source: trunk/components/bio-formats/src/loci/formats/in @ 6985

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(edit) @6967   9 years melissa Fixed SizeT calculation.
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(edit) @6959   9 years melissa Fixed well dimension parsing and calculation, so that the ScanR reader no …
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(edit) @6917   9 years callan Solution for underscores in wavelength names. (Fixes #558)
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(edit) @6845   9 years melissa Added support for Varian FDF files. Closes #474.
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(edit) @6842   9 years melissa Added support for multi-position Zeiss LSM data. Closes #527.
(edit) @6838   9 years melissa One more signedness fix, as pointed out by Rubén Muñoz.
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(edit) @6810   10 years melissa Force the pixel type to be unsigned, regardless of what is actually stored …
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(edit) @6801   10 years melissa * Parse metadata from SimplePCI TIFFs. * Slightly better Z/T detection for …
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(edit) @6797   10 years melissa Added support for FEI TIFF files, specifically those from S-FEG and Helios …
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(edit) @6790   10 years melissa Initial version of ECAT 7 reader. Closes #487.
(edit) @6789   10 years curtis Fix for NullPointerException.
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(edit) @6786   10 years melissa More OME-XML validation fixes, see #520.
(edit) @6784   10 years melissa More OME-XML validation fixes. See #520.
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(edit) @6758   10 years melissa Added support for Perkin-Elmer densitometer data. Closes #490.
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(edit) @6735   10 years melissa * Handful of type checking fixes. See #273. * Strip whitespace from …
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(edit) @6720   10 years melissa Populate physical pixel sizes, if present. Closes #515.
(edit) @6713   10 years melissa Prevent ArithmeticException if stage coordinates are not present.
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(edit) @6697   10 years melissa First attempt at parsing stage coordinates from LSM files.
(edit) @6695   10 years melissa Fixed problems with unaligned RLE-compressed images. Closes #511.
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(edit) @6692   10 years melissa * Updated CellWorXReader to delegate to DeltavisionReader when reading …
(edit) @6690   10 years melissa Initial version of CellWorX .pnl reader.
(edit) @6689   10 years melissa Fixed emission wavelength parsing.
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(edit) @6662   10 years melissa Removed some obsolete hacks that prevented physical sizes from being …
(edit) @6661   10 years melissa Better physical X/Y size parsing.
(edit) @6655   10 years melissa Added MetadataLevel.NO_OVERLAYS, and updated readers accordingly.
(edit) @6645   10 years melissa Fixed Objective parsing when Immersion and Correction are reversed.
(edit) @6635   10 years melissa Be more thorough when searching for the .dv file that matches a .log or …
(edit) @6630   10 years callan Set fill color as well as stroke color for mask ROI.
(edit) @6629   10 years callan Fix shape indexes for ellipse X and Y radii.
(edit) @6628   10 years callan Utilize the shape label rather than a seperate text shape for MIAS ROI.
(edit) @6618   10 years callan Restoring MIAS reader overlay support.
(edit) @6612   10 years melissa Fixed parsing of large OME-XML files and pre-2010-04 files with …
(edit) @6606   10 years curtis Fix bug with fake data generation when rgbChannelCount>1.
(edit) @6601   10 years melissa Added 'unknown' domain and updated various readers to use the unknown …
(edit) @6597   10 years melissa Better XZ/XT scan detection; see  omero:2321.
(edit) @6573   10 years melissa Fixed GZIP pixel data detection for ICS files.
(edit) @6568   10 years melissa Various fixes to OME-XML/OME-TIFF handling, including support for …
(edit) @6567   10 years melissa Fixed how pixels files are found, so that having multiple *.vws files in …
(edit) @6566   10 years melissa Tweaked pixel block detection to work with Slidebook 5.0.0.5 files.
(edit) @6553   10 years melissa Fixed a handful of core metadata and pixels offset bugs in Visitech …
(edit) @6545   10 years curtis For indexed color fake data, return a different LUT for each channel.
(edit) @6534   10 years melissa Fixed a few issues with 16-bit LUTs.
(edit) @6531   10 years callan Re-run of code generation; working copy schema. Huge merge. (See …
(edit) @6527   10 years melissa Tweaked Metamorph reader's type detection so that TIFFs are not …
(edit) @6526   10 years melissa Fixed Detector indices so that Detectors are properly populated and linked …
(edit) @6515   10 years melissa Allow Metamorph reader to pick up TIFF files.
(edit) @6507   10 years melissa Couple of minor reader fixes.
(edit) @6503   10 years melissa Fixed XZ/XT scans to display as they do in Olympus' software.
(edit) @6501   10 years melissa Tweaked isThisType to only pick up valid TIFF files that are in the same …
(edit) @6495   10 years melissa Updated email address.
(edit) @6494   10 years melissa Added support for multi-file OME-TIFF export. Closes #485.
(edit) @6489   10 years melissa Fixed Nikon tag parsing.
(edit) @6487   10 years melissa Minor fixes to make metadata level tests pass.
(edit) @6486   10 years melissa Make sure that CoreMetadata.indexed is set correctly, regardless of the …
(edit) @6484   10 years melissa Updated Channel -> Laser linkage rule in accordance with r6076.
(edit) @6483   10 years melissa Populate Laser.Model, if present. See  omero:2475.
(edit) @6465   10 years melissa Added some debugging statements so that missing TIFF files are reported. …
(edit) @6461   10 years melissa Fixed well ordering bug, courtesy of Rubén Muñoz.
(edit) @6459   10 years melissa Synced up export/MetadataConverter fixes between trunk and 4.2. OME-TIFF …
(edit) @6458   10 years melissa Moved ome.xml.r201004.* to ome.xml.model.* in trunk.
(edit) @6451   10 years callan Need fileLength parsed in parseSeriesTag() for parseImageTag() to be …
(edit) @6443   10 years curtis Fix TextReader.openBytes to work properly.
(edit) @6440   10 years callan Fixing issues with endianness parsing for OME-TIFFs. Re-run of code …
(edit) @6437   10 years curtis Add scaleFactor option to FakeReader for scaling gradient pixel values.
(edit) @6430   10 years melissa * Updated OMEXMLMetadataImpl based on  ome-xml:r618. * Fixed a bunch of …
(edit) @6426   10 years melissa Fixed various metadata population bugs in the FV1000 reader. See …
(edit) @6419   10 years curtis Fix bugs in FakeReader with indexed color.
(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) @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) @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) @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) @6349   10 years melissa Fixed various bugs exposed by test suite.
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