Timeline


and

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 …

07/04/09:

13:28 Changeset [5212] by melissa
Fixed compile error.
13:22 Changeset [5211] by melissa
Added very basic example of working with multiple files. Could use a …
12:51 Ticket #387 (Behavior when overcropping is inconsistent) closed by melissa
fixed: As of r5210, all readers throw an exception if the cropping parameters are …
12:51 Changeset [5210] by melissa
* Added getPlaneSize methods to FormatTools for returning the size of the …
10:59 Changeset [5209] by melissa
Updated stable version number.

07/03/09:

14:21 Changeset [5208] by curtis
Use IMetadata instead of casting between MetadataStore and …
13:43 Ticket #405 (OME-TIFF export erroneously reuses OME metadata from input dataset) created by curtis
The Bio-Formats Exporter plugin feeds the input dataset's OME-XML directly …
12:58 Changeset [5207] by curtis
Record all particles detected, not just ones in the last known positions.
10:27 Changeset [5206] by curtis
Disallow range specification and cropping when virtual stack is enabled.
09:05 Changeset [5205] by melissa
Prevent an exception if there is an open bracket without a matching …
08:07 Changeset [5204] by melissa
Added RoiLink methods to MetadataStore/MetadataRetrieve. These are not …
07:53 Changeset [5203] by melissa
Fixed Detector/DetectorSettings population, as only one detector is …

07/02/09:

11:51 Changeset [5202] by melissa
Fixed indices into planeMax, so getPlaneMaximum(int) returns the correct …

07/01/09:

12:31 Changeset [5201] by curtis
Add call to printTimingPerPlane.
12:23 Changeset [5200] by curtis
Example of timestamp extraction using Bio-Formats.
12:17 Ticket #400 (Remove IFormatReader.openImage in favor of BufferedImageReader class) closed by melissa
fixed: openImage was removed from IFormatReader in r5191.
12:07 Changeset [5199] by curtis
* Split ISO 8601 date format into a separate string constant. * Add …

06/30/09:

16:18 Changeset [5198] by curtis
Better exception message.
16:17 Changeset [5197] by curtis
Fix bug with infinite read loops at EOF.
15:17 Changeset [5196] by curtis
Remove reflection logic for loci.formats.gui.ImageViewer.
13:19 Changeset [5195] by melissa
Fixed problems that prevented reader-altering flags (-stitch, -merge, …
11:46 Changeset [5194] by melissa
Fixed DetectorSettings and PlaneTiming bugs.
10:16 Changeset [5193] by melissa
Reverted mosaic handling logic - mosaics are now stitched on import.
09:10 Ticket #404 (Exporter plugin doesn't preserve metadata) created by melissa
Original metadata (key/value pairs in the "Image Info" window) is not …
09:10 Ticket #403 (Buttons in importer series dialog are misaligned) created by melissa
If the series names are very short (i.e. the window is narrow), then the …

06/29/09:

20:41 Changeset [5192] by melissa
* Removed mosaic stitching logic. Each tile in the mosaic is now …
17:49 Changeset [5191] by curtis
Progress on elimination of AWT references from core Bio-Formats packages. …

06/27/09:

15:56 Changeset [5190] by callan
OME data model fixes: * Plate.Name is a required field * Image.ID needs …

06/26/09:

14:40 Changeset [5189] by curtis
First cut at hack workaround for problem on Windows with certain constants …
13:46 Changeset [5188] by melissa
* Added setDichroicID(String, int, int) to MetadataStore. * …

06/25/09:

21:43 Changeset [5187] by melissa
Lots of InCell updates, including support for .im pixels files and better …
17:44 Changeset [5186] by melissa
Fixed compile error.
17:24 Changeset [5185] by melissa
Initial version of MIAS reader.

06/24/09:

22:30 Changeset [5184] by curtis
Improvements to Bio-Formats ITK plugin: * Better handling of …
22:27 Changeset [5183] by curtis
Some minor improvements to the Boost detection logic.
22:21 Changeset [5182] by curtis
Fix bug in TIFF comment parsing.
14:31 Changeset [5181] by melissa
Minor cleanup; fixed exposure time units.
14:27 Changeset [5180] by melissa
DicomReader now respects isGroupFiles() when determining whether to group …

06/23/09:

15:24 Changeset [5179] by curtis
More improvements.
14:55 Changeset [5178] by melissa
Packbits decompression is now much faster.
14:41 Changeset [5177] by curtis
Use Boost_THREAD_LIBRARY_DEBUG instead of Boost_THREAD_LIBRARY.
14:07 Changeset [5176] by melissa
If there are missing planes, attempt to use TiffReader to determine how …
12:24 Changeset [5175] by melissa
* Several improvements to DICOM file grouping logic. * No longer apply …
09:55 Changeset [5174] by melissa
Adjust image count if an XZ or XT scan is found.

06/22/09:

11:48 Changeset [5173] by melissa
Fixed min/max calculation for signed images.
Note: See TracTimeline for information about the timeline view.