Timeline


and

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 …

05/28/10:

19:32 Changeset [6423] by curtis
Merge ChannelFiller bugfixes to 4.2.
19:32 Changeset [6422] by curtis
Fix more problems with ChannelFiller (some self-inflicted). Seems to work …
16:58 Changeset [6421] by bdezonia
further work on testColorComposite
15:24 Changeset [6420] by curtis
Merge ChannelFiller and FakeReader bugfixes to 4.2.
15:20 Changeset [6419] by curtis
Fix bugs in FakeReader with indexed color.
15:20 Changeset [6418] by curtis
Fix problems with ChannelFiller when lookup table color component count != …
15:19 Changeset [6417] by curtis
Flesh out the IFormatReader javadoc a bit.
10:32 Changeset [6416] by melissa
Fixed physical size Z scaling.
09:28 Changeset [6415] by callan
Merging r6413,r6414 from Trunk
07:48 Changeset [6414] by callan
Fixed some further NPEs when reading OME-TIFF files with no UUID objects.
07:38 Changeset [6413] by callan
General cleanup for metadata classes. Moved and overhauled ome.xml test …

05/27/10:

18:25 Changeset [6412] by curtis
More tweaks to the conflicts list.
18:19 Changeset [6411] by curtis
Update conflicts list for latest bf-cpp with WiscScan.
15:39 Changeset [6410] by bdezonia
some refactoring, some composite test code
15:03 Changeset [6409] by melissa
Several fixes to Leica LEI, ND2, and Perkin Elmer readers.
11:59 Changeset [6408] by curtis
Fix image calibration bug.
11:44 Changeset [6407] by curtis
Temporary(?) hack to speed up text file reading.
11:40 Changeset [6406] by melissa
Updated several TIFF-based readers to populate Image.Description more …
10:46 Changeset [6405] by melissa
Fixed Detector/DetectorSettings population to correspond to what the …
10:03 Changeset [6404] by melissa
Trim the image name before placing it in the original metadata hashtable. …
09:55 Changeset [6403] by bdezonia
Minor edits
09:22 Changeset [6402] by callan
Merging r6401 from Trunk.
09:21 Changeset [6401] by callan
slf4j usage. Re-run of code generation ( ome-xml:r612)
06:16 Changeset [6400] by callan
Merging r6398,r6399 from Trunk
06:14 Changeset [6399] by callan
Initializing filenames and roiFilenames on close() in FV1000Reader.
03:45 Changeset [6398] by callan
Ensure that Image names are populated for Leica LEI when …

05/26/10:

20:24 Changeset [6397] by curtis
Add reader for tabular text data.
20:24 Changeset [6396] by curtis
Fix bug where readLine and readCString returned "" instead of null at EOF.
20:05 Changeset [6395] by melissa
Read tags into a byte array, so that non-String tags are preserved. See …
17:24 Changeset [6394] by bdezonia
More work on color tests
15:58 Changeset [6393] by bdezonia
Some work on color tests
11:09 Changeset [6392] by melissa
Fixed LUT ordering bug. See  omero:2438.
10:49 Changeset [6391] by callan
Merging r6382,r6390 from Trunk
10:34 Changeset [6390] by callan
Re-run of code generation. ( ome-xml:r607)
Note: See TracTimeline for information about the timeline view.