source: branches/4.2/components/bio-formats/src/loci/formats/in @ 6998

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Diff Rev Age Author Log Message
(edit) @6998   10 years melissa Merged base reader changes into 4.2: r6688, r6756, r6757, r6764, r6853, …
(edit) @6997   10 years melissa Merged new readers into 4.2: r6758, r6783, r6790, r6797, r6801, r6845.
(edit) @6996   10 years melissa Merged changes to common component and logging into 4.2: r6696, r6722, …
(edit) @6995   10 years melissa Merged recent ScanR changes: r6720, r6810, r6838, r6959, and r6967.
(edit) @6994   10 years melissa Merged GUI tools changes: r6766 and r6774.
(edit) @6993   10 years melissa Merged minor API additions to 4.2: r6747 and r6798.
(edit) @6992   10 years melissa Merged recent Zeiss LSM changes to 4.2: r6697, r6713, and r6842.
(edit) @6991   10 years melissa Merged r6695 into 4.2.
(edit) @6987   10 years melissa Parse scanner serial numbers from the plate log file.
(edit) @6983   10 years melissa Fixed various dimension ordering bugs in new multi-file Improvision TIFF …
(edit) @6981   10 years melissa Only populate a channel's excitation wavelength if the wavelength is …
(edit) @6970   10 years melissa Support for multi-file Improvision/Volocity TIFF datasets.
(edit) @6958   10 years melissa Fixed error in plane index calculation.
(edit) @6950   10 years curtis Backport r6948,r6949 to 4.2 branch.
(edit) @6947   10 years callan Merging r6715 from Trunk. (See #543)
(edit) @6944   10 years callan Merging r6943 from Trunk. (See #561)
(edit) @6920   10 years callan Merged r6743 and r6872 from Trunk. (See #543)
(edit) @6918   10 years callan Merged r6917 and r6916 from Trunk.
(edit) @6910   10 years callan Merging commits (r6690, r6692, r6735, r6784, r6786) from Trunk with …
(edit) @6856   10 years melissa Fixed sub-image reading for SimplePCI files that contain embedded TIFFs.
(edit) @6836   10 years melissa Fixed Image indexed passed to …
(edit) @6834   10 years melissa Moved MetadataStore calls that depend on MetadataTools.populatePixels(...) …
(edit) @6822   10 years melissa Prevent extra (Logical)Channel objects from being populated.
(edit) @6812   10 years melissa Reverse the order of the rows if a negative height was stored in the file. …
(edit) @6808   10 years melissa If a negative width or height is stored, use the absolute value instead …
(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) @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) @6744   10 years melissa Force buffer reallocation if the previously allocated buffer is too small.
(edit) @6710   10 years melissa * Fixed how ICS files with > 4 channels are read. * Fixed Channel …
(edit) @6706   10 years melissa Tweaked isThisType to automatically return false if the TIFF comment is an …
(edit) @6699   10 years melissa Fixed pixel data offset.
(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) @6681   10 years melissa Only populate Objective.NominalMagnification if the magnification is …
(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) @6626   10 years curtis Backport r6625 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) @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) @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) @6515   10 years melissa Allow Metamorph reader to pick up TIFF files.
(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) @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) @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) @6477   10 years curtis Backport Bio-Formats and Importer bugfixes from trunk.
(edit) @6465   10 years melissa Added some debugging statements so that missing TIFF files are reported. …
(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) @6457   10 years melissa Moved ome.xml.r201004.* to ome.xml.model.*.
(edit) @6430   10 years melissa * Updated OMEXMLMetadataImpl based on  ome-xml:r618. * Fixed a bunch of …
(edit) @6426   10 years melissa Fixed various metadata population bugs in the FV1000 reader. See …
(edit) @6420   10 years curtis Merge ChannelFiller and FakeReader bugfixes to 4.2.
(edit) @6416   10 years melissa Fixed physical size Z scaling.
(edit) @6415   10 years callan Merging r6413,r6414 from Trunk
(edit) @6409   10 years melissa Several fixes to Leica LEI, ND2, and Perkin Elmer readers.
(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) @6400   10 years callan Merging r6398,r6399 from Trunk
(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) @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 …
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