Timeline


and

10/06/09:

19:13 Changeset [5553] by melissa
Fixed a couple of core metadata bugs.
15:43 Changeset [5552] by curtis
Add subclass of FormatException for missing libraries.
15:42 Changeset [5551] by curtis
Fix up Ant build system; add OSGi bundle export to JAR production.
13:58 Changeset [5550] by melissa
* Better bounds checking in FlexReader.getSeriesUsedFiles. * Fixed a few …
12:31 Changeset [5549] by melissa
Fixed getUsedFiles() omissions.
10:45 Ticket #416 (Feedback 17) created by omero-qa
 http://qa.openmicroscopy.org.uk/qa/feedback/17/ primarily testing out …

10/05/09:

09:10 Changeset [5548] by melissa
* Added enumeration checking to OME-XML MetadataStore implementations. * …

10/02/09:

14:36 Changeset [5547] by melissa
Fixed thumbnail scaling for signed images.
13:50 Changeset [5546] by melissa
Fixed type checking when an absolute path is used.
11:55 Changeset [5545] by melissa
Set Detector.Type to PMT when appropriate.
10:37 Changeset [5544] by melissa
Better type checking for .cfg files.
09:05 Changeset [5543] by melissa
Add thumbnail TIFFs to used file list.
08:47 Changeset [5542] by melissa
* Changed signatures of MetadataStore.setMaskPixelsBinData and …

10/01/09:

15:50 Changeset [5541] by melissa
Use value of MultiBand.Channel to link Filters and LogicalChannels.
15:20 Changeset [5540] by melissa
A few tweaks to Detector and Laser population/linkage.
12:12 Changeset [5539] by melissa
Fixed node caching problem.
11:19 Changeset [5538] by melissa
One more fix for sequential LEI data.
08:39 Changeset [5537] by melissa
Fixed Detector and Filter linkages for sequential scan data.

09/30/09:

20:25 Changeset [5536] by melissa
Use separate readers for the input file and converted files.
20:23 Changeset [5535] by melissa
* Removed most calls to MetadataStore.setDisplayOptions* * Make sure that …
16:50 Changeset [5534] by curtis
Update Eclipse JARs and remove a couple of unused imports.
16:32 Changeset [5533] by curtis
Better way of doing OME-XML validation hack.
11:33 Changeset [5532] by melissa
A couple of Quicktime conversion and test suite fixes.

09/29/09:

12:49 Changeset [5531] by melissa
* Allow test-convert target to be run on a directory, in addition to …
10:27 Changeset [5530] by curtis
Add hack to suppress BinData/TiffData validation errors.
10:17 Changeset [5529] by curtis
Working version of OME-XML reordering stylesheet, plus other validation …
10:05 Changeset [5528] by melissa
* Added NetCDF dependencies to Bio-Formats runtime classpath. * Only allow …

09/28/09:

19:05 Ticket #415 (Lossless JPEG codec performs invalid bit operations) created by curtis
Sometimes the lossless JPEG codec attempts to extract a negative number of …
18:56 Changeset [5527] by curtis
Some tweaks to the bit logic.
18:16 Changeset [5526] by curtis
Fixes to Bio-Formats OME-XML reordering stylesheet. But still has issues.
15:35 Changeset [5525] by curtis
Revert unknown file format message, in case anyone was relying on it.
14:37 Changeset [5524] by curtis
New FormatException subclass specifically for files in an unknown format.
14:11 Changeset [5523] by melissa
Lots of findbugs fixes.
14:10 Changeset [5522] by curtis
Minor clean up and argument checking.
13:39 Changeset [5521] by melissa
More changes to ensure that all of the metadata is placed in the metadata …
12:51 Changeset [5520] by melissa
* Leica LIF metadata validation fixes. * Fixed a few problems exposed by …
08:31 Changeset [5519] by melissa
Avoid setting null Detector properties.

09/26/09:

12:19 Changeset [5518] by melissa
* Added PrintDomains to loci.formats.tools. * Better checks for very large …
11:54 Changeset [5517] by melissa
Added two new methods to IFormatReader: boolean isSingleFile(String) …

09/25/09:

22:11 Changeset [5516] by melissa
Work-around for the case when TiffData.FileName is present, but the file …
15:11 Changeset [5515] by melissa
One more fix for multi-Z/multi-T datasets with more than 4 channels.
12:41 Changeset [5514] by melissa
* Revert to populating LogicalChannel.Name and Filter data using the …
11:43 Changeset [5513] by curtis
Small tweaks.
11:42 Changeset [5512] by curtis
Tweak include statement.
11:33 Changeset [5511] by melissa
* Added support for new metadata blocks. * Only link a Filter to a …
08:44 Changeset [5510] by melissa
* LogicalChannel.SecondaryEmissionFilter is now populated * Tweaked the …

09/24/09:

15:17 Changeset [5509] by melissa
More metadata fixes.
14:36 Changeset [5508] by curtis
Remove obsolete OMERO JARs; fix tools-ome target.
12:30 Changeset [5507] by melissa
Return blank planes if files were removed from the dataset.
11:33 Changeset [5506] by melissa
Fixed bug that prevented token replacement from occurring if …

09/23/09:

18:23 Changeset [5505] by curtis
Fix test suite dependencies in Ant targets.
17:28 Changeset [5504] by curtis
Add package statement for LOCI Common library.
16:36 Changeset [5503] by curtis
Fix test suite build path.
16:11 Changeset [5502] by melissa
Ant should now replace "@release.version@" in source files with "trunk" or …
15:18 Changeset [5501] by curtis
Some work on OmeroReader implementation of IFormatReader, for OMERO 4.0.x.
15:12 Changeset [5500] by curtis
Add compilation instructions for Windows.
14:45 Changeset [5499] by melissa
Added logic to handle ICS files produced by Lambert Instruments software.
14:09 Changeset [5498] by melissa
* Removed incorrect population of DetectorSettings.ReadOutRate. * Link …
13:57 Changeset [5497] by melissa
Lots of work on Instrument, LogicalChannel, and ROI metadata for Leica …

09/22/09:

12:21 Changeset [5496] by curtis
Findbugs target should not clean the build. :-P
12:14 Changeset [5495] by curtis
Fix toplevel Findbugs target.
11:15 Changeset [5494] by melissa
Fixed Zeiss LSM endianness bug.
10:58 Changeset [5493] by melissa
A few more fixes to Zeiss LSM, Leica LEI, and Olympus FV1000 metadata …

09/21/09:

20:34 Changeset [5492] by melissa
* Removed channel reordering logic. * Fixed channel naming and …
17:16 Changeset [5491] by melissa
Fixed LogicalChannel, Detector, and Filter population.
15:55 Changeset [5490] by curtis
Combine MetadataStore and MetadataRetrieve Ice interfaces into one …
13:27 Changeset [5489] by melissa
* Parse Mask ROIs from MIAS overlay TIFFs. * Fixed a bug in Base64 …
12:40 Changeset [5488] by curtis
Clean up dependencies.
10:35 Changeset [5487] by melissa
* Fix for OMERO QA #284. * Fixed a few bugs exposed by findbugs.
08:38 Changeset [5486] by melissa
Added findbugs target to root. This change is courtesy of Josh Moore.

09/19/09:

13:44 Changeset [5485] by melissa
Make sure that OMEXMLMetadata objects returned by …

09/18/09:

15:53 Changeset [5484] by melissa
Lots of work on metadata correction/completeness for Leica LEI.
11:43 Changeset [5483] by curtis
Fix some Eclipse warnings.
11:43 Changeset [5482] by curtis
Fix build problems with bf-ice.
11:35 Ticket #408 (Exception when opening files with > 512 series in ImageJ) closed by melissa
fixed: (In [5481]) An exception is no longer thrown if there are more than 512 …
11:35 Changeset [5481] by melissa
An exception is no longer thrown if there are more than 512 series. …
11:23 Changeset [5480] by curtis
Rename Eclipse project.
11:22 Changeset [5479] by curtis
Rename Bio-Formats Ice component to bf-ice.
10:18 Changeset [5478] by curtis
Fix some Eclipse problems and warnings.
08:46 Changeset [5477] by melissa
* Allow CellomicsReader to read *.dib (uncompressed bitmap) files. * …
07:53 Changeset [5476] by melissa
Fixed NPE.

09/17/09:

13:23 Changeset [5475] by callan
Fixed Eclipse classpath.
08:47 Changeset [5474] by melissa
Make sure that wells are sorted in the same order.

09/16/09:

21:35 Changeset [5473] by melissa
* Fixed problems exposed by directory import testing. * Minor progress on …
10:37 Changeset [5472] by melissa
* Removed calls to getGlobalMeta(String). * Background images are now …

09/15/09:

20:56 Changeset [5471] by dscho
Add an AmiraMesh reader This reader, authored by Gregory Jefferis and …
14:23 Changeset [5470] by melissa
* Fixed how findString(String...) behaves if there are multiple arguments. …

09/14/09:

13:14 Changeset [5469] by melissa
Make sure that LogicalChannel.Name is populated for InCell datasets.
11:11 Changeset [5468] by melissa
Do not group multiple plates together.
10:15 Changeset [5467] by curtis
Reorder generated OME-XML using the reorder-2008-09.xsl stylesheet.
08:08 Changeset [5466] by melissa
Fixed off-by-1 in Well.Column.

09/11/09:

15:29 Changeset [5465] by curtis
Throw FormatException if ImageIO returns an invalid BufferedImage.
13:41 Changeset [5464] by melissa
Fixed problem with datasets that have more than 4 channels and multiple Z …

09/10/09:

19:48 Changeset [5463] by curtis
Update Bio-Formats Ice package.
19:41 Changeset [5462] by curtis
Update Ice library to 3.3.1 from 3.2.1.
19:32 Changeset [5461] by curtis
Remove superfluous/obsolete call to MetadataStore.setImageObjective.
19:18 Changeset [5460] by curtis
MetadataStore changes: * Populate ROIs in Image, not DisplayOptions. * …
19:17 Changeset [5459] by curtis
Map timestamp and ROI metadata for LI-FLIM format; thanks to Nick Perry.
19:16 Changeset [5458] by curtis
Use new DateTools.getMillisFromTicks convenience method.
19:16 Changeset [5457] by curtis
Add convenience method for working with split dates in ticks (COBOL).
15:02 Changeset [5456] by curtis
Explicitly print contents of arrays.
13:52 Changeset [5455] by curtis
Simple utility for dumping all TIFF IFDs.
13:40 Changeset [5454] by curtis
First working (?) version of LI-FLIM reader.
13:39 Changeset [5453] by curtis
Fix bugs in float/double normalization algorithm.
09:52 Changeset [5452] by melissa
Override 'void close(boolean)', so that native/legacy readers are closed …

09/09/09:

16:12 Changeset [5451] by melissa
Allow the configuration file to specify multiple folders for a single …
09:21 Changeset [5450] by melissa
Throw a more informative exception if the companion file directory is …

09/08/09:

15:16 Ticket #414 (Serialize reader state) created by curtis
Some formats take a long time to parse. Often the reader implementations …
14:47 Changeset [5449] by curtis
Make DataTools.indexOf work better with nulls.
13:34 Ticket #401 (Split TiffTools into multiple utility classes) closed by curtis
fixed: This work has been completed, with logic split into several classes in a …
08:28 Changeset [5448] by melissa
Use stored Z step and time increment instead of calculating these values.

09/07/09:

15:45 Changeset [5447] by melissa
Minor cleanup, including removal of unused imports and use of generics.
14:18 Changeset [5446] by melissa
Search for .flex files in the 'Screening' and 'Archive' directories of the …
12:43 Changeset [5445] by melissa
Added utility to check for unused imports.
10:09 Changeset [5444] by melissa
Updated metadata documentation.

09/06/09:

23:21 Changeset [5443] by curtis
Fix some Eclipse warnings.
23:03 Changeset [5442] by curtis
Fix Eclipse compile errors.
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