Timeline


and

11/23/07:

08:53 Changeset [3407] by melissa
Fixed endian bug.

11/21/07:

18:40 Changeset [3406] by curtis
Bugfixes, corrections and improvements toward a working 2007-06 OME-XML. …
14:21 Changeset [3405] by melissa
2007 Nov 21 release of LOCI Tools
14:21 Changeset [3404] by melissa
2007 Nov 21 release of LOCI Tools
14:21 Changeset [3403] by melissa
2007 Nov 21 release of LOCI Tools
14:21 Changeset [3402] by melissa
2007 Nov 21 release of LOCI Tools
14:21 Changeset [3401] by melissa
2007 Nov 21 release of LOCI Tools
14:21 Changeset [3400] by melissa
2007 Nov 21 release of LOCI Tools
14:20 Changeset [3399] by melissa
2007 Nov 21 release of LOCI Tools
14:20 Changeset [3398] by melissa
2007 Nov 21 release of LOCI Tools
14:18 Changeset [3397] by melissa
Fixed bug with slicing 12 channel data.
13:24 Changeset [3396] by curtis
Use isInstance rather than equals for class matching test.
13:17 Changeset [3395] by melissa
Added new IFormatReader API method - "IFormatReader[] …
13:16 Changeset [3394] by melissa
Formats that don't support multiple series now set the Image name to null, …

11/20/07:

16:16 Changeset [3393] by curtis
Bugfixes and corrections for 2003 (FC) version.
15:17 Changeset [3392] by melissa
* Fixed SimplePCI endianness * Fixed PICT channel separation bug * Fixed …

11/19/07:

15:18 Changeset [3391] by melissa
Updated for next release.
15:03 Ticket #181 (Investigate LSM data with nonstandard LZW compression) closed by melissa
fixed: r3390. This was less complex than original investigation suggested - just …
15:01 Changeset [3390] by melissa
Double the values of StripByteCounts for files with no RowsPerStrip entry …
14:33 Changeset [3389] by melissa
Automatically apply the LUT, instead of having isIndexed() return true; …
13:07 Changeset [3388] by melissa
Fixed axis size parsing logic.
12:20 Changeset [3387] by curtis
Remove obsolete XML validation helper class.
12:13 Changeset [3386] by curtis
Split LineTracker into separate source file.
11:51 Changeset [3385] by curtis
Allow multiple Plane elements per Pixels.
11:50 Changeset [3384] by curtis
Add handling for node types unsupported by certain versions (e.g., …
11:19 Changeset [3383] by curtis
Add notation for 2003/CA-style ID reference path chains.

11/16/07:

15:27 Changeset [3382] by curtis
Update author information in About dialog.
14:45 Changeset [3381] by curtis
Remove cruft.
14:29 Changeset [3380] by curtis
Readd junit.jar as external library dependency.
14:27 Changeset [3379] by curtis
Move native code to libs folder; update build script.
12:08 Changeset [3378] by curtis
Throw a proper FormatException for various problems.
11:49 Changeset [3377] by melissa
Fixed another endian issue.
11:34 Changeset [3376] by melissa
Fixed endian problem.
09:57 Ticket #204 (Support lossless JPEG in DICOM reader) closed by melissa
fixed: Added support for lossless JPEG in r3369; required libraries were added in …
09:56 Changeset [3375] by melissa
Added JAR/native library files needed to read lossless JPEG.
09:38 Ticket #220 (LZW decoder misbehaves for some LZW-compressed TIFFs) closed by melissa
fixed: r3374. The issue was that we didn't (correctly) support undifferencing of …
09:37 Changeset [3374] by melissa
16 bit data is now undifferenced properly.

11/15/07:

14:50 Ticket #216 (Improve window titles for multi-file datasets) closed by melissa
fixed: r3373; multi-file formats will continue to use the primary file's name.
14:49 Changeset [3373] by melissa
* Removed separate FileStitcher, since data browser integration is much …
14:29 Ticket #218 (Fix memory issue with OLE-based formats) closed by melissa
fixed: Fixed in r3372. Used the solution described above, which changed POI's …
14:27 Changeset [3372] by melissa
* Updated POI to use significantly less memory, which required a few …

11/14/07:

17:46 Changeset [3371] by melissa
Check pixel type before doing user-specified merge; don't pass …
15:23 Changeset [3370] by melissa
Removed unnecessary imports/debugging statements.
13:55 Changeset [3369] by melissa
Lossless JPEG is now supported, if JAI (with native code) is installed. …
12:30 Ticket #220 (LZW decoder misbehaves for some LZW-compressed TIFFs) created by curtis
The files in data/tiff/wayne/mBoeglin_lzw do not decode properly with …
11:22 Changeset [3368] by melissa
* Removed several hacks that were designed to correct for POI …

11/13/07:

18:54 Ticket #219 (Some Slidebook files have incorrect dimensions) closed by melissa
fixed: Fixed, r3367.
18:54 Changeset [3367] by melissa
Fixed sizeC detection.
16:00 Ticket #219 (Some Slidebook files have incorrect dimensions) created by curtis
For an example, see data/slidebook/john/Slide1.sld, which should be 512 …
15:46 Ticket #218 (Fix memory issue with OLE-based formats) created by melissa
Zeiss ZVI, FV1000 OIB, ImagePro IPW and SimplePCI all have significant …
15:40 Ticket #199 (Fix exception with new OIB files) closed by melissa
fixed: Fixed, r3366. This was an issue with POI, not the OIB reader.
15:34 Changeset [3366] by melissa
Updated poi-loci.jar - fixes a couple of bugs with files that have a big …
13:28 Ticket #217 (Write alternate ND2 reader using Nikon SDK) created by melissa
At some point, we should implement an ND2 reader that uses the SDK from …

11/12/07:

13:36 Changeset [3365] by melissa
Added windowless importer - reads options from IJ_Prefs.txt, but doesn't …
12:16 Changeset [3364] by curtis
Fill in setter method bodies; miscellaneous progress.
12:09 Changeset [3363] by melissa
Reset previousImage if the series number was changed.
11:22 Ticket #17 (Bio-Formats importer does not set calibration information for alternate ...) closed by melissa
fixed: Data browser sets calibration information as of r3362.
11:19 Ticket #12 (Override createSubtitle() properly) closed by melissa
fixed: Finished, r3362.
11:19 Ticket #65 (Cache indicators can report erroneous caching situation) closed by melissa
fixed: Seems to be fixed in r3362 - as of that revision, the 4D data browser uses …
11:17 Ticket #211 (Add ImageJ plugin that merges/colorizes channels) closed by melissa
fixed: Finished, r3362.
11:13 Changeset [3362] by melissa
* Lots of work on data browser; it now uses the caching logic in …
08:49 Changeset [3361] by melissa
Read each resolution level into its own series.

11/09/07:

14:08 Ticket #213 (OMETiffReader should parse OriginalMetadata) closed by melissa
fixed: Fixed in r3360. You can check this with …
14:06 Changeset [3360] by melissa
Place OriginalMetadata key/value pairs in the metadata hashtable.
13:59 Changeset [3359] by melissa
Compare the primary file's used file list against FilePattern's file list …
13:16 Changeset [3358] by melissa
Implemented new sub-image API methods - this should have been in r3357.
13:14 Changeset [3357] by melissa
Added new API methods to read sub-images: - BufferedImage openImage(int …
13:11 Changeset [3356] by melissa
Use FormatTools.populatePixels to set MetadataStore's 'Pixels' …
13:08 Changeset [3355] by melissa
* Added two new API methods - 'boolean isInCache(int[])' and 'boolean …
13:04 Changeset [3354] by melissa
close() methods now clear *all* variables; added signed pixel support in …
12:55 Ticket #215 (Stack Slicer window titles must be distinct) closed by melissa
fixed: Fixed, r3353; appropriate Z/C/T coordinates are appended to the original …
12:52 Changeset [3353] by melissa
Append the appropriate Z, C and T indices to the window title.
12:04 Ticket #216 (Improve window titles for multi-file datasets) created by melissa
Right now, if we open a multi-file dataset in ImageJ, the window title is …
12:03 Ticket #215 (Stack Slicer window titles must be distinct) created by curtis
One major reason to use the Stack Slicer plugin is to create multiple …
11:30 Changeset [3352] by curtis
Minor tweaks.
11:29 Changeset [3351] by curtis
Flesh out the metadata guide a bit more.
09:58 Ticket #214 (Add support for InCell1000 HCS format) created by melissa
InCell1000 uses a high-content screening format that is a combination of …
09:57 Ticket #213 (OMETiffReader should parse OriginalMetadata) created by melissa
Right now, OMETiffReader doesn't do anything with OriginalMetadata …

11/08/07:

14:01 Changeset [3350] by curtis
Use properly capitalized pixel type for Uint8.
11:32 Changeset [3349] by curtis
Fix xsi:schemaLocation.
08:33 Ticket #212 (Reading OME-TIFF file with '-nometa' throws exception) closed by melissa
fixed: Fixed in r3348.
08:33 Changeset [3348] by melissa
Retrieve OME-XML block directly from first IFD, without relying on …

11/07/07:

14:09 Changeset [3347] by curtis
Exclude loci.formats.auto package from bio-formats.jar build.
13:54 Changeset [3346] by curtis
Use class resources instead of files directly; output files with proper …
13:46 Changeset [3345] by curtis
Framework for autogenerating MetadataStore/MetadataRetrieve interfaces and …
13:30 Changeset [3344] by curtis
Add one-time dialog for Mac users warning about OLE2 column view crash …

11/06/07:

14:57 Ticket #212 (Reading OME-TIFF file with '-nometa' throws exception) created by melissa
Reading any OME-TIFF file using the '-nometa' option produces the …

11/05/07:

18:59 Changeset [3343] by melissa
Removed unnecessary getIFDs call.
11:25 Changeset [3342] by melissa
Giving lse.xml file to BioRadReader will now open entire dataset.
09:30 Changeset [3341] by melissa
Fixed interleaving bug for real this time.
09:26 Changeset [3340] by melissa
Fixed interleaving bug.
09:02 Changeset [3339] by melissa
Don't try to decompress more bytes than are needed.

11/02/07:

19:08 Ticket #210 (Better file stitching in BioradReader) closed by melissa
fixed: Done in r3338. If an lse.xml file is present, the appropriate .pic files …
14:13 Changeset [3338] by melissa
Find and group PIC files if lse.xml companion file is present.
11:23 Changeset [3337] by melissa
CustomImage can now merge up to 4 channels.
10:48 Ticket #211 (Add ImageJ plugin that merges/colorizes channels) created by melissa
At some point, the importer's merging and colorizing logic should get …

11/01/07:

09:52 Changeset [3336] by melissa
Make sure PixelSizeZ is always parsed, even if SizeZ == 1.
09:44 Ticket #210 (Better file stitching in BioradReader) created by melissa
BioradReader should check the companion files to more accurately detect …

10/31/07:

15:31 Ticket #209 (OME download is broken) created by curtis
The latest version of VisBio fails to download from an OME server, due to …
12:07 Changeset [3335] by melissa
Don't throw an exception if a Z stamp is encountered when we are expecting …
11:55 Changeset [3334] by melissa
More reliable pixel size parsing.
08:04 Ticket #207 (Slicer plugin throws an exception when there is no active image) closed by melissa
fixed: Fixed in r3333.
08:03 Changeset [3333] by melissa
Slicer now implements PlugInFilter, preventing an exception when there are …

10/30/07:

15:21 Ticket #208 (Add information about format versions to web site) created by curtis
The Bio-Formats web site should provide information about which file …
14:47 Ticket #207 (Slicer plugin throws an exception when there is no active image) created by curtis
The Slicer plugin implements PlugIn, which means currently it throws an …
13:22 Ticket #206 (Color merge throws an exception) closed by melissa
fixed: Fixed in r3330.
13:11 Changeset [3332] by melissa
Catch UnsupportedClassVersionError when creating ReflectedUniverse - this …
13:08 Changeset [3331] by melissa
Catch EOFException when parsing image files.
13:03 Changeset [3330] by melissa
Fixed merging bug.
10:49 Changeset [3329] by melissa
Calculate pixel sizes if they aren't stored explicitly.
08:50 Changeset [3328] by melissa
Make sure pixel sizes get reset; check for invalid min/max values before …
08:04 Changeset [3327] by melissa
Set pixel type correctly for signed images.

10/29/07:

10:39 Changeset [3326] by curtis
No more need for omebf script.
10:37 Ticket #206 (Color merge throws an exception) created by curtis
The option to "Merge channels to RGB" can throw an exception. For example, …
10:06 Ticket #205 (Window titles can become too long) closed by melissa
fixed: Fixed in r3325. The window title is now file name plus the series name …
10:05 Changeset [3325] by melissa
Better string trimming.
10:01 Changeset [3324] by melissa
Make sure that window titles are <= 128 chars.
09:33 Changeset [3323] by melissa
Populate PixelSize*, if values exist in metadata; better parsing of …

10/26/07:

15:22 Changeset [3322] by melissa
Fixed endianness.
14:56 Changeset [3321] by melissa
* Removed a bunch of unnecessary axis size calculation logic from …
13:38 Ticket #205 (Window titles can become too long) created by curtis
The Importer plugin currently uses the full path name, plus the image …
13:31 Changeset [3320] by melissa
Multiple series are now correctly detected; replaced evil axis …
12:53 Changeset [3319] by curtis
Remove unnecessary imports.
11:28 Changeset [3318] by curtis
Typo.
11:24 Changeset [3317] by curtis
Workaround for XML parsing bug with SAX on Windows and Mac OS X.
08:52 Changeset [3316] by melissa
Reorganized MetadataStore population logic - calls to setLogicalChannel …
07:36 Changeset [3315] by melissa
Temporary hack to unbreak openBytes(int, byte[]).

10/25/07:

16:10 Changeset [3314] by curtis
Remove unnecessary import.
16:10 Changeset [3313] by curtis
Print exceptions to Results window rather than with IJ.showMessage or …
15:25 Changeset [3312] by curtis
Remove references to the optional loci.formats.tools package.
15:01 Changeset [3311] by melissa
Removed unnecessary import statements.
14:49 Changeset [3310] by curtis
Add NetCDF libraries to build properties.
13:13 Ticket #178 (Add support for Imaris 5.5) closed by melissa
fixed: Done in r3309.
13:12 Changeset [3309] by melissa
Added support for Imaris 5.5 (HDF-based).
07:47 Changeset [3308] by melissa
Implemented openBytes(int).
07:45 Changeset [3307] by melissa
Added command-line flags to ImageConverter (-merge, -separate, -stitch, …
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