (TIFF writer does not support saving tiles whose width is smaller than the ...) created by melissa
See TiffSaver.java:188.
16:46 Changeset [6508] by melissa
* Added basic TIFF tile export. Closes #413. * Throw an exception in …
16:37 Changeset [6507] by melissa
Couple of minor reader fixes.
15:17 Export edited by melissa
(diff)
15:17 Ticket #504 (OME-XML writer does not support saving tiles) created by melissa
15:16 Ticket #503 (JPEG writer does not support saving tiles) created by melissa
15:16 Ticket #502 (JPEG-2000 writer does not support saving tiles) created by melissa
15:15 Ticket #501 (Java writer does not support saving tiles) created by melissa
15:14 Ticket #500 (APNG writer does not support saving tiles) created by melissa
15:13 Ticket #499 (AVI writer does not support saving tiles) created by melissa
14:03 Changeset [6506] by melissa
* Updated JUnit version so that ImageJ plugin tests compile. * Overrode …
13:49 Changeset [6505] by melissa
Added missing header file for OME-XML component.
13:48 Changeset [6504] by melissa
Finished adding Xalan dependency.
13:06 Changeset [6503] by melissa
Fixed XZ/XT scans to display as they do in Olympus' software.
12:44 Changeset [6502] by melissa
Implemented colorizing when SizeC == 1, and fixed color handling when …
11:06 Changeset [6501] by melissa
Tweaked isThisType to only pick up valid TIFF files that are in the same …
10:54 Ticket #495 (Lookup tables are not correctly applied if there is one LUT per channel) closed by melissa
fixed: (In [6500]) Apply one LUT to each channel if the original file contains …
10:54 Changeset [6500] by melissa
Apply one LUT to each channel if the original file contains its own LUTs. …
10:17 Changeset [6499] by melissa
Fixed bug introduced in r6497, for real this time.
10:10 Changeset [6498] by melissa
Fixed bug introduced in r6497.
10:09 Ticket #498 (Consider using either JUnit or TestNG for all tests) created by melissa
Right now, some component tests (common, bio-formats) use TestNG and some …

06/07/10:

18:59 Changeset [6497] by melissa
Throw an exception if ImageProcessor types don't match.
18:46 Ticket #497 (Allow user to specify dimensions during stack concatenation) created by melissa
In the future, the stack concatenation option should prompt the user for …
15:02 Changeset [6496] by melissa
Updated bf-cpp to compile with latest ome.xml.* and loci.formats.meta.* …
11:45 Ticket #326 (Allow "merge to RGB" and "split channels" options to be used ...) closed by melissa
invalid

06/05/10:

14:34 Changeset [6495] by melissa
Updated email address.
12:09 Export edited by melissa
(diff)
11:50 Ticket #485 (Support for writing multi-file OME-TIFF datasets) closed by melissa
fixed: (In [6494]) Added support for multi-file OME-TIFF export. Closes #485.
11:50 Changeset [6494] by melissa
Added support for multi-file OME-TIFF export. Closes #485.

06/04/10:

15:41 Changeset [6493] by bdezonia
improved a number of methods (testComboCropAutoscale, testDatasetGroup, …
14:46 Changeset [6492] by melissa
Fixed Channel indices in MetadataTools.verifyMinimumPopulated.
13:37 Changeset [6491] by melissa
Updated MetadataTools.verifyMinimumPopulated and the MinimumWriter example …
13:25 Changeset [6490] by melissa
Added TextReader to 4.2 branch.
12:52 Changeset [6489] by melissa
Fixed Nikon tag parsing.
12:20 Changeset [6488] by bdezonia
Fixed issue in adjustColorRange() with calculation of max and min
11:12 Changeset [6487] by melissa
Minor fixes to make metadata level tests pass.
10:32 Ticket #496 (Leica lookup tables not applied when metadata collection disabled) closed by melissa
fixed: (In [6486]) Make sure that CoreMetadata.indexed is set correctly, …
10:32 Changeset [6486] by melissa
Make sure that CoreMetadata.indexed is set correctly, regardless of the …
10:23 Changeset [6485] by melissa
Updated metadata level tests to check for isIndexed mismatches. See #496.
10:16 Changeset [6484] by melissa
Updated Channel -> Laser linkage rule in accordance with r6076.
09:58 Changeset [6483] by melissa
Populate Laser.Model, if present. See  omero:2475.
09:44 Changeset [6482] by melissa
Fixed min calculation for cropped planes. See  imagej:59.

06/03/10:

23:44 Ticket #496 (Leica lookup tables not applied when metadata collection disabled) created by curtis
Running showinf with the -nometa flag on `data/leica/joel/sequential scan …
21:53 Changeset [6481] by curtis
Remove debugging statements.
21:50 Changeset [6480] by curtis
Tweak creation of ColorModel.
20:45 Changeset [6479] by curtis
Merge 'Standard ImageJ' bugfix to 4.2
20:44 Changeset [6478] by curtis
Readd support for obsolete "Standard ImageJ" stack view option.
20:25 Changeset [6477] by curtis
Backport Bio-Formats and Importer bugfixes from trunk.
19:38 Changeset [6476] by curtis
Add compatibility later for obsolete color options. This should allow old …
19:37 Changeset [6475] by curtis
Organize methods a little better.
18:39 Ticket #266 (L2D datasets cannot be imported using omebf) closed by melissa
wontfix: OME server is now officially legacy software, so this won't be fixed.
18:36 Ticket #418 (Feedback 134: multithreading issue) closed by melissa
fixed: Closing, as multi-threading seems to be working now. Feel free to reopen …
18:33 Ticket #377 (Some formats take a long time to initialize) closed by melissa
fixed: With r6474, ax2-egcr.sld initializes in ~39s, and vladan.zvi initializes …
18:21 Changeset [6474] by curtis
Add a note about the use of ImporterPrompter in BF.openImagePlus.
18:04 Ticket #310 (Overhaul Bio-Formats Importer) closed by curtis
fixed: Nearly two years later, we finally have a much better API for …
17:51 Changeset [6473] by curtis
Clarify and expound on some TODOs.
17:39 Changeset [6472] by curtis
Remove superfluous StatusListener & StatusEvent classes.
17:18 Changeset [6471] by bdezonia
in middle of writing testColorColorizedSubcases() - incomplete
16:58 Changeset [6470] by curtis
Fix some Eclipse warnings.
16:58 Changeset [6469] by curtis
Force non-overlapping ZCT order when swapping dimensions.
16:21 Changeset [6468] by melissa
Fixed compile errors introduced in r6458.
16:09 Ticket #493 (Series beyond 456 do not appear in ImageJ plugin) closed by curtis
fixed: In r6466, I changed the code to suppress the thumbnails if more than 200 …
16:05 Changeset [6467] by curtis
Fix a couple of minor Mac OS X specific bugs.
15:56 Changeset [6466] by curtis
Fix some problems with the series chooser. If there are more than 200 …
15:46 Changeset [6465] by melissa
Added some debugging statements so that missing TIFF files are reported. …
15:04 Changeset [6464] by melissa
Backported r6463 to 4.1.
14:50 Changeset [6463] by melissa
Don't attempt to read IFDs with offsets beyond the end of the file.
14:13 Ticket #495 (Lookup tables are not correctly applied if there is one LUT per channel) created by melissa
See for example the first series of data/leica/joel/sequential scan …
14:01 Changeset [6462] by melissa
Added test for checking IFormatReader.getCoreMetadata() against the values …
13:10 Changeset [6461] by melissa
Fixed well ordering bug, courtesy of Rubén Muñoz.
13:06 Changeset [6460] by curtis
ijview depends on loci_plugins.jar, not bio-formats.jar.
13:00 Changeset [6459] by melissa
Synced up export/MetadataConverter fixes between trunk and 4.2. OME-TIFF …
12:11 Changeset [6458] by melissa
Moved ome.xml.r201004.* to ome.xml.model.* in trunk.
11:40 Changeset [6457] by melissa
Moved ome.xml.r201004.* to ome.xml.model.*.
10:40 Changeset [6456] by bdezonia
testComboManyOptions() - added verification of crop size
10:29 Changeset [6455] by bdezonia
testComboManyOptions() - enhanced range testing
10:13 Changeset [6454] by bdezonia
testComboManyOptions() - improved and working
10:10 Changeset [6453] by bdezonia
testComboManyOptions - save working version with debug code in place
06:34 Changeset [6452] by callan
Ensure that Pixels LSIDs are created uniquely.
03:59 Changeset [6451] by callan
Need fileLength parsed in parseSeriesTag() for parseImageTag() to be …

06/02/10:

17:19 Changeset [6450] by curtis
Better indexed color logic; still broken in various cases though.
16:56 Changeset [6449] by bdezonia
testComboManyOptions - temp/wrong implementation. Various other changes.
16:06 Changeset [6448] by curtis
Remove obsolete, commented-out code.
15:46 Changeset [6447] by curtis
Fix testDatasetSwapDims.
13:39 Changeset [6446] by curtis
Remove debugging statements.
13:38 Changeset [6445] by curtis
Fix getCoreMetadata with ReaderWrapper implementations.
13:12 Changeset [6444] by melissa
Break out of loop if an AIOOB exception is thrown to prevent an infinite …
12:36 Changeset [6443] by curtis
Fix TextReader.openBytes to work properly.
12:17 Changeset [6442] by curtis
Clean up indexed color table generation a bit.
11:33 Changeset [6441] by bdezonia
Fixed comboConcatSplit code. BF broken here.
11:23 Ticket #491 (Check that Leica LIF physical dimensions are correct) closed by melissa
fixed: TimeIncrements are correct with r6440.
11:17 Ticket #494 (ImageJ importer plugin does not preserve pixel sizes) closed by curtis
fixed: Fixed in r6408.
08:50 Changeset [6440] by callan
Fixing issues with endianness parsing for OME-TIFFs. Re-run of code …

06/01/10:

17:35 Changeset [6439] by bdezonia
Added comboConcatSplitTest(). Other small edits.
17:23 Changeset [6438] by curtis
Fix ijview's Importer package.
17:22 Changeset [6437] by curtis
Add scaleFactor option to FakeReader for scaling gradient pixel values.
17:03 Changeset [6436] by melissa
Merged r6435 to 4.2 branch.
17:02 Changeset [6435] by melissa
Updated metadata support documentation.
14:48 Changeset [6434] by curtis
Throw IllegalArgumentException for invalid Z/C/T step.
14:11 Changeset [6433] by curtis
Fix intensity scaling issue with signed and float pixel types.
14:10 Changeset [6432] by curtis
Fix problem with step size of 0.
13:25 Changeset [6431] by bdezonia
Clarified TODOs at top of file
12:06 Changeset [6430] by melissa
* Updated OMEXMLMetadataImpl based on  ome-xml:r618. * Fixed a bunch of …
10:35 Changeset [6429] by callan
Added missing "continue". (See  omero:#2467 and r6424)
10:34 Changeset [6428] by callan
Reverting r6427.
10:33 Changeset [6427] by callan
Added missing "continue". (See  omero:#2467 and r6424)
10:21 Changeset [6426] by melissa
Fixed various metadata population bugs in the FV1000 reader. See …
10:18 Changeset [6425] by callan
Update of stylesheets ( ome-xml:r617).
09:32 Changeset [6424] by callan
Handle very nasty null reference sources and remove System.err logging in …
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