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Refactor inline expressions expansion into a transformer (#1093)
* refactor inline expressions expansion into a transformer * refactor inline expressions expansion into a transformer * refactor inline expressions expansion into a transformer * refactor inline expressions expansion into a transformer * refactor inline expressions expansion into a transformer --------- Co-authored-by: C.A.P. Linssen <[email protected]>
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142 changes: 142 additions & 0 deletions
142
pynestml/transformers/inline_expression_expansion_transformer.py
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| Original file line number | Diff line number | Diff line change |
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| # -*- coding: utf-8 -*- | ||
| # | ||
| # inline_expression_expansion_transformer.py | ||
| # | ||
| # This file is part of NEST. | ||
| # | ||
| # Copyright (C) 2004 The NEST Initiative | ||
| # | ||
| # NEST is free software: you can redistribute it and/or modify | ||
| # it under the terms of the GNU General Public License as published by | ||
| # the Free Software Foundation, either version 2 of the License, or | ||
| # (at your option) any later version. | ||
| # | ||
| # NEST is distributed in the hope that it will be useful, | ||
| # but WITHOUT ANY WARRANTY; without even the implied warranty of | ||
| # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | ||
| # GNU General Public License for more details. | ||
| # | ||
| # You should have received a copy of the GNU General Public License | ||
| # along with NEST. If not, see <http://www.gnu.org/licenses/>. | ||
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| from __future__ import annotations | ||
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| from typing import List, Optional, Mapping, Any, Union, Sequence | ||
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| import re | ||
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| from pynestml.frontend.frontend_configuration import FrontendConfiguration | ||
| from pynestml.meta_model.ast_inline_expression import ASTInlineExpression | ||
| from pynestml.meta_model.ast_node import ASTNode | ||
| from pynestml.meta_model.ast_ode_equation import ASTOdeEquation | ||
| from pynestml.transformers.transformer import Transformer | ||
| from pynestml.utils.ast_utils import ASTUtils | ||
| from pynestml.utils.logger import Logger, LoggingLevel | ||
| from pynestml.utils.string_utils import removesuffix | ||
| from pynestml.visitors.ast_higher_order_visitor import ASTHigherOrderVisitor | ||
| from pynestml.visitors.ast_parent_visitor import ASTParentVisitor | ||
| from pynestml.visitors.ast_symbol_table_visitor import ASTSymbolTableVisitor | ||
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| class InlineExpressionExpansionTransformer(Transformer): | ||
| r""" | ||
| Make inline expressions self contained, i.e. without any references to other inline expressions. | ||
| Additionally, replace variable symbols referencing inline expressions in defining expressions of ODEs with the corresponding defining expressions from the inline expressions. | ||
| """ | ||
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| _variable_matching_template = r'(\b)({})(\b)' | ||
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| def __init__(self, options: Optional[Mapping[str, Any]] = None): | ||
| super(Transformer, self).__init__(options) | ||
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| def transform(self, models: Union[ASTNode, Sequence[ASTNode]]) -> Union[ASTNode, Sequence[ASTNode]]: | ||
| single = False | ||
| if isinstance(models, ASTNode): | ||
| single = True | ||
| models = [models] | ||
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| for model in models: | ||
| if not model.get_equations_blocks(): | ||
| continue | ||
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| for equations_block in model.get_equations_blocks(): | ||
| self.make_inline_expressions_self_contained(equations_block.get_inline_expressions()) | ||
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| for equations_block in model.get_equations_blocks(): | ||
| self.replace_inline_expressions_through_defining_expressions(equations_block.get_ode_equations(), equations_block.get_inline_expressions()) | ||
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| if single: | ||
| return models[0] | ||
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| return models | ||
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| def make_inline_expressions_self_contained(self, inline_expressions: List[ASTInlineExpression]) -> List[ASTInlineExpression]: | ||
| r""" | ||
| Make inline expressions self contained, i.e. without any references to other inline expressions. | ||
| :param inline_expressions: A sorted list with entries ASTInlineExpression. | ||
| :return: A list with ASTInlineExpressions. Defining expressions don't depend on each other. | ||
| """ | ||
| from pynestml.utils.model_parser import ModelParser | ||
| from pynestml.visitors.ast_symbol_table_visitor import ASTSymbolTableVisitor | ||
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| for source in inline_expressions: | ||
| source_position = source.get_source_position() | ||
| for target in inline_expressions: | ||
| matcher = re.compile(self._variable_matching_template.format(source.get_variable_name())) | ||
| target_definition = str(target.get_expression()) | ||
| target_definition = re.sub(matcher, "(" + str(source.get_expression()) + ")", target_definition) | ||
| old_parent = target.expression.parent_ | ||
| target.expression = ModelParser.parse_expression(target_definition) | ||
| target.expression.update_scope(source.get_scope()) | ||
| target.expression.parent_ = old_parent | ||
| target.expression.accept(ASTParentVisitor()) | ||
| target.expression.accept(ASTSymbolTableVisitor()) | ||
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| def log_set_source_position(node): | ||
| if node.get_source_position().is_added_source_position(): | ||
| node.set_source_position(source_position) | ||
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| target.expression.accept(ASTHigherOrderVisitor(visit_funcs=log_set_source_position)) | ||
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| return inline_expressions | ||
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| @classmethod | ||
| def replace_inline_expressions_through_defining_expressions(self, definitions: Sequence[ASTOdeEquation], | ||
| inline_expressions: Sequence[ASTInlineExpression]) -> Sequence[ASTOdeEquation]: | ||
| r""" | ||
| Replace variable symbols referencing inline expressions in defining expressions of ODEs with the corresponding defining expressions from the inline expressions. | ||
| :param definitions: A list of ODE definitions (**updated in-place**). | ||
| :param inline_expressions: A list of inline expression definitions. | ||
| :return: A list of updated ODE definitions (same as the ``definitions`` parameter). | ||
| """ | ||
| from pynestml.utils.model_parser import ModelParser | ||
| from pynestml.visitors.ast_symbol_table_visitor import ASTSymbolTableVisitor | ||
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| for m in inline_expressions: | ||
| if "mechanism" not in [e.namespace for e in m.get_decorators()]: | ||
| """ | ||
| exclude compartmental mechanism definitions in order to have the | ||
| inline as a barrier inbetween odes that are meant to be solved independently | ||
| """ | ||
| source_position = m.get_source_position() | ||
| for target in definitions: | ||
| matcher = re.compile(self._variable_matching_template.format(m.get_variable_name())) | ||
| target_definition = str(target.get_rhs()) | ||
| target_definition = re.sub(matcher, "(" + str(m.get_expression()) + ")", target_definition) | ||
| old_parent = target.rhs.parent_ | ||
| target.rhs = ModelParser.parse_expression(target_definition) | ||
| target.update_scope(m.get_scope()) | ||
| target.rhs.parent_ = old_parent | ||
| target.rhs.accept(ASTParentVisitor()) | ||
| target.accept(ASTSymbolTableVisitor()) | ||
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| def log_set_source_position(node): | ||
| if node.get_source_position().is_added_source_position(): | ||
| node.set_source_position(source_position) | ||
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| target.accept(ASTHigherOrderVisitor(visit_funcs=log_set_source_position)) | ||
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| return definitions |
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59 changes: 59 additions & 0 deletions
59
tests/nest_tests/resources/beta_function_with_inline_expression_neuron.nestml
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,59 @@ | ||
| """ | ||
| beta_function_with_inline_expression_neuron | ||
| ########################################### | ||
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| Description | ||
| +++++++++++ | ||
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| Used for testing processing of inline expressions. | ||
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| Copyright | ||
| +++++++++ | ||
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| This file is part of NEST. | ||
|
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| Copyright (C) 2004 The NEST Initiative | ||
|
|
||
| NEST is free software: you can redistribute it and/or modify | ||
| it under the terms of the GNU General Public License as published by | ||
| the Free Software Foundation, either version 2 of the License, or | ||
| (at your option) any later version. | ||
|
|
||
| NEST is distributed in the hope that it will be useful, | ||
| but WITHOUT ANY WARRANTY; without even the implied warranty of | ||
| MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | ||
| GNU General Public License for more details. | ||
| You should have received a copy of the GNU General Public License | ||
| along with NEST. If not, see <http://www.gnu.org/licenses/>. | ||
| """ | ||
| model beta_function_with_inline_expression_neuron: | ||
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| parameters: | ||
| tau1 ms = 20 ms ## decay time | ||
| tau2 ms = 10 ms ## rise time | ||
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| state: | ||
| x_ pA/ms = 0 pA/ms | ||
| x pA = 0 pA | ||
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| internals: | ||
| alpha real = 42. | ||
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| equations: | ||
| x' = x_ - x / tau2 | ||
| x_' = - x_ / tau1 | ||
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| recordable inline z pA = x | ||
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| input: | ||
| weighted_input_spikes <- spike | ||
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| output: | ||
| spike | ||
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| update: | ||
| integrate_odes() | ||
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| onReceive(weighted_input_spikes): | ||
| x_ += alpha * (1 / tau2 - 1 / tau1) * pA * weighted_input_spikes * s |
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