source: trunk @ 7446

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Diff Rev Age Author Log Message
(edit) @7446   9 years melissa Parse and apply LUTs stored in the 'u32OffsetChannelColors' block. See …
(edit) @7443   9 years melissa Use the 'uiSequenceCount' attribute to calculate the image count. Closes …
(edit) @7442   9 years melissa Populate channel colors even if the MetadataLevel is set to MINIMUM. This …
(edit) @7433   9 years melissa Make sure that channel names are populated for screen data.
(edit) @7429   9 years melissa Adjust the number of padding bytes based upon the total number of bytes …
(edit) @7428   9 years melissa * Added setValidBitsPerPixel(int) to IFormatWriter. * Updated ICSWriter to …
(edit) @7427   9 years melissa Catch exception when parsing .mdb files, so that .lsm files can be read …
(edit) @7424   9 years hinerm Enhanced BF-ITK build for windows. The dist target is now specific to a …
(edit) @7418   9 years callan More robust InCellReader XML parsing. (See #623) Specifically handled: * …
(edit) @7417   9 years callan Made InCellReader support a little more generic to accomodate InCell 2000 …
(edit) @7402   9 years melissa Moved missing OME-XML messages into OMEXMLServiceImpl. Closes #604.
(edit) @7401   9 years melissa Override openBytes, so that correct pixels are returned for each series.
(edit) @7400   9 years melissa Added series number to one last failure message.
(edit) @7389   9 years callan Resolve OpenlabReader thread safety as it applies to the internal static …
(edit) @7386   9 years melissa Added some debugging to help track down an FV1000 bug.
(edit) @7384   9 years melissa Fixed well row and column indices, because I obviously didn't read r7379
(edit) @7379   9 years melissa Added better type checking to ScreenReader, so it is now included in …
(edit) @7375   9 years melissa Added more sophisticated image name parsing to OpenlabReader. Closes …
(edit) @7374   9 years melissa Fixed series count population assertBlock's Y offset calculation.
(edit) @7373   9 years melissa Sanitize XML before parsing and prevent XML parsing failures from causing …
(edit) @7372   9 years callan Include series in any failures. (See  omero:#3627)
(edit) @7371   9 years callan Extended OMERO openBytes() test case (See  omero:#3627) * Go through every …
(edit) @7370   9 years melissa Some polishing in ScreenReader. Wells are now sorted correctly and SPW …
(edit) @7357   9 years melissa Make sure references are resolved before resetting an OMEXMLMetadata's …
(edit) @7356   9 years melissa Smarter pixel offset detection for Visitech XYS files.
(edit) @7355   9 years melissa Fixed a handful of problems with reading Amira sub-images.
(edit) @7354   9 years melissa Removed erroneous call to skipBytes, so that sub-images of uncompressed …
(edit) @7353   9 years melissa * Allow the same plane to be read multiple times in succession. * Fixed …
(edit) @7352   9 years melissa Restored getFirst(), getLast(), and getStep() as deprecated methods.
(edit) @7351   9 years melissa Fixed AVI reader to allow a compressed plane to be accessed multiple times …
(edit) @7350   9 years melissa * Reader wrapper implementations that manipulate byte arrays now declare …
(edit) @7349   9 years melissa Added method to AWTImageTools for retrieving subimages. Readers now use …
(edit) @7339   9 years melissa Fixed row reversal to work correctly with sub-images.
(edit) @7338   9 years melissa Updated FEI reader to properly support sub-image reading.
(edit) @7337   9 years melissa Fixed plane size and pixel offset calculations when opening a sub-image.
(edit) @7336   9 years melissa Fixed MD5 calculations for planes whose SizeY is odd.
(edit) @7334   9 years melissa Updated what's new for today's release.
(edit) @7333   9 years melissa Initial version of generic screen reader. It still needs a lot of work, …
(edit) @7319   9 years melissa Added Ant target to run OMERO openBytes tests. To use it: 'ant …
(edit) @7318   9 years melissa ImageTools.splitChannels now takes an extra int parameter that specifies …
(edit) @7317   9 years melissa Make image names more easily identifiable in the original metadata.
(edit) @7316   9 years melissa Return a blank plane if a TIFF file is missing, just like we do with many …
(edit) @7315   9 years callan Script to run OMERO openBytes() tests on a suite of files on Hudson.
(edit) @7314   9 years callan Fix a missing variable initialization in the OMERO openBytes() test case.
(edit) @7313   9 years callan Test.java (from  omero:#3627) port to a full blown TestNG test case also …
(edit) @7312   9 years callan Adding required ome-xml project to the test-suite component Eclipse …
(edit) @7311   9 years melissa A couple of fixes for reading a sub-image of the second channel in 2 …
(edit) @7310   9 years hinerm Added code allowing jar paths and trailing slashes (or absence thereof) on …
(edit) @7309   9 years callan Fix min/max calculation in the "slush" area outside the actual pixel count …
(edit) @7287   9 years melissa Parse some more (undocumented) metadata from STK files, including channel …
(edit) @7286   9 years curtis Fix problem with skipping past EOF.
(edit) @7285   9 years curtis Add compression type to original metadata table.
(edit) @7284   9 years callan Fixed minMaxDone population. Much more thorough test case that includes …
(edit) @7283   9 years callan Solution for minima and maxima calculation when using block based …
(edit) @7282   9 years callan Fix documentation locations and header comment in XML annotation test.
(edit) @7281   9 years hinerm Corrected a missing end brace in the BFITK plug-in code.
(edit) @7280   9 years melissa Close readers left open by the openImage/openSubImage macro functions.
(edit) @7278   9 years melissa Fixed one more typo.
(edit) @7277   9 years curtis Fix typo.
(edit) @7276   9 years curtis Clarify Autoscale help text. These changes are based on updated text …
(edit) @7275   9 years melissa Updated metadata support documentation.
(edit) @7274   9 years melissa Updated version numbers to 4.3-DEV.
(edit) @7260   9 years melissa * Skip over empty .lsm files instead of throwing an EOFException. * …
(edit) @7259   9 years melissa Improved stage position parsing.
(edit) @7258   9 years melissa Fixed ImagePlus retrieval methods so that the calibration is properly …
(edit) @7257   9 years melissa Fixed calculation in r7255 so that tests pass again.
(edit) @7256   9 years melissa Fixed interleaving bugs in ImageInfo and ImageTools.make24Bits.
(edit) @7255   9 years melissa Better image count calculation; this fixes the case when we have multiple …
(edit) @7254   9 years melissa Fixed small bug in r7236 that prevented multi-channel 16-bit …
(edit) @7253   9 years melissa Fixed APNG writer to properly handle interleaved little-endian data.
(edit) @7252   9 years melissa Fixed dragging and dropping so that an "Open" dialog is not shown and …
(edit) @7251   9 years melissa Catch IOException when parsing ROIs, so that we can still read the file if …
(edit) @7250   9 years curtis Better parsing of ValidBitCounts.
(edit) @7249   9 years curtis Add debugging statements for FV1000 INI entries.
(edit) @7247   9 years callan Restoring XML annotation write testing (See  omero:#3269); re-run of code …
(edit) @7246   9 years melissa Fixed channel name population.
(edit) @7245   9 years curtis Add ability to specify bitsPerPixel to fake reader.
(edit) @7244   9 years melissa Fixed dimension adjustment for spool files.
(edit) @7242   9 years callan These types of comparisons no longer work and the XML annotation test …
(edit) @7241   9 years callan Fix build, making sure that the stylesheet is included in the ome-xml JAR.
(edit) @7240   9 years callan Proper XML annotation support (See  omero:#3269); re-run of code …
(edit) @7239   9 years melissa Remove BinData elements from a copy of the writer's MetadataRetrieve, …
(edit) @7238   9 years melissa * Added macro functions for retrieving physical size and version …
(edit) @7237   9 years melissa Preserve physical pixel sizes when writing vanilla TIFF files.
(edit) @7236   9 years melissa * Properly unpack 16-bit BufferedImages into a byte array. Fix courtesy …
(edit) @7235   9 years melissa Override get*BitLookupTable() methods so that files with a different LUT …
(edit) @7234   9 years hinerm Updated the bf-itk plug-in so that it no longer tries to instantiate a JVM …
(edit) @7231   9 years melissa Use an ImageWriter instead of a TiffWriter so that OME-TIFF files are …
(edit) @7230   9 years callan File handle open/close logging at the TRACE level and a test case to pick …
(edit) @7229   9 years melissa Prevent NPEs if detector metadata is missing.
(edit) @7228   9 years melissa Added reader for .aim files. Closes #597.
(edit) @7227   9 years melissa Use the sum of all position values stored for a particular position …
(edit) @7226   9 years callan Attempt to fix issues with leaking file handles during planar writing …
(edit) @7225   9 years melissa Switched getPixelTypes()/getPixelTypes(String) delegation, so that …
(edit) @7224   9 years melissa Fixed pixel offset bug.
(edit) @7223   9 years melissa Prevent the 'open' option from being recorded twice. Closes #596. This …
(edit) @7222   9 years melissa Preserve custom color choices. Closes #586.
(edit) @7221   9 years hinerm Modified build.xml to copy platform-specific files from the …
(edit) @7220   9 years melissa Added support for JPEG-compressed AVIs. Closes #569.
(edit) @7218   9 years melissa Fixed ImageViewer's default metadata population; closes #525.
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