def test_make_neuron_post_tree_action():
def post_action(t):
t.bar = 'foo'
rd = RAW_DATA[0]
nrn = utils.make_neuron(rd, post_action)
for t in nrn.neurites:
nt.ok_(hasattr(t, 'bar') and t.bar == 'foo')
def test_make_neuron_no_soma_raises_SomaError():
utils.make_neuron(NO_SOMA_RAW_DATA)
def test_make_neuron():
rd = RAW_DATA[0]
nrn = utils.make_neuron(rd)
nt.ok_(np.all([s[COLS.ID] for s in nrn.soma.iter()] == SOMA_IDS[0]))
_check_trees(nrn.neurites)
from neurom.point_neurite.io.utils import make_neuron
from neurom.point_neurite.point_tree import PointTree
from neurom.point_neurite import bifurcations as bif
from neurom.point_neurite.core import iter_neurites
import math
class MockNeuron(object):
pass
DATA_PATH = './test_data'
SWC_PATH = os.path.join(DATA_PATH, 'swc/')
data = io.load_data(SWC_PATH + 'Neuron.swc')
neuron0 = make_neuron(data)
tree0 = neuron0.neurites[0]
def _make_neuron_tree():
p = [0.0, 0.0, 0.0, 1.0, 1, 1, 2]
T = PointTree(p)
T1 = T.add_child(PointTree([0.0, 1.0, 0.0, 1.0, 1, 1, 2]))
T2 = T1.add_child(PointTree([0.0, 2.0, 0.0, 1.0, 1, 1, 2]))
T3 = T2.add_child(PointTree([0.0, 4.0, 0.0, 2.0, 1, 1, 2]))
T4 = T3.add_child(PointTree([0.0, 5.0, 0.0, 2.0, 1, 1, 2]))
T5 = T4.add_child(PointTree([2.0, 5.0, 0.0, 1.0, 1, 1, 2]))
T6 = T4.add_child(PointTree([0.0, 5.0, 2.0, 1.0, 1, 1, 2]))
T7 = T5.add_child(PointTree([3.0, 5.0, 0.0, 0.75, 1, 1, 2]))
T8 = T7.add_child(PointTree([4.0, 5.0, 0.0, 0.75, 1, 1, 2]))
T9 = T6.add_child(PointTree([0.0, 5.0, 3.0, 0.75, 1, 1, 2]))
T10 = T9.add_child(PointTree([0.0, 6.0, 3.0, 0.75, 1, 1, 2]))
from neurom.point_neurite.io.utils import make_neuron
from neurom import io
from neurom.point_neurite import io as pt_io
from neurom.view import view
from neurom.point_neurite.treefunc import set_tree_type
import os
import numpy as np
import pylab as plt
from neurom.point_neurite.point_tree import PointTree
DATA_PATH = './test_data'
SWC_PATH = os.path.join(DATA_PATH, 'swc/')
pt_raw_data = pt_io.load_data(SWC_PATH + 'Neuron.swc')
pt_neuron = make_neuron(pt_raw_data, set_tree_type)
soma0 = pt_neuron.soma
fst_neuron = io.load_neuron(os.path.join(SWC_PATH, 'Neuron.swc'))
def test_tree():
axes = []
for tree in pt_neuron.neurites:
fig, ax = view.tree(tree)
axes.append(ax)
nt.ok_(axes[0].get_data_ratio() > 1.00 )
nt.ok_(axes[1].get_data_ratio() > 0.80 )
nt.ok_(axes[2].get_data_ratio() > 1.00 )
nt.ok_(axes[3].get_data_ratio() > 0.85 )
tree0 = pt_neuron.neurites[0]
"""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!")
