Timeline


and

05/27/09:

20:07 Changeset [5128] by melissa
Instead of throwing an exception when .pty files are not found, print a …
14:56 Changeset [5127] by melissa
Added utility for printing a list of supported formats, courtesy of Dmitry …
13:17 Changeset [5126] by melissa
Eliminated java.awt.Point from format readers.
12:41 Changeset [5125] by melissa
Reverted type preservation changes from r5037. These changes caused major …

05/26/09:

18:19 Changeset [5124] by melissa
Fixed getUsedFiles bug.
16:14 Ticket #401 (Split TiffTools into multiple utility classes) created by curtis
The TiffTools class has grown very large, and contains functionality for …
16:12 Ticket #400 (Remove IFormatReader.openImage in favor of BufferedImageReader class) created by curtis
Any reference to AWT classes can cause problems on certain systems, …
16:09 Ticket #399 (Remove deprecated methods from AWTImageTools) created by curtis
For the next release of Bio-Formats, we should remove the old, deprecated …
16:07 Ticket #398 (Better support for N-dimensional data) created by curtis
Eliminate IFormatReader.getChannelDimTypes and …
15:57 Changeset [5123] by curtis
Whitespace.
15:56 Changeset [5122] by curtis
Add reminder to fix Eclipse dependency checking later.
13:58 Changeset [5121] by melissa
* Lots of cleanup in PerkinElmerReader. * Reworked the getUsedFiles …

05/25/09:

17:58 Changeset [5120] by melissa
Use unique keys in the metadata hashtable if there are multiple instances …
17:48 Ticket #397 (Add support for .nex file format) created by melissa
ICS files produced by the Nikon BioStation IMq system can have an …
17:18 Changeset [5119] by melissa
* Fixed IPW dimension order. * Some cleanup in ICSReader - fixes a few …

05/20/09:

05:55 Changeset [5118] by curtis
Progress on LOCI plugins preferences refactoring.
03:15 Changeset [5117] by melissa
Eliminate use of java.awt.Rectangle in loci.formats.TiffTools.

05/19/09:

05:26 Changeset [5116] by curtis
Fix proxy generation on non-Windows systems.
01:26 Changeset [5115] by curtis
Fix up Eclipse classpath dependencies. This new way uses "External …

05/18/09:

11:06 Changeset [5114] by melissa
More bug fixes.
11:03 Changeset [5113] by curtis
Respect "quiet" flag in a macro.

05/16/09:

10:27 Ticket #396 (Create bfsave.m script for MATLAB) created by curtis
We provide a bfopen.m script for opening image formats into MATLAB. We …

05/15/09:

08:45 Changeset [5112] by melissa
Various bug fixes.

05/14/09:

16:36 Changeset [5111] by curtis
Minor progress on LOCI plugins refactoring.
11:50 Ticket #395 (Support for non-numerical patterns in FilePattern) created by curtis
FilePattern currently supports only numerical blocks. It would be nice to …
09:58 Changeset [5110] by melissa
Fixed bug in parsing XML from a byte array.
09:52 Changeset [5109] by melissa
Various fixes for reading Metamorph datasets that contain an .nd file.
09:37 Changeset [5108] by melissa
Updated plugins.config to match plugin package structure.

05/13/09:

09:10 Changeset [5107] by curtis
Minor tweaks.

05/12/09:

18:11 Changeset [5106] by gbonamy
Merged with old 5101 revision
18:10 Changeset [5105] by gbonamy
Merged in R5083
16:51 Changeset [5104] by melissa
Fixed memory leaks in OpenlabReader, PictReader and FV1000Reader.
16:07 Ticket #257 (Improve RAUrl) closed by melissa
fixed: (In [5103]) Minor cleanup in common component and improvements to …
16:07 Changeset [5103] by melissa
Minor cleanup in common component and improvements to URLHandle. Closes …
14:41 Changeset [5102] by curtis
Fix problem with HandleExtraFileTypes calling Bio-Formats Importer.

05/11/09:

20:14 Changeset [5101] by gbonamy
Fixed bug. Only itterates over FLEX files
20:04 Changeset [5100] by gbonamy
Updated the comments
20:01 Ticket #394 (Flex file metadata objective extraction incorrect) created by gbonamy
The objective extraction is incorrect (cf. attached Flex Metadata …
10:48 Changeset [5099] by melissa
Fixed tile row/column calculation and ArrayIndexOutOfBoundsException in …

05/10/09:

10:12 Changeset [5098] by melissa
Don't populate more than getSeriesCount() Image elements.

05/08/09:

22:24 Changeset [5097] by gbonamy
Tool to extract Flex file XML.
11:11 Ticket #393 (openThumbImage throws an exception for int16 images) closed by melissa
fixed: (In [5096]) Allow int16 images to be scaled. Closes #393.
11:11 Changeset [5096] by melissa
Allow int16 images to be scaled. Closes #393.
09:13 Changeset [5095] by melissa
Only include log file in used files list if it exists.
07:46 Ticket #393 (openThumbImage throws an exception for int16 images) created by melissa
[…] produces this exception: […]
07:31 Changeset [5094] by melissa
Added getUsedFiles(boolean) to IFormatReader.
07:24 Changeset [5093] by curtis
Fix a bunch of Eclipse warnings.

05/07/09:

17:42 Changeset [5092] by curtis
Progress on LOCI plugins refactoring.
16:39 Changeset [5091] by curtis
Split out crazy reader stack duplication into handy API methods.
14:46 Ticket #390 (Bio-Formats Exporter plugin fails with virtual stacks) closed by melissa
fixed: (In [5090]) Fixed exporting from virtual stacks; closes #390.
14:46 Changeset [5090] by melissa
Fixed exporting from virtual stacks; closes #390.
13:43 Ticket #391 (Bio-Formats Exporter should use saveBytes instead of saveImage) closed by melissa
fixed: (In [5089]) Updated Exporter plugin to use saveBytes instead of saveImage. …
13:43 Changeset [5089] by melissa
Updated Exporter plugin to use saveBytes instead of saveImage. Closes …
13:39 Changeset [5088] by curtis
Remove executable flag from source file.
11:31 Ticket #392 (Endianness problem when exporting 16-bit ICS) closed by melissa
fixed: (In [5087]) Get the endianness from MetadataRetrieve, instead of assuming …
11:31 Changeset [5087] by melissa
Get the endianness from MetadataRetrieve, instead of assuming that the …

05/06/09:

18:24 Ticket #392 (Endianness problem when exporting 16-bit ICS) created by curtis
ICS files written by Bio-Formats may have their endianness reversed. For …
18:19 Ticket #391 (Bio-Formats Exporter should use saveBytes instead of saveImage) created by curtis
The Bio-Formats Exporter plugin extracts arrays from ImageJ …
18:19 Ticket #390 (Bio-Formats Exporter plugin fails with virtual stacks) created by curtis
When trying to export a dataset imported with the "Use virtual stack" …
17:29 Changeset [5086] by curtis
Fix reflection problem with virtual stacks.
15:44 Changeset [5085] by gbonamy
Modification to parse number of channels / series /etc. correction.
13:42 Ticket #389 (Add support for BD Pathway datasets) created by melissa
Example data is in bd-pathway/. These datasets appear to be a collection …
11:13 Changeset [5084] by melissa
Minor fixes to SizeC and SizeT calculation.
10:49 Changeset [5083] by melissa
Cleaned up ExtractFlexMetadata utility.
09:43 Changeset [5082] by melissa
Return channels in the order in which they appear in the file, instead of …
08:02 Changeset [5081] by melissa
Fixed how ConvertToOmeTiff handles multi-series files.

05/05/09:

19:15 Changeset [5080] by gbonamy
Tool to extract the FLEX file metadata
16:10 Changeset [5079] by melissa
If an STK was passed to MetamorphReader, check for an .nd file in the same …
14:07 Ticket #375 (Cannot construct uint32 BufferedImages) closed by melissa
fixed: (In [5078]) Added UnsignedIntBuffer and UnsignedIntColorModel to …
14:07 Changeset [5078] by melissa
Added UnsignedIntBuffer and UnsignedIntColorModel to facilitate unsigned …
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13:14 Changeset [5077] by melissa
Fixed ArrayIndexOutOfBoundsException when opening subimages with …
11:32 Changeset [5076] by melissa
Updated Bio-Formats component to require Java 1.5. Fixes compile errors …

05/04/09:

19:22 Ticket #388 (Flex file metadata extraction) closed by gbonamy
fixed: This bug was fixed.
19:22 Changeset [5075] by gbonamy
Ticket #388 fix. Generate correctly the number of channels. Verify the …
19:14 Changeset [5074] by gbonamy
Takes into consideration the number of series
18:43 Changeset [5073] by gbonamy
Small modifs Included Data Compression set (commented out).
18:20 Ticket #388 (Flex file metadata extraction) created by gbonamy
I have found the reason why the metadata is not correctly extracted from …
14:04 Changeset [5072] by melissa
* Allow IniParser to read resources from packages outside of loci.common. …
14:01 Ticket #313 (Improve Slidebook metadata) closed by melissa
fixed: (In [5071]) Improvements to metadata support; closes #313.
14:01 Changeset [5071] by melissa
Improvements to metadata support; closes #313.
10:07 Changeset [5070] by melissa
More robust axis size detection for Metamorph STK/TIFF files.

05/03/09:

18:35 Changeset [5069] by gbonamy
Updating JRE compliance to 1.5
18:35 Changeset [5068] by gbonamy
Updating JRE compliance to 1.5
18:35 Changeset [5067] by gbonamy
Updating JRE compliance to 1.5
18:34 Changeset [5066] by gbonamy
Updating JRE compliance to 1.5
18:34 Changeset [5065] by gbonamy
Updating JRE compliance to 1.5

05/02/09:

21:20 Changeset [5064] by melissa
Fixed file index calculation.

05/01/09:

15:59 Changeset [5063] by curtis
Fix long lines.
14:55 Changeset [5062] by curtis
Fix problem with file paths starting with dot slash.
14:42 Changeset [5061] by melissa
Separate thumbnail IFDs from regular IFDs.
14:03 Changeset [5060] by melissa
MinimumWriter now populates LogicalChannel.SamplesPerPixel.
13:59 Changeset [5059] by curtis
* Rename RandomAccessStream to RandomAccessInputStream, and RA* …
13:51 Changeset [5058] by melissa
Fixed lookup table indices.
12:45 Ticket #378 (Change bfconvert to open/save byte arrays) closed by melissa
fixed: (In [5057]) * Updated writers to use saveBytes by default. * Updated …
12:44 Changeset [5057] by melissa
* Updated writers to use saveBytes by default. * Updated ImageConverter …
11:32 Changeset [5056] by melissa
Changed behavior of ClassList constructor so that a ClassList can be …

04/30/09:

17:59 Changeset [5055] by curtis
* Perform a standard check for minimum necessary metadata for writing. * …
16:02 Changeset [5054] by curtis
* Update package references for loci.plugins. * Uncomment working byte …
12:02 Changeset [5053] by curtis
Add package statements for LOCI plugins subpackages.

04/29/09:

18:03 Changeset [5052] by curtis
Fix bug with Export when curve fitting is disabled.
17:46 Changeset [5051] by curtis
Fix bugs with "None" fit option, and set to default when bin count is low.
17:00 Changeset [5050] by curtis
Fix ArrayIndexOutOfBoundsException with test_greys.lif.
16:56 Changeset [5049] by curtis
Update to ImageJ v1.42n.
16:56 Changeset [5048] by curtis
Add new ImageProcessor method required by recent versions of ImageJ.
16:55 Changeset [5047] by curtis
Clean up debugging statements.
16:55 Changeset [5046] by curtis
Check for Forms library, which is required now.
16:55 Changeset [5045] by curtis
Tweak online help.
16:25 Changeset [5044] by curtis
Add some debugging statements when ImageJ debug mode is set.
15:53 Changeset [5043] by curtis
* Begin code cleanup for LOCI plugins. * Disable deprecation warnings …
10:53 Changeset [5042] by melissa
When retrieving a primitive type array from an IFD, cast the next largest …
10:30 Changeset [5041] by melissa
Improved isThisType(RandomAccessStream) to allow extensionless ZVI files …
10:25 Changeset [5040] by melissa
Added '-map' option to bfconvert.
08:01 Changeset [5039] by melissa
Prevent TIFFs without OME-XML comment from being detected as OME-TIFF and …

04/28/09:

15:11 Changeset [5038] by melissa
Added various checks to ensure that openBytes doesn't try to read a plane …
13:15 Changeset [5037] by melissa
When writing an IFD, try to preserve each value's type (e.g. don't convert …
12:18 Ticket #380 (Error converting some LEI files to OME-TIFF) closed by melissa
fixed: (In [5036]) Fix for reading/writing an OME-TIFF dataset that doesn't …
12:18 Changeset [5036] by melissa
Fix for reading/writing an OME-TIFF dataset that doesn't contain pixel …
11:13 Changeset [5035] by melissa
* Added 'warning' flag to StatusEvent. * Added 'void warn(String)' method …

04/27/09:

14:04 Changeset [5034] by melissa
Remove padding bytes from images whose width is not a multiple of 4.
12:36 Changeset [5033] by melissa
Updated stack slicer to handle CompositeImages.
11:40 Changeset [5032] by melissa
Fixed how Zeiss ZVI lookup tables are created; fixed problems with …
09:02 Changeset [5031] by melissa
Prevent ClassCastException if the UIC3 tag is a single TiffRational.
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