Timeline


and

01/29/11:

17:12 Ticket #660 (Non-instr versions of the functions not implemented) created by aivar
The marquardt functions as opposed to marquardt_instr functions are empty.
17:11 Ticket #659 (Error field is not filled correctly on time resolved front panel) created by aivar
The NR version of G-J returns an inverted version of A, as well as the …
17:09 Ticket #658 (Global fitting causes problem with Gauss Jordan when B is NULL.) created by aivar
The previous GJ implementation inverts the A matrix when B is NULL. This …
12:44 Ticket #657 (Add fit execution framework) created by paulbarber
Some overall framework to load some data, process in several ways …
12:43 Ticket #656 (Check what is meant by an 'iteration' and provide for this in ecf class.) created by paulbarber
The LOCI LM and GA code allows access to individual iterations of the …
12:42 Ticket #655 (Import ecf global curve library) created by paulbarber
Check source code for licenced code. Add licence and author, …
12:39 Ticket #654 (Basic UI and graphical output) created by paulbarber
Basic C++ (e.g. Qt) and/or java front and and graph plot.
12:38 Ticket #653 (Add support for non-exp fns to curve fitter class) created by paulbarber
e.g. stretched exp, rise time, generic functions.
12:37 Ticket #652 (Create a web site for slim-curve) created by paulbarber
Banner image. Centres/names involved. Links to other web sites and papers …
12:12 Changeset [7611] by aivar
Added float chisq_delta parameter to …
11:55 Changeset [7610] by curtis
Remove unnecessary include folder.
11:54 Changeset [7609] by curtis
Initial CMakeLists build file for slim-curve.
11:43 Changeset [7608] by paulbarber
Utility.h not needed.

01/28/11:

14:38 Changeset [7607] by paulbarber
Added single frequency phasor routine for lifetime. Added Non-negative …
14:37 Changeset [7606] by paulbarber
To compile in TRI2, moved declarations to top of relevant block. Added …

01/27/11:

23:59 Changeset [7605] by aivar
I had inverted the image to correspond with SLIMPlotter, but the natural …
23:57 Changeset [7604] by aivar
I had inverted the image to correspond with SLIMPlotter, but the natural …
23:56 Changeset [7603] by aivar
Thought there might be a bug here, so made the display table more flexible …
23:54 Changeset [7602] by aivar
Added TODO comment.
23:54 Changeset [7601] by aivar
Needed an out of bounds strategy.
23:53 Changeset [7600] by aivar
New 7x7 binner.
23:53 Changeset [7599] by aivar
Deleted some vestigial files.
23:39 Changeset [7598] by aivar
Parameter ordering problems. GrayNRCurveFitter was out of date.
14:50 Changeset [7597] by aivar
Fixed null pointer exception when library not found.
14:49 Changeset [7596] by aivar
Fixed null pointer exception when library not found.

01/26/11:

22:25 Changeset [7595] by curtis
Fix up LOCI Software POM structure.
17:36 Changeset [7594] by aivar
Commented out unused #include <ansi.h>
17:35 Changeset [7593] by aivar
Nar plugin dependency added (temporarily)

01/25/11:

23:21 Changeset [7592] by curtis
Remove obsolete svn:ignore property.
23:13 Changeset [7591] by curtis
Remove obsolete class.
23:12 Changeset [7590] by curtis
Add Deep Zoom plugin to umbrella POM.
22:50 Changeset [7589] by curtis
Remove Bio-Formats ITK project. Bio-Formats has moved to its own …
22:49 Changeset [7588] by curtis
Remove old JRE bundles.
22:43 Changeset [7587] by curtis
Remove Bio-Formats projects, and merge Maven branch. Bio-Formats has …
22:06 Changeset [7586] by curtis
Remove Bio-Formats branches and tags. Bio-Formats has moved to its own …
22:03 Changeset [7585] by curtis
Remove Bio-Formats branches and tags. Bio-Formats has moved to its own …

01/24/11:

18:21 Changeset [7584] by melissa
One more pixel data offset fix.
17:49 Changeset [7583] by melissa
Deprecated superfluous getHexString(byte[]) method.
17:48 Changeset [7582] by melissa
Prevent StringIndexOutOfBoundsException when file names start with "_".
15:50 Changeset [7581] by melissa
Prevent extra Plane(Timing).ExposureTime attributes from being populated.
08:20 Ticket #651 (Allow JPEG-2000 writer to use lossy compression) closed by melissa
fixed: (In [7580]) The JPEG-2000 writer can now use lossy or lossless …
08:20 Changeset [7580] by melissa
The JPEG-2000 writer can now use lossy or lossless compression. Closes …

01/22/11:

15:30 Changeset [7579] by melissa
Prevent potential AIOOB.
15:10 Ticket #651 (Allow JPEG-2000 writer to use lossy compression) created by melissa
getCompressionTypes() should return ["Lossy", "Lossless"], with "Lossless" …
11:50 Changeset [7578] by rlentz
Moved jocl.jar to lib directory and successfully ran sobel example on OSX
11:44 Changeset [7577] by rlentz
Michael Bien created a work around that allowed JOCL to work around a bug …

01/21/11:

23:19 Changeset [7576] by aivar
Project moved to ImageJ
23:13 Changeset [7575] by aivar
Added utility for dealing with native libraries.
22:27 Changeset [7574] by aivar
New utility class for dealing with native libraries.
21:26 Changeset [7573] by melissa
Backported a bunch of recent ND2 fixes to 4.1.
17:53 Changeset [7572] by curtis
Fix up save dialog behavior.
14:39 Changeset [7571] by melissa
Populate all of the wells, even if no image data is associated with them.
13:17 Changeset [7570] by melissa
Sanitize the XML before we parse it.
13:08 Changeset [7569] by curtis
Working version of Save As J2K plugin. Needed to call …
12:38 Changeset [7568] by melissa
Initial version of Metamorph TIFF HCS support.

01/20/11:

17:53 Changeset [7567] by curtis
Minor tweaks; still broken.
17:33 Changeset [7566] by curtis
Initial version of example JPEG2000 export plugin, courtesy of Albert …
14:51 Changeset [7565] by hinerm
Backport -r7564 to 4.2 branch.
14:49 Changeset [7564] by hinerm
Added a "dist" target to the bf-cpp project. Functionally identical to …
14:16 Changeset [7563] by hinerm
Backport r7562 to 4.2 branch.
14:11 Changeset [7562] by hinerm
Modified the dist target for BF-ITK to no longer copy unnecessary files on …
13:24 Changeset [7561] by melissa
Tweaked MetamorphReader's isThisType to prevent it from picking up files …
13:22 Changeset [7560] by melissa
Tweaked well name detection so that column indexes can only contain at …
13:07 Changeset [7559] by melissa
Clarified CLASSPATH requirements.
12:51 Changeset [7558] by melissa
Added some documentation on file export/conversion.
12:46 Ticket #650 (Update tiffcomment to allow editing on the command line) created by melissa
Right now, the only way to edit TIFF comments is using the GUI displayed …
12:45 Changeset [7557] by hinerm
Forward port from branch 4.2 changes - mistakenly committed to a branch …
12:24 Changeset [7556] by hinerm
Added the java class BioFormatsExtensionPrinter to the svn repository. …
12:22 Changeset [7555] by hinerm
Added a new java class to BF-CPP - BioFormatsExtensionPrinter - to …
12:18 Changeset [7554] by curtis
Add variable for controlling number of channels.

01/19/11:

15:40 Ticket #646 (OME-TIFFs cannot be opened in Fiji with file grouping turned on) closed by melissa
fixed: (In [7553]) Prevent an NPE when attempting to stitch datasets that aren't …
15:40 Changeset [7553] by melissa
Prevent an NPE when attempting to stitch datasets that aren't stitchable. …
14:36 Ticket #627 (Slidebook series grouping is not always correct) closed by melissa
fixed: The series grouping should be correct with r7552, but the pixel data still …
14:35 Changeset [7552] by melissa
Group together separate blocks of pixels that belong to the same stack. …
11:38 Changeset [7551] by melissa
Fixed various metadata population problems when working with multi-file …
11:34 Changeset [7550] by curtis
Migrate workflow project to ImageJ repository. New location is …
11:13 Changeset [7549] by curtis
Remove binary libraries (not needed with Maven).
11:11 Changeset [7548] by curtis
Convert LOCI workflow to Maven.

01/18/11:

13:09 Ticket #649 (Add IFormatWriter.saveBytes signatures that accept a Region) created by melissa
...instead of 4 ints specifying the region.
13:09 Ticket #648 (Add reader wrapper that provides simpler tile access) created by melissa
* void setTileWidth(int width) defaults to optimal width * void …
13:04 Ticket #647 (Add conversion convenience methods to FormatTools) created by melissa
Specifically: * static void convert(IFormatReader, IFormatWriter) * …
12:56 Ticket #646 (OME-TIFFs cannot be opened in Fiji with file grouping turned on) created by melissa
To reproduce: * start Fiji * select Plugins > LOCI > Bio-Formats …
12:35 Ticket #645 (Eliminate log4j warning messages) created by melissa
Several Bio-Formats-related tools still display log4j warning messages; …
12:34 Ticket #644 (Parse additional Andor TIFF tags) created by melissa
In particular: […] See the files in data/andor/benjamin/ for examples …
11:55 Changeset [7547] by aivar
Delete extraneous files
11:54 Changeset [7546] by aivar
Delete extraneous files
11:52 Changeset [7545] by aivar
Delete extraneous files
11:44 Changeset [7544] by melissa
Fixed channel name and wavelength population. See  omero:#3865.

01/17/11:

11:29 Ticket #643 (Slidebook files with maximum projections cannot be read) closed by melissa
fixed: The file mentioned above can now be read, but the pixel data for some …
11:27 Changeset [7543] by melissa
One more adjustment to SizeX/SizeY calculations. See #643.
11:07 Changeset [7542] by rlentz
Added eclipse jar export configuration file
11:01 Ticket #626 (Slidebook valid bits per pixel not parsed) closed by melissa
fixed: (In [7541]) Parse valid bits per pixel from Slidebook files. Closes #626.
11:01 Changeset [7541] by melissa
Parse valid bits per pixel from Slidebook files. Closes #626.
10:17 Changeset [7540] by rlentz
No change

01/14/11:

20:46 Changeset [7539] by aivar
JNI NativeLoader
13:18 Ticket #643 (Slidebook files with maximum projections cannot be read) created by melissa
See data/slidebook/vytas/worms.sld.
13:06 Ticket #642 (Add better isThisType tests) created by melissa
Two new tests should be added: * one in loci.formats.utests that times …
11:50 Ticket #612 (Multi-channel indexed color images treated incorrectly) closed by melissa
fixed: (In [7538]) Set 'falseColor' to true, so that lookup tables are not …
11:50 Changeset [7538] by melissa
Set 'falseColor' to true, so that lookup tables are not improperly …
11:22 Ticket #641 (Add support for Zeiss FCS files) created by melissa
See data in data/zeiss-fcs/chris/ and description in …
10:48 Changeset [7537] by rlentz
changed the implementation to floating point
09:15 Changeset [7536] by rlentz
Test from Michael Bien
08:53 Ticket #637 (Plane numbers in status bar are sometimes incorrect) closed by melissa
fixed: (In [7535]) Fixed plane index in status bar. Closes #637.
08:53 Changeset [7535] by melissa
Fixed plane index in status bar. Closes #637.

01/13/11:

21:44 Changeset [7534] by aivar
Multiple changes to get discovery and workflow save/restore to Preferences …
16:28 Changeset [7533] by rlentz
Configured for 64 bit linux.
16:15 Changeset [7532] by rlentz
16:13 Changeset [7531] by rlentz
14:40 Changeset [7530] by hinerm
Update bf-cpp proxy list to match latest Java source files.
14:32 Changeset [7529] by hinerm
Backport latest bf-itk to 4.2 branch.
13:56 Changeset [7528] by melissa
Corrected pixel type for 32-bit images, as Andor/Fluoview assumes that all …
13:46 Changeset [7527] by rlentz
13:29 Ticket #640 (Add a few more options to bfconvert) created by melissa
In particular: * '-range', similar to showinf's '-range' * '-channel', …
12:18 Changeset [7526] by aivar
Copied over workflow stuff from DeepZoom plugin.
12:17 Changeset [7525] by rlentz
10:58 Changeset [7524] by rlentz
Tested SobelFilter Sample under OSX with latest CUDA and jogamp libraries. …
09:47 Changeset [7523] by rlentz
Restructured libs and code to reflect CUDA 3.2 and Jogamp's signed build …

01/12/11:

20:05 Ticket #639 (Make sure that static fields are being used properly) created by melissa
There are several static (non-final) HashMaps/Hashtables throughout the …
20:05 Changeset [7522] by melissa
Make primitive type static variables volatile.
15:34 Changeset [7521] by rlentz
update
15:20 Changeset [7520] by rlentz
update
15:19 Changeset [7519] by rlentz
update
15:19 Changeset [7518] by rlentz
update
15:17 Changeset [7517] by rlentz
update 7
14:40 Changeset [7516] by aivar
You can now create a workflow, save to XML, create another workflow from …
13:20 Changeset [7515] by rlentz
update
12:17 Ticket #638 (Add support for Zeiss LSM files that have differing bits per sample) created by melissa
See the file in data/zeiss-lsm/aaron-o*/. Each non-thumbnail IFD has a …
11:35 Ticket #637 (Plane numbers in status bar are sometimes incorrect) created by melissa
See attached screenshot. Specifying a range of planes to open can cause …
10:39 Ticket #633 (FV1000 LUTs are not displayed correctly in ImageJ) closed by melissa
fixed: (In [7514]) Fixed indexed flag and LUT parsing. Closes #633.
10:39 Changeset [7514] by melissa
Fixed indexed flag and LUT parsing. Closes #633.
10:09 Changeset [7513] by hinerm
Enhanced ant dist script to copy BioFormatsIO.dll to the dist directory.

01/11/11:

21:29 Changeset [7512] by aivar
Made the test plugin input and output names more meaningful.
21:13 Changeset [7511] by aivar
Workflow updates, works with new PluginModule, hooks up to …
21:11 Changeset [7510] by aivar
Added new tests during test-driven development.
21:11 Changeset [7509] by aivar
This package is basically a copy of loci.multiinstanceplugin. Also …
15:07 Ticket #636 (Allow ImageReader to call isThisType(..., false)) created by melissa
There are three pieces to this ticket: 1) Add a setter to ImageReader …
14:28 Changeset [7508] by melissa
Fixed NPE.
14:27 Changeset [7507] by melissa
Backported changes to Openlab reader for importing HCS data.
13:53 Changeset [7506] by rlentz
Updated the Readme text to the following: ( Please ensure installation of …
13:45 Changeset [7505] by rlentz
No change here.
13:44 Changeset [7504] by rlentz
Several updates to clarify the examples provided to enable OpenCL …
13:20 Changeset [7503] by curtis
Backport r7494,r7496 bugfixes to 4.2 branch.
12:56 Changeset [7502] by melissa
Don't overwrite existing image names.
12:40 Changeset [7501] by rlentz
Added a readme This code was developed to show how to use JOCL to …
12:39 Changeset [7500] by melissa
Search more thoroughly for image descriptions. Image descriptions are no …
09:14 Changeset [7499] by melissa
Fixed compile error in r7498.
09:03 Changeset [7498] by melissa
Backported ScreenReader to 4.2.

01/10/11:

20:11 Changeset [7497] by aivar
Fleshed out WorkFlow.finalize. ModuleFactory now has a register method …
16:18 Changeset [7496] by curtis
Fix signedness averaging problem with convertTo8Bit method.
16:14 Changeset [7495] by aivar
Added proper ComponentFactory. Renamed chain -> wire, component -> …
15:56 Changeset [7494] by curtis
Fix problem where custom LUTs override grayscale mode. This happened …
14:22 Changeset [7493] by melissa
Slightly more robust well name checking.
10:25 Changeset [7492] by melissa
Fixed import that caused compile failure in r7491.
10:15 Changeset [7491] by melissa
Merged file grouping and channel name parsing fixes from trunk.

01/07/11:

17:22 Changeset [7490] by aivar
Added method call for Rick's project.
13:38 Changeset [7489] by melissa
Prevent potential NPE if the "Info" property is not set on the ImagePlus …
12:43 Changeset [7488] by melissa
Sanitize OME-XML before attempting to create a MetadataStore.

01/06/11:

10:56 Changeset [7487] by melissa
Use a ConcurrentHashMap instead of a HashMap.

01/05/11:

16:15 Changeset [7486] by melissa
Added optional cacheing of directory listings, courtesy of Lee Kamentsky.
14:19 Ticket #635 (Add support for Image-Pro .ips metadata files) created by melissa
See files in data/imagepro/alex/. The .ips file is some sort of metadata …

01/04/11:

13:09 Ticket #634 (File grouping does not work in ImageJ on Windows) closed by melissa
fixed: (In [7485]) Escape backslashes when finding a pattern. Closes #634.
13:09 Changeset [7485] by melissa
Escape backslashes when finding a pattern. Closes #634.
12:05 Changeset [7484] by melissa
Various fixes to allow retrieval of pixel data from truncated TIFFs.

12/31/10:

14:16 Ticket #272 (Ability to explicitly disable file stitching for certain files) closed by melissa
fixed: This was added in r6349; adding "no_stitch=true" to a .bioformats file …
13:39 Changeset [7483] by melissa
Fixed a handful of bugs introduced in r7481.
11:07 Changeset [7482] by melissa
Moved 'void setWriteSequentially(boolean)' from TiffWriter to …
11:04 Changeset [7481] by melissa
Expanded special strip unpacking case to allow multiple strips.
10:56 Changeset [7480] by melissa
Set a more reasonable timeout when checking for updates.

12/30/10:

13:26 Ticket #634 (File grouping does not work in ImageJ on Windows) created by melissa
The file separator ('\') causes the file pattern to be incorrectly …
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