def __init__(self, data_wrapper, name='Neuron'):
self._data = data_wrapper
neurites, sections = make_neurites(self._data)
soma_check, soma_class = _SOMA_CONFIG[self._data.fmt]
soma = make_soma(self._data.soma_points(), soma_check, soma_class)
super(FstNeuron, self).__init__(soma, neurites, sections, name)
self._points = None
def test_make_Soma_ThreePointCylinder():
with warnings.catch_warnings(record=True):
sm = _soma.make_soma(SOMA_THREEPOINTS_PTS,
soma_class=_soma.SOMA_CYLINDER)
nt.ok_('SomaNeuromorphoThreePointCylinders' in str(sm))
nt.ok_(isinstance(sm, _soma.SomaNeuromorphoThreePointCylinders))
nt.eq_(list(sm.center), [0, 0, 0])
nt.eq_(sm.radius, 44)
def test_invalid_soma_points_2_raises_SomaError():
_soma.make_soma(INVALID_PTS_2)
def check_SomaC(points):
sm = _soma.make_soma(points)
nt.ok_('SomaSimpleContour' in str(sm))
nt.ok_(isinstance(sm, _soma.SomaSimpleContour))
np.testing.assert_allclose(sm.center, (0., 0., 0.), atol=1e-16)
nt.eq_(sm.radius, 1.0)
for diameter_scale, linewidth in it.product((1.0, None),
(0.0, 1.2)):
with get_fig_2d() as (fig, ax):
view.plot_tree(ax, test_section, diameter_scale=diameter_scale, linewidth=linewidth)
with get_fig_3d() as (fig, ax):
view.plot_tree3d(ax, test_section, diameter_scale=diameter_scale, linewidth=linewidth)
soma0 = fst_neuron.soma
# upright, varying radius
soma_2pt_normal_pts = np.array([
[0.0, 0.0, 0.0, 1.0, 1, 1, -1],
[0.0, 10.0, 0.0, 10.0, 1, 2, 1],
])
soma_2pt_normal = make_soma(soma_2pt_normal_pts, soma_class=SOMA_CYLINDER)
# upright, uniform radius, multiple cylinders
soma_3pt_normal_pts = np.array([
[0.0, -10.0, 0.0, 10.0, 1, 1, -1],
[0.0, 0.0, 0.0, 10.0, 1, 2, 1],
[0.0, 10.0, 0.0, 10.0, 1, 3, 2],
])
soma_3pt_normal = make_soma(soma_3pt_normal_pts, soma_class=SOMA_CYLINDER)
# increasing radius, multiple cylinders
soma_4pt_normal_pts = np.array([
[0.0, 0.0, 0.0, 1.0, 1, 1, -1],
[0.0, -10.0, 0.0, 2.0, 1, 2, 1],
[0.0, -10.0, -10.0, 3.0, 1, 3, 2],
[-10.0, -10.0, -10.0, 4.0, 1, 4, 3],
def test_make_Soma_contour():
sm = _soma.make_soma(SOMA_THREEPOINTS_PTS, soma_class=_soma.SOMA_CONTOUR)
nt.ok_('SomaSimpleContour' in str(sm))
nt.ok_(isinstance(sm, _soma.SomaSimpleContour))
nt.eq_(list(sm.center), [0, 0, 0])
nt.assert_almost_equal(sm.radius, 29.33333333, places=5)
def test_make_Soma_ThreePoint():
sm = _soma.make_soma(SOMA_THREEPOINTS_PTS, soma_class=_soma.SOMA_CONTOUR)
nt.ok_('SomaThreePoint' in str(sm))
nt.ok_(isinstance(sm, _soma.SomaThreePoint))
nt.eq_(list(sm.center), [0, 0, 0])
nt.eq_(sm.radius, 44)
def test_make_Soma_contour():
sm = _soma.make_soma(SOMA_THREEPOINTS_PTS, soma_class=_soma.SOMA_CONTOUR)
nt.ok_('SomaSimpleContour' in str(sm))
nt.ok_(isinstance(sm, _soma.SomaSimpleContour))
nt.eq_(list(sm.center), [0, 0, 0])
nt.assert_almost_equal(sm.radius, 29.33333333, places=5)
def test_invalid_soma_points_2_raises_SomaError():
_soma.make_soma(INVALID_PTS_2)
def check_SomaC(points):
sm = _soma.make_soma(points)
nt.ok_('SomaSimpleContour' in str(sm))
nt.ok_(isinstance(sm, _soma.SomaSimpleContour))
np.testing.assert_allclose(sm.center, (0., 0., 0.), atol=1e-16)
nt.eq_(sm.radius, 1.0)
def test_make_Soma_ThreePointCylinder_small_radius():
with warnings.catch_warnings(record=True):
sm = _soma.make_soma(SOMA_THREEPOINTS_PTS_SMALL_RADIUS,
soma_class=_soma.SOMA_CYLINDER)
linewidth=linewidth)
with get_fig_3d() as (fig, ax):
view.plot_tree3d(ax,
test_section,
diameter_scale=diameter_scale,
linewidth=linewidth)
soma0 = fst_neuron.soma
#upright, varying radius
soma_2pt_normal_pts = np.array([
[0.0, 0.0, 0.0, 1.0, 1, 1, -1],
[0.0, 10.0, 0.0, 10.0, 1, 2, 1],
])
soma_2pt_normal = make_soma(soma_2pt_normal_pts, soma_class=SOMA_CYLINDER)
#upright, uniform radius, multiple cylinders
soma_3pt_normal_pts = np.array([
[0.0, -10.0, 0.0, 10.0, 1, 1, -1],
[0.0, 0.0, 0.0, 10.0, 1, 2, 1],
[0.0, 10.0, 0.0, 10.0, 1, 3, 2],
])
soma_3pt_normal = make_soma(soma_3pt_normal_pts, soma_class=SOMA_CYLINDER)
#increasing radius, multiple cylinders
soma_4pt_normal_pts = np.array([
[0.0, 0.0, 0.0, 1.0, 1, 1, -1],
[0.0, -10.0, 0.0, 2.0, 1, 2, 1],
[0.0, -10.0, -10.0, 3.0, 1, 3, 2],
[-10.0, -10.0, -10.0, 4.0, 1, 4, 3],
def test_make_Soma_ThreePoint():
sm = _soma.make_soma(SOMA_THREEPOINTS_PTS)
nt.ok_('SomaThreePoint' in str(sm))
nt.ok_(isinstance(sm, _soma.SomaThreePoint))
nt.assert_items_equal(sm.center, (11, 22, 33))
nt.eq_(sm.radius, 0.0)
def test_make_Soma_SinglePoint():
sm = _soma.make_soma(SOMA_SINGLE_PTS)
nt.ok_('SomaSinglePoint' in str(sm))
nt.ok_(isinstance(sm, _soma.SomaSinglePoint))
nt.assert_items_equal(sm.center, (11, 22, 33))
nt.ok_(sm.radius == 44)
def test_make_Soma_Cylinders():
points = [[0, 0, -10, 40],
[0, 0, 0, 40],
[0, 0, 10, 40],
]
s = _soma.SomaCylinders(points)
# if r = 2*h (ie: as in this case 10 - -10 == 20), then the
# area of a cylinder (excluding end caps) is:
# 2*pi*r*h == 4*pi*r^2 == area of a sphere of radius 20
nt.eq_(s.radius, 20.0)
nt.assert_almost_equal(s.area, 5026.548245743669)
nt.eq_(s.center, [0, 0, -10])
nt.ok_('SomaCylinders' in str(s))
# cylinder: h = 10, r = 20
soma_2pt_normal = np.array([
[0.0, 0.0, 0.0, 20.0, 1, 1, -1],
[0.0, -10.0, 0.0, 20.0, 1, 2, 1],
])
s = _soma.make_soma(soma_2pt_normal, soma_class=_soma.SOMA_CYLINDER)
nt.assert_almost_equal(s.area, 1256.6370614) # see r = 2*h above
nt.eq_(list(s.center), [0., 0., 0.])
#check tapering
soma_2pt_normal = np.array([
[0.0, 0.0, 0.0, 0.0, 1, 1, -1],
[0.0, -10.0, 0.0, 20.0, 1, 2, 1],
])
s = _soma.make_soma(soma_2pt_normal, soma_class=_soma.SOMA_CYLINDER)
nt.assert_almost_equal(s.area, 1404.9629462081452) # cone area, not including 'bottom'
# neuromorpho style
soma_3pt_neuromorpho = np.array([
[0.0, 0.0, 0.0, 10.0, 1, 1, -1],
[0.0, -10.0, 0.0, 10.0, 1, 2, 1],
[0.0, 10.0, 0.0, 10.0, 1, 3, 1],
])
s = _soma.make_soma(soma_3pt_neuromorpho, soma_class=_soma.SOMA_CYLINDER)
nt.ok_('SomaNeuromorphoThreePointCylinders' in str(s))
nt.eq_(list(s.center), [0., 0., 0.])
nt.assert_almost_equal(s.area, 1256.6370614)
# some neuromorpho files don't follow the convention
#but have (ys + rs) as point 2, and have xs different in each line
# ex: http://neuromorpho.org/dableFiles/brumberg/CNG%20version/april11s1cell-1.CNG.swc
soma_3pt_neuromorpho = np.array([
[ 0.0, 0.0, 0.0, 10.0, 1, 1, -1],
[-2.0, 6.0, 0.0, 10.0, 1, 2, 1],
[ 2.0, -6.0, 0.0, 10.0, 1, 3, 1],
])
s = _soma.make_soma(soma_3pt_neuromorpho, soma_class=_soma.SOMA_CYLINDER)
nt.ok_('SomaNeuromorphoThreePointCylinders' in str(s))
nt.eq_(list(s.center), [0., 0., 0.])
nt.assert_almost_equal(s.area, 794.76706126368811)
soma_4pt_normal = np.array([
[0.0, 0.0, 0.0, 0.0, 1, 1, -1],
[0.0, 2.0, 0.0, 2.0, 1, 2, 1],
[0.0, 4.0, 0.0, 4.0, 1, 3, 2],
[0.0, 6.0, 0.0, 6.0, 1, 4, 3],
[0.0, 8.0, 0.0, 8.0, 1, 5, 4],
[0.0, 10.0, 0.0, 10.0, 1, 6, 5],
])
s = _soma.make_soma(soma_4pt_normal, soma_class=_soma.SOMA_CYLINDER)
nt.eq_(list(s.center), [0., 0., 0.])
nt.assert_almost_equal(s.area, 444.288293851) # cone area, not including bottom
def test_make_Soma_Cylinders():
points = [
[0, 0, -10, 40],
[0, 0, 0, 40],
[0, 0, 10, 40],
]
s = _soma.SomaCylinders(points)
# if r = 2*h (ie: as in this case 10 - -10 == 20), then the
# area of a cylinder (excluding end caps) is:
# 2*pi*r*h == 4*pi*r^2 == area of a sphere of radius 20
nt.eq_(s.radius, 20.0)
nt.assert_almost_equal(s.area, 5026.548245743669)
nt.eq_(s.center, [0, 0, -10])
nt.ok_('SomaCylinders' in str(s))
# cylinder: h = 10, r = 20
soma_2pt_normal = np.array([
[0.0, 0.0, 0.0, 20.0, 1, 1, -1],
[0.0, -10.0, 0.0, 20.0, 1, 2, 1],
])
s = _soma.make_soma(soma_2pt_normal, soma_class=_soma.SOMA_CYLINDER)
nt.assert_almost_equal(s.area, 1256.6370614) # see r = 2*h above
nt.eq_(list(s.center), [0., 0., 0.])
#check tapering
soma_2pt_normal = np.array([
[0.0, 0.0, 0.0, 0.0, 1, 1, -1],
[0.0, -10.0, 0.0, 20.0, 1, 2, 1],
])
s = _soma.make_soma(soma_2pt_normal, soma_class=_soma.SOMA_CYLINDER)
nt.assert_almost_equal(
s.area, 1404.9629462081452) # cone area, not including 'bottom'
# neuromorpho style
soma_3pt_neuromorpho = np.array([
[0.0, 0.0, 0.0, 10.0, 1, 1, -1],
[0.0, -10.0, 0.0, 10.0, 1, 2, 1],
[0.0, 10.0, 0.0, 10.0, 1, 3, 1],
])
with warnings.catch_warnings(record=True):
s = _soma.make_soma(soma_3pt_neuromorpho,
soma_class=_soma.SOMA_CYLINDER)
nt.ok_('SomaNeuromorphoThreePointCylinders' in str(s))
nt.eq_(list(s.center), [0., 0., 0.])
nt.assert_almost_equal(s.area, 1256.6370614)
# some neuromorpho files don't follow the convention
#but have (ys + rs) as point 2, and have xs different in each line
# ex: http://neuromorpho.org/dableFiles/brumberg/CNG%20version/april11s1cell-1.CNG.swc
soma_3pt_neuromorpho = np.array([
[0.0, 0.0, 0.0, 10.0, 1, 1, -1],
[-2.0, 6.0, 0.0, 10.0, 1, 2, 1],
[2.0, -6.0, 0.0, 10.0, 1, 3, 1],
])
with warnings.catch_warnings(record=True):
s = _soma.make_soma(soma_3pt_neuromorpho,
soma_class=_soma.SOMA_CYLINDER)
nt.ok_('SomaNeuromorphoThreePointCylinders' in str(s))
nt.eq_(list(s.center), [0., 0., 0.])
nt.assert_almost_equal(s.area, 794.76706126368811)
soma_4pt_normal = np.array([
[0.0, 0.0, 0.0, 0.0, 1, 1, -1],
[0.0, 2.0, 0.0, 2.0, 1, 2, 1],
[0.0, 4.0, 0.0, 4.0, 1, 3, 2],
[0.0, 6.0, 0.0, 6.0, 1, 4, 3],
[0.0, 8.0, 0.0, 8.0, 1, 5, 4],
[0.0, 10.0, 0.0, 10.0, 1, 6, 5],
])
s = _soma.make_soma(soma_4pt_normal, soma_class=_soma.SOMA_CYLINDER)
nt.eq_(list(s.center), [0., 0., 0.])
nt.assert_almost_equal(s.area,
444.288293851) # cone area, not including bottom
def test_make_Soma_SinglePoint():
sm = _soma.make_soma(SOMA_SINGLE_PTS)
nt.ok_('SomaSinglePoint' in str(sm))
nt.ok_(isinstance(sm, _soma.SomaSinglePoint))
nt.eq_(list(sm.center), [11, 22, 33])
nt.ok_(sm.radius == 44)
def test_make_Soma_SinglePoint():
sm = _soma.make_soma(SOMA_SINGLE_PTS)
nt.ok_('SomaSinglePoint' in str(sm))
nt.ok_(isinstance(sm, _soma.SomaSinglePoint))
nt.eq_(list(sm.center), [11, 22, 33])
nt.ok_(sm.radius == 44)
def test_make_Soma_ThreePointCylinder():
sm = _soma.make_soma(SOMA_THREEPOINTS_PTS, soma_class=_soma.SOMA_CYLINDER)
nt.ok_('SomaNeuromorphoThreePointCylinders' in str(sm))
nt.ok_(isinstance(sm, _soma.SomaNeuromorphoThreePointCylinders))
nt.eq_(list(sm.center), [0, 0, 0])
nt.eq_(sm.radius, 44)
def test_make_Soma_ThreePoint():
sm = _soma.make_soma(SOMA_THREEPOINTS_PTS)
nt.ok_('SomaThreePoint' in str(sm))
nt.ok_(isinstance(sm, _soma.SomaThreePoint))
nt.eq_(list(sm.center), [11, 22, 33])
nt.eq_(sm.radius, 0.0)