def test_make_copy():
tree_copy = make_copy(REF_TREE3)
# assert that the two trees have the same values
# first by total nodes
nt.assert_true(len(list(ipreorder(tree_copy))) == len(list(ipreorder(REF_TREE3))))
# then node by node
for val1, val2 in izip(val_iter(ipreorder(tree_copy)), val_iter(ipreorder(REF_TREE3))):
nt.assert_true(all(val1 == val2))
# assert that the tree values do not have the same identity
for val1, val2 in izip(val_iter(ipreorder(tree_copy)), val_iter(ipreorder(REF_TREE3))):
nt.assert_false(val1 is val2)
# create a deepcopy of the original tree for validation
validation_tree = deepcopy(REF_TREE3)
# modify copied tree
tree_copy.value[0:3] = np.array([1000.0, 1000.0, -1000.0])
tree_copy.children[0].add_child(Tree(np.array([0.0, 0.0, 0.0, 1.0, 1.0, 1.0, 1.0])))
# check if anything changed in REF_TREE3 with respect to the validation deepcopy
nt.assert_true(len(list(ipreorder(validation_tree))) == len(list(ipreorder(REF_TREE3))))
for val1, val2 in izip(val_iter(ipreorder(REF_TREE3)), val_iter(ipreorder(validation_tree))):
nt.assert_true(all(val1 == val2))
def _evaluate(tr1, tr2, comp_func):
for v1, v2 in izip(val_iter(ipreorder(tr1)), val_iter(ipreorder(tr2))):
#print "v1 : ", v1[:COLS.R]
#print "v2 : ", v2[:COLS.R]
#print "-" * 10
nt.assert_true(comp_func(v1[:COLS.R], v2[:COLS.R]))
def test_preorder_iteration():
nt.ok_(
list(val_iter(ipreorder(REF_TREE))) ==
[0, 11, 111, 112, 12, 121, 1211, 12111, 12112, 122])
nt.ok_(list(val_iter(ipreorder(REF_TREE.children[0]))) == [11, 111, 112])
nt.ok_(
list(val_iter(ipreorder(REF_TREE.children[1]))) ==
[12, 121, 1211, 12111, 12112, 122])
def test_iter_points(self):
ref_point_radii = []
for t in self.neuron.neurites:
ref_point_radii.extend(p[COLS.R] for p in val_iter(ipreorder(t)))
rads = [r for r in self.neuron.iter_points(lambda p: p[COLS.R])]
nt.assert_true(np.all(ref_point_radii == rads))
def test_iter_points(self):
ref_point_radii = []
for t in self.neuron.neurites:
ref_point_radii.extend(p[COLS.R] for p in val_iter(ipreorder(t)))
rads = [r for r in self.neuron.iter_points(lambda p: p[COLS.R])]
nt.assert_true(np.all(ref_point_radii == rads))
def test_copy():
soma = neuron.make_soma([[0, 0, 0, 1, 1, 1, -1]])
nrn1 = neuron.Neuron(soma, [TREE], name="Rabbit of Caerbannog")
nrn2 = nrn1.copy()
# check if two neurons are identical
# somata
nt.assert_true(isinstance(nrn2.soma, type(nrn1.soma)))
nt.assert_true(nrn1.soma.radius == nrn2.soma.radius)
for v1, v2 in izip(nrn1.soma.iter(), nrn2.soma.iter()):
nt.assert_true(np.allclose(v1, v2))
# neurites
for neu1, neu2 in izip(nrn1.neurites, nrn2.neurites):
nt.assert_true(isinstance(neu2, type(neu1)))
for v1, v2 in izip(val_iter(ipreorder(neu1)), val_iter(ipreorder(neu2))):
nt.assert_true(np.allclose(v1, v2))
# check if the ids are different
# somata
nt.assert_true( nrn1.soma is not nrn2.soma)
# neurites
for neu1, neu2 in izip(nrn1.neurites, nrn2.neurites):
nt.assert_true(neu1 is not neu2)
# check if changes are propagated between neurons
nrn2.soma.radius = 10.
nt.assert_false(nrn1.soma.radius == nrn2.soma.radius)
# neurites
for neu1, neu2 in izip(nrn1.neurites, nrn2.neurites):
for v1, v2 in izip(val_iter(ipreorder(neu1)), val_iter(ipreorder(neu2))):
v2 = np.array([-1000., -1000., -1000., 1000., -100., -100., -100.])
nt.assert_false(any(v1 == v2))
def find_tree_type(tree):
"""
Calculates the 'mean' type of the tree.
Accepted tree types are:
'undefined', 'axon', 'basal', 'apical'
The 'mean' tree type is defined as the type
that is shared between at least 51% of the tree's points.
Returns:
The type of the tree
"""
tree_types = tuple(TreeType)
types = [node[COLS.TYPE] for node in tr.val_iter(tr.ipreorder(tree))]
types = [node[COLS.TYPE] for node in tr.val_iter(tr.ipreorder(tree))]
return tree_types[int(np.median(types))]
def find_tree_type(tree):
"""
Calculates the 'mean' type of the tree.
Accepted tree types are:
'undefined', 'axon', 'basal', 'apical'
The 'mean' tree type is defined as the type
that is shared between at least 51% of the tree's points.
Returns:
The type of the tree
"""
tree_types = tuple(TreeType)
types = [node[COLS.TYPE] for node in tr.val_iter(tr.ipreorder(tree))]
types = [node[COLS.TYPE] for node in tr.val_iter(tr.ipreorder(tree))]
return tree_types[int(np.median(types))]
def test_deep_iteration():
root = t = Tree(0)
for i in range(1, sys.getrecursionlimit() + 2):
child = Tree(i)
t.add_child(child)
t = child
list(ipreorder(root))
list(ipostorder(root))
list(iupstream(t))
def test_deep_iteration():
root = t = Tree(0)
for i in range(1, sys.getrecursionlimit() + 2):
child = Tree(i)
t.add_child(child)
t = child
list(ipreorder(root))
list(ipostorder(root))
list(iupstream(t))
def _check_trees(trees):
for t in trees:
nt.ok_(len(list(tree.ileaf(t))) == 11)
nt.ok_(len(list(tree.iforking_point(t))) == 10)
nt.ok_(len(list(tree.ipreorder(t))) == 211)
nt.ok_(len(list(tree.ipostorder(t))) == 211)
nt.ok_(len(list(tree.isegment(t))) == 210)
leaves = [l for l in tree.ileaf(t)]
# path length from each leaf to root node.
branch_order = [21, 31, 41, 51, 61, 71, 81, 91, 101, 111, 111]
for i, l in enumerate(leaves):
nt.ok_(len(list(tree.iupstream(l))) == branch_order[i])
def _total_rectangles(tree):
'''
Calculate the total number of segments that are required
for the dendrogram. There is a vertical line for each segment
and two horizontal line at each branching point
'''
def f(children):
'''Calculates number of lines needed for the children of a node
'''
return 2 * len(children) if len(children) != 1 else 1
return sum(f(node.children) for node in ipreorder(tree))
def _check_trees(trees):
for t in trees:
nt.ok_(len(list(tree.ileaf(t))) == 11)
nt.ok_(len(list(tree.iforking_point(t))) == 10)
nt.ok_(len(list(tree.ipreorder(t))) == 211)
nt.ok_(len(list(tree.ipostorder(t))) == 211)
nt.ok_(len(list(tree.isegment(t))) == 210)
leaves = [l for l in tree.ileaf(t)]
# path length from each leaf to root node.
branch_order = [21, 31, 41, 51, 61, 71, 81, 91, 101, 111, 111]
for i, l in enumerate(leaves):
nt.ok_(len(list(tree.iupstream(l))) == branch_order[i])
def nonzero_neurite_radii(neuron, threshold=0.0):
'''Check presence of neurite points with radius not above threshold
Arguments:
neuron: Neuron object whose segments will be tested
threshold: value above which a radius is considered to be non-zero
Return: list of IDs of zero-radius points
'''
ids = [[i[COLS.ID] for i in val_iter(ipreorder(t))
if i[COLS.R] <= threshold] for t in neuron.neurites]
return [i for i in chain(*ids)]
def nonzero_neurite_radii(neuron, threshold=0.0):
'''Check presence of neurite points with radius not above threshold
Arguments:
neuron: Neuron object whose segments will be tested
threshold: value above which a radius is considered to be non-zero
Return: list of IDs of zero-radius points
'''
ids = [[
i[COLS.ID] for i in val_iter(ipreorder(t)) if i[COLS.R] <= threshold
] for t in neuron.neurites]
return [i for i in chain(*ids)]
def get_bounding_box(tree):
"""
Returns:
The boundaries of the tree in three dimensions:
[[xmin, ymin, zmin],
[xmax, ymax, zmax]]
"""
min_xyz, max_xyz = (np.array([np.inf, np.inf, np.inf]), np.array([np.NINF, np.NINF, np.NINF]))
for p in val_iter(tr.ipreorder(tree)):
min_xyz = np.minimum(p[: COLS.R], min_xyz)
max_xyz = np.maximum(p[: COLS.R], max_xyz)
return np.array([min_xyz, max_xyz])
def get_bounding_box(tree):
"""
Returns:
The boundaries of the tree in three dimensions:
[[xmin, ymin, zmin],
[xmax, ymax, zmax]]
"""
min_xyz, max_xyz = (np.array([np.inf, np.inf, np.inf]),
np.array([np.NINF, np.NINF, np.NINF]))
for p in val_iter(tr.ipreorder(tree)):
min_xyz = np.minimum(p[:COLS.R], min_xyz)
max_xyz = np.maximum(p[:COLS.R], max_xyz)
return np.array([min_xyz, max_xyz])
def is_monotonic(tree, tol):
'''Check if tree is monotonic, i.e. if each child has smaller or
equal diameters from its parent
Arguments:
tree : tree object
tol: numerical precision
'''
for node in ipreorder(tree):
if node.parent is not None:
if node.value[COLS.R] > node.parent.value[COLS.R] + tol:
return False
return True
def _affineTransformTree(tree, A, t, origin=None):
'''
Apply an affine transform on your tree by applying a linear
transform A (e.g. rotation) and a non-linear transform t (translation)
Input:
A : 3x3 transformation matrix
t : 3x1 translation array
tree : tree object
origin : the point with respect of which the rotation is applied. If
None then the x,y,z of the root node is assumed to be the
origin.
'''
# if no origin is specified, the position from the root node
# becomes the origin
if origin is None:
origin = tree.value[:COLS.R]
for value in val_iter(ipreorder(tree)):
_affineTransformPoint(value, A, t, origin)
def principal_direction_extent(tree):
'''Calculate the extent of a tree, that is the maximum distance between
the projections on the principal directions of the covariance matrix
of the x,y,z points of the nodes of the tree.
Input
tree : a tree object
Returns
extents : the extents for each of the eigenvectors of the cov matrix
eigs : eigenvalues of the covariance matrix
eigv : respective eigenvectors of the covariance matrix
'''
# extract the x,y,z coordinates of all the points in the tree
points = np.array([value[COLS.X: COLS.R]for value in val_iter(ipreorder(tree))])
# center the points around 0.0
points -= np.mean(points, axis=0)
# principal components
_, eigv = pca(points)
extent = np.zeros(3)
for i in range(eigv.shape[1]):
# orthogonal projection onto the direction of the v component
scalar_projs = np.sort(np.array([np.dot(p, eigv[:, i]) for p in points]))
extent[i] = scalar_projs[-1]
if scalar_projs[0] < 0.:
extent -= scalar_projs[0]
return extent
def test_preorder_iteration():
nt.ok_(list(val_iter(ipreorder(REF_TREE))) ==
[0, 11, 111, 112, 12, 121, 1211, 12111, 12112, 122])
nt.ok_(list(val_iter(ipreorder(REF_TREE.children[0]))) == [11, 111, 112])
nt.ok_(list(val_iter(ipreorder(REF_TREE.children[1]))) ==
[12, 121, 1211, 12111, 12112, 122])
def _max_recursion_depth(obj):
''' Estimate recursion depth, which is defined as the number of nodes in a tree
'''
neurites = obj.neurites if hasattr(obj, 'neurites') else [obj]
return max(sum(1 for _ in ipreorder(neu)) for neu in neurites)
def _make_monotonic(neuron):
for neurite in neuron.neurites:
for node in ipreorder(neurite):
if node.parent is not None:
node.value[COLS.R] = node.parent.value[COLS.R] / 2.
if __name__ == '__main__':
filename = 'test_data/swc/Neuron.swc'
rd = load_data(filename)
init_seg_ids = get_initial_segment_ids(rd)
trees = [make_tree(rd, sg) for sg in init_seg_ids]
soma = neuron.make_soma([rd.get_row(si) for si in get_soma_ids(rd)])
for tr in trees:
for p in point_iter(tree.ipreorder(tr)):
print p
print 'Initial segment IDs:', init_seg_ids
nrn = neuron.Neuron(soma, trees)
print 'Neuron soma raw data', [r for r in nrn.soma.iter()]
print 'Neuron soma points', [as_point(p) for p in nrn.soma.iter()]
print 'Neuron tree init points, types'
for tt in nrn.neurites:
print tt.value[COLS.ID], tt.value[COLS.TYPE]
print 'Making neuron 2'
nrn2 = make_neuron(rd)
def _make_flat(neuron):
for neurite in neuron.neurites:
for node in ipreorder(neurite):
if node.parent is not None:
node.value[COLS.Z] = 0.
if __name__ == '__main__':
filename = 'test_data/swc/Neuron.swc'
rd = load_data(filename)
init_seg_ids = get_initial_segment_ids(rd)
trees = [make_tree(rd, sg) for sg in init_seg_ids]
soma = neuron.make_soma([rd.get_row(si) for si in get_soma_ids(rd)])
for tr in trees:
for p in point_iter(tree.ipreorder(tr)):
LOG.debug(p)
LOG.info('Initial segment IDs: %s', init_seg_ids)
nrn = neuron.Neuron(soma, trees)
LOG.info('Neuron soma raw data % s', [r for r in nrn.soma.iter()])
LOG.info('Neuron soma points %s', [as_point(p)
for p in nrn.soma.iter()])
LOG.info('Neuron tree init points, types')
for tt in nrn.neurites:
LOG.info('%s, %s', tt.value[COLS.ID], tt.value[COLS.TYPE])
LOG.info('Making neuron 2')
def _max_diameter(tree):
'''Find max diameter in tree
'''
return 2. * max(node.value[COLS.R] for node in ipreorder(tree))
