source: trunk @ 7236

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Diff Rev Age Author Log Message
(edit) @7236   10 years melissa * Properly unpack 16-bit BufferedImages into a byte array. Fix courtesy …
(edit) @7235   10 years melissa Override get*BitLookupTable() methods so that files with a different LUT …
(edit) @7234   10 years hinerm Updated the bf-itk plug-in so that it no longer tries to instantiate a JVM …
(edit) @7231   10 years melissa Use an ImageWriter instead of a TiffWriter so that OME-TIFF files are …
(edit) @7230   10 years callan File handle open/close logging at the TRACE level and a test case to pick …
(edit) @7229   10 years melissa Prevent NPEs if detector metadata is missing.
(edit) @7228   10 years melissa Added reader for .aim files. Closes #597.
(edit) @7227   10 years melissa Use the sum of all position values stored for a particular position …
(edit) @7226   10 years callan Attempt to fix issues with leaking file handles during planar writing …
(edit) @7225   10 years melissa Switched getPixelTypes()/getPixelTypes(String) delegation, so that …
(edit) @7224   10 years melissa Fixed pixel offset bug.
(edit) @7223   10 years melissa Prevent the 'open' option from being recorded twice. Closes #596. This …
(edit) @7222   10 years melissa Preserve custom color choices. Closes #586.
(edit) @7221   10 years hinerm Modified build.xml to copy platform-specific files from the …
(edit) @7220   10 years melissa Added support for JPEG-compressed AVIs. Closes #569.
(edit) @7218   10 years melissa Fixed ImageViewer's default metadata population; closes #525.
(edit) @7211   10 years melissa Fixed FileFilter construction method so that it unwraps WriterWrappers. …
(edit) @7210   10 years melissa Added series count to series dialog. Closes #590.
(edit) @7207   10 years melissa Switched around tag parsing so that missing UIC2/UIC4 tags do not prevent …
(edit) @7183   10 years melissa Fixed a couple of bugs in ImageConverter.
(edit) @7182   10 years melissa Updated what's new for today's release.
(edit) @7181   10 years hinerm Updated post-build instructions to reflect the removal of ITKFactories …
(edit) @7180   10 years hinerm Modified CmakeLists.txt for the BF-ITK build so that it will no longer …
(edit) @7179   10 years curtis Add BitsPerPixel to Bio-Formats Importer's Original Metadata window.
(edit) @7178   10 years melissa Don't correct the channel count in the case of RGB images.
(edit) @7175   10 years melissa Changed ome-io component back to using Java 1.5.
(edit) @7174   10 years melissa * Updated stylesheets to  ome-xml:r692. * Added test for Channel.Color.
(edit) @7158   10 years melissa Fixes for truncated .dv files from QA #2988 and #2989.
(edit) @7157   10 years melissa Remove any extra channels from OME-TIFF files. See  omero:#3250, QA #2973.
(edit) @7156   10 years melissa Hackish fix for potential IndexOutOfBoundsException; the real fix should …
(edit) @7155   10 years melissa Fix for overwriting TIFF planes.
(edit) @7154   10 years melissa Fixed conversion of LaserMedium attributes with value "Unknown".
(edit) @7153   10 years melissa Only populate LightPath references if the LSIDs are not null.
(edit) @7152   10 years melissa Allow .rec extension for MRC files. isThisType(RandomAccessInputStream) …
(edit) @7151   10 years melissa Updated showinf help text.
(edit) @7150   10 years melissa Updated C++ headers.
(edit) @7149   10 years melissa A bunch of little export fixes.
(edit) @7148   10 years melissa A few fixes for writing planes non-sequentially.
(edit) @7147   10 years melissa Forward ported r7145 and r7146.
(edit) @7144   10 years melissa Finally fixed ND2 field index bug.
(edit) @7143   10 years melissa Fixed a handful of NPEs, AIOOBs, and leaking file handles.
(edit) @7142   10 years melissa Fixed a bug that prevented ROIs from being displayed.
(edit) @7141   10 years melissa * Backported r6227 to 4.1. * Fixed a subtle bug in calculating the pixel …
(edit) @7140   10 years melissa Fixed an NPE and a few plane indexing bugs.
(edit) @7137   10 years melissa Fixed timestamp indices, see  omero:#3121.
(edit) @7129   10 years melissa Fixed stage position indices.
(edit) @7128   10 years melissa Fixed a handful of Javadoc errors.
(edit) @7127   10 years melissa A few more fixes for small bugs exposed during testing.
(edit) @7126   10 years melissa Reversed usage of OMETiffReader's getMetadataStoreForDisplay() and …
(edit) @7125   10 years melissa Fixed a handful of little bugs exposed during testing.
(edit) @7124   10 years melissa Fixed scanline padding and various metadata parsing bugs.
(edit) @7123   10 years melissa Fixed autoscaling for sliced stacks.
(edit) @7122   10 years melissa Fixed TIFF file ordering problems.
(edit) @7106   10 years melissa Updated metadata support documentation.
(edit) @7105   10 years hinerm Adjusted canDoDirect to be true if the image is interleaved (avoiding …
(edit) @7093   10 years melissa Various tweaks to file grouping logic, so that datasets can be read even …
(edit) @7092   10 years melissa Only populate Objective.NominalMagnification if the magnification is …
(edit) @7091   10 years melissa * Attempt to gracefully handle truncated Deltavision files. See QA #2892, …
(edit) @7090   10 years melissa Override get*LookupTable() so that LUTs are returned where appropriate. …
(edit) @7089   10 years melissa Skip over ROI files that do not exist, instead of throwing an exception.
(edit) @7086   10 years melissa A few more file stitching fixes.
(edit) @7085   10 years melissa Close unused file handles.
(edit) @7084   10 years melissa Fixed a few deprecation warnings and compile errors.
(edit) @7083   10 years melissa Added better type detection to the text reader, see  omero:#2740.
(edit) @7076   10 years melissa Fixed potential ArrayIndexOutOfBounds which prevented tests from passing …
(edit) @7075   10 years melissa * Fixed various file stitching bugs. * Removed debugging statement.
(edit) @7074   10 years melissa Parse stage positions from Fluoview/Andor TIFFs.
(edit) @7073   10 years melissa Populate physical sizes for all series.
(edit) @7072   10 years melissa Using bfconvert with an existing output file will now cause that output …
(edit) @7071   10 years melissa Fixed bugs that prevented tests from passing in r7070.
(edit) @7070   10 years melissa Added support for non-numerical file pattern blocks, closes #395. You can …
(edit) @7068   10 years melissa Finally finished fixing original metadata population, closes #564. We now …
(edit) @7066   10 years melissa Allow a different stage position for each plane.
(edit) @7063   10 years melissa Prevent Bio-Rad reader from attempting to initialize ._*.pic files. See …
(edit) @7057   10 years melissa Fixed PICT sub-image reading, see  omero:#3037.
(edit) @7056   10 years melissa Moved SizeT population, so that we do not attempt to populate it when …
(edit) @7055   10 years melissa Standardized storage of stage positions in the original metadata …
(edit) @7054   10 years melissa Reverted r7018, see #570.
(edit) @7053   10 years melissa Parse physical pixel sizes.
(edit) @7052   10 years melissa Fixed a handful of lovely dimension detection bugs.
(edit) @7051   10 years callan Handle NPE when accessing UUID filename. (Fixes downstream  omero:#3038)
(edit) @7050   10 years hinerm Improvement: prevented null assignment of path to libraries
(edit) @7049   10 years hinerm Improvement: The BF-ITK plug-in now detects where its libraries live, vita …
(edit) @7046   10 years melissa Fixed slice updating in the Data Browser; closes #579.
(edit) @7043   10 years melissa Fixed stage position indices, see #576.
(edit) @7042   10 years melissa Parse and apply channel colors stored in ND2 files.
(edit) @7041   10 years melissa Added support for pixel types other than uint8.
(edit) @7040   10 years melissa Progress on reading position data from LSM files. See #576, see #570.
(edit) @7039   10 years melissa Several metadata population fixes.
(edit) @7038   10 years melissa Adjusted original metadata population, so that it doesn't take nearly as …
(edit) @7037   10 years melissa One more very temporary fix that prevents too many Channels from being …
(edit) @7036   10 years hinerm Added private data members to allow use of ChannelSeparators and …
(edit) @7035   10 years hinerm Bug Fixes: read image data from start to start + count, instead of start …
(edit) @7022   10 years melissa Fixed a few little bugs that prevented tests from passing in r7021.
(edit) @7021   10 years melissa Updated FileStitcher and FilePattern to better handle multi-series …
(edit) @7020   10 years melissa Hide temporary files in a subdirectory of /tmp, so that the tests are …
(edit) @7019   10 years melissa Added support for RGB and indexed color images. Closes #567.
(edit) @7018   10 years melissa Sets the Calibration.*Origin values to equal the stage position (if …
(edit) @7014   10 years hinerm Bug Fix: Converted logging functions from Log::getStackTrace to …
(edit) @7013   10 years callan Resolving issues with Reference instances (with their referrer ID) ending …
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