Source code for brian2.codegen.generators.GSL_generator

GSLCodeGenerators for code that uses the ODE solver provided by the GNU Scientific Library (GSL)

import os
import re
import sys

import numpy as np

from brian2.units.fundamentalunits import fail_for_dimension_mismatch
from brian2.core.variables import AuxiliaryVariable, ArrayVariable, Constant
from brian2.core.functions import Function
from brian2.codegen.translation import make_statements
from brian2.codegen.permutation_analysis import (check_for_order_independence,
from brian2.core.preferences import prefs, BrianPreference
from brian2.utils.stringtools import get_identifiers, word_substitute
from brian2.parsing.statements import parse_statement
from brian2.codegen.generators import c_data_type

from brian2.core.preferences import PreferenceError

__all__ = ['GSLCodeGenerator', 'GSLCPPCodeGenerator', 'GSLCythonCodeGenerator']

[docs]def valid_gsl_dir(val): ''' Validate given string to be path containing required GSL files. ''' if val is None: return True if not isinstance(val, str): raise PreferenceError(('Illegal value for GSL directory: %s, ' 'has to be str' % (str(val)))) if not os.path.isdir(val): raise PreferenceError(('Illegal value for GSL directory: %s, ' 'has to be existing directory' % (val))) if any(not os.path.isfile(os.path.join(val, 'gsl', filename)) for filename in ['gsl_odeiv2.h', 'gsl_errno.h', 'gsl_matrix.h']): raise PreferenceError(('Illegal value for GSL directory: %s, ' 'has to contain gsl_odeiv2.h, gsl_errno.h ' 'and gsl_matrix.h' % (val))) return True
prefs.register_preferences( 'GSL', 'Directory containing GSL code', directory=BrianPreference( validator=valid_gsl_dir, docs=("Set path to directory containing GSL header files (gsl_odeiv2.h etc.)" "\nIf this directory is already in Python's include (e.g. because of " "conda installation), this path can be set to None."), default=None ) )
[docs]class GSLCodeGenerator(object): ''' GSL code generator. Notes ----- Approach is to first let the already existing code generator for a target language do the bulk of the translating from abstract_code to actual code. This generated code is slightly adapted to render it GSL compatible. The most critical part here is that the vector_code that is normally contained in a loop in the ```main()``` is moved to the function ```_GSL_func``` that is sent to the GSL integrator. The variables used in the vector_code are added to a struct named ```dataholder``` and their values are set from the Brian namespace just before the scalar code block. ''' def __init__(self, variables, variable_indices, owner, iterate_all, codeobj_class, name, template_name, override_conditional_write=None, allows_scalar_write=False): self.generator = codeobj_class.original_generator_class(variables, variable_indices, owner, iterate_all, codeobj_class, name, template_name, override_conditional_write, allows_scalar_write) self.method_options = dict(owner.state_updater.method_options) self.integrator = owner.state_updater.integrator # default timestep to start with is the timestep of the NeuronGroup itself self.method_options['dt_start'] = owner.dt.variable.get_value()[0] self.variable_flags = owner.state_updater._gsl_variable_flags def __getattr__(self, item): return getattr(self.generator, item) # A series of functions that should be overridden by child class:
[docs] def c_data_type(self, dtype): ''' Get string version of object dtype that is attached to Brian variables. c pp_generator already has this function, but the Cython generator does not, but we need it for GSL code generation. ''' return NotImplementedError
[docs] def initialize_array(self, varname, values): ''' Initialize a static array with given floating point values. E.g. in C++, when called with arguments ``array`` and ``[1.0, 3.0, 2.0]``, this method should return ``double array[] = {1.0, 3.0, 2.0}``. Parameters ---------- varname : str The name of the array variable that should be initialized values : list of float The values that should be assigned to the array Returns ------- code : str One or more lines of array initialization code. ''' raise NotImplementedError
[docs] def var_init_lhs(self, var, type): ''' Get string version of the left hand side of an initializing expression Parameters ---------- var : str type : str Returns ------- code : str For cpp returns type + var, while for cython just var ''' raise NotImplementedError
[docs] def unpack_namespace_single(self, var_obj, in_vector, in_scalar): ''' Writes the code necessary to pull single variable out of the Brian namespace into the generated code. The code created is significantly different between cpp and cython, so I decided to not make this function general over all target languages (i.e. in contrast to most other functions that only have syntactical differences) ''' raise NotImplementedError
# GSL functions that are the same for all target languages:
[docs] def find_function_names(self): ''' Return a list of used function names in the self.variables dictionary Functions need to be ignored in the GSL translation process, because the brian generator already sufficiently dealt with them. However, the brian generator also removes them from the variables dict, so there is no way to check whether an identifier is a function after the brian translation process. This function is called before this translation process and the list of function names is stored to be used in the GSL translation. Returns ------- function_names : list list of strings that are function names used in the code ''' variables = self.variables return [var for var, var_obj in variables.items() if isinstance(var_obj, Function)]
[docs] def is_cpp_standalone(self): ''' Check whether we're running with cpp_standalone. Test if `get_device()` is instance `CPPStandaloneDevice`. Returns ------- is_cpp_standalone : bool whether currently using cpp_standalone device See Also -------- is_constant_and_cpp_standalone : uses the returned value ''' # imports here to avoid circular imports from brian2.devices.device import get_device from brian2.devices.cpp_standalone.device import CPPStandaloneDevice device = get_device() return isinstance(device, CPPStandaloneDevice)
[docs] def is_constant_and_cpp_standalone(self, var_obj): """Check whether self.cpp_standalone and variable is Constant. This check is needed because in the case of using the cpp_standalone device we do not want to apply our GSL variable conversion (var --> _GSL_dataholder.var), because the cpp_standalone code generation process involves replacing constants with their actual value ('freezing'). This results in code that looks like (if for example var = 1.2): _GSL_dataholder.1.2 = 1.2 and _GSL_dataholder->1.2. To prevent repetitive calls to get_device() etc. the outcome of is_cpp_standalone is saved. Parameters ---------- var_obj : `Variable` instance of brian Variable class describing the variable Returns ------- is_cpp_standalone : bool whether the used device is cpp_standalone and the given variable is an instance of Constant """ if not hasattr(self, 'cpp_standalone'): self.cpp_standalone = self.is_cpp_standalone() return isinstance(var_obj, Constant) and self.cpp_standalone
[docs] def find_differential_variables(self, code): ''' Find the variables that were tagged _gsl_{var}_f{ind} and return var, ind pairs. `GSLStateUpdater` tagged differential variables and here we extract the information given in these tags. Parameters ---------- code : list of strings A list of strings containing gsl tagged variables Returns ------- diff_vars : dict A dictionary with variable names as keys and differential equation index as value ''' diff_vars = {} for expr_set in code: for expr in expr_set.split('\n'): expr = expr.strip(' ') try: lhs, op, rhs, comment = parse_statement(expr) except ValueError: pass m ='_gsl_(.+?)_f([0-9]*)$', lhs) if m: diff_vars[] = return diff_vars
[docs] def diff_var_to_replace(self, diff_vars): ''' Add differential variable-related strings that need to be replaced to go from normal brian to GSL code From the code generated by Brian's 'normal' generators (cpp_generator or cython_generator a few bits of text need to be replaced to get GSL compatible code. The bits of text related to differential equation variables are put in the replacer dictionary in this function. Parameters ---------- diff_vars : dict dictionary with variables as keys and differential equation index as value Returns ------- to_replace : dict dictionary with strings that need to be replaced as keys and the strings that will replace them as values ''' variables = self.variables to_replace = {} for var, diff_num in list(diff_vars.items()): to_replace.update(self.var_replace_diff_var_lhs(var, diff_num)) var_obj = variables[var] array_name = self.generator.get_array_name(var_obj, access_data=True) idx_name = '_idx' #TODO: could be dynamic? replace_what = '{var} = {array_name}[{idx_name}]'.format(array_name=array_name, idx_name=idx_name, var=var) replace_with = '{var} = _GSL_y[{ind}]'.format(ind=diff_num, var=var) to_replace[replace_what] = replace_with return to_replace
[docs] def get_dimension_code(self, diff_num): ''' Generate code for function that sets the dimension of the ODE system. GSL needs to know how many differential variables there are in the ODE system. Since the current approach is to have the code in the vector loop the same for all simulations, this dimension is set by an external function. The code for this set_dimension functon is written here. It is assumed the code will be the same for each target language with the exception of some syntactical differences Parameters ---------- diff_num : int Number of differential variables that describe the ODE system Returns ------- set_dimension_code : str The code describing the target language function in a single string ''' code = ['\n{start_declare}int set_dimension(size_t * dimension){open_function}'] code += ['\tdimension[0] = %d{end_statement}'%diff_num] code += ['\treturn GSL_SUCCESS{end_statement}{end_function}'] return ('\n').join(code).format(**self.syntax)
[docs] def yvector_code(self, diff_vars): ''' Generate code for function dealing with GSLs y vector. The values of differential variables have to be transferred from Brian's namespace to a vector that is given to GSL. The transferring from Brian --> y and back from y --> Brian after integration happens in separate functions. The code for these is written here. Parameters ---------- diff_vars : dictionary Dictionary containing variable names as keys (str) and differential variable index as value Returns ------- yvector_code : str The code for the two functions (``_fill_y_vector`` and ``_empty_y_vector``) as single string. ''' fill_y = [("\n{start_declare}int _fill_y_vector(_dataholder *" "_GSL_dataholder, double * _GSL_y, int _idx){open_function}")] empty_y = [("\n{start_declare}int _empty_y_vector(_dataholder * " "_GSL_dataholder, double * _GSL_y, int _idx){" "open_function}")] for var, diff_num in list(diff_vars.items()): diff_num = int(diff_num) array_name = self.generator.get_array_name(self.variables[var], access_data=True) fill_y += [("\t_GSL_y[%d] = _GSL_dataholder{access_pointer}%s[" "_idx]{end_statement}"%(diff_num, array_name))] empty_y += [("\t_GSL_dataholder{access_pointer}%s[_idx] = _GSL_y[" "%d]{end_statement}"%(array_name, diff_num))] fill_y += ['\treturn GSL_SUCCESS{end_statement}{end_function}'] empty_y += ['\treturn GSL_SUCCESS{end_statement}{end_function}'] return ('\n').join(fill_y + empty_y).format(**self.syntax)
[docs] def make_function_code(self, lines): ''' Add lines of GSL translated vector code to 'non-changing' _GSL_func code. Adds nonchanging aspects of GSL _GSL_func code to lines of code written somewhere else (`translate_vector_code`). Here these lines are put between the non-changing parts of the code and the target-language specific syntax is added. Parameters ---------- lines : str Code containing GSL version of equations Returns ------- function_code : str code describing ``_GSL_func`` that is sent to GSL integrator. ''' code = [("\n{start_declare}int _GSL_func(double t, const double " "_GSL_y[], double f[], void * params){open_function}" "\n\t{start_declare}_dataholder * _GSL_dataholder = {open_cast}" "_dataholder *{close_cast} params{end_statement}" "\n\t{start_declare}int _idx = _GSL_dataholder{access_pointer}_idx" "{end_statement}")] code += [lines] code += ["\treturn GSL_SUCCESS{end_statement}{end_function}"] return ('\n').join(code).format(**self.syntax)
[docs] def write_dataholder_single(self, var_obj): ''' Return string declaring a single variable in the ``_dataholder`` struct. Parameters ---------- var_obj : `Variable` Returns ------- code : str string describing this variable object as required for the ``_dataholder`` struct (e.g. ``double* _array_neurongroup_v``) ''' dtype = self.c_data_type(var_obj.dtype) if isinstance(var_obj, ArrayVariable): pointer_name = self.get_array_name(var_obj, access_data=True) try: restrict = self.generator.restrict except AttributeError: restrict = '' if var_obj.scalar or var_obj.size == 1: restrict = '' return '%s* %s %s{end_statement}'%(dtype, restrict, pointer_name) else: return '%s %s{end_statement}'%(dtype,
[docs] def write_dataholder(self, variables_in_vector): ''' Return string with full code for _dataholder struct. Parameters ---------- variables_in_vector : dict dictionary containing variable name as key and `Variable` as value Returns ------- code : str code for _dataholder struct ''' code = ['\n{start_declare}struct _dataholder{open_struct}'] code += ['\tint _idx{end_statement}'] for var, var_obj in list(variables_in_vector.items()): if var == 't' or '_gsl' in var or self.is_constant_and_cpp_standalone(var_obj): continue code += ['\t'+self.write_dataholder_single(var_obj)] code += ['{end_struct}'] return ('\n').join(code).format(**self.syntax)
[docs] def scale_array_code(self, diff_vars, method_options): ''' Return code for definition of ``_GSL_scale_array`` in generated code. Parameters ---------- diff_vars : dict dictionary with variable name (str) as key and differential variable index (int) as value method_options : dict dictionary containing integrator settings Returns ------- code : str full code describing a function returning a array containing doubles with the absolute errors for each differential variable (according to their assigned index in the GSL StateUpdater) ''' # get scale values per variable from method_options abs_per_var = method_options['absolute_error_per_variable'] abs_default = method_options['absolute_error'] if not isinstance(abs_default, float): raise TypeError(("The absolute_error key in method_options should be " "a float. Was type %s" % (str(type(abs_default))))) if abs_per_var is None: diff_scale = {var: float(abs_default) for var in list(diff_vars.keys())} elif isinstance(abs_per_var, dict): diff_scale = {} for var, error in list(abs_per_var.items()): # first do some checks on input if not var in diff_vars: if not var in self.variables: raise KeyError("absolute_error specified for variable " "that does not exist: %s"%var) else: raise KeyError("absolute_error specified for variable " "that is not being integrated: %s"%var) fail_for_dimension_mismatch(error, self.variables[var], ("Unit of absolute_error_per_variable " "for variable %s does not match " "unit of varialbe itself"%var)) # if all these are passed we can add the value for error in base units diff_scale[var] = float(error) # set the variables that are not mentioned to default value for var in list(diff_vars.keys()): if var not in abs_per_var: diff_scale[var] = float(abs_default) else: raise TypeError(("The absolute_error_per_variable key in method_options " "should either be None or a dictionary " "containing the error for each individual state variable. " "Was type %s"%(str(type(abs_per_var))))) # write code return self.initialize_array('_GSL_scale_array', [diff_scale[var] for var in sorted(diff_vars)])
[docs] def find_undefined_variables(self, statements): ''' Find identifiers that are not in ``self.variables`` dictionary. Brian does not save the ``_lio_`` variables it uses anywhere. This is problematic for our GSL implementation because we save the lio variables in the ``_dataholder`` struct (for which we need the datatype of the variables). This function adds the left hand side variables that are used in the vector code to the variable dictionary as `AuxiliaryVariable`\ s (all we need later is the datatype). Parameters ---------- statements : list list of statement objects (need to have the dtype attribute) Notes ----- I keep ``self.variables`` and ``other_variables`` separate so I can distinguish what variables are in the Brian namespace and which ones are defined in the code itself. ''' variables = self.variables other_variables = {} for statement in statements: var, op, expr, comment = (statement.var, statement.op, statement.expr, statement.comment) if var not in variables: other_variables[var] = AuxiliaryVariable(var, dtype=statement.dtype) return other_variables
[docs] def find_used_variables(self, statements, other_variables): ''' Find all the variables used in the right hand side of the given expressions. Parameters ---------- statements : list list of statement objects Returns ------- used_variables : dict dictionary of variables that are used as variable name (str), `Variable` pairs. ''' variables = self.variables used_variables = {} for statement in statements: lhs, op, rhs, comment = (statement.var, statement.op, statement.expr, statement.comment) for var in (get_identifiers(rhs)): if var in self.function_names: continue try: var_obj = variables[var] except KeyError: var_obj = other_variables[var] used_variables[var] = var_obj # save as object because this has # all needed info (dtype, name, isarray) # I don't know a nicer way to do this, the above way misses write # variables (e.g. not_refractory).. read, write, _ = self.array_read_write(statements) for var in (read|write): if var not in used_variables: used_variables[var] = variables[var] # will always be array and # thus exist in variables return used_variables
[docs] def to_replace_vector_vars(self, variables_in_vector, ignore=frozenset()): ''' Create dictionary containing key, value pairs with to be replaced text to translate from conventional Brian to GSL. Parameters ---------- variables_in_vector : dict dictionary with variable name (str), `Variable` pairs of variables occurring in vector code ignore : set, optional set of strings with variable names that should be ignored Returns ------- to_replace : dict dictionary with strings that need to be replaced i.e. _lio_1 will be _GSL_dataholder._lio_1 (in cython) or _GSL_dataholder->_lio_1 (cpp) Notes ----- t will always be added because GSL defines its own t. i.e. for cpp: {'const t = _ptr_array_defaultclock_t[0];' : ''} ''' access_pointer = self.syntax['access_pointer'] to_replace = {} t_in_code = None for var, var_obj in list(variables_in_vector.items()): if == 't': t_in_code = var_obj continue if '_gsl' in var or var in ignore: continue if self.is_constant_and_cpp_standalone(var_obj): # does not have to be processed by GSL generator self.variables_to_be_processed.remove( continue if isinstance(var_obj, ArrayVariable): pointer_name = self.get_array_name(var_obj, access_data=True) to_replace[pointer_name] = '_GSL_dataholder' + access_pointer + pointer_name else: to_replace[var] = '_GSL_dataholder' + access_pointer + var # also make sure t declaration is replaced if in code if t_in_code is not None: t_declare = self.var_init_lhs('t', 'const double ') array_name = self.get_array_name(t_in_code, access_data=True) end_statement = self.syntax['end_statement'] replace_what = ("{t_declare} = {array_name}[0]" "{end_statement}".format(t_declare=t_declare, array_name=array_name, end_statement=end_statement)) to_replace[replace_what] = '' self.variables_to_be_processed.remove('t') return to_replace
[docs] def unpack_namespace(self, variables_in_vector, variables_in_scalar, ignore=frozenset()): ''' Write code that unpacks Brian namespace to cython/cpp namespace. For vector code this means putting variables in _dataholder (i.e. _GSL_dataholder->var or _GSL_dataholder.var = ...) Note that code is written so a variable could occur both in scalar and vector code Parameters ---------- variables_in_vector : dict dictionary with variable name (str), `Variable` pairs of variables occurring in vector code variables_in_scalar : dict dictionary with variable name (str), `Variable` pairs of variables occurring in scalar code ignore : set, optional set of string names of variables that should be ignored Returns ------- unpack_namespace_code : str code fragment unpacking the Brian namespace (setting variables in the _dataholder struct in case of vector) ''' code = [] for var, var_obj in list(self.variables.items()): if var in ignore: continue if self.is_constant_and_cpp_standalone(var_obj): continue in_vector = var in variables_in_vector in_scalar = var in variables_in_scalar if in_vector: self.variables_to_be_processed.remove(var) code += [self.unpack_namespace_single(var_obj, in_vector, in_scalar)] return ('\n').join(code)
[docs] def translate_vector_code(self, code_lines, to_replace): ''' Translate vector code to GSL compatible code by substituting fragments of code. Parameters ---------- code_lines : list list of strings describing the vector_code to_replace: dict dictionary with to be replaced strings (see to_replace_vector_vars and to_replace_diff_vars) Returns ------- vector_code : str New code that is now to be added to the function that is sent to the GSL integrator ''' code = [] for expr_set in code_lines: for line in expr_set.split('\n'): # every line seperate to make tabbing correct code += ['\t' + line] code = ('\n').join(code) code = word_substitute(code, to_replace) # special substitute because of limitations of regex word boundaries with # variable[_idx] for from_sub, to_sub in list(to_replace.items()): m ='\[(\w+)\];?$', from_sub) if m: code = re.sub(re.sub('\[', '\[', from_sub), to_sub, code) if '_gsl' in code: raise AssertionError(('Translation failed, _gsl still in code (should only ' 'be tag, and should be replaced.\n' 'Code:\n%s' % code)) return code
[docs] def translate_scalar_code(self, code_lines, variables_in_scalar, variables_in_vector): ''' Translate scalar code: if calculated variables are used in the vector_code their value is added to the variable in the _dataholder. Parameters ---------- code_lines : list list of strings containing scalar code variables_in_vector : dict dictionary with variable name (str), `Variable` pairs of variables occurring in vector code variables_in_scalar : dict dictionary with variable name (str), `Variable` pairs of variables occurring in scalar code Returns ------- scalar_code : str code fragment that should be injected in the main before the loop ''' code = [] for line in code_lines: m ='(\w+ = .*)', line) try: new_line = var, op, expr, comment = parse_statement(new_line) except (ValueError, AttributeError): code += [line] continue if var in list(variables_in_scalar.keys()): code += [line] elif var in list(variables_in_vector.keys()): if var == 't': continue try: self.variables_to_be_processed.remove(var) except KeyError: raise AssertionError(("Trying to process variable named %s by " "putting its value in the _GSL_dataholder " "based on scalar code, but the variable " "has been processed already." % var)) code += ['_GSL_dataholder.{var} {op} {expr} {comment}'.format( var=var, op=op, expr=expr, comment=comment)] return '\n'.join(code)
[docs] def add_gsl_variables_as_non_scalar(self, diff_vars): ''' Add _gsl variables as non-scalar. In `GSLStateUpdater` the differential equation variables are substituted with GSL tags that describe the information needed to translate the conventional Brian code to GSL compatible code. This function tells Brian that the variables that contain these tags should always be vector variables. If we don't do this, Brian renders the tag-variables as scalar if no vector variables are used in the right hand side of the expression. Parameters ---------- diff_vars : dict dictionary with variables as keys and differential equation index as value ''' for var, ind in list(diff_vars.items()): name = '_gsl_{var}_f{ind}'.format(var=var, ind=ind) self.variables[name] = AuxiliaryVariable(var, scalar=False)
[docs] def add_meta_variables(self, options): if options['use_last_timestep']: try: N = int(self.variables['N'].get_value()) self.owner.variables.add_array('_last_timestep', size=N, values=np.ones(N)*options['dt_start'], dtype=np.float64) except KeyError: # has already been run pass self.variables['_last_timestep'] = self.owner.variables.get('_last_timestep') pointer_last_timestep = self.get_array_name(self.variables['_last_timestep'])+ '[_idx]' else: pointer_last_timestep = None if options['save_failed_steps']: N = int(self.variables['N'].get_value()) try: self.owner.variables.add_array('_failed_steps', size=N, dtype=np.int32) except KeyError: # has already been run pass self.variables['_failed_steps'] = self.owner.variables.get('_failed_steps') pointer_failed_steps = self.get_array_name(self.variables['_failed_steps']) + '[_idx]' else: pointer_failed_steps = None if options['save_step_count']: N = int(self.variables['N'].get_value()) try: self.owner.variables.add_array('_step_count', size=N, dtype=np.int32) except KeyError: # has already been run pass self.variables['_step_count'] = self.owner.variables.get('_step_count') pointer_step_count = self.get_array_name(self.variables['_step_count']) + '[_idx]' else: pointer_step_count = None return {'pointer_last_timestep' : pointer_last_timestep, 'pointer_failed_steps' : pointer_failed_steps, 'pointer_step_count' : pointer_step_count}
[docs] 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(list(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.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.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 list(scalar_code.values())+list(vector_code.values()): for code in code_list: m ='\[(\w+)\]', code) if m is not None: if != '0' and != '_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 list(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 = list(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=list(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 list(pointer_names.items()): kwds[key] = value return scalar_code, vector_code, kwds
[docs]class GSLCythonCodeGenerator(GSLCodeGenerator): syntax = {'end_statement': '', 'access_pointer': '.', 'start_declare': 'cdef ', 'open_function': ':', 'open_struct': ':', 'end_function': '', 'end_struct': '', 'open_cast': '<', 'close_cast': '>', 'diff_var_declaration': ''}
[docs] def c_data_type(self, dtype): return c_data_type(dtype)
[docs] def initialize_array(self, varname, values): value_list = ', '.join(repr(v) for v in values) code = 'cdef double {varname}[{n_values}]\n' code += '{varname}[:] = [{value_list}]' return code.format(varname=varname, value_list=value_list, n_values=len(values))
[docs] def var_replace_diff_var_lhs(self, var, ind): return {'_gsl_{var}_f{ind}'.format(var=var, ind=ind): 'f[{ind}]'.format(ind=ind)}
[docs] def var_init_lhs(self, var, type): return var
[docs] def unpack_namespace_single(self, var_obj, in_vector, in_scalar): code = [] if isinstance(var_obj, ArrayVariable): array_name = self.generator.get_array_name(var_obj) dtype = self.c_data_type(var_obj.dtype) if in_vector: code += [('_GSL_dataholder.{array} = <{dtype} *> ' '_buf_{array}.data'.format(array=array_name, dtype=dtype))] if in_scalar: code += [('{array} = <{dtype} *> ' '_buf_{array}.data'.format(array=array_name, dtype=dtype))] else: if in_vector: code += ['_GSL_dataholder.{var} = _namespace["{var}"]'.format(] if in_scalar: code += ['{var} = _namespace["{var}"]'.format(] return '\n'.join(code)
[docs] @staticmethod def get_array_name( var, access_data=True): # We have to do the import here to avoid circular import dependencies. from brian2.codegen.generators.cython_generator import CythonCodeGenerator return CythonCodeGenerator.get_array_name(var, access_data)
[docs]class GSLCPPCodeGenerator(GSLCodeGenerator): def __getattr__(self, item): return getattr(self.generator, item) syntax = {'end_statement': ';', 'access_pointer': '->', 'start_declare': '', 'open_function': '\n{', 'open_struct' :'\n{', 'end_function': '\n}', 'end_struct': '\n};', 'open_cast': '(', 'close_cast': ')', 'diff_var_declaration': 'const scalar '}
[docs] def c_data_type(self, dtype): return self.generator.c_data_type(dtype)
[docs] def initialize_array(self, varname, values): value_list = ', '.join(repr(v) for v in values) return 'double const %s[] = {%s};' % (varname, value_list)
[docs] def var_replace_diff_var_lhs(self, var, ind): scalar_dtype = self.c_data_type(prefs.core.default_float_dtype) f = 'f[{ind}]'.format(ind=ind) try: if 'unless refractory' in self.variable_flags[var]: return {'_gsl_{var}_f{ind}'.format(var=var, ind=ind) : f, '{scalar_dtype} _gsl_{var}_f{ind};'.format(var=var, ind=ind, scalar_dtype=scalar_dtype): '', '{scalar_dtype} {f};'.format(f=f, scalar_dtype=scalar_dtype): ''} # in case the replacement # of _gsl_var_find to f[ind] happens first except KeyError: pass return {'const {scalar_dtype} _gsl_{var}_f{ind}'.format(scalar_dtype=scalar_dtype, var=var, ind=ind) : f}
[docs] def var_init_lhs(self, var, type): return type + var
[docs] def unpack_namespace_single(self, var_obj, in_vector, in_scalar): if isinstance(var_obj, ArrayVariable): pointer_name = self.get_array_name(var_obj, access_data=True) array_name = self.get_array_name(var_obj) if in_vector: return '_GSL_dataholder.{ptr} = {array};'.format(ptr=pointer_name, array=array_name) else: return '' else: if in_vector: return '_GSL_dataholder.{var} = {var};'.format( else: return ''