def __init__()

in dowhy/causal_graph.py [0:0]

• 67 lines of code
• 17 McCabe index (conditional complexity)

    def __init__(self,
                 treatment_name, outcome_name,
                 graph=None,
                 common_cause_names=None,
                 instrument_names=None,
                 effect_modifier_names=None,
                 mediator_names=None,
                 observed_node_names=None,
                 missing_nodes_as_confounders=False):
        self.treatment_name = parse_state(treatment_name)
        self.outcome_name = parse_state(outcome_name)
        instrument_names = parse_state(instrument_names)
        common_cause_names = parse_state(common_cause_names)
        effect_modifier_names = parse_state(effect_modifier_names)
        mediator_names = parse_state(mediator_names)
        self.logger = logging.getLogger(__name__)

        #re.sub only takes string parameter so the first if is to avoid error
        #if the input is a text file, convert the contained data into string
        if isinstance(graph, str) and re.match(r".*\.txt" , str(graph)): 
            text_file = open(graph , "r")
            graph = text_file.read()
            text_file.close()
 
        if isinstance(graph, str) and re.match(r"^dag", graph):   #Convert daggity output to dot format 
            graph = daggity_to_dot(graph)

        if isinstance(graph, str):
            graph=graph.replace("\n", " ")

        if graph is None:
            self._graph = nx.DiGraph()
            self._graph = self.build_graph(common_cause_names,
                                           instrument_names,
                                           effect_modifier_names,
                                           mediator_names)
        elif re.match(r".*\.dot", graph):
            # load dot file
            try:
                import pygraphviz as pgv
                self._graph = nx.DiGraph(nx.drawing.nx_agraph.read_dot(graph))
            except Exception as e:
                self.logger.error("Pygraphviz cannot be loaded. " + str(e) + "\nTrying pydot...")
                try:
                    import pydot
                    self._graph = nx.DiGraph(nx.drawing.nx_pydot.read_dot(graph))
                except Exception as e:
                    self.logger.error("Error: Pydot cannot be loaded. " + str(e))
                    raise e
        elif re.match(r".*\.gml", graph):
            self._graph = nx.DiGraph(nx.read_gml(graph))
        elif re.match(r".*graph\s*\{.*\}\s*", graph):
            try:
                import pygraphviz as pgv
                self._graph = pgv.AGraph(graph, strict=True, directed=True)
                self._graph = nx.drawing.nx_agraph.from_agraph(self._graph)
            except Exception as e:
                self.logger.error("Error: Pygraphviz cannot be loaded. " + str(e) + "\nTrying pydot ...")
                try:
                    import pydot
                    P_list = pydot.graph_from_dot_data(graph)
                    self._graph = nx.drawing.nx_pydot.from_pydot(P_list[0])
                except Exception as e:
                    self.logger.error("Error: Pydot cannot be loaded. " + str(e))
                    raise e
        elif re.match(".*graph\s*\[.*\]\s*", graph):
            self._graph = nx.DiGraph(nx.parse_gml(graph))
        else:
            self.logger.error("Error: Please provide graph (as string or text file) in dot or gml format.")
            self.logger.error("Error: Incorrect graph format")
            raise ValueError
        if missing_nodes_as_confounders:
            self._graph = self.add_missing_nodes_as_common_causes(observed_node_names)
        # Adding node attributes
        self._graph = self.add_node_attributes(observed_node_names)