Timeline


and

03/03/08:

14:55 Ticket #254 (FV1000 reader doesn't support lookup tables) closed by melissa
fixed: r3762
14:55 Changeset [3762] by melissa
Added LUT support to FV1000Reader.
14:04 Ticket #253 (BioRad reader doesn't support lookup tables) closed by melissa
fixed: r3761
14:04 Changeset [3761] by melissa
Added LUT support and fixed SizeC calculation.
13:12 Ticket #229 (Support multi-series OME-TIFF export) closed by melissa
fixed: r3760
13:12 Changeset [3760] by melissa
Added support for writing multi-series OME-TIFF files.
12:57 Changeset [3759] by curtis
* Fix class loader problem with ImageJ versions prior to 1.38. * Add …

02/29/08:

16:54 Changeset [3758] by curtis
Fix setVar(JVMLinkObject*) to work on non-array primitives, and change …
14:23 Changeset [3757] by melissa
Fixed plane height and offset calculations.
13:55 Changeset [3756] by curtis
Send strings prefixed by length, rather than terminated with newlines …
13:30 Changeset [3755] by curtis
Fix large longs; fix warnings.
12:58 Changeset [3754] by curtis
No need for this file in the repository.
12:57 Changeset [3753] by curtis
* Encapsulate endianness concerns. * Add a command to switch server's …
10:35 Ticket #254 (FV1000 reader doesn't support lookup tables) created by melissa
LUTs can be present in FV1000 OIB/OIF datasets - we should check if a LUT …
10:33 Ticket #253 (BioRad reader doesn't support lookup tables) created by melissa
Lookup tables can be present in BioRad files; we should detect when LUTs …
10:15 Ticket #252 (Bio-Rad reader does not include data.raw files on its used files list) closed by melissa
fixed: r3752
10:14 Changeset [3752] by melissa
data.raw file is now added to BioRad used file list.
10:12 Changeset [3751] by melissa
Cleaned up isThisType implementations - Location.list() is no longer …
09:44 Changeset [3750] by curtis
Fix SAX parsing exception caused by earlier hack/fix.
08:41 Changeset [3749] by curtis
Ignore comments in .bioformats files.

02/28/08:

16:36 Changeset [3748] by curtis
Rewrite configuration manager class to use a tree structure.
16:20 Ticket #252 (Bio-Rad reader does not include data.raw files on its used files list) created by curtis
[…] For consistency, the data.raw companion file should always be …
15:21 Changeset [3747] by curtis
These readers should also not indiscriminately green-light TIFFs.
15:06 Changeset [3746] by curtis
Leica reader should not green-light TIFFs unless it knows they are Leica.
14:25 Changeset [3745] by curtis
More efficient isThisType(String) for ImageReader.
12:52 Ticket #250 (Bio-Rad reader throws StringIndexOutOfBoundsException with some XML ...) closed by melissa
fixed: r3744
12:52 Ticket #251 (Bio-Rad reader sometimes looks for an incorrectly named PIC file) closed by melissa
fixed: r3744
12:51 Changeset [3744] by melissa
Various fixes to BioRad reader.
12:24 Changeset [3743] by curtis
Minor tweaks.

02/27/08:

18:58 Changeset [3742] by ansari
fixed double, float, long, short
17:40 Changeset [3741] by curtis
Fix used files list for PerkinElmer.
17:30 Changeset [3740] by curtis
Increase TestNG memory limit to avoid memory error during results …
17:27 Ticket #251 (Bio-Rad reader sometimes looks for an incorrectly named PIC file) created by curtis
When opening a Bio-Rad PIC file via its companion lse.xml or data.raw …
17:25 Ticket #250 (Bio-Rad reader throws StringIndexOutOfBoundsException with some XML ...) created by curtis
BioRadReader currently uses error-prone string parsing to extract …
17:08 Changeset [3739] by curtis
Allow TIFF reader to redundantly green-light files, since many specific …
16:47 Changeset [3738] by curtis
Remove debugging output.
16:44 Changeset [3737] by curtis
* ImageReader.isThisType(String) no longer needs to default to open=false. …
15:45 Changeset [3736] by curtis
Add a test to exercise isThisType more thoroughly.
15:19 Changeset [3735] by curtis
Do not call super.isThisType unless absolutely necessary.
14:58 Changeset [3734] by melissa
Fixed isThisType problem.
14:50 Changeset [3733] by curtis
BufferedReader does not work; revert to previous revision for now.
14:50 Changeset [3732] by melissa
Miscellaneous bug fixes.
14:46 Changeset [3731] by curtis
Use reader instead of input stream for readLine calls.

02/26/08:

19:21 Changeset [3730] by curtis
Copy resources into classes directory up front, rather than within jar …
13:51 Changeset [3729] by curtis
Skip inapplicable tests rather than trivially passing.

02/25/08:

10:58 Changeset [3728] by melissa
Make sure the MetadataStore is updated to reflect the chosen stack order.
10:23 Changeset [3727] by melissa
* Slight improvements to some isThisType implementations. * Added reader …

02/21/08:

16:27 Changeset [3726] by curtis
Add more tests and fix some bugs.
14:56 Changeset [3725] by curtis
Lots of cleanup and tweaks to JVMLink.
13:17 Changeset [3724] by melissa
Fixed RGB channel swapping.
13:02 Changeset [3723] by melissa
Strip offsets need to be treated as unsigned integers, to handle files …
11:10 Changeset [3722] by melissa
Fixed channel count check in testThumbnailImageDimensions.
10:16 Changeset [3721] by melissa
Populate image creation date in the MetadataStore.
08:50 Changeset [3720] by curtis
Add failure message for testByteArrayDimensions.
07:48 Ticket #249 (Sequential setId calls with BioRadReader do not fully reset state) closed by melissa
fixed: r3719
07:48 Ticket #247 (Sequential setId calls with SVSReader can throw an exception) closed by melissa
fixed: r3719
07:48 Changeset [3719] by melissa
Make sure that the state is fully reset when close() is called.
07:34 Ticket #248 (MetamorphTiffReader.isThisType throws NullPointerException on some files) closed by melissa
fixed: r3718
07:34 Changeset [3718] by melissa
isThisType now returns false if the first IFD's comment is null, instead …

02/20/08:

17:17 Changeset [3717] by curtis
Use factory instead of data provider to generate list of tests.
16:33 Ticket #249 (Sequential setId calls with BioRadReader do not fully reset state) created by curtis
The value of SizeZ differs when initializing a file with a fresh reader …
16:09 Ticket #248 (MetamorphTiffReader.isThisType throws NullPointerException on some files) created by curtis
[…]
15:38 Ticket #247 (Sequential setId calls with SVSReader can throw an exception) created by curtis
When calling setId iteratively on multiple SVS files, an …
13:56 Changeset [3716] by curtis
Fix class name.
13:53 Changeset [3715] by curtis
Progress on TestNG suite.
13:21 Ticket #243 (Thumbnail pixel values are incorrect) closed by melissa
fixed: r3714
13:21 Changeset [3714] by melissa
Fixed thumbnail generation problems.
09:44 Ticket #238 (Exception is thrown when multiple BioRad datasets are in the same ...) closed by melissa
fixed: r3713
09:44 Ticket #246 (Bio-Rad data.raw files are not recognized) closed by melissa
fixed: r3713
09:43 Changeset [3713] by melissa
Improved file grouping and type checking logic.
08:25 Ticket #245 (FV1000 reader dies when analyzing Bio-Rad ROIs) closed by melissa
fixed: r3712
08:16 Changeset [3712] by melissa
Better isThisType(byte[]) implementation; fixed bug with datasets whose …

02/19/08:

19:16 Ticket #244 (NullPointerException in GatanReader) closed by melissa
fixed: r3711
19:16 Changeset [3711] by melissa
Fixed NPE when instrument data is missing.
16:08 Changeset [3710] by curtis
Progress on testing framework.
15:34 Ticket #246 (Bio-Rad data.raw files are not recognized) created by curtis
Though they are returned as part of the used files list for Bio-Rad …
15:33 Ticket #245 (FV1000 reader dies when analyzing Bio-Rad ROIs) created by curtis
[…]
15:30 Ticket #244 (NullPointerException in GatanReader) created by curtis
[…] Other files in the folder have the same issue.
15:27 Changeset [3709] by melissa
Fixed BufferedImage -> byte array conversion for grayscale JPEG planes.
14:15 Changeset [3708] by melissa
More robust wavelength population.
13:52 Changeset [3707] by curtis
Use HTML for slightly nicer About dialog.
13:23 Changeset [3706] by melissa
Removed legacy ZVI reader.
13:18 Ticket #243 (Thumbnail pixel values are incorrect) created by melissa
For certain datasets (e.g. zeiss-zvi/cecilia/Day\ 1\ Naked\ NB\ positive\ …
12:51 Changeset [3705] by melissa
Moved common POI logic to utility class.
09:09 Ticket #242 (Turn off NetCDF debugging output) created by melissa
When reading Imaris HDF files, the message "WARN: Variable data has a …
09:03 Changeset [3704] by melissa
Cleaned up PrairieReader's isThisType.
08:50 Ticket #241 (More robust channel assignment) created by melissa
We naively assign channel 0 to red, channel 1 to green, channel 2 to blue, …
08:41 Ticket #240 (Update OMEROReader to work with 2.3 server) created by melissa
Currently, the OMERO reader (and corresponding ImageJ plugin) only works …

02/18/08:

12:28 Ticket #239 (ArrayIndexOutOfBoundsException for IndexedColorModel and/or DICOM) closed by melissa
fixed: r3703
12:28 Changeset [3703] by melissa
Use Java2D API instead of AWT for scaling thumbnail images.
10:45 Changeset [3702] by melissa
Cleaned up isThisType for Imaris TIFF.

02/15/08:

16:22 Ticket #239 (ArrayIndexOutOfBoundsException for IndexedColorModel and/or DICOM) created by curtis
A recent fix results in the OT-PAL-8-face.dcm image being properly …
14:56 Changeset [3701] by curtis
Fix Javadoc tag warnings.
10:53 Ticket #235 (Add support for new Metamorph format) closed by melissa
fixed: r3700
10:53 Changeset [3700] by melissa
Added reader for Metamorph 7.5 TIFF files.
09:44 Changeset [3699] by melissa
Fixed another shuffleAllTypesToFront bug.
09:35 Changeset [3698] by curtis
Fixed shuffleAllTypesToFront again. Ha ha, testing is good.
09:27 Changeset [3697] by curtis
Fix bug in shuffleAllTypesToFront (hopefully).
08:09 Changeset [3696] by melissa
Record absolute path (not relative path) to preview image files.
07:41 Changeset [3695] by melissa
Added base case, where "All supported file types" filter is already first …

02/14/08:

15:09 Changeset [3694] by melissa
First cut at new OME-TIFF file grouping heuristics. If image/pixels LSIDs …
12:39 Changeset [3693] by curtis
Make JFileChooser file filter logic work with the recent isThisType …
11:38 Changeset [3692] by melissa
Removed a bunch of deprecated methods.
11:32 Changeset [3691] by curtis
Always use "Bitplane Imaris" to describe IMS files, for consistency.
11:30 Changeset [3690] by melissa
Fixed LUT construction bug.
09:27 Ticket #237 (Image planes from LegacyQTReader can no longer be displayed) closed by melissa
fixed: r3689
09:27 Changeset [3689] by melissa
Override openImage(int, int, int, int, int) so that legacy files don't …
09:06 Ticket #238 (Exception is thrown when multiple BioRad datasets are in the same ...) created by melissa
If multiple BioRad PIC datasets are present in the same directory, the …
07:46 Ticket #234 (Bio-Formats Importer plugin problems when cropping multiple series) closed by melissa
fixed: r3688.
07:46 Changeset [3688] by melissa
Labels on "crop on import" box are now unique.

02/13/08:

19:07 Changeset [3687] by curtis
Add JVMLink targets to Ant script.
19:07 Changeset [3686] by curtis
Whitespace and formatting.
18:47 Changeset [3685] by curtis
Add copyright notices to C++ code.
18:44 Changeset [3684] by curtis
Add copyright notices and package doc.
18:24 Changeset [3683] by curtis
First cut at streamlining isThisType implementations.
18:21 Changeset [3682] by curtis
Fix compile errors with Java 1.4.
17:40 Changeset [3681] by curtis
More preview pane bugfixes.
17:33 Changeset [3680] by curtis
Improve preview pane.
15:36 Changeset [3679] by ansari
tiny change to take care of path
15:24 Changeset [3678] by ansari
Initial commit of JVMLink package
14:35 Changeset [3677] by melissa
Better offset detection for JPEG-2000 planes; fixed indexed color bug.

02/12/08:

14:50 Changeset [3676] by melissa
Improved tiling logic.
12:16 Changeset [3675] by curtis
Update what's new for 2008 Feb 12 patch release.
12:08 Changeset [3674] by curtis
2008 Feb 12 release of LOCI Tools
12:08 Changeset [3673] by curtis
2008 Feb 12 release of LOCI Tools
12:08 Changeset [3672] by curtis
2008 Feb 12 release of LOCI Tools
12:08 Changeset [3671] by curtis
2008 Feb 12 release of LOCI Tools
12:08 Changeset [3670] by curtis
2008 Feb 12 release of LOCI Tools
12:08 Changeset [3669] by curtis
2008 Feb 12 release of LOCI Tools
12:08 Changeset [3668] by curtis
2008 Feb 12 release of LOCI Tools
12:08 Changeset [3667] by curtis
2008 Feb 12 release of LOCI Tools
11:59 Changeset [3666] by curtis
Fix bug in ..namedfork/rsrc resource fork style parsing.
11:37 Changeset [3665] by curtis
Lame hack to allow QuickTime reader to recognize extensionless files, …
11:30 Changeset [3664] by melissa
Removed isIndexedAsRGB and setIndexedAsRGB, for real this time.
11:27 Changeset [3663] by melissa
* Removed setIndexedAsRGB and isIndexedAsRGB - ChannelFiller now offers …
07:54 Changeset [3662] by melissa
Added new methods setIndexedAsRGB(boolean) and isIndexedAsRGB(). If …

02/11/08:

19:15 Changeset [3661] by melissa
Fixed pixel type detection.
16:24 Changeset [3660] by curtis
Remove references to loci.formats.test package.
16:22 Changeset [3659] by curtis
Reorganize test suite and integrate with Ant.
13:27 Ticket #236 (QuickTime resource fork parsing on Mac file systems throws ...) closed by melissa
fixed: Should be fixed in r3658. Note that the difference between the ._ and …
13:24 Changeset [3658] by melissa
Fixed offset bug in MJPB codec, and fixed a few problems with QuickTime …
12:11 Ticket #237 (Image planes from LegacyQTReader can no longer be displayed) created by curtis
Attempting to read data/quicktime/curtis/mri-cinepak.mov on a Windows …
11:39 Ticket #236 (QuickTime resource fork parsing on Mac file systems throws ...) created by curtis
When reading a QuickTime movie with split resource fork on a Mac OS X file …
11:11 Changeset [3657] by curtis
Fix bug in resource fork detection; add debugging statements.
09:58 Changeset [3656] by melissa
Don't throw an exception when parsing the maximum pixel value.
09:43 Changeset [3655] by melissa
The byte array passed to openBytes is now properly populated.

02/08/08:

17:29 Changeset [3654] by curtis
2008 Feb 08 release of LOCI Tools
17:29 Changeset [3653] by curtis
2008 Feb 08 release of LOCI Tools
17:29 Changeset [3652] by curtis
2008 Feb 08 release of LOCI Tools
17:29 Changeset [3651] by curtis
2008 Feb 08 release of LOCI Tools
17:29 Changeset [3650] by curtis
2008 Feb 08 release of LOCI Tools
17:29 Changeset [3649] by curtis
2008 Feb 08 release of LOCI Tools
17:29 Changeset [3648] by curtis
2008 Feb 08 release of LOCI Tools
17:29 Changeset [3647] by curtis
2008 Feb 08 release of LOCI Tools
17:20 Changeset [3646] by curtis
Update what's new for today's release.
17:13 Changeset [3645] by curtis
Hook up channel widget logic.
16:47 Changeset [3644] by curtis
More fixes and tweaks to macro options (third time's the charm).
16:24 Changeset [3643] by curtis
Refix Data Browser plugin entry.
16:23 Changeset [3642] by curtis
* Fix Data Browser plugin entry. * Tweak macro parameters some more. * …
16:19 Changeset [3641] by curtis
Fix macro recording with newer importer options.
16:16 Changeset [3640] by curtis
Hook up Data Browser animation logic.
15:10 Changeset [3639] by curtis
CacheIndicator can work with Components other than JScrollBar.
15:09 Changeset [3638] by curtis
* Preliminary version of new Data Browser (CustomWindow). * Revised …
15:06 Changeset [3637] by melissa
Added new Metamorph format to list of stuff we want and updated what's new …
14:19 Changeset [3636] by melissa
Miscellaneous bug fixes.
10:40 Changeset [3635] by curtis
Workaround for Mac OS X Java bug in Bio-Formats Importer options dialog's …
10:25 Changeset [3634] by melissa
Fixed RGB channel count calculation for non-indexed images.
10:14 Changeset [3633] by melissa
Pixel sizes must be read as ints, not floats.
09:40 Changeset [3632] by melissa
Fixed pixel size calculation - pixel sizes of 0 were incorrectly reported …
08:56 Changeset [3631] by curtis
Fix stack ordering bug with virtual stacks.
08:54 Changeset [3630] by melissa
Fixed absolute path problem.
08:42 Changeset [3629] by melissa
Fixed a couple of ChannelFiller-related bugs.
08:23 Changeset [3628] by curtis
Add javadoc explaining the distinction between DimensionSwapper and …
06:28 Changeset [3627] by curtis
* Add FormatTools.getReorderedIndex method sans IFormatReader, similar …
06:22 Changeset [3626] by curtis
Fix typo.
06:22 Changeset [3625] by curtis
Make getMetadataString return String rather than StringBuffer.
00:23 Changeset [3624] by curtis
* Move ImageProcessorSource to loci.plugins; use Util.openProcessor …

02/07/08:

22:35 Changeset [3623] by curtis
Make autoscale and virtual stack options mutually exclusive. Otherwise, …
22:14 Changeset [3622] by curtis
Add missing copyright.
22:13 Changeset [3621] by curtis
Add some missing copyrights; miscellaneous fiddling.
14:40 Changeset [3620] by melissa
Make sure that the MetadataStore's root is non-null, and adjust sizeC to …
14:05 Changeset [3619] by melissa
Corrected for Y-axis inversion.
13:09 Ticket #235 (Add support for new Metamorph format) created by melissa
Metamorph 7.5 introduces a new TIFF-based format that is designed to …
09:56 Changeset [3618] by melissa
Check if the original string is null before trying to remove invalid …
09:43 Changeset [3617] by melissa
Added new MetadataStore implementation (FilterMetadata) - this allows us …

02/06/08:

16:02 Changeset [3616] by curtis
Some work on DisplayOptions and ChannelComponent.
15:42 Changeset [3615] by curtis
Eliminate unnecessary imports.
13:34 Changeset [3614] by melissa
No longer throws an exception if setMetadataFiltered(true) was not called.
12:57 Changeset [3613] by melissa
OIB files always use '/' as the file separator.
10:41 Changeset [3612] by melissa
Replaced 1.5-specific "Boolean.parseBoolean..." calls.
10:01 Changeset [3611] by melissa
Files are now initialized once, instead of at the start of every test.
09:52 Changeset [3610] by melissa
Re-added openBytes signatures that were removed in r3569.
09:33 Changeset [3609] by melissa
Added a couple of extra checks to make sure that Z, C and T sizes are …
09:18 Changeset [3608] by melissa
Fixed pixel type detection.
08:22 Changeset [3607] by melissa
Removed unnecessary width hack.

02/05/08:

14:12 Changeset [3606] by curtis
Add copyright notices.
13:27 Changeset [3605] by curtis
Initial version of metadata framework with working object references …
07:20 Changeset [3604] by melissa
Don't reset currentId when opening an OIB file.
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