def _score(patient_feature):
conn = sqlite3.connect('concept_data/omop_v5')
c = conn.cursor()
# print (json.dumps(patient_feature))
results = []
for name in os.listdir("ucb_spaceship/model"):
if name != ".DS_Store":
model_path = "ucb_spaceship/model/{}/".format(name)
adapter = SpaceshipAdapter(model_path)
top_features = adapter.top_features(patient_feature)
score = adapter.score(patient_feature)
statistics = adapter.model_statistics()
# print ('--top_features and stat--')
# print (top_features)
# print (json.dumps(statistics))
parsed_top_features = []
for top_feature in top_features:
splited = top_feature.split(":", 4);
if splited[0] in ('diagnostic', 'procedure'):
concept_code = splited[1]
concept_code_value = splited[2]
if len(concept_code_value) > 3:
concept_code_value = concept_code_value[:3]+'.'+concept_code_value[3:]
# print ('{}'.format(concept_code))
# print ('{}'.format(concept_code_value))
if concept_code == 'icd-9-cm':
c.execute('SELECT concept_name FROM concept WHERE vocabulary_id="ICD9CM" and concept_code="{}"'.format(concept_code_value))
feature_name = c.fetchone()[0]
# print (feature_name)
elif concept_code == 'cpt':
c.execute('SELECT concept_name FROM concept WHERE vocabulary_id="CPT4" and concept_code="{}"'.format(concept_code_value))
feature_name = c.fetchone()[0]
# print (feature_name)
else:
feature_name = ''
else:
feature_name = splited[1]
parsed_top_features.append({'type':splited[0], 'name':feature_name})
# print(parsed_top_features)
result = {u'model':name, u'score':u'{:.0f}'.format(score*100),u'statistics':statistics,u'top_features':parsed_top_features}
results.append(result)
# statistics = model_statistics(name,model_path)
# result = {u'model':name, u'score':u'{:.0f}'.format(score(config, model_path, patient_feature)*100),u'statistics':statistics,u'top_features':top_features}
# results.append(result)
#
conn.close()
results = sorted(results, key=sort_results, reverse=True)
return results
__author__ = 'suhang'
from ucb_spaceship.spaceship.export.adapter import SpaceshipAdapter
import json
model_path = 'model/ZONISAMIDE/'
adapter = SpaceshipAdapter(model_path)
print (adapter._top_features)
patient_str = '{ "attribute": [ {"name": "DOB","schema": "date_attr","value": "1976-01-01"},{"name":"gender","schema": "cat_attr","value": "F"}],"events": {"diagnostic": {"items": [{ "eventName": "icd-9-cm:7231","timestamp": "2011-07-12T00:00:00-04:00"},{"eventName": "icd-9-cm:78079","timestamp": "2011-07-12T00:00:00-04:00"},{"eventName": "icd-9-cm:3544","timestamp": "2011-07-19T00:00:00-04:00"}],"schema": "bin_event"},"medication": {"items": [{"eventName": "VENLAFAXINE_HCL","stopTime": "2013-06-27T00:00:00-04:00","timestamp": "2013-05-29T00:00:00-04:00","value": 30},{"eventName": "TOPIRAMATE","stopTime": "2013-10-31T00:00:00-04:00","timestamp": "2013-07-29T00:00:00-04:00","value": 30}],"schema": "num_event"},"procedure": {"items": [{"eventName": "cpt:99000","timestamp": "2011-01-10T00:00:00-05:00"},{"eventName": "cpt:81000","timestamp": "2011-01-10T00:00:00-05:00"}],"schema": "bin_event"}},"id": "313"}'
patient = json.loads(patient_str)
import time
begin = time.time()
print (adapter.score(patient))
print (adapter.top_features(patient))
stop = time.time()
print (stop - begin)