pyAgrum-nightly 2.3.0.9.dev202512061764412981__cp310-abi3-macosx_11_0_arm64.whl

pyagrum/lib/mrf2graph.py

@@ -0,0 +1,471 @@
+############################################################################
+#   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                           #
+#                                                                          #
+############################################################################
+
+"""
+The purpose of this module is to provide tools for mapping Markov random field (and inference) in dot language in order to
+be displayed/saved as image.
+"""
+
+import time
+import hashlib
+
+import matplotlib.pyplot as plt
+import pydot as dot
+
+import pyagrum as gum
+import pyagrum.lib._colors as gumcols
+
+from .proba_histogram import saveFigProba
+
+
+def MRF2UGdot(
+  mrf,
+  size="4",
+  nodeColor=None,
+  edgeWidth=None,
+  edgeLabel=None,
+  edgeColor=None,
+  cmapNode=None,
+  cmapEdge=None,
+  showMsg=None,
+):
+  """
+  Create a pydot representation of the Markov random field as an undirected graph
+
+  Parameters
+  ----------
+  mrf: pyagrum.MarkovRandomField
+    The Markov random field
+  size : int |str
+    Size of the rendered graph
+  nodeColor : Dict[int,float]
+    a nodeMap of values (between 0 and 1) to be shown as color of nodes (with special colors for 0 and 1)
+  edgeWidth : Dict[Tuple(int,int),float]
+    a edgeMap of values to be shown as width of edges
+  edgeLabel: Dict[Tuple(int,int),str]
+    an edgeMap of labels to be shown next to edges
+  edgeColor: Dict[Tuple(int,int),float]
+    a edgeMap of values to be shown as color of edges
+  cmapNode : matplotlib.color.colormap
+    color map to show the vals of Nodes
+  cmapEdge : matplotlib.color.colormap
+    color map to show the vals of Edges.
+  showMsg : Dict[int,str]
+     a nodeMap of values to be shown as tooltip
+
+  Returns
+  -------
+  pydot.Dot
+    the desired representation of the MRF as a dot graph
+  """
+  if cmapNode is None:
+    cmapNode = plt.get_cmap(gum.config["notebook", "default_node_cmap"])
+
+  if cmapEdge is None:
+    cmapEdge = plt.get_cmap(gum.config["notebook", "default_edge_cmap"])
+
+  # default
+  maxedges = 100
+  minedges = 0
+
+  if edgeWidth is not None:
+    minedges = min(edgeWidth.values())
+    maxedges = max(edgeWidth.values())
+
+  graph = dot.Dot(graph_type="graph", bgcolor="transparent")
+
+  for n in mrf.names():
+    if nodeColor is None or n not in nodeColor:
+      bgcol = gum.config["notebook", "default_node_bgcolor"]
+      fgcol = gum.config["notebook", "default_node_fgcolor"]
+      res = ""
+    else:
+      bgcol = gumcols.proba2bgcolor(nodeColor[n], cmapNode)
+      fgcol = gumcols.proba2fgcolor(nodeColor[n], cmapNode)
+      res = f" : {nodeColor[n] if showMsg is None else showMsg[n]:2.5f}"
+
+    node = dot.Node(
+      '"' + n + '"', style="filled", fillcolor=bgcol, fontcolor=fgcol, tooltip=f'"({mrf.idFromName(n)}) {n}{res}"'
+    )
+    graph.add_node(node)
+
+  for a in mrf.edges():
+    (n, j) = a
+    pw = 1
+    av = f"{n} — {j}"
+    col = gumcols.getBlackInTheme()
+    lb = ""
+
+    if edgeWidth is not None and a in edgeWidth:
+      if maxedges != minedges:
+        pw = 0.1 + 5 * (edgeWidth[a] - minedges) / (maxedges - minedges)
+      av = f"{n} — {j} : {edgeWidth[a]}"
+
+    if edgeColor is not None and a in edgeColor:
+      col = gumcols.proba2color(edgeColor[a], cmapEdge)
+
+    if edgeLabel is not None and a in edgeLabel:
+      lb = edgeLabel[a]
+
+    edge = dot.Edge(
+      '"' + mrf.variable(a[0]).name() + '"',
+      '"' + mrf.variable(a[1]).name() + '"',
+      label=lb,
+      fontsize="10",
+      penwidth=pw,
+      color=col,
+      tooltip=av,
+    )
+    graph.add_edge(edge)
+
+  if size is None:
+    size = gum.config["notebook", "default_graph_size"]
+  graph.set_size(size)
+  return graph
+
+
+def MRF2FactorGraphdot(mrf, size=None, nodeColor=None, factorColor=None, cmapNode=None, showMsg=None):
+  """
+  Create a pydot representation of the Markov random field as a factor graph
+
+  Parameters
+  ----------
+  mrf: pyagrum.MarkovRandomField
+    the model
+  size: float|str
+    the size of the rendered graph
+  nodeColor: Dict[str,float]
+    a nodeMap of values (between 0 and 1) to be shown as color of nodes (with special colors for 0 and 1)
+  factorColor:
+    a function returning a value (between 0 and 1) to be shown as a color of factor.
+  cmapNode: matplotlib.colors.Colormap
+    colormap for nodes
+  showMsg: Dict[str,str]
+    a nodeMap of values to be shown as tooltip
+
+  Returns
+  -------
+  pydot.Dot
+    the desired representation of the MRF as a dot graph
+  """
+  if cmapNode is None:
+    cmapNode = plt.get_cmap(gum.config["notebook", "default_node_cmap"])
+
+  graph = dot.Dot(graph_type="graph", bgcolor="transparent", layout=gum.config["factorgraph", "graph_layout"])
+
+  for n in mrf.names():
+    if nodeColor is None or n not in nodeColor:
+      bgcol = gum.config["factorgraph", "default_node_bgcolor"]
+      fgcol = gum.config["factorgraph", "default_node_fgcolor"]
+      res = ""
+    else:
+      bgcol = gumcols.proba2bgcolor(nodeColor[n], cmapNode)
+      fgcol = gumcols.proba2fgcolor(nodeColor[n], cmapNode)
+      res = f" : {nodeColor[n] if showMsg is None else showMsg[n]:2.5f}"
+
+    node = dot.Node(
+      '"' + n + '"',
+      style="filled",
+      fillcolor=bgcol,
+      fontcolor=fgcol,
+      shape="rectangle",
+      margin=0.04,
+      width=0,
+      height=0,
+      tooltip=f'"({mrf.idFromName(n)}) {n}{res}"',
+    )
+    graph.add_node(node)
+
+  def factorname(factor):
+    return '"f' + "#".join(map(str, sorted(list(factor)))) + '"'
+
+  for f in mrf.factors():
+    if factorColor is None:
+      bgcol = gum.config["factorgraph", "default_factor_bgcolor"]
+    else:
+      bgcol = gumcols.proba2bgcolor(factorColor(f), cmapNode)
+    node = dot.Node(factorname(f), style="filled", fillcolor=bgcol, shape="point", width=0.1, height=0.1)
+    graph.add_node(node)
+
+  for f in mrf.factors():
+    for n in f:
+      edge = dot.Edge(
+        factorname(f),
+        '"' + mrf.variable(n).name() + '"',
+        color=gumcols.getBlackInTheme(),
+        len=gum.config["factorgraph", "edge_length"],
+      )
+      graph.add_edge(edge)
+
+  if size is None:
+    size = gum.config["notebook", "default_graph_size"]
+  graph.set_size(size)
+  return graph
+
+
+def MRFinference2UGdot(
+  mrf,
+  size=None,
+  engine=None,
+  evs=None,
+  targets=None,
+  nodeColor=None,
+  factorColor=None,
+  arcWidth=None,
+  arcColor=None,
+  cmapNode=None,
+  cmapArc=None,
+  view=None,
+):
+  """
+  create a pydot representation of an inference in a MRF as an UG
+
+  :param pyagrum.MarkovRandomField mrf:
+  :param string size: size of the rendered graph
+  :param pyAgrum Inference engine: inference algorithm used. If None, ShaferShenoyMRFInference will be used
+  :param dictionnary evs: map of evidence
+  :param set targets: set of targets. If targets={} then each node is a target
+  :param nodeColor: a nodeMap of values to be shown as color nodes (with special color for 0 and 1)
+  :param arcWidth: a arcMap of values to be shown as bold arcs
+  :param arcColor: a arcMap of values (between 0 and 1) to be shown as color of arcs
+  :param cmapNode: color map to show the vals of Nodes
+  :param cmapArc: color map to show the vals of Arcs
+
+  :return: the desired representation of the inference
+  """
+  if evs is None:
+    evs = {}
+  if targets is None:
+    targets = {}
+
+  if cmapNode is None:
+    cmapNode = plt.get_cmap(gum.config["notebook", "default_node_cmap"])
+
+  if cmapArc is None:
+    cmapArc = plt.get_cmap(gum.config["notebook", "default_arc_cmap"])
+
+  # default
+  minarcs = 0
+  maxarcs = 100
+
+  if arcWidth is not None:
+    minarcs = min(arcWidth.values())
+    maxarcs = max(arcWidth.values())
+
+  startTime = time.time()
+  if engine is None:
+    ie = gum.ShaferShenoyMRFInference(mrf)
+  else:
+    ie = engine
+  ie.setEvidence(evs)
+  ie.makeInference()
+  stopTime = time.time()
+
+  from tempfile import mkdtemp
+
+  temp_dir = mkdtemp("", "tmp", None)  # with TemporaryDirectory() as temp_dir:
+
+  dotstr = 'graph structs {\n  fontcolor="' + gumcols.getBlackInTheme() + '";bgcolor="transparent";'
+
+  if gum.config.asBool["notebook", "show_inference_time"]:
+    dotstr += f'  label="Inference in {1000 * (stopTime - startTime):6.2f}ms";\n'
+
+  fontname, fontsize = gumcols.fontFromMatplotlib()
+  dotstr += f'  node [fillcolor="{gum.config["notebook", "default_node_bgcolor"]}", style=filled,color="{gum.config["notebook", "default_node_fgcolor"]}",fontname="{fontname}",fontsize="{fontsize}"];\n'
+  dotstr += f'  edge [color="{gumcols.getBlackInTheme()}"];\n'
+
+  for nid in mrf.nodes():
+    name = mrf.variable(nid).name()
+
+    # defaults
+    bgcol = gum.config["notebook", "default_node_bgcolor"]
+    fgcol = gum.config["notebook", "default_node_fgcolor"]
+    if len(targets) == 0 or name in targets or nid in targets:
+      bgcol = gum.config["notebook", "figure_facecolor"]
+
+    if nodeColor is not None and (name in nodeColor or nid in nodeColor):
+      bgcol = gumcols.proba2bgcolor(nodeColor[name], cmapNode)
+      fgcol = gumcols.proba2fgcolor(nodeColor[name], cmapNode)
+
+    # 'hard' colour for evidence (?)
+    if nid in ie.hardEvidenceNodes() | ie.softEvidenceNodes():
+      bgcol = gum.config["notebook", "evidence_bgcolor"]
+      fgcol = gum.config["notebook", "evidence_fgcolor"]
+
+    colorattribute = f'fillcolor="{bgcol}", fontcolor="{fgcol}", color="#000000"'
+
+    if len(targets) == 0 or name in targets or nid in targets:
+      filename = temp_dir + hashlib.md5(name.encode()).hexdigest() + "." + gum.config["notebook", "graph_format"]
+      saveFigProba(ie.posterior(name), filename, bgcolor=bgcol)
+      dotstr += f' "{name}" [shape=rectangle,image="{filename}",label="", {colorattribute}];\n'
+    else:
+      dotstr += f' "{name}" [{colorattribute}]'
+
+  for a in mrf.edges():
+    (n, j) = a
+    pw = 1
+    av = f"{n} — {j}"
+    col = gumcols.getBlackInTheme()
+
+    if arcWidth is not None and (n, j) in arcWidth:
+      if maxarcs != minarcs:
+        pw = 0.1 + 5 * (arcWidth[a] - minarcs) / (maxarcs - minarcs)
+      av = f"{n} — {j} : {arcWidth[a]}"
+
+    if arcColor is not None and a in arcColor:
+      col = gumcols.proba2color(arcColor[a], cmapArc)
+
+    dotstr += f' "{mrf.variable(n).name()}"--"{mrf.variable(j).name()}" [penwidth="{pw}",tooltip="{av}",color="{col}"];'
+  dotstr += "}"
+
+  g = dot.graph_from_dot_data(dotstr)[0]
+
+  if size is None:
+    size = gum.config["notebook", "default_graph_inference_size"]
+  g.set_size(size)
+  g.temp_dir = temp_dir
+
+  return g
+
+
+def MRFinference2FactorGraphdot(
+  mrf, size=None, engine=None, evs=None, targets=None, nodeColor=None, factorColor=None, cmapNode=None
+):
+  """
+  create a pydot representation of an inference in a MRF as an factor graph
+
+  :param pyagrum.MarkovRandomField mrf:
+  :param string size: size of the rendered graph
+  :param pyAgrum Inference engine: inference algorithm used. If None, ShaferShenoyMRFInference will be used
+  :param dictionnary evs: map of evidence
+  :param set targets: set of targets. If targets={} then each node is a target
+  :param nodeColor: a nodeMap of values to be shown as color nodes (with special color for 0 and 1)
+  :param cmapNode: color map to show the vals of Nodes
+
+  :return: the desired representation of the inference
+  """
+  if evs is None:
+    evs = {}
+  if targets is None:
+    targets = {}
+  if cmapNode is None:
+    cmapNode = plt.get_cmap(gum.config["notebook", "default_node_cmap"])
+
+  startTime = time.time()
+  if engine is None:
+    ie = gum.ShaferShenoyMRFInference(mrf)
+  else:
+    ie = engine
+  ie.setEvidence(evs)
+  ie.makeInference()
+  stopTime = time.time()
+
+  from tempfile import mkdtemp
+
+  temp_dir = mkdtemp("", "tmp", None)  # with TemporaryDirectory() as temp_dir:
+  dotstr = f'''graph{{ 
+    layout="{gum.config["factorgraph", "graph_layout"]}";
+    fontcolor="{gumcols.getBlackInTheme()}";
+    bgcolor="transparent";
+  '''
+
+  if gum.config.asBool["notebook", "show_inference_time"]:
+    dotstr += f'  label="Inference in {1000 * (stopTime - startTime):6.2f}ms";\n'
+
+  dotstr += (
+    '  node [fillcolor="'
+    + gum.config["notebook", "default_node_bgcolor"]
+    + '", style=filled,color="'
+    + gum.config["notebook", "default_node_fgcolor"]
+    + '"];'
+    + "\n"
+  )
+  dotstr += '  edge [color="' + gumcols.getBlackInTheme() + '"];' + "\n"
+
+  for nid in mrf.nodes():
+    name = mrf.variable(nid).name()
+
+    # defaults
+    bgcol = gum.config["notebook", "default_node_bgcolor"]
+    fgcol = gum.config["notebook", "default_node_fgcolor"]
+    if len(targets) == 0 or name in targets or nid in targets:
+      bgcol = gum.config["notebook", "figure_facecolor"]
+
+    if nodeColor is not None and (name in nodeColor or nid in nodeColor):
+      bgcol = gumcols.proba2bgcolor(nodeColor[name], cmapNode)
+      fgcol = gumcols.proba2fgcolor(nodeColor[name], cmapNode)
+
+    # 'hard' colour for evidence (?)
+    if nid in ie.hardEvidenceNodes() | ie.softEvidenceNodes():
+      bgcol = gum.config["notebook", "evidence_bgcolor"]
+      fgcol = gum.config["notebook", "evidence_fgcolor"]
+
+    colorattribute = f'fillcolor="{bgcol}", fontcolor="{fgcol}", color="#000000"'
+    if len(targets) == 0 or name in targets or nid in targets:
+      filename = temp_dir + hashlib.md5(name.encode()).hexdigest() + "." + gum.config["notebook", "graph_format"]
+      saveFigProba(ie.posterior(name), filename, bgcolor=bgcol)
+      dotstr += f' "{name}" [shape=rectangle,image="{filename}",label="", {colorattribute}];\n'
+    else:
+      dotstr += f' "{name}" [shape=rectangle,margin=0.04,width=0,height=0,{colorattribute}];\n'
+
+  def factorname(f):
+    return '"f' + "#".join(map(str, sorted(list(f)))) + '"'
+
+  for f in mrf.factors():
+    if factorColor is None:
+      bgcol = gum.config["factorgraph", "default_factor_bgcolor"]
+    else:
+      bgcol = gumcols.proba2bgcolor(factorColor(f), cmapNode)
+    dotstr += f"  {factorname(f)} [style=filled,fillcolor={bgcol},shape=point,width=0.1,height=0.1];\n"
+
+  for f in mrf.factors():
+    col = gumcols.getBlackInTheme()
+    for n in f:
+      dotstr += f' {factorname(f)}->"{mrf.variable(n).name()}" [tooltip="{f}:{n}",color="{col}",fillcolor="{bgcol}",len="{gum.config["factorgraph", "edge_length_inference"]}"];\n'
+  dotstr += "}"
+
+  g = dot.graph_from_dot_data(dotstr)[0]
+
+  if size is None:
+    size = gum.config["notebook", "default_graph_inference_size"]
+  g.set_size(size)
+  g.temp_dir = temp_dir
+
+  return g