def statements(self, new):
try:
old = self._statements
except AttributeError:
old = self.statements
if new == old:
return
old_index = 0
node_index = 0
kept = []
new_nodes = []
defined_symbols = set() # Set of all defined symbols updated so far
for op, s in diff(old, new):
while (node_index < len(self.root.children)
and old_index < len(self.nodes)
and self.root.children[node_index]
is not self.nodes[old_index]):
node = self.root.children[node_index]
kept.append(node)
node_index += 1
if op == '+':
if isinstance(s.expression, Piecewise):
statement_str = self._translate_sympy_piecewise(
s, defined_symbols)
elif re.search('sign', str(s.expression)):
statement_str = self._translate_sympy_sign(s)
else:
statement_str = s.print_custom(self.rvs, self.trans)
node_tree = CodeRecordParser(statement_str).root
for node in node_tree.all('statement'):
if node_index == 0:
node.children.insert(0, AttrToken('LF', '\n'))
if (not node.all('LF') and node_index != 0
or len(self.root.children) > 0
and self.root.children[0].rule != 'empty_line'):
node.children.append(AttrToken('LF', '\n'))
new_nodes.append(node)
kept.append(node)
defined_symbols.add(s.symbol)
elif op == '-':
node_index += 1
old_index += 1
else:
kept.append(self.root.children[node_index])
new_nodes.append(self.root.children[node_index])
node_index += 1
old_index += 1
defined_symbols.add(s.symbol)
if node_index < len(self.root.children): # Remaining non-statements
kept.extend(self.root.children[node_index:])
self.root.children = kept
self.nodes = new_nodes
self._statements = new.copy()
def statements(self, new):
try:
old = self._statements
except AttributeError:
old = self.statements
if new == old:
return
old_index = 0
node_index = 0
kept = []
new_nodes = []
for op, s in diff(old, new):
while (node_index < len(self.root.children)
and old_index < len(self.nodes)
and self.root.children[node_index]
is not self.nodes[old_index]):
node = self.root.children[node_index]
kept.append(node)
node_index += 1
if op == '+':
if isinstance(s.expression, Piecewise):
statement_str = self._translate_sympy_piecewise(s)
elif re.search('sign', str(s.expression)):
statement_str = self._translate_sympy_sign(s)
else:
statement_str = f'\n{repr(s).replace(":", "")}'
node_tree = CodeRecordParser(statement_str).root
node = node_tree.all('statement')[0]
if node_index == 0:
node.children.insert(0, AttrToken('LF', '\n'))
if (node_index != 0 or len(self.root.children) > 0
and self.root.children[0].rule != 'empty_line'):
node.children.append(AttrToken('LF', '\n'))
new_nodes.append(node)
kept.append(node)
elif op == '-':
node_index += 1
old_index += 1
else:
kept.append(self.root.children[node_index])
new_nodes.append(self.root.children[node_index])
node_index += 1
old_index += 1
if node_index < len(self.root.children): # Remaining non-statements
kept.extend(self.root.children[node_index:])
self.root.children = kept
self.nodes = new_nodes
self._statements = new.copy()
def update(self, parameters, first_theta):
"""From a ParameterSet update the THETAs in this record
Currently only updating initial estimates
"""
i = first_theta
for theta in self.root.all('theta'):
name = f'THETA({i})'
param = parameters[name]
new_init = param.init
if float(str(theta.init)) != new_init:
theta.init.tokens[0].value = str(new_init)
fix = bool(theta.find('FIX'))
if fix != param.fix:
if param.fix:
space = AttrToken('WS', ' ')
fix_token = AttrToken('FIX', 'FIX')
theta.children.extend([space, fix_token])
else:
remove_token_and_space(theta, 'FIX')
n = self._multiple(theta)
i += n
def update(self, parameters, first_omega, previous_size):
"""From a ParameterSet update the OMEGAs in this record
returns the next omega number
"""
block = self.root.find('block')
bare_block = self.root.find('bare_block')
if not (block or bare_block):
size = 1
i = first_omega
new_nodes = []
for node in self.root.children:
if node.rule != 'diag_item':
new_nodes.append(node)
else:
sd = bool(node.find('SD'))
fix = bool(node.find('FIX'))
n = node.n.INT if node.find('n') else 1
new_inits = []
new_fix = []
for j in range(i, i + n):
name = f'{self.name}({j},{j})'
if not sd:
value = float(parameters[name].init)
else:
value = parameters[name].init ** 0.5
new_inits.append(value)
new_fix.append(parameters[name].fix)
if n == 1 or (new_inits.count(new_inits[0]) == len(new_inits) and
new_fix.count(new_fix[0]) == len(new_fix)): # All equal?
if float(str(node.init)) != new_inits[0]:
node.init.tokens[0].value = str(new_inits[0])
if new_fix[0] != fix:
if new_fix[0]:
insert_before_or_at_end(node, 'RPAR', [AttrToken('WS', ' '),
AttrToken('FIX', 'FIX')])
else:
remove_token_and_space(node, 'FIX')
new_nodes.append(node)
else:
# Need to split xn
new_children = []
for child in node.children:
if child.rule != 'n':
new_children.append(child)
node.children = new_children
for j, init in enumerate(new_inits):
new_node = AttrTree.transform(node)
if float(str(new_node.init)) != init:
new_node.init.tokens[0].value = str(init)
if new_fix[j] != fix:
insert_before_or_at_end(node, 'RPAR', [AttrToken('WS', ' '),
AttrToken('FIX', 'FIX')])
else:
remove_token_and_space(node, 'FIX')
new_nodes.append(new_node)
if j != len(new_inits) - 1: # Not the last
new_nodes.append(AttrTree.create('ws', {'WS': ' '}))
i += n
self.root.children = new_nodes
next_omega = i
else:
same = bool(self.root.find('same'))
if same:
return first_omega + previous_size, previous_size
size = self.root.block.size.INT
fix, sd, corr, cholesky = self._block_flags()
row = first_omega
col = first_omega
inits = []
new_fix = []
for row in range(first_omega, first_omega + size):
for col in range(first_omega, row + 1):
name = f'{self.name}({row},{col})'
inits.append(parameters[name].init)
new_fix.append(parameters[name].fix)
if len(set(new_fix)) != 1: # Not all true or all false
raise ValueError('Cannot only fix some parameters in block')
A = pharmpy.math.flattened_to_symmetric(inits)
if corr:
for i in range(size):
for j in range(size):
if i != j:
A[i, j] = A[i, j] / (math.sqrt(A[i, i]) * math.sqrt(A[j, j]))
if sd:
np.fill_diagonal(A, A.diagonal()**0.5)
if cholesky:
A = np.linalg.cholesky(A)
inds = np.tril_indices_from(A)
array = list(A[inds])
i = 0
new_nodes = []
for node in self.root.children:
if node.rule != 'omega':
new_nodes.append(node)
else:
n = node.n.INT if node.find('n') else 1
if array[i:i+n].count(array[i]) == n: # All equal?
if float(str(node.init)) != array[i]:
node.init.tokens[0].value = str(array[i])
new_nodes.append(node)
else:
# Need to split xn
new_children = []
for child in node.children:
if child.rule not in ['n', 'LPAR', 'RPAR']:
new_children.append(child)
node.children = new_children
for j, init in enumerate(array[i:i+n]):
new_node = AttrTree.transform(node)
if float(str(new_node.init)) != init:
new_node.init.tokens[0].value = str(init)
new_nodes.append(new_node)
if j != n - 1: # Not the last
new_nodes.append(AttrTree.create('ws', {'WS': ' '}))
i += n
self.root.children = new_nodes
if new_fix[0] != fix:
if new_fix[0]:
insert_after(self.root, 'block', [AttrToken('WS', ' '),
AttrToken('FIX', 'FIX')])
else:
remove_token_and_space(self.root, 'FIX', recursive=True)
next_omega = first_omega + size
return next_omega, size