Timeline


and

11/01/10:

17:32 Ticket #592 (Slidebook pixel data is not always correct) created by melissa
See files in data/slidebook/marjolijn, data/slidebook/roman and …
17:05 Changeset [7148] by melissa
A few fixes for writing planes non-sequentially.
17:00 Ticket #591 (Writers do not support overwriting metadata) created by melissa
See attached test case. In summary, writing some subset of planes using …
08:48 Changeset [7147] by melissa
Forward ported r7145 and r7146.

10/30/10:

12:57 Changeset [7146] by melissa
Added top-level compile target.
12:31 Changeset [7145] by melissa
* Fixed multi-series OME-XML export. * Fixed multi-series OME-TIFF export. …

10/29/10:

16:37 Ticket #590 (Series dialog should indicate the total number of series) created by melissa
The dialog that is shown when there are more than …

10/28/10:

13:35 Changeset [7144] by melissa
Finally fixed ND2 field index bug.
10:43 Changeset [7143] by melissa
Fixed a handful of NPEs, AIOOBs, and leaking file handles.
10:42 Changeset [7142] by melissa
Fixed a bug that prevented ROIs from being displayed.

10/27/10:

21:31 Changeset [7141] by melissa
* Backported r6227 to 4.1. * Fixed a subtle bug in calculating the pixel …
18:22 Ticket #589 (Add support for TIFF files with FillOrder == 2) created by melissa
See example file in data/tiff/john/. In essence, the bits in each byte …

10/26/10:

17:59 Changeset [7140] by melissa
Fixed an NPE and a few plane indexing bugs.
16:20 Ticket #588 (Consider writing decoder for compressed Flex files) created by melissa
The main reason to do this is so that compressed Flex files can be …
14:29 Changeset [7139] by aivar
Select SLIM Curve LMA as default.
14:29 Changeset [7138] by aivar
Select SLIM Curve LMA as default.
10:21 Changeset [7137] by melissa
Fixed timestamp indices, see  omero:#3121.
08:26 Ticket #587 (Move color options to a separate dialog) created by melissa
Instead of the current color options, we could have a "Specify custom …
08:23 Ticket #586 (Preserve custom color options) created by melissa
The "Custom" color option currently does not remember which colors were …
08:21 Ticket #585 (Make error message windows more friendly) created by melissa
It's been pointed out that seeing a stack trace when something goes wrong …

10/25/10:

23:24 Changeset [7136] by aivar
Init start bin.
22:32 Changeset [7135] by aivar
Added 'quit' method to make the UI go away when the user cancels a fit.
22:31 Changeset [7134] by aivar
Added 'quit' method to make the UI go away when the user cancels a fit.
22:30 Changeset [7133] by aivar
Added image stack support for multiple channels. Support for multiple …
22:23 Changeset [7132] by aivar
Add multiple exponential support (doesn't seem to actually work though).
19:46 Changeset [7131] by aivar
Better colorization.
19:45 Changeset [7130] by aivar
A cheap variant of my ThreeColorColorize. Still emphasizes green (my …
18:16 Changeset [7129] by melissa
Fixed stage position indices.
16:20 Changeset [7128] by melissa
Fixed a handful of Javadoc errors.
15:31 Changeset [7127] by melissa
A few more fixes for small bugs exposed during testing.
14:23 Changeset [7126] by melissa
Reversed usage of OMETiffReader's getMetadataStoreForDisplay() and …

10/24/10:

17:28 Changeset [7125] by melissa
Fixed a handful of little bugs exposed during testing.
17:01 Changeset [7124] by melissa
Fixed scanline padding and various metadata parsing bugs.
15:56 Ticket #584 (Data repository cleanup) created by melissa
* Make sure that every file has an accurate configuration file entry. * …
15:42 Changeset [7123] by melissa
Fixed autoscaling for sliced stacks.
14:08 Changeset [7122] by melissa
Fixed TIFF file ordering problems.

10/22/10:

23:05 Changeset [7121] by aivar
Default to "EACH PIXEL" for better demo.
23:01 Changeset [7120] by aivar
Added chiSquare.
23:00 Changeset [7119] by aivar
Added chiSquare.
23:00 Changeset [7118] by aivar
Added chiSquare.
23:00 Changeset [7117] by aivar
Added chiSquare.
22:59 Changeset [7116] by aivar
Tidied up, made all the listeners anonymous inner classes. Added setters …
22:58 Changeset [7115] by aivar
Added quit capability.
22:57 Changeset [7114] by aivar
Added more setters and chiSquare.
22:57 Changeset [7113] by aivar
Removed debugging print statement.
22:56 Changeset [7112] by aivar
Added main loop that does fits based on UI input. Gets and sets …

10/21/10:

21:13 Changeset [7111] by aivar
Fleshed out.
21:12 Changeset [7110] by aivar
Doesn't extend StartStopListener any more.
21:11 Changeset [7109] by aivar
New method to set listener.
21:10 Changeset [7108] by aivar
New UI; not working.
21:10 Changeset [7107] by aivar
Cleanup, rewrote start/stop bars completely.
16:17 Changeset [7106] by melissa
Updated metadata support documentation.
11:02 Changeset [7105] by hinerm
Adjusted canDoDirect to be true if the image is interleaved (avoiding …
08:48 Changeset [7104] by melissa
Updated version numbers to "4.2.1-DEV".
08:40 Changeset [7103] by melissa
Backported r7084 to 4.2.
08:39 Changeset [7102] by melissa
Backported r7055 to 4.2.
08:39 Changeset [7101] by melissa
Backported r7051 to 4.2.
08:38 Changeset [7100] by melissa
Backported r7042 to 4.2.
08:37 Changeset [7099] by melissa
Backported Zeiss LSM stage position changes to 4.2: r7040 and r7043.
08:35 Changeset [7098] by melissa
Backported r7037 to 4.2.
08:34 Changeset [7097] by melissa
Backported file stitching changes to 4.2: r7021, r7022, r7070, r7071, …
08:32 Changeset [7096] by melissa
Backported native component changes to 4.2: r7014, r7035, r7036, r7049, …
08:31 Changeset [7095] by melissa
Backported r7012 and r7013 to 4.2.

10/20/10:

10:37 Changeset [7094] by rlentz
Converted to Maven Project for ease of download

10/19/10:

21:23 Changeset [7093] by melissa
Various tweaks to file grouping logic, so that datasets can be read even …
17:24 Changeset [7092] by melissa
Only populate Objective.NominalMagnification if the magnification is …
14:46 Ticket #583 (DeltaVision OMX read error) closed by melissa
fixed: (In [7091]) * Attempt to gracefully handle truncated Deltavision files. …
14:46 Changeset [7091] by melissa
* Attempt to gracefully handle truncated Deltavision files. See QA #2892, …
14:04 Changeset [7090] by melissa
Override get*LookupTable() so that LUTs are returned where appropriate. …
13:55 Changeset [7089] by melissa
Skip over ROI files that do not exist, instead of throwing an exception.
04:24 Ticket #583 (DeltaVision OMX read error) created by callan
 http://qa.openmicroscopy.org.uk/qa/feedback/2892/ […]

10/18/10:

21:54 Changeset [7088] by aivar
Default to 'each pixel' fit.
21:53 Changeset [7087] by aivar
Commented out excessive printouts that slow down the fit.
18:13 Changeset [7086] by melissa
A few more file stitching fixes.
15:59 Changeset [7085] by melissa
Close unused file handles.
15:48 Changeset [7084] by melissa
Fixed a few deprecation warnings and compile errors.
10:56 Changeset [7083] by melissa
Added better type detection to the text reader, see  omero:#2740.

10/15/10:

21:24 Changeset [7082] by aivar
Removed imagej/ij/1.43, added imagej/ij/2.0-SNAPSHOT, …
21:17 Changeset [7081] by aivar
First plugins config file.
21:16 Changeset [7080] by aivar
Borrowed from SLIMPlotter.
21:15 Changeset [7079] by aivar
Many changes to SLIMProcessor, mostly for automatic plugin.
21:15 Changeset [7078] by aivar
New version of SLIM_Plugin, moved out of the default package.
21:15 Changeset [7077] by aivar
Automatically executed version of SLIM Plugin.

10/14/10:

19:45 Changeset [7076] by melissa
Fixed potential ArrayIndexOutOfBounds which prevented tests from passing …
18:23 Changeset [7075] by melissa
* Fixed various file stitching bugs. * Removed debugging statement.
11:01 Changeset [7074] by melissa
Parse stage positions from Fluoview/Andor TIFFs.

10/13/10:

16:12 Changeset [7073] by melissa
Populate physical sizes for all series.
14:56 Ticket #578 (bfconvert does not properly overwrite or append to files) closed by melissa
fixed: (In [7072]) Using bfconvert with an existing output file will now cause …
14:56 Changeset [7072] by melissa
Using bfconvert with an existing output file will now cause that output …
14:43 Changeset [7071] by melissa
Fixed bugs that prevented tests from passing in r7070.
13:09 Ticket #395 (Support for non-numerical patterns in FilePattern) closed by melissa
fixed: (In [7070]) Added support for non-numerical file pattern blocks, closes …
13:09 Changeset [7070] by melissa
Added support for non-numerical file pattern blocks, closes #395. You can …
12:05 Ticket #576 (Improve Zeiss LSM stage/tile position parsing) closed by melissa
fixed: After reviewing revisions to the 6.0 documentation, it seems as though we …

10/12/10:

16:34 Changeset [7069] by curtis
Minor tweaks.

10/11/10:

16:42 Ticket #564 (Improve original metadata population in OME-XML) closed by melissa
fixed: (In [7068]) Finally finished fixing original metadata population, closes …
16:42 Changeset [7068] by melissa
Finally finished fixing original metadata population, closes #564. We now …
16:33 Changeset [7067] by melissa
Backported r7038 to 4.2.
12:26 Changeset [7066] by melissa
Allow a different stage position for each plane.
11:39 Changeset [7065] by curtis
Fix compile error with Java 1.5.
11:39 Changeset [7064] by curtis
Add bf-imglib dependency to slim-plugin POM.
09:17 Changeset [7063] by melissa
Prevent Bio-Rad reader from attempting to initialize ._*.pic files. See …

10/08/10:

20:12 Changeset [7062] by aivar
Fixed build problem.
20:10 Changeset [7061] by aivar
Extensive changes: Refactored into packages. New interface.
20:10 Changeset [7060] by aivar
Extensive changes: Refactored into packages. New interface.
20:09 Changeset [7059] by aivar
Extensive changes: Refactored into packages. New interface.
20:09 Changeset [7058] by aivar
Extensive changes: Refactored into packages. New interface.
17:32 Changeset [7057] by melissa
Fixed PICT sub-image reading, see  omero:#3037.
17:22 Changeset [7056] by melissa
Moved SizeT population, so that we do not attempt to populate it when …
17:15 Ticket #570 (Populate ImageJ's 'origin' metadata) closed by melissa
fixed: Closing this ticket, as you can now retrieve the stage positions from the …
17:15 Ticket #582 (Consider standarizing some original metadata keys) created by melissa
Comment from Curtis in #570: *snip* > Wayne recently added a new macro …
17:04 Changeset [7055] by melissa
Standardized storage of stage positions in the original metadata …
16:23 Changeset [7054] by melissa
Reverted r7018, see #570.
16:12 Changeset [7053] by melissa
Parse physical pixel sizes.
14:58 Changeset [7052] by melissa
Fixed a handful of lovely dimension detection bugs.
10:27 Changeset [7051] by callan
Handle NPE when accessing UUID filename. (Fixes downstream  omero:#3038)
09:39 Changeset [7050] by hinerm
Improvement: prevented null assignment of path to libraries
09:01 Changeset [7049] by hinerm
Improvement: The BF-ITK plug-in now detects where its libraries live, vita …

10/07/10:

22:51 Changeset [7048] by curtis
Backport latest loci-plugins unit tests to Maven branch.
22:48 Changeset [7047] by curtis
Backport latest loci-plugins trunk to Maven branch.
17:56 Ticket #581 (Add support for DICOM supplement #145) created by melissa
See documentation here: …
17:40 Ticket #579 (Images do not properly update in the Data Browser) closed by melissa
fixed: (In [7046]) Fixed slice updating in the Data Browser; closes #579.
17:40 Changeset [7046] by melissa
Fixed slice updating in the Data Browser; closes #579.
17:30 Changeset [7045] by curtis
Merge latest LOCI Common trunk to Maven branch.
17:28 Changeset [7044] by curtis
Backport latest Bio-Formats trunk to Maven branch.
15:39 Changeset [7043] by melissa
Fixed stage position indices, see #576.
15:09 Changeset [7042] by melissa
Parse and apply channel colors stored in ND2 files.
10:29 Changeset [7041] by melissa
Added support for pixel types other than uint8.

10/06/10:

18:07 Changeset [7040] by melissa
Progress on reading position data from LSM files. See #576, see #570.
16:59 Changeset [7039] by melissa
Several metadata population fixes.
15:02 Ticket #574 (Some Prairie datasets take a long time to initialize on Windows) closed by melissa
fixed: (In [7038]) Adjusted original metadata population, so that it doesn't take …
15:02 Changeset [7038] by melissa
Adjusted original metadata population, so that it doesn't take nearly as …
12:48 Ticket #580 (Virtual stack with split channels, timepoints and/or planes) created by curtis
Currently, the Bio-Formats Importer does not allow the "Use virtual stack" …

10/05/10:

18:11 Ticket #579 (Images do not properly update in the Data Browser) created by melissa
To reproduce: - Select "Plugins > LOCI > Bio-Formats Importer" in …
17:59 Ticket #578 (bfconvert does not properly overwrite or append to files) created by melissa
To reproduce: […] Select 'y' when prompted to overwrite the existing …
12:49 Ticket #577 (Switch Leica LIF reader to use DOM parsing (instead of SAX)) created by melissa
The structure of Leica LIF XML is rather complicated, and in many places …
12:48 Changeset [7037] by melissa
One more very temporary fix that prevents too many Channels from being …
11:36 Changeset [7036] by hinerm
Added private data members to allow use of ChannelSeparators and …
11:35 Changeset [7035] by hinerm
Bug Fixes: read image data from start to start + count, instead of start …
10:47 Ticket #576 (Improve Zeiss LSM stage/tile position parsing) created by melissa
We now have the new 6.0 documentation, along with several example datasets …

10/04/10:

18:58 Changeset [7034] by aivar
Deal with sigma and instrument response.
18:58 Changeset [7033] by aivar
Deal with sigma and instrument response.
18:57 Changeset [7032] by aivar
Deal with sigma and instrument response.
18:57 Changeset [7031] by aivar
Deal with sigma and instrument response.
18:57 Changeset [7030] by aivar
Deal with sigma and instrument response.
18:57 Changeset [7029] by aivar
Deal with sigma and instrument response.
18:56 Changeset [7028] by aivar
Deal with sigma and instrument response.
18:56 Changeset [7027] by aivar
Deal with sigma and instrument response.
18:54 Changeset [7026] by aivar
Deal with sigma and instrument response.
18:54 Changeset [7025] by aivar
Deal with sigma and instrument response.
18:51 Changeset [7024] by aivar
TIdy up code.
18:51 Changeset [7023] by aivar
TIdy up code.
17:45 Changeset [7022] by melissa
Fixed a few little bugs that prevented tests from passing in r7021.
16:07 Ticket #517 (Bio-Formats Importer progress bar is missing on some systems) closed by curtis
worksforme: We are unable to duplicate the problem on our systems. We will reopen the …
13:55 Ticket #296 (Stitching multiple series needs improvement) closed by melissa
fixed: (In [7021]) Updated FileStitcher and FilePattern to better handle …
13:55 Ticket #542 (Multi-series stitching is incorrect) closed by melissa
fixed: (In [7021]) Updated FileStitcher and FilePattern to better handle …
13:55 Changeset [7021] by melissa
Updated FileStitcher and FilePattern to better handle multi-series …

10/03/10:

10:39 Ticket #572 (Location tests can fail when /tmp is under high load) closed by melissa
fixed: (In [7020]) Hide temporary files in a subdirectory of /tmp, so that the …
10:39 Changeset [7020] by melissa
Hide temporary files in a subdirectory of /tmp, so that the tests are …

10/02/10:

16:04 Ticket #567 (LUTs not parsed from .pcx files) closed by melissa
fixed: (In [7019]) Added support for RGB and indexed color images. Closes #567.
16:04 Changeset [7019] by melissa
Added support for RGB and indexed color images. Closes #567.
12:25 Changeset [7018] by melissa
Sets the Calibration.*Origin values to equal the stage position (if …
11:11 Ticket #556 (OME-TIFF reader should use MetadataOnly rather than BinData) closed by melissa
fixed: I'm fairly certain that this was fixed in r6978, but feel free to re-open …
Note: See TracTimeline for information about the timeline view.