def codeprint(code):
if isinstance(code, str):
print deindent(code)
else:
for k, v in code.items():
print k+':'
print indent(deindent(v))
def code_object(self, owner, name, abstract_code, variables, template_name,
variable_indices, codeobj_class=None,
template_kwds=None, override_conditional_write=None,
compiler_kwds=None):
if compiler_kwds is None:
compiler_kwds = {}
name = find_name(name)
codeobj_class = self.code_object_class(codeobj_class)
template = getattr(codeobj_class.templater, template_name)
iterate_all = template.iterate_all
generator = codeobj_class.generator_class(variables=variables,
variable_indices=variable_indices,
owner=owner,
iterate_all=iterate_all,
codeobj_class=codeobj_class,
override_conditional_write=override_conditional_write,
allows_scalar_write=template.allows_scalar_write,
name=name,
template_name=template_name)
if template_kwds is None:
template_kwds = dict()
else:
template_kwds = template_kwds.copy()
logger.diagnostic('%s abstract code:\n%s' % (name, indent(code_representation(abstract_code))))
scalar_code, vector_code, kwds = generator.translate(abstract_code,
dtype=prefs['core.default_float_dtype'])
# Add the array names as keywords as well
for varname, var in variables.items():
if isinstance(var, ArrayVariable):
pointer_name = generator.get_array_name(var)
if var.scalar:
pointer_name += '[0]'
template_kwds[varname] = pointer_name
if hasattr(var, 'resize'):
dyn_array_name = generator.get_array_name(var,
access_data=False)
template_kwds['_dynamic_'+varname] = dyn_array_name
template_kwds.update(kwds)
logger.diagnostic('%s snippet (scalar):\n%s' % (name, indent(code_representation(scalar_code))))
logger.diagnostic('%s snippet (vector):\n%s' % (name, indent(code_representation(vector_code))))
code = template(scalar_code, vector_code,
owner=owner, variables=variables, codeobj_name=name,
variable_indices=variable_indices,
get_array_name=generator.get_array_name,
**template_kwds)
logger.diagnostic('%s code:\n%s' % (name, indent(code_representation(code))))
codeobj = codeobj_class(owner, code, variables, variable_indices,
template_name=template_name,
template_source=template.template_source,
name=name, compiler_kwds=compiler_kwds)
codeobj.compile()
return codeobj
def code_object(self, owner, name, abstract_code, variables, template_name,
variable_indices, codeobj_class=None,
template_kwds=None, override_conditional_write=None,
compiler_kwds=None):
if compiler_kwds is None:
compiler_kwds = {}
name = find_name(name)
codeobj_class = self.code_object_class(codeobj_class)
template = getattr(codeobj_class.templater, template_name)
iterate_all = template.iterate_all
generator = codeobj_class.generator_class(variables=variables,
variable_indices=variable_indices,
owner=owner,
iterate_all=iterate_all,
codeobj_class=codeobj_class,
override_conditional_write=override_conditional_write,
allows_scalar_write=template.allows_scalar_write,
name=name,
template_name=template_name)
if template_kwds is None:
template_kwds = dict()
else:
template_kwds = template_kwds.copy()
logger.diagnostic('%s abstract code:\n%s' % (name, indent(code_representation(abstract_code))))
scalar_code, vector_code, kwds = generator.translate(abstract_code,
dtype=prefs['core.default_float_dtype'])
# Add the array names as keywords as well
for varname, var in variables.iteritems():
if isinstance(var, ArrayVariable):
pointer_name = generator.get_array_name(var)
if var.scalar:
pointer_name += '[0]'
template_kwds[varname] = pointer_name
if hasattr(var, 'resize'):
dyn_array_name = generator.get_array_name(var,
access_data=False)
template_kwds['_dynamic_'+varname] = dyn_array_name
template_kwds.update(kwds)
logger.diagnostic('%s snippet (scalar):\n%s' % (name, indent(code_representation(scalar_code))))
logger.diagnostic('%s snippet (vector):\n%s' % (name, indent(code_representation(vector_code))))
code = template(scalar_code, vector_code,
owner=owner, variables=variables, codeobj_name=name,
variable_indices=variable_indices,
get_array_name=generator.get_array_name,
**template_kwds)
logger.diagnostic('%s code:\n%s' % (name, indent(code_representation(code))))
codeobj = codeobj_class(owner, code, variables, variable_indices,
template_name=template_name,
template_source=template.template_source,
name=name, compiler_kwds=compiler_kwds)
codeobj.compile()
return codeobj
def vectorise_code(self, statements, variables, variable_indices, index='_idx'):
# We treat every statement individually with its own read and write code
# to be on the safe side
lines = []
created_vars = {stmt.var for stmt in statements if stmt.op == ':='}
for statement in statements:
lines.append('# Abstract code: {var} {op} {expr}'.format(var=statement.var,
op=statement.op,
expr=statement.expr))
read, write, indices, conditional_write_vars = self.arrays_helper([statement])
try:
# We make sure that we only add code to `lines` after it went
# through completely
ufunc_lines = []
# No need to load a variable if it is only in read because of
# the in-place operation
if (statement.inplace and
variable_indices[statement.var] != '_idx' and
statement.var not in get_identifiers(statement.expr)):
read = read - {statement.var}
ufunc_lines.extend(self.read_arrays(read, write, indices,
variables, variable_indices))
ufunc_lines.append(self.ufunc_at_vectorisation(statement,
variables,
variable_indices,
conditional_write_vars,
created_vars,
index=index))
# Do not write back such values, the ufuncs have modified the
# underlying array already
if statement.inplace and variable_indices[statement.var] != '_idx':
write = write - {statement.var}
ufunc_lines.extend(self.write_arrays([statement], read, write,
variables,
variable_indices))
lines.extend(ufunc_lines)
except VectorisationError:
logger.warn("Failed to vectorise synapses code, falling back on Python loop: note that "
"this will be very slow! Switch to another code generation target for "
"best performance (e.g. cython or weave).",
once=True)
lines.extend(['_full_idx = _idx',
'for _idx in _full_idx:'])
lines.extend(indent(code) for code in
self.read_arrays(read, write, indices,
variables, variable_indices))
line = self.translate_statement(statement)
line = self.conditional_write(line, statement, variables,
conditional_write_vars,
created_vars)
lines.append(indent(line))
lines.extend(indent(code) for code in
self.write_arrays(statements, read, write,
variables, variable_indices))
lines.append('_idx = _full_idx')
return lines
def translate_one_statement_sequence(self, statements, scalar=False):
variables = self.variables
variable_indices = self.variable_indices
read, write, indices, conditional_write_vars = self.arrays_helper(statements)
lines = []
# index and read arrays (index arrays first)
for varname in itertools.chain(indices, read):
var = variables[varname]
index = variable_indices[varname]
line = '{varname} = {arrayname}[{index}]'.format(varname=varname, arrayname=self.get_array_name(var),
index=index)
lines.append(line)
# the actual code
created_vars = set([])
for stmt in statements:
if stmt.op==':=':
created_vars.add(stmt.var)
line = self.translate_statement(stmt)
if stmt.var in conditional_write_vars:
subs = {}
condvar = conditional_write_vars[stmt.var]
lines.append('if %s:' % condvar)
lines.append(indent(line))
else:
lines.append(line)
# write arrays
for varname in write:
index_var = self.variable_indices[varname]
var = self.variables[varname]
line = self.get_array_name(var, self.variables) + '[' + index_var + '] = ' + varname
lines.append(line)
return lines
def translate_one_statement_sequence(self, statements, scalar=False):
variables = self.variables
variable_indices = self.variable_indices
read, write, indices, conditional_write_vars = self.arrays_helper(statements)
lines = []
# index and read arrays (index arrays first)
for varname in itertools.chain(indices, read):
var = variables[varname]
index = variable_indices[varname]
line = '{varname} = {arrayname}[{index}]'.format(varname=varname, arrayname=self.get_array_name(var),
index=index)
lines.append(line)
# the actual code
for stmt in statements:
if stmt.op == ':=' and not stmt.var in variables:
self.temporary_vars.add((stmt.var, stmt.dtype))
line = self.translate_statement(stmt)
if stmt.var in conditional_write_vars:
subs = {}
condvar = conditional_write_vars[stmt.var]
lines.append('if %s:' % condvar)
lines.append(indent(line))
else:
lines.append(line)
# write arrays
for varname in write:
index_var = self.variable_indices[varname]
var = self.variables[varname]
line = self.get_array_name(var, self.variables) + '[' + index_var + '] = ' + varname
lines.append(line)
return lines
def numerically_check_permutation_code(code):
# numerically checks that a code block used in the test below is permutation-independent by creating a
# presynaptic and postsynaptic group of 3 neurons each, and a full connectivity matrix between them, then
# repeatedly filling in random values for each of the variables, and checking for several random shuffles of
# the synapse order that the result doesn't depend on it. This is a sort of test of the test itself, to make
# sure we didn't accidentally assign a good/bad example to the wrong class.
code = deindent(code)
from collections import defaultdict
vars = get_identifiers(code)
indices = defaultdict(lambda: '_idx')
vals = {}
for var in vars:
if var.endswith('_syn'):
indices[var] = '_idx'
vals[var] = zeros(9)
elif var.endswith('_pre'):
indices[var] ='_presynaptic_idx'
vals[var] = zeros(3)
elif var.endswith('_post'):
indices[var] = '_postsynaptic_idx'
vals[var] = zeros(3)
subs = dict((var, var+'['+idx+']') for var, idx in indices.iteritems())
code = word_substitute(code, subs)
code = '''
from numpy import *
from numpy.random import rand, randn
for _idx in shuffled_indices:
_presynaptic_idx = presyn[_idx]
_postsynaptic_idx = postsyn[_idx]
{code}
'''.format(code=indent(code))
ns = vals.copy()
ns['shuffled_indices'] = arange(9)
ns['presyn'] = arange(9)%3
ns['postsyn'] = arange(9)/3
for _ in xrange(10):
origvals = {}
for k, v in vals.iteritems():
v[:] = randn(len(v))
origvals[k] = v.copy()
exec code in ns
endvals = {}
for k, v in vals.iteritems():
endvals[k] = v.copy()
for _ in xrange(10):
for k, v in vals.iteritems():
v[:] = origvals[k]
shuffle(ns['shuffled_indices'])
exec code in ns
for k, v in vals.iteritems():
try:
assert_allclose(v, endvals[k])
except AssertionError:
raise OrderDependenceError()
def _get_documentation(self):
s = ''
for name in sorted(self._values.keys()):
default = self._default_values[name]
doc = str(self._docs[name])
# Make a link target
s += '.. _brian-pref-{name}:\n\n'.format(name=name.replace('_', '-'))
s += '``{name}`` = ``{default}``\n'.format(name=name,
default=repr(default))
s += indent(deindent(doc))
s += '\n\n'
return s
def translate_to_statements(self, statements, conditional_write_vars):
lines = []
for stmt in statements:
if stmt.op == ':=' and not stmt.var in self.variables:
self.temporary_vars.add((stmt.var, stmt.dtype))
line = self.translate_statement(stmt)
if stmt.var in conditional_write_vars:
subs = {}
condvar = conditional_write_vars[stmt.var]
lines.append('if %s:' % condvar)
lines.append(indent(line))
else:
lines.append(line)
return lines
def translate_to_statements(self, statements, conditional_write_vars):
lines = []
for stmt in statements:
if stmt.op == ':=' and not stmt.var in self.variables:
self.temporary_vars.add((stmt.var, stmt.dtype))
line = self.translate_statement(stmt)
if stmt.var in conditional_write_vars:
subs = {}
condvar = conditional_write_vars[stmt.var]
lines.append(f'if {condvar}:')
lines.append(indent(line))
else:
lines.append(line)
return lines
def _get_one_documentation(self, basename, link_targets):
'''
Document a single category of preferences.
'''
s = ''
if not basename in self.pref_register:
raise ValueError('No preferences under the name "%s" are registered' % basename)
prefdefs, basedoc = self.pref_register[basename]
s += deindent(basedoc, docstring=True).strip() + '\n\n'
for name in sorted(prefdefs.keys()):
pref = prefdefs[name]
name = basename + '.' + name
linkname = name.replace('_', '-').replace('.', '-')
if link_targets:
# Make a link target
s += '.. _brian-pref-{name}:\n\n'.format(name=linkname)
s += '``{name}`` = ``{default}``\n'.format(name=name,
default=pref.representor(pref.default))
s += indent(deindent(pref.docs, docstring=True))
s += '\n\n'
return s
def _get_one_documentation(self, basename, link_targets):
'''
Document a single category of preferences.
'''
s = ''
if not basename in self.pref_register:
raise ValueError('No preferences under the name "%s" are registered' % basename)
prefdefs, basedoc = self.pref_register[basename]
s += deindent(basedoc, docstring=True).strip() + '\n\n'
for name in sorted(prefdefs.keys()):
pref = prefdefs[name]
name = basename + '.' + name
linkname = name.replace('_', '-').replace('.', '-')
if link_targets:
# Make a link target
s += '.. _brian-pref-{name}:\n\n'.format(name=linkname)
s += '``{name}`` = ``{default}``\n'.format(name=name,
default=pref.representor(pref.default))
s += indent(deindent(pref.docs, docstring=True))
s += '\n\n'
return s
def exceptions(self):
exc_list = []
for configuration in self.configurations:
curconfig = []
for ft in self.feature_tests:
sym, txt, exc, tb = self.full_results[configuration.name,
ft.fullname()]
if tb is not None:
curconfig.append((ft.fullname(), tb))
if len(curconfig):
exc_list.append((configuration.name, curconfig))
if len(exc_list)==0:
return ''
r = ''
s = 'Exceptions'
r += s+'\n'+'-'*len(s)+'\n\n'
for config_name, curconfig in exc_list:
s = config_name
r += s+'\n'+'^'*len(s)+'\n\n'
for name, tb in curconfig:
r += name+'::\n\n'+indent(tb)+'\n\n'
return r
def exceptions(self):
exc_list = []
for configuration in self.configurations:
curconfig = []
for ft in self.feature_tests:
sym, txt, exc, tb, runtime, prof_info = self.full_results[
configuration.name, ft.fullname()]
if tb is not None:
curconfig.append((ft.fullname(), tb))
if len(curconfig):
exc_list.append((configuration.name, curconfig))
if len(exc_list) == 0:
return ''
r = ''
s = 'Exceptions'
r += s + '\n' + '-' * len(s) + '\n\n'
for config_name, curconfig in exc_list:
s = config_name
r += s + '\n' + '^' * len(s) + '\n\n'
for name, tb in curconfig:
r += name + '::\n\n' + indent(tb) + '\n\n'
return r
def _get_one_documentation(self, basename, link_targets):
"""
Document a single category of preferences.
"""
s = ''
if not basename in self.pref_register:
raise ValueError(
f"No preferences under the name '{basename}' are registered")
prefdefs, basedoc = self.pref_register[basename]
s += deindent(basedoc, docstring=True).strip() + '\n\n'
for name in sorted(prefdefs.keys()):
pref = prefdefs[name]
name = basename + '.' + name
linkname = name.replace('_', '-').replace('.', '-')
if link_targets:
# Make a link target
s += f".. _brian-pref-{linkname}:\n\n"
s += f"``{name}`` = ``{pref.representor(pref.default)}``\n"
s += indent(deindent(pref.docs, docstring=True))
s += "\n\n"
return s
def apply_code_template(code, template, placeholder='%CODE%'):
'''
Inserts the string ``code`` into ``template`` at ``placeholder``.
The ``code`` is deindented, and inserted into ``template`` with the
indentation level at the place where ``placeholder`` appears. The
placeholder should appear on its own line.
All tab characters are replaced by four spaces.
'''
code = deindent(code)
code = strip_empty_lines(code)
template = template.replace('\t', ' '*4)
lines = template.split('\n')
newlines = []
for line in lines:
if placeholder in line:
indentlevel = len(line)-len(line.lstrip())
newlines.append(indent(code, indentlevel, tab=' '))
else:
newlines.append(line)
return '\n'.join(newlines)
def code_object(self, owner, name, abstract_code, variables, template_name,
variable_indices, codeobj_class=None,
template_kwds=None, override_conditional_write=None):
codeobj_class = self.code_object_class(codeobj_class)
template = getattr(codeobj_class.templater, template_name)
iterate_all = template.iterate_all
generator = codeobj_class.generator_class(variables=variables,
variable_indices=variable_indices,
owner=owner,
iterate_all=iterate_all,
codeobj_class=codeobj_class,
override_conditional_write=override_conditional_write,
allows_scalar_write=template.allows_scalar_write,
name=name,
template_name=template_name)
if template_kwds is None:
template_kwds = dict()
else:
template_kwds = template_kwds.copy()
# Check that all functions are available
for varname, value in variables.iteritems():
if isinstance(value, Function):
try:
value.implementations[codeobj_class]
except KeyError as ex:
# if we are dealing with numpy, add the default implementation
if codeobj_class is NumpyCodeObject:
value.implementations.add_numpy_implementation(value.pyfunc)
else:
raise NotImplementedError(('Cannot use function '
'%s: %s') % (varname, ex))
logger.diagnostic('%s abstract code:\n%s' % (name, indent(code_representation(abstract_code))))
scalar_code, vector_code, kwds = generator.translate(abstract_code,
dtype=prefs['core.default_float_dtype'])
# Add the array names as keywords as well
for varname, var in variables.iteritems():
if isinstance(var, ArrayVariable):
pointer_name = generator.get_array_name(var)
if var.scalar:
pointer_name += '[0]'
template_kwds[varname] = pointer_name
if hasattr(var, 'resize'):
dyn_array_name = generator.get_array_name(var,
access_data=False)
template_kwds['_dynamic_'+varname] = dyn_array_name
template_kwds.update(kwds)
logger.diagnostic('%s snippet (scalar):\n%s' % (name, indent(code_representation(scalar_code))))
logger.diagnostic('%s snippet (vector):\n%s' % (name, indent(code_representation(vector_code))))
name = find_name(name)
code = template(scalar_code, vector_code,
owner=owner, variables=variables, codeobj_name=name,
variable_indices=variable_indices,
get_array_name=generator.get_array_name,
**template_kwds)
logger.diagnostic('%s code:\n%s' % (name, indent(code_representation(code))))
codeobj = codeobj_class(owner, code, variables, variable_indices,
template_name=template_name,
template_source=template.template_source,
name=name)
codeobj.compile()
return codeobj
def vectorise_code(self,
statements,
variables,
variable_indices,
index='_idx'):
created_vars = {stmt.var for stmt in statements if stmt.op == ':='}
try:
lines = []
used_variables = set()
for statement in statements:
lines.append('# Abstract code: {var} {op} {expr}'.format(
var=statement.var, op=statement.op, expr=statement.expr))
# We treat every statement individually with its own read and write code
# to be on the safe side
read, write, indices, conditional_write_vars = self.arrays_helper(
[statement])
# We make sure that we only add code to `lines` after it went
# through completely
ufunc_lines = []
# No need to load a variable if it is only in read because of
# the in-place operation
if (statement.inplace
and variable_indices[statement.var] != '_idx' and
statement.var not in get_identifiers(statement.expr)):
read = read - {statement.var}
ufunc_lines.extend(
self.read_arrays(read, write, indices, variables,
variable_indices))
ufunc_lines.append(
self.ufunc_at_vectorisation(
statement,
variables,
variable_indices,
conditional_write_vars,
created_vars,
used_variables,
))
# Do not write back such values, the ufuncs have modified the
# underlying array already
if statement.inplace and variable_indices[
statement.var] != '_idx':
write = write - {statement.var}
ufunc_lines.extend(
self.write_arrays([statement], read, write, variables,
variable_indices))
lines.extend(ufunc_lines)
except VectorisationError:
if self._use_ufunc_at_vectorisation:
logger.info(
"Failed to vectorise code, falling back on Python loop: note that "
"this will be very slow! Switch to another code generation target for "
"best performance (e.g. cython). First line is: " +
str(statements[0]),
once=True)
lines = []
lines.extend([
'_full_idx = _idx', 'for _idx in _full_idx:',
' _vectorisation_idx = _idx'
])
read, write, indices, conditional_write_vars = self.arrays_helper(
statements)
lines.extend(
indent(code) for code in self.read_arrays(
read, write, indices, variables, variable_indices))
for statement in statements:
line = self.translate_statement(statement)
if statement.var in conditional_write_vars:
lines.append(
indent('if {}:'.format(
conditional_write_vars[statement.var])))
lines.append(indent(line, 2))
else:
lines.append(indent(line))
lines.extend(
indent(code) for code in self.write_arrays(
statements, read, write, variables, variable_indices))
return lines
code = '''
_tmp_V = x
V += _tmp_V*x*dt
'''
specifiers = {
'V':ArrayVariable('_array_V', '_neuron_idx', float64),
'I':ArrayVariable('_array_I', '_neuron_idx', float64),
'x':Subexpression('-(V+I)/tau'),
'tau':Value(float64),
'dt':Value(float64),
'_cond':OutputVariable(bool),
#'_neuron_idx':Index(),
'_neuron_idx':Index(all=False),
}
for lang in [
CLanguage(),
PythonLanguage(),
NumexprPythonLanguage()
]:
print lang.__class__.__name__
print '='*len(lang.__class__.__name__)
output = translate(code, specifiers, float64, lang)
print 'OUTPUT CODE:'
if isinstance(output, str):
print indent(output)
else:
for k, v in output.items():
print k+':'
print indent(v)
print
def create_runner_codeobj(
group,
code,
template_name,
variable_indices=None,
name=None,
check_units=True,
needed_variables=None,
additional_variables=None,
level=0,
run_namespace=None,
template_kwds=None,
override_conditional_write=None,
):
''' Create a `CodeObject` for the execution of code in the context of a
`Group`.
Parameters
----------
group : `Group`
The group where the code is to be run
code : str or dict of str
The code to be executed.
template_name : str
The name of the template to use for the code.
variable_indices : dict-like, optional
A mapping from `Variable` objects to index names (strings). If none is
given, uses the corresponding attribute of `group`.
name : str, optional
A name for this code object, will use ``group + '_codeobject*'`` if
none is given.
check_units : bool, optional
Whether to check units in the statement. Defaults to ``True``.
needed_variables: list of str, optional
A list of variables that are neither present in the abstract code, nor
in the ``USES_VARIABLES`` statement in the template. This is only
rarely necessary, an example being a `StateMonitor` where the
names of the variables are neither known to the template nor included
in the abstract code statements.
additional_variables : dict-like, optional
A mapping of names to `Variable` objects, used in addition to the
variables saved in `group`.
level : int, optional
How far to go up in the stack to find the call frame.
run_namespace : dict-like, optional
An additional namespace that is used for variable lookup (if not
defined, the implicit namespace of local variables is used).
template_kwds : dict, optional
A dictionary of additional information that is passed to the template.
override_conditional_write: list of str, optional
A list of variable names which are used as conditions (e.g. for
refractoriness) which should be ignored.
'''
if isinstance(code, str):
code = {None: code}
msg = 'Creating code object (group=%s, template name=%s) for abstract code:\n' % (
group.name, template_name)
msg += indent(code_representation(code))
logger.debug(msg)
from brian2.devices import get_device
device = get_device()
if override_conditional_write is None:
override_conditional_write = set([])
else:
override_conditional_write = set(override_conditional_write)
if check_units:
for c in code.values():
check_code_units(c,
group,
additional_variables=additional_variables,
level=level + 1,
run_namespace=run_namespace)
codeobj_class = device.code_object_class(group.codeobj_class)
template = getattr(codeobj_class.templater, template_name)
all_variables = dict(group.variables)
if additional_variables is not None:
all_variables.update(additional_variables)
# Determine the identifiers that were used
used_known = set()
unknown = set()
for v in code.values():
_, uk, u = analyse_identifiers(v, all_variables, recursive=True)
used_known |= uk
unknown |= u
logger.debug('Unknown identifiers in the abstract code: ' +
', '.join(unknown))
# Only pass the variables that are actually used
variables = group.resolve_all(used_known | unknown,
additional_variables=additional_variables,
run_namespace=run_namespace,
level=level + 1)
conditional_write_variables = {}
# Add all the "conditional write" variables
for var in variables.itervalues():
cond_write_var = getattr(var, 'conditional_write', None)
if cond_write_var in override_conditional_write:
continue
if cond_write_var is not None and cond_write_var not in variables.values(
):
if cond_write_var.name in variables:
raise AssertionError(
('Variable "%s" is needed for the '
'conditional write mechanism of variable '
'"%s". Its name is already used for %r.') %
(cond_write_var.name, var.name,
variables[cond_write_var.name]))
conditional_write_variables[cond_write_var.name] = cond_write_var
variables.update(conditional_write_variables)
# Add variables that are not in the abstract code, nor specified in the
# template but nevertheless necessary
if needed_variables is None:
needed_variables = []
# Also add the variables that the template needs
variables.update(
group.resolve_all(
set(needed_variables) | set(template.variables),
additional_variables=additional_variables,
run_namespace=run_namespace,
level=level + 1,
do_warn=False)) # no warnings for internally used variables
if name is None:
if group is not None:
name = '%s_%s_codeobject*' % (group.name, template_name)
else:
name = '%s_codeobject*' % template_name
all_variable_indices = copy.copy(group.variables.indices)
if additional_variables is not None:
all_variable_indices.update(additional_variables.indices)
if variable_indices is not None:
all_variable_indices.update(variable_indices)
# Make "conditional write" variables use the same index as the variable
# that depends on them
for varname, var in variables.iteritems():
cond_write_var = getattr(var, 'conditional_write', None)
if cond_write_var is not None:
all_variable_indices[
cond_write_var.name] = all_variable_indices[varname]
# Add the indices needed by the variables
varnames = variables.keys()
for varname in varnames:
var_index = all_variable_indices[varname]
if not var_index in ('_idx', '0'):
variables[var_index] = all_variables[var_index]
return device.code_object(
owner=group,
name=name,
abstract_code=code,
variables=variables,
template_name=template_name,
variable_indices=all_variable_indices,
template_kwds=template_kwds,
codeobj_class=group.codeobj_class,
override_conditional_write=override_conditional_write,
)
def __str__(self):
s = 'def %s(%s):\n%s\n return %s\n' % (self.name,
', '.join(self.args),
indent(self.code),
self.return_expr)
return s
def create_runner_codeobj(group, code, template_name,
user_code=None,
variable_indices=None,
name=None, check_units=True,
needed_variables=None,
additional_variables=None,
level=0,
run_namespace=None,
template_kwds=None,
override_conditional_write=None,
codeobj_class=None
):
''' Create a `CodeObject` for the execution of code in the context of a
`Group`.
Parameters
----------
group : `Group`
The group where the code is to be run
code : str or dict of str
The code to be executed.
template_name : str
The name of the template to use for the code.
user_code : str, optional
The code that had been specified by the user before other code was
added automatically. If not specified, will be assumed to be identical
to ``code``.
variable_indices : dict-like, optional
A mapping from `Variable` objects to index names (strings). If none is
given, uses the corresponding attribute of `group`.
name : str, optional
A name for this code object, will use ``group + '_codeobject*'`` if
none is given.
check_units : bool, optional
Whether to check units in the statement. Defaults to ``True``.
needed_variables: list of str, optional
A list of variables that are neither present in the abstract code, nor
in the ``USES_VARIABLES`` statement in the template. This is only
rarely necessary, an example being a `StateMonitor` where the
names of the variables are neither known to the template nor included
in the abstract code statements.
additional_variables : dict-like, optional
A mapping of names to `Variable` objects, used in addition to the
variables saved in `group`.
level : int, optional
How far to go up in the stack to find the call frame.
run_namespace : dict-like, optional
An additional namespace that is used for variable lookup (if not
defined, the implicit namespace of local variables is used).
template_kwds : dict, optional
A dictionary of additional information that is passed to the template.
override_conditional_write: list of str, optional
A list of variable names which are used as conditions (e.g. for
refractoriness) which should be ignored.
codeobj_class : class, optional
The `CodeObject` class to run code with. If not specified, defaults to
the `group`'s ``codeobj_class`` attribute.
'''
if name is None:
if group is not None:
name = '%s_%s_codeobject*' % (group.name, template_name)
else:
name = '%s_codeobject*' % template_name
if user_code is None:
user_code = code
if isinstance(code, str):
code = {None: code}
user_code = {None: user_code}
msg = 'Creating code object (group=%s, template name=%s) for abstract code:\n' % (group.name, template_name)
msg += indent(code_representation(code))
logger.debug(msg)
from brian2.devices import get_device
device = get_device()
if override_conditional_write is None:
override_conditional_write = set([])
else:
override_conditional_write = set(override_conditional_write)
if check_units:
for c in code.values():
# This is the first time that the code is parsed, catch errors
try:
check_code_units(c, group,
additional_variables=additional_variables,
level=level+1,
run_namespace=run_namespace)
except (SyntaxError, KeyError, ValueError) as ex:
error_msg = _error_msg(c, name)
raise ValueError(error_msg + str(ex))
if codeobj_class is None:
codeobj_class = device.code_object_class(group.codeobj_class)
else:
codeobj_class = device.code_object_class(codeobj_class)
template = getattr(codeobj_class.templater, template_name, None)
if template is None:
codeobj_class_name = codeobj_class.class_name or codeobj_class.__name__
raise AttributeError(('"%s" does not provide a code generation '
'template "%s"') % (codeobj_class_name,
template_name))
all_variables = dict(group.variables)
if additional_variables is not None:
all_variables.update(additional_variables)
# Determine the identifiers that were used
identifiers = set()
user_identifiers = set()
for v, u_v in zip(code.values(), user_code.values()):
_, uk, u = analyse_identifiers(v, all_variables, recursive=True)
identifiers |= uk | u
_, uk, u = analyse_identifiers(u_v, all_variables, recursive=True)
user_identifiers |= uk | u
# Only pass the variables that are actually used
variables = group.resolve_all(identifiers,
user_identifiers,
additional_variables=additional_variables,
run_namespace=run_namespace,
level=level+1)
conditional_write_variables = {}
# Add all the "conditional write" variables
for var in variables.itervalues():
cond_write_var = getattr(var, 'conditional_write', None)
if cond_write_var in override_conditional_write:
continue
if cond_write_var is not None and cond_write_var not in variables.values():
if cond_write_var.name in variables:
raise AssertionError(('Variable "%s" is needed for the '
'conditional write mechanism of variable '
'"%s". Its name is already used for %r.') % (cond_write_var.name,
var.name,
variables[cond_write_var.name]))
conditional_write_variables[cond_write_var.name] = cond_write_var
variables.update(conditional_write_variables)
# Add variables that are not in the abstract code, nor specified in the
# template but nevertheless necessary
if needed_variables is None:
needed_variables = []
# Also add the variables that the template needs
variables.update(group.resolve_all(set(needed_variables) | set(template.variables),
# template variables are not known to the user:
user_identifiers=set(),
additional_variables=additional_variables,
run_namespace=run_namespace,
level=level+1))
all_variable_indices = copy.copy(group.variables.indices)
if additional_variables is not None:
all_variable_indices.update(additional_variables.indices)
if variable_indices is not None:
all_variable_indices.update(variable_indices)
# Make "conditional write" variables use the same index as the variable
# that depends on them
for varname, var in variables.iteritems():
cond_write_var = getattr(var, 'conditional_write', None)
if cond_write_var is not None:
all_variable_indices[cond_write_var.name] = all_variable_indices[varname]
# Add the indices needed by the variables
varnames = variables.keys()
for varname in varnames:
var_index = all_variable_indices[varname]
if not var_index in ('_idx', '0'):
variables[var_index] = all_variables[var_index]
return device.code_object(owner=group,
name=name,
abstract_code=code,
variables=variables,
template_name=template_name,
variable_indices=all_variable_indices,
template_kwds=template_kwds,
codeobj_class=codeobj_class,
override_conditional_write=override_conditional_write,
)
def __str__(self):
s = ''
for k, v in self._templates.items():
s += k+':\n'
s += strip_empty_lines(indent(v))+'\n'
return s
def __str__(self):
s = 'def %s(%s):\n%s\n return %s\n' % (self.name,
', '.join(self.args),
indent(self.code),
self.return_expr)
return s
:maxdepth: 1
:titlesonly:
'''
for tutorial, _ in tutorials:
text += ' ' + tutorial + '\n'
text += '''
.. only:: html
Interactive notebooks and files
-------------------------------
'''
for tutorial, _ in tutorials:
text += indent(
deindent('''
.. |launchbinder{tutid}| image:: http://mybinder.org/badge.svg
.. _launchbinder{tutid}: http://mybinder.org:/repo/brian-team/brian2-binder/notebooks/tutorials/{tutorial}.ipynb
'''.format(tutorial=tutorial, tutid=tutorial.replace('-', ''))))
text += '\n'
for tutorial, title in tutorials:
text += ' * |launchbinder{tutid}|_ :download:`{title} <{tutorial}.ipynb>`\n'.format(
title=title, tutorial=tutorial, tutid=tutorial.replace('-', ''))
text += '''
.. _`Jupyter Notebooks`: http://jupyter-notebook-beginner-guide.readthedocs.org/en/latest/what_is_jupyter.html
.. _`Jupyter`: http://jupyter.org/
.. _`Jupyter Notebook documentation`: http://jupyter.readthedocs.org/
.. [#] Formerly known as "IPython Notebooks".
'''
def create_runner_codeobj(group,
code,
template_name,
run_namespace,
user_code=None,
variable_indices=None,
name=None,
check_units=True,
needed_variables=None,
additional_variables=None,
template_kwds=None,
override_conditional_write=None,
codeobj_class=None):
''' Create a `CodeObject` for the execution of code in the context of a
`Group`.
Parameters
----------
group : `Group`
The group where the code is to be run
code : str or dict of str
The code to be executed.
template_name : str
The name of the template to use for the code.
run_namespace : dict-like
An additional namespace that is used for variable lookup (either
an explicitly defined namespace or one taken from the local
context).
user_code : str, optional
The code that had been specified by the user before other code was
added automatically. If not specified, will be assumed to be identical
to ``code``.
variable_indices : dict-like, optional
A mapping from `Variable` objects to index names (strings). If none is
given, uses the corresponding attribute of `group`.
name : str, optional
A name for this code object, will use ``group + '_codeobject*'`` if
none is given.
check_units : bool, optional
Whether to check units in the statement. Defaults to ``True``.
needed_variables: list of str, optional
A list of variables that are neither present in the abstract code, nor
in the ``USES_VARIABLES`` statement in the template. This is only
rarely necessary, an example being a `StateMonitor` where the
names of the variables are neither known to the template nor included
in the abstract code statements.
additional_variables : dict-like, optional
A mapping of names to `Variable` objects, used in addition to the
variables saved in `group`.
template_kwds : dict, optional
A dictionary of additional information that is passed to the template.
override_conditional_write: list of str, optional
A list of variable names which are used as conditions (e.g. for
refractoriness) which should be ignored.
codeobj_class : class, optional
The `CodeObject` class to run code with. If not specified, defaults to
the `group`'s ``codeobj_class`` attribute.
'''
if name is None:
if group is not None:
name = '%s_%s_codeobject*' % (group.name, template_name)
else:
name = '%s_codeobject*' % template_name
if user_code is None:
user_code = code
if isinstance(code, str):
code = {None: code}
user_code = {None: user_code}
msg = 'Creating code object (group=%s, template name=%s) for abstract code:\n' % (
group.name, template_name)
msg += indent(code_representation(code))
logger.diagnostic(msg)
from brian2.devices import get_device
device = get_device()
if override_conditional_write is None:
override_conditional_write = set([])
else:
override_conditional_write = set(override_conditional_write)
if codeobj_class is None:
codeobj_class = device.code_object_class(group.codeobj_class)
else:
codeobj_class = device.code_object_class(codeobj_class)
template = getattr(codeobj_class.templater, template_name)
template_variables = getattr(template, 'variables', None)
all_variables = dict(group.variables)
if additional_variables is not None:
all_variables.update(additional_variables)
# Determine the identifiers that were used
identifiers = set()
user_identifiers = set()
for v, u_v in zip(code.values(), user_code.values()):
_, uk, u = analyse_identifiers(v, all_variables, recursive=True)
identifiers |= uk | u
_, uk, u = analyse_identifiers(u_v, all_variables, recursive=True)
user_identifiers |= uk | u
# Add variables that are not in the abstract code, nor specified in the
# template but nevertheless necessary
if needed_variables is None:
needed_variables = []
# Resolve all variables (variables used in the code and variables needed by
# the template)
variables = group.resolve_all(
identifiers | set(needed_variables) | set(template_variables),
# template variables are not known to the user:
user_identifiers=user_identifiers,
additional_variables=additional_variables,
run_namespace=run_namespace)
# We raise this error only now, because there is some non-obvious code path
# where Jinja tries to get a Synapse's "name" attribute via syn['name'],
# which then triggers the use of the `group_get_indices` template which does
# not exist for standalone. Putting the check for template == None here
# means we will first raise an error about the unknown identifier which will
# then make Jinja try syn.name
if template is None:
codeobj_class_name = codeobj_class.class_name or codeobj_class.__name__
raise AttributeError(
('"%s" does not provide a code generation '
'template "%s"') % (codeobj_class_name, template_name))
conditional_write_variables = {}
# Add all the "conditional write" variables
for var in variables.itervalues():
cond_write_var = getattr(var, 'conditional_write', None)
if cond_write_var in override_conditional_write:
continue
if cond_write_var is not None:
if (cond_write_var.name in variables
and not variables[cond_write_var.name] is cond_write_var):
logger.diagnostic(('Variable "%s" is needed for the '
'conditional write mechanism of variable '
'"%s". Its name is already used for %r.') %
(cond_write_var.name, var.name,
variables[cond_write_var.name]))
else:
conditional_write_variables[
cond_write_var.name] = cond_write_var
variables.update(conditional_write_variables)
if check_units:
for c in code.values():
# This is the first time that the code is parsed, catch errors
try:
check_units_statements(c, variables)
except (SyntaxError, ValueError) as ex:
error_msg = _error_msg(c, name)
raise ValueError(error_msg + str(ex))
all_variable_indices = copy.copy(group.variables.indices)
if additional_variables is not None:
all_variable_indices.update(additional_variables.indices)
if variable_indices is not None:
all_variable_indices.update(variable_indices)
# Make "conditional write" variables use the same index as the variable
# that depends on them
for varname, var in variables.iteritems():
cond_write_var = getattr(var, 'conditional_write', None)
if cond_write_var is not None:
all_variable_indices[
cond_write_var.name] = all_variable_indices[varname]
# Add the indices needed by the variables
varnames = variables.keys()
for varname in varnames:
var_index = all_variable_indices[varname]
if not var_index in ('_idx', '0'):
variables[var_index] = all_variables[var_index]
return device.code_object(
owner=group,
name=name,
abstract_code=code,
variables=variables,
template_name=template_name,
variable_indices=all_variable_indices,
template_kwds=template_kwds,
codeobj_class=codeobj_class,
override_conditional_write=override_conditional_write,
)
def __str__(self):
s = ''
for k, v in self._templates.items():
s += k + ':\n'
s += strip_empty_lines(indent(v)) + '\n'
return s
:maxdepth: 1
:titlesonly:
'''
for tutorial, _ in tutorials:
text += ' ' + tutorial + '\n'
text += '''
.. only:: html
Interactive notebooks and files
-------------------------------
'''
for tutorial, _ in tutorials:
text += indent(
deindent('''
.. |launchbinder{tutid}| image:: http://mybinder.org/badge.svg
.. _launchbinder{tutid}: https://mybinder.org/v2/gh/brian-team/brian2-binder/master?filepath=tutorials/{tutorial}.ipynb
'''.format(tutorial=tutorial, tutid=tutorial.replace('-', ''))))
text += '\n'
for tutorial, title in tutorials:
text += ' * |launchbinder{tutid}|_ :download:`{title} <{tutorial}.ipynb>`\n'.format(
title=title, tutorial=tutorial, tutid=tutorial.replace('-', ''))
text += '''
.. _`Jupyter Notebooks`: http://jupyter-notebook-beginner-guide.readthedocs.org/en/latest/what_is_jupyter.html
.. _`Jupyter`: http://jupyter.org/
.. _`Jupyter Notebook documentation`: http://jupyter.readthedocs.org/
.. [#] Formerly known as "IPython Notebooks".
'''
def create_runner_codeobj(group, code, template_name,
run_namespace,
user_code=None,
variable_indices=None,
name=None, check_units=True,
needed_variables=None,
additional_variables=None,
template_kwds=None,
override_conditional_write=None,
codeobj_class=None
):
''' Create a `CodeObject` for the execution of code in the context of a
`Group`.
Parameters
----------
group : `Group`
The group where the code is to be run
code : str or dict of str
The code to be executed.
template_name : str
The name of the template to use for the code.
run_namespace : dict-like
An additional namespace that is used for variable lookup (either
an explicitly defined namespace or one taken from the local
context).
user_code : str, optional
The code that had been specified by the user before other code was
added automatically. If not specified, will be assumed to be identical
to ``code``.
variable_indices : dict-like, optional
A mapping from `Variable` objects to index names (strings). If none is
given, uses the corresponding attribute of `group`.
name : str, optional
A name for this code object, will use ``group + '_codeobject*'`` if
none is given.
check_units : bool, optional
Whether to check units in the statement. Defaults to ``True``.
needed_variables: list of str, optional
A list of variables that are neither present in the abstract code, nor
in the ``USES_VARIABLES`` statement in the template. This is only
rarely necessary, an example being a `StateMonitor` where the
names of the variables are neither known to the template nor included
in the abstract code statements.
additional_variables : dict-like, optional
A mapping of names to `Variable` objects, used in addition to the
variables saved in `group`.
template_kwds : dict, optional
A dictionary of additional information that is passed to the template.
override_conditional_write: list of str, optional
A list of variable names which are used as conditions (e.g. for
refractoriness) which should be ignored.
codeobj_class : class, optional
The `CodeObject` class to run code with. If not specified, defaults to
the `group`'s ``codeobj_class`` attribute.
'''
if name is None:
if group is not None:
name = '%s_%s_codeobject*' % (group.name, template_name)
else:
name = '%s_codeobject*' % template_name
if user_code is None:
user_code = code
if isinstance(code, str):
code = {None: code}
user_code = {None: user_code}
msg = 'Creating code object (group=%s, template name=%s) for abstract code:\n' % (group.name, template_name)
msg += indent(code_representation(code))
logger.diagnostic(msg)
from brian2.devices import get_device
device = get_device()
if override_conditional_write is None:
override_conditional_write = set([])
else:
override_conditional_write = set(override_conditional_write)
if codeobj_class is None:
codeobj_class = device.code_object_class(group.codeobj_class)
else:
codeobj_class = device.code_object_class(codeobj_class)
template = getattr(codeobj_class.templater, template_name)
template_variables = getattr(template, 'variables', None)
all_variables = dict(group.variables)
if additional_variables is not None:
all_variables.update(additional_variables)
# Determine the identifiers that were used
identifiers = set()
user_identifiers = set()
for v, u_v in zip(code.values(), user_code.values()):
_, uk, u = analyse_identifiers(v, all_variables, recursive=True)
identifiers |= uk | u
_, uk, u = analyse_identifiers(u_v, all_variables, recursive=True)
user_identifiers |= uk | u
# Add variables that are not in the abstract code, nor specified in the
# template but nevertheless necessary
if needed_variables is None:
needed_variables = []
# Resolve all variables (variables used in the code and variables needed by
# the template)
variables = group.resolve_all(identifiers | set(needed_variables) | set(template_variables),
# template variables are not known to the user:
user_identifiers=user_identifiers,
additional_variables=additional_variables,
run_namespace=run_namespace)
# We raise this error only now, because there is some non-obvious code path
# where Jinja tries to get a Synapse's "name" attribute via syn['name'],
# which then triggers the use of the `group_get_indices` template which does
# not exist for standalone. Putting the check for template == None here
# means we will first raise an error about the unknown identifier which will
# then make Jinja try syn.name
if template is None:
codeobj_class_name = codeobj_class.class_name or codeobj_class.__name__
raise AttributeError(('"%s" does not provide a code generation '
'template "%s"') % (codeobj_class_name,
template_name))
conditional_write_variables = {}
# Add all the "conditional write" variables
for var in variables.itervalues():
cond_write_var = getattr(var, 'conditional_write', None)
if cond_write_var in override_conditional_write:
continue
if cond_write_var is not None:
if (cond_write_var.name in variables and
not variables[cond_write_var.name] is cond_write_var):
logger.diagnostic(('Variable "%s" is needed for the '
'conditional write mechanism of variable '
'"%s". Its name is already used for %r.') % (cond_write_var.name,
var.name,
variables[cond_write_var.name]))
else:
conditional_write_variables[cond_write_var.name] = cond_write_var
variables.update(conditional_write_variables)
if check_units:
for c in code.values():
# This is the first time that the code is parsed, catch errors
try:
check_units_statements(c, variables)
except (SyntaxError, ValueError) as ex:
error_msg = _error_msg(c, name)
raise ValueError(error_msg + str(ex))
all_variable_indices = copy.copy(group.variables.indices)
if additional_variables is not None:
all_variable_indices.update(additional_variables.indices)
if variable_indices is not None:
all_variable_indices.update(variable_indices)
# Make "conditional write" variables use the same index as the variable
# that depends on them
for varname, var in variables.iteritems():
cond_write_var = getattr(var, 'conditional_write', None)
if cond_write_var is not None:
all_variable_indices[cond_write_var.name] = all_variable_indices[varname]
# Check that all functions are available
for varname, value in variables.iteritems():
if isinstance(value, Function):
try:
value.implementations[codeobj_class]
except KeyError as ex:
# if we are dealing with numpy, add the default implementation
from brian2.codegen.runtime.numpy_rt import NumpyCodeObject
if codeobj_class is NumpyCodeObject:
value.implementations.add_numpy_implementation(value.pyfunc)
else:
raise NotImplementedError(('Cannot use function '
'%s: %s') % (varname, ex))
# Gather the additional compiler arguments declared by function
# implementations
all_keywords = [_gather_compiler_kwds(var, codeobj_class)
for var in variables.itervalues()
if isinstance(var, Function)]
compiler_kwds = _merge_compiler_kwds(all_keywords)
# Add the indices needed by the variables
varnames = variables.keys()
for varname in varnames:
var_index = all_variable_indices[varname]
if not var_index in ('_idx', '0'):
variables[var_index] = all_variables[var_index]
return device.code_object(owner=group,
name=name,
abstract_code=code,
variables=variables,
template_name=template_name,
variable_indices=all_variable_indices,
template_kwds=template_kwds,
codeobj_class=codeobj_class,
override_conditional_write=override_conditional_write,
compiler_kwds=compiler_kwds
)
.. toctree::
:maxdepth: 1
:titlesonly:
'''
for tutorial, _ in tutorials:
text += ' ' + tutorial + '\n'
text += '''
.. only:: html
Interactive notebooks and files
-------------------------------
'''
for tutorial, _ in tutorials:
text += indent(deindent('''
.. |launchbinder{tutid}| image:: http://mybinder.org/badge.svg
.. _launchbinder{tutid}: http://mybinder.org:/repo/brian-team/brian2-binder/notebooks/tutorials/{tutorial}.ipynb
'''.format(tutorial=tutorial, tutid=tutorial.replace('-', ''))))
text += '\n'
for tutorial, title in tutorials:
text += ' * |launchbinder{tutid}|_ :download:`{title} <{tutorial}.ipynb>`\n'.format(title=title,
tutorial=tutorial, tutid=tutorial.replace('-', ''))
text += '''
.. _`Jupyter Notebooks`: http://jupyter-notebook-beginner-guide.readthedocs.org/en/latest/what_is_jupyter.html
.. _`Jupyter`: http://jupyter.org/
.. _`Jupyter Notebook documentation`: http://jupyter.readthedocs.org/
.. [#] Formerly known as "IPython Notebooks".
'''
with open(os.path.join(target_dir, 'index.rst'), 'w') as f: