source: branches/4.2 @ 7218

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Diff Rev Age Author Log Message
(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) @7208   10 years melissa Backported r7207 to 4.2.
(edit) @7184   10 years melissa Updated version numbers to "4.2.1".
(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) @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) @7146   10 years melissa Added top-level compile target.
(edit) @7145   10 years melissa * Fixed multi-series OME-XML export. * Fixed multi-series OME-TIFF export. …
(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) @7104   10 years melissa Updated version numbers to "4.2.1-DEV".
(edit) @7103   10 years melissa Backported r7084 to 4.2.
(edit) @7102   10 years melissa Backported r7055 to 4.2.
(edit) @7101   10 years melissa Backported r7051 to 4.2.
(edit) @7100   10 years melissa Backported r7042 to 4.2.
(edit) @7099   10 years melissa Backported Zeiss LSM stage position changes to 4.2: r7040 and r7043.
(edit) @7098   10 years melissa Backported r7037 to 4.2.
(edit) @7097   10 years melissa Backported file stitching changes to 4.2: r7021, r7022, r7070, r7071, …
(edit) @7096   10 years melissa Backported native component changes to 4.2: r7014, r7035, r7036, r7049, …
(edit) @7095   10 years melissa Backported r7012 and r7013 to 4.2.
(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) @7085   10 years melissa Close unused file handles.
(edit) @7083   10 years melissa Added better type detection to the text reader, see  omero:#2740.
(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) @7068   10 years melissa Finally finished fixing original metadata population, closes #564. We now …
(edit) @7067   10 years melissa Backported r7038 to 4.2.
(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) @7053   10 years melissa Parse physical pixel sizes.
(edit) @7052   10 years melissa Fixed a handful of lovely dimension detection bugs.
(edit) @7046   10 years melissa Fixed slice updating in the Data Browser; closes #579.
(edit) @7041   10 years melissa Added support for pixel types other than uint8.
(edit) @7039   10 years melissa Several metadata population fixes.
(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) @7010   10 years melissa Fixed a bug that prevented extra LIF channels from being removed. Closes …
(edit) @7008   10 years melissa Added missing files.
(edit) @7007   10 years melissa Merged remainder of build, test, and SVN/Trac link changes to 4.2.
(edit) @7006   10 years melissa Merged remaining reader changes: r6708, r6727, r6778, r6779, r6782, r6787, …
(edit) @7005   10 years melissa Merged remaining MATLAB, command line tool, and C++ changes into 4.2: …
(edit) @7004   10 years melissa Merged TIFF export fixes into 4.2: r6878, r6976, and r6977.
(edit) @7003   10 years melissa Merged metadata population fixes into 4.2: r6700, r6711, r6719, r6728, …
(edit) @7002   10 years melissa Merged type checking fixes into 4.2: r6724, r6726, r6741, r6746, and …
(edit) @7001   10 years melissa Merged ome-io component changes into 4.2: r6759, r6760, r6761, r6769, …
(edit) @7000   10 years melissa Merged remaining ImageJ plugin changes to 4.2.
(edit) @6999   10 years melissa Merged common XML changes in to 4.2: r6717, r6888, and r6985.
(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) @6975   10 years melissa One more set of ArrayIndexOutOfBounds fixes for certain LZW-compressed …
(edit) @6972   10 years melissa Only apply LUTs to sliced stacks if the original CompositeImage used the …
(edit) @6971   10 years melissa Updated upgrade check status message to be a bit more clear.
(edit) @6970   10 years melissa Support for multi-file Improvision/Volocity TIFF datasets.
(edit) @6968   10 years melissa Prevent ArrayIndexOutOfBoundsException when decompressing certain …
(edit) @6958   10 years melissa Fixed error in plane index calculation.
(edit) @6951   10 years melissa Backported r6714, r6716, r6948, and r6949 to 4.2. See #557.
(edit) @6950   10 years curtis Backport r6948,r6949 to 4.2 branch.
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