source: branches/4.2 @ 7063

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Diff Rev Age Author Log Message
(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.
(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) @6887   10 years melissa Backported r6839, r6840, and r6841 to 4.2.
(edit) @6856   10 years melissa Fixed sub-image reading for SimplePCI files that contain embedded TIFFs.
(edit) @6843   10 years melissa Removed check that prevented multi-file OME-TIFF export from working.
(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) @6753   10 years melissa Fixed saveBytes and savePlane implementations to use the correct image …
(edit) @6744   10 years melissa Force buffer reallocation if the previously allocated buffer is too small.
(edit) @6730   10 years melissa Merged r6729 into 4.2 branch.
(edit) @6710   10 years melissa * Fixed how ICS files with > 4 channels are read. * Fixed Channel …
(edit) @6707   10 years melissa Fixed problems with exporting multi-channel data.
(edit) @6706   10 years melissa Tweaked isThisType to automatically return false if the TIFF comment is an …
(edit) @6705   10 years melissa Fixed bytes per pixel calculation for RGB data.
(edit) @6699   10 years melissa Fixed pixel data offset.
(edit) @6694   10 years melissa Adjust SizeC internally when writing RGB OME-TIFF files. Closes #513.
(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) @6684   10 years melissa Updated what's new and switch trunk component version numbers to 5.0-DEV.
(edit) @6683   10 years curtis Backport r6682 to 4.2 branch.
(edit) @6681   10 years melissa Only populate Objective.NominalMagnification if the magnification is …
(edit) @6680   10 years curtis Backport r6679 to 4.2 branch.
(edit) @6678   10 years melissa Updated component version numbers in 4.2 branch.
(edit) @6677   10 years curtis Backport r6672,r6673,r6676 to 4.2 branch.
(edit) @6674   10 years melissa Fixed how Images are removed from a MetadataStore when exporting one …
(edit) @6669   10 years curtis Backport recent LOCI plugins progress to 4.2 branch.
(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) @6631   10 years melissa Removed obsolete OME-XML model objects.
(edit) @6627   10 years melissa Switched TiffParser logging from 'debug' to 'trace'; see #512.
(edit) @6626   10 years curtis Backport r6625 to 4.2 branch.
(edit) @6615   10 years dscho Avoid "prefix <...> not bound" error when transforming XML When …
(edit) @6614   10 years dscho Fix OME-XML version discovery Some files (Huygens) have an xmlns:ome …
(edit) @6613   10 years melissa Merged r6602 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.
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