Timeline


and

10/13/09:

17:59 Changeset [5589] by melissa
Branched for 4.1 release.
15:49 Changeset [5588] by curtis
* Better separation of Jace and bf-cpp components. * Draft of …
15:26 Changeset [5587] by curtis
Finish transition of readers from openImage to openData.
08:08 Changeset [5586] by melissa
Updated docs to reflect status of XML validation tests.

10/12/09:

16:49 Changeset [5585] by curtis
Better QTJava logic in case of Mac OS X with 64-bit JVM.
15:43 Ticket #417 (Feedback 144:showinf fails on remove invocation) closed by melissa
invalid: This exception is expected, as 'showinf' is attempting to display images. …
15:37 Ticket #419 (Feedback 140: NPE in reader) closed by melissa
fixed: (In [5584]) Fixed name mapping on Windows. Closes #419.
15:37 Changeset [5584] by melissa
Fixed name mapping on Windows. Closes #419.
12:57 Changeset [5583] by melissa
Fixed compile error.
12:44 Changeset [5582] by melissa
Throw MissingLibraryException instead of NPE if jai-imageio.jar is not in …
12:08 Changeset [5581] by melissa
Split MaskPixels.BinData parsing into separate method, which can be called …
10:53 Ticket #415 (Lossless JPEG codec performs invalid bit operations) closed by melissa
fixed: (In [5580]) Fixed bit reading problem in Huffman codec. Closes #415.
10:53 Changeset [5580] by melissa
Fixed bit reading problem in Huffman codec. Closes #415.
10:15 Ticket #405 (OME-TIFF export erroneously reuses OME metadata from input dataset) closed by melissa
fixed: (In [5579]) Modify the input dataset's OME-XML before exporting. Closes …
10:15 Changeset [5579] by melissa
Modify the input dataset's OME-XML before exporting. Closes #405.
09:42 Changeset [5578] by melissa
Correct for incorrectly calculated dimensions.
09:28 Changeset [5577] by melissa
More descriptive series names.
08:24 Ticket #406 (Split channels on export if there are 2 or >=4 16-bit RGB channels) closed by melissa
fixed: (In [5576]) Split 16-bit RGB images before saving to a TIFF file. Closes …
08:24 Changeset [5576] by melissa
Split 16-bit RGB images before saving to a TIFF file. Closes #406.
07:43 Changeset [5575] by melissa
* Allow writers to specify supported pixel types by codec. * Fixed a few …

10/11/09:

13:03 Ticket #411 (Add support for Olympus ScanR) closed by melissa
fixed: (In [5574]) Added Olympus ScanR reader. Closes #411.
13:03 Changeset [5574] by melissa
Added Olympus ScanR reader. Closes #411.
11:25 Ticket #420 (Feedback 145: exported tiffs cannot be opened with) created by omero-qa
 http://qa.openmicroscopy.org.uk/qa/feedback/145/ the issue where …
09:49 Ticket #419 (Feedback 140: NPE in reader) created by omero-qa
 http://qa.openmicroscopy.org.uk/qa/feedback/140/
09:45 Ticket #418 (Feedback 134: multithreading issue) created by omero-qa
 http://qa.openmicroscopy.org.uk/qa/feedback/134/
09:45 Ticket #417 (Feedback 144:showinf fails on remove invocation) created by omero-qa
 http://qa.openmicroscopy.org.uk/qa/feedback/144/ Running `showinf ... …

10/09/09:

11:26 Changeset [5573] by melissa
Better transmission Detector population.
07:57 Changeset [5572] by melissa
Link Lasers to LogicalChannels in the same way that Detectors and Filters …
04:21 Changeset [5571] by melissa
Prevent null values from being passed to MetadataStore setters.
04:04 Changeset [5570] by melissa
More fixes to Detector/Filter linkages.

10/08/09:

23:54 Changeset [5569] by curtis
Add MissingLibraryException to C++ header.
23:53 Changeset [5568] by curtis
Fix gen-bf-cpp problem on Windows.
22:27 Ticket #384 (Generated OME-XML should use proper namespaces where appropriate) closed by curtis
fixed: Fixed in r5529.
16:41 Changeset [5567] by melissa
Fixed emission filter linkages.
16:20 Changeset [5566] by melissa
Fixed duplicate channel names.
13:58 Changeset [5565] by melissa
MIAS reader now respects isMetadataCollected().
13:25 Changeset [5564] by melissa
* Moved getDomains(String) to getPossibleDomains(String). * Added …
12:10 Changeset [5563] by melissa
Fixed channel ordering and transmittance range population bugs.
09:25 Changeset [5562] by melissa
Verify that all variables are cleared when close(false) is called.
09:20 Changeset [5561] by melissa
Added a bunch of debugging statements.
07:55 Changeset [5560] by melissa
Fixed behavior of getSeriesUsedFiles(true) for single-file Metamorph …
04:09 Changeset [5559] by callan
Attempt to fix race condition when working with LSM files in multiple …

10/07/09:

14:37 Changeset [5558] by melissa
More fixes for Detector/Filter/LogicalChannel linkages and wavelength …
12:33 Changeset [5557] by melissa
* Fixed regression with opening indexed color images in ImageJ. * Changed …
11:51 Changeset [5556] by melissa
Fixed last round of Detector and Filter linkage problems.
10:36 Changeset [5555] by melissa
* Added status messages to colorizer plugin. * Faster channel merging for …
09:38 Changeset [5554] by callan
Allow access to the IFormatReader member variable from the …

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.
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