Timeline


and

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, …

09/10/10:

17:48 Ticket #557 (Virtual stack channel-specific LUTs are not preserved) created by curtis
When opening a dataset with channel-specific LUTs as a virtual stack, all …
17:18 Ticket #556 (OME-TIFF reader should use MetadataOnly rather than BinData) created by curtis
When producing an output OME-XML block, the OME-TIFF reader should inject …
17:16 Ticket #555 (OME-TIFF reader resets Image Name) created by curtis
When reading an OME-TIFF file such as multi-channel-4D-series.ome.tif, …
16:51 Changeset [6915] by curtis
Remove obsolete components folder.
16:51 Changeset [6914] by curtis
Initial version of autogen Maven project. Needs cleaning up.
16:02 Changeset [6913] by curtis
Begin migration of autogen project to Maven.
14:50 Ticket #554 (Exporting a multi-series OME-TIFF file results in incorrect pixel data) created by melissa
[…] Evidently produces a file with all series identical.
14:44 Ticket #553 (Add support for Zeiss Axiovision TIFFs) created by melissa
See files in data/zeiss-axiovision/.
14:42 Ticket #552 (Add support for Zeiss .lms files) created by melissa
See files in data/zeiss-lms/.
10:54 Changeset [6912] by curtis
Remove Bio-Formats Ice package for now.

09/09/10:

17:06 Changeset [6911] by curtis
Miscellaneous small tweaks.
16:02 Changeset [6910] by callan
Merging commits (r6690, r6692, r6735, r6784, r6786) from Trunk with …

09/08/10:

18:55 Changeset [6909] by curtis
Remove non-Maven version of test-suite project.
18:50 Changeset [6908] by curtis
Maven version of test-suite project.
17:19 Changeset [6907] by curtis
Tweak Maven repositories list.
16:55 Changeset [6906] by curtis
Maven version of Aivar's standalone ImageJ plugins.
16:45 Changeset [6905] by curtis
Add fiji-lib dependency for slim-plugin; it compiles now.
14:47 Changeset [6904] by aivar
Commented out version 1.0.13 BarRender method to work with version 12 in …

09/07/10:

23:56 Changeset [6903] by curtis
Move Bio-Formats command line tools to default Maven scripts path.
23:54 Changeset [6902] by curtis
Add additional projects to umbrella.
23:51 Changeset [6901] by curtis
Tweak some licenses.
23:51 Changeset [6900] by curtis
POM for Jama.
23:46 Changeset [6899] by curtis
New curve fitter package, migrated from …
23:23 Changeset [6898] by curtis
New curve fitter package, migrated from …
23:20 Changeset [6897] by curtis
Update SLIM Plotter to work with jaolho LMA v1.3.
13:51 Changeset [6896] by curtis
More efficient XML sanitation algorithm.
11:09 Ticket #551 ("waitTime" not parsed from Prairie datasets) created by melissa
The "waitTime" key in the .cfg file should be parsed into both the …
00:07 Changeset [6895] by curtis
Maven version of loci-checks.

09/06/10:

23:58 Changeset [6894] by curtis
Fix ome-editor author.
23:37 Changeset [6893] by curtis
Maven version of ome-editor.
22:58 Changeset [6892] by curtis
Maven version of ome-notes (but still doesn't compile).
15:10 Ticket #549 (Some options should be disabled in the "Standard ImageJ" view mode) closed by melissa
fixed: (In [6891]) Disable color mode options when the stack view is set to …
15:10 Changeset [6891] by melissa
Disable color mode options when the stack view is set to "Standard …
13:05 Ticket #550 (ScanR reader assumes that wells form a square) created by melissa
The number of wells acquired in each row is assumed to be either 0, or …
13:00 Changeset [6890] by melissa
A few fixes for ScanR datasets with missing wells, based on a patch …
12:05 Ticket #547 (Add system property values to ImageJ plugins log) closed by melissa
fixed: (In [6889]) Added system properties to ImageJ plugin log. Closes #547.
12:05 Changeset [6889] by melissa
Added system properties to ImageJ plugin log. Closes #547.
12:04 Changeset [6888] by melissa
Updated XMLTools.sanitizeXML to remove invalid "&#" sequences.
11:06 Changeset [6887] by melissa
Backported r6839, r6840, and r6841 to 4.2.
10:15 Changeset [6886] by melissa
* Improved metadata parsing for Prairie datasets. * Reverted changes to …
07:18 Changeset [6885] by curtis
Maven version of legacy Multi-LUT application.

09/05/10:

22:58 WikiStart edited by curtis
(diff)
22:38 Changeset [6884] by curtis
Maven version of jvmlink project.
22:37 Changeset [6883] by curtis
Update repository links to match new dev server.

09/04/10:

18:24 Changeset [6882] by curtis
Fix out-of-date SVN and Trac paths.
18:13 Changeset [6881] by curtis
Update SVN and Trac paths.

09/03/10:

12:53 Ticket #549 (Some options should be disabled in the "Standard ImageJ" view mode) created by melissa
For instance, the "Colorized" color mode will not work as expected if the …
12:31 Changeset [6880] by melissa
Couple of findbugs fixes, see #546.
11:02 Changeset [6879] by melissa
Added more logging to LocationTest, in an attempt to track down the …
10:48 Ticket #545 (Fix TIFF/OME-TIFF export with JPEG/JPEG-2000 compression) closed by melissa
fixed: (In [6878]) Fixed bugs in writing and reading JPEG- and …
10:48 Changeset [6878] by melissa
Fixed bugs in writing and reading JPEG- and JPEG-2000-compressed TIFFs. …
09:28 Changeset [6877] by melissa
* Return blank planes if pixel data is missing from an OME-XML file. * …
06:01 Ticket #548 (Support OME-XML with BinData.Length = 0) closed by callan
fixed: (In [6876]) Some further test case cleanup. Added a check to ChannelFiller …
06:01 Changeset [6876] by callan
Some further test case cleanup. Added a check to ChannelFiller to handle …
05:59 Ticket #548 (Support OME-XML with BinData.Length = 0) created by callan
It should be possible to at least initialize the reader state when BinData …

09/02/10:

17:07 Changeset [6875] by melissa
Fixed handling of multi-position ND2 datasets.
15:29 Changeset [6874] by curtis
Better series handling when number of series is extremely large.
11:43 Ticket #547 (Add system property values to ImageJ plugins log) created by melissa
In particular, it would be useful to have java.version and java.class.path …
11:33 Changeset [6873] by curtis
Update location of LegacyQTTools class.
10:43 Ticket #543 (OMETiffWriter.close() can leak file descriptors) closed by melissa
fixed: (In [6872]) Fixed OMETiffWriter.close() so that it releases resources even …
10:43 Changeset [6872] by melissa
Fixed OMETiffWriter.close() so that it releases resources even if an …
02:21 Changeset [6871] by callan
Removed erroneous STDERR debugging statement from test case.

09/01/10:

16:59 Changeset [6870] by melissa
Added JUnit JAR to build classpath, and made a few minor tweaks to test …
16:56 Changeset [6869] by curtis
Add a note stating that metadata can also be viewed in Image Info.
16:51 Changeset [6868] by melissa
Merged trunk r6867 into junit-test-suite.
16:34 Ticket #546 (Make findbugs happy) created by melissa
The "LOCI-findbugs" job on OME Hudson now runs the 'findbugs' Ant target …
16:24 Ticket #545 (Fix TIFF/OME-TIFF export with JPEG/JPEG-2000 compression) created by melissa
See, for instance, the output of: […] on the junit-test-suite branch.
16:14 Changeset [6867] by melissa
Migrated data-driven writer tests to JUnit. See #498.
16:13 Changeset [6866] by melissa
Removed support for JPEG/JPEG-2000 compression in OME-XML files, as this …
15:01 Ticket #539 (Skip tests when setId fails) closed by melissa
fixed: (In [6865]) Skip tests if IFormatReader.setId(String) failed. Closes …
15:01 Changeset [6865] by melissa
Skip tests if IFormatReader.setId(String) failed. Closes #539.
13:35 Ticket #544 (Native support for Quicktime Sorenson 1 codec (SVQ1)) created by melissa
See file in data/quicktime/jesper/. This file can be opened using the …
13:06 Changeset [6864] by melissa
Several tweaks to original metadata storage so that FV1000 files do not …
11:59 Changeset [6863] by melissa
Added missing methods that prevented r6862 from compiling.
11:58 Changeset [6862] by melissa
Simplified search for BinData offsets.
10:20 Changeset [6861] by callan
Reverting erroneous debugging in OMEXMLReader from r6860.
10:17 Changeset [6860] by callan
Added a test case (and re-organized some of the mock infrastructure) for …

08/31/10:

14:57 Changeset [6859] by curtis
Remove bogus quote escape characters.
14:51 Changeset [6858] by curtis
Clarify 'Display metadata' option to be less misleading.
09:55 Ticket #543 (OMETiffWriter.close() can leak file descriptors) created by melissa
An exception during writer.close(): […] leads to …
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