Timeline


and

07/30/10:

13:36 Changeset [6754] by melissa
Fixed BGR correction when opening sub-images. See QA #2583.
12:35 Ticket #526 (Parse metadata from S-FEG and Helios NanoLab TIFF files) created by curtis
The S-FEG and Helios NanoLab systems store metadata as key/value pairs in …
10:48 Ticket #525 (Files cannot be saved from ImageViewer unless '-omexml' option was passed ...) created by melissa
To reproduce: […] Select "File > Save". Enter any filename with a …

07/29/10:

20:20 Changeset [6753] by melissa
Fixed saveBytes and savePlane implementations to use the correct image …
14:27 Changeset [6752] by curtis
Document advantages of using the static library class loading approach.
13:41 Ticket #524 (Better documentation for command line tools) created by melissa
bfconvert, in particular, has some dangerously non-intuitive behavior. …
13:22 Ticket #523 (Bio-Formats Windowless Importer is broken) created by curtis
Attempting to use the Bio-Formats Windowless Importer with recent code …
12:59 Changeset [6751] by melissa
No longer use TiffData injection hack when validating OME-XML; OME-XML …
12:49 Changeset [6750] by curtis
Add Bio-Formats Importer to the File>Import menu.
12:16 Ticket #522 (Add support for Fuji LAS 3000 files) created by melissa
See data in data/fuji/venu/. The .img file appears to be raw pixels, and …
11:24 Changeset [6749] by melissa
Fixed OMEReaderWriterServiceImpl dependency checking and ome-io component …

07/28/10:

17:38 Changeset [6748] by melissa
Temporarily commented out URLHandleTest.
16:38 Ticket #519 (Implement new saveImage methods in BufferedImageWriter) closed by melissa
fixed: (In [6747]) * Added 'int getSeries()' method to IFormatWriter. * …
16:38 Changeset [6747] by melissa
* Added 'int getSeries()' method to IFormatWriter. * Implemented …
16:11 Ticket #273 (Some readers do not have sane file type checking) closed by melissa
fixed: (In [6746]) Remainder of type checking fixes. Closes #273.
16:11 Changeset [6746] by melissa
Remainder of type checking fixes. Closes #273.
13:09 Ticket #521 (Make Ant fail when tests fail) closed by melissa
fixed: (In [6745]) Updated overridden test targets to make Ant fail if any of the …
13:08 Changeset [6745] by melissa
Updated overridden test targets to make Ant fail if any of the tests …
10:28 Changeset [6744] by melissa
Force buffer reallocation if the previously allocated buffer is too small.
09:58 Changeset [6743] by melissa
Resolve references immediately, so that they are not lost with the …

07/27/10:

20:18 Changeset [6742] by melissa
More informative failure messages in sane used files test.
20:18 Changeset [6741] by melissa
Several more type checking fixes, see #273. Includes a fix for a very, …
16:12 Changeset [6740] by bselinsky
comments
15:32 Changeset [6739] by curtis
Extend the Boost_ADDITIONAL_VERSIONS hack to help CMake on Windows.
15:28 Changeset [6738] by curtis
Prevent Windows build from requiring dynamic Boost libraries (courtesy of …
14:51 Changeset [6737] by curtis
Fix errors with array allocation.
14:50 Changeset [6736] by curtis
More speed improvements and other cleanup to bfopen.m.
08:06 Changeset [6735] by melissa
* Handful of type checking fixes. See #273. * Strip whitespace from …

07/26/10:

18:39 Changeset [6734] by bselinsky
new
18:38 Changeset [6733] by bselinsky
Update
15:44 Changeset [6732] by curtis
Add a showinf easter egg. ;-)
13:59 Changeset [6731] by curtis
Stop using BufferedImageReader, for faster plane extraction.
11:45 Changeset [6730] by melissa
Merged r6729 into 4.2 branch.
11:43 Changeset [6729] by melissa
Ignore IFDs that do not contain an IMAGE_WIDTH entry. See QA #2570.
11:25 Changeset [6728] by melissa
Switch calls to MetadataTools.populatePixels and …
09:20 Changeset [6727] by melissa
Allow double images to be saved to TIFF.

07/23/10:

13:34 Changeset [6726] by melissa
A few more type checking fixes. See #273.
10:31 Changeset [6725] by curtis
Close file when finished reading data.

07/22/10:

19:16 Changeset [6724] by melissa
Fixed a bunch of type detection problems. See #273.

07/21/10:

19:58 Ticket #521 (Make Ant fail when tests fail) created by melissa
Currently, Ant test targets succeed even if one or more tests failed. To …
17:40 Changeset [6723] by curtis
Readd support for "-debug" flag to showinf and bfconvert.
17:36 Changeset [6722] by curtis
Add a utility method for enabling log4j logging without a configuration …
14:07 Changeset [6721] by bdezonia
whitespace only - a hudson test
11:32 Ticket #515 (Investigate physical size population for ScanR datasets) closed by melissa
fixed: (In [6720]) Populate physical pixel sizes, if present. Closes #515.
11:32 Changeset [6720] by melissa
Populate physical pixel sizes, if present. Closes #515.

07/20/10:

16:56 Changeset [6719] by melissa
Set BinData.Length to "0" to prevent validation errors.
16:55 Ticket #520 (Verify that generated OME-XML validates) created by melissa
r6719 fixed the most common error (missing BinData.Length), but some files …
16:32 Changeset [6718] by bdezonia
no change except whitespace - hudson test
16:11 Changeset [6717] by curtis
Eliminate excessive xmlvalid output.
14:51 Changeset [6716] by curtis
More fixes to LWF license code handling.
12:24 Changeset [6715] by melissa
Close open files to prevent "too many open files" error when exporting …
11:46 Changeset [6714] by curtis
Fix up support for LWF license codes.
09:29 Changeset [6713] by melissa
Prevent ArithmeticException if stage coordinates are not present.
09:05 Ticket #519 (Implement new saveImage methods in BufferedImageWriter) created by melissa
All of the existing saveImage methods in BufferedImageWriter are …
08:56 Changeset [6712] by melissa
Allow sane used file test to be run separately; useful for testing #273.
08:40 Changeset [6711] by melissa
Speed up plane access by using one reader for each constituent file.

07/19/10:

21:21 Changeset [6710] by melissa
* Fixed how ICS files with > 4 channels are read. * Fixed Channel …
19:08 Changeset [6709] by melissa
Added utility that prints out all of the files in a directory that are …
18:12 Changeset [6708] by melissa
Added one more date format to the list of acceptable TIFF date formats.
17:40 Changeset [6707] by melissa
Fixed problems with exporting multi-channel data.
17:35 Ticket #518 (Allow exporter plugin to export to multiple files) created by melissa
In particular, it would be nice to be able to export multi-file OME-TIFF …
14:07 Ticket #517 (Bio-Formats Importer progress bar is missing on some systems) created by curtis
The recent changes to the Bio-Formats Importer have resulted in some cases …
11:33 Changeset [6706] by melissa
Tweaked isThisType to automatically return false if the TIFF comment is an …
10:02 Changeset [6705] by melissa
Fixed bytes per pixel calculation for RGB data.

07/16/10:

11:30 Changeset [6704] by melissa
* Reverted r6703 stupidity. * Fixed Image5D display mode to work with …

07/15/10:

15:23 Changeset [6703] by melissa
Disable the "concatenate series" option when displaying with Image5D. See …
15:14 Changeset [6702] by melissa
* Fixed ROI retrieval logic in ImageJ import plugin. * Updated FV1000 …
14:19 Changeset [6701] by melissa
Fixed View5D instantiation; see #514.

07/14/10:

15:23 Ticket #516 (Allow metadata support documentation to be fully autogenerated) created by melissa
Right now, the metadata support documentation is autogenerated from the …
15:14 Ticket #515 (Investigate physical size population for ScanR datasets) created by melissa
Need to double-check that ScanR physical sizes are being populated …
14:54 Ticket #510 (Some Amira files throw an exception during setId) closed by melissa
invalid: The Amira software does not open either file, so I'm going to assume that …
13:47 Changeset [6700] by melissa
More robust Z position parsing. The value of 'absoluteZ' is now taken …

07/13/10:

17:57 Changeset [6699] by melissa
Fixed pixel data offset.
17:03 Milestone bio-formats-4.2 completed
16:16 Changeset [6698] by curtis
Fix problem with GUI locking when using LOCI Plugins Shortcut Window.
15:39 Changeset [6697] by melissa
First attempt at parsing stage coordinates from LSM files.
15:31 Changeset [6696] by curtis
Add toString method to StatusEvent, for debugging.
15:03 Ticket #514 (Fix Image5D and View5D view modes) created by curtis
There may be an issue with Image5D and View5D view modes, as they were not …
14:18 Ticket #511 (Compressed Amira file not read properly) closed by melissa
fixed: Fixed in r6695.
14:18 Changeset [6695] by melissa
Fixed problems with unaligned RLE-compressed images. Closes #511.
11:00 Ticket #513 (Exporting RGB images to OME-TIFF fails) closed by melissa
fixed: Fixed in r6694.
10:58 Changeset [6694] by melissa
Adjust SizeC internally when writing RGB OME-TIFF files. Closes #513.

07/12/10:

14:45 Ticket #513 (Exporting RGB images to OME-TIFF fails) created by melissa
This macro: […] produces this exception: […]
14:35 Changeset [6693] by melissa
Fixed ArrayIndexOutOfBoundsException when opening sub-images from 16- and …
14:28 Changeset [6692] by melissa
* Updated CellWorXReader to delegate to DeltavisionReader when reading …
13:14 Changeset [6691] by melissa
Backported r6689 to 4.2 branch.
12:57 Changeset [6690] by melissa
Initial version of CellWorX .pnl reader.
12:56 Changeset [6689] by melissa
Fixed emission wavelength parsing.
12:55 Changeset [6688] by curtis
Whitespace.

07/10/10:

09:44 Changeset [6687] by melissa
Fixed channel data is parsed from Leica LIF files that have had one or …

07/09/10:

14:22 Changeset [6686] by curtis
Fix up test targets in Ant build scripts.
10:47 Changeset [6685] by melissa
4.2.0 release of LOCI tools.
10:38 Changeset [6684] by melissa
Updated what's new and switch trunk component version numbers to 5.0-DEV.
10:10 Changeset [6683] by curtis
Backport r6682 to 4.2 branch.
10:09 Changeset [6682] by curtis
Add a flag to disable tests with special requirements. All tests now pass.
10:04 Changeset [6681] by melissa
Only populate Objective.NominalMagnification if the magnification is …
09:48 Changeset [6680] by curtis
Backport r6679 to 4.2 branch.
09:40 Changeset [6679] by curtis
Better handling of 5+ channel data.
08:24 Changeset [6678] by melissa
Updated component version numbers in 4.2 branch.

07/08/10:

16:31 Changeset [6677] by curtis
Backport r6672,r6673,r6676 to 4.2 branch.
16:29 Changeset [6676] by curtis
Fix bug with dimensional extents between multiple series.
15:32 Changeset [6675] by curtis
Fix some Eclipse warnings.
15:22 Changeset [6674] by melissa
Fixed how Images are removed from a MetadataStore when exporting one …
15:13 Changeset [6673] by curtis
Better error handling when constructing base reader object.
15:13 Changeset [6672] by curtis
Fix typo.
15:13 Changeset [6671] by curtis
Define some constants for FakeReader defaults.
15:02 Changeset [6670] by curtis
Use native line endings for Bio-Formats C++ source code.
14:40 Changeset [6669] by curtis
Backport recent LOCI plugins progress to 4.2 branch.
14:35 Changeset [6668] by curtis
Fix autoscaling bugs, and rework autoscaling tests.
13:58 Changeset [6667] by melissa
* Updated undeclared namespace stripping logic to look for namespaces in …
10:39 Matlab edited by melissa
(diff)
10:07 Changeset [6666] by melissa
Catch NullPointerException when attempting to parse OME-XML comments.
09:47 Changeset [6665] by melissa
Only overwrite the dimensions if the new values are sane.

07/07/10:

20:17 Changeset [6664] by melissa
OMETiffReader.isThisType now checks whether or not the OME-XML block can …
15:55 Changeset [6663] by melissa
Merged recent OME-XML and core Bio-Formats changes into the 4.2 branch.
13:48 Changeset [6662] by melissa
Removed some obsolete hacks that prevented physical sizes from being …
12:38 Changeset [6661] by melissa
Better physical X/Y size parsing.
12:01 Changeset [6660] by curtis
Remove unnecessary thumbnail autoscaling logic.
11:54 Changeset [6659] by curtis
Disable 'Record modifications to virtual stack' option (broken anyway).
11:54 Changeset [6658] by curtis
Fix problem with virtual stack pixel types.
11:27 Changeset [6657] by curtis
Use 'uncalibrated' values for CompositeImage min/max.
10:52 Changeset [6656] by curtis
If TimeIncrement is missing, average DeltaT values for ImageJ time …

07/06/10:

19:58 Changeset [6655] by melissa
Added MetadataLevel.NO_OVERLAYS, and updated readers accordingly.
19:02 Changeset [6654] by curtis
Progress on Bio-Formats Importer: * Readd support for Ext.openImage and …
12:07 Changeset [6653] by callan
Move reference handling until after attribute population for FilterSet …
11:56 Changeset [6652] by callan
Re-run of code generation. ( ome-xml:r649)
10:58 Changeset [6651] by callan
Handle class cast exceptions in ROI shape transformation.
09:34 Changeset [6650] by callan
Handle namespace prefixes on nodes during parsing of the DOM.

07/05/10:

11:23 Changeset [6649] by callan
Re-run of code generation; laser pumps can be any light source. …
11:04 Changeset [6648] by melissa
Remove any BinData elements from the OME-XML before it is written to the …
10:17 Changeset [6647] by callan
Messed up logging by having an old version of the enum handler template, …
10:02 Changeset [6646] by melissa
Updated schema location to 2010-06.
09:50 Changeset [6645] by melissa
Fixed Objective parsing when Immersion and Correction are reversed.
09:48 Changeset [6644] by callan
Re-run of code generation; DRY as a possible value for AIR immersion. …

07/02/10:

18:25 Changeset [6643] by curtis
Fix Jace paths to work pre-r46, with commented out code for r46+. Add …
17:13 Changeset [6642] by curtis
Update ome-xml.h to reflect r6631.
16:57 Changeset [6641] by curtis
Update paths to work with new Jace path structure (r52+).
16:49 Changeset [6640] by bdezonia
minor edits. did change maxPixel calc for UINT32.
15:51 Changeset [6639] by curtis
Update autoscale test to check CompositeImage LUT ranges.
15:20 Changeset [6638] by curtis
Enable toggling of debug print statements using DEBUG flag.
15:15 Changeset [6637] by bdezonia
minor edits
14:48 Changeset [6636] by bdezonia
added UINT16 support to all colorTests. added back all virtual modes to …
13:01 Changeset [6635] by melissa
Be more thorough when searching for the .dv file that matches a .log or …
12:53 Changeset [6634] by bdezonia
datasetGroupFiles() improved. Constants fixed for correct style.
12:27 Changeset [6633] by bdezonia
fixed lut testing in testColorCustom. enhanced testColorComposite to …
11:48 WikiStart edited by melissa
(diff)
09:54 Ticket #512 (Logging cleanup) closed by melissa
fixed: (In [6632]) Re-run of code generation ( ome-xml:r646), closes #512.
09:54 Changeset [6632] by melissa
Re-run of code generation ( ome-xml:r646), closes #512.
09:43 Changeset [6631] by melissa
Removed obsolete OME-XML model objects.
06:07 Changeset [6630] by callan
Set fill color as well as stroke color for mask ROI.
05:34 Changeset [6629] by callan
Fix shape indexes for ellipse X and Y radii.
05:08 Changeset [6628] by callan
Utilize the shape label rather than a seperate text shape for MIAS ROI.

07/01/10:

19:30 Changeset [6627] by melissa
Switched TiffParser logging from 'debug' to 'trace'; see #512.
18:59 Changeset [6626] by curtis
Backport r6625 to 4.2 branch.
18:58 Changeset [6625] by curtis
Fix autoscaling problem with >8-bit CompositeImages.
18:07 Changeset [6624] by curtis
Remove obsolete constant from bf-cpp conflicts list.
17:31 Changeset [6623] by bdezonia
make flesh for the color tests. remove unfinished tests. comment out some …
16:17 Changeset [6622] by melissa
Ensure that xmlns:ome elements are preserved during transformation.
15:16 Changeset [6621] by melissa
Merged r6614 and r6615 into trunk.
11:36 Changeset [6620] by bdezonia
some work on composite testing and some code on dimension swapping tests. …
09:08 Changeset [6619] by melissa
Updated stylesheets to  ome-xml:r645.
07:32 Changeset [6618] by callan
Restoring MIAS reader overlay support.
06:16 Changeset [6617] by callan
Support for TagAnnotation and TermAnnotation conversion.
06:07 Changeset [6616] by callan
Re-run of code generation; support for mask bin data. ( ome-xml:r644)
04:40 Changeset [6615] by dscho
Avoid "prefix <...> not bound" error when transforming XML When …
04:40 Changeset [6614] by dscho
Fix OME-XML version discovery Some files (Huygens) have an xmlns:ome …

06/30/10:

21:15 Changeset [6613] by melissa
Merged r6602 to 4.2 branch.
20:48 Changeset [6612] by melissa
Fixed parsing of large OME-XML files and pre-2010-04 files with …
16:13 Changeset [6611] by curtis
Backport r6609,r6610 to 4.2 branch.
16:11 Changeset [6610] by curtis
Change default stack order to XYCZT, to match Hyperstack view option.
16:10 Changeset [6609] by curtis
Fix bug in 'Metadata only' stack view option.
14:44 Changeset [6608] by curtis
Backport r6606,r6607 to 4.2 branch.
14:42 Changeset [6607] by curtis
Fix plane ordering bug with channel separator when effectiveSizeC>1, …
14:31 Ticket #512 (Logging cleanup) created by melissa
Specifically: * change many of the loci.formats.tiff.TiffParser logging …
13:52 Changeset [6606] by curtis
Fix bug with fake data generation when rgbChannelCount>1.
13:12 Changeset [6605] by curtis
Backport r6603,6604 to 4.2 branch.
13:11 Changeset [6604] by curtis
Readd "Standard ImageJ" stack view option. Note that non-hyperstacks …
11:21 Ticket #511 (Compressed Amira file not read properly) created by melissa
See data/amira/jeremy/Virus_Membrane7.am and the corresponding screenshot …
10:31 Ticket #510 (Some Amira files throw an exception during setId) created by melissa
See data/amira/jeremy/HIV_FINAL.hx and …
09:41 Ticket #509 (Add test for macro key regressions) created by melissa
It would be a good idea to add a unit test that checks whether or not old …
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