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Commits on Mar 13, 2012
  1. Add skeleton ZeissAxioVisionReader

    Roger Leigh committed Mar 13, 2012
Commits on Mar 12, 2012
  1. Merge pull request #33 from joshmoore/7239-submods

    melissalinkert committed Mar 12, 2012
    OME build hooks
  2. Merge pull request #35 from ctrueden/scijava

    melissalinkert committed Mar 12, 2012
    Update Bio-Formats POMs to use scijava base POM
Commits on Mar 9, 2012
Commits on Mar 6, 2012
  1. Merge pull request #27 from melissalinkert/sprint8-bug-fixes

    chris-allan committed Mar 6, 2012
    Sprint8 bug fixes
Commits on Feb 29, 2012
  1. ICSWriter: Allow the output order to be changed

    melissalinkert committed Feb 29, 2012
    By default, planes will be written in XYZTC order.  However, there is
    now a 'setOutputOrder(String)' method, so that the ordering may be
    changed with minimal effort.
Commits on Feb 28, 2012
  1. Merge pull request #32 from melissalinkert/sprint9-bug-fixes

    chris-allan committed Feb 28, 2012
    Sprint9 bug fixes
  2. OME build hooks

    joshmoore committed Feb 28, 2012
    build.xml is called by the OME ./build.py-based build
    system. The only two targets that are currently supported
    are "dist" and "clean". "test" etc. will also need hooks.
    
    "dist" calls the regular Bio-Formats build and then calls
    out to ome.xml which re-distributes the jars basd on the
    ivy.xml specification.
    
    This logic can't sit in the build.xml file itself because
    of at least one naming conflict (root.dir)
  3. Add '-xmlspaces' option for specifying indentation

    melissalinkert committed Feb 28, 2012
    Previously, 3 spaces were used for indenting OME-XML.  This isn't
    optimal for all use cases, so now we allow the number of spaces to be
    specified, e.g. '-xmlspaces 4'.  See #8147.
  4. Add '-no-sas' option, to disable SA display

    melissalinkert committed Feb 28, 2012
    See #8148.  Using the '-no-sas' option with '-omexml' will print OME-XML
    that has the StructuredAnnotation elements removed.
    
    To test, verify that 'java loci.formats.tools.ImageInfo -omexml file'
    displays StructuredAnnotations, while 'java loci.formats.tools.ImageInfo
    -no-sas -omexml file' does not.
  5. Ensure that the tile dimensions are not too large

    melissalinkert committed Feb 28, 2012
    The last tile in a row or column is often smaller than the optimal size.
    Instead of just assuming that the optimal dimensions will work, we
    adjust the width and height of the last tile as needed.
    
    This should fix all sorts of failures in the BIOFORMATS-openbytes-performance
    Jenkins job.
  6. Fix possible NPE

    melissalinkert committed Feb 27, 2012
    Introduced in f5fe876da0b5373a3230b250f8567cc4e1fdf04e.
  7. Do not convert OTF elements

    melissalinkert committed Feb 25, 2012
    The OTF element was deprecated in the 2011-06 OME-XML schema.  As it is
    deprecated and often written incorrectly, we now no longer convert it.
    
    See #7886.
  8. Be sure to remove singleton files with no Z index

    melissalinkert committed Feb 25, 2012
    This prevents an ArrayIndexOutOfBoundsException when a single extra file
    is placed first on the list of used files.
    
    Reported by Helio Roque.
  9. Fix outdated statements in the readme files

    melissalinkert committed Feb 25, 2012
    The top-level directory is now 'components/scifio', and Maven 3 is
    supported as of earlier today.
  10. Add missing null check for the ND2Handler

    melissalinkert committed Feb 24, 2012
    Noticed by FindBugs.
  11. Add missing 'break' statements

    melissalinkert committed Feb 24, 2012
    Noticed by FindBugs.
  12. Fill in missing units for the C axis

    melissalinkert committed Feb 24, 2012
    Some software (notably Huygens) does not feel the need to write a unit
    for the C axis.  This causes our poor ICS reader a great deal of
    confusion, as the index into the array of units is now wrong.  So now we
    check for a missing unit, and add in "nm" for the C axis as appropriate.
    
    Reported by Glen MacDonald.
  13. Allow units to be specified as "micrometers"

    melissalinkert committed Feb 24, 2012
    Previously, only "um" and "microns" were allowed.  Since it's all the
    same unit, allow "micrometers" too.
    
    Reported by Glen MacDonald.
  14. Flip the planes upside-down

    melissalinkert committed Feb 23, 2012
    In carefully re-reading the MRC specification, the image origin is
    assumed to be in the lower left corner (not the the upper left corner).
    To correct for this, we now reverse the order of the rows prior to
    returning the image.
  15. Stop parsing tags if we have reached the EOF

    melissalinkert committed Feb 22, 2012
    Noticed by Anthony Luu.
  16. Add some extra diagnostics to the log file

    melissalinkert committed Feb 20, 2012
    The hope is that this will help to track down why a particular directory
    is detected as being invalid.
  17. Only overwrite the channel count for non-RGB data

    melissalinkert committed Feb 17, 2012
    The user is allowed to do whatever they want to the dimensions in
    ImageJ; sometimes, this means that the channel count is changed to 1
    when RGB data is actually stored in the file.
    
    Noticed by Tom Kazimiers.
  18. Fix configuration file path name checking

    melissalinkert committed Feb 17, 2012
    This allows the data tests to run again.
  19. Check MicroManager metadata files more thoroughly

    melissalinkert committed Feb 15, 2012
    ...so that we do not inadvertantly pick up files that do not really
    belong to MicroManager datasets.
    
    Noticed by Tom Kazimiers.
Commits on Feb 27, 2012
  1. Use the last n detector gains and offsets

    melissalinkert committed Feb 27, 2012
    This fixes the detector index so that the last n gains and offsets are
    used, instead of the first n.
    
    See #7897.
  2. Merge pull request #31 from melissalinkert/bf-itk-fixes

    chris-allan committed Feb 27, 2012
    BF-ITK build fix
Commits on Feb 24, 2012
Commits on Feb 17, 2012
  1. Merge pull request #29 from melissalinkert/build-fix

    chris-allan committed Feb 17, 2012
    Build fix: Disable failing encoding tests
  2. Merge pull request #28 from melissalinkert/build-fix

    chris-allan committed Feb 17, 2012
    Build fix: Reintroduce import of loci.common.DataTools
Commits on Feb 16, 2012
  1. Reintroduce import of loci.common.DataTools

    melissalinkert committed Feb 16, 2012
    This was accidentally removed while resolving merge conflicts in
    50877b9.  Resolves build failures.
  2. Merge pull request #3 from melissalinkert/findbugs-happiness

    chris-allan committed Feb 16, 2012
    #4149 - FindBugs fixes