def test_discretizer(self):
reader_gen = DataInMemory(data=self.generated_data)
# check if exception safe
api.discretizer(reader_gen)._chain[-1].get_output()
api.discretizer(reader_gen, transform=api.tica())._chain[-1].get_output()
api.discretizer(reader_gen, cluster=api.cluster_uniform_time())._chain[-1].get_output()
api.discretizer(reader_gen, transform=api.pca(), cluster=api.cluster_regspace(dmin=10))._chain[-1].get_output()
def test_no_transform(self):
reader_xtc = api.source(self.traj_files, top=self.pdb_file)
api.pipeline([reader_xtc,
api.cluster_kmeans(k=10)])._chain[-1].get_output()
api.pipeline([reader_xtc,
api.cluster_regspace(dmin=10)])._chain[-1].get_output()
api.pipeline([reader_xtc,
api.cluster_uniform_time()])._chain[-1].get_output()
def test_regspace_nthreads(self):
for metric in ('euclidean', 'minRMSD'):
self.clustering.estimate(self.src,
n_jobs=1,
dmin=self.dmin,
metric=metric)
cl2 = cluster_regspace(self.src,
n_jobs=2,
dmin=self.dmin,
metric=metric)
np.testing.assert_equal(self.clustering.clustercenters,
cl2.clustercenters)
def test_is_parametrized(self):
# construct pipeline with all possible transformers
p = api.pipeline(
[
api.source(self.traj_files, top=self.pdb_file),
api.tica(),
api.pca(),
api.cluster_kmeans(k=50),
api.cluster_regspace(dmin=50),
api.cluster_uniform_time(k=20)
], run=False
)
self.assertFalse(p._is_parametrized(), "If run=false, the pipeline should not be parametrized.")
p.parametrize()
self.assertTrue(p._is_parametrized(), "If parametrized was called, the pipeline should be parametrized.")
def test_no_transform(self):
reader_xtc = api.source(self.traj_files, top=self.pdb_file)
api.pipeline([reader_xtc, api.cluster_kmeans(k=10)])._chain[-1].get_output()
api.pipeline([reader_xtc, api.cluster_regspace(dmin=10)])._chain[-1].get_output()
api.pipeline([reader_xtc, api.cluster_uniform_time()])._chain[-1].get_output()
def test1d_data(self):
data = np.random.random(100)
cluster_regspace(data, dmin=0.3)
def test1d_data(self):
data = np.random.random(100)
cluster_regspace(data, dmin=0.3)
