def test_load_parameters(self):
"""
Test the method load_parameters.
"""
leaspy_object = Leaspy.load(example_logisticmodel_path)
abstract_model = AbstractModel("dummy_model")
abstract_model.load_parameters(leaspy_object.model.parameters)
self.assertTrue(torch.equal(abstract_model.parameters['g'],
torch.tensor([1.8669992685317993, 2.4921786785125732,
2.471605062484741, 2.1240732669830322])))
self.assertTrue(torch.equal(abstract_model.parameters['v0'],
torch.tensor([-2.8300716876983643, -3.3241398334503174,
-3.4701175689697266, -2.6136295795440674])))
self.assertTrue(torch.equal(abstract_model.parameters['betas'],
torch.tensor([[0.011530596762895584, 0.06039918214082718],
[0.008324957452714443, 0.048168670386075974],
[0.01144738681614399, 0.0822334811091423]])))
self.assertTrue(torch.equal(abstract_model.parameters['tau_mean'], torch.tensor(75.30111694335938)))
self.assertTrue(torch.equal(abstract_model.parameters['tau_std'], torch.tensor(7.103002071380615)))
self.assertTrue(torch.equal(abstract_model.parameters['xi_mean'], torch.tensor(0.0)))
self.assertTrue(torch.equal(abstract_model.parameters['xi_std'], torch.tensor(0.2835913300514221)))
self.assertTrue(torch.equal(abstract_model.parameters['sources_mean'], torch.tensor(0.0)))
self.assertTrue(torch.equal(abstract_model.parameters['sources_std'], torch.tensor(1.0)))
self.assertTrue(torch.equal(abstract_model.parameters['noise_std'], torch.tensor(0.1988248974084854)))
def test_estimate(self):
model_parameters_path = os.path.join(test_data_dir, 'model_parameters',
'fitted_multivariate_model.json')
leaspy = Leaspy.load(model_parameters_path)
ip_path = os.path.join(test_data_dir, 'io', 'outputs', 'ip_save.json')
ip = IndividualParameters.load(ip_path)
timepoints = {'idx1': [78, 81], 'idx2': [91]}
estimations = leaspy.estimate(timepoints, ip)
test = {
'idx1': [[0.9168074, 0.88841885, 0.80543965, 0.9921461],
[0.98348546, 0.9773835, 0.9456895, 0.99938035]],
'idx2': [[0.9999131, 0.9998343, 0.9991264, 0.99999964]]
}
# Test
self.assertEqual(estimations.keys(), test.keys())
for k in estimations.keys():
self.assertTrue(k in test.keys())
for v1, v2 in zip(estimations[k], test[k]):
self.assertTrue((v1 - v2 < 10e-8).all())
def test_acceptation(self):
n_patients = 17
n_draw = 200
# temperature_inv = 1.0
path_model_sampler = os.path.join(test_data_dir, "model_parameters",
"multivariate_model_sampler.json")
path_data = os.path.join(test_data_dir, "io", "data_tiny.csv")
# data = Dataset(Data.from_csv_file(path_data))
leaspy = Leaspy.load(path_model_sampler)
# realizations = leaspy.model.get_realization_object(n_patients)
# Test with taus
var_name = 'tau'
gsampler = GibbsSampler(
leaspy.model.random_variable_informations()[var_name], n_patients)
for i in range(n_draw):
gsampler._update_acceptation_rate(
torch.tensor([1.0] * 10 + [0.0] * 7, dtype=torch.float32))
self.assertAlmostEqual(gsampler.acceptation_temp.mean(),
10 / 17,
delta=0.05)
def test_append_spaceshifts_to_individual_parameters_dataframe(self):
df = pd.DataFrame(data=[[0.1, 70, 0.1, -0.3], [0.2, 73, -0.4, 0.1],
[0.3, 58, -0.6, 0.2]],
index=["idx1", "idx2", "idx3"],
columns=["xi", "tau", "sources_0", "sources_1"])
leaspy = Leaspy.load(
os.path.join(test_data_dir, 'model_parameters', 'test_api.json'))
df_w = append_spaceshifts_to_individual_parameters_dataframe(
df, leaspy)
def test_compute_trajectory_of_population(self):
leaspy = Leaspy.load(
os.path.join(test_data_dir, 'model_parameters', 'test_api.json'))
ip = IndividualParameters.load(
os.path.join(test_data_dir, 'io', 'outputs', 'ip_save.json'))
timepoints = [70, 71, 72, 73, 74, 75, 76]
trajectory = compute_trajectory_of_population(timepoints, ip, leaspy)
#self.assertTrue(torch.is_tensor(trajectory))
# TODO : choose a convention for output type : Numpy or Torch ? For now it seems numpy in api.estimate
self.assertEqual(trajectory.shape[0], 7)
self.assertEqual(trajectory.shape[1], 4)
def test_get_reparametrized_ages(self):
leaspy = Leaspy.load(
os.path.join(test_data_dir, 'model_parameters', 'test_api.json'))
ip = IndividualParameters.load(
os.path.join(test_data_dir, 'io', 'outputs', 'ip_save.json'))
ages = {'idx1': [70, 80], 'idx3': [100]}
reparametrized_ages = get_reparametrized_ages(ages, ip, leaspy)
self.assertEqual(reparametrized_ages.keys(), ages.keys())
self.assertEqual(reparametrized_ages['idx1'],
[78.02704620361328, 89.0787582397461])
self.assertEqual(reparametrized_ages['idx3'], [134.7211151123047])
def test_personalize_scipy(self):
"""
Load logistic model from file, and personalize it to data from ...
:return:
"""
# Inputs
data = Data.from_csv_file(example_data_path)
# Initialize
leaspy = Leaspy.load(example_logisticmodel_path)
# Launch algorithm
algo_personalize_settings = AlgorithmSettings('scipy_minimize', seed=0)
ips, noise_std = leaspy.personalize(data,
settings=algo_personalize_settings,
return_noise=True)
self.assertAlmostEqual(noise_std.item(), 0.1169, delta=0.01)
def test_personalize_scipy_diag_noise(self):
"""
Load logistic model (diag noise) from file, and personalize it to data from ...
:return:
"""
# Inputs
data = Data.from_csv_file(example_data_path)
# Initialize
leaspy = Leaspy.load(example_logisticmodel_diag_noise_path)
# Launch algorithm
algo_personalize_settings = AlgorithmSettings('scipy_minimize', seed=0)
ips, noise_std = leaspy.personalize(data,
settings=algo_personalize_settings,
return_noise=True)
diff_noise = noise_std - torch.tensor([0.3299, 0.1236, 0.1642, 0.2582])
self.assertAlmostEqual((diff_noise**2).sum(), 0., delta=0.01)
def test_personalize_modereal(self):
"""
Load logistic model from file, and personalize it to data from ...
:return:
"""
# Inputs
data = Data.from_csv_file(example_data_path)
# Initialize
leaspy = Leaspy.load(example_logisticmodel_path)
# Launch algorithm
path_settings = os.path.join(os.path.dirname(__file__),
"data/settings_mode_real.json")
algo_personalize_settings = AlgorithmSettings.load(path_settings)
ips, noise_std = leaspy.personalize(data,
settings=algo_personalize_settings,
return_noise=True)
self.assertAlmostEqual(noise_std.item(), 0.12152, delta=0.01)
def test_check_cofactors(self, get_result=False):
"""
Test Leaspy.simulate return a ``ValueError`` if the ``cofactor`` and ``cofactor_state`` parameters given
in the ``AlgorithmSettings`` are invalid.
Parameters
----------
get_result : bool
If set to ``True``, return the leaspy model and result object used to do the test. Else return nothing.
Returns
-------
model : leaspy.Leaspy
results : leaspy.io.outputs.result.Result
"""
data = Data.from_csv_file(example_data_path)
cofactors = pd.read_csv(
os.path.join(test_data_dir, "io/data/data_tiny_covariate.csv"))
cofactors.columns = ("ID", "Treatments")
cofactors['ID'] = cofactors['ID'].apply(lambda x: str(x))
cofactors = cofactors.set_index("ID")
data.load_cofactors(cofactors, ["Treatments"])
model = Leaspy.load(
os.path.join(test_data_dir,
"model_parameters/multivariate_model_sampler.json"))
settings = AlgorithmSettings('mode_real')
individual_parameters = model.personalize(data, settings)
settings = AlgorithmSettings('simulation', cofactor="dummy")
self.assertRaises(ValueError, model.simulate, individual_parameters,
data, settings)
settings = AlgorithmSettings('simulation',
cofactor="Treatments",
cofactor_state="dummy")
self.assertRaises(ValueError, model.simulate, individual_parameters,
data, settings)
if get_result:
return model, individual_parameters, data
def get_individual_parameters(data):
# Data
leaspy_data = convert_data(data)
# Algorithm
settings = AlgorithmSettings('scipy_minimize')
# Leaspy
#leaspy = Leaspy.load(data['model'])
# TO CORRECT
#if data['model']['name'] == 'logistic_parallel':
leaspy = Leaspy.load(data['model'])
#elif data['model']['name'] == 'logistic':
# leaspy = Leaspy.load(os.path.join(os.getcwd(), 'data', 'example', 'parkinson_model.json'))
individual_parameters = leaspy.personalize(leaspy_data, settings=settings)
output = {
'individual_parameters' : individual_parameters["patient"],
'scores': leaspy_data.to_dataframe().values.T.tolist()
}
return output
def test_get_error_distribution_dataframe(self):
model_path = os.path.join(test_data_dir, "model_parameters",
"fitted_multivariate_model.json")
leaspy_session = Leaspy.load(model_path)
self.results.get_error_distribution_dataframe(leaspy_session.model)
def test_sample(self):
"""
Test if samples values are the one expected
:return:
"""
# TODO change this instanciation
n_patients = 17
n_draw = 50
temperature_inv = 1.0
path_model_sampler = os.path.join(test_data_dir, "model_parameters",
"multivariate_model_sampler.json")
path_data = os.path.join(test_data_dir, "io", "data", "data_tiny.csv")
data = Dataset(Data.from_csv_file(path_data))
leaspy = Leaspy.load(path_model_sampler)
realizations = leaspy.model.get_realization_object(n_patients)
# Test with taus
var_name = 'tau'
gsampler = GibbsSampler(
leaspy.model.random_variable_informations()[var_name], n_patients)
random_draws = []
for i in range(n_draw):
gsampler.sample(data, leaspy.model, realizations, temperature_inv)
random_draws.append(
realizations[var_name].tensor_realizations.clone())
stack_random_draws = torch.stack(random_draws)
stack_random_draws_mean = (stack_random_draws[1:, :, :] -
stack_random_draws[:-1, :, :]).mean(dim=0)
stack_random_draws_std = (stack_random_draws[1:, :, :] -
stack_random_draws[:-1, :, :]).std(dim=0)
self.assertAlmostEqual(stack_random_draws_mean.mean(),
0.0160,
delta=0.05)
self.assertAlmostEqual(stack_random_draws_std.mean(),
0.0861,
delta=0.05)
# Test with g
var_name = 'g'
gsampler = GibbsSampler(
leaspy.model.random_variable_informations()[var_name], n_patients)
random_draws = []
for i in range(n_draw):
gsampler.sample(data, leaspy.model, realizations, temperature_inv)
random_draws.append(
realizations[var_name].tensor_realizations.clone())
stack_random_draws = torch.stack(random_draws)
stack_random_draws_mean = (stack_random_draws[1:, :] -
stack_random_draws[:-1, :]).mean(dim=0)
stack_random_draws_std = (stack_random_draws[1:, :] -
stack_random_draws[:-1, :]).std(dim=0)
self.assertAlmostEqual(stack_random_draws_mean.mean(),
4.2792e-05,
delta=0.05)
self.assertAlmostEqual(stack_random_draws_std.mean(),
0.0045,
delta=0.05)
def test_usecase(self):
"""
Functional test of a basic analysis using leaspy package
1 - Data loading
2 - Fit logistic model with MCMC algorithm
3 - Save paramaters & reload (remove created files to keep the repo clean)
4 - Personalize model with 'mode_real' algorithm
5 - Plot results
6 - Simulate new patients
"""
data = Data.from_csv_file(example_data_path)
# Fit
algo_settings = AlgorithmSettings('mcmc_saem', n_iter=10, seed=0)
leaspy = Leaspy("logistic")
leaspy.model.load_hyperparameters({'source_dimension': 2})
leaspy.fit(data, algorithm_settings=algo_settings)
self.model_values_test(leaspy.model)
# Save parameters and check its consistency
path_to_saved_model = os.path.join(test_data_dir, 'model_parameters',
'test_api-copy.json')
leaspy.save(path_to_saved_model)
with open(
os.path.join(test_data_dir, "model_parameters",
'test_api.json'), 'r') as f1:
model_parameters = json.load(f1)
with open(path_to_saved_model) as f2:
model_parameters_new = json.load(f2)
# self.assertTrue(ordered(model_parameters) == ordered(model_parameters_new))
self.assertTrue(
dict_compare_and_display(model_parameters, model_parameters_new))
# Load data and check its consistency
leaspy = Leaspy.load(path_to_saved_model)
os.remove(path_to_saved_model)
self.assertTrue(leaspy.model.is_initialized)
self.model_values_test(leaspy.model)
# Personalize
algo_personalize_settings = AlgorithmSettings('mode_real', seed=0)
individual_parameters = leaspy.personalize(
data, settings=algo_personalize_settings)
# TODO REFORMAT: compute the noise std afterwards
#self.assertAlmostEqual(result.noise_std, 0.21146, delta=0.01)
## Plot TODO
#path_output = os.path.join(os.path.dirname(__file__), '../../_data', "_outputs")
#plotter = Plotter(path_output)
# plotter.plot_mean_trajectory(leaspy.model, save_as="mean_trajectory_plot")
#plt.close()
# Simulate
simulation_settings = AlgorithmSettings('simulation', seed=0)
simulation_results = leaspy.simulate(individual_parameters, data,
simulation_settings)
self.assertTrue(type(simulation_results) == Result)
self.assertTrue(simulation_results.data.headers == data.headers)
n = simulation_settings.parameters['number_of_subjects']
self.assertEqual(simulation_results.data.n_individuals, n)
self.assertEqual(
len(simulation_results.get_parameter_distribution('xi')), n)
self.assertEqual(
len(simulation_results.get_parameter_distribution('tau')), n)
self.assertEqual(
len(
simulation_results.get_parameter_distribution('sources')
['sources0']), n)
# simulation_results.data.to_dataframe().to_csv(os.path.join(
# test_data_dir, "_outputs/simulation/test_api_simulation_df-post_merge-result_fix.csv"), index=False)
# Test the reproducibility of simulate
# round is necessary, writing and reading induces numerical errors of magnitude ~ 1e-13
# BUT ON DIFFERENT MACHINE I CAN SEE ERROR OF MAGNITUDE 1e-5 !!!
# TODO: Can we improve this??
simulation_df = pd.read_csv(
os.path.join(
test_data_dir,
"_outputs/simulation/test_api_simulation_df-post_merge-result_fix.csv"
))
id_simulation_is_reproducible = simulation_df['ID'].equals(
simulation_results.data.to_dataframe()['ID'])
# Check ID before - str doesn't seem to work with numpy.allclose
self.assertTrue(id_simulation_is_reproducible)
round_decimal = 5
simulation_is_reproducible = allclose(
simulation_df.loc[:, simulation_df.columns != 'ID'].values,
simulation_results.data.to_dataframe().
loc[:,
simulation_results.data.to_dataframe().columns != 'ID'].values,
atol=10**(-round_decimal),
rtol=10**(-round_decimal))
# Use of numpy.allclose instead of pandas.testing.assert_frame_equal because of buggy behaviour reported
# in https://github.com/pandas-dev/pandas/issues/22052
# If reproducibility error > 1e-5 => display it + visit with the biggest reproducibility error
error_message = ''
if not simulation_is_reproducible:
# simulation_df = pd.read_csv(
# os.path.join(test_data_dir, "_outputs/simulation/test_api_simulation_df-post_merge-result_fix.csv"))
max_diff = 0.
value_v1 = 0.
value_v2 = 0.
count = 0
tol = 10**(-round_decimal)
actual_simu_df = simulation_results.data.to_dataframe()
for v1, v2 in zip(
simulation_df.loc[:, simulation_df.columns != 'ID'].values.
tolist(), actual_simu_df.
loc[:, actual_simu_df.columns != 'ID'].values.tolist()):
diff = [abs(val1 - val2) for val1, val2 in zip(v1, v2)]
if max(diff) > tol:
count += 1
if max(diff) > max_diff:
value_v1 = v1
value_v2 = v2
max_diff = max(diff)
error_message += '\nTolerance error = %.1e' % tol
error_message += '\nMaximum error = %.3e' % max_diff
error_message += '\n' + str(
[round(v, round_decimal + 1) for v in value_v1])
error_message += '\n' + str(
[round(v, round_decimal + 1) for v in value_v2])
error_message += '\nNumber of simulated visits above tolerance error = %d / %d \n' \
% (count, simulation_df.shape[0])
# For loop before the last self.assert - otherwise no display is made
self.assertTrue(simulation_is_reproducible, error_message)
import os
import sys
import plotly.graph_objects as go
import seaborn as sns
import sys
import numpy as np
from sklearn.decomposition import PCA
sys.path.append("../")
print(os.getcwd())
from leaspy import IndividualParameters, Data, Leaspy
from src.leaspype import get_reparametrized_ages, append_spaceshifts_to_individual_parameters_dataframe
#%% Load Data
path_datadashboard = "data/"
leaspy = Leaspy.load(os.path.join(path_datadashboard, "leaspy.json"))
individual_parameters = IndividualParameters.load(
os.path.join(path_datadashboard, "ip.csv"))
data = Data.from_csv_file(os.path.join(path_datadashboard, "data.csv"))
n_sources = leaspy.model.source_dimension
sources_name = ["sources_{}".format(i) for i in range(n_sources)]
df_data = data.to_dataframe().set_index(["ID", "TIME"])
features = leaspy.model.features
# ind parameters
df_ind = individual_parameters.to_dataframe()
ind_param_names = list(df_ind.columns) + ["pca1", "pca2"]
df_ind = df_ind.reset_index()
# PCA on the w_i
res = append_spaceshifts_to_individual_parameters_dataframe(
name = "personalize_0"
path_output_personalize = os.path.join(output_directory, experiment_folder,
"personalize", name)
if not os.path.exists(path_output_personalize):
os.makedirs(path_output_personalize)
# Get calibrated models paths
model_paths = [
os.path.join(path_output_calibrate, "fold_{}".format(i),
"model_parameters.json") for i in range(n_resampling_iter)
]
# Load estimated leaspy models
leaspy_iter = []
for i in range(n_resampling_iter):
leaspy = Leaspy.load(model_paths[i])
leaspy_iter.append(leaspy)
# Algo settings iter
algo_settings_personalize_iter = []
algo_settings_personalize = AlgorithmSettings(personalize_algorithm,
seed=seed,
n_iter=n_iter_personalize)
for i in range(n_resampling_iter):
algo_settings_personalize_iter.append(algo_settings_personalize)
# Save algo settings
algo_settings_personalize.save(
os.path.join(path_output_personalize, "algo_settings_personalize.json"))