Timeline


and

09/05/10:

22:58 WikiStart edited by curtis
(diff)
22:38 Changeset [6884] by curtis
Maven version of jvmlink project.
22:37 Changeset [6883] by curtis
Update repository links to match new dev server.

09/04/10:

18:24 Changeset [6882] by curtis
Fix out-of-date SVN and Trac paths.
18:13 Changeset [6881] by curtis
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 melissa
For instance, the "Colorized" color mode will not work as expected if the …
12:31 Changeset [6880] by melissa
Couple of findbugs fixes, see #546.
11:02 Changeset [6879] by melissa
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 melissa
fixed: (In [6878]) Fixed bugs in writing and reading JPEG- and …
10:48 Changeset [6878] by melissa
Fixed bugs in writing and reading JPEG- and JPEG-2000-compressed TIFFs. …
09:28 Changeset [6877] by melissa
* 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 callan
fixed: (In [6876]) Some further test case cleanup. Added a check to ChannelFiller …
06:01 Changeset [6876] by callan
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 callan
It should be possible to at least initialize the reader state when BinData …

09/02/10:

17:07 Changeset [6875] by melissa
Fixed handling of multi-position ND2 datasets.
15:29 Changeset [6874] by curtis
Better series handling when number of series is extremely large.
11:43 Ticket #547 (Add system property values to ImageJ plugins log) created by melissa
In particular, it would be useful to have java.version and java.class.path …
11:33 Changeset [6873] by curtis
Update location of LegacyQTTools class.
10:43 Ticket #543 (OMETiffWriter.close() can leak file descriptors) closed by melissa
fixed: (In [6872]) Fixed OMETiffWriter.close() so that it releases resources even …
10:43 Changeset [6872] by melissa
Fixed OMETiffWriter.close() so that it releases resources even if an …
02:21 Changeset [6871] by callan
Removed erroneous STDERR debugging statement from test case.

09/01/10:

16:59 Changeset [6870] by melissa
Added JUnit JAR to build classpath, and made a few minor tweaks to test …
16:56 Changeset [6869] by curtis
Add a note stating that metadata can also be viewed in Image Info.
16:51 Changeset [6868] by melissa
Merged trunk r6867 into junit-test-suite.
16:34 Ticket #546 (Make findbugs happy) created by melissa
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 melissa
See, for instance, the output of: […] on the junit-test-suite branch.
16:14 Changeset [6867] by melissa
Migrated data-driven writer tests to JUnit. See #498.
16:13 Changeset [6866] by melissa
Removed support for JPEG/JPEG-2000 compression in OME-XML files, as this …
15:01 Ticket #539 (Skip tests when setId fails) closed by melissa
fixed: (In [6865]) Skip tests if IFormatReader.setId(String) failed. Closes …
15:01 Changeset [6865] by melissa
Skip tests if IFormatReader.setId(String) failed. Closes #539.
13:35 Ticket #544 (Native support for Quicktime Sorenson 1 codec (SVQ1)) created by melissa
See file in data/quicktime/jesper/. This file can be opened using the …
13:06 Changeset [6864] by melissa
Several tweaks to original metadata storage so that FV1000 files do not …
11:59 Changeset [6863] by melissa
Added missing methods that prevented r6862 from compiling.
11:58 Changeset [6862] by melissa
Simplified search for BinData offsets.
10:20 Changeset [6861] by callan
Reverting erroneous debugging in OMEXMLReader from r6860.
10:17 Changeset [6860] by callan
Added a test case (and re-organized some of the mock infrastructure) for …

08/31/10:

14:57 Changeset [6859] by curtis
Remove bogus quote escape characters.
14:51 Changeset [6858] by curtis
Clarify 'Display metadata' option to be less misleading.
09:55 Ticket #543 (OMETiffWriter.close() can leak file descriptors) created by melissa
An exception during writer.close(): […] leads to …

08/30/10:

14:10 Changeset [6857] by melissa
Added support for multi-chunk AVI files.
09:21 Changeset [6856] by melissa
Fixed sub-image reading for SimplePCI files that contain embedded TIFFs.

08/28/10:

12:53 Changeset [6855] by melissa
Backported r6068 to 4.1.

08/27/10:

17:08 Ticket #542 (Multi-series stitching is incorrect) created by curtis
When stitching a dataset with multiple image series distributed across …
17:04 Changeset [6854] by curtis
Use INFO logging for AxisGuesser main.
17:03 Changeset [6853] by curtis
Use INFO logging in FilePattern main.
14:32 Changeset [6852] by melissa
Prevent a bunch of NPEs.
14:04 Changeset [6851] by melissa
* Added more informative logging. * Make sure that tests fail if files …

08/26/10:

15:38 Changeset [6850] by melissa
Initial version of data-driven JUnit tests, see #498. 'ant …
14:43 Changeset [6849] by curtis
Fix build warnings when using Ant 1.8+.
12:36 Changeset [6848] by curtis
Various improvements to Bio-Formats MATLAB bfopen script: * Better …
11:11 Changeset [6847] by melissa
Removed external URL from Location tests.

08/25/10:

15:55 Changeset [6846] by melissa
Added branch for migrating the data-driven tests to JUnit; see #498.
15:50 TestingNotes edited by melissa
Ordered tickets by priority. (diff)
15:24 Ticket #541 (Add support for Varian FID files) created by melissa
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 melissa
fixed: (In [6845]) Added support for Varian FDF files. Closes #474.
15:23 Changeset [6845] by melissa
Added support for Varian FDF files. Closes #474.
10:18 Changeset [6844] by melissa
Sped up original metadata hashtable population.
08:57 Changeset [6843] by melissa
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 melissa
fixed: (In [6842]) Added support for multi-position Zeiss LSM data. Closes #527.
16:42 Changeset [6842] by melissa
Added support for multi-position Zeiss LSM data. Closes #527.
15:56 TestingNotes edited by melissa
Added links to newly filed tickets. (diff)
15:56 Ticket #540 (Add Hudson jobs to run data-driven tests) created by melissa
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 melissa
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 melissa
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 melissa
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 melissa
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 melissa
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 melissa
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 melissa
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 melissa
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 melissa
Similar to the md5 test for full image planes, it would be a good idea to …
13:03 TestingNotes edited by melissa
(diff)
12:25 Changeset [6841] by melissa
* Updated MetadataConverter to properly handle LightSource attributes. * …
11:02 Changeset [6840] by callan
Support for type resolution of light sources. Re-run of code generation. …
06:59 Changeset [6839] by callan
Mock and tests for SPW model use with OME-XML.

08/23/10:

16:56 Changeset [6838] by melissa
One more signedness fix, as pointed out by Rubén Muñoz.
12:51 Changeset [6837] by curtis
Update bf-cpp invocation script: * Add loci_plugins library to the mix. …
10:26 Changeset [6836] by melissa
Fixed Image indexed passed to …
09:34 Ticket #445 (Feedback 2160: Leica lambda scans) closed by melissa
fixed: I believe this was fixed in 4.2.
09:32 Ticket #450 (Feedback 1489: OMX regression?) closed by melissa
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 melissa
invalid
09:30 Ticket #416 (Feedback 17) closed by melissa
invalid
09:22 Ticket #441 (Feedback 2110 : File handle error on MIAS plate) closed by melissa
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 melissa
fixed: Near as I can tell, this feature is no longer needed. Now that #273 is …
14:05 Changeset [6835] by melissa
A few changes to how pixels and dimension information are found. I'm not …
13:19 TestingNotes edited by melissa
Some updates to list of formats for which we can generate public data. (diff)
12:02 Changeset [6834] by melissa
Moved MetadataStore calls that depend on MetadataTools.populatePixels(...) …
09:47 TestingNotes edited by melissa
(diff)

08/19/10:

20:40 TestingNotes edited by melissa
(diff)
16:28 Changeset [6833] by curtis
Add latest Maven projects to the umbrella.
16:24 Changeset [6832] by curtis
Maven version of ome-plugins project.
16:21 Changeset [6831] by curtis
Add missing flow-cytometry pom.xml.
16:04 Changeset [6830] by curtis
Maven version of flow-cytometry project.
16:04 Changeset [6829] by curtis
Fix VisBio developer list.
15:42 Changeset [6828] by curtis
Migrate miscellaneous utilities to Maven.
15:20 Changeset [6827] by curtis
Convert slim-plotter to Maven project structure.
15:05 Changeset [6826] by melissa
Backported dimension detection changes.
14:50 Changeset [6825] by curtis
Add new projects to umbrella, and ignore target folders.
14:39 Changeset [6824] by curtis
Progress on Mavenization, including ome-io and visbio projects.
14:21 Ticket #529 (Parse metadata from TIFFs produced by Nikon Elements) closed by melissa
fixed: (In [6823]) Added reader for TIFFs produced by Nikon Elements. Closes …
14:21 Changeset [6823] by melissa
Added reader for TIFFs produced by Nikon Elements. Closes #529.
12:52 Changeset [6822] by melissa
Prevent extra (Logical)Channel objects from being populated.

08/18/10:

18:10 TestingNotes created by melissa
Assorted notes on future testing plans
17:46 Changeset [6821] by curtis
Add temporary workaround for Jace bug when class names have underscores.
17:45 Changeset [6820] by curtis
Add boot classpath to AutoProxy classpath.
17:25 Changeset [6819] by melissa
Factored ND2Handler out of NativeND2Reader. See #529.
15:42 Changeset [6818] by curtis
Set main class appropriately in deps jar.
15:37 Changeset [6817] by curtis
Fixed assembly for jar2lib-*-deps.jar.
15:33 Changeset [6816] by melissa
Fixed hack from r6804 so that it won't throw an AIOOB exception.
15:31 Changeset [6815] by curtis
Add assembly for creating jar2lib JAR with dependencies. Still buggy.
15:21 Changeset [6814] by melissa
Reverted a few changes from r6791 that prevented OME-TIFF files from being …
14:44 Changeset [6813] by curtis
Temporary place to house bf-cpp-specific Jar2Lib files.
14:42 Changeset [6812] by melissa
Reverse the order of the rows if a negative height was stored in the file. …
14:18 Changeset [6811] by curtis
Better layout for static resources.
14:09 Changeset [6810] by melissa
Force the pixel type to be unsigned, regardless of what is actually stored …
14:01 Changeset [6809] by curtis
Working version of Jar2Lib.
13:15 Changeset [6808] by melissa
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 melissa
fixed: (In [6807]) * Fixed bug in StringOption that prevented macro keys from …
13:01 Changeset [6807] by melissa
* Fixed bug in StringOption that prevented macro keys from being parsed …

08/17/10:

19:29 Changeset [6806] by curtis
Initial version of Jar2Lib implementation.
15:12 Ticket #530 (BD Pathway reader doesn't fully populate original metadata hashtable) closed by melissa
fixed: (In [6805]) * Added convenience method to loci.common.IniList to flatten …
15:12 Changeset [6805] by melissa
* Added convenience method to loci.common.IniList to flatten the IniTables …
13:17 Changeset [6804] by melissa
Hackish fix for some files that have an incorrect dimension order.
12:44 Changeset [6803] by melissa
Backported r6802 to 4.1 branch.
12:09 Changeset [6802] by melissa
* Ignore missing L2D scans, instead of throwing an exception. * More …
10:20 Changeset [6801] by melissa
* Parse metadata from SimplePCI TIFFs. * Slightly better Z/T detection for …
08:08 Changeset [6800] by melissa
Remove invalid characters from strings that will later be parsed into …

08/16/10:

15:58 Ticket #263 (Bio-Formats configuration dialog) closed by curtis
fixed: > Ability to install native JPEG2000 codec if needed Bio-Formats decodes …
14:51 Matlab edited by melissa
(diff)
14:23 Changeset [6799] by melissa
Fixed a few Bio-Rad Gel offset bugs.
12:37 Changeset [6798] by melissa
Added 'Object getSeriesMetadataValue(String)' to IFormatReader.
12:05 Ticket #526 (Parse metadata from S-FEG and Helios NanoLab TIFF files) closed by melissa
fixed: (In [6797]) Added support for FEI TIFF files, specifically those from …
12:05 Changeset [6797] by melissa
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 melissa
fixed: (In [6796]) Remainder of OME-XML validation fixes. Closes #520.
10:10 Changeset [6796] by melissa
Remainder of OME-XML validation fixes. Closes #520.

08/13/10:

15:53 Changeset [6795] by curtis
Backport r6792 to 4.2 branch.
15:50 Changeset [6794] by curtis
Backport r6789 to 4.2 branch.
13:46 Changeset [6793] by melissa
Changed logging level of missing interface messages from 'warn' to …
11:33 Ticket #528 (LUTs are lost in virtual stack mode) closed by melissa
fixed: (In [6792]) Preserve LUTs in virtual stack mode. Closes #528.
11:33 Changeset [6792] by melissa
Preserve LUTs in virtual stack mode. Closes #528.
09:18 Changeset [6791] by melissa
More OME-XML validation fixes, see #520.
09:06 Ticket #487 (Add support for ECAT7 files) closed by melissa
fixed: (In [6790]) Initial version of ECAT 7 reader. Closes #487.
09:06 Changeset [6790] by melissa
Initial version of ECAT 7 reader. Closes #487.

08/12/10:

14:45 Changeset [6789] by curtis
Fix for NullPointerException.

08/11/10:

17:38 Ticket #523 (Bio-Formats Windowless Importer is broken) closed by melissa
fixed: (In [6788]) If ImporterOptions.getId() returns null, prompt for a file …
17:38 Changeset [6788] by melissa
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 melissa
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 melissa
The metadata is very similar to what is in new ND2 files (i.e. lots of …
16:30 Changeset [6787] by melissa
Added extra sanity check when parsing doubles.
15:48 Changeset [6786] by melissa
More OME-XML validation fixes, see #520.

08/10/10:

14:39 Ticket #524 (Better documentation for command line tools) closed by melissa
fixed: (In [6785]) * bfconvert and showinf now exit if an unknown flag or …
14:39 Changeset [6785] by melissa
* bfconvert and showinf now exit if an unknown flag or argument is …
14:06 Changeset [6784] by melissa
More OME-XML validation fixes. See #520.
07:52 Changeset [6783] by melissa
Removed not-yet-existent CRIReader.

08/09/10:

13:20 Changeset [6782] by melissa
Parse physical pixel sizes for all series, instead of applying the first …
13:07 Changeset [6781] by melissa
Fixed tests in components/bio-formats; all tests should now pass.
11:54 Changeset [6780] by melissa
More thoroughly parse Z position values from single-file datasets.
10:22 Changeset [6779] by melissa
Fixed tag alignment problem.
09:34 Changeset [6778] by melissa
Prevent SlidebookReader from passing a negative int to setSeries.

08/06/10:

17:31 Changeset [6777] by curtis
Fix problem with ij.jar dependency resolution.
16:56 Changeset [6776] by curtis
First cut at Maven-based build system and directory layout for LOCI …
15:56 Changeset [6775] by curtis
Experimental branch for Maven-based builds.
11:39 Ticket #528 (LUTs are lost in virtual stack mode) created by curtis
When opening a single-channel dataset with the Bio-Formats Importer with …
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