added support for plotting BayesNet network structures in XML BIF format

Author: fracpete

CHANGES.rst

@@ -15,6 +15,9 @@ Changelog
 - added `split_commandline` method to module `weka.core.classes`, which splits a command-line
   into classname and option list tuple
 - the `Instances` class (module: `weka.core.dataset`) now supports slicing
+- added methods `plot_xmlbif_graph` and `xmlbif_to_dot` to module `weka.plot.graph` for plotting
+  XML BIF graphs generated by BayesNet using GraphViz
+- added method `plot_graph` to module `weka.plot.graph` to plot dot or XML BIF graphs
 
 
 0.2.10 (2022-06-27)

python/weka/plot/__init__.py

@@ -12,7 +12,7 @@
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
 # __init__.py
-# Copyright (C) 2014-2021 Fracpete (pythonwekawrapper at gmail dot com)
+# Copyright (C) 2014-2022 Fracpete (pythonwekawrapper at gmail dot com)
 
 from weka.core.dataset import Instances
 from weka.core.classes import Random
@@ -44,6 +44,14 @@
 except ImportError:
     pass
 
+# check whether lxml is there
+lxml_available = False
+try:
+    from lxml import etree
+    lxml_available = True
+except ImportError:
+    pass
+
 
 def create_subsample(data, percent, seed=1):
     """

python/weka/plot/graph.py

@@ -12,7 +12,7 @@
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
 # graph.py
-# Copyright (C) 2014-2016 Fracpete (pythonwekawrapper at gmail dot com)
+# Copyright (C) 2014-2022 Fracpete (pythonwekawrapper at gmail dot com)
 
 import logging
 import tempfile
@@ -21,6 +21,8 @@
     from pygraphviz.agraph import AGraph
 if plot.PIL_available:
     from PIL import Image
+if plot.lxml_available:
+    from lxml import etree
 
 # logging setup
 logger = logging.getLogger(__name__)
@@ -30,6 +32,8 @@ def plot_dot_graph(graph, filename=None):
     """
     Plots a graph in graphviz dot notation.
 
+    http://graphviz.org/doc/info/lang.html
+
     :param graph: the dot notation graph
     :type graph: str
     :param filename: the (optional) file to save the generated plot to. The extension determines the file format.
@@ -49,3 +53,70 @@ def plot_dot_graph(graph, filename=None):
     agraph.draw(filename)
     image = Image.open(filename)
     image.show()
+
+
+def xmlbif_to_dot(graph):
+    """
+    Converts the graph in XML BIF notation into a dot graph.
+
+    http://sites.poli.usp.br/p/fabio.cozman/Research/InterchangeFormat/index.html
+
+    :param graph: the graph to convert
+    :type graph: str
+    :return: the graph in dot notation
+    :rtype: str
+    """
+    if not plot.lxml_available:
+        logger.error("lxml is not installed, cannot convert XML BIF graph!")
+        return
+
+    result = list()
+    result.append("digraph {")
+
+    root = etree.fromstring(graph)
+    network = root.find("NETWORK")
+    definitions = network.findall("DEFINITION")
+    for definition in definitions:
+        f = definition.find("FOR")
+        givens = definition.findall("GIVEN")
+        for given in givens:
+            result.append("  %s -> %s;" % (given.text, f.text))
+
+    result.append("}")
+
+    return "\n".join(result)
+
+
+def plot_xmlbif_graph(graph, filename=None):
+    """
+    Plots a graph in XML BIF notation. Only plots the structure, not the tables.
+
+    http://sites.poli.usp.br/p/fabio.cozman/Research/InterchangeFormat/index.html
+
+    :param graph: the XML BIF notation graph
+    :type graph: str
+    :param filename: the (optional) file to save the generated plot to. The extension determines the file format.
+    :type filename: str
+    """
+    if not plot.lxml_available:
+        logger.error("lxml is not installed, cannot convert XML BIF graph!")
+        return
+    plot_dot_graph(xmlbif_to_dot(graph), filename)
+
+
+def plot_graph(graph, filename=None):
+    """
+    Plots a graph in dot or XML BIF notation.
+
+    http://graphviz.org/doc/info/lang.html
+    http://sites.poli.usp.br/p/fabio.cozman/Research/InterchangeFormat/index.html
+
+    :param graph: the dot/XML BIF notation graph
+    :type graph: str
+    :param filename: the (optional) file to save the generated plot to. The extension determines the file format.
+    :type filename: str
+    """
+    if "<BIF" in graph and "<NETWORK>" in graph:
+        return plot_xmlbif_graph(graph, filename=filename)
+    else:
+        return plot_dot_graph(graph, filename=filename)

setup.py

@@ -65,7 +65,7 @@ def _read(f):
     ],
     extras_require={
         'plots': ["matplotlib"],
-        'graphs': ["pygraphviz", "pillow"],
+        'graphs': ["pygraphviz", "pillow", "lxml"],
     },
     entry_points={
         "console_scripts": [