Timeline


and

08/05/09:

15:35 Changeset [5358] by melissa
* Added "sane XML" test to check for common OME-XML errors that are not …
15:13 Changeset [5357] by callan
Math.pow() is incredibly expensive, moving it outside the loop.
14:30 Changeset [5356] by melissa
Use ImageTools.bgrToRgb utility method when possible.
14:12 Changeset [5355] by callan
*sigh* Reverting erroneous changes to Eclipse preferences again.
14:09 Changeset [5354] by callan
Optimize the reading of single channel, 8 or 16 bit greyscale TIFFs and …
14:08 Changeset [5353] by melissa
* Fixed problems with QuickTime files that are not flattened. * Better …
11:16 Changeset [5352] by melissa
Fixed endianness and extended header size calculations.
08:53 Changeset [5351] by melissa
Fixed scaling problems with 16 bit data.

08/04/09:

16:15 Changeset [5350] by curtis
Add support for Paul Barber's time resolved lifetime ICS data.
15:47 Changeset [5349] by curtis
Add DelegateReader.isLegacy() method, and make class abstract.
15:46 Changeset [5348] by curtis
Add support for pixel types beyond uint16 and int16.
15:45 Changeset [5347] by melissa
Be less strict about checking file sizes, to account for differences in …
15:17 Changeset [5346] by melissa
Updated metadata support documentation for HCS formats.
12:35 Changeset [5345] by curtis
Add "-format" command line flag for forcing use of a specific format.
10:29 Changeset [5344] by melissa
* Added min/max arguments to ImageTools.make24Bits methods. * Added …
09:04 Changeset [5343] by melissa
Use a custom DataBuffer for signed short data. This prevents an …

08/03/09:

15:25 Changeset [5342] by melissa
A bunch of improvements to Leica LIF/TCS metadata parsing - still needs …
10:47 Changeset [5341] by melissa
* Fixed COBOL epoch constant. * POITools uses generics when possible. * …

08/01/09:

11:28 Changeset [5340] by curtis
In debug mode, print no exception if header file is missing during type …

07/31/09:

13:16 Ticket #410 (showinf's -fast flag adjusts data too naively) closed by melissa
fixed: (In [5339]) * Fixed scaling problems in make24Bits methods. Closes #410. …
13:16 Changeset [5339] by melissa
* Fixed scaling problems in make24Bits methods. Closes #410. * Added …

07/30/09:

12:30 Changeset [5338] by curtis
Update to latest TIFF API; fix problem with missing methods in …
12:23 Changeset [5337] by melissa
* Eliminated .pty filename length checks. * Use generics in FV1000Reader …

07/29/09:

18:07 Changeset [5336] by curtis
Update to latest TIFF API.
17:55 Changeset [5335] by curtis
Update to latest TIFF API.
17:55 Changeset [5334] by curtis
Finish TiffTools migration; clean up import statements.
16:58 Changeset [5333] by curtis
Fix linker error on Windows (avoid using JInt directly with cout).
14:40 Changeset [5332] by curtis
Tweak text.
14:39 Changeset [5331] by curtis
More reflection testing.
13:11 Changeset [5330] by curtis
Benchmark utility for testing reflection performance.
09:10 Changeset [5329] by melissa
* Style fixes. * Added CodecOptions constructor that takes a CodecOptions …

07/28/09:

21:19 Changeset [5328] by melissa
Ensure that the number of DetectorSettings is less than or equal to the …
19:58 Changeset [5327] by gbonamy
Fixing compilation error. See if importing the …
19:08 Changeset [5326] by gbonamy
Added support for JPEG2000 Lossy compression. Please make sure that the …
16:53 Changeset [5325] by melissa
Updated examples to work with recent revisions. Moved component-specific …
16:11 Ticket #410 (showinf's -fast flag adjusts data too naively) created by curtis
When using the -fast flag with the showinf command line utility, 16-bit …
15:08 Changeset [5324] by curtis
Add MetadataTools.keys(Hashtable) method for easily obtaining sorted keys.
15:07 Changeset [5323] by curtis
Add code for metadata output.
13:55 Changeset [5322] by melissa
Automatically group together .pic files that belong to the same dataset, …
12:50 Changeset [5321] by curtis
Include stdio/stdlib for atoi on Linux; miscellaneous tweaks.
12:06 Changeset [5320] by melissa
getCurrentFile() now returns 'currentId' directly. This prevents an …
11:49 Changeset [5319] by melissa
Fix for file names that contain 'pty', but do not have the '.pty' …
10:40 Changeset [5318] by gbonamy
Fixed improper formating in package.html files.

07/24/09:

11:50 Changeset [5317] by melissa
Smarter .mdb/.lsm file grouping.
11:40 Changeset [5316] by curtis
Read pixels (but do not display) in C++ version of showinf.
11:29 Ticket #409 (int8 BufferedImages are displayed incorrectly) closed by melissa
fixed: (In [5315]) Fixed scaling problems with signed byte data. Closes #409.
11:29 Changeset [5315] by melissa
Fixed scaling problems with signed byte data. Closes #409.
11:21 Changeset [5314] by curtis
* Include LOCI Common library in bf-cpp build. * Progress on C++ version …
10:29 Changeset [5313] by curtis
Avoid bf-cpp compile error with loci.formats.tiff.IFD.IFD constant.
09:54 Changeset [5312] by curtis
Add FilePattern.findPattern(String path) convenience method.
09:11 Changeset [5311] by curtis
Consolidate ImageReader's assertId checks into getReader() method.
08:54 Ticket #409 (int8 BufferedImages are displayed incorrectly) created by melissa
Can be reproduced using data/ics/melissa/signed-8-bit.ics or: […]

07/23/09:

17:00 Changeset [5310] by curtis
Better series macro labels (series_1, series_2, series_3, etc., instead of …
16:59 Changeset [5309] by curtis
Fix potential NullPointerException?
16:58 Changeset [5308] by curtis
Better series names.
16:43 Changeset [5307] by curtis
Add hack to support testing with fake datasets.
16:15 Changeset [5306] by curtis
Fix typos.
16:14 Changeset [5305] by curtis
Add examples of usage to Javadoc.
15:56 Changeset [5304] by curtis
Add "fake" reader for simulating data of various types.
15:04 Changeset [5303] by curtis
Remove mysterious unnecessary constructor.
14:58 Changeset [5302] by curtis
QuickTime should have suffixNecessary = false, not suffixSufficient = …
14:47 Changeset [5301] by curtis
Clean up isThisType implementations.
13:20 Changeset [5300] by curtis
Clean up DataTools byte translation methods: * Deprecate superfluous …
11:11 Changeset [5299] by melissa
If the DV file is a deconvolved file, attempt to parse metadata from the …
10:40 Changeset [5298] by melissa
Populate Detector.Zoom, fixed Image.Name, and swapped …

07/22/09:

16:33 Changeset [5297] by curtis
Fix Windows-specific hacks.
16:11 Changeset [5296] by curtis
Update path to problematic CMYK and RGB constants.
15:13 Ticket #408 (Exception when opening files with > 512 series in ImageJ) created by melissa
Opening data/incell/brian/2008.03.16.13.04.12/2008.03.16.13.04.12.xdce …
14:32 Changeset [5295] by melissa
Fixed transposed row/column dimensions.
14:02 Changeset [5294] by melissa
Use DateTools utility methods to do date/time parsing.
13:25 Changeset [5293] by melissa
Fixed several NPEs and ArrayList usage problems.
08:16 Ticket #407 (Add support for Slidebook spool (.spl) files) created by melissa
Slidebook .sld files are supported, but .spl files are not - a brief …
06:32 Changeset [5292] by callan
Reverting erroneous changes to Eclipse settings.
06:29 Changeset [5291] by callan
* Fixed parsing of different date-time formats. * Fixed issues with IFD …

07/21/09:

17:43 Changeset [5290] by melissa
Fixed macro options to work with 4.0.1 and trunk versions of the importer …
17:32 Changeset [5289] by curtis
Include typedefs for common primitive array types.
17:17 Changeset [5288] by curtis
Eliminate unused variables with potential for NullPointerException.
16:19 Changeset [5287] by curtis
Add MetadataTools.asStore and MetadataTools.asRetrieve convenience …
16:06 Changeset [5286] by melissa
Fixed physical size and objective population.
14:36 Changeset [5285] by melissa
Make sure that minimum metadata is populated, even if OME-XML is …
14:07 Changeset [5284] by melissa
Updated plugin arguments to work with 4.0.1 and trunk versions of …
13:49 Changeset [5283] by melissa
Various MIAS speed improvements. May need a little more work, but a 384 …
08:58 Changeset [5282] by melissa
* Fixed RandomAccessInputStream.readCString() implementation. * Fixed …

07/20/09:

13:23 Changeset [5281] by curtis
Update documentation on Jace to indicate revision 23 or later is needed.
13:17 Changeset [5280] by curtis
Remove JACE_PROXY_API hack (fixed in recent Jace revisions).
13:16 Changeset [5279] by curtis
Remove debugging statements.
12:22 Changeset [5278] by curtis
Only require CMake 2.6.4 on Windows; otherwise require only CMake 2.6.
12:20 Changeset [5277] by curtis
Update to latest Bio-Formats and Jace. Works out of the box now.
10:53 Changeset [5276] by melissa
* FV1000 reader now closes all of its' files. * Removed duplicate …
09:44 Changeset [5275] by melissa
* Set Image.Name to the current file name by default. * TIFF companion …
09:00 Changeset [5274] by melissa
Imaris HDF files now initialize much more quickly. A slightly more …

07/17/09:

15:52 Changeset [5273] by curtis
Fix NullPointerException in Fluoview TIFF comment detection.
15:36 Changeset [5272] by curtis
More progress and bug-fixes for improved TIFF infrastructure.
14:05 Changeset [5271] by curtis
* Progress on object-oriented TIFF logic. * Move debug utility methods …
12:17 Changeset [5270] by melissa
Put overlay TIFFs on list returned by getUsedFiles(true).

07/16/09:

18:46 Changeset [5269] by curtis
Progress on TIFF logic refactoring.
18:24 Changeset [5268] by curtis
* Begin migrating TIFF logic to object-oriented loci.formats.tiff package. …
13:51 Changeset [5267] by curtis
Fix VisBio build targets.
13:32 Changeset [5266] by curtis
Split StatusEchoer into a separate class.
11:34 Changeset [5265] by melissa
Fixed how arrays with one element are parsed.
11:21 Changeset [5264] by melissa
Added reader for Nikon EZ-C1 TIFFs.
08:42 Changeset [5263] by melissa
* Put the Filter/Dichroic name in Filter.Model or Dichroic.Model. * Use …

07/15/09:

17:26 Changeset [5262] by melissa
Preliminary InCell ROI parsing. Text files are supported, but Excel files …
15:13 Changeset [5261] by curtis
Remove unnecessary loci.formats.gui reflection.
15:09 Changeset [5260] by curtis
Remove ReflectedUniverse for XML validation (not supporting Java 1.4 …
14:46 Changeset [5259] by curtis
Use java.lang.reflect.Array instead of ReflectedUniverse.
14:17 Changeset [5258] by melissa
Display an informative message if the JAR file couldn't be renamed.
13:21 Changeset [5257] by melissa
* Filter/FilterSet now populated. * Updated image names so that well …
11:02 Ticket #403 (Buttons in importer series dialog are misaligned) closed by melissa
fixed: (In [5256]) Fixed series dialog layout so that buttons don't overlap. …
11:02 Changeset [5256] by melissa
Fixed series dialog layout so that buttons don't overlap. Closes #403.

07/14/09:

13:42 Changeset [5255] by melissa
Fixed detector binning to be "nxn" instead of "n".
13:20 Ticket #404 (Exporter plugin doesn't preserve metadata) closed by melissa
fixed: (In [5254]) * ImageJ importer now populates OriginalMetadata. * OME-XML …
13:20 Changeset [5254] by melissa
* ImageJ importer now populates OriginalMetadata. * OME-XML and OME-TIFF …
12:30 Changeset [5253] by curtis
Add "formatlist" tool to Bio-Formats command line tools.
11:45 Ticket #406 (Split channels on export if there are 2 or >=4 16-bit RGB channels) created by melissa
While Bio-Formats is capable of reading and writing 16-bit images with …
11:28 Changeset [5252] by melissa
Fixed a couple of minor bugs and sped up isThisType.

07/13/09:

11:31 Changeset [5251] by melissa
Fix for ND2 files where the actual block sizes don't necessarily match the …
10:02 Changeset [5250] by melissa
* Fixed PhysicalSize* calculation for TIFF files. * If there is a file …
09:03 Changeset [5249] by melissa
Populate a Well element for every well in the plate, even if image data is …

07/12/09:

13:53 Changeset [5248] by melissa
Make sure that files beginning with '.' are not added to the …

07/11/09:

11:50 Changeset [5247] by melissa
Parse color for each channel and place it in ChannelComponent.ColorDomain.

07/10/09:

17:14 Changeset [5246] by curtis
* Fix problem where images with duplicate image windows (hopefully). * …
11:36 Changeset [5245] by curtis
Some debugging statements and tweaks.
11:22 Changeset [5244] by melissa
If the tag count is invalid, adjust it and print a debugging message …
04:44 Changeset [5243] by callan
Fixed companion file return values from getUsedFiles().

07/09/09:

22:41 Changeset [5242] by melissa
* Added plate barcode to Plate.Name * Fixed yet another file grouping …
17:28 Changeset [5241] by curtis
Use latest autogenerated bio-formats.h header file.
17:27 Changeset [5240] by curtis
Add autogenerator for Jace header files.
13:53 Changeset [5239] by melissa
Support alternate measurement directory structure.
13:44 Changeset [5238] by curtis
Change FLEX constant back to public (needed to query Flex IFDs outside of …
13:41 Changeset [5237] by curtis
Remove example of connectivity with old OME server.
13:40 Changeset [5236] by curtis
Simple example for extracting LensNA.
09:13 Changeset [5235] by melissa
* Use one reader per TIFF file (reduces plane access time). * Ignore …
06:13 Changeset [5234] by callan
Fixed LightSource LSID population.

07/08/09:

22:44 Changeset [5233] by melissa
Fixed div. by 0. If only one LightSource is referenced in the Flex XML, …
20:23 Changeset [5232] by callan
Fix metadata population for sparsly imaged plates.
18:07 Changeset [5231] by callan
Handle cases where well rows and/or columns are offset (ie. 0,0 is not the …
16:23 Changeset [5230] by melissa
Populate Objective.Immersion with the immersion medium, not the NA of the …
15:04 Changeset [5229] by melissa
Fixed various file grouping and MetadataStore population problems.
14:28 Changeset [5228] by curtis
Clean up flow cytometry values output.

07/07/09:

16:02 Changeset [5227] by melissa
Make sure that pixel type is initialized.
15:32 Changeset [5226] by curtis
Add "-nocore" command line option to suppress output of core metadata.
15:22 Changeset [5225] by curtis
Do not require measurement files to be present.
15:16 Changeset [5224] by melissa
Removed debugging statements.
15:15 Changeset [5223] by melissa
* Added .mea and .res files to getUsedFiles() list. * Fixed SPW …
14:03 Changeset [5222] by curtis
* Update comments in readers.txt; * Move JPEG2000 reader into section …
13:53 Changeset [5221] by melissa
Moved DicomReader to the end of the reader list.
10:04 Changeset [5220] by melissa
Fixed problems with new MIAS plate and cleaned up some of the file …
09:20 Changeset [5219] by melissa
Group Flex files in the same directory.

07/06/09:

20:33 Changeset [5218] by melissa
* Added 'String readString(String)' method to RandomAccessInputStream, …
14:42 Changeset [5217] by curtis
Update example programs to use new BufferedImageReader API.
14:20 Changeset [5216] by curtis
Bring list in line with packaging changes.
12:14 Changeset [5215] by melissa
Fixed compile error.
12:12 Changeset [5214] by melissa
Fixed line lengths.
11:39 Ticket #402 (Split original metadata fields into series-specific tables) closed by melissa
fixed: (In [5213]) * Series-specific metadata is now placed in the …
11:39 Changeset [5213] by melissa
* Series-specific metadata is now placed in the 'seriesMetadata' hashtable …
Note: See TracTimeline for information about the timeline view.