Timeline


and

11/19/09:

16:51 Ticket #438 (Allow readers to report whether or not companion files can be expected) created by melissa
i.e. add something like 'public static boolean hasCompanionFiles()' to …
16:13 Ticket #434 (Feedback 1528: OOM in ZVI) closed by melissa
fixed: (In [5709]) * Various bug fixes. * Reduced amount of memory required by …
16:13 Changeset [5709] by melissa
* Various bug fixes. * Reduced amount of memory required by ZeissZVIReader …
16:02 Changeset [5708] by curtis
Miscellaneous bugfixes (especially with the preview pane).
16:00 Changeset [5707] by curtis
Save VisBio output to a log file.

11/18/09:

12:44 Changeset [5706] by melissa
Prevent NPE if delegate reader was not initialized.
08:10 Changeset [5705] by melissa
Allow Deltavision files to have non-standard extensions.

11/17/09:

19:52 Ticket #437 (Feedback 1692: incell reader OOMs on text parse) closed by melissa
fixed: (In [5704]) Removed InCell ROI parsing; closes #437.
19:52 Changeset [5704] by melissa
Removed InCell ROI parsing; closes #437.
17:54 Ticket #437 (Feedback 1692: incell reader OOMs on text parse) created by omero-qa
 http://qa.openmicroscopy.org.uk/qa/feedback/1692/
15:13 Changeset [5703] by melissa
Fixed LUT parsing for multi-file BioRad datasets.
14:28 Changeset [5702] by curtis
Better logging for C++ proxy generation.
13:50 Changeset [5701] by curtis
Fix problem with -preload: do not create a DIS if the RAF was directly …
13:25 Changeset [5700] by curtis
Add debug messages to Location mapping methods.
13:24 Changeset [5699] by curtis
Better feedback when caching data with "-preload" flag.
11:54 Ticket #436 (Improve ND2 initialization time) created by melissa
Many Nikon ND2 files (particularly the JPEG-2000 variant) take a long time …

11/16/09:

15:34 Changeset [5698] by curtis
Eliminate CMake policy warnings.
15:24 Changeset [5697] by curtis
Workaround for AutoProxy's extreme logging verbosity.
13:46 Changeset [5696] by melissa
Always ignore the file pattern if fileGroupOption(id) == MUST_GROUP.
12:55 Changeset [5695] by melissa
Fixed AIOOB.
12:20 Ticket #435 (Feedback 1526: String index error) closed by melissa
fixed: (In [5694]) Prevent StringIndexOutOfBoundsException when parsing Objective …
12:20 Changeset [5694] by melissa
Prevent StringIndexOutOfBoundsException when parsing Objective data. …
11:46 Changeset [5693] by melissa
* Throw a more informative exception if an invalid file pattern is passed …
11:35 Changeset [5692] by curtis
Some fixes for compiling Bio-Formats C++ bindings on Windows: * Set …
10:15 Changeset [5691] by melissa
One more Filter linkage fix.
09:00 Changeset [5690] by melissa
Populate Shape.StrokeColor.

11/15/09:

17:30 Changeset [5689] by callan
Merging r5688 from Trunk
17:29 Changeset [5688] by callan
Handling cases where the plane index is not present
15:46 Changeset [5687] by melissa
Fixed linkages for simultaneous scan files.

11/14/09:

13:37 Changeset [5686] by melissa
Tiling fixes.

11/13/09:

12:03 Changeset [5685] by melissa
MIAS masks are now packed bit masks.
09:54 Ticket #435 (Feedback 1526: String index error) created by omero-qa
 http://qa.openmicroscopy.org.uk/qa/feedback/1526/
09:44 Ticket #434 (Feedback 1528: OOM in ZVI) created by omero-qa
 http://qa.openmicroscopy.org.uk/qa/feedback/1528/

11/12/09:

04:13 Changeset [5684] by callan
Merging r5628 and r5651 from Trunk

11/11/09:

10:57 Changeset [5683] by melissa
Reduced initialization time for Flex datasets.
07:58 Ticket #385 (Generated OME-XML has an invalid DisplayOptions element) closed by melissa
fixed: DisplayOptions is not populated as of r5535.

11/10/09:

16:27 Changeset [5682] by curtis
Relicense Bio-Formats C++ bindings and Bio-Formats ITK plugin under a …
13:50 Changeset [5681] by melissa
Ensure that the XML string starts with '<'.
12:19 Changeset [5680] by melissa
Prevent StringIndexOutOfBoundsException when parsing key/value pairs.

11/09/09:

15:10 Changeset [5679] by melissa
Tweaked tiled image handling.
09:06 Changeset [5678] by melissa
Place timestamps in original metadata hashtable and populate …
08:13 Changeset [5677] by melissa
Prevent measurement files from being duplicated in the used file list.

11/07/09:

11:35 Changeset [5676] by melissa
Tweaked pixel offset calculation.

11/06/09:

08:25 Changeset [5675] by melissa
Check that TIFF comment has not been truncated.

11/05/09:

16:24 Changeset [5674] by curtis
Tweak error messages.
15:13 Changeset [5673] by curtis
Preallocate byte buffer.
14:22 Changeset [5672] by curtis
Vastly improved performance for Bio-Formats ITK plugin.

11/04/09:

16:40 Changeset [5671] by curtis
Progress on Bio-Formats ITK plugin. But still broken.
16:39 Changeset [5670] by curtis
Add convenience method for getting stack trace string.
12:44 Changeset [5669] by curtis
Add note to look into using Java enums later.
12:42 Changeset [5668] by curtis
Add IFD.getIFDTextValue convenience method; clean up a few IFD calls.
12:10 Changeset [5667] by curtis
More LOCI logos.
11:18 Changeset [5666] by curtis
Fix OSGi version numbers to match latest 4.1.0 release.
10:36 Changeset [5665] by melissa
Prevent AIOOB if the tile index is greater than the total number of tiles.
09:52 Ticket #430 (Feedback 1018: ArrayIndexOutOfBounds in ZeissLSM) closed by melissa
fixed: (In [5664]) Several minor bugfixes. Closes #430.
09:52 Changeset [5664] by melissa
Several minor bugfixes. Closes #430.

11/03/09:

15:36 Changeset [5663] by curtis
Add exception handling for Bio-Formats calls.
12:38 Changeset [5662] by curtis
Minor tweak.
10:02 Changeset [5661] by melissa
Override fileGroupOption(String) and populate WellSample.ImageRef.
09:48 Changeset [5660] by melissa
Ensure that the series is correct before constructing a virtual stack.

11/02/09:

16:12 Changeset [5659] by melissa
Fixed bugs exposed by test suite.
11:40 Changeset [5658] by melissa
Sequential Leica LIFs now populate DetectorSettings and …

10/30/09:

14:29 Ticket #433 (Consider adding getBitsPerPixel() to IFormatReader) created by melissa
'int getBitsPerPixel()' would complement the existing 'int getPixelType()' …
11:15 Changeset [5657] by melissa
Merged r5655 and r5656 into 4.1 branch.
11:02 Changeset [5656] by melissa
Don't allow close() to clear the 'isBigTiff' flag.
10:59 Changeset [5655] by melissa
Only populate Plane attributes if the plane index is smaller than the …

10/29/09:

12:17 Changeset [5654] by melissa
Removed unnecessary method and fixed exception with multi-Image datasets.
12:02 Changeset [5653] by melissa
Merged r5635 and r5652 into 4.1 branch.
10:57 Changeset [5652] by melissa
Updated to support multiple positions and multiple timepoints. Based on a …
09:03 Changeset [5651] by melissa
Fixed Mask indices.

10/28/09:

14:48 Changeset [5650] by curtis
Cease blanket namespace usage, to avoid global name conflicts.
14:45 Changeset [5649] by curtis
Fix Bio-Formats ITK plugin compilation.
14:26 Changeset [5648] by curtis
Cease blanket namespace usage, to avoid global name conflicts.
13:49 Changeset [5647] by melissa
* Added loci.tests.EnumTest for testing enumeration package. * Updated …
13:17 Changeset [5646] by curtis
Fix Bio-Formats OSGi version.
12:57 Changeset [5645] by curtis
Fix JAR manifests.
12:43 Changeset [5644] by melissa
* IEnumerationProvider methods now throw EnumerationException. * Finished …
12:30 Changeset [5643] by curtis
Split out OSGi generation into its own target.
11:55 Changeset [5642] by callan
* Fixed up some class hierarchy issues, now using "Enumeration" interface …
06:42 Changeset [5641] by callan
Enumeration types from ROI, SPW and OME schema. Fixed issues with …

10/27/09:

22:16 Changeset [5640] by melissa
Added enumeration classes. Binning and PixelType classes were omitted, as …
20:49 Changeset [5639] by melissa
Updated IEnumerationHandler interface.
17:06 Changeset [5638] by melissa
Fixed time increment calculation.
15:04 Changeset [5637] by melissa
Tweaked axis order if 'field' and 'T' are the only axes.
13:22 Changeset [5636] by curtis
Add accessors to get IFDs from the TIFF reader.
11:38 Changeset [5635] by melissa
Ensure that all .res files are picked up if a .mea file is selected.
08:37 Changeset [5634] by melissa
Changed trunk version number to 4.2-DEV.
08:25 Ticket #429 (Feedback 1020 : ArrayIndexOutOfBounds w/ InCell) closed by melissa
fixed: Resolved in r5633.
08:23 Changeset [5633] by melissa
Prevent AIOOB exceptions if a malformed text file is encountered. Closes …
07:49 Ticket #432 (Feedback 1022: bioformats version # is still 4.0.1) closed by melissa
fixed: (In [5632]) Updated version number in trunk. Closes #432.
07:49 Changeset [5632] by melissa
Updated version number in trunk. Closes #432.
02:53 Ticket #432 (Feedback 1022: bioformats version # is still 4.0.1) created by omero-qa
 http://qa.openmicroscopy.org.uk/qa/feedback/1022/
02:33 Ticket #431 (Feedback 1012: ArrayIndexOutOfBound in Slidebook) created by omero-qa
 http://qa.openmicroscopy.org.uk/qa/feedback/1012/
02:32 Ticket #430 (Feedback 1018: ArrayIndexOutOfBounds in ZeissLSM) created by omero-qa
 http://qa.openmicroscopy.org.uk/qa/feedback/1018/
02:27 Ticket #429 (Feedback 1020 : ArrayIndexOutOfBounds w/ InCell) created by omero-qa
 http://qa.openmicroscopy.org.uk/qa/feedback/1020/

10/26/09:

20:26 Changeset [5631] by melissa
Some improvements to tile stitching logic. Images with missing tiles are …
18:41 Ticket #428 (Add enumeration for OME-XML versions) created by melissa
The enumerations interfaces …
18:34 Ticket #427 (Add support for Imacon (.fff) files) created by melissa
Preliminary research indicates that this is a TIFF-based file format, …
15:02 Changeset [5630] by melissa
Enumeration interfaces are now typed, and no longer use concrete …
14:03 Changeset [5629] by melissa
* Initial version of enumeration interfaces. * Added …

10/23/09:

09:40 Changeset [5628] by melissa
Don't populate any Mask attributes if parseMasks is set to false.
07:34 Ticket #399 (Remove deprecated methods from AWTImageTools) closed by melissa
fixed: Deprecated methods removed by Curtis by r5590.

10/21/09:

09:07 Changeset [5627] by melissa
Added debugging statement and more informative error messages.
07:29 Milestone bio-formats-4.1 completed
Bio-Formats release corresponding to OMERO Beta 4.1. The primary focuses …
07:18 Changeset [5626] by melissa
4.1 release of LOCI Tools

10/20/09:

08:47 Changeset [5625] by melissa
* Tweaked ordering of used file list. * Updated metadata support docs. * …
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