def __init__(self, objective, chain, folder=None, parent=None):
QtWidgets.QDialog.__init__(self, parent)
self.setupUi(self)
self.objective = objective
self.folder = folder
self.chain = chain
if folder is None:
self.folder = os.getcwd()
if self.chain is None:
model_file_name, ok = QtWidgets.QFileDialog.getOpenFileName(
self, "Select chain file")
if not ok:
return
self.folder = os.path.dirname(model_file_name)
try:
self.chain = load_chain(model_file_name)
except Exception as e:
# a chain load will go wrong quite often I'd expect
self.chain = None
print(repr(e))
return
if len(self.chain.shape) == 3:
steps, walkers, varys = self.chain.shape
self.chain_size.setText(
f"steps: {steps}, walkers: {walkers}, varys: {varys}")
else:
steps, temps, walkers, varys = self.chain.shape
self.chain_size.setText(f"steps: {steps}, temps: {temps}, "
f"walkers: {walkers}, varys: {varys}")
self.total_samples.setText("Total samples: {}".format(steps * walkers))
self.burn.setMaximum(steps - 1)
self.thin.setMaximum(steps - 1)
acfs = autocorrelation_chain(self.chain)
time = integrated_time(acfs, tol=1, quiet=True)
self.autocorrelation_time.setText(
f"Estimated Autocorrelation Time: {time}")
def test_best_weighted(self):
assert_equal(len(self.objective.varying_parameters()), 4)
self.objective.setp(self.p0)
f = CurveFitter(self.objective, nwalkers=100)
res = f.fit('least_squares', jac='3-point')
output = res.x
assert_almost_equal(output, self.best_weighted, 3)
assert_almost_equal(self.objective.chisqr(),
self.best_weighted_chisqr, 5)
# compare the residuals
res = (self.data.y - self.model(self.data.x)) / self.data.y_err
assert_equal(self.objective.residuals(), res)
# compare objective.covar to the best_weighted_errors
uncertainties = [param.stderr for param in self.params]
assert_allclose(uncertainties, self.best_weighted_errors, rtol=0.005)
# we're also going to try the checkpointing here.
checkpoint = os.path.join(self.tmpdir, 'checkpoint.txt')
# compare samples to best_weighted_errors
np.random.seed(1)
f.sample(steps=101, random_state=1, verbose=False, f=checkpoint)
process_chain(self.objective, f.chain, nburn=50, nthin=10)
uncertainties = [param.stderr for param in self.params]
assert_allclose(uncertainties, self.best_weighted_errors, rtol=0.07)
# test that the checkpoint worked
check_array = np.loadtxt(checkpoint)
check_array = check_array.reshape(101, f._nwalkers, f.nvary)
assert_allclose(check_array, f.chain)
# test loading the checkpoint
chain = load_chain(checkpoint)
assert_allclose(chain, f.chain)
f.initialise('jitter')
f.sample(steps=2, nthin=4, f=checkpoint, verbose=False)
assert_equal(f.chain.shape[0], 2)
def test_best_weighted(self):
assert_equal(len(self.objective.varying_parameters()), 4)
self.objective.setp(self.p0)
f = CurveFitter(self.objective, nwalkers=100)
res = f.fit("least_squares", jac="3-point")
output = res.x
assert_almost_equal(output, self.best_weighted, 3)
assert_almost_equal(self.objective.chisqr(), self.best_weighted_chisqr,
5)
# compare the residuals
res = (self.data.y - self.model(self.data.x)) / self.data.y_err
assert_equal(self.objective.residuals(), res)
# compare objective.covar to the best_weighted_errors
uncertainties = [param.stderr for param in self.params]
assert_allclose(uncertainties, self.best_weighted_errors, rtol=0.005)
# we're also going to try the checkpointing here.
checkpoint = os.path.join(self.tmpdir, "checkpoint.txt")
# compare samples to best_weighted_errors
np.random.seed(1)
f.sample(steps=201, random_state=1, verbose=False, f=checkpoint)
process_chain(self.objective, f.chain, nburn=50, nthin=10)
uncertainties = [param.stderr for param in self.params]
assert_allclose(uncertainties, self.best_weighted_errors, rtol=0.07)
# test that the checkpoint worked
check_array = np.loadtxt(checkpoint)
check_array = check_array.reshape(201, f._nwalkers, f.nvary)
assert_allclose(check_array, f.chain)
# test loading the checkpoint
chain = load_chain(checkpoint)
assert_allclose(chain, f.chain)
f.initialise("jitter")
f.sample(steps=2, nthin=4, f=checkpoint, verbose=False)
assert_equal(f.chain.shape[0], 2)
# we should be able to produce 2 * 100 steps from the generator
g = self.objective.pgen(ngen=20000000000)
s = [i for i, a in enumerate(g)]
assert_equal(np.max(s), 200 - 1)
g = self.objective.pgen(ngen=200)
pvec = next(g)
assert_equal(pvec.size, len(self.objective.parameters.flattened()))
# check that all the parameters are returned via pgen, not only those
# being varied.
self.params[0].vary = False
f = CurveFitter(self.objective, nwalkers=100)
f.initialise("jitter")
f.sample(steps=2, nthin=4, f=checkpoint, verbose=False)
g = self.objective.pgen(ngen=100)
pvec = next(g)
assert_equal(pvec.size, len(self.objective.parameters.flattened()))
# the following test won't work because of emcee/gh226.
# chain = load_chain(checkpoint)
# assert_(chain.shape == f.chain.shape)
# assert_allclose(chain, f.chain)
# try reproducing best fit with parallel tempering
self.params[0].vary = True
f = CurveFitter(self.objective, nwalkers=100, ntemps=10)
f.fit("differential_evolution", seed=1)
f.sample(steps=201, random_state=1, verbose=False)
process_chain(self.objective, f.chain, nburn=50, nthin=15)
print(self.params[0].chain.shape, self.params[0].chain)
uncertainties = [param.stderr for param in self.params]
assert_allclose(uncertainties, self.best_weighted_errors, rtol=0.07)