source: branches @ 6830

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Diff Rev Age Author Log Message
(edit) @6830   10 years curtis Maven version of flow-cytometry project.
(edit) @6829   10 years curtis Fix VisBio developer list.
(edit) @6828   10 years curtis Migrate miscellaneous utilities to Maven.
(edit) @6827   10 years curtis Convert slim-plotter to Maven project structure.
(edit) @6826   10 years melissa Backported dimension detection changes.
(edit) @6825   10 years curtis Add new projects to umbrella, and ignore target folders.
(edit) @6824   10 years curtis Progress on Mavenization, including ome-io and visbio projects.
(edit) @6822   10 years melissa Prevent extra (Logical)Channel objects from being populated.
(edit) @6821   10 years curtis Add temporary workaround for Jace bug when class names have underscores.
(edit) @6820   10 years curtis Add boot classpath to AutoProxy classpath.
(edit) @6818   10 years curtis Set main class appropriately in deps jar.
(edit) @6817   10 years curtis Fixed assembly for jar2lib-*-deps.jar.
(edit) @6815   10 years curtis Add assembly for creating jar2lib JAR with dependencies. Still buggy.
(edit) @6813   10 years curtis Temporary place to house bf-cpp-specific Jar2Lib files.
(edit) @6812   10 years melissa Reverse the order of the rows if a negative height was stored in the file. …
(edit) @6811   10 years curtis Better layout for static resources.
(edit) @6809   10 years curtis Working version of Jar2Lib.
(edit) @6808   10 years melissa If a negative width or height is stored, use the absolute value instead …
(edit) @6806   10 years curtis Initial version of Jar2Lib implementation.
(edit) @6803   10 years melissa Backported r6802 to 4.1 branch.
(edit) @6802   10 years melissa * Ignore missing L2D scans, instead of throwing an exception. * More …
(edit) @6800   10 years melissa Remove invalid characters from strings that will later be parsed into …
(edit) @6795   10 years curtis Backport r6792 to 4.2 branch.
(edit) @6794   10 years curtis Backport r6789 to 4.2 branch.
(edit) @6777   10 years curtis Fix problem with ij.jar dependency resolution.
(edit) @6776   10 years curtis First cut at Maven-based build system and directory layout for LOCI …
(edit) @6775   10 years curtis Experimental branch for Maven-based builds.
(edit) @6767   10 years melissa Fixed a couple of silly Photoshop bugs.
(edit) @6765   10 years melissa Only populate Objective.NominalMagnification if the magnification stored …
(edit) @6754   10 years melissa Fixed BGR correction when opening sub-images. See QA #2583.
(edit) @6753   10 years melissa Fixed saveBytes and savePlane implementations to use the correct image …
(edit) @6744   10 years melissa Force buffer reallocation if the previously allocated buffer is too small.
(edit) @6730   10 years melissa Merged r6729 into 4.2 branch.
(edit) @6710   10 years melissa * Fixed how ICS files with > 4 channels are read. * Fixed Channel …
(edit) @6707   10 years melissa Fixed problems with exporting multi-channel data.
(edit) @6706   10 years melissa Tweaked isThisType to automatically return false if the TIFF comment is an …
(edit) @6705   10 years melissa Fixed bytes per pixel calculation for RGB data.
(edit) @6699   10 years melissa Fixed pixel data offset.
(edit) @6694   10 years melissa Adjust SizeC internally when writing RGB OME-TIFF files. Closes #513.
(edit) @6693   10 years melissa Fixed ArrayIndexOutOfBoundsException when opening sub-images from 16- and …
(edit) @6691   10 years melissa Backported r6689 to 4.2 branch.
(edit) @6687   10 years melissa Fixed channel data is parsed from Leica LIF files that have had one or …
(edit) @6684   10 years melissa Updated what's new and switch trunk component version numbers to 5.0-DEV.
(edit) @6683   10 years curtis Backport r6682 to 4.2 branch.
(edit) @6681   10 years melissa Only populate Objective.NominalMagnification if the magnification is …
(edit) @6680   10 years curtis Backport r6679 to 4.2 branch.
(edit) @6678   10 years melissa Updated component version numbers in 4.2 branch.
(edit) @6677   10 years curtis Backport r6672,r6673,r6676 to 4.2 branch.
(edit) @6674   10 years melissa Fixed how Images are removed from a MetadataStore when exporting one …
(edit) @6669   10 years curtis Backport recent LOCI plugins progress to 4.2 branch.
(edit) @6667   10 years melissa * Updated undeclared namespace stripping logic to look for namespaces in …
(edit) @6666   10 years melissa Catch NullPointerException when attempting to parse OME-XML comments.
(edit) @6665   10 years melissa Only overwrite the dimensions if the new values are sane.
(edit) @6664   10 years melissa OMETiffReader.isThisType now checks whether or not the OME-XML block can …
(edit) @6663   10 years melissa Merged recent OME-XML and core Bio-Formats changes into the 4.2 branch.
(edit) @6635   10 years melissa Be more thorough when searching for the .dv file that matches a .log or …
(edit) @6631   10 years melissa Removed obsolete OME-XML model objects.
(edit) @6627   10 years melissa Switched TiffParser logging from 'debug' to 'trace'; see #512.
(edit) @6626   10 years curtis Backport r6625 to 4.2 branch.
(edit) @6615   10 years dscho Avoid "prefix <...> not bound" error when transforming XML When …
(edit) @6614   10 years dscho Fix OME-XML version discovery Some files (Huygens) have an xmlns:ome …
(edit) @6613   10 years melissa Merged r6602 to 4.2 branch.
(edit) @6611   10 years curtis Backport r6609,r6610 to 4.2 branch.
(edit) @6608   10 years curtis Backport r6606,r6607 to 4.2 branch.
(edit) @6605   10 years curtis Backport r6603,6604 to 4.2 branch.
(edit) @6599   10 years curtis Backport r6598 to 4.2 branch.
(edit) @6597   10 years melissa Better XZ/XT scan detection; see  omero:2321.
(edit) @6596   10 years curtis Backport r6595 to 4.2 branch.
(edit) @6593   10 years curtis Backport r6592 to 4.2 branch.
(edit) @6589   10 years curtis Backport r6588 to 4.2 branch.
(edit) @6586   10 years curtis Backport r6585 to 4.2 branch.
(edit) @6584   10 years curtis Backport recent bugfixes to 4.2 branch.
(edit) @6577   10 years melissa Merged r6576 to 4.2 branch.
(edit) @6573   10 years melissa Fixed GZIP pixel data detection for ICS files.
(edit) @6567   10 years melissa Fixed how pixels files are found, so that having multiple *.vws files in …
(edit) @6566   10 years melissa Tweaked pixel block detection to work with Slidebook 5.0.0.5 files.
(edit) @6564   10 years curtis Backport r6563 to 4.2 branch.
(edit) @6562   10 years curtis Backport indexed color fix to 4.2 branch.
(edit) @6559   10 years curtis Backport colorization fix for filled indices to 4.2 branch.
(edit) @6557   10 years curtis Backport 16-bit LUT fix to 4.2 branch.
(edit) @6555   10 years curtis Merge color mode progress to 4.2 branch.
(edit) @6553   10 years melissa Fixed a handful of core metadata and pixels offset bugs in Visitech …
(edit) @6534   10 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. …
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