Timeline


and

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.

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.

04/13/09:

14:17 Changeset [4997] by melissa
Added preliminary support for ROIs to ZeissLSMReader; some ROI types are …
11:40 Changeset [4996] by curtis
Build hack to insert missing export symbol into Jace proxy Object header.

04/12/09:

17:30 Ticket #258 (Move Zip detection logic to ZipReader) closed by melissa
fixed: (In [4995]) * Moved logic for opening Zip, GZip and BZip2 streams from …
17:30 Changeset [4995] by melissa
* Moved logic for opening Zip, GZip and BZip2 streams from …
12:50 Ticket #373 (Writers do not preserve color lookup tables) closed by melissa
fixed: (In [4994]) APNGWriter now preserves the LUT associated with the first …
12:50 Changeset [4994] by melissa
APNGWriter now preserves the LUT associated with the first image that is …

04/10/09:

15:04 Changeset [4993] by melissa
TiffTools.writeImage now saves the LUT associated with the image being …
11:26 Changeset [4992] by curtis
Update URL of VisAD javadocs.
10:02 Changeset [4991] by melissa
Added logic to TiffReader that will attempt to read as much pixel data as …

04/09/09:

16:50 Changeset [4990] by curtis
When debugging, print a warning if next IFD offset is invalid.
16:21 Changeset [4989] by curtis
Respect "insane" debug setting in TIFF debugging output.
16:17 Changeset [4988] by curtis
Use FormatHandler debug flag to decide whether to dump TIFF debugging …
11:29 Changeset [4987] by melissa
Fixed Z/T axis swapping in ImagePro files.

04/08/09:

17:29 Ticket #376 (Add support for writing lossless JPEGs) created by melissa
Lossless JPEG allows for up to 16 bits per pixel; we should update …
17:00 Changeset [4986] by melissa
Some fixes for channel/series size calculation.

04/07/09:

20:46 Ticket #374 (Cannot construct int8 BufferedImages) closed by melissa
fixed: (In [4985]) Added SignedByteBuffer for use in constructing BufferedImages …
20:46 Changeset [4985] by melissa
Added SignedByteBuffer for use in constructing BufferedImages of type …
11:55 Changeset [4984] by melissa
Populate Plate.WellOriginX and Plate.WellOriginY.
10:48 Ticket #333 (Decide how to handle XZ and XT scans) closed by melissa
fixed: (In [4983]) Swap Y and Z if an XZ scan is encountered, or Y and T if an XT …
10:48 Changeset [4983] by melissa
Swap Y and Z if an XZ scan is encountered, or Y and T if an XT scan is …
09:21 Changeset [4982] by melissa
Make sure that the .mdb file is not a directory.
08:48 Changeset [4981] by melissa
Changed capitalization of getters/setters for Thumbnail.href.

04/06/09:

14:50 Changeset [4980] by melissa
* Added version constants to loci.formats.FormatTools, so that the version …
14:43 Changeset [4979] by curtis
Call close when finished reading the image planes.
13:25 Ticket #231 (Improve bfconvert) closed by melissa
fixed: (In [4978]) Allow bfconvert to save to multiple files; run bfconvert with …
13:25 Changeset [4978] by melissa
Allow bfconvert to save to multiple files; run bfconvert with no options …
13:17 Changeset [4977] by melissa
Fixed problem with writing images to an existing TIFF file.
10:25 Changeset [4976] by melissa
Throw a more informative exception if constituent TIFF/STK files are …
09:50 Changeset [4975] by melissa
Set Objective.Immersion to "Unknown" if the value in the file is null or …
09:49 Changeset [4974] by melissa
Fixed how SizeC is calculated if an AXIS_4 or AXIS_9 note is found.
08:07 Changeset [4973] by melissa
- Added new SPW attributes to MetadataStore/MetadataRetrieve: * …
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