source: trunk/components/bio-formats/src @ 6419

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Diff Rev Age Author Log Message
(edit) @6419   10 years curtis Fix bugs in FakeReader with indexed color.
(edit) @6418   10 years curtis Fix problems with ChannelFiller when lookup table color component count != …
(edit) @6417   10 years curtis Flesh out the IFormatReader javadoc a bit.
(edit) @6416   10 years melissa Fixed physical size Z scaling.
(edit) @6414   10 years callan Fixed some further NPEs when reading OME-TIFF files with no UUID objects.
(edit) @6413   10 years callan General cleanup for metadata classes. Moved and overhauled ome.xml test …
(edit) @6409   10 years melissa Several fixes to Leica LEI, ND2, and Perkin Elmer readers.
(edit) @6407   10 years curtis Temporary(?) hack to speed up text file reading.
(edit) @6406   10 years melissa Updated several TIFF-based readers to populate Image.Description more …
(edit) @6405   10 years melissa Fixed Detector/DetectorSettings population to correspond to what the …
(edit) @6404   10 years melissa Trim the image name before placing it in the original metadata hashtable. …
(edit) @6399   10 years callan Initializing filenames and roiFilenames on close() in FV1000Reader.
(edit) @6398   10 years callan Ensure that Image names are populated for Leica LEI when …
(edit) @6397   10 years curtis Add reader for tabular text data.
(edit) @6395   10 years melissa Read tags into a byte array, so that non-String tags are preserved. See …
(edit) @6392   10 years melissa Fixed LUT ordering bug. See  omero:2438.
(edit) @6389   10 years melissa Prevent each EmissionFilterRef from being populated multiple times.
(edit) @6388   10 years melissa Fixed a bunch of Leica LIF metadata population bugs.
(edit) @6383   10 years melissa Make sure that references get resolved before dumping OME-XML; otherwise, …
(edit) @6381   10 years melissa Fixed bug in file renaming logic.
(edit) @6378   10 years melissa Tweaked MetamorphReader.isThisType so that Prairie TIFFs are not picked …
(edit) @6377   10 years melissa Merged r6376 back to trunk.
(edit) @6373   10 years callan Removed another location of the same problem resolved with r6372.
(edit) @6372   10 years callan Passing the metadata store down to planar TIFF reader causes metadata …
(edit) @6371   10 years melissa Merged r6370 back to trunk.
(edit) @6369   10 years melissa Fixed a few SimplePCI dimension bugs.
(edit) @6368   10 years melissa A few more LSM-related fixes.
(edit) @6367   10 years melissa Prevent StringIndexOutOfBoundsException.
(edit) @6362   10 years callan Re-run of code generation for enumeration handlers. Moved enumeration …
(edit) @6361   10 years melissa Fixed several TIFF, Zeiss LSM and Zeiss ZVI bugs exposed during testing.
(edit) @6360   10 years callan Fixing illumination parsing for FV1000 files.
(edit) @6359   10 years callan Restoring LEI file to getUsedFiles().
(edit) @6358   10 years melissa Added missing implementations of isSingleFile(String), …
(edit) @6356   10 years callan Fixed broken instrument parsing for Leica LEI. (See  omero:#2410)
(edit) @6355   10 years melissa Don't swap bits if the number of bits per pixel is less than or equal to …
(edit) @6354   10 years melissa Prevent NumberFormatException from being thrown when parsing the number of …
(edit) @6353   10 years melissa Call MetadataTools.populatePixels(...) after all of the CoreMetadata …
(edit) @6352   10 years melissa Fixed Well -> WellSample linkage. See  omero:2406.
(edit) @6350   10 years melissa Skip over TIFF tiles/strips that have StripByteCounts == 0. See …
(edit) @6349   10 years melissa Fixed various bugs exposed by test suite.
(edit) @6339   10 years melissa Fixed IFD entry count calculation for BigTIFF files. See  omero:2390.
(edit) @6337   10 years melissa Fixed LightPath and Image population to prevent AIOOB exceptions. See …
(edit) @6336   10 years melissa Fixed Image -> ROI link. See  omero:2381.
(edit) @6335   10 years melissa Moved SizeT population to prevent it from being 0. See  omero:2377.
(edit) @6334   10 years melissa * Prevent PICT reader from reporting width or height less than 0. * Fixd …
(edit) @6333   10 years melissa * Removed hopefully obsolete hack from RandomAccessInputStream.findString. …
(edit) @6332   10 years melissa Fixed ROI transformation population, see  omero:2373.
(edit) @6329   10 years melissa Fixed a couple of bugs exposed by the test suite.
(edit) @6328   10 years melissa Fixed a few multi-file export problems. Closes #486.
(edit) @6327   10 years melissa Fixed NPE when closing NetCDF files. See  omero:#2378.
(edit) @6323   10 years melissa Fixed a couple of dimension calculation bugs.
(edit) @6320   10 years curtis Use Double.isNaN for clarity instead of equality test (same performance …
(edit) @6319   10 years curtis Change gradient to always start at smallest possible value for integer …
(edit) @6317   10 years melissa Fix for plates that do not have well labels, courtesy of Rubén Muñoz.
(edit) @6316   10 years melissa Parse XY dimensions from IFD.PAGE_NAME entry, if present.
(edit) @6315   10 years melissa Updated Filter population to use new LightPath model.
(edit) @6313   10 years melissa Fixed field count and image names, courtesy of Rubén Muñoz.
(edit) @6310   10 years curtis Whitespace.
(edit) @6309   10 years curtis Fix bug with 8-bit indexed color when less than 3 channels.
(edit) @6308   10 years curtis Add fake filename parameter checks.
(edit) @6306   10 years melissa Exported OME-XML files can now be read.
(edit) @6305   10 years curtis If indexed is set and pixel type is uint8 or uint16, generate LUTs.
(edit) @6304   10 years curtis Minor tweaks.
(edit) @6303   10 years melissa Fixed bug that caused get*BitLookupTable() to return null if openBytes had …
(edit) @6301   10 years melissa Added 'boolean hasCompanionFiles()' to IFormatReader. See #438.
(edit) @6300   10 years melissa Switched a few logging statements from 'debug' to 'trace'.
(edit) @6299   10 years curtis Add bounds checking for laser wavelength.
(edit) @6298   10 years curtis Fix compile error in TIFF pixels test.
(edit) @6294   10 years melissa Added API for tiled image and multi-file export (see #413 and #486). …
(edit) @6290   10 years melissa Fixed NPE in FileStitcher.setGroupFiles.
(edit) @6289   10 years curtis Fix showinf documentation for -nogroup option.
(edit) @6279   10 years curtis Fix a bunch of warnings.
(edit) @6272   10 years melissa Transforming from old OME-XML versions to 2010-04 *finally* works.
(edit) @6267   10 years melissa Fixed calls to IMinMaxStore.setChannelGlobalMinMax(...).
(edit) @6266   10 years melissa Re-added AggregateMetadata, DummyMetadata, and FilterMetadata.
(edit) @6264   10 years curtis Allow toggling of patternIds flag in existing FileStitcher.
(edit) @6263   10 years curtis Use List/ArrayList instead of Vector.
(edit) @6262   10 years curtis Fix some warnings.
(edit) @6256   10 years melissa Added command line flag to disable file grouping.
(edit) @6254   10 years melissa Adjust the dimensions if the dimensions stored in the file do not match …
(edit) @6252   10 years curtis Skip file existence check for fake files in FileStitcher.
(edit) @6243   10 years melissa * Fixed timestamp parsing bugs in Andor/Fluoview TIFF reader. Closes …
(edit) @6236   10 years curtis Add a hack to skip file existence check for .fake files.
(edit) @6234   10 years melissa * Fixed compile errors introduced in r6230. * Added transformations from …
(edit) @6233   10 years melissa Populate original metadata using StructuredAnnotations.
(edit) @6232   10 years melissa OME-XML generation should work now.
(edit) @6231   10 years melissa Added loci.formats.ome.OMEXMLMetadataImpl, which should have been in …
(edit) @6230   10 years melissa Updated to new MetadataStore/MetadataRetrieve APIs. This may temporarily …
(edit) @6228   10 years curtis Change certain logger warnings to debug instead, to avoid extraneous …
(edit) @6221   10 years melissa Fixed Nikon type, compression, and image count detection bugs.
(edit) @6218   10 years melissa * Cache previously opened LSM plane if channels are being split. * …
(edit) @6217   10 years melissa Reduced Zeiss LSM IFD parsing time.
(edit) @6208   10 years curtis Minor fix to showinf output.
(edit) @6207   10 years melissa Fixed parsing of ND filter from log file.
(edit) @6205   10 years melissa Prevent NPE if ROI file is missing.
(edit) @6203   10 years melissa Removed SPA-LEED reader, which hasn't yet been committed.
(edit) @6198   10 years melissa Tweaked matching priorities so that reordering works again.
(edit) @6197   10 years melissa * Added Molecular Imaging and JPK readers. See #412. * Minor cleanup in …
(edit) @6193   10 years melissa Added RHK Technologies reader. See #412.
(edit) @6191   10 years melissa Added SBIG reader and fixed a NIfTI type detection bug. See #412.
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