def get_pifs_from_Citrination(client, dataset_id_list):
all_hits = []
for dataset in dataset_id_list:
query = PifSystemReturningQuery(
from_index=0,
size=100,
query=DataQuery(dataset=DatasetQuery(id=Filter(equal=dataset))))
current_result = client.search(query)
while current_result.hits is not None:
all_hits.extend(current_result.hits)
n_current_hits = len(current_result.hits)
#n_hits += n_current_hits
query.from_index += n_current_hits
current_result = client.search(query)
pifs = [x.system for x in all_hits]
return pifs
def query_to_mdf_records(query=None, dataset_id=None, mdf_acl=None):
"""Evaluate a query and return a list of MDF records
If a datasetID is specified by there is no query, a simple
whole dataset query is formed for the user
"""
if not query and not dataset_id:
raise ValueError("Either query or dataset_id must be specified")
if query and dataset_id:
raise ValueError(
"Both query and dataset_id were specified; pick one or the other.")
if not query:
query = PifSystemReturningQuery(
query=DataQuery(dataset=DatasetQuery(id=Filter(equal=dataset_id))),
size=10000 # Don't pull down all the results by default
)
client = get_client()
if not mdf_acl:
raise ValueError(
'Access controls (mdf_acl) must be specified. Use ["public"] for public access'
)
pif_result = client.pif_search(query)
if len(pif_result.hits) == 0:
return []
example_uid = pif_result.hits[0].system.uid
dataset_query = DatasetReturningQuery(
query=DataQuery(system=PifSystemQuery(uid=Filter(equal=example_uid))),
size=1 # we only expect one dataset to hit
)
dataset_result = client.dataset_search(dataset_query)
records = []
for hit in pif_result.hits:
records.append(
pif_to_mdf_record(hit.system, dataset_result.hits[0], mdf_acl))
return records
def run_sequential_learning(client:CitrinationClient, view_id:int, dataset_id:int,
num_candidates_per_iter:int,
design_effort:int, wait_time:int,
num_sl_iterations:int, input_properties:List[str],
target:List[str], print_output:bool,
true_function:Callable[[np.ndarray], float],
score_type:str,
) -> Tuple[List[float], List[float]]:
'''Runs SL design
:param client: Client object
:type client: CitrinationClient
:param view_id: View ID
:type view_id: int
:param dataset_id: Dataset ID
:type dataset_id: int
:param num_candidates_per_iter: Candidates in a batch
:type num_candidates_per_iter: int
:param design_effort: Effort from 1-30
:type design_effort: int
:param wait_time: Wait time in seconds before polling API
:type wait_time: int
:param num_sl_iterations: SL iterations to run
:type num_sl_iterations: int
:param input_properties: Inputs
:type input_properties: List[str]
:param target: ("Output property", {"Min", "Max"})
:type target: List[str]
:param print_output: Whether or not to print outputs
:type print_output: bool
:param true_function: Actual function for evaluating measured/true values
:type true_function: Callable[[np.ndarray], float]
:param score_type: MLI or MEI
:type score_type: str
:return: 2-tuple: list of predicted scores/uncertainties; list of measured scores/uncertainties
:rtype: Tuple[List[float], List[float]]
'''
best_sl_pred_vals = []
best_sl_measured_vals = []
_wait_on_ingest(client, dataset_id, wait_time, print_output)
for i in range(num_sl_iterations):
if print_output:
print(f"\n---STARTING SL ITERATION #{i+1}---")
_wait_on_ingest(client, dataset_id, wait_time, print_output)
_wait_on_data_view(client, dataset_id, view_id, wait_time, print_output)
# Submit a design run
design_id = client.submit_design_run(
data_view_id=view_id,
num_candidates=num_candidates_per_iter,
effort=design_effort,
target=Target(*target),
constraints=[],
sampler="Default"
).uuid
if print_output:
print(f"Created design run with ID {design_id}")
_wait_on_design_run(client, design_id, view_id, wait_time, print_output)
# Compute the best values with uncertainties as a list of (value, uncertainty)
if score_type == "MEI":
candidates = client.get_design_run_results(view_id, design_id).best_materials
else:
candidates = client.get_design_run_results(view_id, design_id).next_experiments
values_w_uncertainties = [
(
m["descriptor_values"][target[0]],
m["descriptor_values"][f"Uncertainty in {target[0]}"]
) for m in candidates
]
# Find and save the best predicted value
if target[1] == "Min":
best_value_w_uncertainty = min(values_w_uncertainties, key=lambda x: x[0])
else:
best_value_w_uncertainty = max(values_w_uncertainties, key=lambda x: x[0])
best_sl_pred_vals.append(best_value_w_uncertainty)
if print_output:
print(f"SL iter #{i+1}, best predicted (value, uncertainty) = {best_value_w_uncertainty}")
# Update dataset w/ new candidates
new_x_vals = []
for material in candidates:
new_x_vals.append(np.array(
[float(material["descriptor_values"][x]) for x in input_properties]
))
temp_dataset_fpath = f"design-{design_id}.json"
write_dataset_from_func(true_function, temp_dataset_fpath, new_x_vals)
upload_data_and_get_id(
client,
"", # No name needed for updating a dataset
temp_dataset_fpath,
given_dataset_id=dataset_id
)
_wait_on_ingest(client, dataset_id, wait_time, print_output)
if print_output:
print(f"Dataset updated: {len(new_x_vals)} candidates added")
query_dataset = PifSystemReturningQuery(size=9999,
query=DataQuery(
dataset=DatasetQuery(
id=Filter(equal=str(dataset_id))
)))
query_result = client.search.pif_search(query_dataset)
if print_output:
print(f"New dataset contains {query_result.total_num_hits} PIFs")
# Update measured values in new dataset
dataset_y_values = []
for hit in query_result.hits:
# Assume last prop is output if following this script
dataset_y_values.append(
float(hit.system.properties[-1].scalars[0].value)
)
if target[1] == "Min":
best_sl_measured_vals.append(min(dataset_y_values))
else:
best_sl_measured_vals.append(max(dataset_y_values))
# Retrain model w/ wait times
client.data_views.retrain(view_id)
_wait_on_data_view(client, dataset_id, view_id, wait_time, print_output)
if print_output:
print("SL finished!\n")
return (best_sl_pred_vals, best_sl_measured_vals)
def load_data_zT():
results_dir = setResDir()
## Metadata
keys_response = [
'Seebeck coefficient; squared', 'Electrical resistivity',
'Thermal conductivity'
]
sign = np.array([
+1, # Seebeck
-1, # Electric resistivity
-1 # Thermal conductivity
])
## Load data, if possible
# --------------------------------------------------
try:
df_X_all = pd.read_csv(results_dir + file_features)
X_all = df_X_all.drop(df_X_all.columns[0], axis=1).values
df_Y_all = pd.read_csv(results_dir + file_responses)
Y_all = df_Y_all.drop(df_Y_all.columns[0], axis=1).values
print("Cached data loaded.")
except FileNotFoundError:
## Data Import
# --------------------------------------------------
# Initialize client
print("Accessing data from Citrination...")
site = 'https://citrination.com' # Citrination
client = CitrinationClient(api_key=os.environ['CITRINATION_API_KEY'],
site=site)
search_client = client.search
# Aluminum dataset
dataset_id = 178480 # ucsb_te_roomtemp_seebeck
system_query = PifSystemReturningQuery(
size=1000,
query=DataQuery(dataset=DatasetQuery(id=Filter(
equal=str(dataset_id)))))
query_result = search_client.pif_search(system_query)
print(" Found {} PIFs in dataset {}.".format(
query_result.total_num_hits, dataset_id))
## Wrangle
# --------------------------------------------------
pifs = [x.system for x in query_result.hits]
# Utility function will tabularize PIFs
df_response = pifs2df(pifs)
# Down-select columns to play well with to_numeric
df_response = df_response[[
'Seebeck coefficient', 'Electrical resistivity',
'Thermal conductivity'
]]
df_response = df_response.apply(pd.to_numeric)
# Parse chemical compositions
formulas = [pif.chemical_formula for pif in pifs]
df_comp = pd.DataFrame(columns=['chemical_formula'], data=formulas)
# Join
df_data = pd.concat([df_comp, df_response], axis=1)
print(" Accessed data.")
# Featurize
print("Featurizing data...")
df_data['composition'] = df_data['chemical_formula'].apply(
get_compostion)
f = MultipleFeaturizer([
cf.Stoichiometry(),
cf.ElementProperty.from_preset("magpie"),
cf.ValenceOrbital(props=['avg']),
cf.IonProperty(fast=True)
])
X = np.array(f.featurize_many(df_data['composition']))
# Find valid response values
keys_original = [
'Seebeck coefficient', 'Electrical resistivity',
'Thermal conductivity'
]
index_valid_response = {
key: df_data[key].dropna().index.values
for key in keys_original
}
index_valid_all = df_data[keys_original].dropna().index.values
X_all = X[index_valid_all, :]
Y_all = df_data[keys_original].iloc[index_valid_all].values
# Manipulate columns for proper objective values
Y_all[:, 0] = Y_all[:, 0]**2 # Squared seebeck
print(" Data prepared; {0:} valid observations.".format(
X_all.shape[0]))
# Cache data
pd.DataFrame(data=X_all).to_csv(results_dir + file_features)
pd.DataFrame(data=Y_all, columns=keys_response).to_csv(results_dir +
file_responses)
print("Data cached in results directory.")
return X_all, Y_all, sign, keys_response, prefix
def get_data(self,
formula=None,
prop=None,
data_type=None,
reference=None,
min_measurement=None,
max_measurement=None,
from_record=None,
data_set_id=None,
max_results=None):
"""
Gets raw api data from Citrine in json format. See api_link for more
information on input parameters
Args:
formula: (str) filter for the chemical formula field; only those
results that have chemical formulas that contain this string
will be returned
prop: (str) name of the property to search for
data_type: (str) 'EXPERIMENTAL'/'COMPUTATIONAL'/'MACHINE_LEARNING';
filter for properties obtained from experimental work,
computational methods, or machine learning.
reference: (str) filter for the reference field; only those
results that have contributors that contain this string
will be returned
min_measurement: (str/num) minimum of the property value range
max_measurement: (str/num) maximum of the property value range
from_record: (int) index of first record to return (indexed from 0)
data_set_id: (int) id of the particular data set to search on
max_results: (int) number of records to limit the results to
Returns: (list) of jsons/pifs returned by Citrine's API
"""
json_data = []
start = from_record if from_record else 0
per_page = 100
refresh_time = 3 # seconds to wait between search calls
# Construct all of the relevant queries from input args
formula_query = ChemicalFieldQuery(filter=ChemicalFilter(
equal=formula))
prop_query = PropertyQuery(
name=FieldQuery(filter=Filter(equal=prop)),
value=FieldQuery(
filter=Filter(min=min_measurement, max=max_measurement)),
data_type=FieldQuery(filter=Filter(equal=data_type)))
ref_query = ReferenceQuery(doi=FieldQuery(filter=Filter(
equal=reference)))
system_query = PifSystemQuery(chemical_formula=formula_query,
properties=prop_query,
references=ref_query)
dataset_query = DatasetQuery(id=Filter(equal=data_set_id))
data_query = DataQuery(system=system_query, dataset=dataset_query)
while True:
# use per_page=max_results, eg: in case of max_results=68 < 100
if max_results and max_results < per_page:
pif_query = PifSystemReturningQuery(query=data_query,
from_index=start,
size=max_results)
else:
pif_query = PifSystemReturningQuery(query=data_query,
from_index=start,
size=per_page)
# Check if any results found
if "hits" not in self.client.search.pif_search(
pif_query).as_dictionary():
raise KeyError("No results found!")
data = self.client.search.pif_search(
pif_query).as_dictionary()["hits"]
size = len(data)
start += size
json_data.extend(data)
# check if limit is reached
if max_results and len(json_data) > max_results:
# get first multiple of 100 records
json_data = json_data[:max_results]
break
if size < per_page: # break out of last loop of results
break
time.sleep(refresh_time)
return json_data