Timeline


and

02/27/10:

14:13 Changeset [5974] by melissa
Fixed how 32-bit AVIs are handled.

02/26/10:

18:55 Changeset [5973] by curtis
Add example for writing 24-bit RGB movies.
17:18 Changeset [5972] by melissa
Added Gatan .dm2 reader and fixed a couple of Gatan .dm3 bugs. See #412.
14:33 Changeset [5971] by melissa
Added missing isThisType(RandomAccessInputStream) implementations to …
14:33 Changeset [5970] by melissa
Consolidated a lot of pixel unpacking logic. See #466.
11:52 Changeset [5969] by callan
#466 Converting PhotoInterp into a Java 1.5+ enum
11:20 Changeset [5968] by callan
#466 Test cases for TiffRational; validates r5967
10:56 Changeset [5967] by callan
#466 TiffRational type safety adjustment
08:17 Changeset [5966] by callan
#466 Cleaned up a couple cases where TreeSet is a useful replacement for …
08:01 Changeset [5965] by callan
Made Nikon codec decompression test a little more thorough.
06:32 Changeset [5964] by callan
#466 Converting IDF types to a Java 1.5+ enum
06:05 Changeset [5963] by callan
Fixed interface / abstract class usage mismatch.
06:02 Changeset [5962] by callan
#466 Made TiffCompression enum instances a little bit more elegant and …
05:35 Changeset [5961] by callan
Fixed a bug where seek() was called on an already closed stream.

02/25/10:

17:28 Changeset [5960] by curtis
Better error message if IFD indices don't line up.
17:14 Changeset [5959] by curtis
Quick fix to a problem with "Merge channels" when not using virtual …
15:07 Changeset [5958] by melissa
* Altered IFD retrieval methods in TiffParser to be a little more …
12:20 Changeset [5957] by callan
#466 Converting TiffCompression into a Java 1.5+ enum
10:13 BioFormatsService edited by callan
(diff)
04:57 BioFormatsService created by callan

02/23/10:

21:23 Changeset [5956] by melissa
Removed some unnecessary TIFF parsing methods and cleaned up how BigTIFF …
15:20 Changeset [5955] by melissa
Fixed typo.
15:05 Changeset [5954] by melissa
Populate WellSample.ImageRef.
14:27 Ticket #464 (Review runtime dependencies) closed by melissa
fixed
14:27 Changeset [5953] by melissa
Updated calls to TiffTools to use TiffParser instead, and removed …
11:48 Changeset [5952] by callan
Test case for lossless JPEG2000 compression.
09:18 Changeset [5951] by melissa
Fixed NPE, courtesy of Jon Armond.
05:16 Changeset [5950] by callan
Cleaning up un-used import
05:04 Changeset [5949] by callan
#464 Some further POI fork tests with an Excel document

02/22/10:

15:16 Changeset [5948] by melissa
Added another MDB service test.
11:55 Changeset [5947] by melissa
Added a few more NetCDF tests.

02/19/10:

15:45 Changeset [5946] by melissa
Added a few more OME-XML tests.
14:35 Changeset [5945] by melissa
Fixed packages for OME I/O tests and removed extra TestNG XML file.
14:17 Changeset [5944] by melissa
* Moved OME I/O tests to ome-io component. * Added dependency check to …
10:17 Changeset [5943] by callan
#464 Added LuraWave service * Stub in stubs component for …
08:39 Changeset [5942] by callan
Stubs component; holds stubs of third party classes
08:22 Changeset [5941] by callan
#464 Minimal test cases for POI, OME reader/writer, OME-XML MDB and NetCDF …
08:17 Changeset [5940] by callan
Fixing imports in loci-plugins component
07:51 Changeset [5939] by callan
#464 Re-organizing the JAIIIOService a bit, adding a test case to cover it
06:06 Changeset [5938] by callan
#464 Various cleanup changes: * Normalized all service packages to …

02/18/10:

13:05 Changeset [5937] by callan
#464 Removing some usage of ReflectedUniverse where OMEReaderWriterService …
12:15 Changeset [5936] by melissa
Prevent a NegativeArraySizeException if the record size information is …
10:45 Changeset [5935] by callan
#464 Implementation of OME reader/writer service (includes test cases)

02/17/10:

15:47 Changeset [5934] by melissa
Prevent NPEs when parsing primitive type values.
14:46 Changeset [5933] by melissa
Set Z/T physical dimensions to 0 if the corresponding axis length is 1.
13:20 Changeset [5932] by melissa
Added reader for Photoshop TIFF files.
11:48 Changeset [5931] by melissa
Switched root test target to use overridden test targets in bio-formats …
11:30 Changeset [5930] by melissa
Each component's 'test' target now depends on 'jar'.
11:23 Changeset [5929] by callan
Fixed missing MDB test case
11:00 Changeset [5928] by callan
Adding missing AbstractService
10:56 Changeset [5927] by callan
Adding dependency check test cases to default test target
10:39 Changeset [5926] by callan
#464 Addition of AbstractService and some more aggressive dependency …
10:38 Changeset [5925] by callan
Updating Eclipse project settings for bio-formats and common components.
10:37 Changeset [5924] by callan
Fixing Eclipse classpath.
08:15 Changeset [5923] by melissa
Tweaked gain parsing to allow for double values.

02/16/10:

14:33 Changeset [5922] by melissa
Override lookup table accessor methods.
14:12 Changeset [5921] by melissa
Added service for reading JPEG-2000 data using JAI Image I/O. See #464.
12:31 Changeset [5920] by melissa
Updated ImageViewer to use OME Notes service.
12:22 Changeset [5919] by melissa
* Added service for MDB Tools. See #464. * Added documentation to …
12:10 Changeset [5918] by callan
#464 NetCDFService implemented with relevant readers adjusted
05:31 Changeset [5917] by callan
Fixing classpath and empty dependency package.

02/15/10:

14:35 Changeset [5916] by callan
Commiting missing ServiceException
12:54 Changeset [5915] by callan
#464 Add ServiceException and switch OMEXMLService over to its use
11:15 Changeset [5914] by melissa
Added getData methods to SignedShortBuffer.
10:56 Changeset [5913] by melissa
Added LOCI POI service and fixed several bugs in service-related resource …

02/13/10:

10:31 Changeset [5912] by melissa
Added reader for Hamamatsu .his files. See #412.

02/12/10:

15:30 Changeset [5911] by curtis
Add documentation for isThisTypeFast macro function.
15:18 Changeset [5910] by curtis
Add "isThisTypeFast" macro function for calling isThisType(id, false).
13:05 Changeset [5909] by melissa
Added reader for VG SAM .dti files. See #412.
12:30 Changeset [5908] by melissa
Added reader for Unisoku files. See #412.
10:58 Changeset [5907] by melissa
Added reader for Oxford Instruments' SPM files. See #412.
09:32 Ticket #389 (Add support for BD Pathway datasets) closed by melissa
fixed: (In [5906]) Added BD Pathway reader, courtesy of Shawn Garbett. Closes …
09:32 Changeset [5906] by melissa
Added BD Pathway reader, courtesy of Shawn Garbett. Closes #389.

02/11/10:

15:04 Changeset [5905] by melissa
Re-added log4j to classpath.
14:38 Changeset [5904] by melissa
Moved dependency version information to scan-deps.pl. Updated …
14:12 Changeset [5903] by melissa
Added provider for ByteArrayHandles constructed from existing byte arrays …
13:39 Changeset [5902] by melissa
Fixed compile errors introduced in r5898.
10:21 Changeset [5901] by melissa
Fixed IMetadata template for bf-ice.
10:21 Changeset [5900] by callan
Updating with MetadataAutgen as of r5899
10:15 Changeset [5899] by callan
Fixing OMEXMLMetadata template.
09:30 Changeset [5898] by callan
#464 OME-XML and OME Notes services "for real" * Moved ServiceFactory and …

02/10/10:

15:17 Changeset [5897] by melissa
* Fixed bug that caused ByteArrayHandles constructed from byte arrays to …
12:18 Ticket #473 (Support for CRi .im3 format) created by curtis
We would like to add support for CRi's .im3 format, used with its HCS …

02/09/10:

19:02 Changeset [5896] by melissa
Upgraded many of the dependency JARs, and removed a few that are no longer …
14:03 Ticket #472 (Bio-Formats plugin for OpenImageIO) created by curtis
It would be cool to create an  OpenImageIO
13:06 WikiStart edited by curtis
(diff)
13:06 WikiStart edited by curtis
(diff)
08:10 Changeset [5895] by melissa
Fixed bugs in writing differenced and signed TIFF data.
07:57 Changeset [5894] by callan
#464 A version of dependency injection for review

02/08/10:

12:59 Changeset [5893] by melissa
* Reverted to using 'img.getData.getPixels' to retrieve the pixel data, …
11:10 Changeset [5892] by melissa
A few more improvements to metadata parsing.
08:37 Changeset [5891] by melissa
Adjusted isThisType to check for any version number, not just "3.9a".

02/05/10:

14:53 Changeset [5890] by abhinav
Fix proxies classpath to include flow-cytometry.h.
14:34 Changeset [5889] by curtis
Remove .rec extension for the moment, and add Johannes's comment about …
14:32 Changeset [5888] by curtis
Add rec, st and ali extensions to MRC in readers.txt comments. We will …
14:30 Changeset [5887] by curtis
Add rec, st and ali suffixes as valid MRC extensions.
09:31 Ticket #469 (Problems autoscaling 1-bit data) closed by melissa
fixed: (In [5886]) Fixed autoscaling to use actual minimum and maximum pixel …
09:31 Changeset [5886] by melissa
Fixed autoscaling to use actual minimum and maximum pixel values. Closes …

02/04/10:

15:32 Changeset [5885] by curtis
Add flow-cytometry.h to Bio-Formats C++ bindings.
15:17 Ticket #463 (Utility class review) closed by melissa
fixed: See r5849 - r5851, r5853, r5855, r5860, r5862 - r5866, r5876, and r5877.
13:17 Ticket #471 (1-bit TIFF data has incorrect valid bits per pixel) closed by melissa
fixed: (In [5884]) Correctly set valid bits per pixel for TIFF files. Closes …
13:17 Changeset [5884] by melissa
Correctly set valid bits per pixel for TIFF files. Closes #471.
12:05 Changeset [5883] by melissa
Fixed off-by-one error in physical size calculations.
10:39 Ticket #462 (Review logging infrastructure) closed by melissa
fixed: See also r5852.

02/03/10:

16:27 Ticket #470 (Problems decoding 1-bit LZW data) closed by melissa
fixed: Duplicate of #468, resolved in r5882. The problem was not with LZW …
15:47 Ticket #468 (TIFF pixel data is incorrect for bit depths that are not a multiple of 8) closed by melissa
fixed: (In [5882]) Fixed how pixels are unpacked when the number of bits per …
15:47 Changeset [5882] by melissa
Fixed how pixels are unpacked when the number of bits per sample is not …
14:44 Ticket #471 (1-bit TIFF data has incorrect valid bits per pixel) created by curtis
TIFF files with 1 bit per sample (i.e., an IFD entry with BitsPerSample …
14:41 Ticket #470 (Problems decoding 1-bit LZW data) created by curtis
1-bit LZW data has strange artifacts after decoding. TiffJAIReader
14:39 Ticket #469 (Problems autoscaling 1-bit data) created by curtis
With some (maybe all?) 1-bit datasets, the image appears initially black …
14:06 Changeset [5881] by curtis
Clean up import statements.
14:01 Changeset [5880] by curtis
Add TIFF JAI-based reader for reading TIFFs with Java Advanced Imaging. …
13:06 Changeset [5879] by curtis
Fix tools dependencies.
11:59 Changeset [5878] by curtis
Add flow-cytometry.jar to loci_tools.jar bundle.

02/02/10:

07:51 Changeset [5877] by callan
#463 Cleanup of locations of inefficient legacy DataTools usage * With …
07:26 Changeset [5876] by callan
#463 ByteArrayHandle changes to use direct buffer manipulations * Large …
04:55 Changeset [5875] by callan
* Adding ByteBuffer read/write capabilities to the RA streams * Removed a …
04:44 Changeset [5874] by callan
* Implemented NIOFileHandle ByteBuffer read/write operations. * Adjusted …

02/01/10:

14:57 Changeset [5873] by melissa
Fixed RGB uint32 BufferedImage construction.
13:16 Changeset [5872] by melissa
Tweaked pixel size calculation to account for non-zero axis start …
12:19 Changeset [5871] by melissa
Tweaked dimension order calculation for XZ and XT scans.
11:08 Changeset [5870] by melissa
Added tests for reading to and writing from a ByteBuffer.
10:50 Changeset [5869] by melissa
Added methods for reading to and writing from a ByteBuffer.
09:17 Changeset [5868] by melissa
Fixes for reading DICOMs from a URL.
08:40 Changeset [5867] by melissa
Ported r5857 to cleanup, with appropriate logging changes.
07:06 Changeset [5866] by callan
#463 Clean up DataTools imports
06:39 Changeset [5865] by callan
#463 Clean up now unused thread local.
06:25 Changeset [5864] by callan
#463 DataTools initial cleanup; removing now unused read/write methods
06:24 Changeset [5863] by callan
#463 Complete port of AWTiffTools away from DataTools
06:17 Changeset [5862] by callan
#463 Ported TIFF saver to use RandomAccessOutputStream for writeIFDValue
06:05 Changeset [5861] by callan
Add constructor for byte array handle to take an initial capacity.
03:59 Changeset [5860] by callan
#463 DataTools removal for QTWriter

01/31/10:

14:34 Changeset [5859] by melissa
Fixed how NIOFileHandle and ByteArrayHandle read and write UTF strings.

01/29/10:

15:41 Changeset [5858] by melissa
* RandomAccessInputStream updates: removed checkEfficiency and replaced …
15:12 Changeset [5857] by curtis
Progress on Bio-Formats Importer refactoring. Probably some new bugs.
12:42 Changeset [5856] by callan
#463 Further changes to allow for DataTools overhaul
12:40 Changeset [5855] by callan
#459 Added capability for the output stream to wrap an existing handle
11:39 Changeset [5854] by callan
Fixing bad AVIWriter conflict resolution against r5852.
11:22 Changeset [5853] by callan
#436 Transitioned AVIWriter away from DataTools static method calls
10:05 Changeset [5852] by melissa
* Changed XMLTools imports; fixes compile errors. * Changed 'status' …
06:05 Changeset [5851] by callan
#436 Removed un-used and thread unsafe static XML factory
05:24 Changeset [5850] by callan
#463 try/finally block sanity for closing files
05:05 Changeset [5849] by callan
#463 Completed XMLTools review: * Fixed thread safety issues with static …

01/28/10:

14:57 Changeset [5848] by melissa
Finished removing references to Log and LogTools; all components should …
09:09 Ticket #460 (Add tests for I/O classes) closed by melissa
fixed: Completed in r5847. Tests are in …
09:07 Ticket #461 (Review build system for testing components in isolation) closed by melissa
fixed: Completed in r5847. Tests for any component can be run using 'ant test' …
09:06 Ticket #459 (I/O class review) closed by melissa
fixed: Completed in r5847.
05:13 Changeset [5847] by callan
* Switch to class parallelization * Remove useless TestNG Ant task …
05:02 Changeset [5846] by callan
Try to avoid printing control characters and ASCII garbage in XML files.
05:01 Changeset [5845] by callan
Adding log4j to the external Eclipse project classpath.
04:38 Changeset [5844] by callan
Fixing Eclipse classpaths for slf4j.
04:12 Changeset [5843] by callan
Test suite name that's easier for Hudson to digest
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