class TestRegSpaceClustering(unittest.TestCase):
@classmethod
def setUpClass(cls):
super(TestRegSpaceClustering, cls).setUpClass()
np.random.seed(0)
def setUp(self):
self.dmin = 0.3
self.clustering = RegularSpaceClustering(dmin=self.dmin)
self.clustering.data_producer = RandomDataSource()
def testAlgo(self):
self.clustering.parametrize()
# correct type of dtrajs
assert types.is_int_array(self.clustering.dtrajs[0])
# assert distance for each centroid is at least dmin
for c in itertools.combinations(self.clustering.clustercenters, 2):
if np.allclose(c[0], c[1]): # skip equal pairs
continue
dist = np.linalg.norm(c[0] - c[1], 2)
self.assertGreaterEqual(
dist, self.dmin, "centroid pair\n%s\n%s\n has smaller"
" distance than dmin(%f): %f" % (c[0], c[1], self.dmin, dist))
def testAssignment(self):
self.clustering.parametrize()
assert len(self.clustering.clustercenters) > 1
# num states == num _clustercenters?
self.assertEqual(
len(np.unique(self.clustering.dtrajs)),
len(self.clustering.clustercenters),
"number of unique states in dtrajs"
" should be equal.")
data_to_cluster = np.random.random((1000, 3))
self.clustering.assign(data_to_cluster, stride=1)
def testSpreadData(self):
self.clustering.data_producer = RandomDataSource(a=-2, b=2)
self.clustering.dmin = 2
self.clustering.parametrize()
def test1d_data(self):
data = np.random.random(100)
cluster_regspace(data, dmin=0.3)
class TestRegSpaceClustering(unittest.TestCase):
@classmethod
def setUpClass(cls):
super(TestRegSpaceClustering, cls).setUpClass()
np.random.seed(0)
def setUp(self):
self.dmin = 0.3
self.clustering = RegularSpaceClustering(dmin=self.dmin)
self.clustering.data_producer = RandomDataSource()
def testAlgo(self):
self.clustering.parametrize()
# correct type of dtrajs
assert types.is_int_array(self.clustering.dtrajs[0])
# assert distance for each centroid is at least dmin
for c in itertools.combinations(self.clustering.clustercenters, 2):
if np.allclose(c[0], c[1]): # skip equal pairs
continue
dist = np.linalg.norm(c[0] - c[1], 2)
self.assertGreaterEqual(dist, self.dmin,
"centroid pair\n%s\n%s\n has smaller"
" distance than dmin(%f): %f"
% (c[0], c[1], self.dmin, dist))
def testAssignment(self):
self.clustering.parametrize()
assert len(self.clustering.clustercenters) > 1
# num states == num _clustercenters?
self.assertEqual(len(np.unique(self.clustering.dtrajs)), len(
self.clustering.clustercenters), "number of unique states in dtrajs"
" should be equal.")
data_to_cluster = np.random.random((1000, 3))
self.clustering.assign(data_to_cluster, stride=1)
def testSpreadData(self):
self.clustering.data_producer = RandomDataSource(a=-2, b=2)
self.clustering.dmin = 2
self.clustering.parametrize()
def test1d_data(self):
data = np.random.random(100)
cluster_regspace(data, dmin=0.3)
def fit(self, data):
""" performs clustering of data
Parameters
----------
data: np.ndarray
array of data points to cluster
merge: int
minimal number of frames within each cluster. Smaller clusters are merged into next big one
"""
# if n_clusters is given and no r, estimate n_clusters
if self.radius is None:
from htmd.clustering.kcenters import KCenter
estClust = KCenter(n_clusters=self.n_clusters)
estClust.fit(data)
self.radius = estClust.distance.max()
logger.info("Estimated radius = {}".format(self.radius))
from pyemma.coordinates.clustering.regspace import RegularSpaceClustering
self._reg = RegularSpaceClustering(dmin=self.radius)
self.labels_ = self._reg.fit_transform(data).flatten()
class TestRegSpaceClustering(unittest.TestCase):
@classmethod
def setUpClass(cls):
super(TestRegSpaceClustering, cls).setUpClass()
np.random.seed(0)
def setUp(self):
self.dmin = 0.3
self.clustering = RegularSpaceClustering(dmin=self.dmin)
self.clustering.data_producer = RandomDataSource()
#self.pr = cProfile.Profile()
#self.pr.enable()
#print "*" * 80
def tearDown(self):
pass
# from pstats import Stats
# p = Stats(self.pr)
# p.strip_dirs()
#
# p.sort_stats('cumtime')
# p.print_stats()
#
# print "*" * 80
def testAlgo(self):
self.clustering.parametrize()
assert self.clustering.dtrajs[0].dtype == int
# assert distance for each centroid is at least dmin
for c in itertools.combinations(self.clustering.clustercenters, 2):
if np.allclose(c[0], c[1]): # skip equal pairs
continue
dist = np.linalg.norm(c[0] - c[1], 2)
self.assertGreaterEqual(dist, self.dmin, "centroid pair\n%s\n%s\n has smaller"
" distance than dmin(%f): %f" % (c[0], c[1], self.dmin, dist))
def testAssignment(self):
self.clustering.parametrize()
assert len(self.clustering.clustercenters) > 1
# num states == num _clustercenters?
self.assertEqual(len(np.unique(self.clustering.dtrajs)), len(
self.clustering.clustercenters), "number of unique states in dtrajs"
" should be equal.")
def testSpreadData(self):
self.clustering.data_producer = RandomDataSource(a=-2, b=2)
self.clustering.dmin = 2
self.clustering.parametrize()
def fit(self, data):
""" performs clustering of data
Parameters
----------
data: np.ndarray
array of data points to cluster
merge: int
minimal number of frames within each cluster. Smaller clusters are merged into next big one
"""
# if n_clusters is given and no r, estimate n_clusters
if self.radius is None:
estClust = KCenter(n_clusters=self.n_clusters)
estClust.fit(data)
self.radius = estClust.distance.max()
logger.info("Estimated radius = {}".format(self.radius))
from pyemma.coordinates.clustering.regspace import RegularSpaceClustering
self._reg = RegularSpaceClustering(dmin=self.radius)
self.labels_ = self._reg.fit_transform(data).flatten()
class RegCluster(BaseEstimator, ClusterMixin, TransformerMixin):
""" Class to perform regular clustering of a given data set
RegCluster can be passed a radius or an approximate number of clusters. If a number of clusters is passed, KCenter
clustering is used to estimate the necessary radius. RegCluster randomly chooses a point and assigns all points
within the radius of this point to the same cluster. Then it proceeds with the nearest point, which is not yet
assigned to a cluster and puts all unassigned points within the radius of this point in the next cluster and so on.
Parameters
----------
radius: float
radius of clusters
n_clusters: int
desired number of clusters
Examples
--------
>>> cluster = RegCluster(radius=5.1)
>>> cluster.fit(data)
Attributes
----------
cluster_centers: list
list with the points, which are the centers of the clusters
centerFrames : list
list of indices of center points in data array
labels_ : list
list with number of cluster of each frame
clusterSize_ : list
list with number of frames in each cluster
"""
def __init__(self, radius=None, n_clusters=None):
if radius is None and n_clusters is None:
raise RuntimeError("radius or n_clusters needs to be set")
self.radius = radius
self.n_clusters = n_clusters
self.labels_ = []
def fit(self, data):
""" performs clustering of data
Parameters
----------
data: np.ndarray
array of data points to cluster
merge: int
minimal number of frames within each cluster. Smaller clusters are merged into next big one
"""
# if n_clusters is given and no r, estimate n_clusters
if self.radius is None:
from htmd.clustering.kcenters import KCenter
estClust = KCenter(n_clusters=self.n_clusters)
estClust.fit(data)
self.radius = estClust.distance.max()
logger.info("Estimated radius = {}".format(self.radius))
from pyemma.coordinates.clustering.regspace import RegularSpaceClustering
self._reg = RegularSpaceClustering(dmin=self.radius)
self.labels_ = self._reg.fit_transform(data).flatten()
@property
def cluster_centers_(self):
return self._reg.clustercenters
@property
def clusterSize(self):
return np.bincount(self.labels_)
class RegCluster(BaseEstimator, ClusterMixin, TransformerMixin):
""" Class to perform regular clustering of a given data set
RegCluster can be passed a radius or an approximate number of clusters. If a number of clusters is passed, KCenter
clustering is used to estimate the necessary radius. RegCluster randomly chooses a point and assigns all points
within the radius of this point to the same cluster. Then it proceeds with the nearest point, which is not yet
assigned to a cluster and puts all unassigned points within the radius of this point in the next cluster and so on.
Parameters
----------
radius: float
radius of clusters
n_clusters: int
desired number of clusters
Examples
--------
>>> cluster = RegCluster(radius=5.1)
>>> cluster.fit(data)
Attributes
----------
cluster_centers: list
list with the points, which are the centers of the clusters
centerFrames : list
list of indices of center points in data array
labels_ : list
list with number of cluster of each frame
clusterSize_ : list
list with number of frames in each cluster
"""
def __init__(self, radius=None, n_clusters=None):
if radius is None and n_clusters is None:
raise RuntimeError("radius or n_clusters needs to be set")
self.radius = radius
self.n_clusters = n_clusters
self.labels_ = []
def fit(self, data):
""" performs clustering of data
Parameters
----------
data: np.ndarray
array of data points to cluster
merge: int
minimal number of frames within each cluster. Smaller clusters are merged into next big one
"""
# if n_clusters is given and no r, estimate n_clusters
if self.radius is None:
from htmd.clustering.kcenters import KCenter
estClust = KCenter(n_clusters=self.n_clusters)
estClust.fit(data)
self.radius = estClust.distance.max()
logger.info("Estimated radius = {}".format(self.radius))
from pyemma.coordinates.clustering.regspace import RegularSpaceClustering
self._reg = RegularSpaceClustering(dmin=self.radius)
self.labels_ = self._reg.fit_transform(data).flatten()
@property
def cluster_centers_(self):
return self._reg.clustercenters
@property
def clusterSize(self):
return np.bincount(self.labels_)
def setUp(self):
self.dmin = 0.3
self.clustering = RegularSpaceClustering(dmin=self.dmin)
self.src = RandomDataSource()
class TestRegSpaceClustering(unittest.TestCase):
def setUp(self):
self.dmin = 0.3
self.clustering = RegularSpaceClustering(dmin=self.dmin)
self.src = RandomDataSource()
def test_algorithm(self):
self.clustering.estimate(self.src)
# correct type of dtrajs
assert types.is_int_vector(self.clustering.dtrajs[0])
# assert distance for each centroid is at least dmin
for c in itertools.combinations(self.clustering.clustercenters, 2):
if np.allclose(c[0], c[1]): # skip equal pairs
continue
dist = np.linalg.norm(c[0] - c[1], 2)
self.assertGreaterEqual(
dist, self.dmin, "centroid pair\n%s\n%s\n has smaller"
" distance than dmin(%f): %f" % (c[0], c[1], self.dmin, dist))
def test_assignment(self):
self.clustering.estimate(self.src)
assert len(self.clustering.clustercenters) > 1
# num states == num _clustercenters?
self.assertEqual(
len(np.unique(self.clustering.dtrajs)),
len(self.clustering.clustercenters),
"number of unique states in dtrajs"
" should be equal.")
data_to_cluster = np.random.random((1000, 3))
self.clustering.assign(data_to_cluster, stride=1)
def test_spread_data(self):
src = RandomDataSource(a=-2, b=2)
self.clustering.dmin = 2
self.clustering.estimate(src)
def test1d_data(self):
data = np.random.random(100)
cluster_regspace(data, dmin=0.3)
def test_non_existent_metric(self):
src = RandomDataSource(a=-2, b=2)
self.clustering.dmin = 2
self.clustering.metric = "non_existent_metric"
with self.assertRaises(ValueError):
self.clustering.estimate(src)
def test_minRMSD_metric(self):
src = RandomDataSource(a=-2, b=2)
self.clustering.dmin = 2
self.clustering.metric = "minRMSD"
self.clustering.estimate(src)
data_to_cluster = np.random.random((1000, 3))
self.clustering.assign(data_to_cluster, stride=1)
def test_too_small_dmin_should_warn(self):
self.clustering.dmin = 1e-8
max_centers = 50
self.clustering.max_centers = max_centers
import warnings
with warnings.catch_warnings(record=True) as w:
# Cause all warnings to always be triggered.
warnings.simplefilter("always")
# Trigger a warning.
self.clustering.estimate(self.src)
assert w
assert len(w) == 1
assert len(self.clustering.clustercenters) == max_centers
# assign data
out = self.clustering.get_output()
assert len(out) == self.clustering.number_of_trajectories()
assert len(out[0]) == self.clustering.trajectory_lengths()[0]
def setUp(self):
self.dmin = 0.3
self.clustering = RegularSpaceClustering(dmin=self.dmin)
self.clustering.data_producer = RandomDataSource()
def setUp(self):
self.dmin = 0.3
self.clustering = RegularSpaceClustering(dmin=self.dmin)
self.clustering.data_producer = RandomDataSource()