source: trunk @ 5588

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(edit) @5588   11 years curtis * Better separation of Jace and bf-cpp components. * Draft of …
(edit) @5587   11 years curtis Finish transition of readers from openImage to openData.
(edit) @5586   11 years melissa Updated docs to reflect status of XML validation tests.
(edit) @5585   11 years curtis Better QTJava logic in case of Mac OS X with 64-bit JVM.
(edit) @5584   11 years melissa Fixed name mapping on Windows. Closes #419.
(edit) @5583   11 years melissa Fixed compile error.
(edit) @5582   11 years melissa Throw MissingLibraryException instead of NPE if jai-imageio.jar is not in …
(edit) @5581   11 years melissa Split MaskPixels.BinData parsing into separate method, which can be called …
(edit) @5580   11 years melissa Fixed bit reading problem in Huffman codec. Closes #415.
(edit) @5579   11 years melissa Modify the input dataset's OME-XML before exporting. Closes #405.
(edit) @5578   11 years melissa Correct for incorrectly calculated dimensions.
(edit) @5577   11 years melissa More descriptive series names.
(edit) @5576   11 years melissa Split 16-bit RGB images before saving to a TIFF file. Closes #406.
(edit) @5575   11 years melissa * Allow writers to specify supported pixel types by codec. * Fixed a few …
(edit) @5574   11 years melissa Added Olympus ScanR reader. Closes #411.
(edit) @5573   11 years melissa Better transmission Detector population.
(edit) @5572   11 years melissa Link Lasers to LogicalChannels in the same way that Detectors and Filters …
(edit) @5571   11 years melissa Prevent null values from being passed to MetadataStore setters.
(edit) @5570   11 years melissa More fixes to Detector/Filter linkages.
(edit) @5569   11 years curtis Add MissingLibraryException to C++ header.
(edit) @5568   11 years curtis Fix gen-bf-cpp problem on Windows.
(edit) @5567   11 years melissa Fixed emission filter linkages.
(edit) @5566   11 years melissa Fixed duplicate channel names.
(edit) @5565   11 years melissa MIAS reader now respects isMetadataCollected().
(edit) @5564   11 years melissa * Moved getDomains(String) to getPossibleDomains(String). * Added …
(edit) @5563   11 years melissa Fixed channel ordering and transmittance range population bugs.
(edit) @5562   11 years melissa Verify that all variables are cleared when close(false) is called.
(edit) @5561   11 years melissa Added a bunch of debugging statements.
(edit) @5560   11 years melissa Fixed behavior of getSeriesUsedFiles(true) for single-file Metamorph …
(edit) @5559   11 years callan Attempt to fix race condition when working with LSM files in multiple …
(edit) @5558   11 years melissa More fixes for Detector/Filter/LogicalChannel linkages and wavelength …
(edit) @5557   11 years melissa * Fixed regression with opening indexed color images in ImageJ. * Changed …
(edit) @5556   11 years melissa Fixed last round of Detector and Filter linkage problems.
(edit) @5555   11 years melissa * Added status messages to colorizer plugin. * Faster channel merging for …
(edit) @5554   11 years callan Allow access to the IFormatReader member variable from the …
(edit) @5553   11 years melissa Fixed a couple of core metadata bugs.
(edit) @5552   11 years curtis Add subclass of FormatException for missing libraries.
(edit) @5551   11 years curtis Fix up Ant build system; add OSGi bundle export to JAR production.
(edit) @5550   11 years melissa * Better bounds checking in FlexReader.getSeriesUsedFiles. * Fixed a few …
(edit) @5549   11 years melissa Fixed getUsedFiles() omissions.
(edit) @5548   11 years melissa * Added enumeration checking to OME-XML MetadataStore implementations. * …
(edit) @5547   11 years melissa Fixed thumbnail scaling for signed images.
(edit) @5546   11 years melissa Fixed type checking when an absolute path is used.
(edit) @5545   11 years melissa Set Detector.Type to PMT when appropriate.
(edit) @5544   11 years melissa Better type checking for .cfg files.
(edit) @5543   11 years melissa Add thumbnail TIFFs to used file list.
(edit) @5542   11 years melissa * Changed signatures of MetadataStore.setMaskPixelsBinData and …
(edit) @5541   11 years melissa Use value of MultiBand.Channel to link Filters and LogicalChannels.
(edit) @5540   11 years melissa A few tweaks to Detector and Laser population/linkage.
(edit) @5539   11 years melissa Fixed node caching problem.
(edit) @5538   11 years melissa One more fix for sequential LEI data.
(edit) @5537   11 years melissa Fixed Detector and Filter linkages for sequential scan data.
(edit) @5536   11 years melissa Use separate readers for the input file and converted files.
(edit) @5535   11 years melissa * Removed most calls to MetadataStore.setDisplayOptions* * Make sure that …
(edit) @5534   11 years curtis Update Eclipse JARs and remove a couple of unused imports.
(edit) @5533   11 years curtis Better way of doing OME-XML validation hack.
(edit) @5532   11 years melissa A couple of Quicktime conversion and test suite fixes.
(edit) @5531   11 years melissa * Allow test-convert target to be run on a directory, in addition to …
(edit) @5530   11 years curtis Add hack to suppress BinData/TiffData validation errors.
(edit) @5529   11 years curtis Working version of OME-XML reordering stylesheet, plus other validation …
(edit) @5528   11 years melissa * Added NetCDF dependencies to Bio-Formats runtime classpath. * Only allow …
(edit) @5527   11 years curtis Some tweaks to the bit logic.
(edit) @5526   11 years curtis Fixes to Bio-Formats OME-XML reordering stylesheet. But still has issues.
(edit) @5525   11 years curtis Revert unknown file format message, in case anyone was relying on it.
(edit) @5524   11 years curtis New FormatException subclass specifically for files in an unknown format.
(edit) @5523   11 years melissa Lots of findbugs fixes.
(edit) @5522   11 years curtis Minor clean up and argument checking.
(edit) @5521   11 years melissa More changes to ensure that all of the metadata is placed in the metadata …
(edit) @5520   11 years melissa * Leica LIF metadata validation fixes. * Fixed a few problems exposed by …
(edit) @5519   11 years melissa Avoid setting null Detector properties.
(edit) @5518   11 years melissa * Added PrintDomains to loci.formats.tools. * Better checks for very large …
(edit) @5517   11 years melissa Added two new methods to IFormatReader: boolean isSingleFile(String) …
(edit) @5516   11 years melissa Work-around for the case when TiffData.FileName is present, but the file …
(edit) @5515   11 years melissa One more fix for multi-Z/multi-T datasets with more than 4 channels.
(edit) @5514   11 years melissa * Revert to populating LogicalChannel.Name and Filter data using the …
(edit) @5513   11 years curtis Small tweaks.
(edit) @5512   11 years curtis Tweak include statement.
(edit) @5511   11 years melissa * Added support for new metadata blocks. * Only link a Filter to a …
(edit) @5510   11 years melissa * LogicalChannel.SecondaryEmissionFilter is now populated * Tweaked the …
(edit) @5509   11 years melissa More metadata fixes.
(edit) @5508   11 years curtis Remove obsolete OMERO JARs; fix tools-ome target.
(edit) @5507   11 years melissa Return blank planes if files were removed from the dataset.
(edit) @5506   11 years melissa Fixed bug that prevented token replacement from occurring if …
(edit) @5505   11 years curtis Fix test suite dependencies in Ant targets.
(edit) @5504   11 years curtis Add package statement for LOCI Common library.
(edit) @5503   11 years curtis Fix test suite build path.
(edit) @5502   11 years melissa Ant should now replace "@release.version@" in source files with "trunk" or …
(edit) @5501   11 years curtis Some work on OmeroReader implementation of IFormatReader, for OMERO 4.0.x.
(edit) @5500   11 years curtis Add compilation instructions for Windows.
(edit) @5499   11 years melissa Added logic to handle ICS files produced by Lambert Instruments software.
(edit) @5498   11 years melissa * Removed incorrect population of DetectorSettings.ReadOutRate. * Link …
(edit) @5497   11 years melissa Lots of work on Instrument, LogicalChannel, and ROI metadata for Leica …
(edit) @5496   11 years curtis Findbugs target should not clean the build. :-P
(edit) @5495   11 years curtis Fix toplevel Findbugs target.
(edit) @5494   11 years melissa Fixed Zeiss LSM endianness bug.
(edit) @5493   11 years melissa A few more fixes to Zeiss LSM, Leica LEI, and Olympus FV1000 metadata …
(edit) @5492   11 years melissa * Removed channel reordering logic. * Fixed channel naming and …
(edit) @5491   11 years melissa Fixed LogicalChannel, Detector, and Filter population.
(edit) @5490   11 years curtis Combine MetadataStore and MetadataRetrieve Ice interfaces into one …
(edit) @5489   11 years melissa * Parse Mask ROIs from MIAS overlay TIFFs. * Fixed a bug in Base64 …
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