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)))
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])
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])
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)))