def test_integration(self, cleanup_files, root_dir):
setup_file_path = os.path.join(root_dir, 'test_setup.yaml')
predictor = predictors.FCPredictor(setup_file=setup_file_path)
predictor.fit(epochs=100, batch_size=128)
predictor.print_score()
y_test_1 = predictor.predict(predictor.test_data)
predictor.save_model('integration_test_model.h5')
assert os.path.isfile('integration_test_model.h5')
predictor.save_training_history('integration_training_history.csv')
assert os.path.isfile('integration_training_history.csv')
predictor = predictors.FCPredictor(saved_model='integration_test_model.h5')
y_test_2 = predictor.predict(predictor.test_data)
for par in predictor.regressors:
np.testing.assert_almost_equal(y_test_1[par].values, y_test_2[par].values)
for par in predictor.classifiers:
np.testing.assert_array_equal(y_test_1[par].values, y_test_2[par].values)
def test_process_targets(self):
data = np.random.normal(10, 3, size=100)
df = pd.DataFrame(data={'M1final': data, 'qfinal': data})
p = preprocessing.StandardScaler()
p.fit(df[['M1final']])
processors = dict(M1final=p,
qfinal = None,)
predictor = predictors.FCPredictor()
predictor.processors = processors
predictor.regressors = ['M1final', 'qfinal']
Y = predictor._process_targets(df)
# check that the output is a list
assert type(Y) == list
# check that both parameters are included
assert len(Y) == 2
# check that one array is transformed and the other not
np.testing.assert_almost_equal(np.mean(Y[0]), 0)
np.testing.assert_almost_equal(np.std(Y[0]), 1)
np.testing.assert_array_equal(Y[1], df[['qfinal']].values)
def test_process_features(self):
data = np.random.normal(10, 3, size=100)
df = pd.DataFrame(data={'M1':data, 'qinit':data})
p = preprocessing.StandardScaler()
p.fit(df[['M1']])
processors = dict(M1=p,
qinit = p,)
predictor = predictors.FCPredictor()
predictor.processors = processors
predictor.features = ['M1', 'qinit']
X = predictor._process_features(df)
# check that the output shape is correct
assert X.shape == (100,2)
# check that all arrays are transformed
np.testing.assert_almost_equal(np.mean(X[:,0]), 0)
np.testing.assert_almost_equal(np.std(X[:,0]), 1)
np.testing.assert_almost_equal(np.mean(X[:,1]), 0)
np.testing.assert_almost_equal(np.std(X[:,0]), 1)
def test_append_to_history(self):
predictor = predictors.FCPredictor()
predictor.regressors = ['M1final', 'qfinal']
predictor.classifiers = []
data = {'M1final_mae': [0.3, 0.2],
'val_M1final_mae': [0.31, 0.21],
'M1final_loss': [1.5, 1.3],
'val_M1final_loss': [1.6, 1.4],
'qfinal_mae': [0.3, 0.2],
'val_qfinal_mae': [0.31, 0.21],
'qfinal_loss': [1.5, 1.3],
'val_qfinal_loss': [1.6, 1.4],
'training_run': [1, 1]}
history1 = pd.DataFrame(data=data)
history1.index.name = 'epoch'
predictor.history = history1
data = {'M1final_mae': [0.1, 0.0],
'val_M1final_mae': [0.11, 0.01],
'M1final_loss': [1.2, 1.1],
'val_M1final_loss': [1.3, 1.2],
'qfinal_mae': [0.1, 0.0],
'val_qfinal_mae': [0.11, 0.01],
'qfinal_loss': [1.2, 1.1],
'val_qfinal_loss': [1.3, 1.2],
}
history2 = pd.DataFrame(data=data)
history2.index.name = 'epoch'
data = {'M1final_mae': [0.3, 0.2, 0.1, 0.0],
'val_M1final_mae': [0.31, 0.21, 0.11, 0.01],
'M1final_loss': [1.5, 1.3, 1.2, 1.1],
'val_M1final_loss': [1.6, 1.4, 1.3, 1.2],
'qfinal_mae': [0.3, 0.2, 0.1, 0.0],
'val_qfinal_mae': [0.31, 0.21, 0.11, 0.01],
'qfinal_loss': [1.5, 1.3, 1.2, 1.1],
'val_qfinal_loss': [1.6, 1.4, 1.3, 1.2],
'training_run': [1, 1, 2, 2]}
history_expected = pd.DataFrame(data=data)
history_expected.index.name = 'epoch'
predictor._append_to_history(history2)
history = predictor.history
assert history.equals(history_expected), \
"\nExpected dataframe: \n{}\nGot dataframe: \n {}".format(history_expected.to_string(),
history.to_string())
def test_train_model(self):
# WARNING: test only checks that some kind of training happened by asserting that the weights are different
predictor = predictors.FCPredictor(setup_file=base_path / 'test_setup.yaml')
weights = predictor.model.layers[1].get_weights()[0]
predictor.train_data = predictor.train_data.iloc[0:200]
predictor.fit(epochs=2, batch_size=50)
weights_new = predictor.model.layers[1].get_weights()[0]
with pytest.raises(AssertionError):
np.testing.assert_almost_equal(weights, weights_new)
def test_make_from_setup(self):
predictor = predictors.FCPredictor(setup_file=base_path / 'test_setup.yaml')
Xpars_ = ['M1', 'qinit', 'Pinit', 'FeHinit']
Yregressors_ = ['Pfinal', 'qfinal']
Yclassifiers_ = ['product', 'binary_type']
# test reading the X and Y variables
assert all([a in predictor.features for a in Xpars_])
assert all([a in predictor.regressors for a in Yregressors_])
assert all([a in predictor.classifiers for a in Yclassifiers_])
# test making the preprocessors
pp = predictor.processors
for par in Xpars_:
assert par in pp, "{} does not have a preprocessor".format(par)
assert pp[par].__class__ == preprocessing.StandardScaler, \
"{} does not have the correct preprocessor.".format(par) + \
" expected {}, got {}".format(preprocessing.StandardScaler, pp[par].__class__)
for par in Yregressors_:
assert par in pp, "{} does not have a preprocessor".format(par)
assert pp[par] == None, "{} does not have the correct preprocessor.".format(par) + \
" expected None, got {}".format(pp[par].__class__)
for par in Yclassifiers_:
assert par in pp, "{} does not have a preprocessor".format(par)
assert pp[par].__class__ == preprocessing.OneHotEncoder, \
"{} does not have the correct preprocessor.".format(par) + \
" expected {}, got {}".format(preprocessing.OneHotEncoder,pp[par].__class__)
# test making the model
mod = predictor.model
assert len(mod.layers) == 11, \
"Model does not have correct number of layers, expected" + \
" {}, got {}".format(11, len(mod.layers))
assert mod.input.shape[1] == len(Xpars_), \
"Model input does not have correct shape, expected " + \
"{}, got {}".format(len(Xpars_),mod.input.shape[1])
assert len(mod.output) == len(Yregressors_) + len(Yclassifiers_), \
"Model does not have correct number of outputs, expected" + \
" {}, got {}".format(len(Yregressors_) + len(Yclassifiers_), len(mod.output))
def test_make_from_setup_with_data(self):
setup = """
features:
- M1
- qinit
regressors:
- Pfinal
classifiers:
- product
"""
setup = yaml.safe_load(setup)
data = pd.read_csv(base_path / 'BesanconGalactic_summary.txt')
predictor = predictors.FCPredictor(setup=setup, data=data)
assert predictor.train_data is not None
assert predictor.test_data is not None
assert len(predictor.train_data) + len(predictor.test_data) == len(data)
def test_make_from_saved_model(self, root_dir):
predictor = predictors.FCPredictor(saved_model=os.path.join(root_dir, 'test_model_FC.h5'))
Xpars_ = ['M1', 'qinit', 'Pinit', 'FeHinit']
Yregressors_ = ['Pfinal', 'qfinal']
Yclassifiers_ = ['product', 'binary_type']
# test reading the X and Y variables
assert all([a in predictor.features for a in Xpars_])
assert all([a in predictor.regressors for a in Yregressors_])
assert all([a in predictor.classifiers for a in Yclassifiers_])
# test making the preprocessors
pp = predictor.processors
for par in Xpars_:
assert par in pp, "{} does not have a preprocessor".format(par)
assert pp[par].__class__ == preprocessing.MinMaxScaler
for par in Yclassifiers_:
assert par in pp, "{} does not have a preprocessor".format(par)
assert pp[par].__class__ == preprocessing.OneHotEncoder
# test making the model
mod = predictor.model
assert len(mod.layers) == 8, \
"Model does not have correct number of layers, expected {}, got {}".format(8, len(mod.layers))
assert mod.input.shape[1] == len(Xpars_), \
"Model input does not have correct shape, expected {}, got {}".format(len(Xpars_), mod.input.shape[1])
assert len(mod.output) == len(Yregressors_) + len(Yclassifiers_), \
"Model does not have correct number of outputs, expected {}, got {}".format(len(Yregressors_) +
len(Yclassifiers_),
len(mod.output))
# test that the training data is loaded again
assert predictor.train_data is not None
assert predictor.test_data is not None
def test_predict(self, root_dir):
# FIXME: for now only check that the predict function returns the correct format, don't check actual predictions
data = pd.read_csv(base_path / 'BesanconGalactic_summary.txt').iloc[0:10]
assert os.path.isfile(os.path.join(root_dir, 'test_model_FC.h5'))
model_path = os.path.join(root_dir, 'test_model_FC.h5')
predictor = predictors.FCPredictor(saved_model=model_path)
res = predictor.predict(data=data)
# check that the dimensions are correct
assert res.shape[0] == 10, "expected 10 predicted rows, got: {}.\n".format(res.shape[0]) +\
" all data:\n{}".format(res)
assert res.shape[1] == 4, "expected 4 predicted columns, got: {}.\n".format(res.shape[1]) + \
" all data:\n{}".format(res)
# check the columns:
for ypar in 'Pfinal qfinal product binary_type'.split():
assert ypar in res.columns, "Expected {} in columns, only".format(ypar) + \
" got: {}.\nall data:\n{}".format(list(res.columns), res)
import os
import pandas as pd
from nnaps import predictors
stability_model = predictors.FCPredictor(
saved_model=os.path.join('MESAbps', 'models', 'model_stability.h5'))
stable_model = predictors.FCPredictor(
saved_model=os.path.join('MESAbps', 'models', 'model_stable_systems.h5'))
ce_model = predictors.FCPredictor(
saved_model=os.path.join('MESAbps', 'models', 'model_ce_systems.h5'))
NECESSARY_PARAMETERS = ['M1_init', 'q_init', 'P_init', 'FeH_init']
def correct_input_pars(df):
for parname in NECESSARY_PARAMETERS:
if not parname in df.columns.values:
return False
return True
def get_missing_input_pars(df):
missing = []
for parname in NECESSARY_PARAMETERS:
if parname not in df.columns.values:
missing.append(parname)