source: trunk/components/bio-formats/src @ 6606

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Diff Rev Age Author Log Message
(edit) @6606   10 years curtis Fix bug with fake data generation when rgbChannelCount>1.
(edit) @6602   10 years melissa Throw a nicer exception if LuraWaveServiceImpl is instantiated with …
(edit) @6601   10 years melissa Added 'unknown' domain and updated various readers to use the unknown …
(edit) @6600   10 years melissa Fixed and uncommented most of the AnnotationRef conversion logic (and a …
(edit) @6597   10 years melissa Better XZ/XT scan detection; see  omero:2321.
(edit) @6582   10 years callan Re-run of code generation; fixes UUID population in OMEXMLMetadataImpl. …
(edit) @6576   10 years melissa Added experimental support for an alternate JPEG-2000 compression code.
(edit) @6573   10 years melissa Fixed GZIP pixel data detection for ICS files.
(edit) @6570   10 years curtis Minor tweaks.
(edit) @6568   10 years melissa Various fixes to OME-XML/OME-TIFF handling, including support for …
(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) @6565   10 years callan Fixing constructor of OMEXMLMetadataImpl
(edit) @6561   10 years curtis Do not fill indices for true color data if LUT is compatible with ImageJ.
(edit) @6556   10 years curtis Fix problem with signed LUT indices.
(edit) @6554   10 years curtis Progress on proper handling of color modes.
(edit) @6553   10 years melissa Fixed a handful of core metadata and pixels offset bugs in Visitech …
(edit) @6551   10 years callan Updating stylesheets. ( ome-xml:r640)
(edit) @6549   10 years callan More verbose tracing to track problems with stylesheet transforms.
(edit) @6548   10 years callan Moving transformed XML logging dump to the TRACE level.
(edit) @6545   10 years curtis For indexed color fake data, return a different LUT for each channel.
(edit) @6544   10 years melissa Reverting r6536, as r6543 fixes the underlying problems in ListAnnotation.
(edit) @6540   10 years callan Support for 2010-06 schema translation.
(edit) @6538   10 years callan Updating stylesheets from  ome-xml:r635.
(edit) @6536   10 years melissa Temporarily commented out ListAnnotationRef population.
(edit) @6534   10 years melissa Fixed a few issues with 16-bit LUTs.
(edit) @6531   10 years callan Re-run of code generation; working copy schema. Huge merge. (See …
(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) @6520   10 years curtis Remove dependency on OME Notes, in favor of loci.formats.gui.XMLWindow. …
(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) @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) @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) @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) @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) @6473   10 years curtis Clarify and expound on some TODOs.
(edit) @6465   10 years melissa Added some debugging statements so that missing TIFF files are reported. …
(edit) @6463   10 years melissa Don't attempt to read IFDs with offsets beyond the end of the file.
(edit) @6461   10 years melissa Fixed well ordering bug, courtesy of Rubén Muñoz.
(edit) @6459   10 years melissa Synced up export/MetadataConverter fixes between trunk and 4.2. OME-TIFF …
(edit) @6458   10 years melissa Moved ome.xml.r201004.* to ome.xml.model.* in trunk.
(edit) @6452   10 years callan Ensure that Pixels LSIDs are created uniquely.
(edit) @6451   10 years callan Need fileLength parsed in parseSeriesTag() for parseImageTag() to be …
(edit) @6448   10 years curtis Remove obsolete, commented-out code.
(edit) @6446   10 years curtis Remove debugging statements.
(edit) @6445   10 years curtis Fix getCoreMetadata with ReaderWrapper implementations.
(edit) @6443   10 years curtis Fix TextReader.openBytes to work properly.
(edit) @6440   10 years callan Fixing issues with endianness parsing for OME-TIFFs. Re-run of code …
(edit) @6437   10 years curtis Add scaleFactor option to FakeReader for scaling gradient pixel values.
(edit) @6430   10 years melissa * Updated OMEXMLMetadataImpl based on  ome-xml:r618. * Fixed a bunch of …
(edit) @6428   10 years callan Reverting r6427.
(edit) @6427   10 years callan Added missing "continue". (See  omero:#2467 and r6424)
(edit) @6426   10 years melissa Fixed various metadata population bugs in the FV1000 reader. See …
(edit) @6425   10 years callan Update of stylesheets ( ome-xml:r617).
(edit) @6422   10 years curtis Fix more problems with ChannelFiller (some self-inflicted). Seems to work …
(edit) @6419   10 years curtis Fix bugs in FakeReader with indexed color.
(edit) @6418   10 years curtis Fix problems with ChannelFiller when lookup table color component count != …
(edit) @6417   10 years curtis Flesh out the IFormatReader javadoc a bit.
(edit) @6416   10 years melissa Fixed physical size Z scaling.
(edit) @6414   10 years callan Fixed some further NPEs when reading OME-TIFF files with no UUID objects.
(edit) @6413   10 years callan General cleanup for metadata classes. Moved and overhauled ome.xml test …
(edit) @6409   10 years melissa Several fixes to Leica LEI, ND2, and Perkin Elmer readers.
(edit) @6407   10 years curtis Temporary(?) hack to speed up text file reading.
(edit) @6406   10 years melissa Updated several TIFF-based readers to populate Image.Description more …
(edit) @6405   10 years melissa Fixed Detector/DetectorSettings population to correspond to what the …
(edit) @6404   10 years melissa Trim the image name before placing it in the original metadata hashtable. …
(edit) @6399   10 years callan Initializing filenames and roiFilenames on close() in FV1000Reader.
(edit) @6398   10 years callan Ensure that Image names are populated for Leica LEI when …
(edit) @6397   10 years curtis Add reader for tabular text data.
(edit) @6395   10 years melissa Read tags into a byte array, so that non-String tags are preserved. See …
(edit) @6392   10 years melissa Fixed LUT ordering bug. See  omero:2438.
(edit) @6389   10 years melissa Prevent each EmissionFilterRef from being populated multiple times.
(edit) @6388   10 years melissa Fixed a bunch of Leica LIF metadata population bugs.
(edit) @6383   10 years melissa Make sure that references get resolved before dumping OME-XML; otherwise, …
(edit) @6381   10 years melissa Fixed bug in file renaming logic.
(edit) @6378   10 years melissa Tweaked MetamorphReader.isThisType so that Prairie TIFFs are not picked …
(edit) @6377   10 years melissa Merged r6376 back to trunk.
(edit) @6373   10 years callan Removed another location of the same problem resolved with r6372.
(edit) @6372   10 years callan Passing the metadata store down to planar TIFF reader causes metadata …
(edit) @6371   10 years melissa Merged r6370 back to trunk.
(edit) @6369   10 years melissa Fixed a few SimplePCI dimension bugs.
(edit) @6368   10 years melissa A few more LSM-related fixes.
(edit) @6367   10 years melissa Prevent StringIndexOutOfBoundsException.
(edit) @6362   10 years callan Re-run of code generation for enumeration handlers. Moved enumeration …
(edit) @6361   10 years melissa Fixed several TIFF, Zeiss LSM and Zeiss ZVI bugs exposed during testing.
(edit) @6360   10 years callan Fixing illumination parsing for FV1000 files.
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