Timeline


and

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.

01/07/10:

13:39 Changeset [5776] by curtis
Add writer for saving images as Java source code. Unfortunately, images …
12:47 Changeset [5775] by melissa
If a lookup table is only present in the first IFD, apply it to all …
11:36 Changeset [5774] by melissa
Created branch for Bio-Formats cleanup work (thread-safeness, I/O review, …
11:29 Changeset [5773] by melissa
Ported Flex/TIFF efficiency changes to 4.1 branch.

01/06/10:

09:51 Changeset [5772] by melissa
When possible, only parse the first IFD from the first file.

01/05/10:

12:28 Changeset [5771] by melissa
Ported r5770 to 4.1 branch.

01/04/10:

14:42 Changeset [5770] by melissa
Tweaked dimension calculation for multi-channel ImageJ TIFFs.
14:32 Ticket #456 (Add support for half-float pixel data in TIFF files) closed by melissa
fixed: (In [5769]) Added support for half float and half double pixels. Closes …
14:32 Changeset [5769] by melissa
Added support for half float and half double pixels. Closes #456.
14:21 Changeset [5768] by curtis
Fix some comments.
11:46 Changeset [5767] by curtis
Improvements to bfopen.m suggested by Cris Luengo.
10:46 Changeset [5766] by melissa
Tweaked TiffIFDEntry retrieval.

12/31/09:

11:08 Changeset [5765] by melissa
One more isThisType tweak.
09:54 Changeset [5764] by melissa
Tweaked isThisType so that .wav files are not detected as AVIs.

12/30/09:

10:58 Changeset [5763] by melissa
Set the tile length to equal the image length if it was originally less …
10:17 Ticket #431 (Feedback 1012: ArrayIndexOutOfBound in Slidebook) closed by melissa
fixed: For those who don't have access to the QA, here is the error: …
10:17 Changeset [5762] by melissa
Tweaked SizeT calculation to prevent an AIOOB.
09:21 Changeset [5761] by melissa
* Better handling of large images in ChannelSeparator. * Minor cleanup in …

12/28/09:

12:34 Changeset [5760] by melissa
A few more tweaks to speed up Flex parsing.
09:17 Ticket #457 (Add support for Bio-Rad Gel format) created by melissa
See sample files in data/biorad-gel/sylvain. These files can be opened by …
09:03 Ticket #456 (Add support for half-float pixel data in TIFF files) created by melissa
Storage of half-float data is defined here: …

12/23/09:

15:49 Changeset [5759] by melissa
Prevent an NPE if the EXIF IFD is invalid.
14:00 Changeset [5758] by melissa
Various tweaks to make Flex parsing faster.

12/22/09:

09:46 Changeset [5757] by melissa
Tweaks to allow TIFFs with missing IFD pointers to be read.

12/18/09:

12:29 Ticket #446 (Feedback 2147: ArrayIndexOutOfBounds with ZeissLsm) closed by melissa
duplicate: Duplicate of #430, which was fixed in r5664.
12:26 Ticket #449 (Feedback 152: IOException rather than FormatExcept) closed by melissa
fixed: (In [5756]) Throw FormatException if XML is malformed. Closes #449.
12:25 Changeset [5756] by melissa
Throw FormatException if XML is malformed. Closes #449.
12:20 Ticket #453 (Feedback 879: invalid opcode in PictReader) closed by melissa
fixed: (In [5755]) * Tweaked file length check. * Added support for …
12:20 Changeset [5755] by melissa
* Tweaked file length check. * Added support for JPEG-compressed PICT …
09:35 Ticket #455 (Add support for Zip files with multiple entries) created by melissa
See leica-lif/stefan/spe_export.zip.
09:31 Changeset [5754] by melissa
Make it clear that multi-file Zips are not supported.
09:20 Ticket #454 (Feedback 860: NumberFormatException for PE) closed by melissa
fixed: (In [5753]) Catch NumberFormatException when parsing stage positions. …
09:20 Changeset [5753] by melissa
Catch NumberFormatException when parsing stage positions. Closes #454.
09:17 Ticket #454 (Feedback 860: NumberFormatException for PE) created by omero-qa
*  http://qa.openmicroscopy.org.uk/qa/feedback/860/ * …
09:14 Ticket #452 (Feedback 939: eps "max search length") closed by melissa
fixed: (In [5752]) More informative exceptions for invalid PE datasets and files …
09:14 Changeset [5752] by melissa
More informative exceptions for invalid PE datasets and files of length 0. …
09:10 Ticket #453 (Feedback 879: invalid opcode in PictReader) created by omero-qa
 http://qa.openmicroscopy.org.uk/qa/feedback/879/ and …
09:04 Ticket #452 (Feedback 939: eps "max search length") created by omero-qa
 http://qa.openmicroscopy.org.uk/qa/feedback/939/
09:00 Changeset [5751] by melissa
Throw a more informative exception if the strip offsets are missing.
08:54 Ticket #451 (Feedback 1021: ArrayIndexOutOfBounds in IncellRead) closed by melissa
fixed: This was fixed in r5704.
08:51 Ticket #444 (Feedback 2163: ArrayIndexOutOfBound on MicroManage) closed by melissa
fixed: (In [5750]) Be more aggressive about looking for TIFF files, and throw a …
08:51 Changeset [5750] by melissa
Be more aggressive about looking for TIFF files, and throw a better …
08:51 Ticket #451 (Feedback 1021: ArrayIndexOutOfBounds in IncellRead) created by omero-qa
 http://qa.openmicroscopy.org.uk/qa/feedback/1021/ Another one which …
08:45 Ticket #450 (Feedback 1489: OMX regression?) created by omero-qa
 http://qa.openmicroscopy.org.uk/qa/feedback/1489/ Will send email to …
08:27 Ticket #448 (Feedback 1689) closed by melissa
fixed: This was fixed in r5705.
08:04 Ticket #447 (Feedback 2138: unknown file format "...ome.xml") closed by melissa
fixed: (In [5749]) Prevent UnknownFormatException for OME-XML files that do not …
08:04 Changeset [5749] by melissa
Prevent UnknownFormatException for OME-XML files that do not have the …
07:44 Ticket #449 (Feedback 152: IOException rather than FormatExcept) created by omero-qa
 http://qa.openmicroscopy.org.uk/qa/feedback/152/ Wouldn't we assume a …
05:36 Ticket #448 (Feedback 1689) created by omero-qa
 http://qa.openmicroscopy.org.uk/qa/feedback/1689/ Just cleaning up qa. …
05:16 Ticket #447 (Feedback 2138: unknown file format "...ome.xml") created by omero-qa
 http://qa.openmicroscopy.org.uk/qa/feedback/2138/
04:22 Ticket #446 (Feedback 2147: ArrayIndexOutOfBounds with ZeissLsm) created by omero-qa
 http://qa.openmicroscopy.org.uk/qa/feedback/2147/
04:16 Ticket #445 (Feedback 2160: Leica lambda scans) created by omero-qa
 http://qa.openmicroscopy.org.uk/qa/feedback/2160/
04:15 Ticket #444 (Feedback 2163: ArrayIndexOutOfBound on MicroManage) created by omero-qa
 http://qa.openmicroscopy.org.uk/qa/feedback/2163/

12/17/09:

13:51 Ticket #407 (Add support for Slidebook spool (.spl) files) closed by melissa
fixed: (In [5748]) Tweaked Slidebook reader to work with spool files. Closes …
13:51 Changeset [5748] by melissa
Tweaked Slidebook reader to work with spool files. Closes #407.
12:00 Ticket #383 (Generated OME-TIFF files have elements in the wrong order) closed by curtis
fixed: This problem was fixed a while ago in r5467. It uses a stylesheet (thanks …
09:15 Changeset [5747] by melissa
One more exposure time parsing fix.
08:50 Changeset [5746] by melissa
Fixed bug in exposure time parsing, thanks to Simon Blanchoud.

12/16/09:

15:07 Changeset [5745] by melissa
Allow file grouping across multiple directories.
09:43 Changeset [5744] by melissa
Swapped plate naming conventions for plates with > 26 rows and added spot …

12/15/09:

15:36 Ticket #433 (Consider adding getBitsPerPixel() to IFormatReader) closed by melissa
fixed: (In [5743]) Added 'getBitsPerPixel()' to IFormatReader. Closes #433.
15:36 Changeset [5743] by melissa
Added 'getBitsPerPixel()' to IFormatReader. Closes #433.
14:57 Changeset [5742] by curtis
Eliminate needless complexity.
13:54 Changeset [5741] by curtis
Fix ND2 padding issue for images with odd widths.
08:59 Changeset [5740] by melissa
Added Ant target to create a Zip file containing the Javadocs.
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