def parameters(self, first_theta):
"""Get a parameter set for this theta record.
first_theta is the number of the first theta in this record
"""
pset = ParameterSet()
current_theta = first_theta
for theta in self.root.all('theta'):
init = theta.init.tokens[0].eval
fix = bool(theta.find('FIX'))
if theta.find('low'):
if theta.low.find('NEG_INF'):
lower = min_lower_bound
else:
lower = theta.low.tokens[0].eval
else:
lower = min_lower_bound
if theta.find('up'):
if theta.up.find('POS_INF'):
upper = max_upper_bound
else:
upper = theta.up.tokens[0].eval
else:
upper = max_upper_bound
multiple = theta.find('n')
if multiple:
n = multiple.INT
else:
n = 1
for i in range(0, n):
new_par = Parameter(f'THETA({current_theta})', init, lower,
upper, fix)
current_theta += 1
pset.add(new_par)
return pset
def test_pset_remove_fixed():
p1 = Parameter('Y', 9, fix=False)
p2 = Parameter('X', 3, fix=True)
p3 = Parameter('Z', 1, fix=False)
pset = ParameterSet([p1, p2, p3])
pset.remove_fixed()
assert len(pset) == 2
assert pset['Y'] == Parameter('Y', 9)
def test_pset_fix():
p1 = Parameter('Y', 9, fix=False)
p2 = Parameter('X', 3, fix=True)
p3 = Parameter('Z', 1, fix=False)
pset = ParameterSet([p1, p2, p3])
assert pset.fix == {'Y': False, 'X': True, 'Z': False}
fixedness = {'Y': True, 'X': True, 'Z': True}
pset.fix = fixedness
assert pset.fix == {'Y': True, 'X': True, 'Z': True}
def test_pset_eq():
p1 = Parameter('Y', 9)
p2 = Parameter('X', 3)
p3 = Parameter('Z', 1)
pset1 = ParameterSet([p1, p2, p3])
pset2 = ParameterSet([p1, p2])
assert pset1 != pset2
pset3 = ParameterSet([p1, p3, p2])
assert pset1 != pset3
assert pset1 == pset1
def parameters(self):
"""Get the ParameterSet of all parameters
"""
try:
return self._parameters
except AttributeError:
pass
next_theta = 1
params = ParameterSet()
for theta_record in self.control_stream.get_records('THETA'):
thetas = theta_record.parameters(next_theta)
params.update(thetas)
next_theta += len(thetas)
next_omega = 1
previous_size = None
for omega_record in self.control_stream.get_records('OMEGA'):
omegas, next_omega, previous_size = omega_record.parameters(
next_omega, previous_size)
params.update(omegas)
next_sigma = 1
previous_size = None
for sigma_record in self.control_stream.get_records('SIGMA'):
sigmas, next_sigma, previous_size = sigma_record.parameters(
next_sigma, previous_size)
params.update(sigmas)
self._parameters = params
return params
def test_pset_names():
p1 = Parameter('Y', 9)
p2 = Parameter('X', 3)
p3 = Parameter('Z', 1)
pset = ParameterSet([p1, p2, p3])
assert pset.names == ['Y', 'X', 'Z']
assert pset.symbols == [symbol('Y'), symbol('X'), symbol('Z')]
def test_pset_index():
p = Parameter('Y', 9)
pset = ParameterSet((p, ))
assert len(pset) == 1
assert pset['Y'] is p
p2 = Parameter('Z', 5)
pset.add(p2)
assert len(pset) == 2
# Check that the parameter set keeps the insertion order upon iteration
for i, param in enumerate(pset):
if i == 0:
assert param is p
else:
assert param is p2
def test_pset_inits():
p1 = Parameter('Y', 9)
p2 = Parameter('X', 3)
p3 = Parameter('Z', 1)
pset = ParameterSet([p1, p2, p3])
pset.inits = {'X': 28}
assert len(pset) == 3
assert pset['X'] == Parameter('X', 28)
assert pset['Y'] == Parameter('Y', 9)
assert pset['Z'] == Parameter('Z', 1)
with pytest.raises(KeyError):
pset.inits = {'CL': 0}
pset.inits = {'X': 0, 'Y': 2, 'Z': 5}
assert len(pset) == 3
assert pset['X'] == Parameter('X', 0)
assert pset['Y'] == Parameter('Y', 2)
assert pset['Z'] == Parameter('Z', 5)
def test_pset_repr():
p1 = Parameter('Y', 9, fix=False)
pset = ParameterSet([p1])
assert type(repr(pset)) == str
assert type(pset._repr_html_()) == str
pset = ParameterSet()
assert type(repr(pset)) == str
assert type(pset._repr_html_()) == str
def _read_parameters(self):
next_theta = 1
params = ParameterSet()
for theta_record in self.control_stream.get_records('THETA'):
thetas = theta_record.parameters(next_theta,
seen_labels=set(params.names))
params.update(thetas)
next_theta += len(thetas)
next_omega = 1
previous_size = None
for omega_record in self.control_stream.get_records('OMEGA'):
omegas, next_omega, previous_size = omega_record.parameters(
next_omega, previous_size, seen_labels=set(params.names))
params.update(omegas)
next_sigma = 1
previous_size = None
for sigma_record in self.control_stream.get_records('SIGMA'):
sigmas, next_sigma, previous_size = sigma_record.parameters(
next_sigma, previous_size, seen_labels=set(params.names))
params.update(sigmas)
self._parameters = params
self._old_parameters = params.copy()
def parameters(self, start_omega, previous_size):
"""Get a ParameterSet for this omega record
"""
row = start_omega
block = self.root.find('block')
bare_block = self.root.find('bare_block')
same = bool(self.root.find('same'))
parameters = ParameterSet()
if not (block or bare_block):
for node in self.root.all('diag_item'):
init = node.init.NUMERIC
fixed = bool(node.find('FIX'))
sd = bool(node.find('SD'))
var = bool(node.find('VAR'))
n = node.n.INT if node.find('n') else 1
if sd and var:
raise ModelSyntaxError(f'Initial estimate for {self.name.upper} cannot be both'
f' on SD and VAR scale\n{self.root}')
if init == 0 and not fixed:
raise ModelSyntaxError(f'If initial estimate for {self.name.upper} is 0 it'
f' must be set to FIX')
if sd:
init = init ** 2
for _ in range(n):
name = f'{self.name}({row},{row})'
param = Parameter(name, init, lower=0, fix=fixed)
parameters.add(param)
row += 1
size = 1
next_omega = row
else:
inits = []
if bare_block:
size = previous_size
else:
size = self.root.block.size.INT
fix, sd, corr, cholesky = self._block_flags()
for node in self.root.all('omega'):
init = node.init.NUMERIC
n = node.n.INT if node.find('n') else 1
inits += [init] * n
if not same:
if size != pharmpy.math.triangular_root(len(inits)):
raise ModelSyntaxError('Wrong number of inits in BLOCK')
if not cholesky:
A = pharmpy.math.flattened_to_symmetric(inits)
if corr:
for i in range(size):
for j in range(size):
if i != j:
if sd:
A[i, j] = A[i, i] * A[j, j] * A[i, j]
else:
A[i, j] = math.sqrt(A[i, i]) * math.sqrt(A[j, j]) * A[i, j]
if sd:
np.fill_diagonal(A, A.diagonal()**2)
else:
L = np.zeros((size, size))
inds = np.tril_indices_from(L)
L[inds] = inits
A = L @ L.T
for i in range(size):
for j in range(0, i + 1):
name = f'{self.name}({i + start_omega},{j + start_omega})'
init = A[i, j]
lower = None if i != j else 0
param = Parameter(name, init, lower=lower, fix=fix)
parameters.add(param)
next_omega = start_omega + size
return parameters, next_omega, size
def test_pset_lower_upper():
p1 = Parameter('X', 0, lower=-1, upper=1)
p2 = Parameter('Y', 1, lower=0)
pset = ParameterSet([p1, p2])
assert pset.lower == {'X': -1, 'Y': 0}
assert pset.upper == {'X': 1, 'Y': sympy.oo}
def parameters(self, first_theta, seen_labels=None):
"""Get a parameter set for this theta record.
first_theta is the number of the first theta in this record
"""
if seen_labels is None:
seen_labels = set()
pset = ParameterSet()
current_theta = first_theta
for theta in self.root.all('theta'):
init = theta.init.tokens[0].eval
fix = bool(theta.find('FIX'))
if theta.find('low'):
if theta.low.find('NEG_INF'):
lower = min_lower_bound
else:
lower = theta.low.tokens[0].eval
else:
lower = min_lower_bound
if theta.find('up'):
if theta.up.find('POS_INF'):
upper = max_upper_bound
else:
upper = theta.up.tokens[0].eval
else:
upper = max_upper_bound
multiple = theta.find('n')
if multiple:
n = multiple.INT
else:
n = 1
for i in range(0, n):
name = None
import pharmpy.plugins.nonmem as nonmem
if nonmem.conf.parameter_names == 'comment':
# needed to avoid circular import with Python 3.6
found = False
for subnode in self.root.tree_walk():
if id(subnode) == id(theta):
if found:
break
else:
found = True
continue
if found and subnode.rule == 'NEWLINE':
m = re.search(r';\s*([a-zA-Z_]\w*)', str(subnode))
if m:
name = m.group(1)
break
if name in seen_labels:
warnings.warn(
f'The parameter name {name} is duplicated. Falling back to basic '
f'NONMEM names.')
name = None
if not name:
name = f'THETA({current_theta})'
seen_labels.add(name)
new_par = Parameter(name, init, lower, upper, fix)
current_theta += 1
pset.add(new_par)
if not self.name_map:
self.name_map = {
name: first_theta + i
for i, name in enumerate(pset.names)
}
return pset