Timeline


and

09/17/10:

17:32 WikiStart edited by curtis
(diff)
17:31 WikiStart edited by curtis
(diff)
17:30 Changeset [6957] by curtis
Merge native projects with main projects tree.
17:28 Changeset [6956] by curtis
Add SLIM-curve project.
16:02 Ticket #514 (Fix Image5D and View5D view modes) closed by curtis
fixed: I reviewed the View5D code, and there is simply no way to avoid invoking a …
13:04 Changeset [6955] by curtis
Remove obsolete ignore rules.
13:02 Changeset [6954] by curtis
Ignore Eclipse metadata files.

09/16/10:

15:34 Ticket #562 (MIAS import fails with NPE) closed by melissa
fixed: (In [6953]) Allow MIAS text files to be passed to MIASReader.setId. …
15:34 Changeset [6953] by melissa
Allow MIAS text files to be passed to MIASReader.setId. Closes #562.
13:54 Ticket #555 (OME-TIFF reader resets Image Name) closed by melissa
fixed: (In [6952]) Prevent Image names from being overwritten. Closes #555.
13:54 Changeset [6952] by melissa
Prevent Image names from being overwritten. Closes #555.
13:43 Changeset [6951] by melissa
Backported r6714, r6716, r6948, and r6949 to 4.2. See #557.
13:39 Changeset [6950] by curtis
Backport r6948,r6949 to 4.2 branch.
13:21 Ticket #557 (Virtual stack channel-specific LUTs are not preserved) closed by melissa
fixed: (In [6949]) Ensure that LUTs are properly preserved when using a virtual …
13:21 Changeset [6949] by melissa
Ensure that LUTs are properly preserved when using a virtual stack. …
09:50 Changeset [6948] by melissa
Don't apply lookup tables if there is more than one channel and we cannot …
09:09 Ticket #563 (Add support for OME-TIFF files produced by Leica Matrix scanner) created by melissa
These are similar to "Leica OME" files, see #386. The primary difference …
05:43 Changeset [6947] by callan
Merging r6715 from Trunk. (See #543)

09/15/10:

12:23 Changeset [6946] by curtis
Remove broken Bio-Formats Ice component, for now.
12:01 Ticket #551 ("waitTime" not parsed from Prairie datasets) closed by melissa
fixed: (In [6945]) Parse 'waitTime' from Prairie datasets. Closes #551.
12:01 Changeset [6945] by melissa
Parse 'waitTime' from Prairie datasets. Closes #551.
08:40 Ticket #562 (MIAS import fails with NPE) created by melissa
Data: …
07:09 Changeset [6944] by callan
Merging r6943 from Trunk. (See #561)
07:08 Ticket #561 (ServiceFactory file handle leak) closed by callan
fixed: (In [6943]) Solution to potential service factory file handle leak. (Fixes …
07:08 Changeset [6943] by callan
Solution to potential service factory file handle leak. (Fixes #561)
07:07 Ticket #561 (ServiceFactory file handle leak) created by callan
It is possible for instantiations of the ServiceFactory to leak file …

09/14/10:

20:34 Changeset [6942] by aivar
Added m_free, describes which parameters are free vs. fixed. Commented out …
20:32 Changeset [6941] by aivar
Added m_free, describes which parameters are free vs. fixed.
20:30 Changeset [6940] by aivar
Removed m_free: This information belongs to the curvefitter instance, not …
20:29 Changeset [6939] by aivar
Handles m_free, which parameters are free vs. fixed. Loads dynamic library …
20:26 Changeset [6938] by aivar
Handles m_free, which parameters are free vs. fixed.
18:22 Changeset [6937] by curtis
Remove obsolete test folder.
16:35 Changeset [6936] by curtis
Fix up license for utils project.
16:30 Changeset [6935] by curtis
Fix typo in ome-notes license link.
16:29 Changeset [6934] by curtis
Fix up license for test-suite project.
16:20 Changeset [6933] by curtis
Fix up license for flow-cytometry project.
16:16 Changeset [6932] by curtis
Fix up license for slim-plugin project.
16:05 Changeset [6931] by curtis
Fix up license for jvmlink project.
16:02 Changeset [6930] by curtis
Fix up license for lwf-stubs project.
15:58 Changeset [6929] by curtis
Fix up license for multi-lut project.
15:53 Changeset [6928] by curtis
Fix up license for loci-checks project.
15:49 Changeset [6927] by curtis
Fix up license for misc-plugins project.
15:49 Changeset [6926] by curtis
Fix up license for jar2lib project.
15:48 Changeset [6925] by curtis
Fix up license for curve-fitter project.
14:51 Changeset [6963] by rlentz
12:06 Changeset [6924] by curtis
Use line comments for proper function documentation.
10:49 Changeset [6923] by callan
Fixing infinite loop introduced by merging r6367 from Trunk. (See #560)
10:44 Changeset [6962] by rlentz
latest
10:10 Changeset [6922] by callan
Merging r6367 from Trunk. (See #560)
07:47 Ticket #560 (Fix multi-line description MetaMorph ND files) created by callan
When a MetaMorph ND file has a multi-line description setId() fails with …
06:27 Changeset [6921] by callan
A solution for file handles being left hanging around after close() on …

09/13/10:

16:59 Changeset [6961] by rlentz
16:25 Changeset [6960] by rlentz
Initial import.
12:12 Ticket #559 (LSM reader XT linescan opened as XY) created by curtis
From Dan White: The y dim is a single pixel, and the other dim is time, …
09:57 Changeset [6920] by callan
Merged r6743 and r6872 from Trunk. (See #543)
08:11 Changeset [6919] by callan
Merging r6917 from Trunk.
08:05 Changeset [6918] by callan
Merged r6917 and r6916 from Trunk.
07:53 Ticket #558 (MetaMorph ND handling for underscores) closed by callan
fixed: (In [6917]) Solution for underscores in wavelength names. (Fixes #558)
07:53 Changeset [6917] by callan
Solution for underscores in wavelength names. (Fixes #558)
07:52 Changeset [6916] by callan
Moved the 'getHandle()' log statement to the TRACE level to avoid DEBUG …
07:15 Ticket #558 (MetaMorph ND handling for underscores) created by callan
When an underscore is present in the wavelength name in the ND file, …

09/10/10:

17:48 Ticket #557 (Virtual stack channel-specific LUTs are not preserved) created by curtis
When opening a dataset with channel-specific LUTs as a virtual stack, all …
17:18 Ticket #556 (OME-TIFF reader should use MetadataOnly rather than BinData) created by curtis
When producing an output OME-XML block, the OME-TIFF reader should inject …
17:16 Ticket #555 (OME-TIFF reader resets Image Name) created by curtis
When reading an OME-TIFF file such as multi-channel-4D-series.ome.tif, …
16:51 Changeset [6915] by curtis
Remove obsolete components folder.
16:51 Changeset [6914] by curtis
Initial version of autogen Maven project. Needs cleaning up.
16:02 Changeset [6913] by curtis
Begin migration of autogen project to Maven.
14:50 Ticket #554 (Exporting a multi-series OME-TIFF file results in incorrect pixel data) created by melissa
[…] Evidently produces a file with all series identical.
14:44 Ticket #553 (Add support for Zeiss Axiovision TIFFs) created by melissa
See files in data/zeiss-axiovision/.
14:42 Ticket #552 (Add support for Zeiss .lms files) created by melissa
See files in data/zeiss-lms/.
10:54 Changeset [6912] by curtis
Remove Bio-Formats Ice package for now.

09/09/10:

17:06 Changeset [6911] by curtis
Miscellaneous small tweaks.
16:02 Changeset [6910] by callan
Merging commits (r6690, r6692, r6735, r6784, r6786) from Trunk with …

09/08/10:

18:55 Changeset [6909] by curtis
Remove non-Maven version of test-suite project.
18:50 Changeset [6908] by curtis
Maven version of test-suite project.
17:19 Changeset [6907] by curtis
Tweak Maven repositories list.
16:55 Changeset [6906] by curtis
Maven version of Aivar's standalone ImageJ plugins.
16:45 Changeset [6905] by curtis
Add fiji-lib dependency for slim-plugin; it compiles now.
14:47 Changeset [6904] by aivar
Commented out version 1.0.13 BarRender method to work with version 12 in …

09/07/10:

23:56 Changeset [6903] by curtis
Move Bio-Formats command line tools to default Maven scripts path.
23:54 Changeset [6902] by curtis
Add additional projects to umbrella.
23:51 Changeset [6901] by curtis
Tweak some licenses.
23:51 Changeset [6900] by curtis
POM for Jama.
23:46 Changeset [6899] by curtis
New curve fitter package, migrated from …
23:23 Changeset [6898] by curtis
New curve fitter package, migrated from …
23:20 Changeset [6897] by curtis
Update SLIM Plotter to work with jaolho LMA v1.3.
13:51 Changeset [6896] by curtis
More efficient XML sanitation algorithm.
11:09 Ticket #551 ("waitTime" not parsed from Prairie datasets) created by melissa
The "waitTime" key in the .cfg file should be parsed into both the …
00:07 Changeset [6895] by curtis
Maven version of loci-checks.

09/06/10:

23:58 Changeset [6894] by curtis
Fix ome-editor author.
23:37 Changeset [6893] by curtis
Maven version of ome-editor.
22:58 Changeset [6892] by curtis
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 melissa
fixed: (In [6891]) Disable color mode options when the stack view is set to …
15:10 Changeset [6891] by melissa
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 melissa
The number of wells acquired in each row is assumed to be either 0, or …
13:00 Changeset [6890] by melissa
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 melissa
fixed: (In [6889]) Added system properties to ImageJ plugin log. Closes #547.
12:05 Changeset [6889] by melissa
Added system properties to ImageJ plugin log. Closes #547.
12:04 Changeset [6888] by melissa
Updated XMLTools.sanitizeXML to remove invalid "&#" sequences.
11:06 Changeset [6887] by melissa
Backported r6839, r6840, and r6841 to 4.2.
10:15 Changeset [6886] by melissa
* Improved metadata parsing for Prairie datasets. * Reverted changes to …
07:18 Changeset [6885] by curtis
Maven version of legacy Multi-LUT application.

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.
Note: See TracTimeline for information about the timeline view.