[2, 10],
[43, 51],
[1, 2, 3]]
INIT_IDS = [[4, 215, 426, 637],
[],
[4],
[4],
[4],
[2, 10],
[3, 11],
[44, 52],
[4]]
RAW_DATA = [utils.load_data(f) for f in FILES]
NO_SOMA_RAW_DATA = utils.load_data(NO_SOMA_FILE)
class MockNeuron(object):
def __init__(self, trees):
self.neurites = trees
def test_get_soma_ids():
for i, d in enumerate(RAW_DATA):
nt.ok_(utils.get_soma_ids(d) == SOMA_IDS[i])
def test_get_initial_neurite_segment_ids():
for i, d in enumerate(RAW_DATA):
def test_load_neurolucida_ascii():
f_ = os.path.join(DATA_PATH, 'neurolucida', 'sample.asc')
ascii = utils.load_data(f_)
nt.ok_(isinstance(ascii, DataWrapper))
nt.eq_(len(ascii.data_block), 18)
"""Calculate inter-segment angles"""
import logging
import numpy as np
from neurom.core.dataformat import COLS
from neurom.point_neurite import triplets as trip
from neurom.point_neurite.io.utils import load_data, make_neuron
from neurom.point_neurite.core import iter_neurites
# 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 iter_neurites(tt, trip.meander_angle):
LOG.debug("Angle %f", a)
if np.isnan(a):
LOG.warn("Found NaN angle. Check for zero length segments!")
