def test_write_to_subexpression():
variables = {
'a': Subexpression(name='a', dtype=np.float32,
owner=FakeGroup(variables={}), device=None,
expr='2*z'),
'z': Variable(name='z')
}
# Writing to a subexpression is not allowed
code = 'a = z'
with pytest.raises(SyntaxError):
make_statements(code, variables, np.float32)
def test_repeated_subexpressions():
variables = {
'a':
Subexpression(name='a',
dtype=np.float32,
owner=FakeGroup(variables={}),
device=None,
expr='2*z'),
'x':
Variable(name='x'),
'y':
Variable(name='y'),
'z':
Variable(name='z')
}
# subexpression a (referring to z) is used twice, but can be reused the
# second time (no change to z)
code = '''
x = a
y = a
'''
scalar_stmts, vector_stmts = make_statements(code, variables, np.float32)
assert len(scalar_stmts) == 0
assert [stmt.var for stmt in vector_stmts] == ['a', 'x', 'y']
assert vector_stmts[0].constant
code = '''
x = a
z *= 2
'''
scalar_stmts, vector_stmts = make_statements(code, variables, np.float32)
assert len(scalar_stmts) == 0
assert [stmt.var for stmt in vector_stmts] == ['a', 'x', 'z']
# Note that we currently do not mark the subexpression as constant in this
# case, because its use after the "z *=2" line would actually redefine it.
# Our algorithm is currently not smart enough to detect that it is actually
# not used afterwards
# a refers to z, therefore we have to redefine a after z changed, and a
# cannot be constant
code = '''
x = a
z *= 2
y = a
'''
scalar_stmts, vector_stmts = make_statements(code, variables, np.float32)
assert len(scalar_stmts) == 0
assert [stmt.var for stmt in vector_stmts] == ['a', 'x', 'z', 'a', 'y']
assert not any(stmt.constant for stmt in vector_stmts)
def test_nested_subexpressions():
'''
This test checks that code translation works with nested subexpressions.
'''
code = '''
x = a + b + c
c = 1
x = a + b + c
d = 1
x = a + b + c
'''
variables = {
'a': Subexpression(name='a', dtype=np.float32, owner=FakeGroup(variables={}), device=None,
expr='b*b+d'),
'b': Subexpression(name='b', dtype=np.float32, owner=FakeGroup(variables={}), device=None,
expr='c*c*c'),
'c': Variable(name='c'),
'd': Variable(name='d'),
}
scalar_stmts, vector_stmts = make_statements(code, variables, np.float32)
assert len(scalar_stmts) == 0
evalorder = ''.join(stmt.var for stmt in vector_stmts)
# This is the order that variables ought to be evaluated in (note that
# previously this test did not expect the last "b" evaluation, because its
# value did not change (c was not changed). We have since removed this
# subexpression caching, because it did not seem to apply in practical
# use cases)
assert evalorder == 'baxcbaxdbax'
def translate(self, code, dtype):
'''
Translates an abstract code block into the target language.
'''
scalar_statements = {}
vector_statements = {}
for ac_name, ac_code in code.iteritems():
scalar_statements[ac_name], vector_statements[
ac_name] = make_statements(ac_code, self.variables, dtype)
for vs in vector_statements.itervalues():
# Check that the statements are meaningful independent on the order of
# execution (e.g. for synapses)
try:
check_for_order_independence(vs, self.variables,
self.variable_indices)
except OrderDependenceError:
# If the abstract code is only one line, display it in full
if len(vs) <= 1:
error_msg = 'Abstract code: "%s"\n' % vs[0]
else:
error_msg = ('%d lines of abstract code, first line is: '
'"%s"\n') % (len(vs), vs[0])
logger.warn(('Came across an abstract code block that is not '
'well-defined: the outcome may depend on the '
'order of execution. ' + error_msg))
return self.translate_statement_sequence(scalar_statements,
vector_statements)
def test_nested_subexpressions():
'''
This test checks that code translation works with nested subexpressions.
'''
code = '''
x = a + b + c
c = 1
x = a + b + c
d = 1
x = a + b + c
'''
variables = {
'a': Subexpression(name='a', dtype=np.float32, owner=FakeGroup(variables={}), device=None,
expr='b*b+d'),
'b': Subexpression(name='b', dtype=np.float32, owner=FakeGroup(variables={}), device=None,
expr='c*c*c'),
'c': Variable(name='c'),
'd': Variable(name='d'),
}
scalar_stmts, vector_stmts = make_statements(code, variables, np.float32)
assert len(scalar_stmts) == 0
evalorder = ''.join(stmt.var for stmt in vector_stmts)
# This is the order that variables ought to be evaluated in (note that
# previously this test did not expect the last "b" evaluation, because its
# value did not change (c was not changed). We have since removed this
# subexpression caching, because it did not seem to apply in practical
# use cases)
assert evalorder == 'baxcbaxdbax'
def translate(self, code, dtype):
'''
Translates an abstract code block into the target language.
'''
scalar_statements = {}
vector_statements = {}
for ac_name, ac_code in code.iteritems():
scalar_statements[ac_name], vector_statements[ac_name] = make_statements(ac_code,
self.variables,
dtype)
for vs in vector_statements.itervalues():
# Check that the statements are meaningful independent on the order of
# execution (e.g. for synapses)
try:
check_for_order_independence(vs,
self.variables,
self.variable_indices)
except OrderDependenceError:
# If the abstract code is only one line, display it in full
if len(vs) <= 1:
error_msg = 'Abstract code: "%s"\n' % vs[0]
else:
error_msg = ('%d lines of abstract code, first line is: '
'"%s"\n') % (len(vs), vs[0])
logger.warn(('Came across an abstract code block that is not '
'well-defined: the outcome may depend on the '
'order of execution. ' + error_msg))
return self.translate_statement_sequence(scalar_statements,
vector_statements)
def test_nested_subexpressions():
'''
This test checks that code translation works with nested subexpressions.
'''
code = '''
x = a + b + c
c = 1
x = a + b + c
d = 1
x = a + b + c
'''
variables = {
'a':
Subexpression(name='a',
unit=Unit(1),
dtype=np.float32,
owner=FakeGroup(variables={}),
device=None,
expr='b*b+d'),
'b':
Subexpression(name='b',
unit=Unit(1),
dtype=np.float32,
owner=FakeGroup(variables={}),
device=None,
expr='c*c*c'),
'c':
Variable(unit=None, name='c'),
'd':
Variable(unit=None, name='d'),
}
stmts = make_statements(code, variables, np.float32)
evalorder = ''.join(stmt.var for stmt in stmts)
# This is the order that variables ought to be evaluated in
assert evalorder == 'baxcbaxdax'
def translate(self, code, dtype):
'''
Translates an abstract code block into the target language.
'''
scalar_statements = {}
vector_statements = {}
for ac_name, ac_code in code.iteritems():
statements = make_statements(ac_code,
self.variables,
dtype,
optimise=True,
blockname=ac_name)
scalar_statements[ac_name], vector_statements[ac_name] = statements
for vs in vector_statements.itervalues():
# Check that the statements are meaningful independent on the order of
# execution (e.g. for synapses)
try:
if self.has_repeated_indices(vs): # only do order dependence if there are repeated indices
check_for_order_independence(vs,
self.variables,
self.variable_indices)
except OrderDependenceError:
# If the abstract code is only one line, display it in full
if len(vs) <= 1:
error_msg = 'Abstract code: "%s"\n' % vs[0]
else:
error_msg = ('%d lines of abstract code, first line is: '
'"%s"\n') % (len(vs), vs[0])
logger.warn(('Came across an abstract code block that may not be '
'well-defined: the outcome may depend on the '
'order of execution. You can ignore this warning if '
'you are sure that the order of operations does not '
'matter. ' + error_msg))
return self.translate_statement_sequence(scalar_statements,
vector_statements)
def translate(self, code, dtype):
'''
Translates an abstract code block into the target language.
'''
statements = {}
for ac_name, ac_code in code.iteritems():
statements[ac_name] = make_statements(ac_code, self.variables, dtype)
return self.translate_statement_sequence(statements)
def translate(self, code, dtype):
'''
Translates an abstract code block into the target language.
'''
statements = {}
for ac_name, ac_code in code.iteritems():
statements[ac_name] = make_statements(ac_code, self.variables, dtype)
return self.translate_statement_sequence(statements)
def test_automatic_augmented_assignments():
# We test that statements that could be rewritten as augmented assignments
# are correctly rewritten (using sympy to test for symbolic equality)
variables = {
'x': ArrayVariable('x', owner=None, size=10, device=device),
'y': ArrayVariable('y', owner=None, size=10, device=device),
'z': ArrayVariable('y', owner=None, size=10, device=device),
'b': ArrayVariable('b', owner=None, size=10, dtype=bool,
device=device),
'clip': DEFAULT_FUNCTIONS['clip'],
'inf': DEFAULT_CONSTANTS['inf']
}
statements = [
# examples that should be rewritten
# Note that using our approach, we will never get -= or /= but always
# the equivalent += or *= statements
('x = x + 1.0', 'x += 1.0'),
('x = 2.0 * x', 'x *= 2.0'),
('x = x - 3.0', 'x += -3.0'),
('x = x/2.0', 'x *= 0.5'),
('x = y + (x + 1.0)', 'x += y + 1.0'),
('x = x + x', 'x *= 2.0'),
('x = x + y + z', 'x += y + z'),
('x = x + y + z', 'x += y + z'),
# examples that should not be rewritten
('x = 1.0/x', 'x = 1.0/x'),
('x = 1.0', 'x = 1.0'),
('x = 2.0*(x + 1.0)', 'x = 2.0*(x + 1.0)'),
('x = clip(x + y, 0.0, inf)', 'x = clip(x + y, 0.0, inf)'),
('b = b or False', 'b = b or False')
]
for orig, rewritten in statements:
scalar, vector = make_statements(orig, variables, np.float32)
try: # we augment the assertion error with the original statement
assert len(
scalar
) == 0, 'Did not expect any scalar statements but got ' + str(
scalar)
assert len(
vector
) == 1, 'Did expect a single statement but got ' + str(vector)
statement = vector[0]
expected_var, expected_op, expected_expr, _ = parse_statement(
rewritten)
assert expected_var == statement.var, 'expected write to variable %s, not to %s' % (
expected_var, statement.var)
assert expected_op == statement.op, 'expected operation %s, not %s' % (
expected_op, statement.op)
# Compare the two expressions using sympy to allow for different order etc.
sympy_expected = str_to_sympy(expected_expr)
sympy_actual = str_to_sympy(statement.expr)
assert sympy_expected == sympy_actual, (
'RHS expressions "%s" and "%s" are not identical' %
(sympy_to_str(sympy_expected), sympy_to_str(sympy_actual)))
except AssertionError as ex:
raise AssertionError(
'Transformation for statement "%s" gave an unexpected result: %s'
% (orig, str(ex)))
def test_repeated_subexpressions():
variables = {
'a': Subexpression(name='a', dtype=np.float32,
owner=FakeGroup(variables={}), device=None,
expr='2*z'),
'x': Variable(name='x'),
'y': Variable(name='y'),
'z': Variable(name='z')
}
# subexpression a (referring to z) is used twice, but can be reused the
# second time (no change to z)
code = '''
x = a
y = a
'''
scalar_stmts, vector_stmts = make_statements(code, variables, np.float32)
assert len(scalar_stmts) == 0
assert [stmt.var for stmt in vector_stmts] == ['a', 'x', 'y']
assert vector_stmts[0].constant
code = '''
x = a
z *= 2
'''
scalar_stmts, vector_stmts = make_statements(code, variables, np.float32)
assert len(scalar_stmts) == 0
assert [stmt.var for stmt in vector_stmts] == ['a', 'x', 'z']
# Note that we currently do not mark the subexpression as constant in this
# case, because its use after the "z *=2" line would actually redefine it.
# Our algorithm is currently not smart enough to detect that it is actually
# not used afterwards
# a refers to z, therefore we have to redefine a after z changed, and a
# cannot be constant
code = '''
x = a
z *= 2
y = a
'''
scalar_stmts, vector_stmts = make_statements(code, variables, np.float32)
assert len(scalar_stmts) == 0
assert [stmt.var for stmt in vector_stmts] == ['a', 'x', 'z', 'a', 'y']
assert not any(stmt.constant for stmt in vector_stmts)
def test_automatic_augmented_assignments():
# We test that statements that could be rewritten as augmented assignments
# are correctly rewritten (using sympy to test for symbolic equality)
variables = {
'x': ArrayVariable('x', owner=None, size=10,
device=device),
'y': ArrayVariable('y', owner=None, size=10,
device=device),
'z': ArrayVariable('y', owner=None, size=10,
device=device),
'b': ArrayVariable('b', owner=None, size=10,
dtype=np.bool, device=device),
'clip': DEFAULT_FUNCTIONS['clip'],
'inf': DEFAULT_CONSTANTS['inf']
}
statements = [
# examples that should be rewritten
# Note that using our approach, we will never get -= or /= but always
# the equivalent += or *= statements
('x = x + 1', 'x += 1'),
('x = 2 * x', 'x *= 2'),
('x = x - 3', 'x += -3'),
('x = x/2', 'x *= 0.5'),
('x = y + (x + 1)', 'x += y + 1'),
('x = x + x', 'x *= 2'),
('x = x + y + z', 'x += y + z'),
('x = x + y + z', 'x += y + z'),
# examples that should not be rewritten
('x = 1/x', 'x = 1/x'),
('x = 1', 'x = 1'),
('x = 2*(x + 1)', 'x = 2*(x + 1)'),
('x = clip(x + y, 0, inf)', 'x = clip(x + y, 0, inf)'),
('b = b or False', 'b = b or False')
]
for orig, rewritten in statements:
scalar, vector = make_statements(orig, variables, np.float32)
try: # we augment the assertion error with the original statement
assert len(scalar) == 0, 'Did not expect any scalar statements but got ' + str(scalar)
assert len(vector) == 1, 'Did expect a single statement but got ' + str(vector)
statement = vector[0]
expected_var, expected_op, expected_expr, _ = parse_statement(rewritten)
assert expected_var == statement.var, 'expected write to variable %s, not to %s' % (expected_var, statement.var)
assert expected_op == statement.op, 'expected operation %s, not %s' % (expected_op, statement.op)
# Compare the two expressions using sympy to allow for different order etc.
sympy_expected = str_to_sympy(expected_expr)
sympy_actual = str_to_sympy(statement.expr)
assert sympy_expected == sympy_actual, ('RHS expressions "%s" and "%s" are not identical' % (sympy_to_str(sympy_expected),
sympy_to_str(sympy_actual)))
except AssertionError as ex:
raise AssertionError('Transformation for statement "%s" gave an unexpected result: %s' % (orig, str(ex)))
def check_permutation_code(code):
from collections import defaultdict
vars = get_identifiers(code)
indices = defaultdict(lambda: '_idx')
for var in vars:
if var.endswith('_syn'):
indices[var] = '_idx'
elif var.endswith('_pre'):
indices[var] ='_presynaptic_idx'
elif var.endswith('_post'):
indices[var] = '_postsynaptic_idx'
variables = dict()
for var in indices:
variables[var] = ArrayVariable(var, 1, None, 10, device)
variables['_presynaptic_idx'] = ArrayVariable(var, 1, None, 10, device)
variables['_postsynaptic_idx'] = ArrayVariable(var, 1, None, 10, device)
scalar_statements, vector_statements = make_statements(code, variables, float64)
check_for_order_independence(vector_statements, variables, indices)
def check_permutation_code(code):
from collections import defaultdict
vars = get_identifiers(code)
indices = defaultdict(lambda: '_idx')
for var in vars:
if var.endswith('_syn'):
indices[var] = '_idx'
elif var.endswith('_pre'):
indices[var] = '_presynaptic_idx'
elif var.endswith('_post'):
indices[var] = '_postsynaptic_idx'
variables = dict()
for var in indices:
variables[var] = ArrayVariable(var, 1, None, 10, device)
variables['_presynaptic_idx'] = ArrayVariable(var, 1, None, 10, device)
variables['_postsynaptic_idx'] = ArrayVariable(var, 1, None, 10, device)
scalar_statements, vector_statements = make_statements(
code, variables, float64)
check_for_order_independence(vector_statements, variables, indices)
def translate(self, code, dtype):
"""
Translates an abstract code block into the target language.
"""
scalar_statements = {}
vector_statements = {}
for ac_name, ac_code in code.items():
statements = make_statements(ac_code,
self.variables,
dtype,
optimise=True,
blockname=ac_name)
scalar_statements[ac_name], vector_statements[ac_name] = statements
for vs in vector_statements.values():
# Check that the statements are meaningful independent on the order of
# execution (e.g. for synapses)
try:
if self.has_repeated_indices(
vs
): # only do order dependence if there are repeated indices
check_for_order_independence(vs, self.variables,
self.variable_indices)
except OrderDependenceError:
# If the abstract code is only one line, display it in full
if len(vs) <= 1:
error_msg = f"Abstract code: '{vs[0]}'\n"
else:
error_msg = (
f"{len(vs)} lines of abstract code, first line is: "
f"'{vs[0]}'\n")
logger.warn(
('Came across an abstract code block that may not be '
'well-defined: the outcome may depend on the '
'order of execution. You can ignore this warning if '
'you are sure that the order of operations does not '
'matter. ' + error_msg))
translated = self.translate_statement_sequence(scalar_statements,
vector_statements)
return translated
def test_nested_subexpressions():
'''
This test checks that code translation works with nested subexpressions.
'''
code = '''
x = a + b + c
c = 1
x = a + b + c
d = 1
x = a + b + c
'''
variables = {
'a': Subexpression(name='a', unit=Unit(1), dtype=np.float32, owner=FakeGroup(variables={}), device=None,
expr='b*b+d'),
'b': Subexpression(name='b', unit=Unit(1), dtype=np.float32, owner=FakeGroup(variables={}), device=None,
expr='c*c*c'),
'c': Variable(unit=None, name='c'),
'd': Variable(unit=None, name='d'),
}
stmts = make_statements(code, variables, np.float32)
evalorder = ''.join(stmt.var for stmt in stmts)
# This is the order that variables ought to be evaluated in
assert evalorder=='baxcbaxdax'
from brian2.core.variables import Variable, ArrayVariable
owner = None
code = '''
x = a*b+c
'''
variables = {
'a': ArrayVariable('a', Unit(1), owner, 10, get_device()),
'b': ArrayVariable('b', Unit(1), owner, 10, get_device()),
'x': ArrayVariable('x', Unit(1), owner, 10, get_device()),
}
namespace = {}
variable_indices = {'a': '_idx', 'b': '_idx', 'x': '_idx'}
gen = CythonCodeGenerator(variables,
variable_indices,
owner,
iterate_all=True,
codeobj_class=None)
#print gen.translate_expression('a*b+c')
#print gen.translate_statement(Statement('x', '=', 'a*b+c', '', float))
stmts = make_statements(code, variables, float)
#for stmt in stmts:
# print stmt
print '\n'.join(gen.translate_one_statement_sequence(stmts))
def code_object(self,
owner,
name,
abstract_code,
variables,
template_name,
variable_indices,
codeobj_class=None,
template_kwds=None,
override_conditional_write=None):
if template_kwds == None:
template_kwds = {}
if hasattr(self, 'profile'):
template_kwds['profile'] = self.profile
no_or_const_delay_mode = False
if isinstance(
owner, (SynapticPathway, Synapses)
) and "delay" in owner.variables and owner.variables["delay"].scalar:
# catches Synapses(..., delay=...) syntax, does not catch the case when no delay is specified at all
no_or_const_delay_mode = True
template_kwds["no_or_const_delay_mode"] = no_or_const_delay_mode
if template_name == "synapses":
##################################################################
# This code is copied from CodeGenerator.translate() and CodeGenerator.array_read_write()
# and should give us a set of variables to which will be written in `vector_code`
vector_statements = {}
for ac_name, ac_code in abstract_code.iteritems():
statements = make_statements(ac_code,
variables,
prefs['core.default_float_dtype'],
optimise=True,
blockname=ac_name)
_, vector_statements[ac_name] = statements
write = set()
for statements in vector_statements.itervalues():
for stmt in statements:
write.add(stmt.var)
write = set(varname for varname, var in variables.items()
if isinstance(var, ArrayVariable) and varname in write)
##################################################################
prepost = template_kwds['pathway'].prepost
synaptic_effects = "synapse"
for varname in variables.iterkeys():
if varname in write:
idx = variable_indices[varname]
if (prepost == 'pre' and idx == '_postsynaptic_idx') or (
prepost == 'post' and idx == '_presynaptic_idx'):
# The SynapticPathways 'target' group variables are modified
if synaptic_effects == "synapse":
synaptic_effects = "target"
if (prepost == 'pre' and idx == '_presynaptic_idx') or (
prepost == 'post' and idx == '_postsynaptic_idx'):
# The SynapticPathways 'source' group variables are modified
synaptic_effects = "source"
template_kwds["synaptic_effects"] = synaptic_effects
print('debug syn effect mdoe ', synaptic_effects)
logger.debug(
"Synaptic effects of Synapses object {syn} modify {mod} group variables."
.format(syn=name, mod=synaptic_effects))
if template_name in [
"synapses_create_generator", "synapses_create_array"
]:
if owner.multisynaptic_index is not None:
template_kwds["multisynaptic_idx_var"] = owner.variables[
owner.multisynaptic_index]
codeobj = super(CUDAStandaloneDevice, self).code_object(
owner,
name,
abstract_code,
variables,
template_name,
variable_indices,
codeobj_class=codeobj_class,
template_kwds=template_kwds,
override_conditional_write=override_conditional_write)
return codeobj
def translate(
self, code, dtype
): # TODO: it's not so nice we have to copy the contents of this function..
'''
Translates an abstract code block into the target language.
'''
# first check if user code is not using variables that are also used by GSL
reserved_variables = [
'_dataholder', '_fill_y_vector', '_empty_y_vector',
'_GSL_dataholder', '_GSL_y', '_GSL_func'
]
if any([var in self.variables for var in reserved_variables]):
# import here to avoid circular import
raise ValueError(("The variables %s are reserved for the GSL "
"internal code." % (str(reserved_variables))))
# if the following statements are not added, Brian translates the
# differential expressions in the abstract code for GSL to scalar statements
# in the case no non-scalar variables are used in the expression
diff_vars = self.find_differential_variables(code.values())
self.add_gsl_variables_as_non_scalar(diff_vars)
# add arrays we want to use in generated code before self.generator.translate() so
# brian does namespace unpacking for us
pointer_names = self.add_meta_variables(self.method_options)
scalar_statements = {}
vector_statements = {}
for ac_name, ac_code in code.iteritems():
statements = make_statements(ac_code,
self.variables,
dtype,
optimise=True,
blockname=ac_name)
scalar_statements[ac_name], vector_statements[ac_name] = statements
for vs in vector_statements.itervalues():
# Check that the statements are meaningful independent on the order of
# execution (e.g. for synapses)
try:
if self.has_repeated_indices(
vs
): # only do order dependence if there are repeated indices
check_for_order_independence(
vs, self.generator.variables,
self.generator.variable_indices)
except OrderDependenceError:
# If the abstract code is only one line, display it in ful l
if len(vs) <= 1:
error_msg = 'Abstract code: "%s"\n' % vs[0]
else:
error_msg = (
'%_GSL_driver lines of abstract code, first line is: '
'"%s"\n') % (len(vs), vs[0])
# save function names because self.generator.translate_statement_sequence
# deletes these from self.variables but we need to know which identifiers
# we can safely ignore (i.e. we can ignore the functions because they are
# handled by the original generator)
self.function_names = self.find_function_names()
scalar_code, vector_code, kwds = self.generator.translate_statement_sequence(
scalar_statements, vector_statements)
############ translate code for GSL
# first check if any indexing other than '_idx' is used (currently not supported)
for code_list in scalar_code.values() + vector_code.values():
for code in code_list:
m = re.search('\[(\w+)\]', code)
if m is not None:
if m.group(1) != '0' and m.group(1) != '_idx':
from brian2.stateupdaters.base import UnsupportedEquationsException
raise UnsupportedEquationsException(
("Equations result in state "
"updater code with indexing "
"other than '_idx', which "
"is currently not supported "
"in combination with the "
"GSL stateupdater."))
# differential variable specific operations
to_replace = self.diff_var_to_replace(diff_vars)
GSL_support_code = self.get_dimension_code(len(diff_vars))
GSL_support_code += self.yvector_code(diff_vars)
# analyze all needed variables; if not in self.variables: put in separate dic.
# also keep track of variables needed for scalar statements and vector statements
other_variables = self.find_undefined_variables(
scalar_statements[None] + vector_statements[None])
variables_in_scalar = self.find_used_variables(scalar_statements[None],
other_variables)
variables_in_vector = self.find_used_variables(vector_statements[None],
other_variables)
# so that _dataholder holds diff_vars as well, even if they don't occur
# in the actual statements
for var in diff_vars.keys():
if not var in variables_in_vector:
variables_in_vector[var] = self.variables[var]
# lets keep track of the variables that eventually need to be added to
# the _GSL_dataholder somehow
self.variables_to_be_processed = variables_in_vector.keys()
# add code for _dataholder struct
GSL_support_code = self.write_dataholder(
variables_in_vector) + GSL_support_code
# add e.g. _lio_1 --> _GSL_dataholder._lio_1 to replacer
to_replace.update(
self.to_replace_vector_vars(variables_in_vector,
ignore=diff_vars.keys()))
# write statements that unpack (python) namespace to _dataholder struct
# or local namespace
GSL_main_code = self.unpack_namespace(variables_in_vector,
variables_in_scalar, ['t'])
# rewrite actual calculations described by vector_code and put them in _GSL_func
func_code = self.translate_one_statement_sequence(
vector_statements[None], scalar=False)
GSL_support_code += self.make_function_code(
self.translate_vector_code(func_code, to_replace))
scalar_func_code = self.translate_one_statement_sequence(
scalar_statements[None], scalar=True)
# rewrite scalar code, keep variables that are needed in scalar code normal
# and add variables to _dataholder for vector_code
GSL_main_code += '\n' + self.translate_scalar_code(
scalar_func_code, variables_in_scalar, variables_in_vector)
if len(self.variables_to_be_processed) > 0:
raise AssertionError(
("Not all variables that will be used in the vector "
"code have been added to the _GSL_dataholder. This "
"might mean that the _GSL_func is using unitialized "
"variables."
"\nThe unprocessed variables "
"are: %s" % (str(self.variables_to_be_processed))))
scalar_code['GSL'] = GSL_main_code
kwds['define_GSL_scale_array'] = self.scale_array_code(
diff_vars, self.method_options)
kwds['n_diff_vars'] = len(diff_vars)
kwds['GSL_settings'] = dict(self.method_options)
kwds['GSL_settings']['integrator'] = self.integrator
kwds['support_code_lines'] += GSL_support_code.split('\n')
kwds['t_array'] = self.get_array_name(self.variables['t']) + '[0]'
kwds['dt_array'] = self.get_array_name(self.variables['dt']) + '[0]'
kwds['define_dt'] = 'dt' not in variables_in_scalar
kwds['cpp_standalone'] = self.is_cpp_standalone()
for key, value in pointer_names.items():
kwds[key] = value
return scalar_code, vector_code, kwds
from pylab import *
from brian2 import *
from brian2.codegen.generators.cython_generator import CythonCodeGenerator
from brian2.codegen.statements import Statement
from brian2.codegen.translation import make_statements
from brian2.core.variables import Variable, ArrayVariable
owner = None
code = '''
x = a*b+c
'''
variables = {'a':ArrayVariable('a', Unit(1), owner, 10, get_device()),
'b':ArrayVariable('b', Unit(1), owner, 10, get_device()),
'x':ArrayVariable('x', Unit(1), owner, 10, get_device()),
}
namespace = {}
variable_indices = {'a': '_idx', 'b': '_idx', 'x': '_idx'}
gen = CythonCodeGenerator(variables, variable_indices, owner, iterate_all=True, codeobj_class=None)
#print gen.translate_expression('a*b+c')
#print gen.translate_statement(Statement('x', '=', 'a*b+c', '', float))
stmts = make_statements(code, variables, float)
#for stmt in stmts:
# print stmt
print '\n'.join(gen.translate_one_statement_sequence(stmts))
# expr=statement.expr)
# line = word_substitute(line, subs)
# lines.append(line)
# return '\n'.join(lines)
if __name__ == '__main__':
from brian2.codegen.translation import make_statements
from brian2.core.variables import ArrayVariable
from brian2 import device
from numpy import float64
code = '''
w_syn = v_pre
v_pre += -a_syn # change operator -= or += to see efficient/inefficient code
x_post = y_post
'''
indices = {
'w_syn': '_idx',
'a_syn': '_idx',
'u_pre': '_presynaptic_idx',
'v_pre': '_presynaptic_idx',
'x_post': '_postsynaptic_idx',
'y_post': '_postsynaptic_idx'
}
variables = dict()
for var in indices:
variables[var] = ArrayVariable(var, 1, None, 10, device)
scalar_statements, vector_statements = make_statements(
code, variables, float64)
print vectorise_synapses_code(vector_statements, variables, indices)
def translate(self, code, dtype): # TODO: it's not so nice we have to copy the contents of this function..
'''
Translates an abstract code block into the target language.
'''
# first check if user code is not using variables that are also used by GSL
reserved_variables = ['_dataholder', '_fill_y_vector', '_empty_y_vector',
'_GSL_dataholder', '_GSL_y', '_GSL_func']
if any([var in self.variables for var in reserved_variables]):
# import here to avoid circular import
raise ValueError(("The variables %s are reserved for the GSL "
"internal code."%(str(reserved_variables))))
# if the following statements are not added, Brian translates the
# differential expressions in the abstract code for GSL to scalar statements
# in the case no non-scalar variables are used in the expression
diff_vars = self.find_differential_variables(code.values())
self.add_gsl_variables_as_non_scalar(diff_vars)
# add arrays we want to use in generated code before self.generator.translate() so
# brian does namespace unpacking for us
pointer_names = self.add_meta_variables(self.method_options)
scalar_statements = {}
vector_statements = {}
for ac_name, ac_code in code.iteritems():
statements = make_statements(ac_code,
self.variables,
dtype,
optimise=True,
blockname=ac_name)
scalar_statements[ac_name], vector_statements[ac_name] = statements
for vs in vector_statements.itervalues():
# Check that the statements are meaningful independent on the order of
# execution (e.g. for synapses)
try:
if self.has_repeated_indices(vs): # only do order dependence if there are repeated indices
check_for_order_independence(vs,
self.generator.variables,
self.generator.variable_indices)
except OrderDependenceError:
# If the abstract code is only one line, display it in ful l
if len(vs) <= 1:
error_msg = 'Abstract code: "%s"\n' % vs[0]
else:
error_msg = ('%_GSL_driver lines of abstract code, first line is: '
'"%s"\n') % (len(vs), vs[0])
# save function names because self.generator.translate_statement_sequence
# deletes these from self.variables but we need to know which identifiers
# we can safely ignore (i.e. we can ignore the functions because they are
# handled by the original generator)
self.function_names = self.find_function_names()
scalar_code, vector_code, kwds = self.generator.translate_statement_sequence(scalar_statements,
vector_statements)
############ translate code for GSL
# first check if any indexing other than '_idx' is used (currently not supported)
for code_list in scalar_code.values()+vector_code.values():
for code in code_list:
m = re.search('\[(\w+)\]', code)
if m is not None:
if m.group(1) != '0' and m.group(1) != '_idx':
from brian2.stateupdaters.base import UnsupportedEquationsException
raise UnsupportedEquationsException(("Equations result in state "
"updater code with indexing "
"other than '_idx', which "
"is currently not supported "
"in combination with the "
"GSL stateupdater."))
# differential variable specific operations
to_replace = self.diff_var_to_replace(diff_vars)
GSL_support_code = self.get_dimension_code(len(diff_vars))
GSL_support_code += self.yvector_code(diff_vars)
# analyze all needed variables; if not in self.variables: put in separate dic.
# also keep track of variables needed for scalar statements and vector statements
other_variables = self.find_undefined_variables(scalar_statements[None] +
vector_statements[None])
variables_in_scalar = self.find_used_variables(scalar_statements[None],
other_variables)
variables_in_vector = self.find_used_variables(vector_statements[None],
other_variables)
# so that _dataholder holds diff_vars as well, even if they don't occur
# in the actual statements
for var in diff_vars.keys():
if not var in variables_in_vector:
variables_in_vector[var] = self.variables[var]
# lets keep track of the variables that eventually need to be added to
# the _GSL_dataholder somehow
self.variables_to_be_processed = variables_in_vector.keys()
# add code for _dataholder struct
GSL_support_code = self.write_dataholder(variables_in_vector) + GSL_support_code
# add e.g. _lio_1 --> _GSL_dataholder._lio_1 to replacer
to_replace.update(self.to_replace_vector_vars(variables_in_vector,
ignore=diff_vars.keys()))
# write statements that unpack (python) namespace to _dataholder struct
# or local namespace
GSL_main_code = self.unpack_namespace(variables_in_vector, variables_in_scalar, ['t'])
# rewrite actual calculations described by vector_code and put them in _GSL_func
func_code = self.translate_one_statement_sequence(vector_statements[None],
scalar=False)
GSL_support_code += self.make_function_code(self.translate_vector_code(func_code,
to_replace))
scalar_func_code = self.translate_one_statement_sequence(scalar_statements[None],
scalar=True)
# rewrite scalar code, keep variables that are needed in scalar code normal
# and add variables to _dataholder for vector_code
GSL_main_code += '\n' + self.translate_scalar_code(scalar_func_code,
variables_in_scalar,
variables_in_vector)
if len(self.variables_to_be_processed) > 0:
raise AssertionError(("Not all variables that will be used in the vector "
"code have been added to the _GSL_dataholder. This "
"might mean that the _GSL_func is using unitialized "
"variables."
"\nThe unprocessed variables "
"are: %s" % (str(self.variables_to_be_processed))))
scalar_code['GSL'] = GSL_main_code
kwds['define_GSL_scale_array'] = self.scale_array_code(diff_vars,
self.method_options)
kwds['n_diff_vars'] = len(diff_vars)
kwds['GSL_settings'] = dict(self.method_options)
kwds['GSL_settings']['integrator'] = self.integrator
kwds['support_code_lines'] += GSL_support_code.split('\n')
kwds['t_array'] = self.get_array_name(self.variables['t']) + '[0]'
kwds['dt_array'] = self.get_array_name(self.variables['dt']) + '[0]'
kwds['define_dt'] = 'dt' not in variables_in_scalar
kwds['cpp_standalone'] = self.is_cpp_standalone()
for key, value in pointer_names.items():
kwds[key] = value
return scalar_code, vector_code, kwds
from codeprint import codeprint
abstract = """
V += w
"""
specifiers = {
"V": ArrayVariable("_array_V", "_postsynaptic_idx", float64),
"w": ArrayVariable("_array_w", "_synapse_idx", float64),
"_spiking_synapse_idx": Index(),
"_postsynaptic_idx": Index(all=False),
"_synapse_idx": Index(all=False),
"_presynaptic_idx": Index(all=False),
}
intermediate = make_statements(abstract, specifiers, float64)
print "ABSTRACT CODE:"
print abstract
print "INTERMEDIATE STATEMENTS:"
print
for stmt in intermediate:
print stmt
print
for lang in [PythonLanguage(), CPPLanguage()]:
innercode = translate(abstract, specifiers, float64, lang)
code = lang.apply_template(innercode, lang.template_synapses())
print lang.__class__.__name__
print "=" * len(lang.__class__.__name__)
codeprint(code)
from codeprint import codeprint
test_compile = True
do_plot = True
tau = 10 * ms # external variable
eqs = '''
dV/dt = (-V + I + J)/tau : 1
dI/dt = -I/tau : 1
J = V * 0.1 : 1
'''
from brian2.stateupdaters.integration import euler, rk2, rk4
G = NeuronGroup(1, eqs, method=rk4)
intermediate = make_statements(G.abstract_code, G.specifiers, float64)
print 'EQUATIONS:'
print eqs
print 'ABSTRACT CODE:'
print G.abstract_code
print 'INTERMEDIATE STATEMENTS:'
print
for stmt in intermediate:
print stmt
print
def getlang(cls, *args, **kwds):
try:
return cls(*args, **kwds)
except Exception as e:
# subs[var] = '{var}[{idx}]'.format(var=var, idx=idx)
# for statement in statements:
# line = ' {var} {op} {expr}'.format(var=statement.var, op=statement.op,
# expr=statement.expr)
# line = word_substitute(line, subs)
# lines.append(line)
# return '\n'.join(lines)
if __name__=='__main__':
from brian2.codegen.translation import make_statements
from brian2.core.variables import ArrayVariable
from brian2 import device
from numpy import float64
code = '''
w_syn = v_pre
v_pre += -a_syn # change operator -= or += to see efficient/inefficient code
x_post = y_post
'''
indices = {'w_syn': '_idx',
'a_syn': '_idx',
'u_pre': '_presynaptic_idx',
'v_pre': '_presynaptic_idx',
'x_post': '_postsynaptic_idx',
'y_post': '_postsynaptic_idx'}
variables = dict()
for var in indices:
variables[var] = ArrayVariable(var, 1, None, 10, device)
scalar_statements, vector_statements = make_statements(code, variables, float64)
print vectorise_synapses_code(vector_statements, variables, indices)