source: branches/4.2 @ 6902

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Diff Rev Age Author Log Message
(edit) @6887   9 years melissa Backported r6839, r6840, and r6841 to 4.2.
(edit) @6856   9 years melissa Fixed sub-image reading for SimplePCI files that contain embedded TIFFs.
(edit) @6843   9 years melissa Removed check that prevented multi-file OME-TIFF export from working.
(edit) @6836   9 years melissa Fixed Image indexed passed to …
(edit) @6834   9 years melissa Moved MetadataStore calls that depend on MetadataTools.populatePixels(...) …
(edit) @6822   9 years melissa Prevent extra (Logical)Channel objects from being populated.
(edit) @6812   9 years melissa Reverse the order of the rows if a negative height was stored in the file. …
(edit) @6808   9 years melissa If a negative width or height is stored, use the absolute value instead …
(edit) @6802   9 years melissa * Ignore missing L2D scans, instead of throwing an exception. * More …
(edit) @6800   9 years melissa Remove invalid characters from strings that will later be parsed into …
(edit) @6795   9 years curtis Backport r6792 to 4.2 branch.
(edit) @6794   9 years curtis Backport r6789 to 4.2 branch.
(edit) @6767   9 years melissa Fixed a couple of silly Photoshop bugs.
(edit) @6765   9 years melissa Only populate Objective.NominalMagnification if the magnification stored …
(edit) @6754   9 years melissa Fixed BGR correction when opening sub-images. See QA #2583.
(edit) @6753   9 years melissa Fixed saveBytes and savePlane implementations to use the correct image …
(edit) @6744   9 years melissa Force buffer reallocation if the previously allocated buffer is too small.
(edit) @6730   9 years melissa Merged r6729 into 4.2 branch.
(edit) @6710   9 years melissa * Fixed how ICS files with > 4 channels are read. * Fixed Channel …
(edit) @6707   9 years melissa Fixed problems with exporting multi-channel data.
(edit) @6706   9 years melissa Tweaked isThisType to automatically return false if the TIFF comment is an …
(edit) @6705   9 years melissa Fixed bytes per pixel calculation for RGB data.
(edit) @6699   9 years melissa Fixed pixel data offset.
(edit) @6694   9 years melissa Adjust SizeC internally when writing RGB OME-TIFF files. Closes #513.
(edit) @6693   9 years melissa Fixed ArrayIndexOutOfBoundsException when opening sub-images from 16- and …
(edit) @6691   9 years melissa Backported r6689 to 4.2 branch.
(edit) @6687   9 years melissa Fixed channel data is parsed from Leica LIF files that have had one or …
(edit) @6684   9 years melissa Updated what's new and switch trunk component version numbers to 5.0-DEV.
(edit) @6683   9 years curtis Backport r6682 to 4.2 branch.
(edit) @6681   9 years melissa Only populate Objective.NominalMagnification if the magnification is …
(edit) @6680   9 years curtis Backport r6679 to 4.2 branch.
(edit) @6678   9 years melissa Updated component version numbers in 4.2 branch.
(edit) @6677   9 years curtis Backport r6672,r6673,r6676 to 4.2 branch.
(edit) @6674   9 years melissa Fixed how Images are removed from a MetadataStore when exporting one …
(edit) @6669   9 years curtis Backport recent LOCI plugins progress to 4.2 branch.
(edit) @6667   9 years melissa * Updated undeclared namespace stripping logic to look for namespaces in …
(edit) @6666   9 years melissa Catch NullPointerException when attempting to parse OME-XML comments.
(edit) @6665   9 years melissa Only overwrite the dimensions if the new values are sane.
(edit) @6664   9 years melissa OMETiffReader.isThisType now checks whether or not the OME-XML block can …
(edit) @6663   9 years melissa Merged recent OME-XML and core Bio-Formats changes into the 4.2 branch.
(edit) @6635   9 years melissa Be more thorough when searching for the .dv file that matches a .log or …
(edit) @6631   9 years melissa Removed obsolete OME-XML model objects.
(edit) @6627   9 years melissa Switched TiffParser logging from 'debug' to 'trace'; see #512.
(edit) @6626   9 years curtis Backport r6625 to 4.2 branch.
(edit) @6615   9 years dscho Avoid "prefix <...> not bound" error when transforming XML When …
(edit) @6614   9 years dscho Fix OME-XML version discovery Some files (Huygens) have an xmlns:ome …
(edit) @6613   9 years melissa Merged r6602 to 4.2 branch.
(edit) @6611   9 years curtis Backport r6609,r6610 to 4.2 branch.
(edit) @6608   9 years curtis Backport r6606,r6607 to 4.2 branch.
(edit) @6605   9 years curtis Backport r6603,6604 to 4.2 branch.
(edit) @6599   9 years curtis Backport r6598 to 4.2 branch.
(edit) @6597   9 years melissa Better XZ/XT scan detection; see  omero:2321.
(edit) @6596   9 years curtis Backport r6595 to 4.2 branch.
(edit) @6593   9 years curtis Backport r6592 to 4.2 branch.
(edit) @6589   9 years curtis Backport r6588 to 4.2 branch.
(edit) @6586   9 years curtis Backport r6585 to 4.2 branch.
(edit) @6584   9 years curtis Backport recent bugfixes to 4.2 branch.
(edit) @6577   9 years melissa Merged r6576 to 4.2 branch.
(edit) @6573   9 years melissa Fixed GZIP pixel data detection for ICS files.
(edit) @6567   9 years melissa Fixed how pixels files are found, so that having multiple *.vws files in …
(edit) @6566   9 years melissa Tweaked pixel block detection to work with Slidebook 5.0.0.5 files.
(edit) @6564   9 years curtis Backport r6563 to 4.2 branch.
(edit) @6562   9 years curtis Backport indexed color fix to 4.2 branch.
(edit) @6559   9 years curtis Backport colorization fix for filled indices to 4.2 branch.
(edit) @6557   9 years curtis Backport 16-bit LUT fix to 4.2 branch.
(edit) @6555   9 years curtis Merge color mode progress to 4.2 branch.
(edit) @6553   9 years melissa Fixed a handful of core metadata and pixels offset bugs in Visitech …
(edit) @6534   9 years melissa Fixed a few issues with 16-bit LUTs.
(edit) @6527   10 years melissa Tweaked Metamorph reader's type detection so that TIFFs are not …
(edit) @6526   10 years melissa Fixed Detector indices so that Detectors are properly populated and linked …
(edit) @6525   10 years melissa Merged r6520 to 4.2.
(edit) @6524   10 years melissa Merged r6521 and a bunch of ImageJ plugin changes to 4.2.
(edit) @6523   10 years curtis Backport Stack Slicer macro fix to 4.2 branch.
(edit) @6517   10 years melissa Fixed scan-deps.pl warnings.
(edit) @6516   10 years melissa Eliminated several deprecation warnings.
(edit) @6515   10 years melissa Allow Metamorph reader to pick up TIFF files.
(edit) @6514   10 years melissa Javadoc tweaks.
(edit) @6509   10 years melissa Adjust strip offsets if 32-bit signed values are being used in > 2 GB …
(edit) @6508   10 years melissa * Added basic TIFF tile export. Closes #413. * Throw an exception in …
(edit) @6507   10 years melissa Couple of minor reader fixes.
(edit) @6505   10 years melissa Added missing header file for OME-XML component.
(edit) @6504   10 years melissa Finished adding Xalan dependency.
(edit) @6503   10 years melissa Fixed XZ/XT scans to display as they do in Olympus' software.
(edit) @6501   10 years melissa Tweaked isThisType to only pick up valid TIFF files that are in the same …
(edit) @6500   10 years melissa Apply one LUT to each channel if the original file contains its own LUTs. …
(edit) @6497   10 years melissa Throw an exception if ImageProcessor types don't match.
(edit) @6496   10 years melissa Updated bf-cpp to compile with latest ome.xml.* and loci.formats.meta.* …
(edit) @6495   10 years melissa Updated email address.
(edit) @6494   10 years melissa Added support for multi-file OME-TIFF export. Closes #485.
(edit) @6492   10 years melissa Fixed Channel indices in MetadataTools.verifyMinimumPopulated.
(edit) @6491   10 years melissa Updated MetadataTools.verifyMinimumPopulated and the MinimumWriter example …
(edit) @6490   10 years melissa Added TextReader to 4.2 branch.
(edit) @6489   10 years melissa Fixed Nikon tag parsing.
(edit) @6487   10 years melissa Minor fixes to make metadata level tests pass.
(edit) @6486   10 years melissa Make sure that CoreMetadata.indexed is set correctly, regardless of the …
(edit) @6485   10 years melissa Updated metadata level tests to check for isIndexed mismatches. See #496.
(edit) @6484   10 years melissa Updated Channel -> Laser linkage rule in accordance with r6076.
(edit) @6483   10 years melissa Populate Laser.Model, if present. See  omero:2475.
(edit) @6482   10 years melissa Fixed min calculation for cropped planes. See  imagej:59.
(edit) @6479   10 years curtis Merge 'Standard ImageJ' bugfix to 4.2
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