Timeline


and

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

01/27/10:

13:35 Ticket #468 (TIFF pixel data is incorrect for bit depths that are not a multiple of 8) created by melissa
See for example: tiff/samples/imagemagick/flower-minisblack-strip-06.tif …
13:11 Changeset [5842] by melissa
Removed loci.common.Log and loci.common.LogTools, in favor of SLF4J …
12:05 Changeset [5841] by callan
Make parallel testing and testng.xml file re-use possible via Ant.
10:05 Changeset [5840] by callan
Fixing test target classpath
09:00 Changeset [5839] by melissa
Fixed return value when EOF is encountered.
08:29 Changeset [5838] by melissa
Fixed TestNG JAR detection.
08:29 Changeset [5837] by callan
Updating strings to for new TestNG JAR version.
06:22 Changeset [5836] by callan
Using group attributes to specify test case run configurations in …
04:50 Changeset [5835] by callan
Fixed remaining TODOs in NIOFileHandle and added test cases: * readLine() …

01/26/10:

13:57 Changeset [5834] by curtis
Move Bio-Formats-specific utilities into Bio-Formats component utility …
11:34 Changeset [5833] by curtis
Add a check to ImageReader for invalid IDs. This check results in …
09:50 Changeset [5832] by melissa
Fixed implementation of writeByte(int).
09:30 Changeset [5831] by callan
* Write tests for all the data types * Fixed problems with double …

01/25/10:

14:14 Changeset [5830] by melissa
* Added LEO EM reader. See #412. * Updated FITS reader to allow the 'fts' …
12:57 Changeset [5829] by melissa
Added Targa reader. See #412.

01/22/10:

14:35 Changeset [5828] by melissa
Added method to retrieve the format name for a particular file.
13:41 Changeset [5827] by melissa
Fixed a few bugs in 16 and 24 bit float support, courtesy of Chris Lesiak.
12:18 Changeset [5826] by melissa
Fixed float/double parsing for ND2 files that have a decimal delimiter not …
11:53 Ticket #467 (Support for Group 3 Fax TIFF compression) created by curtis
Bio-Formats does not currently support CCITT T.4 bi-level encoding (Group …
11:51 Changeset [5825] by callan
* Tests for reads with byte arrays on buffer alignment * Fixed NIO file …
10:10 Changeset [5824] by melissa
* Changed URLHandle to be read-only. * Added URLHandleTest to testng.xml.
09:03 Changeset [5823] by callan
* Added byte array and byte sub array tests from Brian * Fixed issue with …
08:20 Changeset [5822] by callan
Switched to usage of validateLength().
08:16 Changeset [5821] by callan
* Fixing most NIOFileHandle write methods * Added test cases for writing …

01/21/10:

16:18 Changeset [5820] by melissa
When parsing an option, look for the option's label if the key is missing.
13:27 Changeset [5819] by melissa
* Fixed bug in NIOFileHandle.read(byte[], int, int) * Updated …
12:06 Changeset [5818] by melissa
Corrected documentation and removed trailing whitespace.
09:29 Changeset [5817] by melissa
Added root 'test' target and modified component 'test' targets to succeed …

01/20/10:

15:51 Changeset [5816] by melissa
Added Ant 'test' target for each component. This will compile everything …
14:01 Changeset [5815] by melissa
* Fixed URLHandle to work with non-HTTP URLs. * Fixed URLHandle tests. …
13:14 Changeset [5814] by melissa
Fixed a handful of bugs exposed by the I/O tests. URLHandle tests still …
12:17 Changeset [5813] by callan
Re-architecting TestNG usage so that we can run a "suite" against any …
11:29 Changeset [5812] by melissa
Tweaked metadata hashtable population.
10:58 Changeset [5811] by melissa
Parse stage position and pinhole size metadata.
10:09 Changeset [5810] by callan
Fixing Eclipse classpath for TestNG JAR
07:19 Changeset [5809] by callan
* Proper end of file exception semantics * Buffers are no longer page …

01/19/10:

14:35 Ticket #382 (Generated OME-TIFF files have invalid UUID elements) closed by melissa
fixed: (In [5808]) Fixed UUID population. Closes #382.
14:35 Changeset [5808] by melissa
Fixed UUID population. Closes #382.
14:25 Ticket #420 (Feedback 145: exported tiffs cannot be opened with) closed by melissa
fixed: Closing this ticket, as we've been able to open exported TIFFs since r5516
14:19 Changeset [5807] by melissa
Removed unused imports.
14:10 Changeset [5806] by melissa
* Added tests for loci.common.BZip2Handle and loci.common.URLHandle. * …
07:34 Changeset [5805] by melissa
Removed check for zero length, as it causes too many problems.
05:57 Changeset [5804] by callan
Fixed typo.
05:51 Changeset [5803] by callan
Removing some unused imports.
05:21 Changeset [5802] by callan
* Added test case for buffer alignment * Fixed buffer rewinding bug as …
04:44 Changeset [5801] by callan
Configurable buffer sizes for added utility and testing.
04:25 Changeset [5800] by callan
* Normalized test class naming * Test cases for float and double

01/18/10:

16:27 Changeset [5799] by melissa
Preserve pixel dimensions.

01/15/10:

14:26 Changeset [5798] by melissa
* Tweaked pixel type enumeration to allow the "double" type. * Fixed a bug …
12:48 Changeset [5797] by melissa
Added priority attributes to two rules, to prevent "Ambiguous rule match" …
11:49 Changeset [5796] by melissa
* Added test classes for loci.common.ByteArrayHandle and …
10:20 Changeset [5795] by melissa
* Added test class for loci.common.GZipHandle. * Fixed a couple of bugs …

01/14/10:

14:58 Changeset [5794] by melissa
* Implemented getOrder() and setOrder(ByteOrder) for StreamHandle and …
14:06 Changeset [5793] by melissa
* Tweaked comments/trailing whitespace in NIOFileHandle and …
11:59 Changeset [5792] by callan
Test case for endianness
11:41 Changeset [5791] by melissa
Upgraded to TestNG 5.11 JDK 1.5, so that new I/O tests can be compiled.
11:39 Changeset [5790] by callan
Added endianness to the I/O API.
10:34 Changeset [5789] by callan
* Normalized test case method names * Added positive and negative values …

01/13/10:

12:52 Changeset [5788] by melissa
Parse Z positions from UIC1 tag.
12:30 Changeset [5787] by callan
* Test cases for "char" from Brian * Renamed uint8 test cases to fall in …
11:23 Ticket #458 (Bio-Formats Exporter drops metadata for non-imported images) closed by melissa
fixed: (In [5786]) Ensure that calibration information is preserved, regardless …
11:23 Changeset [5786] by melissa
Ensure that calibration information is preserved, regardless of how the …
10:53 Ticket #466 (Review TIFF parsing logic) created by melissa
Need to ensure that everything in loci.formats.tiff: * Is thread-safe. …
10:52 Ticket #465 (Add tests for ImageJ plugin) created by melissa
Add tests to ensure that cleanup work (especially ticket #464) does not …
10:50 Ticket #464 (Review runtime dependencies) created by melissa
For every dependency (including those in the 'forks' component), we want …
10:43 Ticket #463 (Utility class review) created by melissa
Review the following classes in loci.common: * Ini* * XMLTools * …
10:38 Ticket #462 (Review logging infrastructure) created by melissa
Primary classes to review are loci.common.Log and loci.common.LogTools, …
10:36 Ticket #461 (Review build system for testing components in isolation) created by melissa
To make cleanup work easier BioFormatsCleanup?, it would be nice to …
10:31 Ticket #460 (Add tests for I/O classes) created by melissa
Add unit tests for each of the following classes in loci.common, and any …
10:27 Ticket #459 (I/O class review) created by melissa
Review the following classes/interfaces in loci.common: * BZip2Handle * …
06:57 Changeset [5785] by callan
NIO based IRandomAccess and InputStream implementations * TestNG test …
00:36 Changeset [5784] by curtis
Support uncompressed data with Compression=0 as well.

01/12/10:

16:04 Changeset [5783] by mike
Updated bf-cpp conflicts file
13:06 Changeset [5782] by melissa
* Moved CompressedRandomAccess to StreamHandle. * Moved a bunch of …
10:51 Changeset [5781] by melissa
Removed 'int read()' and 'void setLength(long)' from IRandomAccess.
10:24 Changeset [5780] by melissa
Updated documentation for IRandomAccess.
08:56 Changeset [5779] by melissa
* Added alternate magic number for JPEG-2000 compression. * Fixed how …

01/11/10:

15:10 Changeset [5778] by melissa
Removed file handle caching logic from RandomAccessInputStream, and …
14:25 Changeset [5777] by curtis
Fix data typing error with doublesToBytes.
14:01 Ticket #458 (Bio-Formats Exporter drops metadata for non-imported images) created by curtis
The Bio-Formats Exporter does not preserve metadata when saving unless the …
13:43 Ticket #317 (Add file format extension filter to Bio-Formats Exporter) closed by curtis
fixed: This issue was addressed in r4833.
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