Timeline


and

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 …
13:57 TracInstall edited by trac
(diff)
13:57 TracGuide edited by trac
(diff)
13:57 TracRss edited by trac
(diff)
13:57 TracRevisionLog edited by trac
(diff)
13:57 TracIni edited by trac
(diff)
13:57 TracTickets edited by trac
(diff)
13:57 TracFineGrainedPermissions edited by trac
(diff)
13:57 TracFastCgi edited by trac
(diff)
13:57 TracCgi edited by trac
(diff)
13:57 TracRoadmap edited by trac
(diff)
13:57 TracNavigation edited by trac
(diff)
13:57 TracBrowser edited by trac
(diff)
13:57 TracModWSGI created by trac
13:57 TracSupport edited by trac
(diff)
13:57 TracPermissions edited by trac
(diff)
13:57 WikiRestructuredTextLinks edited by trac
(diff)
13:57 TracReports edited by trac
(diff)
13:57 TracEnvironment edited by trac
(diff)
13:57 WikiProcessors edited by trac
(diff)
13:57 WikiMacros edited by trac
(diff)
13:57 TracStandalone edited by trac
(diff)
13:57 TracPlugins edited by trac
(diff)
13:57 WikiFormatting edited by trac
(diff)
13:57 TracUnicode edited by trac
(diff)
13:57 TracModPython edited by trac
(diff)
13:57 TracNotification edited by trac
(diff)
13:57 InterWiki edited by trac
(diff)
13:57 TracWorkflow edited by trac
(diff)
13:57 TracQuery edited by trac
(diff)
13:57 WikiRestructuredText edited by trac
(diff)
13:57 TracUpgrade edited by trac
(diff)
13:57 TracLinks edited by trac
(diff)
13:57 TracSyntaxColoring edited by trac
(diff)
13:57 TracAdmin edited by trac
(diff)
13:57 TracInterfaceCustomization edited by trac
(diff)
13:57 TracTicketsCustomFields edited by trac
(diff)
13:57 InterTrac edited by trac
(diff)
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.

04/24/09:

18:18 Changeset [5030] by curtis
Remove restriction where resolution needed to be square and a power of …
16:10 Ticket #387 (Behavior when overcropping is inconsistent) created by curtis
It is possible to "overcrop" by specifying an x,y,w,h larger than the size …
14:13 Changeset [5029] by melissa
Fixed ClassCastException and added lookup table support to ZeissZVIReader.
12:35 Ticket #386 (Add support for Leica OME data) created by melissa
"Leica OME" datasets contain an {LOME}MetaData.xml file, a set of TIFF …
10:12 Ticket #381 (Channel discrepancy when converting from indexed true color to OME-TIFF) closed by melissa
fixed: (In [5028]) Override get8BitLookupTable() and get16BitLookupTable(). …
10:12 Changeset [5028] by melissa
Override get8BitLookupTable() and get16BitLookupTable(). Closes #381.

04/23/09:

22:26 Ticket #379 (EOFException reading some LEI datasets) closed by melissa
fixed: Mostly fixed in r5027. An EOFException will still be thrown when …
22:22 Changeset [5027] by melissa
LeicaReader.initFile(String) no longer requires a constituent TIFF file to …
15:51 Ticket #385 (Generated OME-XML has an invalid DisplayOptions element) created by curtis
[…] It is not clear whether we should be using DisplayOptions at all, …
15:47 Ticket #349 (Fix known OME-XML validation errors) closed by curtis
fixed: Refiled to be more specific; see ticket #384.
15:46 Ticket #384 (Generated OME-XML should use proper namespaces where appropriate) created by curtis
In particular, CustomAttributes and SemanticTypeDefinitions elements need …
15:34 Changeset [5026] by curtis
Add reporting of false color to showinf.
15:16 Ticket #383 (Generated OME-TIFF files have elements in the wrong order) created by curtis
There are many cases, but for example, according to the OME-XML schema, …
15:10 Ticket #382 (Generated OME-TIFF files have invalid UUID elements) created by curtis
A TiffData element with a UUID child must include CDATA with a UUID string …
15:01 Ticket #381 (Channel discrepancy when converting from indexed true color to OME-TIFF) created by curtis
[…] If the -expand flag is used, then three non-indexed channels are …
14:56 Ticket #380 (Error converting some LEI files to OME-TIFF) created by curtis
[…]
14:54 Ticket #379 (EOFException reading some LEI datasets) created by curtis
[…]
13:05 Changeset [5025] by curtis
Fix showinf handling of -version flag.
11:34 Changeset [5024] by melissa
Make sure that all readers convert the exposure time to seconds before …
11:05 Changeset [5023] by melissa
Fixed compile error and corrected for the fact the Metamorph files store …
10:49 Changeset [5022] by melissa
Metamorph TIFF files now correctly populate PlaneTiming.ExposureTime.
10:30 Changeset [5021] by melissa
Escape backslashes when constructing an output file name.
10:17 Ticket #315 (Investigate how to handle ROIs and overlays within proprietary file ...) closed by melissa
fixed: (In [5020]) Added ROI support to NativeND2Reader. Closes #315.
10:17 Changeset [5020] by melissa
Added ROI support to NativeND2Reader. Closes #315.

04/22/09:

14:27 Changeset [5019] by melissa
Updated ZVI reader to support additional ROI types. See #315.

04/21/09:

15:33 Changeset [5018] by melissa
Reduced ZVI initialization time and updated the ZVI reader to parse data …
10:02 Changeset [5017] by melissa
Populate new Shape attributes and ROI transforms.
09:29 Changeset [5016] by melissa
Changed format name reported by JPEGWriter to match the name reported by …
09:28 Changeset [5015] by melissa
Added option to print the version information.

04/20/09:

17:28 Changeset [5014] by curtis
Fix readme to note that C++ bindings now compile on Windows.
13:58 Changeset [5013] by melissa
Added (experimental) font/color attributes for Shape to MetadataStore and …

04/17/09:

13:28 Changeset [5012] by melissa
Print a warning if the SizeX, SizeY, BigEndian, or PixelType values …
12:47 Changeset [5011] by melissa
Finished support for 3-point circles and ellipses.
09:48 Changeset [5010] by melissa
Make sure LogicalChannel.SamplesPerPixel matches the SamplesPerPixel …
08:45 Changeset [5009] by curtis
Cleaner token filtering.

04/16/09:

15:54 Changeset [5008] by curtis
If no lifetime or spectra sub-channel information is present, default to …
15:50 Changeset [5007] by curtis
If OME-XML and TIFF IFD SamplesPerPixel values do not match, use the TIFF …
09:42 Changeset [5006] by melissa
Fix for datasets in which the number of channels per timepoint is not …

04/15/09:

14:47 Changeset [5005] by curtis
Eliminate Slim Plotter's direct dependency on SDTReader.
10:12 Changeset [5004] by melissa
Use well row/column names in the image names.

04/14/09:

14:39 Changeset [5003] by melissa
Fixed compile error.
13:29 Changeset [5002] by melissa
Use image numbers indexed from 1 when creating artifical image names.
13:08 Ticket #378 (Change bfconvert to open/save byte arrays) created by melissa
Right now, bfconvert (loci.formats.tools.ImageConverter) opens and saves …
12:21 Ticket #377 (Some formats take a long time to initialize) created by melissa
Files in some formats - notably Slidebook and Zeiss ZVI - take a very long …
11:45 Changeset [5001] by curtis
Add a check to gen-meta-support to ensure omexml.version is set.
11:32 Changeset [5000] by curtis
Fix javadoc.
11:31 Changeset [4999] by curtis
Fix broken links.
08:14 Changeset [4998] by melissa
Better metadata population for Li-Cor .l2d datasets.
Note: See TracTimeline for information about the timeline view.