Source code for networkx.drawing.nx_agraph

"""
***************
Graphviz AGraph
***************

Interface to pygraphviz AGraph class.

Examples
--------
>>> G = nx.complete_graph(5)
>>> A = nx.nx_agraph.to_agraph(G)
>>> H = nx.nx_agraph.from_agraph(A)

See Also
--------
 - Pygraphviz: http://pygraphviz.github.io/
 - Graphviz:      https://www.graphviz.org
 - DOT Language:  http://www.graphviz.org/doc/info/lang.html
"""
import os
import tempfile
import networkx as nx

__all__ = [
    "from_agraph",
    "to_agraph",
    "write_dot",
    "read_dot",
    "graphviz_layout",
    "pygraphviz_layout",
    "view_pygraphviz",
]


[docs]def from_agraph(A, create_using=None): """Returns a NetworkX Graph or DiGraph from a PyGraphviz graph. Parameters ---------- A : PyGraphviz AGraph A graph created with PyGraphviz create_using : NetworkX graph constructor, optional (default=None) Graph type to create. If graph instance, then cleared before populated. If `None`, then the appropriate Graph type is inferred from `A`. Examples -------- >>> K5 = nx.complete_graph(5) >>> A = nx.nx_agraph.to_agraph(K5) >>> G = nx.nx_agraph.from_agraph(A) Notes ----- The Graph G will have a dictionary G.graph_attr containing the default graphviz attributes for graphs, nodes and edges. Default node attributes will be in the dictionary G.node_attr which is keyed by node. Edge attributes will be returned as edge data in G. With edge_attr=False the edge data will be the Graphviz edge weight attribute or the value 1 if no edge weight attribute is found. """ if create_using is None: if A.is_directed(): if A.is_strict(): create_using = nx.DiGraph else: create_using = nx.MultiDiGraph else: if A.is_strict(): create_using = nx.Graph else: create_using = nx.MultiGraph # assign defaults N = nx.empty_graph(0, create_using) if A.name is not None: N.name = A.name # add graph attributes N.graph.update(A.graph_attr) # add nodes, attributes to N.node_attr for n in A.nodes(): str_attr = {str(k): v for k, v in n.attr.items()} N.add_node(str(n), **str_attr) # add edges, assign edge data as dictionary of attributes for e in A.edges(): u, v = str(e[0]), str(e[1]) attr = dict(e.attr) str_attr = {str(k): v for k, v in attr.items()} if not N.is_multigraph(): if e.name is not None: str_attr["key"] = e.name N.add_edge(u, v, **str_attr) else: N.add_edge(u, v, key=e.name, **str_attr) # add default attributes for graph, nodes, and edges # hang them on N.graph_attr N.graph["graph"] = dict(A.graph_attr) N.graph["node"] = dict(A.node_attr) N.graph["edge"] = dict(A.edge_attr) return N
[docs]def to_agraph(N): """Returns a pygraphviz graph from a NetworkX graph N. Parameters ---------- N : NetworkX graph A graph created with NetworkX Examples -------- >>> K5 = nx.complete_graph(5) >>> A = nx.nx_agraph.to_agraph(K5) Notes ----- If N has an dict N.graph_attr an attempt will be made first to copy properties attached to the graph (see from_agraph) and then updated with the calling arguments if any. """ try: import pygraphviz except ImportError as e: raise ImportError("requires pygraphviz " "http://pygraphviz.github.io/") from e directed = N.is_directed() strict = nx.number_of_selfloops(N) == 0 and not N.is_multigraph() A = pygraphviz.AGraph(name=N.name, strict=strict, directed=directed) # default graph attributes A.graph_attr.update(N.graph.get("graph", {})) A.node_attr.update(N.graph.get("node", {})) A.edge_attr.update(N.graph.get("edge", {})) A.graph_attr.update( (k, v) for k, v in N.graph.items() if k not in ("graph", "node", "edge") ) # add nodes for n, nodedata in N.nodes(data=True): A.add_node(n) # Add node data a = A.get_node(n) a.attr.update({k: str(v) for k, v in nodedata.items()}) # loop over edges if N.is_multigraph(): for u, v, key, edgedata in N.edges(data=True, keys=True): str_edgedata = {k: str(v) for k, v in edgedata.items() if k != "key"} A.add_edge(u, v, key=str(key)) # Add edge data a = A.get_edge(u, v) a.attr.update(str_edgedata) else: for u, v, edgedata in N.edges(data=True): str_edgedata = {k: str(v) for k, v in edgedata.items()} A.add_edge(u, v) # Add edge data a = A.get_edge(u, v) a.attr.update(str_edgedata) return A
[docs]def write_dot(G, path): """Write NetworkX graph G to Graphviz dot format on path. Parameters ---------- G : graph A networkx graph path : filename Filename or file handle to write """ A = to_agraph(G) A.write(path) A.clear() return
[docs]def read_dot(path): """Returns a NetworkX graph from a dot file on path. Parameters ---------- path : file or string File name or file handle to read. """ try: import pygraphviz except ImportError as e: raise ImportError( "read_dot() requires pygraphviz " "http://pygraphviz.github.io/" ) from e A = pygraphviz.AGraph(file=path) gr = from_agraph(A) A.clear() return gr
[docs]def graphviz_layout(G, prog="neato", root=None, args=""): """Create node positions for G using Graphviz. Parameters ---------- G : NetworkX graph A graph created with NetworkX prog : string Name of Graphviz layout program root : string, optional Root node for twopi layout args : string, optional Extra arguments to Graphviz layout program Returns ------- Dictionary of x, y, positions keyed by node. Examples -------- >>> G = nx.petersen_graph() >>> pos = nx.nx_agraph.graphviz_layout(G) >>> pos = nx.nx_agraph.graphviz_layout(G, prog="dot") Notes ----- This is a wrapper for pygraphviz_layout. """ return pygraphviz_layout(G, prog=prog, root=root, args=args)
[docs]def pygraphviz_layout(G, prog="neato", root=None, args=""): """Create node positions for G using Graphviz. Parameters ---------- G : NetworkX graph A graph created with NetworkX prog : string Name of Graphviz layout program root : string, optional Root node for twopi layout args : string, optional Extra arguments to Graphviz layout program Returns ------- node_pos : dict Dictionary of x, y, positions keyed by node. Examples -------- >>> G = nx.petersen_graph() >>> pos = nx.nx_agraph.graphviz_layout(G) >>> pos = nx.nx_agraph.graphviz_layout(G, prog="dot") Notes ----- If you use complex node objects, they may have the same string representation and GraphViz could treat them as the same node. The layout may assign both nodes a single location. See Issue #1568 If this occurs in your case, consider relabeling the nodes just for the layout computation using something similar to:: >>> H = nx.convert_node_labels_to_integers(G, label_attribute="node_label") >>> H_layout = nx.nx_agraph.pygraphviz_layout(G, prog="dot") >>> G_layout = {H.nodes[n]["node_label"]: p for n, p in H_layout.items()} """ try: import pygraphviz except ImportError as e: raise ImportError("requires pygraphviz " "http://pygraphviz.github.io/") from e if root is not None: args += f"-Groot={root}" A = to_agraph(G) A.layout(prog=prog, args=args) node_pos = {} for n in G: node = pygraphviz.Node(A, n) try: xs = node.attr["pos"].split(",") node_pos[n] = tuple(float(x) for x in xs) except: print("no position for node", n) node_pos[n] = (0.0, 0.0) return node_pos
@nx.utils.open_file(5, "w+b") def view_pygraphviz( G, edgelabel=None, prog="dot", args="", suffix="", path=None, show=True ): """Views the graph G using the specified layout algorithm. Parameters ---------- G : NetworkX graph The machine to draw. edgelabel : str, callable, None If a string, then it specifes the edge attribute to be displayed on the edge labels. If a callable, then it is called for each edge and it should return the string to be displayed on the edges. The function signature of `edgelabel` should be edgelabel(data), where `data` is the edge attribute dictionary. prog : string Name of Graphviz layout program. args : str Additional arguments to pass to the Graphviz layout program. suffix : str If `filename` is None, we save to a temporary file. The value of `suffix` will appear at the tail end of the temporary filename. path : str, None The filename used to save the image. If None, save to a temporary file. File formats are the same as those from pygraphviz.agraph.draw. show : bool, default = True Whether to display the graph with :mod:`PIL.Image.show`, default is `True`. If `False`, the rendered graph is still available at `path`. Returns ------- path : str The filename of the generated image. A : PyGraphviz graph The PyGraphviz graph instance used to generate the image. Notes ----- If this function is called in succession too quickly, sometimes the image is not displayed. So you might consider time.sleep(.5) between calls if you experience problems. """ if not len(G): raise nx.NetworkXException("An empty graph cannot be drawn.") # If we are providing default values for graphviz, these must be set # before any nodes or edges are added to the PyGraphviz graph object. # The reason for this is that default values only affect incoming objects. # If you change the default values after the objects have been added, # then they inherit no value and are set only if explicitly set. # to_agraph() uses these values. attrs = ["edge", "node", "graph"] for attr in attrs: if attr not in G.graph: G.graph[attr] = {} # These are the default values. edge_attrs = {"fontsize": "10"} node_attrs = { "style": "filled", "fillcolor": "#0000FF40", "height": "0.75", "width": "0.75", "shape": "circle", } graph_attrs = {} def update_attrs(which, attrs): # Update graph attributes. Return list of those which were added. added = [] for k, v in attrs.items(): if k not in G.graph[which]: G.graph[which][k] = v added.append(k) def clean_attrs(which, added): # Remove added attributes for attr in added: del G.graph[which][attr] if not G.graph[which]: del G.graph[which] # Update all default values update_attrs("edge", edge_attrs) update_attrs("node", node_attrs) update_attrs("graph", graph_attrs) # Convert to agraph, so we inherit default values A = to_agraph(G) # Remove the default values we added to the original graph. clean_attrs("edge", edge_attrs) clean_attrs("node", node_attrs) clean_attrs("graph", graph_attrs) # If the user passed in an edgelabel, we update the labels for all edges. if edgelabel is not None: if not callable(edgelabel): def func(data): return "".join([" ", str(data[edgelabel]), " "]) else: func = edgelabel # update all the edge labels if G.is_multigraph(): for u, v, key, data in G.edges(keys=True, data=True): # PyGraphviz doesn't convert the key to a string. See #339 edge = A.get_edge(u, v, str(key)) edge.attr["label"] = str(func(data)) else: for u, v, data in G.edges(data=True): edge = A.get_edge(u, v) edge.attr["label"] = str(func(data)) if path is None: ext = "png" if suffix: suffix = f"_{suffix}.{ext}" else: suffix = f".{ext}" path = tempfile.NamedTemporaryFile(suffix=suffix, delete=False) else: # Assume the decorator worked and it is a file-object. pass # Write graph to file A.draw(path=path, format=None, prog=prog, args=args) path.close() # Show graph in a new window (depends on platform configuration) if show: from PIL import Image Image.open(path.name).show() return path.name, A def display_pygraphviz(graph, path, format=None, prog=None, args=""): """Internal function to display a graph in OS dependent manner. Parameters ---------- graph : PyGraphviz graph A PyGraphviz AGraph instance. path : file object An already opened file object that will be closed. format : str, None An attempt is made to guess the output format based on the extension of the filename. If that fails, the value of `format` is used. prog : string Name of Graphviz layout program. args : str Additional arguments to pass to the Graphviz layout program. Notes ----- If this function is called in succession too quickly, sometimes the image is not displayed. So you might consider time.sleep(.5) between calls if you experience problems. """ from PIL import Image import warnings warnings.warn( "display_pygraphviz is deprecated and will be removed in NetworkX 3.0. " "To view a graph G using pygraphviz, use nx.nx_agraph.view_pygraphviz(G). " "To view a graph from file, consider an image processing libary like " "`Pillow`, e.g. ``PIL.Image.open(path.name).show()``", DeprecationWarning, ) if format is None: filename = path.name format = os.path.splitext(filename)[1].lower()[1:] if not format: # Let the draw() function use its default format = None # Save to a file and display in the default viewer. # We must close the file before viewing it. graph.draw(path, format, prog, args) path.close() Image.open(filename).show()