def test_get_n_segments(self):
nt.assert_equal(_nrt.n_segments(self.sec_nrn),
get('number_of_segments', self.ref_nrn)[0])
for t in NeuriteType:
nt.assert_equal(
_nrt.n_segments(self.sec_nrn, neurite_type=t),
get('number_of_segments', self.ref_nrn, neurite_type=t)[0])
def test_get_n_segments(self):
nt.assert_equal(_nrt.n_segments(self.sec_nrn.neurites[0]),
get('number_of_segments', self.ref_nrn.neurites[0])[0])
nt.assert_equal(_nrt.n_segments(self.sec_nrn), get('number_of_segments', self.ref_nrn)[0])
for t in NeuriteType:
nt.assert_equal(_nrt.n_segments(self.sec_nrn, neurite_type=t),
get('number_of_segments', self.ref_nrn, neurite_type=t)[0])
def test_n_segments():
n_segments = _nf.n_segments(SIMPLE)
nt.eq_(n_segments, 6)
# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
'''Compatibility between NL and H5 files'''
# pylint: disable=protected-access
import numpy as np
import neurom as nm
from neurom.fst import _neuritefunc as _nf
nrn_h5 = nm.load_neuron('test_data/h5/v1/bio_neuron-001.h5')
nrn_asc = nm.load_neuron('test_data/neurolucida/bio_neuron-001.asc')
print 'h5 number of sections: %s' % nm.get('number_of_sections', nrn_h5)[0]
print 'nl number of sections: %s\n' % nm.get('number_of_sections', nrn_asc)[0]
print 'h5 number of segments: %s' % nm.get('number_of_segments', nrn_h5)[0]
print 'nl number of segments: %s\n' % nm.get('number_of_segments', nrn_asc)[0]
print 'h5 total neurite length: %s' % np.sum(nm.get('section_lengths', nrn_h5))
print 'nl total neurite length: %s\n' % np.sum(nm.get('section_lengths', nrn_asc))
print 'h5 principal direction extents: %s' % nm.get('principal_direction_extents', nrn_h5)
print 'nl principal direction extents: %s' % nm.get('principal_direction_extents', nrn_asc)
print '\nNumber of neurites:'
for nt in nm.NeuriteType:
print nt, _nf.n_neurites(nrn_h5, neurite_type=nt),\
_nf.n_neurites(nrn_asc, neurite_type=nt)
print '\nNumber of segments:'
for nt in nm.NeuriteType:
print nt, _nf.n_segments(nrn_h5, neurite_type=nt),\
_nf.n_segments(nrn_asc, neurite_type=nt)
def test_n_segments():
n_segments = _nf.n_segments(SIMPLE)
nt.eq_(n_segments, 6)
import numpy as np
import neurom as nm
from neurom.fst import _neuritefunc as _nf
nrn_h5 = nm.load_neuron('test_data/h5/v1/bio_neuron-001.h5')
nrn_asc = nm.load_neuron('test_data/neurolucida/bio_neuron-001.asc')
print('h5 number of sections: %s' % nm.get('number_of_sections', nrn_h5)[0])
print('nl number of sections: %s\n' % nm.get('number_of_sections', nrn_asc)[0])
print('h5 number of segments: %s' % nm.get('number_of_segments', nrn_h5)[0])
print('nl number of segments: %s\n' % nm.get('number_of_segments', nrn_asc)[0])
print('h5 total neurite length: %s' %
np.sum(nm.get('section_lengths', nrn_h5)))
print('nl total neurite length: %s\n' %
np.sum(nm.get('section_lengths', nrn_asc)))
print('h5 principal direction extents: %s' %
nm.get('principal_direction_extents', nrn_h5))
print('nl principal direction extents: %s' %
nm.get('principal_direction_extents', nrn_asc))
print('\nNumber of neurites:')
for nt in iter(nm.NeuriteType):
print(nt, _nf.n_neurites(nrn_h5, neurite_type=nt),
_nf.n_neurites(nrn_asc, neurite_type=nt))
print('\nNumber of segments:')
for nt in iter(nm.NeuriteType):
print(nt, _nf.n_segments(nrn_h5, neurite_type=nt),
_nf.n_segments(nrn_asc, neurite_type=nt))
