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Add initial structure for decompressing JPEG XR images (assist #8493). #1014

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merged 60 commits into from Apr 23, 2014

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bpindelski
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This PR adds a Bio-Formats module named ome-jxr. This module implements part of the ITU-T T.832 recommendation for "Still-image compression – JPEG XR". The main blocker encountered during work on the business logic was the lack of proper bit-level stream readers in Java (and Bio-Formats). The code implements the specification up to point 8.4.22.6. Comments have been left in places where the requirement of an enum or class was unknown before the decompression stage. Outstanding tasks can be seen in https://trac.openmicroscopy.org/ome/ticket/8493.

For discussion during code review:

  • the ITU-T spec mentions global variables and codestream-level variables. I think a globally visible store of variables needed during the decompression process would make the code cleaner (reduced number of private class members),
  • class hierarchy,
  • test coverage and construction.

WARNING: This implementation is incomplete. Please see the comment below for the current status (March 2016)

Blazej Pindelski and others added 30 commits March 28, 2014 14:03
The PixelFormat class has still an ugly byte array as the common
part. This might need a bit of work. Also unit tests are missing.
This allows for another metadata class to be present:
one for the IFD and one for the image header
metadata.
@mtbc
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mtbc commented Apr 1, 2014

Travis failure.

@joshmoore
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Re-launched maven travis job.

@melissalinkert
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Temporarily excluding as this fails BIOFORMATS-5.1-merge-build due to a findbugs warning (http://ci.openmicroscopy.org/view/Bio-Formats/job/BIOFORMATS-5.1-merge-build/113/findbugsResult/new/?)

@melissalinkert
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Exclude removed as findbugs is expected to be fixed.

melissalinkert added a commit that referenced this pull request Apr 23, 2014
Add initial structure for decompressing JPEG XR images (assist #8493).
@melissalinkert melissalinkert merged commit d97fd41 into ome:develop Apr 23, 2014
@melissalinkert
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--no-rebase

@bpindelski bpindelski deleted the jpegxr branch April 30, 2014 11:04
@sbesson sbesson added this to the 5.1.0-m1 milestone Oct 14, 2014
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sbesson commented Mar 1, 2016

Following this initial effort, more information about the cost of trying to implement JPEG-XR can be read at http://lists.openmicroscopy.org.uk/pipermail/ome-users/2015-September/005616.html and http://blog.openmicroscopy.org/file-formats/community/2016/01/06/format-support/ .

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5 participants