def test_neuron():
fig, ax = view.neuron(neuron0)
nt.ok_(np.allclose(ax.get_xlim(), (-70.328535157399998, 94.7472627179)) )
nt.ok_(np.allclose(ax.get_ylim(), (-87.600171997199993, 78.51626225230001)) )
fig, ax = view.neuron(neuron0, plane='wrong')
nt.ok_(ax == 'No such plane found! Please select one of: xy, xz, yx, yz, zx, zy.')
plt.close('all')
def neuron_morphology_dendrogram(neuron, suptitle='Neuron Morphology'):
'''Figure of dendrogram and morphology view
'''
from neurom.view import view
import pylab as pl
view.neuron(neuron, new_fig=True, plane='xz', subplot=121,
title='', xlabel='', ylabel='', xticks=[], yticks=[])
dendrogram(neuron, show_diameters=True, new_fig=False, subplot=122, rotation='right', title='')
pl.suptitle(suptitle)
def test_neuron():
fig, ax = view.neuron(fst_neuron)
nt.ok_(np.allclose(ax.get_xlim(), (-70.328535157399998, 94.7472627179)) )
nt.ok_(np.allclose(ax.get_ylim(), (-87.600171997199993, 78.51626225230001)) )
nt.ok_(ax.get_title() == fst_neuron.name)
fig, ax = view.neuron(fst_neuron, xlim=(0,100), ylim=(0,100))
nt.ok_(np.allclose(ax.get_xlim(), (0, 100)) )
nt.ok_(np.allclose(ax.get_ylim(), (0, 100)) )
nt.ok_(ax.get_title() == fst_neuron.name)
fig, ax = view.neuron(fst_neuron, plane='wrong')
nt.ok_(ax == 'No such plane found! Please select one of: xy, xz, yx, yz, zx, zy.')
plt.close('all')
def neuron_morphology_dendrogram(neuron, suptitle='Neuron Morphology'):
'''Figure of dendrogram and morphology view
'''
from neurom.view import view
import pylab as pl
view.neuron(neuron,
new_fig=True,
plane='xz',
subplot=121,
title='',
xlabel='',
ylabel='',
xticks=[],
yticks=[])
dendrogram(neuron,
show_diameters=True,
new_fig=False,
subplot=122,
rotation='right',
title='')
pl.suptitle(suptitle)
def test_neuron_no_neurites():
filename = os.path.join(SWC_PATH, 'point_soma.swc')
f, a = view.neuron(io.load_neuron(filename))
def test_neuron_no_neurites():
filename = os.path.join(SWC_PATH, 'point_soma.swc')
f, a = view.neuron(load_neuron(filename))
