pyAgrum-nightly 2.3.1.9.dev202512261765915415__cp310-abi3-macosx_10_15_x86_64.whl

pyagrum/clg/GaussianVariable.py

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+############################################################################
+#   This file is part of the aGrUM/pyAgrum library.                        #
+#                                                                          #
+#   Copyright (c) 2005-2025 by                                             #
+#       - Pierre-Henri WUILLEMIN(_at_LIP6)                                 #
+#       - Christophe GONZALES(_at_AMU)                                     #
+#                                                                          #
+#   The aGrUM/pyAgrum library is free software; you can redistribute it    #
+#   and/or modify it under the terms of either :                           #
+#                                                                          #
+#    - the GNU Lesser General Public License as published by               #
+#      the Free Software Foundation, either version 3 of the License,      #
+#      or (at your option) any later version,                              #
+#    - the MIT license (MIT),                                              #
+#    - or both in dual license, as here.                                   #
+#                                                                          #
+#   (see https://agrum.gitlab.io/articles/dual-licenses-lgplv3mit.html)    #
+#                                                                          #
+#   This aGrUM/pyAgrum library is distributed in the hope that it will be  #
+#   useful, but WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED,          #
+#   INCLUDING BUT NOT LIMITED TO THE WARRANTIES MERCHANTABILITY or FITNESS #
+#   FOR A PARTICULAR PURPOSE  AND NONINFRINGEMENT. IN NO EVENT SHALL THE   #
+#   AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER #
+#   LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE,        #
+#   ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR  #
+#   OTHER DEALINGS IN THE SOFTWARE.                                        #
+#                                                                          #
+#   See LICENCES for more details.                                         #
+#                                                                          #
+#   SPDX-FileCopyrightText: Copyright 2005-2025                            #
+#       - Pierre-Henri WUILLEMIN(_at_LIP6)                                 #
+#       - Christophe GONZALES(_at_AMU)                                     #
+#   SPDX-License-Identifier: LGPL-3.0-or-later OR MIT                      #
+#                                                                          #
+#   Contact  : info_at_agrum_dot_org                                       #
+#   homepage : http://agrum.gitlab.io                                      #
+#   gitlab   : https://gitlab.com/agrumery/agrum                           #
+#                                                                          #
+############################################################################
+
+"""
+class GaussianVariable: Continuous Gaussian Variable
+"""
+
+
+class GaussianVariable:
+  def __init__(self, name: str, mu: float, sigma: float):
+    self._mu = mu
+    self._sigma = sigma
+    self._name = name
+
+  def __repr__(self):
+    return str(self)
+
+  def name(self) -> str:
+    """
+    Returns the name of the variable.
+
+    Returns
+    -------
+    str
+      The name of the variable.
+    """
+    return self._name
+
+  def mu(self) -> float:
+    """
+    Returns the mean of the variable.
+
+    Returns
+    -------
+    float
+      The mean of the variable.
+    """
+    return self._mu
+
+  def sigma(self) -> float:
+    """
+    Returns the standard deviation of the variable.
+
+    Returns
+    -------
+    float
+      The standard deviation of the variable.
+    """
+    return self._sigma
+
+  def setMu(self, mu: float):
+    """
+    Set the mean of the variable.
+
+    Parameters
+    ----------
+    mu : float
+      The new mean of the variable.
+    """
+    self._mu = mu
+
+  def setSigma(self, sigma: float):
+    """
+    Set the standard deviation of the variable.
+
+    Parameters
+    ----------
+    sigma : float
+      The new standard deviation of the variable.
+    """
+    self._sigma = sigma
+
+  def __str__(self) -> str:
+    return f"{self._name}:{self._mu}[{self._sigma}]"

pyagrum/clg/SEM.py

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+############################################################################
+#   This file is part of the aGrUM/pyAgrum library.                        #
+#                                                                          #
+#   Copyright (c) 2005-2025 by                                             #
+#       - Pierre-Henri WUILLEMIN(_at_LIP6)                                 #
+#       - Christophe GONZALES(_at_AMU)                                     #
+#                                                                          #
+#   The aGrUM/pyAgrum library is free software; you can redistribute it    #
+#   and/or modify it under the terms of either :                           #
+#                                                                          #
+#    - the GNU Lesser General Public License as published by               #
+#      the Free Software Foundation, either version 3 of the License,      #
+#      or (at your option) any later version,                              #
+#    - the MIT license (MIT),                                              #
+#    - or both in dual license, as here.                                   #
+#                                                                          #
+#   (see https://agrum.gitlab.io/articles/dual-licenses-lgplv3mit.html)    #
+#                                                                          #
+#   This aGrUM/pyAgrum library is distributed in the hope that it will be  #
+#   useful, but WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED,          #
+#   INCLUDING BUT NOT LIMITED TO THE WARRANTIES MERCHANTABILITY or FITNESS #
+#   FOR A PARTICULAR PURPOSE  AND NONINFRINGEMENT. IN NO EVENT SHALL THE   #
+#   AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER #
+#   LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE,        #
+#   ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR  #
+#   OTHER DEALINGS IN THE SOFTWARE.                                        #
+#                                                                          #
+#   See LICENCES for more details.                                         #
+#                                                                          #
+#   SPDX-FileCopyrightText: Copyright 2005-2025                            #
+#       - Pierre-Henri WUILLEMIN(_at_LIP6)                                 #
+#       - Christophe GONZALES(_at_AMU)                                     #
+#   SPDX-License-Identifier: LGPL-3.0-or-later OR MIT                      #
+#                                                                          #
+#   Contact  : info_at_agrum_dot_org                                       #
+#   homepage : http://agrum.gitlab.io                                      #
+#   gitlab   : https://gitlab.com/agrumery/agrum                           #
+#                                                                          #
+############################################################################
+
+"""
+This module contains the SEM class, which is used to parse a SEM into a CLG model or convert a CLG model into a SEM.
+"""
+
+import re
+import warnings
+
+from .CLG import CLG
+from .GaussianVariable import GaussianVariable
+
+
+class SEM:
+  """
+  This class is used to parse a SEM into a CLG model or convert a CLG model into a SEM.
+
+  code
+  ----
+
+  sem = SEM('''
+  # hyper parameters
+  A = 4[5]
+  B = 3[5]
+  C = -2[5]
+
+  # equations
+  D = A[.2]  # D is a noisy version of A
+  E = 1 + D + 2
+  B[2]
+  F = E + C + 3.5*B + E[0.001]
+  ''')
+  """
+
+  NUMBER = r"[0-9]*\.?[0-9]*"
+  ID = r"[a-zA-Z_]\w*"
+  FIND_VAR = rf"^({ID})$"
+  FIND_STDDEV = rf"^\[({NUMBER})\]$"
+  FIND_FLOAT = rf"^({NUMBER})$"
+  FIND_TERM = rf"^({NUMBER})\*?({ID})$"
+
+  _reg_variable = re.compile(FIND_VAR)
+  _reg_stddev = re.compile(FIND_STDDEV)
+  _reg_term = re.compile(FIND_TERM)
+  _reg_float = re.compile(FIND_FLOAT)
+
+  def __init__(self):
+    """
+    Constructor
+    """
+    warnings.warn("SEM has not to be instantiated.")
+
+  @staticmethod
+  def _check_token(s, pos, pattern):
+    """
+    Check if the string s[pos:] matches the pattern.
+    If it does, return the match and the position of the next character.
+    If it does not, return None, None.
+
+    Parameters
+    ----------
+    s : str
+      The string to be checked.
+    pos : int
+      The position in the string where to start the check.
+    pattern : re.Pattern
+      The pattern to be matched.
+
+    Returns
+    -------
+    Tuple[str, int] or Tuple[None, None]
+      The match and the position of the next character if the string matches the pattern.
+    """
+    res = pattern.match(s[pos:])
+    if res is None:
+      return None, None
+    else:
+      return res.group(1), res.end()
+
+  @staticmethod
+  def _parse_line(s: str):
+    """
+    This function parses a line of a SEM.
+
+    Parameters
+    ----------
+    s : str
+      The line to be parsed.
+
+    Returns
+    -------
+    Tuple[str, Dict[str, str | float], float]
+      The name of the variable, the dictionary of the terms and the standard deviation.
+    """
+
+    ss = s.split("#")[0]
+    ss = "".join(ss.split())
+    # allow every tokens to be separated with "+"
+    ss = ss.replace("-+", "-")
+    ss = ss.replace("-", "+-")
+    ss = ss.replace("=", "=+")
+    ss = ss.replace("[", "+[")
+
+    # to be sure there are now empty tokens
+    tokens = [s for s in ss.split("+") if s != ""]
+
+    token = tokens.pop()
+    if SEM._reg_stddev.match(token) is None:
+      raise SyntaxError(f"{token=} not recognized as a stdev")
+    stddev = token[1:-1]
+
+    tokens.reverse()
+    token = tokens.pop()
+    if token[-1] != "=":
+      raise SyntaxError("No affectation operator ('=')")
+    variable = token[:-1]
+    if SEM._reg_variable.match(variable) is None:
+      raise SyntaxError(f"{variable=} not a variable")
+
+    terms = {}
+    for token in tokens:
+      # get rid of "-" at the beginning of token
+      if token[0] == "-":
+        coef = -1
+        token = token[1:]
+      else:
+        coef = 1
+
+      if (m := SEM._reg_variable.match(token)) is not None:
+        var = m.group(0)
+      elif (m := SEM._reg_float.match(token)) is not None:
+        coef *= float(m.group(0))
+        var = ""
+      elif (m := SEM._reg_term.match(token)) is not None:
+        coef *= float(m.group(1))
+        var = m.group(2)
+      else:
+        break
+
+      # allow more than one term for the same variable (or more than one constant)
+      if var in terms:
+        terms[var] += coef
+      else:
+        terms[var] = coef
+
+    if len(terms) > len(tokens):
+      raise SyntaxError("Some tokens not recognized")
+    if len(terms) + 2 < len(tokens):
+      raise SyntaxError("Tokens after stddev")
+
+    return variable, terms, float(stddev)
+
+  @staticmethod
+  def toclg(sem: str) -> CLG:
+    """
+    This function parses a SEM into a CLG model.
+
+    Parameters
+    ----------
+    sem : str
+      The SEM to be parsed.
+
+    Returns
+    -------
+    CLG
+      The CLG model corresponding to the SEM.
+    """
+
+    canonic_form = []
+    for line in re.split("\n+", sem):
+      line = line.strip()
+      if line == "":
+        continue
+      if line[0] == "#":
+        continue
+      if "=" in line:  # new equation
+        canonic_form.append(line)
+      else:
+        if len(canonic_form) == 0:
+          raise SyntaxError(f"Line '{line}' is not an equation.")
+        canonic_form[-1] += line
+
+    # parsing the canonic_form
+    clg = CLG()
+    arcs = []
+    arcs = []
+    for line in canonic_form:
+      try:
+        var, terms, stddev = SEM._parse_line(line)
+      except SyntaxError as e:
+        raise SyntaxError(f"In line {line}, {e.msg()}.")
+      mu = 0
+      for parent in terms:
+        if parent == "":
+          mu = terms[""]
+        else:
+          arcs.append((parent, var, terms[parent]))
+      clg.add(GaussianVariable(var, mu, stddev))
+    for head, tail, coef in arcs:
+      clg.addArc(head, tail, coef)
+
+    return clg
+
+  @staticmethod
+  def tosem(clg: CLG) -> str:
+    """
+    This function converts a CLG model into a SEM.
+
+    Parameters
+    ----------
+    clg : CLG
+      The CLG model to be converted.
+
+    Returns
+    -------
+    lines : str
+      The SEM corresponding to the CLG model.
+    """
+
+    lines = ""
+    for node in clg.topologicalOrder():
+      line = ""
+
+      # after the "="
+      for parent in clg.parents(node):
+        if clg._arc2coef[(parent, node)] == 1:
+          line += f"+{clg._id2var[parent].name()}"
+        elif clg._arc2coef[(parent, node)] < 0:
+          line += f"-{-clg._arc2coef[(parent, node)]}{clg._id2var[parent].name()}"
+        else:
+          line += f"+{clg._arc2coef[(parent, node)]}{clg._id2var[parent].name()}"
+      line += f"[{clg._id2var[node].sigma()}]"
+
+      # before the "="
+      line = clg._id2var[node].name() + "=" + str(clg._id2var[node].mu()) + line
+      line = line.replace("=0+", "=")  # remove the 0
+
+      lines += line + "\n"
+
+    return lines
+
+  @staticmethod
+  def saveCLG(clg: CLG, filename: str):
+    """
+    Save the CLG as a SEM to a file.
+
+    Parameters
+    ----------
+    clg : CLG
+      The CLG model to be saved.
+    filename : str
+      The name of the file containing the SEM of CLG.
+    """
+    with open(filename, "w") as file:
+      file.write(SEM.tosem(clg))
+
+  @staticmethod
+  def loadCLG(filename: str) -> CLG:
+    """
+    Load the CLG from the file containing a SEM.
+
+    Parameters
+    ----------
+    filename : str
+      The name of the file containing the SEM of CLG.
+
+    Returns
+    -------
+    the loaded CLG
+    """
+    with open(filename, "r") as file:
+      sem = file.read()
+
+    return SEM.toclg(sem)

pyagrum/clg/__init__.py

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+############################################################################
+#   This file is part of the aGrUM/pyAgrum library.                        #
+#                                                                          #
+#   Copyright (c) 2005-2025 by                                             #
+#       - Pierre-Henri WUILLEMIN(_at_LIP6)                                 #
+#       - Christophe GONZALES(_at_AMU)                                     #
+#                                                                          #
+#   The aGrUM/pyAgrum library is free software; you can redistribute it    #
+#   and/or modify it under the terms of either :                           #
+#                                                                          #
+#    - the GNU Lesser General Public License as published by               #
+#      the Free Software Foundation, either version 3 of the License,      #
+#      or (at your option) any later version,                              #
+#    - the MIT license (MIT),                                              #
+#    - or both in dual license, as here.                                   #
+#                                                                          #
+#   (see https://agrum.gitlab.io/articles/dual-licenses-lgplv3mit.html)    #
+#                                                                          #
+#   This aGrUM/pyAgrum library is distributed in the hope that it will be  #
+#   useful, but WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED,          #
+#   INCLUDING BUT NOT LIMITED TO THE WARRANTIES MERCHANTABILITY or FITNESS #
+#   FOR A PARTICULAR PURPOSE  AND NONINFRINGEMENT. IN NO EVENT SHALL THE   #
+#   AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER #
+#   LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE,        #
+#   ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR  #
+#   OTHER DEALINGS IN THE SOFTWARE.                                        #
+#                                                                          #
+#   See LICENCES for more details.                                         #
+#                                                                          #
+#   SPDX-FileCopyrightText: Copyright 2005-2025                            #
+#       - Pierre-Henri WUILLEMIN(_at_LIP6)                                 #
+#       - Christophe GONZALES(_at_AMU)                                     #
+#   SPDX-License-Identifier: LGPL-3.0-or-later OR MIT                      #
+#                                                                          #
+#   Contact  : info_at_agrum_dot_org                                       #
+#   homepage : http://agrum.gitlab.io                                      #
+#   gitlab   : https://gitlab.com/agrumery/agrum                           #
+#                                                                          #
+############################################################################
+
+""" """
+
+__author__ = "Pierre-Henri Wuillemin, Zhe Huang"
+__copyright__ = "(c) 2022-2023 PARIS"
+
+from .canonicalForm import CanonicalForm
+from .CLG import CLG, randomCLG
+from .forwardSampling import ForwardSampling
+from .GaussianVariable import GaussianVariable
+from .variableElimination import CLGVariableElimination
+from .learning import CLGLearner
+from .SEM import SEM
+
+__all__ = [
+  "CanonicalForm",
+  "CLG",
+  "randomCLG",
+  "ForwardSampling",
+  "GaussianVariable",
+  "CLGVariableElimination",
+  "CLGLearner",
+  "SEM",
+]