Timeline


and

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 …

12/29/10:

20:35 Changeset [7479] by aivar
Added comments.
17:41 Ticket #619 (Add tests for ScreenReader) closed by melissa
fixed: (In [7478]) Added tests for screen detection. Closes #619.
17:41 Changeset [7478] by melissa
Added tests for screen detection. Closes #619.
17:40 Changeset [7477] by melissa
Allow sparse plates.
17:39 Changeset [7476] by melissa
Prevent a NPE when calling isThisType on a file with no parent directory.
15:45 Changeset [7475] by melissa
Attach non-well files as companion metadata files.
14:05 Ticket #624 (Allow FileStitcher to stitch files with multiple series) closed by melissa
fixed: (In [7474]) Allow multi-series files to be stitched if the file pattern …
14:05 Changeset [7474] by melissa
Allow multi-series files to be stitched if the file pattern contains only …
13:06 Changeset [7473] by melissa
Make type detection slightly more restrictive; this should allow the tests …
12:47 Ticket #628 (Update ScreenReader to handle InCell 3000 data) closed by melissa
fixed: (In [7472]) Added more flexible plate/well detection, so that InCell 3000 …
12:47 Changeset [7472] by melissa
Added more flexible plate/well detection, so that InCell 3000 datasets are …
09:11 Ticket #613 (Investigate consolidating 'showinf' and 'bfview') closed by melissa
fixed: (In [7471]) 'bfview' now has the same behavior as 'showinf', except that a …
09:11 Changeset [7471] by melissa
'bfview' now has the same behavior as 'showinf', except that a deprecation …

12/28/10:

12:05 Ticket #580 (Virtual stack with split channels, timepoints and/or planes) closed by melissa
fixed: (In [7470]) Allow virtual stacks to be sliced. Closes #580.
12:05 Changeset [7470] by melissa
Allow virtual stacks to be sliced. Closes #580.

12/27/10:

17:24 Changeset [7469] by melissa
Removed duplicate variable declaration, which prevented 2008-09 and …
16:39 Changeset [7468] by aivar
Grayscale image wasn't showing up.
15:29 Ticket #601 (Investigate using MediaUtil for block-based JPEG decoding) closed by melissa
fixed: After some investigation, I have yet to find a way to retrieve the …
14:40 Changeset [7467] by melissa
Fixed NPE introduced in r7433.
14:37 Changeset [7466] by melissa
Fixed one more IFD caching bug.
13:34 Ticket #631 (EPS coloring is often incorrect) closed by melissa
fixed: (In [7465]) Fixed how EPS images with two channels are handled. Closes …
13:34 Changeset [7465] by melissa
Fixed how EPS images with two channels are handled. Closes #631.
10:47 Ticket #603 (Move get/setMetadataOptions methods to IFormatReader) closed by melissa
invalid: The [get,set]MetadataOptions methods are actually declared in the …
10:41 Ticket #630 (Bio-Rad LUTs do not look correct) closed by melissa
fixed: (In [7464]) Reset ColorModel after setting the display range; this …
10:41 Changeset [7464] by melissa
Reset ColorModel after setting the display range; this prevents LUTs from …
09:49 Ticket #632 (Some metadata is not populated for Zeiss LSM files) closed by melissa
fixed: (In [7463]) Preserve user name and emission wavelengths. Closes #632.
09:49 Changeset [7463] by melissa
Preserve user name and emission wavelengths. Closes #632.

12/24/10:

16:15 Ticket #479 (Add support for Trestle slide data) closed by melissa
fixed: (In [7462]) * Fixed various TIFF-parsing related problems introduced in …
16:15 Changeset [7462] by melissa
* Fixed various TIFF-parsing related problems introduced in r7459. * …
15:15 Changeset [7461] by melissa
Fixed a bug in ZipHandle.isZipFile(String) that was introduced in r7460.
14:50 Ticket #608 (Zip file URLs are not supported) closed by melissa
fixed: (In [7460]) Updated ZipHandle and ZipReader to use a ZipInputStream …
14:50 Changeset [7460] by melissa
Updated ZipHandle and ZipReader to use a ZipInputStream instead of a …
14:49 Changeset [7459] by melissa
Fill in IFD values after the IFDs have been parsed, thus reducing the …
11:54 Changeset [7458] by melissa
A few small speed improvements for reading Openlab files.

12/23/10:

18:53 Changeset [7457] by aivar
Resources directory.
18:40 Changeset [7456] by aivar
More documentation.
13:02 Changeset [7455] by melissa
Added initial version of Trestle reader, see #479.
11:50 Changeset [7454] by melissa
Made PGM parsing more flexible, as required for #479.
10:48 Ticket #599 (Add optimal tile size methods) closed by melissa
fixed: (In [7453]) Added methods for retrieving the optimal size of a sub-image. …
10:48 Changeset [7453] by melissa
Added methods for retrieving the optimal size of a sub-image. Closes …
09:21 Ticket #568 (Review results of testing project) closed by melissa
fixed: Many of the issues reported here were invalid or have since been fixed. …
09:20 Ticket #633 (FV1000 LUTs are not displayed correctly in ImageJ) created by melissa
See data/fv1000/jean-claude/villositerat0heurea.oib. The first channel …
09:19 Ticket #632 (Some metadata is not populated for Zeiss LSM files) created by melissa
See data/zeiss-lsm/gaetan/blastocyste.lsm: - the user name "adenot" is …
09:17 Ticket #631 (EPS coloring is often incorrect) created by melissa
See data/eps/frank/075095##_F_3C.eps. The main part of the image should …
09:15 Ticket #630 (Bio-Rad LUTs do not look correct) created by melissa
See biorad/chris/4C_tweek12;nSyb_PLC-PH-GFP_HRPstain.pic. With the LUT …

12/22/10:

17:09 Ticket #629 (Add support for Leica Stereo Microscope data) created by melissa
See files in data/leica-sm/grant/. It looks to be one or more plain TIFFs …
17:01 Changeset [7452] by melissa
Fixed .nd/.stk file searching, to prevent problems with multiple …
14:20 Changeset [7451] by melissa
Append 'Z' to the dimension order string when appropriate. See …
12:45 Ticket #622 (.aim to TIFF conversion is not quite right) closed by melissa
invalid: This is actually a set of problems in ImageJ's native TIFF reader. I can …
12:35 Changeset [7450] by curtis
Update legacy auto-display plugin package name.
12:13 Ticket #628 (Update ScreenReader to handle InCell 3000 data) created by melissa
InCell 3000 files have names like this: 20041103 1049_01_REF-1049-03 - …
12:11 Ticket #443 (Add support for IN Cell 3000 datasets) closed by melissa
fixed: (In [7449]) Added reader for InCell 3000 files. Closes #443.
12:11 Changeset [7449] by melissa
Added reader for InCell 3000 files. Closes #443.

12/21/10:

16:51 Changeset [7448] by melissa
One more fix to 'uiSequenceCount' parsing. This really definitely fixes …
12:49 Ticket #627 (Slidebook series grouping is not always correct) created by melissa
See files in slidebook/glen/Loci sld/. D3 Timelapse3.sld should be a pair …
12:46 Ticket #626 (Slidebook valid bits per pixel not parsed) created by melissa
See 12-bit files in slidebook/glen/Loci sld/.

12/20/10:

16:00 Changeset [7447] by melissa
Prevent setSeries(int) from being called incorrectly.
15:42 Ticket #617 (Channel order is reversed in some LSM files) closed by melissa
fixed: r7446 fixes the channel coloring. However, this data will not display …
15:40 Changeset [7446] by melissa
Parse and apply LUTs stored in the 'u32OffsetChannelColors' block. See …
14:15 Changeset [7445] by curtis
Use updated auto-plugin package name in slim-plugin.
10:06 Ticket #625 (Add support for MetaXpress data) created by melissa
See files in data/metaxpress/. Datasets consist of an MSSQL database …
01:25 Changeset [7444] by aivar
Hooking in PluginLinker to PluginComponent. See PluginComponent TODO …

12/17/10:

17:16 Ticket #621 (Some ND2 files are not read completely) closed by melissa
fixed: (In [7443]) Use the 'uiSequenceCount' attribute to calculate the image …
17:16 Changeset [7443] by melissa
Use the 'uiSequenceCount' attribute to calculate the image count. Closes …
17:15 Changeset [7442] by melissa
Populate channel colors even if the MetadataLevel is set to MINIMUM. This …
16:22 Changeset [7441] by aivar
Deleting those pesky local deletes.
16:21 Changeset [7440] by aivar
Made Chain an outer class so that WorkFlow can report chains. Worked on …
16:20 Changeset [7439] by aivar
Renamed XMLTest to SerializeDeserializeTest. Made TestComponent really …
16:10 Changeset [7438] by aivar
Changed package to 'xmllight'. Split XMLHelper into XMLParser and …
13:49 Ticket #624 (Allow FileStitcher to stitch files with multiple series) created by melissa
See files in data/fv1000/aryeh/061010 plate 1/. It's important to check …
13:22 Changeset [7437] by aivar
Handles nested workflows.
13:22 Changeset [7436] by aivar
Renamed.
13:21 Changeset [7435] by aivar
Refactored XMLHelper into XMLParser and XMLWriter. Worked on factories.
13:20 Changeset [7434] by aivar
Refactored XMLHelper into XMLParser and XMLWriter.
12:16 Changeset [7433] by melissa
Make sure that channel names are populated for screen data.
11:05 Changeset [7432] by aivar
More javadoc.
02:00 Changeset [7431] by aivar
Workflow passes unit test: Create a workflow programmatically and export …

12/16/10:

18:27 Changeset [7430] by aivar
Added "loci.workflow" package. Instead of having a singleton that passes …
17:15 Ticket #610 (Some AVI files have skewed scanlines) closed by melissa
fixed: (In [7429]) Adjust the number of padding bytes based upon the total number …
17:15 Changeset [7429] by melissa
Adjust the number of padding bytes based upon the total number of bytes …
15:48 Ticket #611 (ICS export should preserve more metadata) closed by melissa
fixed: (In [7428]) * Added setValidBitsPerPixel(int) to IFormatWriter. * Updated …
15:48 Changeset [7428] by melissa
* Added setValidBitsPerPixel(int) to IFormatWriter. * Updated ICSWriter to …
11:00 Changeset [7427] by melissa
Catch exception when parsing .mdb files, so that .lsm files can be read …

12/15/10:

23:54 Changeset [7426] by aivar
Added a workflow class that creates a pipeline of plugins but looks just …
23:29 Changeset [7425] by aivar
Added a workflow class that creates a pipeline of plugins but looks just …
13:20 Changeset [7424] by hinerm
Enhanced BF-ITK build for windows. The dist target is now specific to a …
12:44 Changeset [7423] by curtis
Remove obsolete loci.nodescheduler package.
11:53 Changeset [7422] by aivar
Catch up with commits.
11:20 Changeset [7421] by aivar
Catch up with commits.
11:17 Changeset [7420] by aivar
Catch up with commits.

12/14/10:

15:48 Changeset [7419] by aivar
Catch up with commits.
09:29 Ticket #623 (Expand InCell support to cover InCell 2000) closed by callan
fixed
07:17 Changeset [7418] by callan
More robust InCellReader XML parsing. (See #623) Specifically handled: * …
05:23 Changeset [7417] by callan
Made InCellReader support a little more generic to accomodate InCell 2000 …
05:18 Ticket #623 (Expand InCell support to cover InCell 2000) created by callan

12/13/10:

16:15 Changeset [7416] by aivar
Does a 'convertToRGB( )' on source image. Sort of memory-intensive but …
12:48 Changeset [7415] by aivar
More documentation.
12:48 Changeset [7414] by aivar
More documentation.
12:47 Changeset [7413] by aivar
More documentation.
12:47 Changeset [7412] by aivar
More documentation.
12:47 Changeset [7411] by aivar
More documentation.
12:47 Changeset [7410] by aivar
More documentation.
12:46 Changeset [7409] by aivar
More documentation.
12:46 Changeset [7408] by aivar
More documentation.
12:46 Changeset [7407] by aivar
More documentation.
12:45 Changeset [7406] by aivar
More documentation.
12:45 Changeset [7405] by aivar
More documentation.

12/12/10:

22:36 Changeset [7404] by curtis
Ignore Eclipse metadata for deep-zoom-plugin.
22:18 Changeset [7403] by curtis
Remove extraneous svn:executable flags.

12/11/10:

13:49 Ticket #604 (Move "no OME-XML" message out of OMETiffReader) closed by melissa
fixed: (In [7402]) Moved missing OME-XML messages into OMEXMLServiceImpl. Closes …
13:49 Changeset [7402] by melissa
Moved missing OME-XML messages into OMEXMLServiceImpl. Closes #604.
12:51 Changeset [7401] by melissa
Override openBytes, so that correct pixels are returned for each series.
12:34 Changeset [7400] by melissa
Added series number to one last failure message.
12:18 Ticket #622 (.aim to TIFF conversion is not quite right) created by melissa
Specifically: […]
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