Timeline


and

04/15/10:

17:05 Changeset [6129] by melissa
Updated more readers to respect MetadataOptions, and added some TIFF IFD …
14:37 Changeset [6128] by curtis
Fix some Eclipse warnings, clean up imports, minor progress on Importer …

04/14/10:

16:47 Changeset [6127] by melissa
Updated a few more readers to respect MetadataOptions.
11:56 Changeset [6126] by melissa
Fixed bug that caused a bunch of extra garbage bytes to be written to the …
11:50 Changeset [6125] by curtis
Improve robustness of color map parsing.
11:49 Changeset [6124] by curtis
Add explicit bounds checking to unpackBytes. Makes for nicer error …
11:12 Changeset [6123] by melissa
Hopefully fixed XML parsing problems introduced in r6000.

04/13/10:

16:21 Changeset [6122] by melissa
Set physical Z size, even if instrument data is not present.
16:01 Ticket #455 (Add support for Zip files with multiple entries) closed by melissa
fixed: (In [6121]) Preliminary support for reading Zip files with multiple …
16:01 Changeset [6121] by melissa
Preliminary support for reading Zip files with multiple entries. Closes …
15:05 Changeset [6120] by curtis
Remove tabs.
14:54 Changeset [6119] by curtis
Add note about alternate location for compiled class files.
12:22 Changeset [6118] by melissa
* Updated a few more readers to respect MetadataOptions. * Added utility …

04/12/10:

18:04 Changeset [6117] by melissa
* Updated Imaris readers to respect MetadataOptions. * Fixed a couple of …
15:44 Changeset [6116] by melissa
Updated a few more readers to respect MetadataOptions.
10:31 Ticket #484 (Investigate usage of FileChannel.map(...)) closed by melissa
fixed: See r6093 and r6100.
09:30 Changeset [6115] by bselinsky
Add Usage Messages and error handling

04/09/10:

15:37 Changeset [6114] by curtis
Begin rearranging some code.
14:27 Changeset [6113] by melissa
Fixed various whitespace issues in AmiraParameters, and updated a few more …
12:55 Changeset [6112] by melissa
Updated several readers to respect MetadataOptions.
09:59 Changeset [6111] by melissa
Fixed how channel indices are reset.
09:41 Changeset [6110] by bselinsky
add jar file support
09:40 Changeset [6109] by bselinsky
add jar file support
09:09 Ticket #487 (Add support for ECAT7 files) created by melissa
See examples files in data/ecat7/mark/.

04/08/10:

16:29 Changeset [6108] by melissa
Fixed a couple of TIFF export bugs.
14:34 Changeset [6107] by melissa
Make sure that all RandomAccessInputStreams are closed.
14:29 Changeset [6106] by bselinsky
add dependency lift file
14:08 Changeset [6105] by melissa
Prevent Image.CreationDate and PlaneTiming.DeltaT from being populated …
11:35 Changeset [6104] by melissa
* Make sure that DV log files are detected regardless of the …
11:25 Changeset [6103] by bselinsky
Adding options flags
11:23 Changeset [6102] by bselinsky
Adding option flags
10:40 Changeset [6101] by bselinsky
new
05:52 Changeset [6100] by callan
Moved byte buffer map() vs. allocate() to a static block and the state …

04/07/10:

17:22 Changeset [6099] by melissa
* Fixed a DICOM offset bug. * Prevent Packbits codec from seeking past the …
14:36 Changeset [6098] by melissa
* Allow the comment delimiter to be changed in IniParser. * Fixed a whole …

04/06/10:

21:51 Changeset [6097] by melissa
Fixed NPE.
18:59 Changeset [6096] by melissa
Moved plane index parsing; this substantially reduces parsing time.
13:35 Changeset [6095] by melissa
Cleaned up BD Pathway reader a bit; the reader now parses more metadata …
11:10 Changeset [6094] by melissa
* Prevent Leica reader from reading beyond the end of the file. * Fixed a …
10:29 Changeset [6093] by callan
Added byte buffer provider to compartmentalize the usage of map() vs. …
02:50 Changeset [6092] by callan
Removed an unused import and fixed a potential null pointer exception as …

04/02/10:

16:27 Changeset [6091] by melissa
Updated Flex reader to respect MetadataOptions.
13:07 Changeset [6090] by melissa
Updated InCell 1000 reader to respect MetadataOptions.

04/01/10:

14:57 Changeset [6089] by melissa
Updated ICS reader to respect MetadataOptions.
11:50 Changeset [6088] by melissa
Updated ScanR reader to respect MetadataOptions.
11:32 Changeset [6087] by melissa
Porting LIFReader changes from r6009 to 4.1 branch.
10:18 Changeset [6086] by melissa
Updated Leica LIF and Leica TCS readers to respect MetadataOptions.

03/31/10:

17:20 Ticket #481 (scan-deps.pl does not detect that unit tests depend upon log4j JARs) closed by curtis
fixed: Fixed in r6085. First of all, slf4j-log4j12-1.5.10.jar and …
17:10 Changeset [6085] by curtis
Fix problem with scan-deps and LOCI Common package. See ticket #481 for …
17:07 Changeset [6084] by melissa
Updated native ND2 reader to respect MetadataOptions.
16:39 Changeset [6083] by curtis
Add log4j libraries to LibraryChecker.
11:19 Changeset [6082] by melissa
Cache instances of OMEXMLService and ServiceFactory, instead of creating …
10:49 Changeset [6081] by melissa
Prevent dimensions stored in the text descriptions from overwriting …
10:13 Changeset [6080] by melissa
Updated Zeiss LSM reader to respect MetadataOptions.
09:37 Changeset [6079] by melissa
Updated MIAS reader to respect MetadataOptions.

03/30/10:

15:57 Changeset [6078] by melissa
* Deprecated setMetadataCollected/isMetadataCollected in favor of …
15:35 Changeset [6077] by melissa
* Fixed a bug in POIServiceImpl.getInputStream(String). * Fixed a bug in …
12:18 Changeset [6076] by melissa
Corrected LightSourceSettings.Attenuation population. See …
12:17 Changeset [6075] by melissa
Updated FV1000 reader to respect MetadataOptions.

03/29/10:

11:01 Changeset [6074] by callan
PIXELS_ONLY --> MINIMUM metadata level.
10:03 Changeset [6073] by melissa
Minor cleanup in Micromanager reader; openBytes will now return a blank …
09:19 Changeset [6072] by melissa
* Added more generic metadata configuration test. * Fixed a handful of …

03/26/10:

15:58 Changeset [6071] by melissa
* Filled in implementations of IMetadataConfigurable methods. * Updated …
12:14 Ticket #457 (Add support for Bio-Rad Gel format) closed by melissa
fixed: (In [6070]) Added support for Bio-Rad Gel (.1sc) files. Closes #457.
12:14 Changeset [6070] by melissa
Added support for Bio-Rad Gel (.1sc) files. Closes #457.
12:01 Changeset [6069] by callan
A scaffold to support metadata configurability of readers.

03/25/10:

10:55 Changeset [6068] by melissa
Catch NumberFormatException when parsing exposure times, and adjust SizeC …
10:54 Changeset [6067] by melissa
Allow Zeiss LSM datasets to contain non-LSM TIFF files.
09:41 Ticket #486 (Generalize support for writing multiple files) created by curtis
While bfconvert has support for exporting to multiple files, this …
09:23 Ticket #485 (Support for writing multi-file OME-TIFF datasets) created by curtis
Currently, bfconvert does not support writing a single image series over …

03/24/10:

17:09 Ticket #476 (AVI files saved using one writer per plane are broken) closed by melissa
fixed: (In [6066]) Allow AVI files to be written using one writer per plane. …
17:09 Changeset [6066] by melissa
Allow AVI files to be written using one writer per plane. Closes #476.
11:28 Changeset [6065] by melissa
Fixed off-by-1 in well column indexing.
10:31 Changeset [6064] by melissa
Ported r6063 to 4.1 branch.

03/23/10:

15:58 Ticket #484 (Investigate usage of FileChannel.map(...)) created by melissa
Prior to r6060, NIOFileHandle used the 'map' method in FileChannel to read …
15:54 Ticket #483 (Add support for Matlab matrix files) created by melissa
See data in data/matlab/daniel/.
13:48 Changeset [6063] by melissa
Allow the number of samples per pixel to be greater than the size of the …
13:02 Changeset [6062] by melissa
Improved parsing for version 2 Andor TIFF files and fixed how IFDs with …

03/22/10:

21:45 Ticket #482 (Expand LOCI Hudson job) created by melissa
Right now, the 'LOCI' job on hudson.openmicroscopy.org.uk only runs 'ant …
21:40 Changeset [6061] by melissa
Avoid skipping beyond the end of the file.
19:04 Changeset [6060] by melissa
* Fixed TIFF offset reading, so that zero offsets are not adjusted. * …
19:02 Ticket #481 (scan-deps.pl does not detect that unit tests depend upon log4j JARs) created by melissa
Several of the tests in the 'common' and 'bio-formats' components fail if …
10:05 Changeset [6059] by callan
Fixed a problem with MDB parsing where previously eaten exceptions (when …
08:46 Changeset [6058] by melissa
Eliminated a few deprecation warnings.
07:38 Changeset [6057] by callan
Removing unnecessary commented out code.
07:36 Changeset [6056] by callan
Performing the NIO out of memory exception handling in the try block to …

03/20/10:

04:46 Changeset [6055] by curtis
Use boxing in a few places.

03/19/10:

15:33 Changeset [6054] by curtis
Better ImageJ metadata parsing: * Also populates TimeIncrement. * …
13:54 Changeset [6053] by melissa
* Fixed compile errors in bf-cpp. * Fixed several bugs exposed by …
13:50 Changeset [6052] by curtis
Add scan-deps target to toplevel Ant script.
12:54 Changeset [6051] by melissa
Fixed NPE.
12:10 Changeset [6050] by curtis
Clean up some copyright notices, and fix scan-deps.pl handling of …
11:16 Changeset [6049] by curtis
Fix build of lwf-stubs.jar, and clean up toplevel build script a bit.
10:49 Changeset [6048] by curtis
Fix path to lwf-stubs.jar.
10:48 Changeset [6047] by curtis
Fix Eclipse compile errors with VisBio tests, and remove unneeded …
10:37 Changeset [6046] by curtis
Ignore lwf-stubs build directory.
10:36 Changeset [6045] by curtis
Fix various dependency problems exposed by scan-deps.pl.

03/18/10:

19:10 Changeset [6044] by melissa
Added '.map' as a valid MRC extension. See OMERO #1934.
16:47 Changeset [6043] by melissa
* Better plate name detection. * Well labelling fixes from Bram Gerritsen.
15:01 Changeset [6042] by melissa
Attempt to retrieve dimension information from plane names.
13:18 Changeset [6041] by curtis
Some Javadoc cleanup and additions.
07:45 Changeset [6040] by curtis
Readd some static MetadataTools methods, deprecated, to ease migration of …
04:59 Changeset [6039] by curtis
Add scroll bars as needed to main Bio-Formats Importer dialog.

03/17/10:

16:46 Changeset [6038] by melissa
Fixed compile errors in Bio-Formats utils.
16:06 Changeset [6037] by melissa
Add key/value pairs that map normalized channel indices to 'real' channel …
14:09 Changeset [6036] by melissa
Adjusted physical size Z to account for the fact that it is stored in …
12:11 Changeset [6035] by curtis
Reset default Visual Studio compiler to VS9 2008.
10:43 Changeset [6034] by melissa
* Fixed 16-bit lookup table handling in ImageJ. * Prevent IFD.printIFD …
07:21 Changeset [6033] by curtis
Parse spacing from ImageJ-style TIFF metadata.
05:34 Changeset [6032] by curtis
More robust handling of SVN metadata in Ant.

03/16/10:

16:01 Changeset [6031] by melissa
* Fixed well labeling bug, courtesy of Bram Gerritsen. * Fixed NPE when …
15:26 Changeset [6030] by melissa
Fixed a couple of bugs with reading > 2 GB ICS datasets.
13:29 Changeset [6029] by melissa
* Prevent an NPE in …
04:24 Changeset [6028] by curtis
Fix LOCI common utils compilation.
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