def main():
#constants
timeRangesToUse = [[1, 2499], [2549, 2999], [3049, 4999], [5049, 14999],
[15049, 19999], [20049, 29999], [30049, 64999],
[65049, 69999], [70049, -1]]
true_parameters = [
2.26E-04, 0.0699, 3.45E-05, 0.05462, 0.0873, 8.92E-03, 5.150E-3,
0.03158, 0.1524
]
model = ChannelModelPintsWrapper()
data = pd.read_csv("data/averaged-data.txt", delim_whitespace=True)
dat = extract_time_ranges(data.values, timeRangesToUse)
times = dat[:, 0]
values = dat[:, 1]
current = model.simulate(true_parameters, times)
plt.plot(times, values)
plt.plot(times, current)
plt.show()
problem = pints.SingleOutputProblem(model, times, values)
error = pints.SumOfSquaresError(problem)
boundaries = MarkovModelBoundaries()
x0 = np.array([0.1] * 9)
found_parameters, found_value = pints.optimise(error,
true_parameters,
boundaries=boundaries)
print(found_parameters, found_value)
def test_optimise(self):
""" Tests :meth: `pints.optimise()`. """
r = pints.toy.TwistedGaussianLogPDF(2, 0.01)
x = np.array([0, 1.01])
s = 0.01
b = pints.RectangularBoundaries([-0.01, 0.95], [0.01, 1.05])
with StreamCapture():
x, f = pints.optimise(r, x, s, b, method=pints.XNES)
self.assertEqual(x.shape, (2, ))
self.assertTrue(f < 1e-6)
def main():
#constants
timeRangesToUse = [[1,2499], [2549,2999], [3049,4999], [5049,14999], [15049,19999], [20049,29999], [30049,64999], [65049,69999], [70049,-1]]
starting_parameters = [3.87068845e-04, 5.88028759e-02, 6.46971727e-05, 4.87408447e-02, 8.03073893e-02, 7.36295506e-03, 5.32908518e-03, 3.32254316e-02, 6.56614672e-02]
model = ChannelModelPintsWrapper()
data = pd.read_csv("data/averaged-data.txt", delim_whitespace=True)
dat = extract_time_ranges(data.values, timeRangesToUse)
times=dat[:,0]
values=dat[:,1]
current = model.simulate(starting_parameters, times)
problem = pints.SingleOutputProblem(model, times, values)
error = pints.SumOfSquaresError(problem)
boundaries = MarkovModelBoundaries()
x0 = np.array([0.1]*9)
found_parameters, found_value = pints.optimise(error, starting_parameters, boundaries=boundaries)
print(found_parameters, found_value)
def optimise(self):
"""
Parameter inference using SNES (Seperable Natural Evolution Strategy).
Returns:
---------------
found_parameters:
- found optimal parameters
"""
#Define a score function, i.e the sum of squares error
score = pints.SumOfSquaresError(self.problem)
#Define the boundaries for F and k according to literature
boundaries = pints.RectangularBoundaries([0.01, 0.01], [1.0, 1.0])
#Starting point within the boundaries
x0 = [0.05, 0.05]
#Run SNES
found_parameters, found_value = pints.optimise(score, x0, boundaries=boundaries, method=pints.SNES)
return found_parameters
def inference(model, values, times):
# Create an object with links to the model and time series
problem = pints.SingleOutputProblem(model, times, values)
# Create a log-likelihood function (adds an extra parameter!)
log_likelihood = pints.GaussianLogLikelihood(problem)
# Create a uniform prior over both the parameters and the new noise variable
lower_bounds = np.array([1e-3, 0.0, 0.4, 0.1, 1e-6, 8.0, 1e-4])
upper_bounds = np.array([10.0, 0.4, 0.6, 100.0, 100e-6, 10.0, 0.2])
log_prior = pints.UniformLogPrior(lower_bounds, upper_bounds)
# Create a posterior log-likelihood (log(likelihood * prior))
log_posterior = pints.LogPosterior(log_likelihood, log_prior)
# Choose starting points for 3 mcmc chains
# params = ['k0', 'E0', 'a', 'Ru', 'Cdl', 'freq', 'sigma']
start_parameters = np.array(
[0.0101, 0.214, 0.53, 8.0, 20.0e-6, 9.0152, 0.01])
transform = pints.ComposedTransformation(
pints.LogTransformation(1),
pints.RectangularBoundariesTransformation(lower_bounds[1:],
upper_bounds[1:]),
)
sigma0 = [0.1 * (h - l) for l, h in zip(lower_bounds, upper_bounds)]
boundaries = pints.RectangularBoundaries(lower_bounds, upper_bounds)
found_parameters, found_value = pints.optimise(log_posterior,
start_parameters,
sigma0,
boundaries,
transform=transform,
method=pints.CMAES)
xs = [
found_parameters * 1.001,
found_parameters * 1.002,
found_parameters * 1.003,
]
for x in xs:
x[5] = found_parameters[5]
print('start_parameters', start_parameters)
print('found_parameters', found_parameters)
print('lower_bounds', lower_bounds)
print('upper_bounds', upper_bounds)
# Create mcmc routine with four chains
mcmc = pints.MCMCController(log_posterior,
3,
xs,
method=pints.HaarioBardenetACMC,
transform=transform)
# Add stopping criterion
mcmc.set_max_iterations(10000)
# Run!
chains = mcmc.run()
# Save chains for plotting and analysis
pickle.dump((xs, pints.GaussianLogLikelihood, log_prior, chains,
'HaarioBardenetACMC'), open('results.pickle', 'wb'))
def n_parameters(self):
return self.n
lpdf = LogisticAPI(
'https://mighty-badlands-12664.herokuapp.com/pints-team/benchmarks/1.0.0/')
real_parameters = [0.015, 500, 10]
## Select some boundaries
boundaries = pints.RectangularBoundaries([0, 400, 0], [0.03, 600, 20])
## Perform an optimization with boundaries and hints
x0 = 0.01, 450, 5
sigma0 = [0.01, 100, 10]
found_parameters, found_value = pints.optimise(lpdf,
x0,
sigma0,
boundaries,
method=pints.CMAES)
## Show score of true solution
print('log likelihood at true solution: ')
print(lpdf(real_parameters))
#
## Compare parameters with original
print('Found solution: True parameters:')
for k, x in enumerate(found_parameters):
print(pints.strfloat(x) + ' ' + pints.strfloat(real_parameters[k]))
s = myokit.Simulation(model, prot)
# Format the values list to use it in PINTS
fit_values = values[0] + values[1]
# Calling PINTS library
# Parameters : [CL, Vc, Qp1, Vp1, Qp2, Vp2]
initial_point = [5.4, 8.5, 18.6, 8.3, 1.7, 32.8]
problem = pints.SingleOutputProblem(model=MyModel(),
times=np.linspace(0, 24, 10),
values=fit_values)
boundaries = pints.RectangularBoundaries([3, 5, 7, 5, 0.5, 30],
[15, 15, 30, 20, 5, 60])
error_measure = pints.SumOfSquaresError(problem)
found_parameters, found_value = pints.optimise(error_measure,
initial_point,
boundaries=boundaries,
method=pints.XNES)
#%% Running the simulation with found parameters
# Reset the variables to initial state for the plot
s.reset()
# Use parameters returned from optimisation or user-defined parameters set
parameters = [6.7, 10.1, 17.8, 9.4, 1.4, 18.3]
plot_parameters = found_parameters
s.set_constant('constants.CL', plot_parameters[0])
s.set_constant('plasma.Vc', plot_parameters[1])
s.set_constant('constants.kp1', plot_parameters[2])
s.set_constant('compartment_1.V1', plot_parameters[3])
s.set_constant('constants.kp2', plot_parameters[4])
s.set_constant('compartment_2.V2', plot_parameters[5])
def main(args, output_dir="", ms_to_remove_after_spike=50):
output_dir = os.path.join(args.output, output_dir)
if not os.path.exists(output_dir):
os.mkdir(output_dir)
# Constants
if ms_to_remove_after_spike == 0:
indices_to_remove = None
else:
spikes = [2500, 3000, 5000, 15000, 20000, 30000, 65000, 70000]
indices_to_remove = [[spike, spike + ms_to_remove_after_spike*10] for spike in spikes]
indices_to_use = remove_indices(list(range(80000)), indices_to_remove)
# indices_to_use = [[1,2499], [2549,2999], [3049,4999], [5049,14999], [15049,19999], [20049,29999], [30049,64999], [65049,69999], [70049,-1]]
starting_parameters = [3.87068845e-04, 5.88028759e-02, 6.46971727e-05, 4.87408447e-02, 8.03073893e-02, 7.36295506e-03, 5.32908518e-03, 3.32254316e-02, 6.56614672e-02]
plt.rcParams['axes.axisbelow'] = True
data = pd.read_csv(args.data_file_path, delim_whitespace=True)
print("outputting to {}".format(args.output))
if not os.path.exists(args.data_file_path):
print("Input file not provided. Doing nothing.")
return
par = Params()
skip = int(par.timestep/0.1)
dat = data.values[indices_to_use]
times=dat[:,0]
values=dat[:,1]
model = PintsWrapper(par, args, times)
current = model.simulate(starting_parameters, times)
if args.plot:
plt.plot(times, values)
plt.plot(model.times_to_use, current)
plt.show()
problem = pints.SingleOutputProblem(model, times, values)
error = pints.SumOfSquaresError(problem)
boundaries = Boundaries()
x0 = starting_parameters
found_parameters, found_value = pints.optimise(error, starting_parameters, boundaries=boundaries)
# found_parameters = np.array([2.26E-04, 0.0699, 3.45E-05, 0.05462, 0.0873, 8.92E-03, 5.150E-3, 0.03158, 0.1524])
# found_value = 100
print("finished! found parameters : {} ".format(found_parameters, found_value))
# Find error sensitivities
funcs = model.funcs
current, sens = funcs.SimulateForwardModelSensitivities(found_parameters)
sens = (sens * found_parameters[None,:]).T
for i, vec in enumerate(sens):
plt.plot(times, vec, label="state_variable".format(i))
plt.title("Output sensitivities for four gate Markov Model")
if args.plot:
plt.show()
else:
plt.savefig(os.path.join(output_dir, "output_sensitivities"))
plt.clf()
# Estimate the various of the i.i.d Gaussian noise
nobs = len(times)
sigma2 = sum((current - values)**2)/(nobs-1)
# Compute the Fischer information matrix
FIM = sens @ sens.T/sigma2
cov = FIM**-1
eigvals = np.linalg.eigvals(FIM)
for i in range(0, par.n_params):
for j in range(i+1, par.n_params):
parameters_to_view = np.array([i,j])
sub_cov = cov[parameters_to_view[:,None], parameters_to_view]
eigen_val, eigen_vec = np.linalg.eigh(sub_cov)
eigen_val=eigen_val.real
if eigen_val[0] > 0 and eigen_val[1] > 0:
print("COV_{},{} : well defined".format(i, j))
cov_ellipse(sub_cov, q=[0.75, 0.9, 0.99])
plt.ylabel("parameter {}".format(i))
plt.xlabel("parameter {}".format(j))
if args.plot:
plt.show()
else:
plt.savefig(os.path.join(output_dir, "covariance_for_parameters_{}_{}".format(i,j)))
plt.clf()
else:
print("COV_{},{} : negative eigenvalue".format(i,j))
print('Eigenvalues of FIM:\n{}'.format(eigvals))
print("Covariance matrix is: \n{}".format(cov))
plt.plot(data["time"], data["current"], label="averaged data")
plt.plot(times, current, label="current")
plt.legend()
if args.plot:
plt.show()
else:
plt.savefig(os.path.join(output_dir, "fit"))
plt.clf()
return times, found_parameters