Python sholl_crossings Examples

Example #1

def test_sholl_crossings_simple():
    center = SIMPLE.soma.center
    radii = []
    nt.eq_(list(_nf.sholl_crossings(SIMPLE, center, radii=radii)), [])

    radii = [1.0]
    nt.eq_([2], list(_nf.sholl_crossings(SIMPLE, center, radii=radii)))

    radii = [1.0, 5.1]
    nt.eq_([2, 4], list(_nf.sholl_crossings(SIMPLE, center, radii=radii)))

    radii = [1., 4., 5.]
    nt.eq_([2, 4, 5], list(_nf.sholl_crossings(SIMPLE, center, radii=radii)))

Example #2

File: test_neuronfunc.py Project: joewgraham/NeuroM

def test_sholl_analysis_custom():
    # recreate morphs from Fig 2 of
    # http://dx.doi.org/10.1016/j.jneumeth.2014.01.016
    radii = np.arange(10, 81, 10)
    center = 0, 0, 0
    morph_A = load_swc("""\
 1 1   0  0  0 1. -1
 2 3   0  0  0 1.  1
 3 3  80  0  0 1.  2
 4 4   0  0  0 1.  1
 5 4 -80  0  0 1.  4""")
    nt.eq_(list(_nf.sholl_crossings(morph_A, center, radii=radii)),
           [2, 2, 2, 2, 2, 2, 2, 2])

    morph_B = load_swc("""\
 1 1   0   0  0 1. -1
 2 3   0   0  0 1.  1
 3 3  35   0  0 1.  2
 4 3  51  10  0 1.  3
 5 3  51   5  0 1.  3
 6 3  51   0  0 1.  3
 7 3  51  -5  0 1.  3
 8 3  51 -10  0 1.  3
 9 4 -35   0  0 1.  2
10 4 -51  10  0 1.  9
11 4 -51   5  0 1.  9
12 4 -51   0  0 1.  9
13 4 -51  -5  0 1.  9
14 4 -51 -10  0 1.  9
                       """)
    nt.eq_(list(_nf.sholl_crossings(morph_B, center, radii=radii)),
           [2, 2, 2, 10, 10, 0, 0, 0])

    morph_C = load_swc("""\
 1 1   0   0  0 1. -1
 2 3   0   0  0 1.  1
 3 3  65   0  0 1.  2
 4 3  85  10  0 1.  3
 5 3  85   5  0 1.  3
 6 3  85   0  0 1.  3
 7 3  85  -5  0 1.  3
 8 3  85 -10  0 1.  3
 9 4  65   0  0 1.  2
10 4  85  10  0 1.  9
11 4  85   5  0 1.  9
12 4  85   0  0 1.  9
13 4  85  -5  0 1.  9
14 4  85 -10  0 1.  9
                       """)
    nt.eq_(list(_nf.sholl_crossings(morph_C, center, radii=radii)),
           [2, 2, 2, 2, 2, 2, 10, 10])

Example #3

def test_sholl_crossings_simple():
    center = SIMPLE.soma.center
    radii = []
    assert (list(_nf.sholl_crossings(SIMPLE, center, radii=radii)) ==
           [])

    radii = [1.0]
    assert ([2] ==
           list(_nf.sholl_crossings(SIMPLE, center, radii=radii)))

    radii = [1.0, 5.1]
    assert ([2, 4] ==
           list(_nf.sholl_crossings(SIMPLE, center, radii=radii)))

    radii = [1., 4., 5.]
    assert ([2, 4, 5] ==
           list(_nf.sholl_crossings(SIMPLE, center, radii=radii)))
    
    assert ([1, 1, 2] ==
           list(_nf.sholl_crossings(list(SIMPLE.sections[:2]), center, radii=radii)))