def _featurize_single(self,
structure: Structure) -> Union[np.array, list, list]:
"""Finds metals in the structure, featurizes the metal sites and collects the features
Args:
structure (pymatgen.Structure): Structure to featurize
Returns:
Union[np.array, list, list]: [description]
"""
get_feat = GetFeatures(structure, '')
features = get_feat.return_features()
metal_indices = get_feat.metal_indices
X = []
feat_dict_list = FeatureCollector.create_dict_for_feature_table_from_dict(
features)
for feat_dict in feat_dict_list:
X.append(feat_dict['feature'])
X = np.vstack(X)
(
X,
_,
) = FeatureCollector._select_features_return_names( # pylint:disable=protected-access
self.featureset, X)
metals = [site.species_string for site in get_feat.metal_sites]
return X, metal_indices, metals
def test_featurization():
s = Structure.from_file(
os.path.join(THIS_DIR, '..', 'examples', 'structures',
'BaO2_mp-1105_computed.cif'))
featurizer = GetFeatures(s, '')
feat = featurizer.return_features()
assert len(feat) == 2
assert len(feat[0]['feature']) == len(feat[1]['feature']) == 129
def test_featurization():
"""Test the basic featurizer"""
structure = Structure.from_file(
os.path.join(THIS_DIR, "..", "..", "examples", "structures",
"BaO2_mp-1105_computed.cif"))
featurizer = GetFeatures(structure, "")
feat = featurizer.return_features()
assert len(feat) == 2
assert len(feat[0]["feature"]) == len(feat[1]["feature"]) == 129
def featurize_single(structure, outdir=OUTDIR):
if Path(structure).stem not in ALREADY_FEATURIZED:
try:
gf = GetFeatures.from_file(structure, outdir) # pylint:disable=invalid-name
gf.run_featurization()
except Exception:
pass
def featurize_single(structure, outdir=OUTDIR):
"""Runs featurization on one structure."""
if Path(structure).stem not in ALREADY_FEATURIZED:
try:
gf = GetFeatures.from_file(structure, outdir) # pylint:disable=invalid-name
gf._run_featurization() # pylint:disable=protected-access
except Exception: # pylint:disable=broad-except
pass
def featurize_single(structure, outdir=OUTDIR):
gf = GetFeatures.from_file(structure, outdir) # pylint:disable=invalid-name
gf.run_featurization()
def featurize_single(structure, outdir=OUTDIR):
"""Featurize one structure"""
gf = GetFeatures.from_file(structure, outdir) # pylint:disable=invalid-name
gf._run_featurization() # pylint:disable=protected-access
def main(structure, outdir):
"""
CLI function
"""
gf = GetFeatures.from_file(structure, outdir, 60) # pylint: disable=invalid-name
gf.run_featurization()