def loadTree(self, reinitialize=0, segments=False):
"""
Load the T-tree morphology in memory
6--5--4--7--8
|
|
1
If `segments` is ``True``, tree is:
12--11--8---9--10
|
7
|
6
|
5
|
4
|
1
Standard associated computational tree is:
12------8------10
|
1
"""
if not hasattr(self, 'tree') or reinitialize:
fname = 'Ttree_segments.swc' if segments else 'Ttree.swc'
self.tree = MorphTree(os.path.join(MORPHOLOGIES_PATH_PREFIX, fname), types=[1,3,4])
def loadTree(self, reinitialize=0, segments=False):
"""
Load the T-tree morphology in memory
6--5--4--7--8
|
|
1
If `segments` is ``True``, tree is:
12--11--8---9--10
|
7
|
6
|
5
|
4
|
1
Standard associated computational tree is:
12------8------10
|
1
"""
if not hasattr(self, 'tree') or reinitialize:
print('>>> loading T-tree <<<')
fname = 'Ttree_segments.swc' if segments else 'Ttree.swc'
self.tree = MorphTree('test_morphologies/' + fname,
types=[1, 3, 4])
def reduceMorphology():
"""
Reduces the number of nodes on the morphology for computational efficiency
Returns
-------
m_tree: `neat.MorphTree`
The original morphology
morph_tree: `neat.MorphTree`
The reduced morphology
locs: list of locations
The recording locations in the coordinates of the original morphology
morph_locs: list of locations
The recording locations in the coordinates of the reduced tree
"""
m_tree = MorphTree(file_n='datafiles/ACCPyr.swc')
locs = [LOC_SOMA, LOC_DEND]
# create a downsampled tree for efficiency
m_tree.setCompTree()
m_tree.distributeLocsUniform(50., add_bifurcations=True, name='downsampled')
morph_tree = m_tree.createNewTree('downsampled', store_loc_inds=True)
# get the reduced loc inds
locinds = m_tree.getNearestLocinds(locs, name='downsampled')
locinds_nt = [n.content['loc ind'] for n in morph_tree]
nodeinds_newloc = [np.where(locinds_nt == loc_ind)[0][0] for loc_ind in locinds]
nodes = [node for ii, node in enumerate(morph_tree) if ii in nodeinds_newloc]
morph_locs = [(n.index, 1.) for n in nodes]
return m_tree, morph_tree, locs, morph_locs
def testMultiCylinderSoma(self):
mtree = MorphTree(os.path.join(MORPHOLOGIES_PATH_PREFIX, 'multicylinder_soma.swc'))
for n, idx in zip(mtree, [1,7,8,9,10]):
assert n.index == idx
idxs = [1,2,3,7,8,9,10]
for ii, n in enumerate(mtree.__iter__(skip_inds=[])):
assert n.index == idxs[ii]
s_radius = np.sqrt(2.*np.pi*10. * 5. / (4.*np.pi))
assert mtree[1].R == s_radius
assert np.allclose(mtree[1].xyz, np.array([0.,2.5,0.]))
def testThreePointSoma(self):
mtree = MorphTree(os.path.join(MORPHOLOGIES_PATH_PREFIX, 'threepoint_soma.swc'))
for n, idx in zip(mtree, [1,4,5]):
assert n.index == idx
idxs = [1,2,3,4,5]
for ii, n in enumerate(mtree.__iter__(skip_inds=[])):
assert n.index == idxs[ii]
s_surface = 2. * np.pi * 5. * 5. + \
2. * np.pi * 5. * 5.
s_radius = np.sqrt(s_surface / (4.*np.pi))
assert mtree[1].R == s_radius
def testThreePointSoma(self):
mtree = MorphTree('test_morphologies/threepoint_soma.swc')
for n, idx in zip(mtree, [1,4,5]):
assert n.index == idx
idxs = [1,2,3,4,5]
for ii, n in enumerate(mtree.__iter__(skip_inds=[])):
assert n.index == idxs[ii]
s_surface = 2. * np.pi * 5. * 5. + \
2. * np.pi * 5. * 5.
s_radius = np.sqrt(s_surface / (4.*np.pi))
assert mtree[1].R == s_radius
def loadTree(self, reinitialize=0):
'''
Load the T-tree morphology in memory
6--5--4--7--8
|
|
1
Standard associated computational tree is:
6-----4-----8
|
|
1
'''
if not hasattr(self, 'tree') or reinitialize:
print '>>> loading T-tree <<<'
fname = 'test_morphologies/Ttree.swc'
self.tree = MorphTree(fname, types=[1,3,4])
def testWrongSoma(self):
with pytest.raises(ValueError):
MorphTree(os.path.join(MORPHOLOGIES_PATH_PREFIX, 'wrong_soma.swc'))
class TestMorphTree():
def loadTree(self, reinitialize=0, segments=False):
"""
Load the T-tree morphology in memory
6--5--4--7--8
|
|
1
If `segments` is ``True``, tree is:
12--11--8---9--10
|
7
|
6
|
5
|
4
|
1
Standard associated computational tree is:
12------8------10
|
1
"""
if not hasattr(self, 'tree') or reinitialize:
fname = 'Ttree_segments.swc' if segments else 'Ttree.swc'
self.tree = MorphTree(os.path.join(MORPHOLOGIES_PATH_PREFIX, fname), types=[1,3,4])
def testLocEquality(self):
self.loadTree()
loc1 = MorphLoc((4,.5), self.tree)
loc2 = MorphLoc((4,.5), self.tree)
loc3 = MorphLoc((4,.7), self.tree)
assert loc1 == (4,.5) and (4,.5) == loc1
assert loc1 == {'node': 4, 'x':.5} and {'node': 4, 'x':.5} == loc1
assert loc1 == loc2 and loc2 == loc1
assert loc1 != (4,.7) and (4,.7) != loc1
assert loc1 != {'node': 5, 'x':.5} and {'node': 5, 'x':.5} != loc1
assert loc1 != loc3 and loc3 != loc1
loc4 = MorphLoc((1,.5), self.tree)
assert loc4 == (1,.8) and loc4 != (4,.5)
def testIteration(self):
self.loadTree()
indices = [node.index for node in self.tree]
assert 2 not in indices and 3 not in indices
assert set(indices) == set([1,4,5,6,7,8])
indices = [node.index for node in self.tree.nodes]
assert 2 not in indices and 3 not in indices
assert set(indices) == set([1,4,5,6,7,8])
def testStructure(self):
self.loadTree()
# check root
root = self.tree[1]
assert root.parent_node == None
assert len(root.child_nodes) == 1 \
and set([node.index for node in root.child_nodes]) == set([4])
# check bifurcation node
bifur = self.tree[4]
assert bifur.parent_node == root
assert len(bifur.child_nodes) == 2 \
and set([node.index for node in bifur.child_nodes]) == set([5,7])
# check branch nodes
bn1 = self.tree[5]
assert bn1.parent_node == bifur
assert len(bn1.child_nodes) == 1 and bn1.child_nodes[0].index == 6
bn2 = self.tree[7]
assert bn2.parent_node == bifur
assert len(bn2.child_nodes) == 1 and bn2.child_nodes[0].index == 8
# check leaf nodes
leaf1 = self.tree[6]
assert leaf1.parent_node == bn1
assert len(leaf1.child_nodes) == 0
leaf2 = self.tree[8]
assert leaf2.parent_node == bn2
assert len(leaf2.child_nodes) == 0
def testGeometry(self):
self.loadTree()
# check root
root = self.tree[1]
assert np.allclose(root.xyz, np.array([0.,0.,0.]))
assert np.allclose(root.R, 10.)
assert np.allclose(root.L, 0.)
assert root.swc_type == 1
# check bifurcation node
bifur = self.tree[4]
assert np.allclose(bifur.xyz, np.array([100.,0.,0.]))
assert np.allclose(bifur.R, 1.)
assert np.allclose(bifur.L, 100.)
assert bifur.swc_type == 4
# check branch nodes
bn1 = self.tree[5]
assert np.allclose(bn1.xyz, np.array([100.,50.,0.]))
assert np.allclose(bn1.R, 1.)
assert np.allclose(bn1.L, 50.)
assert bn1.swc_type == 4
bn2 = self.tree[7]
assert np.allclose(bn2.xyz, np.array([100.,-50.,0.]))
assert np.allclose(bn2.R, 1.)
assert np.allclose(bn2.L, 50.)
assert bn2.swc_type == 4
# check leaf nodes
leaf1 = self.tree[6]
assert np.allclose(leaf1.xyz, np.array([100.,100.,0.]))
assert np.allclose(leaf1.R, .5)
assert np.allclose(leaf1.L, 50.)
assert leaf1.swc_type == 4
leaf2 = self.tree[8]
assert np.allclose(leaf2.xyz, np.array([100.,-100.,0.]))
assert np.allclose(leaf2.R, .5)
assert np.allclose(leaf2.L, 50.)
assert leaf2.swc_type == 4
def testCompTree0(self):
self.loadTree(reinitialize=1)
# check exception when treetype is invalid
with pytest.raises(ValueError):
self.tree.treetype = 'bla'
# check exception when computational tree has not been set
with pytest.raises(ValueError):
self.tree.treetype = 'computational'
# initialize the comptree
self.tree.setCompTree(eps=1.)
# set computational tree as primary tree
self.tree.treetype = 'computational'
# check root node
root = self.tree[1]
assert root.parent_node == None
assert len(root.child_nodes) == 1 \
and set([node.index for node in root.child_nodes]) == set([4])
assert np.allclose(root.xyz, np.array([0.,0.,0.]))
assert np.allclose(root.R, 10.)
assert np.allclose(root.L, 0.)
assert root.swc_type == 1
# check bifurcation node
bifur = self.tree[4]
assert bifur.parent_node == root
assert len(bifur.child_nodes) == 2 \
and set([node.index for node in bifur.child_nodes]) == set([6,8])
assert np.allclose(bifur.xyz, np.array([100.,0.,0.]))
assert np.allclose(bifur.R, 1.)
assert np.allclose(bifur.L, 100.)
assert bifur.swc_type == 4
# check leaf nodes
leaf1 = self.tree[6]
assert leaf1.parent_node == bifur
assert len(leaf1.child_nodes) == 0
assert np.allclose(leaf1.xyz, np.array([100.,100.,0.]))
assert np.allclose(leaf1.R, .75)
assert np.allclose(leaf1.L, 100.)
assert leaf1.swc_type == 4
leaf2 = self.tree[8]
assert leaf2.parent_node == bifur
assert len(leaf2.child_nodes) == 0
assert np.allclose(leaf2.xyz, np.array([100.,-100.,0.]))
assert np.allclose(leaf2.R, .75)
assert np.allclose(leaf2.L, 100.)
# test nodes getter
assert len(self.tree.nodes) == 4
leafs = self.tree.leafs
assert np.allclose([leafs[0].L, leafs[1].L], [100., 100.])
self.tree.treetype = 'original'
assert len(self.tree.nodes) == 6
leafs = self.tree.leafs
assert np.allclose([leafs[0].L, leafs[1].L], [50., 50.])
# remove the computational tree
self.tree.removeCompTree()
with pytest.raises(ValueError):
self.tree.treetype = 'computational'
for node in self.tree:
assert not node.used_in_comp_tree
def testInputArgConversion(self):
self.loadTree()
nodes = self.tree._convertNodeArgToNodes(None)
assert self.tree.nodes == nodes
nodes = self.tree._convertNodeArgToNodes(self.tree[4])
assert self.tree.gatherNodes(self.tree[4]) == nodes
nodes = self.tree._convertNodeArgToNodes('apical')
assert self.tree.getNodesInApicalSubtree() == nodes
nodes = self.tree._convertNodeArgToNodes('basal')
assert self.tree.getNodesInBasalSubtree() == nodes
nodes = self.tree._convertNodeArgToNodes('axonal')
assert self.tree.getNodesInAxonalSubtree() == nodes
nodes_ = [self.tree[5], self.tree[7]]
nodes = self.tree._convertNodeArgToNodes(nodes_)
assert nodes_ == nodes
with pytest.raises(ValueError):
self.tree._convertNodeArgToNodes('wrong arg')
self.tree._convertNodeArgToNodes(5)
# with the computational tree
self.tree.setCompTree(set_as_primary_tree=1, eps=1.)
nodes = self.tree._convertNodeArgToNodes(None)
assert self.tree.nodes == nodes
nodes = self.tree._convertNodeArgToNodes(self.tree[4])
assert self.tree.gatherNodes(self.tree[4]) == nodes
nodes = self.tree._convertNodeArgToNodes('apical')
assert self.tree.getNodesInApicalSubtree() == nodes
nodes = self.tree._convertNodeArgToNodes('basal')
assert self.tree.getNodesInBasalSubtree() == nodes
nodes = self.tree._convertNodeArgToNodes('axonal')
assert self.tree.getNodesInAxonalSubtree() == nodes
nodes__ = [self.tree[6], self.tree[8]]
nodes = self.tree._convertNodeArgToNodes(nodes_)
assert nodes_ != nodes
assert nodes__ == nodes
def testLocFunctionality(self):
self.loadTree()
# locs in the original tree
self.tree.treetype = 'original'
locs = [MorphLoc({'node': 1, 'x': .5}, self.tree),
MorphLoc({'node': 4, 'x': .5}, self.tree),
MorphLoc({'node': 5, 'x': .5}, self.tree),
MorphLoc({'node': 7, 'x': .5}, self.tree),
MorphLoc({'node': 6, 'x': .5}, self.tree),
MorphLoc({'node': 8, 'x': .5}, self.tree)]
# set the computational tree
self.tree.setCompTree(eps=1.)
self.tree.treetype = 'computational'
for loc in locs: loc._setComputationalLoc()
assert locs[0].comp_loc == locs[0].loc
assert locs[1].comp_loc == locs[1].loc
assert locs[2].comp_loc == {'node': 6, 'x': .25}
assert locs[3].comp_loc == {'node': 8, 'x': .25}
assert locs[4].comp_loc == {'node': 6, 'x': .75}
assert locs[5].comp_loc == {'node': 8, 'x': .75}
def testPathLength(self):
self.loadTree()
# lengths in the original tree
self.tree.treetype = 'original'
# test lengths
L = self.tree.pathLength({'node': 1, 'x': 1.}, {'node': 1, 'x': .4})
assert np.allclose(L, 0.)
L = self.tree.pathLength({'node': 4, 'x': 1.}, {'node': 1, 'x': .4})
assert np.allclose(L, 100.)
L = self.tree.pathLength({'node': 4, 'x': 1.}, {'node': 1, 'x': .6})
assert np.allclose(L, 100.)
L = self.tree.pathLength({'node': 4, 'x': 1.}, {'node': 4, 'x': 1.})
assert np.allclose(L, 0.)
L = self.tree.pathLength({'node': 4, 'x': 1.}, {'node': 5, 'x': 0.})
assert np.allclose(L, 0.)
L = self.tree.pathLength({'node': 4, 'x': .5}, {'node': 5, 'x': .2})
assert np.allclose(L, 60.)
L = self.tree.pathLength({'node': 5, 'x': .2}, {'node': 4, 'x': .5})
assert np.allclose(L, 60.)
L = self.tree.pathLength({'node': 5, 'x': .2}, {'node': 7, 'x': .2})
assert np.allclose(L, 20.)
L = self.tree.pathLength({'node': 8, 'x': .2}, {'node': 4, 'x': .5})
assert np.allclose(L, 110.)
# lengths in the original tree
self.tree.setCompTree()
self.tree.treetype = 'computational'
# test lengths
L = self.tree.pathLength({'node': 1, 'x': 1.}, {'node': 1, 'x': .4})
assert np.allclose(L, 0.)
L = self.tree.pathLength({'node': 4, 'x': 1.}, {'node': 1, 'x': .4})
assert np.allclose(L, 100.)
L = self.tree.pathLength({'node': 4, 'x': 1.}, {'node': 1, 'x': .6})
assert np.allclose(L, 100.)
L = self.tree.pathLength({'node': 4, 'x': 1.}, {'node': 4, 'x': 1.})
assert np.allclose(L, 0.)
L = self.tree.pathLength({'node': 4, 'x': 1.}, {'node': 5, 'x': 0.})
assert np.allclose(L, 0.)
L = self.tree.pathLength({'node': 4, 'x': .5}, {'node': 5, 'x': .2})
assert np.allclose(L, 60.)
L = self.tree.pathLength({'node': 5, 'x': .2}, {'node': 4, 'x': .5})
assert np.allclose(L, 60.)
L = self.tree.pathLength({'node': 5, 'x': .2}, {'node': 7, 'x': .2})
assert np.allclose(L, 20.)
L = self.tree.pathLength({'node': 8, 'x': .2}, {'node': 4, 'x': .5})
assert np.allclose(L, 110.)
def testLocStorageRetrievalLookup(self):
self.loadTree()
locs = [(1,.5), (1, 1.), (4, 1.), (4, .5), (5, .5),
(5, 1.), (6, .5), (6, 1.), (8, .5), (8, 1.)]
with pytest.warns(UserWarning):
self.tree.storeLocs(locs, 'testlocs')
# with pytest.raises(ValueError):
# self.tree.storeLocs(locs, 'testlocs')
locs = [(1,.5), (4, 1.), (4, .5), (5, .5),
(5, 1.), (6, .5), (6, 1.), (8, .5), (8, 1.)]
self.tree.storeLocs(locs, 'testlocs')
# test retrieval
with pytest.raises(KeyError):
self.tree.getLocs('wronglocs')
locs_ = [(loc['node'], loc['x'])
for loc in self.tree.getLocs('testlocs')]
assert locs_ == locs
# test getting node indices
with pytest.raises(KeyError):
self.tree.getNodeIndices('wronglocs')
assert [1,4,4,5,5,6,6,8,8] == self.tree.getNodeIndices('testlocs').tolist()
# test get x-coords
with pytest.raises(KeyError):
self.tree.getXCoords('wronglocs')
assert np.allclose([.5,1.,.5,.5,1.,.5,1.,.5,1.],
self.tree.getXCoords('testlocs'))
# test get locinds on non-empty node
locinds = self.tree.getLocindsOnNode('testlocs', self.tree[4])
assert locinds == [2,1]
# test get locinds on empty node
locinds = self.tree.getLocindsOnNode('testlocs', self.tree[7])
assert locinds == []
with pytest.raises(KeyError):
self.tree.getLocindsOnNode('wronglocs', self.tree[7])
# test locinds on path
path = self.tree.pathBetweenNodes(self.tree[6], self.tree[8])
locinds = self.tree.getLocindsOnPath('testlocs',
self.tree[6], self.tree[8], xstart=.5, xstop=1.)
assert locinds == [5,4,3,1,7,8]
path = self.tree.pathBetweenNodes(self.tree[7], self.tree[7])
locinds = self.tree.getLocindsOnPath('testlocs',
self.tree[7], self.tree[7], xstart=0., xstop=1.)
assert locinds == []
path = self.tree.pathBetweenNodes(self.tree[4], self.tree[4])
locinds = self.tree.getLocindsOnPath('testlocs',
self.tree[4], self.tree[4], xstart=0., xstop=.9)
assert locinds == [2]
path = self.tree.pathBetweenNodes(self.tree[1], self.tree[1])
locinds = self.tree.getLocindsOnPath('testlocs',
self.tree[1], self.tree[1], xstart=0., xstop=.9)
assert locinds == [0]
path = self.tree.pathBetweenNodes(self.tree[4], self.tree[1])
locinds = self.tree.getLocindsOnPath('testlocs',
self.tree[4], self.tree[1], xstart=.9, xstop=.9)
assert locinds == [2,0]
locinds = self.tree.getLocindsOnPath('testlocs',
self.tree[7], self.tree[7], xstart=.1, xstop=.9)
assert locinds == []
# test locinds on branch
branch = self.tree.pathBetweenNodes(self.tree[4], self.tree[5])
locinds = self.tree.getLocindsOnNodes('testlocs', branch)
assert locinds == [2,1,3,4]
# test locinds on basal/apical/axonal subtrees
locinds = self.tree.getLocindsOnNodes('testlocs', 'basal')
assert locinds == []
locinds = self.tree.getLocindsOnNodes('testlocs', 'axonal')
assert locinds == []
locinds = self.tree.getLocindsOnNodes('testlocs', 'apical')
assert locinds == [2,1,3,4,5,6,7,8]
# test locinds on subtree
nodes = self.tree.getNodesInSubtree(self.tree[5], self.tree[4])
locinds = self.tree.getLocindsOnNodes('testlocs', nodes)
assert locinds == [2,1,3,4,5,6]
# find the nearest locs
locs = [(1,.5), (4, .5), (5, .4), (5, 1.),
(6, .5), (6, 1.), (8, .5), (8, 1.)]
self.tree.storeLocs(locs, 'testlocs2')
locinds = self.tree.getNearestLocinds([(7, .5), (1,.6), (6, .1), (6, .7)],
'testlocs2', direction=0)
res = self.tree.getNearestLocinds([(6, .1)],
'testlocs2', direction=0)
assert locinds == [2, 0, 3, 4]
locinds = self.tree.getNearestLocinds([(7, .5), (1,.6), (6, .1), (6, .7)],
'testlocs2', direction=1)
assert locinds == [2, 0, 3, 4]
locinds = self.tree.getNearestLocinds([(7, .5), (1,.6), (6, .1), (6, .7)],
'testlocs2', direction=2)
assert locinds == [6, 0, 4, 5]
# find the leaf locs
locinds = self.tree.getLeafLocinds('testlocs2')
assert locinds == [5,7]
# find the neartest locs
locs = [(4, .1), (4, .4), (4, .7)]
self.tree.storeLocs(locs, 'testlocs3')
locinds0 = self.tree.getNearestLocinds([(4, .4)],
'testlocs3', direction=0)
locinds1 = self.tree.getNearestLocinds([(4, .4)],
'testlocs3', direction=1)
locinds2 = self.tree.getNearestLocinds([(4, .4)],
'testlocs3', direction=2)
assert locinds0[0] == 1
assert locinds1[0] == 1
assert locinds2[0] == 1
def testNearestNeighbours(self):
self.loadTree()
locs1 = [(4,1.), (5,.5), (7,.5)]
inds = self.tree.getNearestNeighbourLocinds((5,.7), locs1)
assert set(inds) == {1}
inds = self.tree.getNearestNeighbourLocinds((6,.7), locs1)
assert set(inds) == {1}
inds = self.tree.getNearestNeighbourLocinds((5,.5), locs1)
assert set(inds) == {1}
inds = self.tree.getNearestNeighbourLocinds((5,.4), locs1)
assert set(inds) == {0,1}
locs2 = [(4,.9), (5,.5), (7,.5)]
inds = self.tree.getNearestNeighbourLocinds((5,.4), locs2)
assert set(inds) == {0,1,2}
locs3 = [(1,.5), (4,.9), (7,.5)]
inds = self.tree.getNearestNeighbourLocinds((4,.8), locs3)
assert set(inds) == {0,1}
locs4 = [(5,.9), (6,.9), (7,.5), (8,.9)]
inds = self.tree.getNearestNeighbourLocinds((1,.5), locs4)
assert set(inds) == {0,2}
def testDistances(self):
self.loadTree()
locs = [(1,.5), (4, 1.), (5, .5), (6, .5), (6, 1.)]
self.tree.storeLocs(locs, 'testlocs')
# compute the distances to soma
d2s = self.tree.distancesToSoma('testlocs')
assert np.allclose(d2s, np.array([0.,100.,125.,175.,200.]))
d2b = self.tree.distancesToBifurcation('testlocs')
assert np.allclose(d2b, np.array([0.,100.,25.,75.,100.]))
def testLocDistribution(self):
self.loadTree()
# check comptree resetting
self.tree.setCompTree()
self.tree.treetype = 'computational'
self.tree.distributeLocsOnNodes(np.array([90.,140.,190.]), [])
assert self.tree.treetype == 'computational'
self.tree.treetype = 'original'
# test loc distribution on nodes
locs = self.tree.distributeLocsOnNodes(np.array([90.,140.,190.]),
[self.tree[6], self.tree[8]])
assert locs[0] == {'node': 6, 'x': 4./5.} \
and locs[1] == {'node': 8, 'x': 4./5.} \
and len(locs) == 2
locs = self.tree.distributeLocsOnNodes(np.array([190.,190.]),
[self.tree[6]])
assert locs[0] == locs[1] and locs[0] == {'node': 6, 'x': 4./5.}
locs = self.tree.distributeLocsOnNodes(np.array([]),
[self.tree[6]])
assert len(locs) == 0
locs = self.tree.distributeLocsOnNodes(np.array([100.]),
[self.tree[4], self.tree[5]])
assert locs[0] == {'node': 4, 'x': 1.}
# derived loc distribution functions
locs = self.tree.distributeLocsOnNodes(np.array([150.,100.]))
assert locs[0] == {'node': 4, 'x': 1.} \
and locs[1] == {'node': 5, 'x': 1.} \
and locs[2] == {'node': 7, 'x': 1.}
nodes = self.tree.pathBetweenNodes(self.tree[5], self.tree[6])
locs = self.tree.distributeLocsOnNodes(np.array([50.,120.,170.]),
node_arg=nodes)
assert locs[0] == {'node': 5, 'x': 2./5.} \
and locs[1] == {'node': 6, 'x': 2./5.}
locs = self.tree.distributeLocsOnNodes(np.array([70.,120.]),
node_arg='basal')
assert len(locs) == 0
locs = self.tree.distributeLocsOnNodes(np.array([70.,120.]),
node_arg='apical')
assert locs[0] == {'node': 4, 'x': 7./10.} \
and locs[1] == {'node': 5, 'x': 2./5.} \
and locs[2] == {'node': 7, 'x': 2./5.}
nodes = self.tree.getNodesInSubtree(self.tree[6], self.tree[4])
locs = self.tree.distributeLocsOnNodes(np.array([70.,120]),
node_arg=nodes)
assert locs[0] == {'node': 4, 'x': 7./10.} \
and locs[1] == {'node': 5, 'x': 2./5.}
# test uniform loc distribution
locs = self.tree.distributeLocsUniform(50.)
checklocs = [{'node': 1, 'x': .8},
{'node': 4, 'x': 1./2.}, {'node': 4, 'x': 1.},
{'node': 5, 'x': 1.}, {'node': 6, 'x': 1.},
{'node': 7, 'x': 1.}, {'node': 8, 'x': 1.}]
for (loc, checkloc) in zip(locs, checklocs):
assert loc == checkloc
locs = self.tree.distributeLocsUniform(50., node_arg=self.tree[5])
checklocs = [{'node': 5, 'x': 1.}, {'node': 6, 'x': 1.}]
for (loc, checkloc) in zip(locs, checklocs):
assert loc == checkloc
# test random loc distribution
locs = self.tree.distributeLocsRandom(10)
assert len(locs) > 0
for node in self.tree:
assert 'tag' not in node.content
locs = self.tree.distributeLocsRandom(10, node_arg='basal', add_soma=0)
assert len(locs) == 0
with pytest.raises(ValueError):
self.tree.distributeLocsRandom(10, node_arg='bad type')
def testTreeCreation(self):
self.loadTree(self)
locs = [(1,.5),(4,.5),(4,1.),(5,1.),(6,1.),(7,1.),(8,1.)]
self.tree.storeLocs(locs, 'newtree_test')
# create the new tree
new_tree = self.tree.createNewTree('newtree_test')
new_xyzs = [(0.,0.,0.),
(50.,0.,0.),
(100.,0.,0.),
(100.,50.,0.),
(100.,100.,0.),
(100.,-50.,0.),
(100.,-100.,0.)]
new_inds = [1,4,5,6,7,8,9]
for ii, new_node in enumerate(new_tree):
assert np.allclose(new_xyzs[ii], new_node.xyz)
assert new_inds[ii] == new_node.index
def testPlotting(self, pshow=0):
self.loadTree()
self.tree.setCompTree()
# create the x-axis
self.tree.makeXAxis(50.)
assert np.allclose(self.tree.xaxis,
np.array([0.,50.,100.,150.,200.,200.,250.]))
# find x-values
locs = [(4.,.7),(5,.9), (7,.8)]
xvals = self.tree.getXValues(locs)
assert np.allclose([50.,150.,200.], xvals)
xvals = self.tree.getXValues([])
assert len(xvals) == 0
# plot on x-axis
parr = np.array([1.,2.,3.,4.,5.,4.,3.])
pl.figure('plot 1d test orig')
# original tree
lines = self.tree.plot1D(pl.gca(), parr, c='r')
assert np.abs(self.tree.xaxis[-1] - 250.) < 1e-5
assert len(lines) == len(self.tree.getLeafLocinds('xaxis'))
assert np.allclose(lines[0].get_data()[1], parr[0:5])
assert np.allclose(lines[1].get_data()[1], parr[5:])
xarr = np.array([0.,50.,100.,150.,200.,200.,250.])
assert np.allclose(lines[0].get_data()[0], xarr[0:5])
assert np.allclose(lines[1].get_data()[0], xarr[5:])
assert lines[0].get_color() == 'r'
# update the lines
parr_ = np.array([5.,4.,3.,2.,1.,2.,3.])
self.tree.setLineData(lines, parr_)
assert np.allclose(lines[0].get_data()[1], parr_[0:5])
assert np.allclose(lines[1].get_data()[1], parr_[5:])
# test x-axis coloring (just sees if function runs)
self.tree.colorXAxis(pl.gca(), pl.get_cmap('jet'))
# computational tree
self.tree.treetype = 'computational'
pl.figure('plot 1d test comp')
lines = self.tree.plot1D(pl.gca(), parr, c='r')
assert np.abs(self.tree.xaxis[-1] - 250.) < 1e-5
assert len(lines) == len(self.tree.getLeafLocinds('xaxis'))
assert np.allclose(lines[0].get_data()[1], parr[0:5])
assert np.allclose(lines[1].get_data()[1], parr[5:])
xarr = np.array([0.,50.,100.,150.,200.,200.,250.])
assert np.allclose(lines[0].get_data()[0], xarr[0:5])
assert np.allclose(lines[1].get_data()[0], xarr[5:])
assert lines[0].get_color() == 'r'
# test x-axis coloring (just sees if function runs)
self.tree.colorXAxis(pl.gca(), pl.get_cmap('jet'))
# a true distance from soma plot
parr = np.array([1.,2.,3.,4.,5.,4.,3.])
pl.figure('plot d2s test')
lines = self.tree.plotTrueD2S(pl.gca(),parr)
assert len(lines) == len(self.tree.getLeafLocinds('xaxis'))
assert np.allclose(lines[0].get_data()[1], parr[0:5])
assert np.allclose(lines[1].get_data()[1], parr[5:])
assert np.allclose(lines[0].get_data()[0], self.tree.d2s['xaxis'][0:5])
assert np.allclose(lines[1].get_data()[0], self.tree.d2s['xaxis'][5:])
# test 2D plotting (just sees if function runs)
pl.figure('plot morphology test')
cs = {node.index: node.index for node in self.tree}
marklocs = [(1,.5), (4,.8), (6,.2)]
locargs = {'marker': 'o', 'mfc': 'r', 'ms': 6}
marklabels = {0: r'soma', 1: r'$\mu$'}
labelargs = {'fontsize': 8}
self.tree.plot2DMorphology(pl.gca(), cs=cs, cmap=pl.get_cmap('summer'),
plotargs={'lw':2},
marklocs=marklocs, locargs=locargs,
marklabels=marklabels, labelargs=labelargs,
textargs={'fontsize': 24},
cb_draw=True)
if pshow: pl.show()
def testCompTree(self):
self.loadTree(reinitialize=1, segments=True)
self.tree.setCompTree()
# check whether amount of nodes is correct
self.tree.treetype = 'original'
assert len(self.tree.nodes) == 10
assert len([node for node in self.tree]) == 10
self.tree.treetype = 'computational'
assert len(self.tree.nodes) == 4
assert len([node for node in self.tree]) == 4
# check whether computational nodes are correct
for node in self.tree: assert node.index in [1,8,10,12]
# check whether returned nodes from `MorphTree._convertNodeArgToNodes`
# are correct
ns_orig = self.tree._nodes_orig
ns_comp = self.tree._convertNodeArgToNodes(ns_orig)
assert [n.index for n in ns_comp] == [1,8,10,12]
ns_comp = self.tree._convertNodeArgToNodes('apical')
assert [n.index for n in ns_comp] == [8,10,12]
ns_comp = self.tree._convertNodeArgToNodes('basal')
assert [n.index for n in ns_comp] == []
ns_comp = [self.tree._convertNodeArgToNodes(n)[0] for n in ns_orig]
assert [n.index for n in ns_comp] == [1,8,8,8,8,8,10,10,12,12]
# assert whether returned nodes have correct structure
assert self.tree[5] == None
assert self.tree[6] == None
assert self.tree[7] == None
assert self.tree[9] == None
assert self.tree[11] == None
assert self.tree[1].parent_node == None
assert self.tree[8].parent_node.index == 1
assert self.tree[10].parent_node.index == 8
assert self.tree[12].parent_node.index == 8
assert self.tree[1].child_nodes[0].index == 8
assert [cn.index for cn in self.tree[8].child_nodes] == [10,12]
assert self.tree[10].child_nodes == []
assert self.tree[12].child_nodes == []
# change radius of a node and check whether computational tree is correct
# (i) below threshold
self.tree.treetype = 'original'
self.tree[5].R += 1e-12
self.tree.setCompTree()
self.tree.treetype = 'computational'
for node in self.tree: assert node.index in [1,8,10,12]
# (i1) above threshold, one node
self.tree.treetype = 'original'
self.tree[5].R += 1e-2
self.tree.setCompTree(eps=1e-9)
self.tree.treetype = 'computational'
for node in self.tree: assert node.index in [1,4,5,8,10,12]
# (i2) above threshold, two consecutive nodes
self.tree.treetype = 'original'
self.tree[4].R += 1e-2
self.tree.setCompTree()
self.tree.treetype = 'computational'
for node in self.tree: assert node.index in [1,5,8,10,12]
def testThreePointSoma(self):
mtree = MorphTree(os.path.join(MORPHOLOGIES_PATH_PREFIX, 'threepoint_soma.swc'))
for n, idx in zip(mtree, [1,4,5]):
assert n.index == idx
idxs = [1,2,3,4,5]
for ii, n in enumerate(mtree.__iter__(skip_inds=[])):
assert n.index == idxs[ii]
s_surface = 2. * np.pi * 5. * 5. + \
2. * np.pi * 5. * 5.
s_radius = np.sqrt(s_surface / (4.*np.pi))
assert mtree[1].R == s_radius
def testMultiCylinderSoma(self):
mtree = MorphTree(os.path.join(MORPHOLOGIES_PATH_PREFIX, 'multicylinder_soma.swc'))
for n, idx in zip(mtree, [1,7,8,9,10]):
assert n.index == idx
idxs = [1,2,3,7,8,9,10]
for ii, n in enumerate(mtree.__iter__(skip_inds=[])):
assert n.index == idxs[ii]
s_radius = np.sqrt(2.*np.pi*10. * 5. / (4.*np.pi))
assert mtree[1].R == s_radius
assert np.allclose(mtree[1].xyz, np.array([0.,2.5,0.]))
def testWrongSoma(self):
with pytest.raises(ValueError):
MorphTree(os.path.join(MORPHOLOGIES_PATH_PREFIX, 'wrong_soma.swc'))
def testWrongSoma(self):
with pytest.raises(ValueError):
mtree = MorphTree('test_morphologies/wrong_soma.swc')
class TestMorphTree():
def loadTree(self, reinitialize=0):
'''
Load the T-tree morphology in memory
6--5--4--7--8
|
|
1
Standard associated computational tree is:
6-----4-----8
|
|
1
'''
if not hasattr(self, 'tree') or reinitialize:
print '>>> loading T-tree <<<'
fname = 'test_morphologies/Ttree.swc'
self.tree = MorphTree(fname, types=[1,3,4])
def testLocEquality(self):
self.loadTree()
loc1 = MorphLoc((4,.5), self.tree)
loc2 = MorphLoc((4,.5), self.tree)
loc3 = MorphLoc((4,.7), self.tree)
assert loc1 == (4,.5) and (4,.5) == loc1
assert loc1 == {'node': 4, 'x':.5} and {'node': 4, 'x':.5} == loc1
assert loc1 == loc2 and loc2 == loc1
assert loc1 != (4,.7) and (4,.7) != loc1
assert loc1 != {'node': 5, 'x':.5} and {'node': 5, 'x':.5} != loc1
assert loc1 != loc3 and loc3 != loc1
loc4 = MorphLoc((1,.5), self.tree)
assert loc4 == (1,.8) and loc4 != (4,.5)
def testIteration(self):
self.loadTree()
indices = [node.index for node in self.tree]
assert 2 not in indices and 3 not in indices
assert set(indices) == set([1,4,5,6,7,8])
indices = [node.index for node in self.tree.nodes]
assert 2 not in indices and 3 not in indices
assert set(indices) == set([1,4,5,6,7,8])
def testStructure(self):
self.loadTree()
# check root
root = self.tree[1]
assert root.parent_node == None
assert len(root.child_nodes) == 1 \
and set([node.index for node in root.child_nodes]) == set([4])
# check bifurcation node
bifur = self.tree[4]
assert bifur.parent_node == root
assert len(bifur.child_nodes) == 2 \
and set([node.index for node in bifur.child_nodes]) == set([5,7])
# check branch nodes
bn1 = self.tree[5]
assert bn1.parent_node == bifur
assert len(bn1.child_nodes) == 1 and bn1.child_nodes[0].index == 6
bn2 = self.tree[7]
assert bn2.parent_node == bifur
assert len(bn2.child_nodes) == 1 and bn2.child_nodes[0].index == 8
# check leaf nodes
leaf1 = self.tree[6]
assert leaf1.parent_node == bn1
assert len(leaf1.child_nodes) == 0
leaf2 = self.tree[8]
assert leaf2.parent_node == bn2
assert len(leaf2.child_nodes) == 0
def testGeometry(self):
self.loadTree()
# check root
root = self.tree[1]
assert np.allclose(root.xyz, np.array([0.,0.,0.]))
assert np.allclose(root.R, 10.)
assert np.allclose(root.L, 0.)
assert root.swc_type == 1
# check bifurcation node
bifur = self.tree[4]
assert np.allclose(bifur.xyz, np.array([100.,0.,0.]))
assert np.allclose(bifur.R, 1.)
assert np.allclose(bifur.L, 100.)
assert bifur.swc_type == 4
# check branch nodes
bn1 = self.tree[5]
assert np.allclose(bn1.xyz, np.array([100.,50.,0.]))
assert np.allclose(bn1.R, 1.)
assert np.allclose(bn1.L, 50.)
assert bn1.swc_type == 4
bn2 = self.tree[7]
assert np.allclose(bn2.xyz, np.array([100.,-50.,0.]))
assert np.allclose(bn2.R, 1.)
assert np.allclose(bn2.L, 50.)
assert bn2.swc_type == 4
# check leaf nodes
leaf1 = self.tree[6]
assert np.allclose(leaf1.xyz, np.array([100.,100.,0.]))
assert np.allclose(leaf1.R, .5)
assert np.allclose(leaf1.L, 50.)
assert leaf1.swc_type == 4
leaf2 = self.tree[8]
assert np.allclose(leaf2.xyz, np.array([100.,-100.,0.]))
assert np.allclose(leaf2.R, .5)
assert np.allclose(leaf2.L, 50.)
assert leaf2.swc_type == 4
def testComptree(self):
self.loadTree(reinitialize=1)
# check exception when treetype is invalid
with pytest.raises(ValueError):
self.tree.treetype = 'bla'
# check exception when computational tree has not been set
with pytest.raises(ValueError):
self.tree.treetype = 'computational'
# initialize the comptree
self.tree.setCompTree()
# set computational tree as primary tree
self.tree.treetype = 'computational'
# check root node
root = self.tree[1]
assert root.parent_node == None
assert len(root.child_nodes) == 1 \
and set([node.index for node in root.child_nodes]) == set([4])
assert np.allclose(root.xyz, np.array([0.,0.,0.]))
assert np.allclose(root.R, 10.)
assert np.allclose(root.L, 0.)
assert root.swc_type == 1
# check bifurcation node
bifur = self.tree[4]
assert bifur.parent_node == root
assert len(bifur.child_nodes) == 2 \
and set([node.index for node in bifur.child_nodes]) == set([6,8])
assert np.allclose(bifur.xyz, np.array([100.,0.,0.]))
assert np.allclose(bifur.R, 1.)
assert np.allclose(bifur.L, 100.)
assert bifur.swc_type == 4
# check leaf nodes
leaf1 = self.tree[6]
assert leaf1.parent_node == bifur
assert len(leaf1.child_nodes) == 0
assert np.allclose(leaf1.xyz, np.array([100.,100.,0.]))
assert np.allclose(leaf1.R, .75)
assert np.allclose(leaf1.L, 100.)
assert leaf1.swc_type == 4
leaf2 = self.tree[8]
assert leaf2.parent_node == bifur
assert len(leaf2.child_nodes) == 0
assert np.allclose(leaf2.xyz, np.array([100.,-100.,0.]))
assert np.allclose(leaf2.R, .75)
assert np.allclose(leaf2.L, 100.)
# test nodes getter
assert len(self.tree.nodes) == 4
leafs = self.tree.leafs
assert np.allclose([leafs[0].L, leafs[1].L], [100., 100.])
self.tree.treetype = 'original'
assert len(self.tree.nodes) == 6
leafs = self.tree.leafs
assert np.allclose([leafs[0].L, leafs[1].L], [50., 50.])
# remove the computational tree
self.tree.removeComptree()
with pytest.raises(ValueError):
self.tree.treetype = 'computational'
for node in self.tree:
assert not node.used_in_comptree
def testInputArgConversion(self):
self.loadTree()
nodes = self.tree._convertNodeArgToNodes(None)
assert self.tree.nodes == nodes
nodes = self.tree._convertNodeArgToNodes(self.tree[4])
assert self.tree.gatherNodes(self.tree[4]) == nodes
nodes = self.tree._convertNodeArgToNodes('apical')
assert self.tree.getNodesInApicalSubtree() == nodes
nodes = self.tree._convertNodeArgToNodes('basal')
assert self.tree.getNodesInBasalSubtree() == nodes
nodes = self.tree._convertNodeArgToNodes('axonal')
assert self.tree.getNodesInAxonalSubtree() == nodes
nodes_ = [self.tree[5], self.tree[7]]
nodes = self.tree._convertNodeArgToNodes(nodes_)
assert nodes_ == nodes
with pytest.raises(ValueError):
self.tree._convertNodeArgToNodes('wrong arg')
self.tree._convertNodeArgToNodes(5)
# with the computational tree
self.tree.setCompTree(set_as_primary_tree=1)
nodes = self.tree._convertNodeArgToNodes(None)
assert self.tree.nodes == nodes
nodes = self.tree._convertNodeArgToNodes(self.tree[4])
assert self.tree.gatherNodes(self.tree[4]) == nodes
nodes = self.tree._convertNodeArgToNodes('apical')
assert self.tree.getNodesInApicalSubtree() == nodes
nodes = self.tree._convertNodeArgToNodes('basal')
assert self.tree.getNodesInBasalSubtree() == nodes
nodes = self.tree._convertNodeArgToNodes('axonal')
assert self.tree.getNodesInAxonalSubtree() == nodes
nodes__ = [self.tree[6], self.tree[8]]
nodes = self.tree._convertNodeArgToNodes(nodes_)
assert nodes_ != nodes
assert nodes__ == nodes
def testLocFunctionality(self):
self.loadTree()
# locs in the original tree
self.tree.treetype = 'original'
locs = [MorphLoc({'node': 1, 'x': .5}, self.tree),
MorphLoc({'node': 4, 'x': .5}, self.tree),
MorphLoc({'node': 5, 'x': .5}, self.tree),
MorphLoc({'node': 7, 'x': .5}, self.tree),
MorphLoc({'node': 6, 'x': .5}, self.tree),
MorphLoc({'node': 8, 'x': .5}, self.tree)]
# set the computational tree
self.tree.setCompTree()
self.tree.treetype = 'computational'
for loc in locs: loc._setComputationalLoc()
assert locs[0].comp_loc == locs[0].loc
assert locs[1].comp_loc == locs[1].loc
assert locs[2].comp_loc == {'node': 6, 'x': .25}
assert locs[3].comp_loc == {'node': 8, 'x': .25}
assert locs[4].comp_loc == {'node': 6, 'x': .75}
assert locs[5].comp_loc == {'node': 8, 'x': .75}
def testPathLength(self):
self.loadTree()
# lengths in the original tree
self.tree.treetype = 'original'
# test lengths
L = self.tree.pathLength({'node': 1, 'x': 1.}, {'node': 1, 'x': .4})
assert np.allclose(L, 0.)
L = self.tree.pathLength({'node': 4, 'x': 1.}, {'node': 1, 'x': .4})
assert np.allclose(L, 100.)
L = self.tree.pathLength({'node': 4, 'x': 1.}, {'node': 1, 'x': .6})
assert np.allclose(L, 100.)
L = self.tree.pathLength({'node': 4, 'x': 1.}, {'node': 4, 'x': 1.})
assert np.allclose(L, 0.)
L = self.tree.pathLength({'node': 4, 'x': 1.}, {'node': 5, 'x': 0.})
assert np.allclose(L, 0.)
L = self.tree.pathLength({'node': 4, 'x': .5}, {'node': 5, 'x': .2})
assert np.allclose(L, 60.)
L = self.tree.pathLength({'node': 5, 'x': .2}, {'node': 4, 'x': .5})
assert np.allclose(L, 60.)
L = self.tree.pathLength({'node': 5, 'x': .2}, {'node': 7, 'x': .2})
assert np.allclose(L, 20.)
L = self.tree.pathLength({'node': 8, 'x': .2}, {'node': 4, 'x': .5})
assert np.allclose(L, 110.)
# lengths in the original tree
self.tree.setCompTree()
self.tree.treetype = 'computational'
# test lengths
L = self.tree.pathLength({'node': 1, 'x': 1.}, {'node': 1, 'x': .4})
assert np.allclose(L, 0.)
L = self.tree.pathLength({'node': 4, 'x': 1.}, {'node': 1, 'x': .4})
assert np.allclose(L, 100.)
L = self.tree.pathLength({'node': 4, 'x': 1.}, {'node': 1, 'x': .6})
assert np.allclose(L, 100.)
L = self.tree.pathLength({'node': 4, 'x': 1.}, {'node': 4, 'x': 1.})
assert np.allclose(L, 0.)
L = self.tree.pathLength({'node': 4, 'x': 1.}, {'node': 5, 'x': 0.})
assert np.allclose(L, 0.)
L = self.tree.pathLength({'node': 4, 'x': .5}, {'node': 5, 'x': .2})
assert np.allclose(L, 60.)
L = self.tree.pathLength({'node': 5, 'x': .2}, {'node': 4, 'x': .5})
assert np.allclose(L, 60.)
L = self.tree.pathLength({'node': 5, 'x': .2}, {'node': 7, 'x': .2})
assert np.allclose(L, 20.)
L = self.tree.pathLength({'node': 8, 'x': .2}, {'node': 4, 'x': .5})
assert np.allclose(L, 110.)
def testLocStorageRetrievalLookup(self):
self.loadTree()
locs = [(1,.5), (1, 1.), (4, 1.), (4, .5), (5, .5),
(5, 1.), (6, .5), (6, 1.), (8, .5), (8, 1.)]
with pytest.warns(UserWarning):
self.tree.storeLocs(locs, 'testlocs')
# with pytest.raises(ValueError):
# self.tree.storeLocs(locs, 'testlocs')
locs = [(1,.5), (4, 1.), (4, .5), (5, .5),
(5, 1.), (6, .5), (6, 1.), (8, .5), (8, 1.)]
self.tree.storeLocs(locs, 'testlocs')
# test retrieval
with pytest.raises(KeyError):
self.tree.getLocs('wronglocs')
locs_ = [(loc['node'], loc['x'])
for loc in self.tree.getLocs('testlocs')]
assert locs_ == locs
# test getting node indices
with pytest.raises(KeyError):
self.tree.getNodeIndices('wronglocs')
assert [1,4,4,5,5,6,6,8,8] == self.tree.getNodeIndices('testlocs').tolist()
# test get x-coords
with pytest.raises(KeyError):
self.tree.getXCoords('wronglocs')
assert np.allclose([.5,1.,.5,.5,1.,.5,1.,.5,1.],
self.tree.getXCoords('testlocs'))
# test get locinds on non-empty node
locinds = self.tree.getLocindsOnNode('testlocs', self.tree[4])
assert locinds == [2,1]
# test get locinds on empty node
locinds = self.tree.getLocindsOnNode('testlocs', self.tree[7])
assert locinds == []
with pytest.raises(KeyError):
self.tree.getLocindsOnNode('wronglocs', self.tree[7])
# test locinds on path
path = self.tree.pathBetweenNodes(self.tree[6], self.tree[8])
locinds = self.tree.getLocindsOnPath('testlocs',
self.tree[6], self.tree[8], xstart=.5, xstop=1.)
assert locinds == [5,4,3,1,7,8]
path = self.tree.pathBetweenNodes(self.tree[7], self.tree[7])
locinds = self.tree.getLocindsOnPath('testlocs',
self.tree[7], self.tree[7], xstart=0., xstop=1.)
assert locinds == []
path = self.tree.pathBetweenNodes(self.tree[4], self.tree[4])
locinds = self.tree.getLocindsOnPath('testlocs',
self.tree[4], self.tree[4], xstart=0., xstop=.9)
assert locinds == [2]
path = self.tree.pathBetweenNodes(self.tree[1], self.tree[1])
locinds = self.tree.getLocindsOnPath('testlocs',
self.tree[1], self.tree[1], xstart=0., xstop=.9)
assert locinds == [0]
path = self.tree.pathBetweenNodes(self.tree[4], self.tree[1])
locinds = self.tree.getLocindsOnPath('testlocs',
self.tree[4], self.tree[1], xstart=.9, xstop=.9)
assert locinds == [2,0]
locinds = self.tree.getLocindsOnPath('testlocs',
self.tree[7], self.tree[7], xstart=.1, xstop=.9)
assert locinds == []
# test locinds on branch
branch = self.tree.pathBetweenNodes(self.tree[4], self.tree[5])
locinds = self.tree.getLocindsOnNodes('testlocs', branch)
assert locinds == [2,1,3,4]
# test locinds on basal/apical/axonal subtrees
locinds = self.tree.getLocindsOnNodes('testlocs', 'basal')
assert locinds == []
locinds = self.tree.getLocindsOnNodes('testlocs', 'axonal')
assert locinds == []
locinds = self.tree.getLocindsOnNodes('testlocs', 'apical')
assert locinds == [2,1,3,4,5,6,7,8]
# test locinds on subtree
nodes = self.tree.getNodesInSubtree(self.tree[5], self.tree[4])
locinds = self.tree.getLocindsOnNodes('testlocs', nodes)
assert locinds == [2,1,3,4,5,6]
# find the nearest locs
locs = [(1,.5), (4, .5), (5, .4), (5, 1.),
(6, .5), (6, 1.), (8, .5), (8, 1.)]
self.tree.storeLocs(locs, 'testlocs2')
locinds = self.tree.getNearestLocinds([(7, .5), (1,.6), (6, .1), (6, .7)],
'testlocs2', direction=0)
res = self.tree.getNearestLocinds([(6, .1)],
'testlocs2', direction=0)
assert locinds == [2, 0, 3, 4]
locinds = self.tree.getNearestLocinds([(7, .5), (1,.6), (6, .1), (6, .7)],
'testlocs2', direction=1)
assert locinds == [2, 0, 3, 4]
locinds = self.tree.getNearestLocinds([(7, .5), (1,.6), (6, .1), (6, .7)],
'testlocs2', direction=2)
assert locinds == [6, 0, 4, 5]
# find the leaf locs
locinds = self.tree.getLeafLocinds('testlocs2')
assert locinds == [5,7]
# find the neartest locs
locs = [(4, .1), (4, .4), (4, .7)]
self.tree.storeLocs(locs, 'testlocs3')
locinds0 = self.tree.getNearestLocinds([(4, .4)],
'testlocs3', direction=0)
locinds1 = self.tree.getNearestLocinds([(4, .4)],
'testlocs3', direction=1)
locinds2 = self.tree.getNearestLocinds([(4, .4)],
'testlocs3', direction=2)
assert locinds0[0] == 1
assert locinds1[0] == 1
assert locinds2[0] == 1
def testDistances(self):
self.loadTree()
locs = [(1,.5), (4, 1.), (5, .5), (6, .5), (6, 1.)]
self.tree.storeLocs(locs, 'testlocs')
# compute the distances to soma
d2s = self.tree.distancesToSoma('testlocs')
assert np.allclose(d2s, np.array([0.,100.,125.,175.,200.]))
d2b = self.tree.distancesToBifurcation('testlocs')
assert np.allclose(d2b, np.array([0.,100.,25.,75.,100.]))
def testLocDistribution(self):
self.loadTree()
# check comptree resetting
self.tree.setCompTree()
self.tree.treetype = 'computational'
self.tree.distributeLocsOnNodes(np.array([90.,140.,190.]), [])
assert self.tree.treetype == 'computational'
self.tree.treetype = 'original'
# test loc distribution on nodes
locs = self.tree.distributeLocsOnNodes(np.array([90.,140.,190.]),
[self.tree[6], self.tree[8]])
assert locs[0] == {'node': 6, 'x': 4./5.} \
and locs[1] == {'node': 8, 'x': 4./5.} \
and len(locs) == 2
locs = self.tree.distributeLocsOnNodes(np.array([190.,190.]),
[self.tree[6]])
assert locs[0] == locs[1] and locs[0] == {'node': 6, 'x': 4./5.}
locs = self.tree.distributeLocsOnNodes(np.array([]),
[self.tree[6]])
assert len(locs) == 0
locs = self.tree.distributeLocsOnNodes(np.array([100.]),
[self.tree[4], self.tree[5]])
assert locs[0] == {'node': 4, 'x': 1.}
# derived loc distribution functions
locs = self.tree.distributeLocsOnNodes(np.array([150.,100.]))
assert locs[0] == {'node': 4, 'x': 1.} \
and locs[1] == {'node': 5, 'x': 1.} \
and locs[2] == {'node': 7, 'x': 1.}
nodes = self.tree.pathBetweenNodes(self.tree[5], self.tree[6])
locs = self.tree.distributeLocsOnNodes(np.array([50.,120.,170.]),
node_arg=nodes)
assert locs[0] == {'node': 5, 'x': 2./5.} \
and locs[1] == {'node': 6, 'x': 2./5.}
locs = self.tree.distributeLocsOnNodes(np.array([70.,120.]),
node_arg='basal')
assert len(locs) == 0
locs = self.tree.distributeLocsOnNodes(np.array([70.,120.]),
node_arg='apical')
assert locs[0] == {'node': 4, 'x': 7./10.} \
and locs[1] == {'node': 5, 'x': 2./5.} \
and locs[2] == {'node': 7, 'x': 2./5.}
nodes = self.tree.getNodesInSubtree(self.tree[6], self.tree[4])
locs = self.tree.distributeLocsOnNodes(np.array([70.,120]),
node_arg=nodes)
assert locs[0] == {'node': 4, 'x': 7./10.} \
and locs[1] == {'node': 5, 'x': 2./5.}
# test uniform loc distribution
locs = self.tree.distributeLocsUniform(50.)
checklocs = [{'node': 1, 'x': .8},
{'node': 4, 'x': 1./2.}, {'node': 4, 'x': 1.},
{'node': 5, 'x': 1.}, {'node': 6, 'x': 1.},
{'node': 7, 'x': 1.}, {'node': 8, 'x': 1.}]
for (loc, checkloc) in zip(locs, checklocs):
assert loc == checkloc
locs = self.tree.distributeLocsUniform(50., node_arg=self.tree[5])
for loc in locs: print loc
checklocs = [{'node': 5, 'x': 1.}, {'node': 6, 'x': 1.}]
for (loc, checkloc) in zip(locs, checklocs):
assert loc == checkloc
# test random loc distribution
locs = self.tree.distributeLocsRandom(10)
assert len(locs) > 0
for node in self.tree:
assert 'tag' not in node.content
locs = self.tree.distributeLocsRandom(10, node_arg='basal', add_soma=0)
assert len(locs) == 0
with pytest.raises(ValueError):
self.tree.distributeLocsRandom(10, node_arg='bad type')
def testTreeCreation(self):
self.loadTree(self)
locs = [(1,.5),(4,.5),(4,1.),(5,1.),(6,1.),(7,1.),(8,1.)]
self.tree.storeLocs(locs, 'newtree_test')
# create the new tree
new_tree = self.tree.createNewTree('newtree_test')
new_xyzs = [(0.,0.,0.),
(50.,0.,0.),
(100.,0.,0.),
(100.,50.,0.),
(100.,100.,0.),
(100.,-50.,0.),
(100.,-100.,0.)]
new_inds = [1,4,5,6,7,8,9]
for ii, new_node in enumerate(new_tree):
assert np.allclose(new_xyzs[ii], new_node.xyz)
assert new_inds[ii] == new_node.index
def testPlotting(self, pshow=0):
self.loadTree()
self.tree.setCompTree()
# create the x-axis
self.tree.makeXAxis(50.)
assert np.allclose(self.tree.xaxis,
np.array([0.,50.,100.,150.,200.,200.,250.]))
# find x-values
locs = [(4.,.7),(5,.9), (7,.8)]
xvals = self.tree.getXValues(locs)
assert np.allclose([50.,150.,200.], xvals)
xvals = self.tree.getXValues([])
assert len(xvals) == 0
# plot on x-axis
parr = np.array([1.,2.,3.,4.,5.,4.,3.])
pl.figure('plot 1d test orig')
# original tree
lines = self.tree.plot1D(pl.gca(), parr, c='r')
assert np.abs(self.tree.xaxis[-1] - 250.) < 1e-5
assert len(lines) == len(self.tree.getLeafLocinds('xaxis'))
assert np.allclose(lines[0].get_data()[1], parr[0:5])
assert np.allclose(lines[1].get_data()[1], parr[5:])
xarr = np.array([0.,50.,100.,150.,200.,200.,250.])
assert np.allclose(lines[0].get_data()[0], xarr[0:5])
assert np.allclose(lines[1].get_data()[0], xarr[5:])
assert lines[0].get_color() == 'r'
# update the lines
parr_ = np.array([5.,4.,3.,2.,1.,2.,3.])
self.tree.setLineData(lines, parr_)
assert np.allclose(lines[0].get_data()[1], parr_[0:5])
assert np.allclose(lines[1].get_data()[1], parr_[5:])
# test x-axis coloring (just sees if function runs)
self.tree.colorXAxis(pl.gca(), pl.get_cmap('jet'))
# computational tree
self.tree.treetype = 'computational'
pl.figure('plot 1d test comp')
lines = self.tree.plot1D(pl.gca(), parr, c='r')
assert np.abs(self.tree.xaxis[-1] - 250.) < 1e-5
assert len(lines) == len(self.tree.getLeafLocinds('xaxis'))
assert np.allclose(lines[0].get_data()[1], parr[0:5])
assert np.allclose(lines[1].get_data()[1], parr[5:])
xarr = np.array([0.,50.,100.,150.,200.,200.,250.])
assert np.allclose(lines[0].get_data()[0], xarr[0:5])
assert np.allclose(lines[1].get_data()[0], xarr[5:])
assert lines[0].get_color() == 'r'
# test x-axis coloring (just sees if function runs)
self.tree.colorXAxis(pl.gca(), pl.get_cmap('jet'))
# a true distance from soma plot
parr = np.array([1.,2.,3.,4.,5.,4.,3.])
pl.figure('plot d2s test')
lines = self.tree.plotTrueD2S(pl.gca(),parr)
assert len(lines) == len(self.tree.getLeafLocinds('xaxis'))
assert np.allclose(lines[0].get_data()[1], parr[0:5])
assert np.allclose(lines[1].get_data()[1], parr[5:])
assert np.allclose(lines[0].get_data()[0], self.tree.d2s['xaxis'][0:5])
assert np.allclose(lines[1].get_data()[0], self.tree.d2s['xaxis'][5:])
# test 2D plotting (just sees if function runs)
pl.figure('plot morphology test')
cs = {node.index: node.index for node in self.tree}
marklocs = [(1,.5), (4,.8), (6,.2)]
locargs = {'marker': 'o', 'mfc': 'r', 'ms': 6}
marklabels = {0: r'soma', 1: r'$\mu$'}
labelargs = {'fontsize': 8}
self.tree.plot2DMorphology(pl.gca(), cs=cs, cmap=pl.get_cmap('summer'),
plotargs={'lw':2},
marklocs=marklocs, locargs=locargs,
marklabels=marklabels, labelargs=labelargs,
textargs={'fontsize': 24},
cb_draw=True)
if pshow: pl.show()