source: trunk/components/bio-formats/src/loci/formats/in @ 6329

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Diff Rev Age Author Log Message
(edit) @6329   10 years melissa Fixed a couple of bugs exposed by the test suite.
(edit) @6323   10 years melissa Fixed a couple of dimension calculation bugs.
(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) @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) @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) @6299   10 years curtis Add bounds checking for laser wavelength.
(edit) @6294   10 years melissa Added API for tiled image and multi-file export (see #413 and #486). …
(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) @6262   10 years curtis Fix some warnings.
(edit) @6254   10 years melissa Adjust the dimensions if the dimensions stored in the file do not match …
(edit) @6243   10 years melissa * Fixed timestamp parsing bugs in Andor/Fluoview TIFF reader. Closes …
(edit) @6230   10 years melissa Updated to new MetadataStore/MetadataRetrieve APIs. This may temporarily …
(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) @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) @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.
(edit) @6190   10 years melissa * Updated remaining readers to respect MetadataOptions. * Added bounds …
(edit) @6189   10 years curtis Fix for NullPointerException, courtesy of Lee Kamentsky.
(edit) @6188   10 years melissa * Updated a few more readers to respect MetadataOptions. * Fixed a couple …
(edit) @6162   10 years melissa Fixed NPE.
(edit) @6156   10 years melissa Updated several more readers to respect MetadataOptions.
(edit) @6154   10 years curtis Create only one codec per instance of NativeND2Reader. This change avoids …
(edit) @6148   10 years melissa Updated the remainder of the SXM readers to respect MetadataOptions.
(edit) @6141   10 years curtis Use generics where appropriate; fix miscellaneous warnings and issues.
(edit) @6140   10 years melissa Updated more readers to respect MetadataOptions.
(edit) @6139   10 years melissa Fixed a couple of bugs that prevented Nikon images with more than one …
(edit) @6129   10 years melissa Updated more readers to respect MetadataOptions, and added some TIFF IFD …
(edit) @6128   10 years curtis Fix some Eclipse warnings, clean up imports, minor progress on Importer …
(edit) @6127   10 years melissa Updated a few more readers to respect MetadataOptions.
(edit) @6125   10 years curtis Improve robustness of color map parsing.
(edit) @6122   10 years melissa Set physical Z size, even if instrument data is not present.
(edit) @6121   10 years melissa Preliminary support for reading Zip files with multiple entries. Closes …
(edit) @6118   10 years melissa * Updated a few more readers to respect MetadataOptions. * Added utility …
(edit) @6117   10 years melissa * Updated Imaris readers to respect MetadataOptions. * Fixed a couple of …
(edit) @6116   10 years melissa Updated a few more readers to respect MetadataOptions.
(edit) @6113   10 years melissa Fixed various whitespace issues in AmiraParameters, and updated a few more …
(edit) @6112   10 years melissa Updated several readers to respect MetadataOptions.
(edit) @6111   10 years melissa Fixed how channel indices are reset.
(edit) @6107   10 years melissa Make sure that all RandomAccessInputStreams are closed.
(edit) @6104   10 years melissa * Make sure that DV log files are detected regardless of the …
(edit) @6099   10 years melissa * Fixed a DICOM offset bug. * Prevent Packbits codec from seeking past the …
(edit) @6098   10 years melissa * Allow the comment delimiter to be changed in IniParser. * Fixed a whole …
(edit) @6097   10 years melissa Fixed NPE.
(edit) @6096   10 years melissa Moved plane index parsing; this substantially reduces parsing time.
(edit) @6095   10 years melissa Cleaned up BD Pathway reader a bit; the reader now parses more metadata …
(edit) @6094   10 years melissa * Prevent Leica reader from reading beyond the end of the file. * Fixed a …
(edit) @6092   10 years callan Removed an unused import and fixed a potential null pointer exception as …
(edit) @6091   10 years melissa Updated Flex reader to respect MetadataOptions.
(edit) @6090   10 years melissa Updated InCell 1000 reader to respect MetadataOptions.
(edit) @6089   10 years melissa Updated ICS reader to respect MetadataOptions.
(edit) @6088   10 years melissa Updated ScanR reader to respect MetadataOptions.
(edit) @6086   10 years melissa Updated Leica LIF and Leica TCS readers to respect MetadataOptions.
(edit) @6084   10 years melissa Updated native ND2 reader to respect MetadataOptions.
(edit) @6081   10 years melissa Prevent dimensions stored in the text descriptions from overwriting …
(edit) @6080   10 years melissa Updated Zeiss LSM reader to respect MetadataOptions.
(edit) @6079   10 years melissa Updated MIAS reader to respect MetadataOptions.
(edit) @6078   10 years melissa * Deprecated setMetadataCollected/isMetadataCollected in favor of …
(edit) @6077   10 years melissa * Fixed a bug in POIServiceImpl.getInputStream(String). * Fixed a bug in …
(edit) @6076   10 years melissa Corrected LightSourceSettings.Attenuation population. See …
(edit) @6075   10 years melissa Updated FV1000 reader to respect MetadataOptions.
(edit) @6074   10 years callan PIXELS_ONLY --> MINIMUM metadata level.
(edit) @6073   10 years melissa Minor cleanup in Micromanager reader; openBytes will now return a blank …
(edit) @6072   10 years melissa * Added more generic metadata configuration test. * Fixed a handful of …
(edit) @6071   10 years melissa * Filled in implementations of IMetadataConfigurable methods. * Updated …
(edit) @6070   10 years melissa Added support for Bio-Rad Gel (.1sc) files. Closes #457.
(edit) @6069   10 years callan A scaffold to support metadata configurability of readers.
(edit) @6068   10 years melissa Catch NumberFormatException when parsing exposure times, and adjust SizeC …
(edit) @6067   10 years melissa Allow Zeiss LSM datasets to contain non-LSM TIFF files.
(edit) @6065   10 years melissa Fixed off-by-1 in well column indexing.
(edit) @6062   10 years melissa Improved parsing for version 2 Andor TIFF files and fixed how IFDs with …
(edit) @6061   10 years melissa Avoid skipping beyond the end of the file.
(edit) @6058   10 years melissa Eliminated a few deprecation warnings.
(edit) @6055   10 years curtis Use boxing in a few places.
(edit) @6054   10 years curtis Better ImageJ metadata parsing: * Also populates TimeIncrement. * …
(edit) @6053   10 years melissa * Fixed compile errors in bf-cpp. * Fixed several bugs exposed by …
(edit) @6051   10 years melissa Fixed NPE.
(edit) @6044   10 years melissa Added '.map' as a valid MRC extension. See OMERO #1934.
(edit) @6043   10 years melissa * Better plate name detection. * Well labelling fixes from Bram Gerritsen.
(edit) @6042   10 years melissa Attempt to retrieve dimension information from plane names.
(edit) @6037   10 years melissa Add key/value pairs that map normalized channel indices to 'real' channel …
(edit) @6036   10 years melissa Adjusted physical size Z to account for the fact that it is stored in …
(edit) @6034   10 years melissa * Fixed 16-bit lookup table handling in ImageJ. * Prevent IFD.printIFD …
(edit) @6033   10 years curtis Parse spacing from ImageJ-style TIFF metadata.
(edit) @6031   10 years melissa * Fixed well labeling bug, courtesy of Bram Gerritsen. * Fixed NPE when …
(edit) @6030   10 years melissa Fixed a couple of bugs with reading > 2 GB ICS datasets.
(edit) @6029   10 years melissa * Prevent an NPE in …
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