Source code for gemseo.wrappers.matlab.matlab_discipline

# -*- coding: utf-8 -*-
# Copyright 2021 IRT Saint Exupéry,
# This program is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License version 3 as published by the Free Software Foundation.
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# Lesser General Public License for more details.
# You should have received a copy of the GNU Lesser General Public License
# along with this program; if not, write to the Free Software Foundation,
# Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.

# -*-mode: python; py-indent-offset: 4; tab-width: 8; coding:utf-8 -*-
# Copyright (c) 2018 IRT-AESE.
# All rights reserved.

# Contributors:
#    INITIAL AUTHORS - API and implementation and/or documentation
#        :author: François Gallard: initial Scilab version
#        :author: Arthur Piat: conversion Scilab to Matlab and complementary features
#        :author: Nicolas Roussouly: GEMSEO integration

"""Definition of the Matlab discipline.


This module contains the :class:`.MatlabDiscipline`
which enables to automatically create a wrapper of any Matlab function.
This class can be used in order to interface any Matlab code
and to use it inside a MDO process.

import logging
import os
import re
from os.path import exists, join
from typing import List, Mapping, Optional, Sequence, Union

import matlab.engine
import numpy as np

from gemseo.core.discipline import MDODiscipline
from gemseo.utils.py23_compat import Path
from gemseo.wrappers.matlab.engine import get_matlab_engine
from gemseo.wrappers.matlab.matlab_data_processor import (
from gemseo.wrappers.matlab.matlab_parser import MatlabParser

LOGGER = logging.getLogger(__name__)

[docs]class MatlabDiscipline(MDODiscipline): """Base wrapper for matlab discipline. Generates a discipline of given matlab function and wrap it to be executed with GEMSEO. Can be used on encrypted, MATLAB build-in and user made function. Examples: >>> # build the discipline from the MATLAB function "function.m" >>> disc = MatlabDiscipline("function.m") >>> # Execute the discipline >>> disc.execute({"x" : array([2.]), "y" : array([1.])}) >>> >>> # build discipline with initial data from MATLAB file >>> disc = MatlabDiscipline("function.m", matlab_data_file="data.mat") >>> # execute discipline from default values >>> disc.execute() >>> >>> # build discipline from MATLAB file located in matlab_files directory >>> disc = MatlabDiscipline("function.m", search_file="matlab_files") >>> >>> # build discipline with jacobian returned by the matlab function >>> disc = MatlabDiscipline("function.m", is_jac_returned_by_func=True) >>> disc.execute({"x" : array([2.]), "y" : array([1.])}) >>> # print jacboian values >>> print(disc.jac) Note: If ``is_jac_returned_by_func`` is True, jacobian matrices must be returned by the matlab function itself. In such case, function outputs must contain standard output as well as new outputs for jacobian terms. These new outputs must follow naming convention described in function :meth:`MatlabDiscipline._get_jac_name`. They can be returned in any order. """ JAC_PREFIX = "jac_" def __init__( self, matlab_fct, # type: Union[str, Path] input_data_list=None, # type: Optional[Sequence[str]] output_data_list=None, # type: Optional[Sequence[str]] add_subfold_path=False, # type: bool search_file=None, # type: Optional[str] matlab_engine_name="matlab", # type: str matlab_data_file=None, # type: Optional[Union[str, Path]] name=None, # type: Optional[str] clean_cache_each_n=None, # type: Optional[int] input_grammar_file=None, # type: Optional[str] output_grammar_file=None, # type: Optional[str] auto_detect_grammar_files=False, # type: bool check_opt_data=True, # type: bool cache_type=MDODiscipline.SIMPLE_CACHE, # type: str grammar_type=MDODiscipline.JSON_GRAMMAR_TYPE, # type: str cache_file_path=None, # type: Optional[str] is_jac_returned_by_func=False, # type: bool ): # type: (...) -> None # noqa: D205,D212,D415 """ Args: matlab_fct: The path of the Matlab file or Name of the function. input_data_list: The list of input variables. output_data_list: The list of output variables. add_subfold_path: If True, add all sub-folder to matlab engine path.. search_file: The root directory to launch the research of matlab file. matlab_engine_name: The name of the singleton used for this discipline. matlab_data_file: The .mat file or path containing default values of data. name: The name of discipline. clean_cache_each_n: Iteration interval at which matlab workspace is cleaned. input_grammar_file: The file for input grammar description, if None, name + "_input.json" is used. output_grammar_file: The file for output grammar description. auto_detect_grammar_files: If no input and output grammar files are provided, auto_detect_grammar_files uses a naming convention to associate a grammar file to a discipline: searches in the "comp_dir" directory containing the discipline source file for files basenames _input.json and _output.json. check_opt_data: If true, check input and output data of discipline, pass if False. cache_type: The type of cache policy, SIMPLE_CACHE or HDF5_CACHE. grammar_type: The type of grammar to use for IO declaration either JSON_GRAMMAR_TYPE or SIMPLE_GRAMMAR_TYPE. cache_file_path: The file to store the data, mandatory when HDF caching is used. is_jac_returned_by_func: If True, the jacobian matrices should be returned of matlab function with standard outputs. Default is False. If True, the conventional name 'jac_dout_din' is used as jacobian term of any output 'out' with respect to input 'in'. """ super(MatlabDiscipline, self).__init__( name=name, input_grammar_file=input_grammar_file, output_grammar_file=output_grammar_file, auto_detect_grammar_files=auto_detect_grammar_files, cache_type=cache_type, grammar_type=grammar_type, cache_file_path=cache_file_path, ) self.__fct_name = None matlab_fct = str(matlab_fct) if input_data_list is None or output_data_list is None: parser = MatlabParser() if search_file is not None: path = self.search_file(matlab_fct, search_file) parser.parse(path) if matlab_data_file is not None and not exists(str(matlab_data_file)): matlab_data_file = self.search_file( str(matlab_data_file), search_file, ".mat" ) else: parser.parse(matlab_fct) input_data = parser.inputs output_data = parser.outputs function_path = ( / parser.function_name).with_suffix(".m") else: function_path = matlab_fct if input_data_list is not None: input_data = input_data_list if output_data_list is not None: output_data = output_data_list self.__engine = get_matlab_engine(matlab_engine_name) self.__inputs = input_data self.__outputs = output_data # init size with -1 -> means that size is currently unknown self.__is_size_known = False self.__inputs_size = {var: -1 for var in self.__inputs} self.__outputs_size = {var: -1 for var in self.__outputs} # self.outputs can be filtered here self.__is_jac_returned_by_func = is_jac_returned_by_func self.__jac_output_names = [] self.__jac_output_indices = [] if self.__is_jac_returned_by_func: self.__filter_jacobian_in_outputs() self.__check_function(function_path, add_subfold_path) self.__check_opt_data = check_opt_data self.cleaning_interval = clean_cache_each_n self.__init_default_data( matlab_data_file, input_grammar_file, output_grammar_file, auto_detect_grammar_files, ) self.data_processor = MatlabDataProcessor() if self.__is_jac_returned_by_func: self.__reorder_and_check_jacobian_consistency() @property def function_name(self): # type: (...) -> str """Return the name of the function.""" return self.__fct_name
[docs] @staticmethod def search_file( file_name, # type: str root_dir, # type: str extension=".m", # type: str ): # type: (...) -> str """Locate recursively a file in the given root directory. Args: file_name: The name of the file to be located. root_dir: The root directory to launch the research. extension: The extension of the file in case not given by user. Returns: The path of the given file. Raises: IOError: * If two files are found in same directory; * If no file is found. """ found_file = False re_matfile = re.compile(r"\S+\.\S*") grps = if grps is None: file_name = file_name + extension file_path = "" for subdir, _, files in os.walk(str(root_dir)): for file_loc in files: if file_loc == file_name: if found_file: msg = "At least two files {} were in directory {}".format( file_name, root_dir ) msg += "\n File one: {};".format(file_path) msg += "\n File two: {}.".format(join(subdir, file_loc)) raise IOError(msg) found_file = True file_path = join(subdir, file_loc) dir_name = subdir if not found_file: raise IOError( "No file: {}, found in directory: {}.".format(file_name, root_dir) )"File: %s found in directory: %s.", file_name, dir_name) return file_path
def __check_function( self, matlab_fct, # type: Union[str, Path] add_subfold_path, # type: bool ): # type (...) --> None """Check the availability of the prescribed MATLAB function. The function manages encrypted, build-in and user made function and unify their use. Args: matlab_fct: A name for the matlab function to be wrapped. add_subfold_path: If true, add all sub-folders of the function to matlab search path. Raises: NameError: If the function (or file) does not exist. """ path = Path(matlab_fct) if path.exists(): # Test if the file exists in the system self.__engine.add_path(path.parent, add_subfolder=add_subfold_path) self.__fct_name = path.stem elif self.__engine.exist(matlab_fct)[0]: # If file does not exist, try to find an existing build-in function in # engine self.__fct_name = matlab_fct else: # If no file and build-in function exist, raise error msg = 'No existing file or function "{}".'.format(matlab_fct) raise NameError(msg) def __init_default_data( self, matlab_data_file, # type: str input_grammar_file, # type: str output_grammar_file, # type: str auto_detect_grammar_files, # type: bool ): # type: (...) -> None """Initialize default data of the discipline. Args: matlab_data_file: The path to the .mat containing default values of data input_grammar_file: The file for input grammar description, if None, name + "_input.json" is used. output_grammar_file: The file for output grammar description. auto_detect_grammar_files: If True, no input and output grammar files. """ if matlab_data_file is not None: saved_values = convert_array_from_matlab( load_matlab_file(str(matlab_data_file).replace(".mat", "")) ) if input_grammar_file is None and not auto_detect_grammar_files: # Here, we temporary init inputs data with an array of # size 1 but that could not be the right size... # The right size can be known from either matlab_data_file or evaluating # the matlab function inputs_dict = dict.fromkeys(self.__inputs, np.array([0.1])) if matlab_data_file is not None: inputs_dict = self.__update_default_val( inputs_dict.copy(), saved_values ) if output_grammar_file is None and not auto_detect_grammar_files: # same remark as above about the size outputs_dict = dict.fromkeys(self.__outputs, np.array([0.1])) if matlab_data_file is not None: outputs_dict = self.__update_default_val( outputs_dict.copy(), saved_values ) self.input_grammar.initialize_from_base_dict(inputs_dict) self.output_grammar.initialize_from_base_dict(outputs_dict) # If none input matlab data is prescribed, we cannot know # the size of inputs and outputs. Thus we must evaluate # the function in order to know the sizes if matlab_data_file is not None: self.__is_size_known = True for in_name, val in inputs_dict.items(): self.__inputs_size[in_name] = len(val) for out_name, val in outputs_dict.items(): self.__outputs_size[out_name] = len(val) default_values = inputs_dict.copy() default_values.update(outputs_dict) self.default_inputs = default_values def __filter_jacobian_in_outputs(self): # type: (...) -> None """Filter jacobians in outputs names. This function is applied when _is_jac_returned_by_func is True. In such case, the function extracts the jacobian component from the list of output names returned by the matlab function. It thus fills _jac_output_names attributes as well as _jac_output_indices which corresponds to indices of jacobian component in the list of outputs returned by the matlab function. After applying this function, _outputs attribute no longer contains jacobian output names but only standard outputs. In order to filter jacobian component, this function just checks that jacobian names are prefixed by 'jac_'. """ output_names = list(self.__outputs) # select jacobian output and remove them from self.outputs for i, out_name in enumerate(self.__outputs): if out_name[0:4] == self.JAC_PREFIX: self.__jac_output_names.append(out_name) self.__jac_output_indices.append(i) output_names.remove(out_name) # here self.outputs only contains output responses (no jacobian) self.__outputs = output_names def __reorder_and_check_jacobian_consistency(self): # type: (...) -> None """This function checks jacobian output consistency. This function is used when _is_jac_returned_by_func is True. The function is called after calling jacobian filtering :meth:`MatlabDiscipline._filter_jacobian_in_outputs`. It enables to: * check that all outputs have a jacobian matrix with respect to all inputs; * reorder the list of jacobian names (and indices) following the order from iterating over outputs then inputs lists; In order to check that all jacobian components exist, the function uses the conventional naming described in :meth:`MatlabDiscipline._get_jac_name`. Raises: ValueError: * If the number of jacobian outputs is wrong; * If a specific jacobian output has the wrong name. """ conventional_jac_names = self.__get_conventional_jac_names() new_indices = [-1] * len(conventional_jac_names) if len(conventional_jac_names) != len(self.__jac_output_names): raise ValueError( "The number of jacobian outputs does " "not correspond to what it should be. " "Make sure that all outputs have a jacobian " "matrix with respect to inputs." ) not_found = [] for i, name in enumerate(conventional_jac_names): try: idx = self.__jac_output_names.index(name) new_indices[i] = self.__jac_output_indices[idx] except ValueError: not_found.append(name) if not_found: raise ValueError( "Jacobian terms {} are not found in the " "list of conventional names. It is reminded that " "jacobian terms' name should be " "such as 'jac_dout_din'".format(not_found) ) self.__jac_output_names = conventional_jac_names self.__jac_output_indices = new_indices def __get_conventional_jac_names(self): # type: (...) -> List[str] """Return the list of jacobian names following the conventional naming. The conventional naming is described in :meth:`MatlabDiscipline._get_jac_name`. """ return [ self.__get_jac_name(out_var, in_var) for out_var in self.__outputs for in_var in self.__inputs ] def __get_jac_name( self, out_var, # type: str in_var, # type: str ): # type: (...) -> str """Return the name of jacobian given input and ouput variables. The conventional naming of jacobian component is the following: if outputs have any names ``out_1``, ``out_2``... and inputs are ``in_1``, ``in_2``... Therefore, names of jacobian components returned by the matlab function must be: ``jac_dout_1_din_1``, ``jac_dout_1_din_2``, ``jac_dout_2_din_1``, ``jac_dout_2_din_2``... which means that the names must be prefixed by ``jac_``, and followed by ``doutput`` and ``dinput`` seperated by ``_``. Args: out_var: The output variable name. in_var: The input variable name. Returns: The jacobian matrix name of output with respect to input. """ return str( "{prefix}d{outv}_d{inv}".format( prefix=self.JAC_PREFIX, outv=out_var, inv=in_var ) )
[docs] def check_input_data( self, input_data, # type: Mapping[str, np.ndarray] raise_exception=True, # type: bool ): # type: (...) -> None # noqa: D102 if self.__check_opt_data: super(MatlabDiscipline, self).check_input_data( input_data, raise_exception=raise_exception )
[docs] def check_output_data( self, raise_exception=True # type: bool ): # type(...) -> None # noqa: D102 if self.__check_opt_data: super(MatlabDiscipline, self).check_output_data( raise_exception=raise_exception )
def _run(self): # type: (...) -> None """Run the Matlab discipline. If jacobian values are returned by the matlab function, they are filtered and used in order to fill :attr:`MatlabDiscipline.jac`. Raises: ValueError: * If the execution of the matlab function fails. * If the size of the jacobian output matrix is wrong. """ # import pudb;pudb.set_trace() input_vals = self.get_input_data() list_of_values = [input_vals.get(k) for k in self.__inputs if k in input_vals] try: out_vals = self.__engine.execute_function( self.__fct_name, *list_of_values, nargout=len(self.__outputs) + len(self.__jac_output_names) ) except matlab.engine.MatlabExecutionError: LOGGER.error("Discipline: %s execution failed", raise # filter output values if jacobian is returned jac_vals = [] if self.__is_jac_returned_by_func: out_vals = np.array(out_vals, dtype=object) jac_vals = [out_vals[idx] for idx in self.__jac_output_indices] out_vals = np.delete(out_vals, self.__jac_output_indices) # --> now out_vals only contains output responses (no jacobian) if self.cleaning_interval is not None: if self._n_calls.value % self.cleaning_interval == 0: self.__engine.execute_function("clear", "all", nargout=0) "MATLAB cache cleaned: Discipline called %s times", self._n_calls.value, ) out_names = self.__outputs if len(out_names) == 1: self.store_local_data(**{out_names[0]: double2array(out_vals)}) else: for out_n, out_v in zip(out_names, out_vals): self.store_local_data(**{out_n: double2array(out_v)}) if not self.__is_size_known: for i, var in enumerate(self.__inputs): self.__inputs_size[var] = len(list_of_values[i]) for var in self.__outputs: self.__outputs_size[var] = len(self.local_data[var]) self.__is_size_known = True if self.__is_jac_returned_by_func: # fill jac dict self._init_jacobian() cpt = 0 for out_name in self.__outputs: self.jac[out_name] = {} for in_name in self.__inputs: self.jac[out_name][in_name] = np.atleast_2d(jac_vals[cpt]) if self.jac[out_name][in_name].shape != ( self.__outputs_size[out_name], self.__inputs_size[in_name], ): raise ValueError( "Jacobian term 'jac_d{}_d{}' " "has the wrong size {} whereas it should " "be {}.".format( out_name, in_name, self.jac[out_name][in_name].shape, ( self.__outputs_size[out_name], self.__inputs_size[in_name], ), ) ) cpt += 1 self._is_linearized = True @staticmethod def __update_default_val( inputs_dict, # type: dict updating_dict, # type: dict ): # type: (...) -> dict """Update only presented key with new values from another dict. Args: inputs_dict: The dict to be updated. updating_dict: The dict containing new values. Returns: The ``inputs_dict`` with only matching keys from ``updating_dict`` updated. """ for key in updating_dict: if key in inputs_dict.keys(): inputs_dict[key] = updating_dict[key] return inputs_dict
[docs] def save_data_to_matlab( self, file_path # type: Union[str, Path] ): # type: (...) -> None """Save local data to matlab .mat format. Args: file_path: The path where to save the file. """ file_path = Path(file_path) save_matlab_file(self.local_data, file_path=file_path) msg = "Local data of discipline {} exported to {}.mat successfully.".format(, )
@property def cleaning_interval(self): # type: (...) -> int """Get and/or set the flushing interval for matlab disciplines.""" return self.__cleaning_interval @cleaning_interval.setter def cleaning_interval(self, cleaning_interval): if cleaning_interval is not None: is_integer = cleaning_interval % 1 == 0 if not is_integer: raise ValueError( "The parameter 'cleaning_interval' argument must be an integer." ) self.__cleaning_interval = cleaning_interval