def test_register_neurite_feature_nrns():
def npts(neurite):
return len(neurite.points)
def vol(neurite):
return neurite.volume
fst.register_neurite_feature('foo', npts)
n_points_ref = [len(n.points) for n in iter_neurites(NRNS)]
n_points = fst.get('foo', NRNS)
assert_items_equal(n_points, n_points_ref)
# test neurite type filtering
n_points_ref = [len(n.points) for n in iter_neurites(NRNS, filt=_is_type(NeuriteType.axon))]
n_points = fst.get('foo', NRNS, neurite_type=NeuriteType.axon)
assert_items_equal(n_points, n_points_ref)
fst.register_neurite_feature('bar', vol)
n_volume_ref = [n.volume for n in iter_neurites(NRNS)]
n_volume = fst.get('bar', NRNS)
assert_items_equal(n_volume, n_volume_ref)
# test neurite type filtering
n_volume_ref = [n.volume for n in iter_neurites(NRNS, filt=_is_type(NeuriteType.axon))]
n_volume = fst.get('bar', NRNS, neurite_type=NeuriteType.axon)
assert_items_equal(n_volume, n_volume_ref)
def test_register_neurite_feature_pop():
def npts(neurite):
return len(neurite.points)
def vol(neurite):
return neurite.volume
fst.register_neurite_feature('foo', npts)
n_points_ref = [len(n.points) for n in iter_neurites(POP)]
n_points = fst.get('foo', POP)
assert_items_equal(n_points, n_points_ref)
# test neurite type filtering
n_points_ref = [len(n.points) for n in iter_neurites(POP,
filt=_is_type(NeuriteType.basal_dendrite))]
n_points = fst.get('foo', POP, neurite_type=NeuriteType.basal_dendrite)
assert_items_equal(n_points, n_points_ref)
fst.register_neurite_feature('bar', vol)
n_volume_ref = [n.volume for n in iter_neurites(POP)]
n_volume = fst.get('bar', POP)
assert_items_equal(n_volume, n_volume_ref)
# test neurite type filtering
n_volume_ref = [n.volume for n in iter_neurites(POP, filt=_is_type(NeuriteType.basal_dendrite))]
n_volume = fst.get('bar', POP, neurite_type=NeuriteType.basal_dendrite)
assert_items_equal(n_volume, n_volume_ref)
def test_register_neurite_feature_pop():
def npts(neurite):
return len(neurite.points)
def vol(neurite):
return neurite.volume
fst.register_neurite_feature('foo', npts)
n_points_ref = [len(n.points) for n in iter_neurites(POP)]
n_points = fst.get('foo', POP)
assert_items_equal(n_points, n_points_ref)
# test neurite type filtering
n_points_ref = [len(n.points) for n in iter_neurites(POP,
filt=_is_type(NeuriteType.basal_dendrite))]
n_points = fst.get('foo', POP, neurite_type=NeuriteType.basal_dendrite)
assert_items_equal(n_points, n_points_ref)
fst.register_neurite_feature('bar', vol)
n_volume_ref = [n.volume for n in iter_neurites(POP)]
n_volume = fst.get('bar', POP)
assert_items_equal(n_volume, n_volume_ref)
# test neurite type filtering
n_volume_ref = [n.volume for n in iter_neurites(POP, filt=_is_type(NeuriteType.basal_dendrite))]
n_volume = fst.get('bar', POP, neurite_type=NeuriteType.basal_dendrite)
assert_items_equal(n_volume, n_volume_ref)
def test_register_neurite_feature_nrns():
def npts(neurite):
return len(neurite.points)
def vol(neurite):
return neurite.volume
fst.register_neurite_feature('foo', npts)
n_points_ref = [len(n.points) for n in iter_neurites(NRNS)]
n_points = fst.get('foo', NRNS)
assert_items_equal(n_points, n_points_ref)
# test neurite type filtering
n_points_ref = [len(n.points) for n in iter_neurites(NRNS, filt=_is_type(NeuriteType.axon))]
n_points = fst.get('foo', NRNS, neurite_type=NeuriteType.axon)
assert_items_equal(n_points, n_points_ref)
fst.register_neurite_feature('bar', vol)
n_volume_ref = [n.volume for n in iter_neurites(NRNS)]
n_volume = fst.get('bar', NRNS)
assert_items_equal(n_volume, n_volume_ref)
# test neurite type filtering
n_volume_ref = [n.volume for n in iter_neurites(NRNS, filt=_is_type(NeuriteType.axon))]
n_volume = fst.get('bar', NRNS, neurite_type=NeuriteType.axon)
assert_items_equal(n_volume, n_volume_ref)
def test_get_segment_midpoint(self):
for ntyp in nm.NEURITE_TYPES:
pts = fst.get('segment_midpoints', self.fst_pop, neurite_type=ntyp)
ref_xyz = (get('segment_x_coordinates', self.ref_pop, neurite_type=ntyp),
get('segment_y_coordinates', self.ref_pop, neurite_type=ntyp),
get('segment_z_coordinates', self.ref_pop, neurite_type=ntyp))
for i in xrange(3):
_equal(pts[:, i], ref_xyz[i])
def _check_neurite_feature(self, ftr, debug=False, rtol=1e-05, atol=1e-08):
self._check_neuron_feature(ftr, debug, rtol, atol)
for t in NeuriteType:
_close(fst.get(ftr, self.fst_pop, neurite_type=t),
get(ftr, self.ref_pop, neurite_type=t), debug, rtol, atol)
def _check_neuron_feature(self, ftr, debug=False, rtol=1e-05, atol=1e-08):
_close(fst.get(ftr, self.fst_pop), get(ftr, self.ref_pop),
debug, rtol, atol)
