11:23 Changeset [6649] by callan
Re-run of code generation; laser pumps can be any light source. …
11:04 Changeset [6648] by melissa
Remove any BinData elements from the OME-XML before it is written to the …
10:17 Changeset [6647] by callan
Messed up logging by having an old version of the enum handler template, …
10:02 Changeset [6646] by melissa
Updated schema location to 2010-06.
09:50 Changeset [6645] by melissa
Fixed Objective parsing when Immersion and Correction are reversed.
09:48 Changeset [6644] by callan
Re-run of code generation; DRY as a possible value for AIR immersion. …


18:25 Changeset [6643] by curtis
Fix Jace paths to work pre-r46, with commented out code for r46+. Add …
17:13 Changeset [6642] by curtis
Update ome-xml.h to reflect r6631.
16:57 Changeset [6641] by curtis
Update paths to work with new Jace path structure (r52+).
16:49 Changeset [6640] by bdezonia
minor edits. did change maxPixel calc for UINT32.
15:51 Changeset [6639] by curtis
Update autoscale test to check CompositeImage LUT ranges.
15:20 Changeset [6638] by curtis
Enable toggling of debug print statements using DEBUG flag.
15:15 Changeset [6637] by bdezonia
minor edits
14:48 Changeset [6636] by bdezonia
added UINT16 support to all colorTests. added back all virtual modes to …
13:01 Changeset [6635] by melissa
Be more thorough when searching for the .dv file that matches a .log or …
12:53 Changeset [6634] by bdezonia
datasetGroupFiles() improved. Constants fixed for correct style.
12:27 Changeset [6633] by bdezonia
fixed lut testing in testColorCustom. enhanced testColorComposite to …
11:48 WikiStart edited by melissa
09:54 Ticket #512 (Logging cleanup) closed by melissa
fixed: (In [6632]) Re-run of code generation ( ome-xml:r646), closes #512.
09:54 Changeset [6632] by melissa
Re-run of code generation ( ome-xml:r646), closes #512.
09:43 Changeset [6631] by melissa
Removed obsolete OME-XML model objects.
06:07 Changeset [6630] by callan
Set fill color as well as stroke color for mask ROI.
05:34 Changeset [6629] by callan
Fix shape indexes for ellipse X and Y radii.
05:08 Changeset [6628] by callan
Utilize the shape label rather than a seperate text shape for MIAS ROI.


19:30 Changeset [6627] by melissa
Switched TiffParser logging from 'debug' to 'trace'; see #512.
18:59 Changeset [6626] by curtis
Backport r6625 to 4.2 branch.
18:58 Changeset [6625] by curtis
Fix autoscaling problem with >8-bit CompositeImages.
18:07 Changeset [6624] by curtis
Remove obsolete constant from bf-cpp conflicts list.
17:31 Changeset [6623] by bdezonia
make flesh for the color tests. remove unfinished tests. comment out some …
16:17 Changeset [6622] by melissa
Ensure that xmlns:ome elements are preserved during transformation.
15:16 Changeset [6621] by melissa
Merged r6614 and r6615 into trunk.
11:36 Changeset [6620] by bdezonia
some work on composite testing and some code on dimension swapping tests. …
09:08 Changeset [6619] by melissa
Updated stylesheets to  ome-xml:r645.
07:32 Changeset [6618] by callan
Restoring MIAS reader overlay support.
06:16 Changeset [6617] by callan
Support for TagAnnotation and TermAnnotation conversion.
06:07 Changeset [6616] by callan
Re-run of code generation; support for mask bin data. ( ome-xml:r644)
04:40 Changeset [6615] by dscho
Avoid "prefix <...> not bound" error when transforming XML When …
04:40 Changeset [6614] by dscho
Fix OME-XML version discovery Some files (Huygens) have an xmlns:ome …


21:15 Changeset [6613] by melissa
Merged r6602 to 4.2 branch.
20:48 Changeset [6612] by melissa
Fixed parsing of large OME-XML files and pre-2010-04 files with …
16:13 Changeset [6611] by curtis
Backport r6609,r6610 to 4.2 branch.
16:11 Changeset [6610] by curtis
Change default stack order to XYCZT, to match Hyperstack view option.
16:10 Changeset [6609] by curtis
Fix bug in 'Metadata only' stack view option.
14:44 Changeset [6608] by curtis
Backport r6606,r6607 to 4.2 branch.
14:42 Changeset [6607] by curtis
Fix plane ordering bug with channel separator when effectiveSizeC>1, …
14:31 Ticket #512 (Logging cleanup) created by melissa
Specifically: * change many of the loci.formats.tiff.TiffParser logging …
13:52 Changeset [6606] by curtis
Fix bug with fake data generation when rgbChannelCount>1.
13:12 Changeset [6605] by curtis
Backport r6603,6604 to 4.2 branch.
13:11 Changeset [6604] by curtis
Readd "Standard ImageJ" stack view option. Note that non-hyperstacks …
11:21 Ticket #511 (Compressed Amira file not read properly) created by melissa
See data/amira/jeremy/Virus_Membrane7.am and the corresponding screenshot …
10:31 Ticket #510 (Some Amira files throw an exception during setId) created by melissa
See data/amira/jeremy/HIV_FINAL.hx and …
09:41 Ticket #509 (Add test for macro key regressions) created by melissa
It would be a good idea to add a unit test that checks whether or not old …


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. …


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.


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.


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).


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 files.
10:22 Changeset [6565] by callan
Fixing constructor of OMEXMLMetadataImpl


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


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.


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
13:18 Changeset [6534] by melissa
Fixed a few issues with 16-bit LUTs.


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 …


05:24 Matlab edited by melissa
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 …


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


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


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.


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.


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
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": […]


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
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
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
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 …


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


14:34 Changeset [6495] by melissa
Updated email address.
12:09 Export edited by melissa
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.
Note: See TracTimeline for information about the timeline view.