Timeline
09/06/10:
- 23:58 Changeset [6894] by
- Fix ome-editor author.
- 23:37 Changeset [6893] by
- Maven version of ome-editor.
- 22:58 Changeset [6892] by
- Maven version of ome-notes (but still doesn't compile).
- 15:10 Ticket #549 (Some options should be disabled in the "Standard ImageJ" view mode) closed by
- fixed: (In [6891]) Disable color mode options when the stack view is set to …
- 15:10 Changeset [6891] by
- Disable color mode options when the stack view is set to "Standard …
- 13:05 Ticket #550 (ScanR reader assumes that wells form a square) created by
- The number of wells acquired in each row is assumed to be either 0, or …
- 13:00 Changeset [6890] by
- A few fixes for ScanR datasets with missing wells, based on a patch …
- 12:05 Ticket #547 (Add system property values to ImageJ plugins log) closed by
- fixed: (In [6889]) Added system properties to ImageJ plugin log. Closes #547.
- 12:05 Changeset [6889] by
- Added system properties to ImageJ plugin log. Closes #547.
- 12:04 Changeset [6888] by
- Updated XMLTools.sanitizeXML to remove invalid "&#" sequences.
- 11:06 Changeset [6887] by
- Backported r6839, r6840, and r6841 to 4.2.
- 10:15 Changeset [6886] by
- * Improved metadata parsing for Prairie datasets. * Reverted changes to …
- 07:18 Changeset [6885] by
- Maven version of legacy Multi-LUT application.
09/05/10:
- 22:58 WikiStart edited by
- (diff)
- 22:38 Changeset [6884] by
- Maven version of jvmlink project.
- 22:37 Changeset [6883] by
- Update repository links to match new dev server.
09/04/10:
- 18:24 Changeset [6882] by
- Fix out-of-date SVN and Trac paths.
- 18:13 Changeset [6881] by
- Update SVN and Trac paths.
09/03/10:
- 12:53 Ticket #549 (Some options should be disabled in the "Standard ImageJ" view mode) created by
- For instance, the "Colorized" color mode will not work as expected if the …
- 12:31 Changeset [6880] by
- Couple of findbugs fixes, see #546.
- 11:02 Changeset [6879] by
- Added more logging to LocationTest, in an attempt to track down the …
- 10:48 Ticket #545 (Fix TIFF/OME-TIFF export with JPEG/JPEG-2000 compression) closed by
- fixed: (In [6878]) Fixed bugs in writing and reading JPEG- and …
- 10:48 Changeset [6878] by
- Fixed bugs in writing and reading JPEG- and JPEG-2000-compressed TIFFs. …
- 09:28 Changeset [6877] by
- * Return blank planes if pixel data is missing from an OME-XML file. * …
- 06:01 Ticket #548 (Support OME-XML with BinData.Length = 0) closed by
- fixed: (In [6876]) Some further test case cleanup. Added a check to ChannelFiller …
- 06:01 Changeset [6876] by
- Some further test case cleanup. Added a check to ChannelFiller to handle …
- 05:59 Ticket #548 (Support OME-XML with BinData.Length = 0) created by
- It should be possible to at least initialize the reader state when BinData …
09/02/10:
- 17:07 Changeset [6875] by
- Fixed handling of multi-position ND2 datasets.
- 15:29 Changeset [6874] by
- Better series handling when number of series is extremely large.
- 11:43 Ticket #547 (Add system property values to ImageJ plugins log) created by
- In particular, it would be useful to have java.version and java.class.path …
- 11:33 Changeset [6873] by
- Update location of LegacyQTTools class.
- 10:43 Ticket #543 (OMETiffWriter.close() can leak file descriptors) closed by
- fixed: (In [6872]) Fixed OMETiffWriter.close() so that it releases resources even …
- 10:43 Changeset [6872] by
- Fixed OMETiffWriter.close() so that it releases resources even if an …
- 02:21 Changeset [6871] by
- Removed erroneous STDERR debugging statement from test case.
09/01/10:
- 16:59 Changeset [6870] by
- Added JUnit JAR to build classpath, and made a few minor tweaks to test …
- 16:56 Changeset [6869] by
- Add a note stating that metadata can also be viewed in Image Info.
- 16:51 Changeset [6868] by
- Merged trunk r6867 into junit-test-suite.
- 16:34 Ticket #546 (Make findbugs happy) created by
- The "LOCI-findbugs" job on OME Hudson now runs the 'findbugs' Ant target …
- 16:24 Ticket #545 (Fix TIFF/OME-TIFF export with JPEG/JPEG-2000 compression) created by
- See, for instance, the output of: […] on the junit-test-suite branch.
- 16:14 Changeset [6867] by
- Migrated data-driven writer tests to JUnit. See #498.
- 16:13 Changeset [6866] by
- Removed support for JPEG/JPEG-2000 compression in OME-XML files, as this …
- 15:01 Ticket #539 (Skip tests when setId fails) closed by
- fixed: (In [6865]) Skip tests if IFormatReader.setId(String) failed. Closes …
- 15:01 Changeset [6865] by
- Skip tests if IFormatReader.setId(String) failed. Closes #539.
- 13:35 Ticket #544 (Native support for Quicktime Sorenson 1 codec (SVQ1)) created by
- See file in data/quicktime/jesper/. This file can be opened using the …
- 13:06 Changeset [6864] by
- Several tweaks to original metadata storage so that FV1000 files do not …
- 11:59 Changeset [6863] by
- Added missing methods that prevented r6862 from compiling.
- 11:58 Changeset [6862] by
- Simplified search for BinData offsets.
- 10:20 Changeset [6861] by
- Reverting erroneous debugging in OMEXMLReader from r6860.
- 10:17 Changeset [6860] by
- Added a test case (and re-organized some of the mock infrastructure) for …
08/31/10:
- 14:57 Changeset [6859] by
- Remove bogus quote escape characters.
- 14:51 Changeset [6858] by
- Clarify 'Display metadata' option to be less misleading.
- 09:55 Ticket #543 (OMETiffWriter.close() can leak file descriptors) created by
- An exception during writer.close(): […] leads to …
08/30/10:
- 14:10 Changeset [6857] by
- Added support for multi-chunk AVI files.
- 09:21 Changeset [6856] by
- Fixed sub-image reading for SimplePCI files that contain embedded TIFFs.
08/28/10:
- 12:53 Changeset [6855] by
- Backported r6068 to 4.1.
08/27/10:
- 17:08 Ticket #542 (Multi-series stitching is incorrect) created by
- When stitching a dataset with multiple image series distributed across …
- 17:04 Changeset [6854] by
- Use INFO logging for AxisGuesser main.
- 17:03 Changeset [6853] by
- Use INFO logging in FilePattern main.
- 14:32 Changeset [6852] by
- Prevent a bunch of NPEs.
- 14:04 Changeset [6851] by
- * Added more informative logging. * Make sure that tests fail if files …
08/26/10:
- 15:38 Changeset [6850] by
- Initial version of data-driven JUnit tests, see #498. 'ant …
- 14:43 Changeset [6849] by
- Fix build warnings when using Ant 1.8+.
- 12:36 Changeset [6848] by
- Various improvements to Bio-Formats MATLAB bfopen script: * Better …
- 11:11 Changeset [6847] by
- Removed external URL from Location tests.
08/25/10:
- 15:55 Changeset [6846] by
- Added branch for migrating the data-driven tests to JUnit; see #498.
- 15:50 TestingNotes edited by
- Ordered tickets by priority. (diff)
- 15:24 Ticket #541 (Add support for Varian FID files) created by
- See data in data/varian-mri//*.fid. This is a different format from …
- 15:23 Ticket #474 (Add support for Varian FDF format) closed by
- fixed: (In [6845]) Added support for Varian FDF files. Closes #474.
- 15:23 Changeset [6845] by
- Added support for Varian FDF files. Closes #474.
- 10:18 Changeset [6844] by
- Sped up original metadata hashtable population.
- 08:57 Changeset [6843] by
- Removed check that prevented multi-file OME-TIFF export from working.
08/24/10:
- 16:42 Ticket #527 (Add support for multiple positions in one Zeiss LSM file) closed by
- fixed: (In [6842]) Added support for multi-position Zeiss LSM data. Closes #527.
- 16:42 Changeset [6842] by
- Added support for multi-position Zeiss LSM data. Closes #527.
- 15:56 TestingNotes edited by
- Added links to newly filed tickets. (diff)
- 15:56 Ticket #540 (Add Hudson jobs to run data-driven tests) created by
- At a minimum, we probably want one job that runs on a set of known good …
- 15:53 Ticket #539 (Skip tests when setId fails) created by
- If the first test for a file fails because setId failed, then we should …
- 15:51 Ticket #538 (Allow MD5 tests to accept an alternate hash) created by
- JPEG-compressed planes, for instance, have different MD5 sums on Linux and …
- 15:47 Ticket #537 (Add tests for non-core metadata consistency) created by
- It would be nice to be able to test metadata beyond core metadata (so we'd …
- 15:47 Ticket #536 (Consider changing test configuration file format) created by
- A lot of the config files need updating anyway, so now might be an OK time …
- 15:44 Ticket #535 (Allow tests to be run on files in memory) created by
- To improve speed, there should be an option to map all of the files into …
- 15:41 Ticket #534 (Add test for consistent type checking) created by
- We could add a field to the config files that gives the name of the reader …
- 15:41 Ticket #533 (Add test that reads planes in a random order) created by
- All of our tests right now read planes sequentially from 0 to n, but most …
- 15:39 Ticket #532 (Add test for leaking file handles) created by
- File handles that are left open are known to cause a problem on Windows, …
- 15:38 Ticket #531 (Add md5 test for sub-images) created by
- Similar to the md5 test for full image planes, it would be a good idea to …
- 13:03 TestingNotes edited by
- (diff)
- 12:25 Changeset [6841] by
- * Updated MetadataConverter to properly handle LightSource attributes. * …
- 11:02 Changeset [6840] by
- Support for type resolution of light sources. Re-run of code generation. …
- 06:59 Changeset [6839] by
- Mock and tests for SPW model use with OME-XML.
08/23/10:
- 16:56 Changeset [6838] by
- One more signedness fix, as pointed out by Rubén Muñoz.
- 12:51 Changeset [6837] by
- Update bf-cpp invocation script: * Add loci_plugins library to the mix. …
- 10:26 Changeset [6836] by
- Fixed Image indexed passed to …
- 09:34 Ticket #445 (Feedback 2160: Leica lambda scans) closed by
- fixed: I believe this was fixed in 4.2.
- 09:32 Ticket #450 (Feedback 1489: OMX regression?) closed by
- invalid: Never received the problematic file, and Deltavision files seem to be …
- 09:30 Ticket #421 (Feedback 853: flex reader finds other directories) closed by
- invalid
- 09:30 Ticket #416 (Feedback 17) closed by
- invalid
- 09:22 Ticket #441 (Feedback 2110 : File handle error on MIAS plate) closed by
- invalid: Closing as invalid, as this plate has been imported many times without …
08/20/10:
- 14:30 Ticket #423 (Feedback 856: Add "get imported file-endings" method) closed by
- fixed: Near as I can tell, this feature is no longer needed. Now that #273 is …
- 14:05 Changeset [6835] by
- A few changes to how pixels and dimension information are found. I'm not …
- 13:19 TestingNotes edited by
- Some updates to list of formats for which we can generate public data. (diff)
- 12:02 Changeset [6834] by
- Moved MetadataStore calls that depend on MetadataTools.populatePixels(...) …
- 09:47 TestingNotes edited by
- (diff)
08/19/10:
- 20:40 TestingNotes edited by
- (diff)
- 16:28 Changeset [6833] by
- Add latest Maven projects to the umbrella.
- 16:24 Changeset [6832] by
- Maven version of ome-plugins project.
- 16:21 Changeset [6831] by
- Add missing flow-cytometry pom.xml.
- 16:04 Changeset [6830] by
- Maven version of flow-cytometry project.
- 16:04 Changeset [6829] by
- Fix VisBio developer list.
- 15:42 Changeset [6828] by
- Migrate miscellaneous utilities to Maven.
- 15:20 Changeset [6827] by
- Convert slim-plotter to Maven project structure.
- 15:05 Changeset [6826] by
- Backported dimension detection changes.
- 14:50 Changeset [6825] by
- Add new projects to umbrella, and ignore target folders.
- 14:39 Changeset [6824] by
- Progress on Mavenization, including ome-io and visbio projects.
- 14:21 Ticket #529 (Parse metadata from TIFFs produced by Nikon Elements) closed by
- fixed: (In [6823]) Added reader for TIFFs produced by Nikon Elements. Closes …
- 14:21 Changeset [6823] by
- Added reader for TIFFs produced by Nikon Elements. Closes #529.
- 12:52 Changeset [6822] by
- Prevent extra (Logical)Channel objects from being populated.
08/18/10:
- 18:10 TestingNotes created by
- Assorted notes on future testing plans
- 17:46 Changeset [6821] by
- Add temporary workaround for Jace bug when class names have underscores.
- 17:45 Changeset [6820] by
- Add boot classpath to AutoProxy classpath.
- 17:25 Changeset [6819] by
- Factored ND2Handler out of NativeND2Reader. See #529.
- 15:42 Changeset [6818] by
- Set main class appropriately in deps jar.
- 15:37 Changeset [6817] by
- Fixed assembly for jar2lib-*-deps.jar.
- 15:33 Changeset [6816] by
- Fixed hack from r6804 so that it won't throw an AIOOB exception.
- 15:31 Changeset [6815] by
- Add assembly for creating jar2lib JAR with dependencies. Still buggy.
- 15:21 Changeset [6814] by
- Reverted a few changes from r6791 that prevented OME-TIFF files from being …
- 14:44 Changeset [6813] by
- Temporary place to house bf-cpp-specific Jar2Lib files.
- 14:42 Changeset [6812] by
- Reverse the order of the rows if a negative height was stored in the file. …
- 14:18 Changeset [6811] by
- Better layout for static resources.
- 14:09 Changeset [6810] by
- Force the pixel type to be unsigned, regardless of what is actually stored …
- 14:01 Changeset [6809] by
- Working version of Jar2Lib.
- 13:15 Changeset [6808] by
- If a negative width or height is stored, use the absolute value instead …
- 13:01 Ticket #509 (Add test for macro key regressions) closed by
- fixed: (In [6807]) * Fixed bug in StringOption that prevented macro keys from …
- 13:01 Changeset [6807] by
- * Fixed bug in StringOption that prevented macro keys from being parsed …
08/17/10:
- 19:29 Changeset [6806] by
- Initial version of Jar2Lib implementation.
- 15:12 Ticket #530 (BD Pathway reader doesn't fully populate original metadata hashtable) closed by
- fixed: (In [6805]) * Added convenience method to loci.common.IniList to flatten …
- 15:12 Changeset [6805] by
- * Added convenience method to loci.common.IniList to flatten the IniTables …
- 13:17 Changeset [6804] by
- Hackish fix for some files that have an incorrect dimension order.
- 12:44 Changeset [6803] by
- Backported r6802 to 4.1 branch.
- 12:09 Changeset [6802] by
- * Ignore missing L2D scans, instead of throwing an exception. * More …
- 10:20 Changeset [6801] by
- * Parse metadata from SimplePCI TIFFs. * Slightly better Z/T detection for …
- 08:08 Changeset [6800] by
- Remove invalid characters from strings that will later be parsed into …
08/16/10:
- 15:58 Ticket #263 (Bio-Formats configuration dialog) closed by
- fixed: > Ability to install native JPEG2000 codec if needed Bio-Formats decodes …
- 14:51 Matlab edited by
- (diff)
- 14:23 Changeset [6799] by
- Fixed a few Bio-Rad Gel offset bugs.
- 12:37 Changeset [6798] by
- Added 'Object getSeriesMetadataValue(String)' to IFormatReader.
- 12:05 Ticket #526 (Parse metadata from S-FEG and Helios NanoLab TIFF files) closed by
- fixed: (In [6797]) Added support for FEI TIFF files, specifically those from …
- 12:05 Changeset [6797] by
- Added support for FEI TIFF files, specifically those from S-FEG and Helios …
- 10:10 Ticket #520 (Verify that generated OME-XML validates) closed by
- fixed: (In [6796]) Remainder of OME-XML validation fixes. Closes #520.
- 10:10 Changeset [6796] by
- Remainder of OME-XML validation fixes. Closes #520.
08/13/10:
- 15:53 Changeset [6795] by
- Backport r6792 to 4.2 branch.
- 15:50 Changeset [6794] by
- Backport r6789 to 4.2 branch.
- 13:46 Changeset [6793] by
- Changed logging level of missing interface messages from 'warn' to …
- 11:33 Ticket #528 (LUTs are lost in virtual stack mode) closed by
- fixed: (In [6792]) Preserve LUTs in virtual stack mode. Closes #528.
- 11:33 Changeset [6792] by
- Preserve LUTs in virtual stack mode. Closes #528.
- 09:18 Changeset [6791] by
- More OME-XML validation fixes, see #520.
- 09:06 Ticket #487 (Add support for ECAT7 files) closed by
- fixed: (In [6790]) Initial version of ECAT 7 reader. Closes #487.
- 09:06 Changeset [6790] by
- Initial version of ECAT 7 reader. Closes #487.
08/12/10:
- 14:45 Changeset [6789] by
- Fix for NullPointerException.
08/11/10:
- 17:38 Ticket #523 (Bio-Formats Windowless Importer is broken) closed by
- fixed: (In [6788]) If ImporterOptions.getId() returns null, prompt for a file …
- 17:38 Changeset [6788] by
- If ImporterOptions.getId() returns null, prompt for a file regardless of …
- 17:01 Ticket #530 (BD Pathway reader doesn't fully populate original metadata hashtable) created by
- BD Pathway datasets have lots of metadata that can't be properly mapped to …
- 16:35 Ticket #529 (Parse metadata from TIFFs produced by Nikon Elements) created by
- The metadata is very similar to what is in new ND2 files (i.e. lots of …
- 16:30 Changeset [6787] by
- Added extra sanity check when parsing doubles.
- 15:48 Changeset [6786] by
- More OME-XML validation fixes, see #520.
08/10/10:
- 14:39 Ticket #524 (Better documentation for command line tools) closed by
- fixed: (In [6785]) * bfconvert and showinf now exit if an unknown flag or …
- 14:39 Changeset [6785] by
- * bfconvert and showinf now exit if an unknown flag or argument is …
- 14:06 Changeset [6784] by
- More OME-XML validation fixes. See #520.
- 07:52 Changeset [6783] by
- Removed not-yet-existent CRIReader.
08/09/10:
- 13:20 Changeset [6782] by
- Parse physical pixel sizes for all series, instead of applying the first …
- 13:07 Changeset [6781] by
- Fixed tests in components/bio-formats; all tests should now pass.
- 11:54 Changeset [6780] by
- More thoroughly parse Z position values from single-file datasets.
- 10:22 Changeset [6779] by
- Fixed tag alignment problem.
- 09:34 Changeset [6778] by
- Prevent SlidebookReader from passing a negative int to setSeries.
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