Timeline


and

11/12/10:

21:30 Changeset [7206] by aivar
Added analysis plugin. Made gray scale a separate class.
21:16 Changeset [7205] by aivar
Kludged up this class to fix a problem with IJ's StackWindow.
21:13 Changeset [7204] by aivar
Interface that communicates pixel selection by clicking on the gray scale …
21:10 Changeset [7203] by aivar
Made a separate interface to display the gray scale image. Handles …
21:09 Changeset [7202] by aivar
Made a separate class to display the gray scale image. Handles multiple …
21:09 Changeset [7201] by aivar
Tidied up comment.
21:08 Changeset [7200] by aivar
Loads a plugin to analyze fit results, using SezPoz.
21:07 Changeset [7199] by aivar
Annotation for plugins that analyze fit results.
21:07 Changeset [7198] by aivar
Interface for plugins that analyze fit results.
21:05 Changeset [7197] by aivar
A VisAD analysis plugin.
21:05 Changeset [7196] by aivar
Stub of an export to text plugin.
21:04 Changeset [7195] by aivar
Dynamically sets minimum, as well as maximum. TIdied up code & added …
21:03 Changeset [7194] by aivar
Dynamically sets minimum, as well as maximum. TIdied up code & added …
21:03 Changeset [7193] by aivar
Dynamically sets minimum, as well as maximum. TIdied up code & added …
21:03 Changeset [7192] by aivar
Dynamically sets minimum, as well as maximum. TIdied up code & added …
21:02 Changeset [7191] by aivar
Dynamically sets minimum, as well as maximum. TIdied up code & added …
21:02 Changeset [7190] by aivar
Dynamically sets minimum, as well as maximum. TIdied up code & added …
21:02 Changeset [7189] by aivar
Dynamically sets minimum, as well as maximum. TIdied up code & added …
21:02 Changeset [7188] by aivar
Dynamically sets minimum, as well as maximum. TIdied up code & added …
21:01 Changeset [7187] by aivar
Save channel with pixel, as well as x and y.
21:01 Changeset [7186] by aivar
Save channel with pixel, as well as x and y.
13:02 Milestone bio-formats-4.2.1 completed
12:24 Changeset [7185] by melissa
Tagged 4.2.1 release of LOCI tools.
10:08 Ticket #598 (ImageViewer's file chooser extensions are wrong) created by melissa
If you select "File > Save" from ImageViewer, the resulting file chooser …
09:58 Changeset [7184] by melissa
Updated version numbers to "4.2.1".
08:49 Changeset [7183] by melissa
Fixed a couple of bugs in ImageConverter.
08:46 Ticket #525 (Files cannot be saved from ImageViewer unless '-omexml' option was passed ...) reopened by melissa
With this command: […] This exception now appears when trying to save …

11/11/10:

11:13 Ticket #597 (Add support for .aim files) created by melissa
See files in data/aim/harry. The image dimensions start at 0x38; they are …
09:04 Changeset [7182] by melissa
Updated what's new for today's release.

11/10/10:

09:30 Changeset [7181] by hinerm
Updated post-build instructions to reflect the removal of ITKFactories …
09:27 Changeset [7180] by hinerm
Modified CmakeLists.txt for the BF-ITK build so that it will no longer …

11/09/10:

16:52 Changeset [7179] by curtis
Add BitsPerPixel to Bio-Formats Importer's Original Metadata window.
15:42 Ticket #596 (Recorded macros contain "open" twice) created by melissa
If you attempt to record a macro for the Bio-Formats Importer plugin, you …
15:26 Changeset [7178] by melissa
Don't correct the channel count in the case of RGB images.
10:01 Changeset [7177] by rlentz
Added developer comments
09:48 Changeset [7176] by rlentz
Test Update

11/08/10:

20:58 Changeset [7175] by melissa
Changed ome-io component back to using Java 1.5.
12:23 Changeset [7174] by melissa
* Updated stylesheets to  ome-xml:r692. * Added test for Channel.Color.
11:26 Changeset [7173] by rlentz
Demo using EJB components on Glassfish, supporting multi-language …
11:20 Changeset [7172] by rlentz
Demo using EJB components on Glassfish, supporting multi-language …
11:19 Changeset [7171] by rlentz
Initial import of the 'server side' implementation for the EJB, Hessian …
10:50 Changeset [7170] by rlentz
Demo using EJB components on Glassfish, supporting multi-language …

11/06/10:

09:50 Changeset [7169] by melissa
Backported r6515, r6527, and most of r7071 to fix a few problems with …

11/05/10:

21:46 Changeset [7168] by aivar
Switched to tau from lambda. Added stretched exponential fitting. …
21:38 Changeset [7167] by aivar
Added setFittedComponents and refineFit, to enable cumulative curve …
21:37 Changeset [7166] by aivar
Added setFittedComponents and refineFit, to enable cumulative curve …
21:35 Changeset [7165] by aivar
Comment added.
21:35 Changeset [7164] by aivar
Comment added.
21:32 Changeset [7163] by aivar
Convert lambda to tau.
21:31 Changeset [7162] by aivar
Convert lambda to tau.
21:29 Changeset [7161] by aivar
Added get/set X/Y, needed to save fit results.
21:27 Changeset [7160] by aivar
Was using lambda, now use tau.
21:26 Changeset [7159] by aivar
Added get/set X/Y, these are needed to save the fit results.
15:51 Changeset [7158] by melissa
Fixes for truncated .dv files from QA #2988 and #2989.
12:42 Changeset [7157] by melissa
Remove any extra channels from OME-TIFF files. See  omero:#3250, QA #2973.
10:32 Changeset [7156] by melissa
Hackish fix for potential IndexOutOfBoundsException; the real fix should …

11/04/10:

17:58 Ticket #595 (Overwriting compressed planes doesn't always work) created by melissa
If the new plane's compressed size is less than or equal to the old …
17:50 Changeset [7155] by melissa
Fix for overwriting TIFF planes.
13:41 Changeset [7154] by melissa
Fixed conversion of LaserMedium attributes with value "Unknown".
12:20 Ticket #594 (Double-check Image -> ROI linkages) created by melissa
Right now, I think most (all?) of the readers that populate ROIs do not …
11:54 SlideFormats edited by melissa
(diff)
10:49 Changeset [7153] by melissa
Only populate LightPath references if the LSIDs are not null.
10:26 Changeset [7152] by melissa
Allow .rec extension for MRC files. isThisType(RandomAccessInputStream) …

11/03/10:

16:14 Changeset [7151] by melissa
Updated showinf help text.
13:31 Changeset [7150] by melissa
Updated C++ headers.

11/02/10:

20:05 Changeset [7149] by melissa
A bunch of little export fixes.
10:40 Ticket #593 (Add support for Micro-CT VOL files) created by melissa
See data in micro-ct/amin/.

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 …
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