Timeline


and

03/03/09:

16:51 Changeset [4892] by curtis
Reuse the same buffer for each image plane, and remove obsolete comments.
16:12 Changeset [4891] by curtis
Ignore build directory.
16:08 Changeset [4890] by curtis
Fix various bugs with Bio-Formats ITK plugin. Also works on Mac OS X now.
16:00 Changeset [4889] by curtis
On Mac OS X, copy libjace.jnilib to libjace.dylib, to avoid linker …
16:00 Changeset [4888] by curtis
Add isMac property, set when platform is Mac OS X.
15:35 Changeset [4887] by melissa
Override getUsedFiles() to return both the image and header file names.
14:30 Ticket #356 (Add support for Analyze 7.5 format) closed by melissa
fixed: (In [4886]) Added support for Analyze 7.5 files; closes #356.
14:30 Changeset [4886] by melissa
Added support for Analyze 7.5 files; closes #356.
12:52 Changeset [4885] by curtis
Trim Leica TCS metadata key/value pairs.
12:50 Changeset [4884] by curtis
Always trim key names when adding original metadata fields.
10:37 Changeset [4883] by melissa
Added missing java.xml.
09:58 Changeset [4882] by melissa
Removed unused tag.
09:43 Changeset [4881] by melissa
4.0.0 release of LOCI Tools
09:31 Changeset [4880] by melissa
4.0.0 release of LOCI Tools
08:45 Changeset [4879] by melissa
Synced 4.0.0 branch to r4878 (including r4804).
08:42 Ticket #364 (Group DICOM files using the 'Instance Number' tag) created by melissa
Instead of grouping DICOM files according to the file names, we should use …
08:02 Changeset [4878] by melissa
Catch NumberFormatException when parsing plane data from the deconvolution …
00:00 Milestone bio-formats-4.0 completed
Bio-Formats release corresponding to OMERO Beta 4. The primary goals of …

03/02/09:

17:01 Changeset [4877] by curtis
Add license to readme file.
16:31 Changeset [4876] by curtis
Flesh out readme file with build instructions and current status.
16:17 Ticket #363 (AWTImageTools.openImage misrepresents negative pixel values for int16) created by curtis
When reading an int16 BufferedImage using the AWTImageTools.openImage …
15:00 Changeset [4875] by curtis
When filtering metadata fields, check for empty strings after performing …
14:33 Ticket #359 (Exception when reading signed 16 bit images) closed by curtis
fixed: (In [4874]) Use USHORT instead of SHORT for 16-bit integer …
14:33 Changeset [4874] by curtis
Use USHORT instead of SHORT for 16-bit integer SignedColorModel. Fixes …
09:53 Changeset [4873] by melissa
Added IPLab-Mac and ARF metadata documentation.
08:11 Changeset [4872] by melissa
Synced 4.0.0 branch with trunk, excluding r4804.

03/01/09:

13:48 Changeset [4871] by melissa
The custom colorize option is now recorded correctly by the macro …
12:30 Changeset [4870] by melissa
Updated metadata support documentation.

02/28/09:

13:15 Changeset [4869] by melissa
Updated what's new for 4.0.0 release.
12:52 Changeset [4868] by melissa
Plane names are stored in the metadata hashtable with keys of the form …

02/27/09:

19:20 Changeset [4867] by curtis
Set Deltavision extended header fields to public visibility, for easier …
19:13 Changeset [4866] by curtis
Always preserve data type of non-string original metadata values.
19:01 Changeset [4865] by curtis
Add showinf option to suppress metadata filtering.
19:01 Changeset [4864] by curtis
Change behavior of original metadata table: * Preserve the original data …
18:00 Changeset [4863] by curtis
Record extended header objects, but not individual header fields, into the …
17:52 Changeset [4862] by curtis
Progress on DeltavisionReader refactoring.
17:30 Changeset [4861] by curtis
Remove unnecessary getters for nested private class.
17:15 Changeset [4860] by curtis
Begin refactoring of DeltaVisionReader.initFile to be more modular.
17:15 Changeset [4859] by curtis
Add a little documentation about build system variables.
16:23 Changeset [4858] by melissa
Throw more informative exceptions if ome-xml.jar is missing.
15:38 Changeset [4857] by curtis
Remove previous build folder, to avoid misleading issues during test.
15:05 Changeset [4856] by curtis
Copy .dylib and .jnilib in addition to .so.
15:05 Changeset [4855] by curtis
Eliminate hardcoded ITK path.
14:52 Changeset [4854] by curtis
Add a simple script to facilitate building the Bio-Formats ITK plugin.
13:25 Changeset [4853] by melissa
Fixed how PictReader detects the pixel type and channel count.

02/26/09:

19:55 Changeset [4852] by melissa
Fixed various ImageJ plugin problems (mostly macro related). The custom …
18:29 Changeset [4851] by curtis
First cut at Bio-Formats ITK Image IO plugin implementation. Numerous …
18:28 Changeset [4850] by curtis
Move more includes into bioformats.h, for convenience.
11:23 Changeset [4849] by curtis
Remove hardcoded paths and other improvements, courtesy of Zack Galbreath.

02/25/09:

19:00 Changeset [4848] by curtis
Fix up MIPAV Bio-Formats plugin: * call calcMinMax() to correctly scale …
17:55 Changeset [4847] by curtis
Tweak Mac OS X notes.
17:53 Changeset [4846] by curtis
Add more future Boost versions to the list, to tide things over until the …
17:31 Changeset [4845] by curtis
On OS X, name Jace library as libjace.jnilib rather than libjace.dylib. …
16:08 Changeset [4844] by curtis
Compiles on Mac OS X, but still doesn't run successfully.
15:20 Changeset [4843] by curtis
Update include paths to reflect new bf-cpp directory structure.
14:26 Changeset [4842] by curtis
Add "-r 6" flag to Jace SVN checkout instructions, since versions newer …

02/24/09:

16:56 Changeset [4841] by curtis
Some work on Mac OS X compilation directions for bf-cpp.
15:16 Changeset [4840] by curtis
Tweaks to the showinfJNI standalone example: * Include stdlib.h for exit …
15:04 Changeset [4839] by curtis
Add 64-bit Linux compile command; use constant for number of JVM options.
12:12 Changeset [4838] by melissa
Fixed segmentation fault and added check to see if JVM was successfully …
11:25 Changeset [4837] by curtis
Add (possibly incorrect) 32-bit Linux compilation instructions.

02/23/09:

18:12 Changeset [4836] by curtis
Slim Plotter improvements: * Changed export to create one file per …
10:32 Changeset [4835] by melissa
* Add a blank channel to 2-channel data when converting to AVI. * Fixed …
09:16 Changeset [4834] by melissa
Allow channels to be merged if the original images have color lookup …

02/20/09:

14:44 Changeset [4833] by curtis
Show available output formats in the Bio-Formats Exporter file filter. …
14:03 Changeset [4832] by melissa
For each writer, test all possible compression types (instead of assuming …
13:53 Changeset [4831] by melissa
Added "String getCompression()" method to IFormatWriter API.
13:48 Changeset [4830] by curtis
Add brief compilation and execution instructions for Mac OS X.
12:36 Changeset [4829] by mike
09:30 Changeset [4828] by curtis
Add Bio-Formats plugin for MIPAV (mostly working).
09:09 Changeset [4827] by curtis
Add copyright notices, and more detail to the readme.

02/19/09:

21:18 Changeset [4826] by melissa
Added fix for Openlab files whose pixel type does not match the pixel type …
15:52 Changeset [4825] by curtis
* Move Bio-Formats C++ bindings to native subfolder. * Add some quick …
15:45 Changeset [4824] by curtis
Add skeleton for Bio-Formats ITK plugin.
15:37 Changeset [4823] by curtis
Add readme with details on prerequisites and compilation.
12:50 Changeset [4822] by curtis
Better build system for Bio-Formats C++ bindings on Linux.
12:28 Changeset [4821] by melissa
Make sure temporary file name prefix is at least 3 characters long.
10:39 Ticket #362 (Clean up delegation to legacy readers) created by melissa
For formats that have multiple readers (QuickTime and ND2), we should …

02/18/09:

14:13 Changeset [4820] by melissa
Fixed a few more bugs exposed by the writer test suite.
12:13 Changeset [4819] by melissa
Propagate QTReader's MetadataStore to LegacyQTReader.
11:03 Changeset [4818] by melissa
Parse pixel sizes from axis notes with type 'VARIABLE'.
10:23 Changeset [4817] by melissa
One more fix for axis notes with extraneous spaces.
09:52 Changeset [4816] by melissa
Changed how axis notes are parsed - extraneous spaces and '=' characters …
09:26 Changeset [4815] by melissa
Fixed how the number of padding bytes is computed.

02/17/09:

14:42 Ticket #361 (Move JPEG-2000 logic into its' own reader) created by melissa
Right now, ND2Reader doubles as the reader for JPEG-2000 files. This is a …
14:41 Ticket #360 (J2K files not supported) created by melissa
JPEG-2000 files with the extension '.j2k' are not supported. These files …
14:12 Changeset [4814] by melissa
Sync 4.0 branch with trunk. r4803 is omitted because it breaks some …
13:19 Changeset [4813] by melissa
Ant targets for reader tests now only run reader tests (instead of all …
12:04 Ticket #327 (Allow ImageJ plugin to check for updates) closed by melissa
fixed: (In [4812]) Added ImageJ plugin that will download the latest trunk, daily …
12:04 Changeset [4812] by melissa
Added ImageJ plugin that will download the latest trunk, daily or stable …
08:07 Changeset [4811] by melissa
Delete converted files once the tests finish.
08:06 Changeset [4810] by melissa
Fixed bug that prevented Data Browser from being displayed if "Use Virtual …

02/16/09:

21:00 Changeset [4809] by melissa
Fixed a couple of bugs in the conversion test, as well as a couple of bugs …
14:58 Ticket #341 (Add unit tests for writers) closed by melissa
fixed: (In [4808]) Added TestNG test to ensure that file conversion works. Closes …
14:58 Changeset [4808] by melissa
Added TestNG test to ensure that file conversion works. Closes #341.
10:05 Changeset [4807] by melissa
Added SPW population for Flex files. Some metadata is still missing.
10:03 Changeset [4806] by melissa
Fixed minor bugs exposed by test suite.

02/13/09:

13:28 Ticket #359 (Exception when reading signed 16 bit images) created by melissa
As of r4804, attempting to read a signed 16-bit image throws the following …
09:27 Ticket #332 (Report field count for multifield data) closed by melissa
fixed: (In [4805]) Split each field into its' own series. Closes #332.
09:27 Changeset [4805] by melissa
Split each field into its' own series. Closes #332.

02/12/09:

14:35 Changeset [4804] by curtis
Fix up DataTools and AWTImageTools data manipulation and image …
10:52 Changeset [4803] by melissa
Make sure that the LightSource type is populated.

02/11/09:

20:09 Changeset [4802] by curtis
Readd method to fix compile errors... but why is 'boolean signed' unused?
18:54 Changeset [4801] by curtis
Eliminate superfluous method signature.
11:47 Changeset [4800] by melissa
Fixed Pixels IDs.
10:58 Changeset [4799] by melissa
Check that LogicalChannel index is valid before linking a LightSource to a …

02/10/09:

22:22 Changeset [4798] by melissa
Only link a LightSource to an Image if LightSource/LightSourceSettings …
18:56 Ticket #358 (Investigate JHOVE for file format recognition) created by curtis
The  JHOVE library from Harvard is an …
12:44 Ticket #357 (Some TIFFs cannot be read) closed by melissa
fixed: (In [4797]) Make sure that *all* of the RowsPerStrip entries are less than …
12:44 Changeset [4797] by melissa
Make sure that *all* of the RowsPerStrip entries are less than or equal to …
12:29 Changeset [4796] by melissa
Fixed Colorizer plugin to work with datasets that have one lookup table …
11:50 Ticket #357 (Some TIFFs cannot be read) created by melissa
TIFFs that are missing the RowsPerStrip IFD entry throw the following …
09:58 Changeset [4795] by melissa
Clicking the "Animate" button now actually animates the image, instead of …
09:48 Changeset [4794] by melissa
Explicitly set the Detector ID.

02/09/09:

12:22 Ticket #356 (Add support for Analyze 7.5 format) created by melissa
The Analyze 7.5 specification is in specs/analyze/ANALYZE75.PDF. The …
11:51 Ticket #355 (Data Browser displays time series data incorrectly) closed by melissa
fixed: (In [4793]) Fixed how the Data Browser handles single dimension, non-Z …
11:51 Changeset [4793] by melissa
Fixed how the Data Browser handles single dimension, non-Z data. Closes …
09:44 Ticket #355 (Data Browser displays time series data incorrectly) created by melissa
See the attached screenshot - even though Bio-Formats detects that the …
09:33 Changeset [4792] by melissa
Updated IFormatWriter Javadocs to make it clear that saveImage methods …
09:00 Changeset [4791] by melissa
Throw a more informative exception if vector data is encountered.
08:12 Changeset [4790] by melissa
Sync 4.0 branch with trunk r4789.
08:03 Changeset [4789] by melissa
Only set LogicalChannel attributes for channels that are present in the …

02/06/09:

16:37 Ticket #354 (Bio-Formats writers should use the loci.common I/O classes) created by curtis
Many of the writer subclasses in loci.formats.out were written before we …
16:05 Changeset [4788] by curtis
Example demonstrating how to read image data from a byte array (and in the …
15:21 Ticket #353 (Vector .psd files not supported) created by melissa
All four of the .psd files in bio-formats/logo/ throw this exception: …
14:18 Changeset [4787] by melissa
Only populate Plane attributes for planes that have a timestamp.
12:54 Changeset [4786] by melissa
Removed unnecessary dimension swapping logic.
10:48 Changeset [4785] by melissa
InCellReader now explicitly calls MetadataStore.setImageID.
08:22 Changeset [4784] by melissa
Updated 4.0 release branch to reflect trunk.

02/05/09:

18:37 Changeset [4783] by curtis
Fix NullPointerException bug Steve Lamont found.
15:27 Ticket #351 (Metadata completeness - InCell 1000) closed by melissa
fixed: (In [4782]) Fixed a bunch of dimension detection problems, and improved …
15:27 Changeset [4782] by melissa
Fixed a bunch of dimension detection problems, and improved metadata …
14:42 Changeset [4781] by curtis
Offset adjustment and general cleanup for ARF reader. Works on sample …
08:07 Changeset [4780] by melissa
Fixed NPE.

02/04/09:

19:31 Changeset [4779] by curtis
Update org.apache.poi to loci.poi in documentation and configuration …
18:05 Changeset [4778] by curtis
Initial untested reader for Axon Raw Format (ARF), from Johannes …
18:00 Changeset [4777] by curtis
Fix typo.
14:24 Changeset [4776] by melissa
Created branch for 4.0.0 release.
14:19 Ticket #340 (Metadata completeness - Leica LEI/LIF) closed by melissa
fixed: (In [4775]) LIFReader now populates more metadata; closes #340.
14:19 Changeset [4775] by melissa
LIFReader now populates more metadata; closes #340.
13:45 Ticket #352 (Add support for NIfTI format) created by melissa
See  http://nifti.nimh.nih.gov/nifti-1/ for specification and sample data.
09:32 Ticket #351 (Metadata completeness - InCell 1000) created by melissa
We need to go through all of our InCell 1000 datasets and make sure that …

02/03/09:

17:40 Changeset [4774] by melissa
Fixed InCellReader's timestamps and element references.
15:32 Changeset [4773] by curtis
Fix compile errors.
14:34 Changeset [4772] by melissa
Changed package names of POI fork from org.apache.poi.* to loci.poi.* to …

02/02/09:

12:19 Changeset [4771] by melissa
Fixed how exposure times and ND filter settings are parsed from …
12:03 Changeset [4770] by melissa
Added preliminary support for iVision files - most pixel data can be read, …
09:28 Ticket #339 (Metadata completeness - Metamorph STK) closed by melissa
fixed: Closed by r4769.
09:27 Ticket #340 (Metadata completeness - Leica LEI/LIF) reopened by melissa
r4769 closed #339, not this ticket.
09:25 Ticket #340 (Metadata completeness - Leica LEI/LIF) closed by melissa
fixed: (In [4769]) Fixed a couple of metadata population bugs; closes #340.
09:25 Changeset [4769] by melissa
Fixed a couple of metadata population bugs; closes #340.
09:12 Changeset [4768] by melissa
Updated metadata support documentation for MetamorphReader. Also added a …
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