source: trunk @ 7076

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Diff Rev Age Author Log Message
(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 …
(edit) @7012   10 years callan Fix a couple small issues with the SPW model mock and In/Out test.
(edit) @7010   10 years melissa Fixed a bug that prevented extra LIF channels from being removed. Closes …
(edit) @7009   10 years melissa Fixed SVN/Trac links.
(edit) @6989   10 years melissa Fixed TiffRationalTest, based on changes in r6988.
(edit) @6988   10 years melissa Fixed a couple of issues exposed by Findbugs. See #546.
(edit) @6987   10 years melissa Parse scanner serial numbers from the plate log file.
(edit) @6986   10 years melissa Minor fixes to (hopefully) prevent AIOOB.
(edit) @6985   10 years melissa Handle XML parsing errors using SLF4J. Eliminates annoying "[Fatal Error] …
(edit) @6983   10 years melissa Fixed various dimension ordering bugs in new multi-file Improvision TIFF …
(edit) @6982   10 years melissa Tweaked component.runtime-cp for the ome-xml component and updated the …
(edit) @6981   10 years melissa Only populate a channel's excitation wavelength if the wavelength is …
(edit) @6978   10 years melissa OMETiffReader now populates its' MetadataStore in such as way as to …
(edit) @6977   10 years melissa Fixed TiffParser constructor, so that it effectively does not modify the …
(edit) @6976   10 years melissa Several fixes for writing BigTIFFs and multi-series OME-TIFFs. Closes …
(edit) @6975   10 years melissa One more set of ArrayIndexOutOfBounds fixes for certain LZW-compressed …
(edit) @6974   10 years curtis Fix Ant configuration error with bf-itk.
(edit) @6973   10 years curtis Update bf-cpp header file.
(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) @6969   10 years melissa Scan TiffData elements for 1-indexed indices before assembling list of …
(edit) @6968   10 years melissa Prevent ArrayIndexOutOfBoundsException when decompressing certain …
(edit) @6967   10 years melissa Fixed SizeT calculation.
(edit) @6965   10 years melissa Tweaked field index calculation.
(edit) @6959   10 years melissa Fixed well dimension parsing and calculation, so that the ScanR reader no …
(edit) @6958   10 years melissa Fixed error in plane index calculation.
(edit) @6953   10 years melissa Allow MIAS text files to be passed to MIASReader.setId. Closes #562.
(edit) @6952   10 years melissa Prevent Image names from being overwritten. Closes #555.
(edit) @6949   10 years melissa Ensure that LUTs are properly preserved when using a virtual stack. …
(edit) @6948   10 years melissa Don't apply lookup tables if there is more than one channel and we cannot …
(edit) @6946   10 years curtis Remove broken Bio-Formats Ice component, for now.
(edit) @6945   10 years melissa Parse 'waitTime' from Prairie datasets. Closes #551.
(edit) @6943   10 years callan Solution to potential service factory file handle leak. (Fixes #561)
(edit) @6924   10 years curtis Use line comments for proper function documentation.
Diff Rev Age Author Log Message
(edit) @6916   10 years callan Moved the 'getHandle()' log statement to the TRACE level to avoid DEBUG …
(edit) @6896   10 years curtis More efficient XML sanitation algorithm.
(edit) @6891   10 years melissa Disable color mode options when the stack view is set to "Standard …
(edit) @6890   10 years melissa A few fixes for ScanR datasets with missing wells, based on a patch …
(edit) @6889   10 years melissa Added system properties to ImageJ plugin log. Closes #547.
(edit) @6888   10 years melissa Updated XMLTools.sanitizeXML to remove invalid "&#" sequences.
(edit) @6886   10 years melissa * Improved metadata parsing for Prairie datasets. * Reverted changes to …
(edit) @6882   10 years curtis Fix out-of-date SVN and Trac paths.
(edit) @6881   10 years curtis Update SVN and Trac paths.
(edit) @6880   10 years melissa Couple of findbugs fixes, see #546.
(edit) @6879   10 years melissa Added more logging to LocationTest, in an attempt to track down the …
(edit) @6878   10 years melissa Fixed bugs in writing and reading JPEG- and JPEG-2000-compressed TIFFs. …
(edit) @6877   10 years melissa * Return blank planes if pixel data is missing from an OME-XML file. * …
(edit) @6876   10 years callan Some further test case cleanup. Added a check to ChannelFiller to handle …
(edit) @6875   10 years melissa Fixed handling of multi-position ND2 datasets.
(edit) @6874   10 years curtis Better series handling when number of series is extremely large.
(edit) @6873   10 years curtis Update location of LegacyQTTools class.
(edit) @6872   10 years melissa Fixed OMETiffWriter.close() so that it releases resources even if an …
(edit) @6871   10 years callan Removed erroneous STDERR debugging statement from test case.
(edit) @6869   10 years curtis Add a note stating that metadata can also be viewed in Image Info.
(edit) @6866   10 years melissa Removed support for JPEG/JPEG-2000 compression in OME-XML files, as this …
(edit) @6864   10 years melissa Several tweaks to original metadata storage so that FV1000 files do not …
(edit) @6863   10 years melissa Added missing methods that prevented r6862 from compiling.
(edit) @6862   10 years melissa Simplified search for BinData offsets.
(edit) @6861   10 years callan Reverting erroneous debugging in OMEXMLReader from r6860.
(edit) @6860   10 years callan Added a test case (and re-organized some of the mock infrastructure) for …
(edit) @6859   10 years curtis Remove bogus quote escape characters.
(edit) @6858   10 years curtis Clarify 'Display metadata' option to be less misleading.
(edit) @6857   10 years melissa Added support for multi-chunk AVI files.
(edit) @6856   10 years melissa Fixed sub-image reading for SimplePCI files that contain embedded TIFFs.
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