def test_feature_addition(self):
""" Add feature data from multiple sources to FeatureTable. """
d = self.dataset
new_data = pd.DataFrame(np.array([
[0.001, 0.1, 0.003],
[0.02, 0.0008, 0.0003],
[0.001, 0.002, 0.05]]),
index=['study1', 'study4', 'study6'], columns=['g1', 'g2', 'g3'])
# Replace all features
d.add_features(new_data, append=False)
self.assertEqual(d.feature_table.data.shape, (3, 3))
self.assertAlmostEqual(d.feature_table.data['g2']['study4'], 0.0008)
# Outer merge and ignore duplicate features
d = get_test_dataset()
d.add_features(new_data)
self.assertEqual(d.feature_table.data.shape, (6, 7))
self.assertEqual(d.feature_table.data['g2']['study2'], 0.0)
self.assertEqual(d.feature_table.data['g1']['study1'], 0.02)
# Outer merge but overwrite old features with new ones
d = get_test_dataset()
d.add_features(new_data, duplicates='replace')
self.assertEqual(d.feature_table.data.shape, (6, 7))
self.assertEqual(d.feature_table.data['g1']['study1'], 0.001)
# Left join (i.e., keep only old rows) and rename conflicting features
d = get_test_dataset()
d.add_features(new_data, merge='left', duplicates='merge')
self.assertEqual(d.feature_table.data.shape, (5, 8))
self.assertEqual(d.feature_table.data['g1_y']['study1'], 0.001)
# Apply threshold
d = get_test_dataset()
d.add_features(new_data, min_studies=2, threshold=0.003)
self.assertEqual(d.feature_table.data.shape, (6, 6))
def test_plot_brain():
"""Ensure that utils.plot_brain returns a matplotlib figure.
"""
from gclda.utils import plot_brain
ns_dset = get_test_dataset()
underlay = ns_dset.masker.volume
test_file = join(get_test_data_path(), 'continuous.nii.gz')
test_data = nib.load(test_file).get_data()
fig = plot_brain(test_data, underlay)
assert isinstance(fig, matplotlib.figure.Figure)
def setUpClass(self):
""" Create a new Dataset and add features. """
self.dataset = get_test_dataset()
self.real_dataset = get_test_dataset(prefix='test_real')
def setUp(self):
""" Create a new Dataset and add features. """
self.dataset = get_test_dataset()
self.real_dataset = get_test_dataset(prefix='test_real')
def setUp(self):
""" Create a new Dataset and add features. """
self.dataset = get_test_dataset()
def setUp(self):
""" Create a new Dataset and add features. """
self.dataset = get_test_dataset()