def test_mass_grid(self):
"""
Check that the mass-based grid is constructed correctly.
"""
## Test typical input - should be sorted
levels = utl.define_density_mass_grid(self.unique_density)
answer = np.sort(self.unique_density)
assert_array_equal(answer, levels)
## Test more levels than density values (answer is the same as typical
# input).
levels = utl.define_density_mass_grid(self.unique_density,
num_levels=self.n * 2)
assert_array_equal(answer, levels)
## Test fewer levels than density values.
levels = utl.define_density_mass_grid(self.unique_density,
num_levels=2)
answer = np.array([1, 10])
assert_array_equal(answer, levels)
## Test negative values.
levels = utl.define_density_mass_grid(self.generic_array)
answer = np.sort(self.generic_array)
assert_array_equal(answer, levels)
## Test uniform input.
levels = utl.define_density_mass_grid(self.uniform_density)
self.assertItemsEqual(levels, [1.])
def test_mass_grid(self):
"""
Check that the mass-based grid is constructed correctly.
"""
## Test typical input - should be sorted
levels = utl.define_density_mass_grid(self.unique_density)
answer = np.sort(self.unique_density)
assert_array_equal(answer, levels)
## Test more levels than density values (answer is the same as typical
# input).
levels = utl.define_density_mass_grid(self.unique_density,
num_levels=self.n * 2)
assert_array_equal(answer, levels)
## Test fewer levels than density values.
levels = utl.define_density_mass_grid(self.unique_density,
num_levels=2)
answer = np.array([1, 10])
assert_array_equal(answer, levels)
## Test negative values.
levels = utl.define_density_mass_grid(self.generic_array)
answer = np.sort(self.generic_array)
assert_array_equal(answer, levels)
## Test uniform input.
levels = utl.define_density_mass_grid(self.uniform_density)
self.assertItemsEqual(levels, [1.])
def construct_tree_from_graph(adjacency_list, density, prune_threshold=None,
num_levels=None, verbose=False):
"""
Construct a level set tree from a similarity graph and a density estimate.
Parameters
----------
adjacency_list : list [list]
Adjacency list of the k-nearest neighbors graph on the data. Each entry
contains the indices of the `k` closest neighbors to the data point at
the same row index.
density : list [float]
Estimate of the density function, evaluated at the data points
represented by the keys in `adjacency_list`.
prune_threshold : int, optional
Leaf nodes with fewer than this number of members are recursively
merged into larger nodes. If 'None' (the default), then no pruning
is performed.
num_levels : list int, optional
Number of density levels in the constructed tree. If None (default),
`num_levels` is internally set to be the number of rows in `X`.
verbose : bool, optional
If True, a progress indicator is printed at every 100th level of tree
construction.
Returns
-------
T : levelSetTree
See the LevelSetTree class for attributes and method definitions.
See Also
--------
construct_tree, LevelSetTree
Examples
--------
>>> X = numpy.random.rand(100, 2)
>>> knn_graph, radii = debacl.utils.knn_graph(X, k=8)
>>> density = debacl.utils.knn_density(radii, n=100, p=2, k=8)
>>> tree = debacl.construct_tree_from_graph(knn_graph, density,
... prune_threshold=5)
>>> print tree
+----+-------------+-----------+------------+----------+------+--------+----------+
| id | start_level | end_level | start_mass | end_mass | size | parent | children |
+----+-------------+-----------+------------+----------+------+--------+----------+
| 0 | 0.000 | 0.768 | 0.000 | 0.390 | 100 | None | [1, 2] |
| 1 | 0.768 | 1.494 | 0.390 | 0.790 | 30 | 0 | [7, 8] |
| 2 | 0.768 | 4.812 | 0.390 | 1.000 | 31 | 0 | [] |
| 7 | 1.494 | 2.375 | 0.790 | 0.950 | 6 | 1 | [] |
| 8 | 1.494 | 2.308 | 0.790 | 0.940 | 5 | 1 | [] |
+----+-------------+-----------+------------+----------+------+--------+----------+
"""
## Initialize the graph and cluster tree
levels = _utl.define_density_mass_grid(density, num_levels=num_levels)
G = _nx.from_dict_of_lists(
{i: neighbors for i, neighbors in enumerate(adjacency_list)})
T = LevelSetTree(density, levels)
## Figure out roots of the tree
cc0 = _nx.connected_components(G)
for i, c in enumerate(cc0): # c is only the vertex list, not the subgraph
T._subgraphs[i] = G.subgraph(c)
T.nodes[i] = ConnectedComponent(
i, parent=None, children=[], start_level=0., end_level=None,
start_mass=0., end_mass=None, members=c)
# Loop through the removal grid
previous_level = 0.
n = float(len(adjacency_list))
for i, level in enumerate(levels):
if verbose and i % 100 == 0:
_logging.info("iteration {}".format(i))
## figure out which points to remove, i.e. the background set.
bg = _np.where((density > previous_level) & (density <= level))[0]
previous_level = level
## compute the mass after the current bg set is removed
old_vcount = sum([x.number_of_nodes()
for x in T._subgraphs.itervalues()])
current_mass = 1. - ((old_vcount - len(bg)) / n)
# loop through active components, i.e. subgraphs
deactivate_keys = [] # subgraphs to deactivate at the iter end
activate_subgraphs = {} # new subgraphs to add at the end of the iter
for (k, H) in T._subgraphs.iteritems():
## remove nodes at the current level
H.remove_nodes_from(bg)
## check if subgraph has vanished
if H.number_of_nodes() == 0:
T.nodes[k].end_level = level
T.nodes[k].end_mass = current_mass
deactivate_keys.append(k)
else: # subgraph hasn't vanished
## check if subgraph now has multiple connected components
# NOTE: this is *the* bottleneck
if not _nx.is_connected(H):
## deactivate the parent subgraph
T.nodes[k].end_level = level
T.nodes[k].end_mass = current_mass
deactivate_keys.append(k)
## start a new subgraph & node for each child component
cc = _nx.connected_components(H)
for c in cc:
new_key = max(T.nodes.keys()) + 1
T.nodes[k].children.append(new_key)
activate_subgraphs[new_key] = H.subgraph(c)
T.nodes[new_key] = ConnectedComponent(
new_key, parent=k, children=[], start_level=level,
end_level=None, start_mass=current_mass,
end_mass=None, members=c)
# update active components
for k in deactivate_keys:
del T._subgraphs[k]
T._subgraphs.update(activate_subgraphs)
## Prune the tree
if prune_threshold is not None:
T = T.prune(threshold=prune_threshold)
return T