source: trunk @ 7106

Revision Log Mode:


Legend:

Added
Modified
Copied or renamed
Diff Rev Age Author Log Message
(edit) @7106   9 years melissa Updated metadata support documentation.
(edit) @7105   9 years hinerm Adjusted canDoDirect to be true if the image is interleaved (avoiding …
(edit) @7093   9 years melissa Various tweaks to file grouping logic, so that datasets can be read even …
(edit) @7092   9 years melissa Only populate Objective.NominalMagnification if the magnification is …
(edit) @7091   9 years melissa * Attempt to gracefully handle truncated Deltavision files. See QA #2892, …
(edit) @7090   9 years melissa Override get*LookupTable() so that LUTs are returned where appropriate. …
(edit) @7089   9 years melissa Skip over ROI files that do not exist, instead of throwing an exception.
(edit) @7086   9 years melissa A few more file stitching fixes.
(edit) @7085   9 years melissa Close unused file handles.
(edit) @7084   9 years melissa Fixed a few deprecation warnings and compile errors.
(edit) @7083   9 years melissa Added better type detection to the text reader, see  omero:#2740.
(edit) @7076   9 years melissa Fixed potential ArrayIndexOutOfBounds which prevented tests from passing …
(edit) @7075   9 years melissa * Fixed various file stitching bugs. * Removed debugging statement.
(edit) @7074   9 years melissa Parse stage positions from Fluoview/Andor TIFFs.
(edit) @7073   9 years melissa Populate physical sizes for all series.
(edit) @7072   9 years melissa Using bfconvert with an existing output file will now cause that output …
(edit) @7071   9 years melissa Fixed bugs that prevented tests from passing in r7070.
(edit) @7070   9 years melissa Added support for non-numerical file pattern blocks, closes #395. You can …
(edit) @7068   9 years melissa Finally finished fixing original metadata population, closes #564. We now …
(edit) @7066   9 years melissa Allow a different stage position for each plane.
(edit) @7063   9 years melissa Prevent Bio-Rad reader from attempting to initialize ._*.pic files. See …
(edit) @7057   9 years melissa Fixed PICT sub-image reading, see  omero:#3037.
(edit) @7056   9 years melissa Moved SizeT population, so that we do not attempt to populate it when …
(edit) @7055   9 years melissa Standardized storage of stage positions in the original metadata …
(edit) @7054   9 years melissa Reverted r7018, see #570.
(edit) @7053   9 years melissa Parse physical pixel sizes.
(edit) @7052   9 years melissa Fixed a handful of lovely dimension detection bugs.
(edit) @7051   9 years callan Handle NPE when accessing UUID filename. (Fixes downstream  omero:#3038)
(edit) @7050   9 years hinerm Improvement: prevented null assignment of path to libraries
(edit) @7049   9 years hinerm Improvement: The BF-ITK plug-in now detects where its libraries live, vita …
(edit) @7046   9 years melissa Fixed slice updating in the Data Browser; closes #579.
(edit) @7043   9 years melissa Fixed stage position indices, see #576.
(edit) @7042   9 years melissa Parse and apply channel colors stored in ND2 files.
(edit) @7041   9 years melissa Added support for pixel types other than uint8.
(edit) @7040   9 years melissa Progress on reading position data from LSM files. See #576, see #570.
(edit) @7039   9 years melissa Several metadata population fixes.
(edit) @7038   9 years melissa Adjusted original metadata population, so that it doesn't take nearly as …
(edit) @7037   9 years melissa One more very temporary fix that prevents too many Channels from being …
(edit) @7036   9 years hinerm Added private data members to allow use of ChannelSeparators and …
(edit) @7035   9 years hinerm Bug Fixes: read image data from start to start + count, instead of start …
(edit) @7022   9 years melissa Fixed a few little bugs that prevented tests from passing in r7021.
(edit) @7021   9 years melissa Updated FileStitcher and FilePattern to better handle multi-series …
(edit) @7020   9 years melissa Hide temporary files in a subdirectory of /tmp, so that the tests are …
(edit) @7019   9 years melissa Added support for RGB and indexed color images. Closes #567.
(edit) @7018   9 years melissa Sets the Calibration.*Origin values to equal the stage position (if …
(edit) @7014   9 years hinerm Bug Fix: Converted logging functions from Log::getStackTrace to …
(edit) @7013   9 years callan Resolving issues with Reference instances (with their referrer ID) ending …
(edit) @7012   9 years callan Fix a couple small issues with the SPW model mock and In/Out test.
(edit) @7010   9 years melissa Fixed a bug that prevented extra LIF channels from being removed. Closes …
(edit) @7009   9 years melissa Fixed SVN/Trac links.
(edit) @6989   9 years melissa Fixed TiffRationalTest, based on changes in r6988.
(edit) @6988   9 years melissa Fixed a couple of issues exposed by Findbugs. See #546.
(edit) @6987   9 years melissa Parse scanner serial numbers from the plate log file.
(edit) @6986   9 years melissa Minor fixes to (hopefully) prevent AIOOB.
(edit) @6985   9 years melissa Handle XML parsing errors using SLF4J. Eliminates annoying "[Fatal Error] …
(edit) @6983   9 years melissa Fixed various dimension ordering bugs in new multi-file Improvision TIFF …
(edit) @6982   9 years melissa Tweaked component.runtime-cp for the ome-xml component and updated the …
(edit) @6981   9 years melissa Only populate a channel's excitation wavelength if the wavelength is …
(edit) @6978   9 years melissa OMETiffReader now populates its' MetadataStore in such as way as to …
(edit) @6977   9 years melissa Fixed TiffParser constructor, so that it effectively does not modify the …
(edit) @6976   9 years melissa Several fixes for writing BigTIFFs and multi-series OME-TIFFs. Closes …
(edit) @6975   9 years melissa One more set of ArrayIndexOutOfBounds fixes for certain LZW-compressed …
(edit) @6974   9 years curtis Fix Ant configuration error with bf-itk.
(edit) @6973   9 years curtis Update bf-cpp header file.
(edit) @6972   9 years melissa Only apply LUTs to sliced stacks if the original CompositeImage used the …
(edit) @6971   9 years melissa Updated upgrade check status message to be a bit more clear.
(edit) @6970   9 years melissa Support for multi-file Improvision/Volocity TIFF datasets.
(edit) @6969   9 years melissa Scan TiffData elements for 1-indexed indices before assembling list of …
(edit) @6968   9 years melissa Prevent ArrayIndexOutOfBoundsException when decompressing certain …
(edit) @6967   9 years melissa Fixed SizeT calculation.
(edit) @6965   9 years melissa Tweaked field index calculation.
(edit) @6959   9 years melissa Fixed well dimension parsing and calculation, so that the ScanR reader no …
(edit) @6958   9 years melissa Fixed error in plane index calculation.
(edit) @6953   9 years melissa Allow MIAS text files to be passed to MIASReader.setId. Closes #562.
(edit) @6952   9 years melissa Prevent Image names from being overwritten. Closes #555.
(edit) @6949   9 years melissa Ensure that LUTs are properly preserved when using a virtual stack. …
(edit) @6948   9 years melissa Don't apply lookup tables if there is more than one channel and we cannot …
(edit) @6946   9 years curtis Remove broken Bio-Formats Ice component, for now.
(edit) @6945   9 years melissa Parse 'waitTime' from Prairie datasets. Closes #551.
(edit) @6943   9 years callan Solution to potential service factory file handle leak. (Fixes #561)
(edit) @6924   9 years curtis Use line comments for proper function documentation.
(edit) @6917   9 years callan Solution for underscores in wavelength names. (Fixes #558)
(edit) @6916   9 years callan Moved the 'getHandle()' log statement to the TRACE level to avoid DEBUG …
(edit) @6896   9 years curtis More efficient XML sanitation algorithm.
(edit) @6891   9 years melissa Disable color mode options when the stack view is set to "Standard …
(edit) @6890   9 years melissa A few fixes for ScanR datasets with missing wells, based on a patch …
(edit) @6889   9 years melissa Added system properties to ImageJ plugin log. Closes #547.
(edit) @6888   9 years melissa Updated XMLTools.sanitizeXML to remove invalid "&#" sequences.
(edit) @6886   9 years melissa * Improved metadata parsing for Prairie datasets. * Reverted changes to …
(edit) @6882   9 years curtis Fix out-of-date SVN and Trac paths.
(edit) @6881   9 years curtis Update SVN and Trac paths.
(edit) @6880   9 years melissa Couple of findbugs fixes, see #546.
(edit) @6879   9 years melissa Added more logging to LocationTest, in an attempt to track down the …
(edit) @6878   9 years melissa Fixed bugs in writing and reading JPEG- and JPEG-2000-compressed TIFFs. …
(edit) @6877   9 years melissa * Return blank planes if pixel data is missing from an OME-XML file. * …
(edit) @6876   9 years callan Some further test case cleanup. Added a check to ChannelFiller to handle …
(edit) @6875   9 years melissa Fixed handling of multi-position ND2 datasets.
(edit) @6874   9 years curtis Better series handling when number of series is extremely large.
(edit) @6873   9 years curtis Update location of LegacyQTTools class.
(edit) @6872   9 years melissa Fixed OMETiffWriter.close() so that it releases resources even if an …
Note: See TracRevisionLog for help on using the revision log.