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Commits on Mar 13, 2012
  1. Add skeleton ZeissAxioVisionReader

    Roger Leigh authored
Commits on Mar 12, 2012
  1. @melissalinkert

    Merge pull request #33 from joshmoore/7239-submods

    melissalinkert authored
    OME build hooks
  2. @melissalinkert

    Merge pull request #35 from ctrueden/scijava

    melissalinkert authored
    Update Bio-Formats POMs to use scijava base POM
Commits on Mar 9, 2012
  1. @ctrueden
Commits on Mar 6, 2012
  1. @chris-allan
Commits on Feb 29, 2012
  1. @melissalinkert

    ICSWriter: Allow the output order to be changed

    melissalinkert authored
    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. @chris-allan
  2. @joshmoore

    OME build hooks

    joshmoore authored
    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. @melissalinkert

    Add '-xmlspaces' option for specifying indentation

    melissalinkert authored
    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. @melissalinkert

    Add '-no-sas' option, to disable SA display

    melissalinkert authored
    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. @melissalinkert

    Ensure that the tile dimensions are not too large

    melissalinkert authored
    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. @melissalinkert

    Fix possible NPE

    melissalinkert authored
    Introduced in f5fe876da0b5373a3230b250f8567cc4e1fdf04e.
  7. @melissalinkert

    Do not convert OTF elements

    melissalinkert authored
    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. @melissalinkert

    Be sure to remove singleton files with no Z index

    melissalinkert authored
    This prevents an ArrayIndexOutOfBoundsException when a single extra file
    is placed first on the list of used files.
    
    Reported by Helio Roque.
  9. @melissalinkert

    Fix outdated statements in the readme files

    melissalinkert authored
    The top-level directory is now 'components/scifio', and Maven 3 is
    supported as of earlier today.
  10. @melissalinkert

    Add missing null check for the ND2Handler

    melissalinkert authored
    Noticed by FindBugs.
  11. @melissalinkert

    Add missing 'break' statements

    melissalinkert authored
    Noticed by FindBugs.
  12. @melissalinkert
  13. @melissalinkert

    Fill in missing units for the C axis

    melissalinkert authored
    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.
  14. @melissalinkert

    Allow units to be specified as "micrometers"

    melissalinkert authored
    Previously, only "um" and "microns" were allowed.  Since it's all the
    same unit, allow "micrometers" too.
    
    Reported by Glen MacDonald.
  15. @melissalinkert

    Flip the planes upside-down

    melissalinkert authored
    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.
  16. @melissalinkert

    Stop parsing tags if we have reached the EOF

    melissalinkert authored
    Noticed by Anthony Luu.
  17. @melissalinkert

    Add some extra diagnostics to the log file

    melissalinkert authored
    The hope is that this will help to track down why a particular directory
    is detected as being invalid.
  18. @melissalinkert
  19. @melissalinkert

    Only overwrite the channel count for non-RGB data

    melissalinkert authored
    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.
  20. @melissalinkert

    Fix configuration file path name checking

    melissalinkert authored
    This allows the data tests to run again.
  21. @melissalinkert

    Check MicroManager metadata files more thoroughly

    melissalinkert authored
    ...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. @melissalinkert

    Use the last n detector gains and offsets

    melissalinkert authored
    This fixes the detector index so that the last n gains and offsets are
    used, instead of the first n.
    
    See #7897.
  2. @chris-allan

    Merge pull request #31 from melissalinkert/bf-itk-fixes

    chris-allan authored
    BF-ITK build fix
Commits on Feb 24, 2012
  1. @melissalinkert
Commits on Feb 17, 2012
  1. @chris-allan

    Merge pull request #29 from melissalinkert/build-fix

    chris-allan authored
    Build fix: Disable failing encoding tests
  2. @melissalinkert
  3. @chris-allan

    Merge pull request #28 from melissalinkert/build-fix

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

    Reintroduce import of loci.common.DataTools

    melissalinkert authored
    This was accidentally removed while resolving merge conflicts in
    50877b9.  Resolves build failures.
  2. @chris-allan

    Merge pull request #3 from melissalinkert/findbugs-happiness

    chris-allan authored
    #4149 - FindBugs fixes
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