Merge f9c5996 into 0d5187a

gala/features/__init__.py

@@ -10,6 +10,7 @@
     base, \
     contact, \
     convex_hull, \
+    default, \
     graph, \
     histogram, \
     inclusion, \
@@ -18,5 +19,6 @@
     orientation, \
     squiggliness
 
-__all__ = ['base', 'contact', 'convex_hull', 'graph', 'histogram', 'inclusion',
-    'io', 'moments', 'orientation', 'squiggliness']
+__all__ = ['base', 'contact', 'convex_hull', 'default',
+           'graph', 'histogram', 'inclusion',
+           'io', 'moments', 'orientation', 'squiggliness']

gala/features/default.py

@@ -0,0 +1,45 @@
+from . import base, moments, histogram, graph, contact
+
+def paper_em():
+    """Return the feature manager used in the PLoS ONE paper.
+
+    This manager was used both for the FIBSEM segmentation (with
+    multi-channel probabilities) and the SNEMI3D segmentation. [1]_
+
+    Returns
+    -------
+    comp : `base.Composite` feature manager
+        The feature manager to use for graph agglomeration.
+
+    References
+    ----------
+    .. [1] http://brainiac2.mit.edu/SNEMI3D/content/gala-serial-2d-watershed
+    """
+    fm = moments.Manager()
+    fh = histogram.Manager(25, 0, 1, [0.1, 0.5, 0.9])
+    fg = graph.Manager()
+    return base.Composite(children=[fm, fh, fg])
+
+
+def snemi3d():
+    """Return the best-performing feature manager for SNEMI3D.
+
+    This correspond's to Neal Donnelly's last submission in 2014 [1]_.
+
+    Returns
+    -------
+    comp : feature manager
+        Same as the `paper_em` manager but including also a `contact`
+        manager.
+
+    References
+    ----------
+    .. [1] http://brainiac2.mit.edu/SNEMI3D/content/gala-new-watersheds
+    """
+    fm = moments.Manager()
+    fh = histogram.Manager(25, 0, 1, [0.1, 0.5, 0.9])
+    fg = graph.Manager()
+    fc = contact.Manager()
+    return base.Composite(children=[fm, fh, fg, fc])
+
+

tests/test_defaults.py

@@ -0,0 +1,63 @@
+from __future__ import absolute_import
+import os
+from six.moves import map
+from six.moves import range
+
+D = os.path.dirname(os.path.abspath(__file__))
+
+import numpy as np
+from numpy.testing import assert_equal, assert_allclose
+
+from gala import agglo
+from gala import evaluate as ev
+from gala.features import default
+
+
+fn_prob = os.path.join(D, 'toy-data/test-01-probabilities.txt')
+prob = np.loadtxt(fn_prob)
+fn_ws = os.path.join(D, 'toy-data/test-01-watershed.txt')
+ws = np.loadtxt(fn_ws, dtype=np.uint32)
+fn_gt = os.path.join(D, 'toy-data/test-01-groundtruth.txt')
+results = np.loadtxt(fn_gt, dtype=np.uint32)
+
+
+ans12 = np.array(
+      [3.00, 2.00, 4.67, 6.00, 32.67,0.50, 0.00, 0.00, 0.00, 0.00, 0.00,
+       0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00,
+       0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.50, 0.01, 0.04, 0.99,
+       3.00, 4.00, 7.00, 1.29, 1.92, 2.05, 9.00, 0.75, 0.00, 0.00, 0.00,
+       0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00,
+       0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.25, 0.01,
+       0.03, 0.98, 4.00, 3.50, 2.00, 1.00, 0.00, 0.00, 0.00, 0.00, 0.00,
+       0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00,
+       0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00,
+       1.00, 0.96, 0.98, 1.00, 2.00, 4.00, 0.71, 2.75, 3.95, 23.67, 0.03,
+       -1.00, 0.50])
+
+
+contact = np.array(
+      [1.00, 1.50, 0.60, 2.10, 1.00, 1.50, 0.60,
+       2.10, 1.00, 1.50, 0.60, 2.10, 0.00, 0.41,
+       -0.51,0.74, 0.00, 0.41,-0.51, 0.74, 0.00,
+       0.41,-0.51, 0.74,-0.41,-1.25, 0.67, 0.29])
+
+
+def test_paper_em():
+    feat = default.paper_em()
+    g = agglo.Rag(ws, prob, feature_manager=feat)
+    assert_allclose(feat(g, 1, 2), ans12, atol=0.01)
+
+
+def test_snemi():
+    feat = default.snemi3d()
+    g = agglo.Rag(ws, prob, feature_manager=feat)
+    # contact are edge features, so they are inserted just before the 8
+    # difference features in the base paper_em vector.
+    expected = np.concatenate((ans12[:-8], contact, ans12[-8:]))
+    assert_allclose(feat(g, 1, 2), expected, atol=0.01)
+
+
+if __name__ == '__main__':
+    from numpy import testing
+    testing.run_module_suite()
+