# # ChangeLog for / # # Generated by Trac 0.12.2 # 02/16/20 12:52:21 Mon, 29 Oct 2007 15:39:04 GMT curtis [3326] * trunk/loci/formats/ome/omebf (deleted) No more need for omebf script. Mon, 29 Oct 2007 15:05:29 GMT melissa [3325] * trunk/loci/plugins/Importer.java (modified) Better string trimming. Mon, 29 Oct 2007 15:01:26 GMT melissa [3324] * trunk/loci/plugins/Importer.java (modified) Make sure that window titles are <= 128 chars. Mon, 29 Oct 2007 14:33:06 GMT melissa [3323] * trunk/loci/formats/in/ImarisHDFReader.java (modified) Populate PixelSize*, if values exist in metadata; better parsing of ... Fri, 26 Oct 2007 20:22:06 GMT melissa [3322] * trunk/loci/formats/in/ND2Reader.java (modified) Fixed endianness. Fri, 26 Oct 2007 19:56:20 GMT melissa [3321] * trunk/loci/formats/in/AVIReader.java (modified) * trunk/loci/formats/in/ImarisReader.java (modified) * trunk/loci/formats/in/ND2Reader.java (modified) * trunk/loci/formats/in/OIBReader.java (modified) * Removed a bunch of unnecessary axis size calculation logic from ... Fri, 26 Oct 2007 18:31:35 GMT melissa [3320] * trunk/loci/formats/in/ND2Reader.java (modified) Multiple series are now correctly detected; replaced evil axis ... Fri, 26 Oct 2007 17:53:20 GMT curtis [3319] * trunk/loci/formats/in/DicomReader.java (modified) Remove unnecessary imports. Fri, 26 Oct 2007 16:28:12 GMT curtis [3318] * trunk/loci/formats/in/FlexReader.java (modified) Typo. Fri, 26 Oct 2007 16:24:29 GMT curtis [3317] * trunk/loci/formats/in/FlexReader.java (modified) Workaround for XML parsing bug with SAX on Windows and Mac OS X. Fri, 26 Oct 2007 13:52:48 GMT melissa [3316] * trunk/loci/formats/in/ImarisHDFReader.java (modified) Reorganized MetadataStore population logic - calls to setLogicalChannel ... Fri, 26 Oct 2007 12:36:48 GMT melissa [3315] * trunk/loci/formats/in/OpenlabReader.java (modified) Temporary hack to unbreak openBytes(int, byte[]). Thu, 25 Oct 2007 21:10:56 GMT curtis [3314] * trunk/loci/plugins/Importer.java (modified) Remove unnecessary import. Thu, 25 Oct 2007 21:10:35 GMT curtis [3313] * trunk/loci/plugins/Importer.java (modified) * trunk/loci/plugins/LociFunctions.java (modified) Print exceptions to Results window rather than with IJ.showMessage or ... Thu, 25 Oct 2007 20:25:44 GMT curtis [3312] * trunk/loci/formats/ImageReader.java (modified) * trunk/loci/formats/ImageWriter.java (modified) Remove references to the optional loci.formats.tools package. Thu, 25 Oct 2007 20:01:25 GMT melissa [3311] * trunk/loci/formats/in/ImarisHDFReader.java (modified) Removed unnecessary import statements. Thu, 25 Oct 2007 19:49:48 GMT curtis [3310] * trunk/build.properties (modified) * trunk/build.xml (modified) Add NetCDF libraries to build properties. Thu, 25 Oct 2007 18:12:20 GMT melissa [3309] * trunk/build.xml (modified) * trunk/jar/bufr-1.1.00.jar (added) * trunk/jar/grib-5.1.03.jar (added) * trunk/jar/netcdf-4.0.jar (added) * trunk/jar/slf4j-jdk14.jar (added) * trunk/loci/formats/in/ImarisHDFReader.java (added) * trunk/loci/formats/in/ImarisTiffReader.java (modified) * trunk/loci/formats/readers.txt (modified) Added support for Imaris 5.5 (HDF-based). Thu, 25 Oct 2007 12:47:39 GMT melissa [3308] * trunk/loci/formats/ChannelSeparator.java (modified) Implemented openBytes(int). Thu, 25 Oct 2007 12:45:48 GMT melissa [3307] * trunk/loci/formats/tools/ImageConverter.java (modified) * trunk/loci/formats/tools/ImageInfo.java (modified) Added command-line flags to ImageConverter (-merge, -separate, -stitch, ... Wed, 24 Oct 2007 21:17:49 GMT curtis [3306] * trunk/loci/formats/TiffTools.java (modified) Fix problem with LuraWave compression. Tue, 23 Oct 2007 14:52:28 GMT melissa [3305] * trunk/loci/plugins/Importer.java (modified) * trunk/loci/plugins/ImporterOptions.java (modified) * trunk/loci/plugins/Slicer.java (added) * trunk/loci/plugins/plugins.config (modified) Added stack slicing plugin, which replaces the channel splitting logic ... Tue, 23 Oct 2007 13:15:27 GMT melissa [3304] * trunk/loci/formats/in/BaseTiffReader.java (modified) * trunk/loci/formats/in/ZeissLSMReader.java (modified) Better indexed color support in Zeiss LSM. Mon, 22 Oct 2007 14:07:41 GMT melissa [3303] * trunk/loci/formats/in/ND2Reader.java (modified) Minor adjustment to offset calculation. Fri, 19 Oct 2007 15:54:16 GMT melissa [3302] * trunk/loci/formats/in/BaseTiffReader.java (modified) * trunk/loci/formats/in/ZeissLSMReader.java (modified) Set indexed = false if the lookup table is too small. Thu, 18 Oct 2007 18:56:14 GMT melissa [3301] * trunk/loci/formats/in/AVIReader.java (modified) Temporarily commented out Cinepak logic. Thu, 18 Oct 2007 18:42:09 GMT melissa [3300] * trunk/loci/formats/TiffIFDEntry.java (modified) * trunk/loci/formats/TiffTools.java (modified) Changed TiffIFDEntry's 'offset' field to 'long'; calls to ... Thu, 18 Oct 2007 18:09:23 GMT melissa [3299] * trunk/loci/formats/in/BMPReader.java (modified) Alpha channel is now handled correctly. Thu, 18 Oct 2007 15:43:17 GMT melissa [3298] * trunk/loci/formats/in/OIFReader.java (modified) Fixed filename parsing logic. Thu, 18 Oct 2007 13:27:58 GMT melissa [3297] * trunk/loci/formats/ChannelFiller.java (modified) Fixed openBytes(int, byte[]) so it no longer returns all zeros. Wed, 17 Oct 2007 20:10:45 GMT curtis [3296] * trunk/loci/formats/TiffTools.java (modified) * trunk/utils/TiffComment.java (modified) Print a message if no TIFF comment is found, rather than throwing an ... Wed, 17 Oct 2007 19:14:06 GMT melissa [3295] * tags/loci-tools-2007-Oct-17/loci/plugins (copied) 2007 Oct 17 release of LOCI Tools Wed, 17 Oct 2007 19:14:06 GMT melissa [3294] * tags/loci-tools-2007-Oct-17/loci/ome (copied) 2007 Oct 17 release of LOCI Tools Wed, 17 Oct 2007 19:14:06 GMT melissa [3293] * tags/loci-tools-2007-Oct-17/loci/formats (copied) 2007 Oct 17 release of LOCI Tools Wed, 17 Oct 2007 19:14:05 GMT melissa [3292] * tags/loci-tools-2007-Oct-17/jar (copied) 2007 Oct 17 release of LOCI Tools Wed, 17 Oct 2007 19:14:05 GMT melissa [3291] * tags/loci-tools-2007-Oct-17/checkstyle.xml (copied) 2007 Oct 17 release of LOCI Tools Wed, 17 Oct 2007 19:14:05 GMT melissa [3290] * tags/loci-tools-2007-Oct-17/build.xml (copied) 2007 Oct 17 release of LOCI Tools Wed, 17 Oct 2007 19:14:05 GMT melissa [3289] * tags/loci-tools-2007-Oct-17/build.properties (copied) 2007 Oct 17 release of LOCI Tools Wed, 17 Oct 2007 19:14:04 GMT melissa [3288] * tags/loci-tools-2007-Oct-17 (added) * tags/loci-tools-2007-Oct-17/loci (added) 2007 Oct 17 release of LOCI Tools Wed, 17 Oct 2007 19:08:32 GMT melissa [3287] * trunk/loci/formats/doc/whats-new.txt (modified) Updated what's new for today's release. Wed, 17 Oct 2007 19:03:51 GMT melissa [3286] * trunk/loci/formats/in/ZeissZVIReader.java (modified) Fixed Z/T reversal. Wed, 17 Oct 2007 15:11:30 GMT melissa [3285] * trunk/loci/formats/in/AVIReader.java (modified) If bmpColorsUsed == 0, set it to 2^bitsPerPixel. Wed, 17 Oct 2007 15:05:02 GMT melissa [3284] * trunk/loci/formats/in/PictReader.java (modified) Corrected pixel type for 5-5-5 RGB data. Wed, 17 Oct 2007 14:34:39 GMT melissa [3283] * trunk/loci/formats/in/DicomReader.java (modified) Make sure elementLength/compression indicators are reset. Wed, 17 Oct 2007 13:37:19 GMT melissa [3282] * trunk/loci/formats/in/DicomReader.java (modified) Fixed case logic for setting pixel scale value. Wed, 17 Oct 2007 13:02:47 GMT melissa [3281] * trunk/loci/formats/DataTools.java (modified) * trunk/loci/formats/FormatReader.java (modified) * trunk/loci/formats/MinMaxCalculator.java (modified) * trunk/loci/formats/in/DicomReader.java (modified) * trunk/loci/formats/tools/ImageInfo.java (modified) * trunk/loci/plugins/Util.java (modified) Finished logic to correctly handle signed data. Tue, 16 Oct 2007 17:38:12 GMT melissa [3280] * trunk/loci/plugins/Util.java (modified) Correctly handle signed data. Tue, 16 Oct 2007 16:10:26 GMT melissa [3279] * trunk/loci/formats/TiffTools.java (modified) * trunk/loci/formats/codec/BaseCodec.java (modified) * trunk/loci/formats/codec/Codec.java (modified) * trunk/loci/formats/codec/JPEGCodec.java (modified) * trunk/loci/formats/codec/PackbitsCodec.java (modified) * trunk/loci/formats/in/DicomReader.java (modified) * trunk/loci/formats/in/PSDReader.java (modified) * trunk/loci/formats/in/PictReader.java (modified) * Added new API method to loci.formats.codec.Codec to allow ... Tue, 16 Oct 2007 13:22:15 GMT melissa [3278] * trunk/loci/formats/ChannelFiller.java (modified) * trunk/loci/formats/FormatReader.java (modified) * trunk/loci/formats/ImageTools.java (modified) Fixed indexed to RGB conversion. Mon, 15 Oct 2007 17:33:20 GMT curtis [3277] * trunk/loci/plugins/Importer.java (modified) * trunk/loci/plugins/ImporterOptions.java (modified) Fix problems with duplicate macro options. Mon, 15 Oct 2007 15:21:53 GMT melissa [3276] * trunk/loci/formats/in/LIFReader.java (modified) * trunk/loci/plugins/Importer.java (modified) * Fixed bug with "open each channel in new window" + "specify range". * ... Sun, 14 Oct 2007 16:02:55 GMT melissa [3275] * trunk/loci/formats/FormatTools.java (modified) * trunk/loci/formats/in/OMETiffReader.java (modified) * trunk/loci/plugins/Importer.java (modified) Fixed ZCT calculation for indexed color images. Sat, 13 Oct 2007 18:25:14 GMT melissa [3274] * trunk/loci/formats/in/OMETiffReader.java (modified) Don't need to manually prepend directory name to file name. Fri, 12 Oct 2007 20:30:46 GMT curtis [3273] * trunk/utils/MakeTestOmeTiff.java (modified) Fix little bug in arg parsing. Fri, 12 Oct 2007 18:04:02 GMT melissa [3272] * trunk/loci/formats/TiffTools.java (modified) More tiling/BigTIFF fixes. Fri, 12 Oct 2007 16:33:27 GMT melissa [3271] * trunk/loci/formats/in/OMETiffReader.java (modified) Corrected image count calculation if we have indexed color planes. Fri, 12 Oct 2007 13:46:09 GMT melissa [3270] * trunk/loci/formats/TiffTools.java (modified) Fixed tiling bug and added remaining BigTIFF types. Thu, 11 Oct 2007 20:17:49 GMT melissa [3269] * trunk/loci/formats/TiffTools.java (modified) * trunk/loci/formats/in/NikonReader.java (modified) Initial implementation of BigTIFF. Thu, 11 Oct 2007 19:32:43 GMT melissa [3268] * trunk/loci/formats/ImageTools.java (modified) * trunk/loci/formats/TiffTools.java (modified) * trunk/loci/formats/in/EPSReader.java (modified) * trunk/loci/formats/in/ND2Reader.java (modified) Removed several hacks that added an extra blank channel if C == 2. Thu, 11 Oct 2007 18:45:37 GMT melissa [3267] * trunk/loci/formats/ImageTools.java (modified) * trunk/loci/formats/TwoChannelColorSpace.java (added) Added new ColorSpace for 2-channel images; updated ImageTools ... Thu, 11 Oct 2007 17:46:53 GMT melissa [3266] * trunk/loci/formats/in/OMETiffReader.java (modified) Fixed plane number -> IFD mapping for primary file. Thu, 11 Oct 2007 17:23:08 GMT curtis [3265] * trunk/loci/formats/DataTools.java (modified) * trunk/loci/formats/ImageTools.java (modified) Clean up and debug image construction methods. Thu, 11 Oct 2007 17:22:43 GMT curtis [3264] * trunk/loci/formats/TiffTools.java (modified) Use BYTES_PER_ENTRY instead of hardcoded 12 where relevant. Thu, 11 Oct 2007 17:20:56 GMT curtis [3263] * trunk/loci/formats/in/OMETiffReader.java (modified) Rename "used" to "usedFiles" so it is easier to search. Thu, 11 Oct 2007 15:51:23 GMT curtis [3262] * trunk/loci/formats/codec/MSVideoCodec.java (modified) Remove unnecessary imports. Thu, 11 Oct 2007 14:49:55 GMT melissa [3261] * trunk/loci/formats/in/OMETiffReader.java (modified) Only parse the primary file once. Thu, 11 Oct 2007 14:26:32 GMT curtis [3260] * trunk/utils/TiffComment.java (modified) TiffComment now has a trivial implementation thanks to ... Thu, 11 Oct 2007 14:17:01 GMT curtis [3259] * trunk/loci/formats/TiffTools.java (modified) * trunk/loci/formats/in/BaseTiffReader.java (modified) * trunk/loci/formats/in/OMETiffReader.java (modified) * Add TiffTools.getComment convenience method. * Some efficiency ... Thu, 11 Oct 2007 13:27:06 GMT melissa [3258] * trunk/loci/plugins/Exporter.java (modified) Removed option to force compatible pixel type. Wed, 10 Oct 2007 22:26:11 GMT curtis [3257] * trunk/loci/formats/ImageTools.java (modified) Standardize getPixels methods to use a single sample model checker ... Wed, 10 Oct 2007 20:12:03 GMT curtis [3256] * trunk/loci/plugins/Exporter.java (modified) Comment out reference to broken makeType method. Wed, 10 Oct 2007 20:10:46 GMT curtis [3255] * trunk/loci/formats/gui/DataConverter.java (modified) Comment out reference to broken makeType method. Wed, 10 Oct 2007 20:09:41 GMT curtis [3254] * trunk/loci/formats/ImageTools.java (modified) Fix getPixels implementations to never use makeType, and get rid of ... Wed, 10 Oct 2007 17:24:16 GMT melissa [3253] * trunk/loci/formats/ChannelSeparator.java (modified) * trunk/loci/formats/DataTools.java (modified) * trunk/loci/formats/FormatReader.java (modified) * trunk/loci/formats/ImageTools.java (modified) * trunk/loci/formats/TiffTools.java (modified) All byte array to float array conversions are now handled by ... Wed, 10 Oct 2007 16:19:24 GMT melissa [3252] * trunk/loci/formats/TiffTools.java (modified) Fixed bug in fake rows per strip calculation. Wed, 10 Oct 2007 15:52:02 GMT melissa [3251] * trunk/loci/formats/FormatWriter.java (modified) Added default saveBytes implementations. To use saveBytes, a ... Tue, 09 Oct 2007 20:06:41 GMT curtis [3250] * trunk/loci/formats/gui/DataConverter.java (modified) Disable editing of file path text boxes for now. Tue, 09 Oct 2007 19:35:38 GMT melissa [3249] * trunk/loci/formats/in/LegacyQTReader.java (modified) * trunk/loci/formats/in/QTReader.java (modified) Fixed pixel type mismatch. Tue, 09 Oct 2007 18:57:12 GMT melissa [3248] * trunk/loci/formats/in/OMETiffReader.java (modified) Fixed series/currentSeries typo; update file map along with IFD map. Tue, 09 Oct 2007 18:38:32 GMT melissa [3247] * trunk/loci/formats/in/ZeissZVIReader.java (modified) Added support for JPEG-compressed ZVI images. Tue, 09 Oct 2007 18:17:41 GMT melissa [3246] * trunk/loci/formats/in/OMETiffReader.java (modified) Fixed one last bug. Tue, 09 Oct 2007 17:55:42 GMT melissa [3245] * trunk/loci/formats/in/OMETiffReader.java (modified) Parse XML using SAX. Mon, 08 Oct 2007 18:58:42 GMT melissa [3244] * trunk/loci/plugins/CustomImage.java (modified) * trunk/loci/plugins/Importer.java (modified) * trunk/loci/plugins/ImporterOptions.java (modified) Added option to open each plane in a separate window; fixed CustomImage ... Mon, 08 Oct 2007 17:27:44 GMT curtis [3243] * trunk/loci/plugins/Importer.java (modified) Echo status message events to the ImageJ status bar. Mon, 08 Oct 2007 17:18:25 GMT curtis [3242] * trunk/loci/formats/FormatTools.java (modified) Add Javadoc for getReorderedIndex. Mon, 08 Oct 2007 17:14:08 GMT curtis [3241] * trunk/loci/formats/in/OMETiffReader.java (modified) Another status message, indicating parsing of each constituent OME- TIFF ... Mon, 08 Oct 2007 17:08:52 GMT curtis [3240] * trunk/loci/formats/in/OMETiffReader.java (modified) Add status message for each TIFF file checked. Mon, 08 Oct 2007 17:07:59 GMT melissa [3239] * trunk/loci/formats/in/LIFReader.java (modified) Fixed bug with >2GB files. Mon, 08 Oct 2007 16:53:46 GMT melissa [3238] * trunk/loci/formats/in/OMETiffReader.java (modified) Improved logic for mapping plane numbers to IFDs - scrambled TiffData ... Mon, 08 Oct 2007 15:06:11 GMT melissa [3237] * trunk/loci/formats/in/BaseTiffReader.java (modified) Fixed sizeC calculation for RGBA TIFFs. Sat, 06 Oct 2007 00:23:08 GMT curtis [3236] * trunk/utils/MakeTestOmeTiff.java (modified) Use openmicroscopy.org, not org.openmicroscopy, for IDs. Fri, 05 Oct 2007 20:33:52 GMT curtis [3235] * trunk/utils/MakeTestOmeTiff.java (modified) Fix typo in Pixels IDs. Fri, 05 Oct 2007 20:19:01 GMT curtis [3234] * trunk/loci/formats/doc/whats-new.txt (modified) Brief what's new for minor 2007 Oct 5 Bio-Formats release. Fri, 05 Oct 2007 19:55:11 GMT curtis [3233] * trunk/utils/MakeTestOmeTiff.java (modified) Fix bug with scramble feature. Fri, 05 Oct 2007 19:43:57 GMT curtis [3232] * trunk/utils/MakeTestOmeTiff.java (modified) Fix multi-Image and multi-Pixels TiffData tags; first cut at IFD ... Fri, 05 Oct 2007 18:14:16 GMT curtis [3231] * trunk/utils/MakeTestOmeTiff.java (modified) Generator now distinguishes between multiple Images vs multiple Pixels. Fri, 05 Oct 2007 18:05:41 GMT melissa [3230] * trunk/loci/formats/in/OMETiffReader.java (modified) Fixed width/height mismatch detection, TiffData scrambling in single- ... Fri, 05 Oct 2007 16:54:53 GMT curtis [3229] * trunk/utils/MakeTestOmeTiff.java (modified) OME-TIFF sample data generator now writes OME-TIFF with multiple series. ... Fri, 05 Oct 2007 15:51:48 GMT curtis [3228] * trunk/utils/MakeTestOmeTiff.java (modified) Progress on OME-TIFF sample file generator. Currently generates plain ... Fri, 05 Oct 2007 15:09:04 GMT melissa [3227] * trunk/loci/formats/in/OMETiffReader.java (modified) Fixed min TiffData calculation.