def test_i_segment_meander_angles():
T = NEURON_TREE
ref = [math.pi * a for a in (1.0, 1.0, 1.0, 0.5, 0.5, 1.0, 1.0, 1.0, 0.5)]
for i, m in enumerate(i_segment_meander_angle(T)):
nt.assert_almost_equal(m, ref[i])
# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
'''Calculate inter-segment angles'''
import logging
import numpy as np
from neurom.core.dataformat import COLS
from neurom.io.readers import load_data
from neurom.io.utils import make_neuron
from neurom.analysis.morphtree import i_segment_meander_angle
# root level logger. This would be a top level application logger.
logging.basicConfig()
LOG = logging.getLogger()
LOG.setLevel(logging.DEBUG)
fmt = logging.Formatter('%(asctime)s - %(name)s - %(levelname)s - %(message)s')
LOG.handlers[0].setFormatter(fmt)
if __name__ == '__main__':
filename = 'test_data/swc/Neuron.swc'
rd = load_data(filename)
nrn = make_neuron(rd)
for tt in nrn.neurites:
print 'Tree ID: {0}, type: {1}'.format(tt.value[COLS.ID],
tt.value[COLS.TYPE])
for a in i_segment_meander_angle(tt):
LOG.debug('Angle %f', a)
if np.isnan(a):
LOG.warn('Found NaN angle. Check for zero length segments!')
'''Calculate inter-segment angles'''
import logging
import numpy as np
from neurom.core.dataformat import COLS
from neurom.io.readers import load_data
from neurom.io.utils import make_neuron
from neurom.analysis.morphtree import i_segment_meander_angle
# root level logger. This would be a top level application logger.
logging.basicConfig()
LOG = logging.getLogger()
LOG.setLevel(logging.DEBUG)
fmt = logging.Formatter('%(asctime)s - %(name)s - %(levelname)s - %(message)s')
LOG.handlers[0].setFormatter(fmt)
if __name__ == '__main__':
filename = 'test_data/swc/Neuron.swc'
rd = load_data(filename)
nrn = make_neuron(rd)
for tt in nrn.neurites:
print 'Tree ID: {0}, type: {1}'.format(tt.value[COLS.ID], tt.value[COLS.TYPE])
for a in i_segment_meander_angle(tt):
LOG.debug('Angle %f', a)
if np.isnan(a):
LOG.warn('Found NaN angle. Check for zero length segments!')