Timeline


and

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 …

09/30/10:

18:19 Ticket #482 (Expand LOCI Hudson job) closed by melissa
fixed: The only task left in this ticket is integrating bf-cpp with Hudson, which …
17:58 Ticket #575 (Make it easier to get/set the pixels' compression type) created by melissa
The reader API currently does not have any way of providing the …
15:19 Ticket #574 (Some Prairie datasets take a long time to initialize on Windows) created by melissa
See data in prairie/pam/092910-psf/. These datasets initialize very …
14:35 Changeset [7017] by aivar
Debugging: print out info on pixels with 'bad' fit: calculated lifetime …
14:31 Changeset [7016] by aivar
Added SLIMCURVE fit algorithms.
14:30 Changeset [7015] by aivar
Added SLIMCURVE fit algorithms.
11:28 Ticket #566 (Fix tests in ome-xml component) closed by melissa
fixed: LOCI Hudson runs 'ant test-ome-xml' starting with build #242.
11:05 Changeset [7014] by hinerm
Bug Fix: Converted logging functions from Log::getStackTrace to …
10:35 Ticket #573 (Add support for Olympus CellSens .vsi data) created by melissa
See files in /data/cellsens/. There is also Windows-only viewer here: …
04:54 Ticket #572 (Location tests can fail when /tmp is under high load) created by callan
When /tmp is under high load and is changing significantly underneath the …
04:52 Ticket #571 (Bug when Pump is used in a LightSourceSettings) closed by callan
fixed: (In [7013]) Resolving issues with Reference instances (with their referrer …
04:52 Changeset [7013] by callan
Resolving issues with Reference instances (with their referrer ID) ending …
04:17 Changeset [7012] by callan
Fix a couple small issues with the SPW model mock and In/Out test.
04:15 Ticket #571 (Bug when Pump is used in a LightSourceSettings) created by callan
If a Pump is then referenced in a LightSourceSettings, there is a …

09/29/10:

20:00 Ticket #570 (Populate ImageJ's 'origin' metadata) created by melissa
The ImageJ import plugin should be populating the '*Origin' fields in …
19:49 Ticket #569 (Add support for JPEG-compressed AVIs) created by melissa
It would be nice if the AVI reader could handle AVIs with JPEG-compressed …
19:42 Ticket #568 (Review results of testing project) created by melissa
See notes and screenshots in /scratch/josh/. #567 should be fixed first, …
19:41 Ticket #567 (LUTs not parsed from .pcx files) created by melissa
See .pcx files in /scratch/josh/Screenshots/. ImageMagick displays them …
10:43 Changeset [7011] by rlentz
10:25 Changeset [7010] by melissa
Fixed a bug that prevented extra LIF channels from being removed. Closes …

09/28/10:

15:21 Changeset [7009] by melissa
Fixed SVN/Trac links.
14:46 Changeset [7008] by melissa
Added missing files.
14:34 Changeset [7007] by melissa
Merged remainder of build, test, and SVN/Trac link changes to 4.2.
13:09 Changeset [7006] by melissa
Merged remaining reader changes: r6708, r6727, r6778, r6779, r6782, r6787, …
12:47 Changeset [7005] by melissa
Merged remaining MATLAB, command line tool, and C++ changes into 4.2: …
11:30 Changeset [7004] by melissa
Merged TIFF export fixes into 4.2: r6878, r6976, and r6977.
11:28 Changeset [7003] by melissa
Merged metadata population fixes into 4.2: r6700, r6711, r6719, r6728, …
11:21 Changeset [7002] by melissa
Merged type checking fixes into 4.2: r6724, r6726, r6741, r6746, and …
11:15 Changeset [7001] by melissa
Merged ome-io component changes into 4.2: r6759, r6760, r6761, r6769, …
11:12 Changeset [7000] by melissa
Merged remaining ImageJ plugin changes to 4.2.
11:08 Changeset [6999] by melissa
Merged common XML changes in to 4.2: r6717, r6888, and r6985.
11:06 Changeset [6998] by melissa
Merged base reader changes into 4.2: r6688, r6756, r6757, r6764, r6853, …
11:03 Changeset [6997] by melissa
Merged new readers into 4.2: r6758, r6783, r6790, r6797, r6801, r6845.
10:59 Changeset [6996] by melissa
Merged changes to common component and logging into 4.2: r6696, r6722, …
10:48 Changeset [6995] by melissa
Merged recent ScanR changes: r6720, r6810, r6838, r6959, and r6967.
10:44 Changeset [6994] by melissa
Merged GUI tools changes: r6766 and r6774.
10:42 Changeset [6993] by melissa
Merged minor API additions to 4.2: r6747 and r6798.
10:33 Changeset [6992] by melissa
Merged recent Zeiss LSM changes to 4.2: r6697, r6713, and r6842.
10:29 Changeset [6991] by melissa
Merged r6695 into 4.2.

09/27/10:

16:03 Changeset [6990] by curtis
Backport r6985 to maven branch.
13:56 Changeset [6989] by melissa
Fixed TiffRationalTest, based on changes in r6988.
13:35 Changeset [6988] by melissa
Fixed a couple of issues exposed by Findbugs. See #546.
13:29 Changeset [6987] by melissa
Parse scanner serial numbers from the plate log file.
13:07 Changeset [6986] by melissa
Minor fixes to (hopefully) prevent AIOOB.
12:52 Changeset [6985] by melissa
Handle XML parsing errors using SLF4J. Eliminates annoying "[Fatal Error] …

09/24/10:

17:11 Changeset [6984] by curtis
Generate Javadocs as part of site generation.
13:17 Changeset [6983] by melissa
Fixed various dimension ordering bugs in new multi-file Improvision TIFF …
12:10 Changeset [6982] by melissa
Tweaked component.runtime-cp for the ome-xml component and updated the …
11:01 Changeset [6981] by melissa
Only populate a channel's excitation wavelength if the wavelength is …

09/23/10:

20:14 Changeset [6980] by curtis
Fix slim-plugin compile errors in Eclipse.
19:47 Changeset [6979] by curtis
Require Java 1.6 for ome-io.
15:19 Ticket #566 (Fix tests in ome-xml component) created by melissa
'ant test-ome-xml' in the root directory currently fails. Once the tests …
15:18 Changeset [6978] by melissa
OMETiffReader now populates its' MetadataStore in such as way as to …
14:03 Ticket #565 (Expand (and clean up) use of new 'setWriteSequentially' method) created by melissa
In r6976, TiffWriter was given a new method: 'void …
11:26 Ticket #564 (Improve original metadata population in OME-XML) created by melissa
There are a few things that should be done: * Change the value of the …
11:15 Changeset [6977] by melissa
Fixed TiffParser constructor, so that it effectively does not modify the …
10:36 Ticket #554 (Exporting a multi-series OME-TIFF file results in incorrect pixel data) closed by melissa
fixed: (In [6976]) Several fixes for writing BigTIFFs and multi-series OME-TIFFs. …
10:36 Changeset [6976] by melissa
Several fixes for writing BigTIFFs and multi-series OME-TIFFs. Closes …

09/22/10:

13:43 Changeset [6975] by melissa
One more set of ArrayIndexOutOfBounds fixes for certain LZW-compressed …
13:26 Changeset [6974] by curtis
Fix Ant configuration error with bf-itk.
13:03 Changeset [6973] by curtis
Update bf-cpp header file.
10:55 Changeset [6972] by melissa
Only apply LUTs to sliced stacks if the original CompositeImage used the …
10:34 Changeset [6971] by melissa
Updated upgrade check status message to be a bit more clear.

09/21/10:

17:37 Changeset [6970] by melissa
Support for multi-file Improvision/Volocity TIFF datasets.
10:52 Changeset [6969] by melissa
Scan TiffData elements for 1-indexed indices before assembling list of …

09/20/10:

19:34 Changeset [6968] by melissa
Prevent ArrayIndexOutOfBoundsException when decompressing certain …
14:58 Changeset [6967] by melissa
Fixed SizeT calculation.
14:55 Changeset [6966] by aivar
Added SLIMCURVE fit algorithms. Worked on JavaDoc.
12:57 Changeset [6965] by melissa
Tweaked field index calculation.
12:30 Changeset [6964] by curtis
Move Rick's OpenCL deconvolution project into projects subtree.
11:18 Ticket #550 (ScanR reader assumes that wells form a square) closed by melissa
fixed: Fixed in r6959.
11:16 Changeset [6959] by melissa
Fixed well dimension parsing and calculation, so that the ScanR reader no …
10:53 Changeset [6958] by melissa
Fixed error in plane index calculation.

09/17/10:

17:32 WikiStart edited by curtis
(diff)
17:31 WikiStart edited by curtis
(diff)
17:30 Changeset [6957] by curtis
Merge native projects with main projects tree.
17:28 Changeset [6956] by curtis
Add SLIM-curve project.
16:02 Ticket #514 (Fix Image5D and View5D view modes) closed by curtis
fixed: I reviewed the View5D code, and there is simply no way to avoid invoking a …
13:04 Changeset [6955] by curtis
Remove obsolete ignore rules.
13:02 Changeset [6954] by curtis
Ignore Eclipse metadata files.

09/16/10:

15:34 Ticket #562 (MIAS import fails with NPE) closed by melissa
fixed: (In [6953]) Allow MIAS text files to be passed to MIASReader.setId. …
15:34 Changeset [6953] by melissa
Allow MIAS text files to be passed to MIASReader.setId. Closes #562.
13:54 Ticket #555 (OME-TIFF reader resets Image Name) closed by melissa
fixed: (In [6952]) Prevent Image names from being overwritten. Closes #555.
13:54 Changeset [6952] by melissa
Prevent Image names from being overwritten. Closes #555.
13:43 Changeset [6951] by melissa
Backported r6714, r6716, r6948, and r6949 to 4.2. See #557.
13:39 Changeset [6950] by curtis
Backport r6948,r6949 to 4.2 branch.
13:21 Ticket #557 (Virtual stack channel-specific LUTs are not preserved) closed by melissa
fixed: (In [6949]) Ensure that LUTs are properly preserved when using a virtual …
13:21 Changeset [6949] by melissa
Ensure that LUTs are properly preserved when using a virtual stack. …
09:50 Changeset [6948] by melissa
Don't apply lookup tables if there is more than one channel and we cannot …
09:09 Ticket #563 (Add support for OME-TIFF files produced by Leica Matrix scanner) created by melissa
These are similar to "Leica OME" files, see #386. The primary difference …
05:43 Changeset [6947] by callan
Merging r6715 from Trunk. (See #543)

09/15/10:

12:23 Changeset [6946] by curtis
Remove broken Bio-Formats Ice component, for now.
12:01 Ticket #551 ("waitTime" not parsed from Prairie datasets) closed by melissa
fixed: (In [6945]) Parse 'waitTime' from Prairie datasets. Closes #551.
12:01 Changeset [6945] by melissa
Parse 'waitTime' from Prairie datasets. Closes #551.
08:40 Ticket #562 (MIAS import fails with NPE) created by melissa
Data: …
07:09 Changeset [6944] by callan
Merging r6943 from Trunk. (See #561)
07:08 Ticket #561 (ServiceFactory file handle leak) closed by callan
fixed: (In [6943]) Solution to potential service factory file handle leak. (Fixes …
07:08 Changeset [6943] by callan
Solution to potential service factory file handle leak. (Fixes #561)
07:07 Ticket #561 (ServiceFactory file handle leak) created by callan
It is possible for instantiations of the ServiceFactory to leak file …

09/14/10:

20:34 Changeset [6942] by aivar
Added m_free, describes which parameters are free vs. fixed. Commented out …
20:32 Changeset [6941] by aivar
Added m_free, describes which parameters are free vs. fixed.
20:30 Changeset [6940] by aivar
Removed m_free: This information belongs to the curvefitter instance, not …
20:29 Changeset [6939] by aivar
Handles m_free, which parameters are free vs. fixed. Loads dynamic library …
20:26 Changeset [6938] by aivar
Handles m_free, which parameters are free vs. fixed.
18:22 Changeset [6937] by curtis
Remove obsolete test folder.
16:35 Changeset [6936] by curtis
Fix up license for utils project.
16:30 Changeset [6935] by curtis
Fix typo in ome-notes license link.
16:29 Changeset [6934] by curtis
Fix up license for test-suite project.
16:20 Changeset [6933] by curtis
Fix up license for flow-cytometry project.
16:16 Changeset [6932] by curtis
Fix up license for slim-plugin project.
16:05 Changeset [6931] by curtis
Fix up license for jvmlink project.
16:02 Changeset [6930] by curtis
Fix up license for lwf-stubs project.
15:58 Changeset [6929] by curtis
Fix up license for multi-lut project.
15:53 Changeset [6928] by curtis
Fix up license for loci-checks project.
15:49 Changeset [6927] by curtis
Fix up license for misc-plugins project.
15:49 Changeset [6926] by curtis
Fix up license for jar2lib project.
15:48 Changeset [6925] by curtis
Fix up license for curve-fitter project.
14:51 Changeset [6963] by rlentz
12:06 Changeset [6924] by curtis
Use line comments for proper function documentation.
10:49 Changeset [6923] by callan
Fixing infinite loop introduced by merging r6367 from Trunk. (See #560)
10:44 Changeset [6962] by rlentz
latest
10:10 Changeset [6922] by callan
Merging r6367 from Trunk. (See #560)
07:47 Ticket #560 (Fix multi-line description MetaMorph ND files) created by callan
When a MetaMorph ND file has a multi-line description setId() fails with …
06:27 Changeset [6921] by callan
A solution for file handles being left hanging around after close() on …

09/13/10:

16:59 Changeset [6961] by rlentz
16:25 Changeset [6960] by rlentz
Initial import.
12:12 Ticket #559 (LSM reader XT linescan opened as XY) created by curtis
From Dan White: The y dim is a single pixel, and the other dim is time, …
09:57 Changeset [6920] by callan
Merged r6743 and r6872 from Trunk. (See #543)
08:11 Changeset [6919] by callan
Merging r6917 from Trunk.
08:05 Changeset [6918] by callan
Merged r6917 and r6916 from Trunk.
07:53 Ticket #558 (MetaMorph ND handling for underscores) closed by callan
fixed: (In [6917]) Solution for underscores in wavelength names. (Fixes #558)
07:53 Changeset [6917] by callan
Solution for underscores in wavelength names. (Fixes #558)
07:52 Changeset [6916] by callan
Moved the 'getHandle()' log statement to the TRACE level to avoid DEBUG …
07:15 Ticket #558 (MetaMorph ND handling for underscores) created by callan
When an underscore is present in the wavelength name in the ND file, …
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