source: trunk @ 6896

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Diff Rev Age Author Log Message
(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(edit) @6882   9 years curtis Fix out-of-date SVN and Trac paths.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 …
(edit) @6871   9 years callan Removed erroneous STDERR debugging statement from test case.
(edit) @6869   9 years curtis Add a note stating that metadata can also be viewed in Image Info.
(edit) @6866   9 years melissa Removed support for JPEG/JPEG-2000 compression in OME-XML files, as this …
(edit) @6864   9 years melissa Several tweaks to original metadata storage so that FV1000 files do not …
(edit) @6863   9 years melissa Added missing methods that prevented r6862 from compiling.
(edit) @6862   9 years melissa Simplified search for BinData offsets.
(edit) @6861   9 years callan Reverting erroneous debugging in OMEXMLReader from r6860.
(edit) @6860   9 years callan Added a test case (and re-organized some of the mock infrastructure) for …
(edit) @6859   9 years curtis Remove bogus quote escape characters.
(edit) @6858   9 years curtis Clarify 'Display metadata' option to be less misleading.
(edit) @6857   9 years melissa Added support for multi-chunk AVI files.
(edit) @6856   9 years melissa Fixed sub-image reading for SimplePCI files that contain embedded TIFFs.
(edit) @6854   9 years curtis Use INFO logging for AxisGuesser main.
(edit) @6853   9 years curtis Use INFO logging in FilePattern main.
(edit) @6852   9 years melissa Prevent a bunch of NPEs.
(edit) @6849   9 years curtis Fix build warnings when using Ant 1.8+.
(edit) @6848   9 years curtis Various improvements to Bio-Formats MATLAB bfopen script: * Better …
(edit) @6847   9 years melissa Removed external URL from Location tests.
(edit) @6845   9 years melissa Added support for Varian FDF files. Closes #474.
(edit) @6844   9 years melissa Sped up original metadata hashtable population.
(edit) @6843   9 years melissa Removed check that prevented multi-file OME-TIFF export from working.
(edit) @6842   9 years melissa Added support for multi-position Zeiss LSM data. Closes #527.
(edit) @6841   9 years melissa * Updated MetadataConverter to properly handle LightSource attributes. * …
(edit) @6840   9 years callan Support for type resolution of light sources. Re-run of code generation. …
(edit) @6839   9 years callan Mock and tests for SPW model use with OME-XML.
(edit) @6838   9 years melissa One more signedness fix, as pointed out by Rubén Muñoz.
(edit) @6836   9 years melissa Fixed Image indexed passed to …
(edit) @6835   9 years melissa A few changes to how pixels and dimension information are found. I'm not …
(edit) @6834   9 years melissa Moved MetadataStore calls that depend on MetadataTools.populatePixels(...) …
(edit) @6823   9 years melissa Added reader for TIFFs produced by Nikon Elements. Closes #529.
(edit) @6822   9 years melissa Prevent extra (Logical)Channel objects from being populated.
(edit) @6819   9 years melissa Factored ND2Handler out of NativeND2Reader. See #529.
(edit) @6816   9 years melissa Fixed hack from r6804 so that it won't throw an AIOOB exception.
(edit) @6814   9 years melissa Reverted a few changes from r6791 that prevented OME-TIFF files from being …
(edit) @6812   9 years melissa Reverse the order of the rows if a negative height was stored in the file. …
(edit) @6810   9 years melissa Force the pixel type to be unsigned, regardless of what is actually stored …
(edit) @6808   9 years melissa If a negative width or height is stored, use the absolute value instead …
(edit) @6807   9 years melissa * Fixed bug in StringOption that prevented macro keys from being parsed …
(edit) @6805   9 years melissa * Added convenience method to loci.common.IniList to flatten the IniTables …
(edit) @6804   9 years melissa Hackish fix for some files that have an incorrect dimension order.
(edit) @6802   9 years melissa * Ignore missing L2D scans, instead of throwing an exception. * More …
(edit) @6801   9 years melissa * Parse metadata from SimplePCI TIFFs. * Slightly better Z/T detection for …
(edit) @6800   9 years melissa Remove invalid characters from strings that will later be parsed into …
(edit) @6799   9 years melissa Fixed a few Bio-Rad Gel offset bugs.
(edit) @6798   9 years melissa Added 'Object getSeriesMetadataValue(String)' to IFormatReader.
(edit) @6797   9 years melissa Added support for FEI TIFF files, specifically those from S-FEG and Helios …
(edit) @6796   9 years melissa Remainder of OME-XML validation fixes. Closes #520.
(edit) @6793   9 years melissa Changed logging level of missing interface messages from 'warn' to …
Diff Rev Age Author Log Message
(edit) @6791   9 years melissa More OME-XML validation fixes, see #520.
(edit) @6790   9 years melissa Initial version of ECAT 7 reader. Closes #487.
Diff Rev Age Author Log Message
(edit) @6788   9 years melissa If ImporterOptions.getId() returns null, prompt for a file regardless of …
(edit) @6787   9 years melissa Added extra sanity check when parsing doubles.
(edit) @6786   9 years melissa More OME-XML validation fixes, see #520.
(edit) @6785   9 years melissa * bfconvert and showinf now exit if an unknown flag or argument is …
(edit) @6784   9 years melissa More OME-XML validation fixes. See #520.
(edit) @6783   9 years melissa Removed not-yet-existent CRIReader.
(edit) @6782   9 years melissa Parse physical pixel sizes for all series, instead of applying the first …
(edit) @6781   9 years melissa Fixed tests in components/bio-formats; all tests should now pass.
(edit) @6780   9 years melissa More thoroughly parse Z position values from single-file datasets.
(edit) @6779   9 years melissa Fixed tag alignment problem.
(edit) @6778   9 years melissa Prevent SlidebookReader from passing a negative int to setSeries.
(edit) @6774   9 years curtis More robust behavior when ome-xml service is unavailable. But still …
(edit) @6773   9 years curtis Update minimum ImageJ version to 1.43, since …
(edit) @6772   9 years curtis Update service properties to match OMEReaderWriterService package change.
(edit) @6771   9 years curtis Fix SVN and Trac links for OMEReaderWriterService.
(edit) @6770   9 years curtis Fix ome-io test compile errors.
(edit) @6769   9 years curtis Remove soft dependency on ome-io from bio-formats component. The ome-io …
(edit) @6768   9 years melissa Fixed several OME-XML validation issues. See #520.
(edit) @6767   9 years melissa Fixed a couple of silly Photoshop bugs.
(edit) @6766   9 years melissa Fixed file export from ImageViewer. Closes #525.
(edit) @6765   9 years melissa Only populate Objective.NominalMagnification if the magnification stored …
(edit) @6764   9 years melissa Fixed implementation of getCurrentFile() in ImageReader. This is the real …
(edit) @6763   9 years melissa Adjusted AnalyzeReader's isThisType implementations, so that AnalyzeReader …
(edit) @6762   9 years melissa Initial work on fully autogenerated metadata support documentation; it's a …
(edit) @6761   9 years curtis Update OMERO library version number to 4.2.0.
(edit) @6760   9 years curtis Remove tabs.
(edit) @6759   9 years curtis Update OmeroReader to use OMERO 4.2 API.
(edit) @6758   9 years melissa Added support for Perkin-Elmer densitometer data. Closes #490.
(edit) @6757   9 years melissa Reverted r6756, so that plugin tests no longer fail.
(edit) @6756   9 years melissa Always reinitialize the 'core' variable; this prevents tests in …
(edit) @6755   9 years melissa Ignore 'readme.txt' files.
(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 …
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