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Tree-based agglomeration #32

Merged
merged 45 commits into from
Oct 15, 2014
Merged

Tree-based agglomeration #32

merged 45 commits into from
Oct 15, 2014

Commits on Jan 23, 2014

  1. Add support for tree agglomeration

    @jni
    jni committed Jan 23, 2014
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  2. Add missing rename_node function

    @jni
    jni committed Jan 23, 2014
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  3. Bug fix: mistyped 'qitem' instead of 'qlink'

    @jni
    jni committed Jan 23, 2014
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  4. Update tests for tree agglomeration

    @jni
    jni committed Jan 23, 2014
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  5. Add function to remove merged boundaries

    @jni
    jni committed Jan 23, 2014
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  6. Remove merged boundaries when getting segmentation

    @jni
    jni committed Jan 23, 2014
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  7. Major bug fix: peek only at valid queue items 

    MergeQueue.peek() was designed to look at the next item in the merge
queue without popping it. However, the next item *could* be invalid,
and cause a merge of a valid item past threshold!

This commit fixes that by having peek() discard invalid items until a
valid one is at the front of the queue.
    @jni
    jni committed Jan 23, 2014
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  8. Change feature testing to use update node ids

    @jni
    jni committed Jan 23, 2014
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Commits on Feb 10, 2014

  1. Update RIG creation to use watershed, not segmentation

    @jni
    jni committed Feb 10, 2014
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  2. Update refine_post_merge_boundaries to use tree agglo

    @jni
    jni committed Feb 10, 2014
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  3. Bug fix: reset tree height after ladder agglo

    @jni
    jni committed Feb 10, 2014
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Commits on Feb 25, 2014

  1. Change call order for tree merge 

    Tree merging was causing the sp2segment map to be incorrect when the
merge boundaries were being refined. Postponing the merge until after
boundary refinement fixes the issue.
    @jni
    jni committed Feb 25, 2014
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Commits on Feb 26, 2014

  1. Update contingency table to allow sequential node renaming

    @jni
    jni committed Feb 26, 2014
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  2. Update tests to allow 1-1 matching of segmentations

    @jni
    jni committed Feb 26, 2014
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Commits on Feb 28, 2014

  1. Update region intersection graph during merge 

    The region intersection graph allows quick computation of current VI
and rand index during an agglomeration run.
    @jni
    jni committed Feb 28, 2014
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  2. Update requirement to viridis 0.2

    @jni
    jni committed Feb 28, 2014
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Commits on Apr 8, 2014

  1. Update default RIG length when no ground truth 

    I doubled the size of the contingency table, but when there is no
contingency table, I hadn't doubled the size of the ones() array,
resulting in an IndexError. This is now fixed.
    @jni
    jni committed Apr 8, 2014
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Commits on Sep 9, 2014

  1. added optimized.pyx for Cython, and tests for its functions

    @NealJMD
    NealJMD committed Sep 9, 2014
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  2. added missing kwarg to classify.py function

    @NealJMD
    NealJMD committed Sep 9, 2014
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  3. modified imio.read_h5_stack to not fail with kwargs for other imio fu… 

    …nctions
    @NealJMD
    NealJMD committed Sep 9, 2014
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  4. stop agglo.py tracking 'extent' set after features are built

    @NealJMD
    NealJMD committed Sep 9, 2014
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  5. optimize 'histogram' and 'moments' feature computations with Cython

    @NealJMD
    NealJMD committed Sep 9, 2014
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  6. added 'contact' feature, which helped win SNEMI3D

    @NealJMD
    NealJMD committed Sep 9, 2014
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  7. added adjusted Rand error metric to evaluate.py

    @NealJMD
    NealJMD committed Sep 9, 2014
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Commits on Sep 17, 2014

  1. fixed u code style and docstrings

    @NealJMD
    NealJMD committed Sep 17, 2014
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Commits on Sep 23, 2014

  1. convert .travis.yml to build from Conda

    @NealJMD
    NealJMD committed Sep 23, 2014
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  2. added Cython linkage to setup.py

    @NealJMD
    NealJMD committed Sep 23, 2014
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  3. fix test_gala.py for sklearn 0.15

    @NealJMD
    NealJMD committed Sep 23, 2014
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  4. fixed up README install instructions

    @NealJMD
    NealJMD committed Sep 23, 2014
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  5. added test_optimized.py to README test instructions

    @NealJMD
    NealJMD committed Sep 23, 2014
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Commits on Sep 30, 2014

  1. more docstrings and test style

    @NealJMD
    NealJMD committed Sep 30, 2014
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Commits on Oct 7, 2014

  1. allow setting random state in RF classifier for meaningful test_gala … 

    …tests
    @NealJMD
    NealJMD committed Oct 7, 2014
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  2. remove outdated import warnings

    @NealJMD
    NealJMD committed Oct 7, 2014
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Commits on Oct 8, 2014

  1. fixed ordering of adapted rand error return values

    @NealJMD
    NealJMD committed Oct 8, 2014
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Commits on Oct 9, 2014

  1. Merge pull request #3 from NealJMD/optimized 

     - added optimized.pyx for Cython, and tests for its functions
 - added missing kwarg to classify.py function
 - modified imio.read_h5_stack to not fail with kwargs for other imio function args
 - stop agglo.py tracking 'extent' set after features are built
 - optimize 'histogram' and 'moments' feature computations with Cython
 - added 'contact' feature, which helped win SNEMI3D
 - added adjusted Rand error metric to evaluate.py
 - dramatically improved testing framework
 - updated travis build to use Conda
 - updated README with all the goodies
 - other minor improvements
    @jni
    jni committed Oct 9, 2014
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Commits on Oct 11, 2014

  1. Remove unused imports in tests

    @jni
    jni committed Oct 11, 2014
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Commits on Oct 14, 2014

  1. Update tests to allow running from root dir

    @jni
    jni committed Oct 14, 2014
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Commits on Oct 15, 2014

  1. Add pytest setup file

    @jni
    jni committed Oct 15, 2014
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  2. Use local imports in agglo.py

    @jni
    jni committed Oct 15, 2014
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  3. Ignore neuroproof dependent tests, test generators

    @jni
    jni committed Oct 15, 2014
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  4. Fix up doctests

    @jni
    jni committed Oct 15, 2014
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  5. Run doctests by default

    @jni
    jni committed Oct 15, 2014
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  6. Use pytest to run tests

    @jni
    jni committed Oct 15, 2014
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  7. Add support for test coverage measurement

    @jni
    jni committed Oct 15, 2014
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  8. Add coveralls support on travis

    @jni
    jni committed Oct 15, 2014
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