How to get the coordinates from layout from graphviz?

Question

I have been working with pygraph on some project. I completed this example, it works fine.

Now, the problem is the following: the graph is drawn in a picture format (gif). What I need is to get the actual coordinates for each node for the graph layout shown on the gif image. How do I do this? I've been trying and trying, but couldn't find solution to this problem. I thought the the problem's solution would be somehow with manipulating one of the two following lines:

gv.layout(gvv,'dot')
gv.render(gvv,'png','europe.png')

Thanks in advance!

Answer 1

You can add the layout information into the graph with :

gv.render(gvv)

and then find out the position of a node getting its attribute pos :

n_france = gv.findnode(gvv, "France")
pos = gv.getv(n_france, "pos")

Then depending on what you want to do, you might need to convert dot coordinates into png image coordinates. You can get useful information from here :

http://www.graphviz.org/faq/#FaqCoordTransformation

It explains in great details the computation from the graph-units to image pixels.

Hope that this is what you are looking for.

Answer 2

I just found a similar solution that works perfectly for my needs

pos = nx.drawing.nx_agraph.graphviz_layout(G, prog='dot', args='-Grankdir=LR')

cheers!

Answer 3

Using pydotplus you can load in and parse a dot/gv file and interrogate the data structure pydotplus produces, but this internal representation seems not to initially possess all the node attributes, like pos, unless they were already in the file.
But you can also call .write_dot() to produce a much more verbose dot file version. If you parse this then the resulting data structure seems to have pos of all the nodes (and even pos for the splines)

Note: maybe best to index the nodes by name not by index because any text with square brackets after it in the verbose file will be parsed as a node, so the node list may have spurious extra elements.

In the following (slightly edited) experiment at the Spyder prompt I have a terse dot file interior.gv (that does not have pos for nodes) which I .graph_from_dot_file(), then .write_dot(). Then .graph_from_dot_file() again on the verbose generated file, and so find the pos as required.

import pydotplus as pdp

interior = pdp.graphviz.graph_from_dot_file('interior.gv')

interior.write_dot('interior2.dot')
Out[210]: True

interior2 = pdp.graphviz.graph_from_dot_file('interior2.dot')

interior2.get_nodes()[3].get_pos()
Out[214]: '"213.74,130"'

Answer 4

Networkx can do this:

import networkx as nx

def setup_europe():
    G = nx.Graph()

    G.add_edge("Portugal", "Spain")
    G.add_edge("Spain","France")
    G.add_edge("France","Belgium")
    G.add_edge("France","Germany")
    G.add_edge("France","Italy")
    G.add_edge("Belgium","Netherlands")
    G.add_edge("Germany","Belgium")
    G.add_edge("Germany","Netherlands")
    G.add_edge("England","Wales")
    G.add_edge("England","Scotland")
    G.add_edge("Scotland","Wales")
    G.add_edge("Switzerland","Austria")
    G.add_edge("Switzerland","Germany")
    G.add_edge("Switzerland","France")
    G.add_edge("Switzerland","Italy")
    G.add_edge("Austria","Germany")
    G.add_edge("Austria","Italy")
    G.add_edge("Austria","Czech Republic")
    G.add_edge("Austria","Slovakia")
    G.add_edge("Austria","Hungary")
    G.add_edge("Denmark","Germany")
    G.add_edge("Poland","Czech Republic")
    G.add_edge("Poland","Slovakia")
    G.add_edge("Poland","Germany")
    G.add_edge("Czech Republic","Slovakia")
    G.add_edge("Czech Republic","Germany")
    G.add_edge("Slovakia","Hungary")
    return G

G = setup_europe()

Write a dot file:

nx.write_dot(G, '/tmp/out.dot')

Compute the position of the nodes:

pos = nx.pygraphviz_layout(G, prog = 'dot')
print(pos)
# {'Netherlands': (713.86, 167.0), 'Italy': (473.86, 389.0), 'Czech Republic': (100.86, 241.0), 'Portugal': (879.86, 315.0), 'England': (1024.9, 241.0), 'Denmark': (568.86, 167.0), 'Poland': (100.86, 167.0), 'Scotland': (1024.9, 389.0), 'France': (571.86, 315.0), 'Belgium': (713.86, 19.0), 'Austria': (320.86, 167.0), 'Slovakia': (156.86, 315.0), 'Wales': (990.86, 315.0), 'Switzerland': (473.86, 241.0), 'Hungary': (294.86, 241.0), 'Germany': (465.86, 93.0), 'Spain': (879.86, 241.0)}

Render an png:

agraph = nx.to_agraph(G)
agraph.draw("/tmp/europe.png", format = 'png', prog = 'dot')

Answer 5

Using just pydot/dot you can do it by generating the SVG and then reading the position of the nodes from the SVG. It is a bit hacky, but works reliably enough

from xml.dom import minidom
import pydot
from io import BytesIO
def extract_node_positions(
    in_dot: pydot.Dot
) -> Dict[str, Tuple[str, float, float]]:
    """
    Extract the x,y positions from a pydot graph by rendering
    Args:
        in_dot: the graph to render

    Returns:
        a list of all the nodes

    Examples:
        >>> g = pydot.Dot()
        >>> g.add_node(pydot.Node("A"))
        >>> g.add_node(pydot.Node("B"))
        >>> g.add_node(pydot.Node("C"))
        >>> g.add_edge(pydot.Edge("A", "B"))
        >>> g.add_edge(pydot.Edge("B", "C"))
        >>> extract_node_positions(g)
        {'A': ('A', 27.0, -157.8), 'B': ('B', 27.0, -85.8), 'C': ('C', 27.0, -13.8)}
    """
    node_mapping = {f'node{i}': k.get_name() 
                    for i, k in enumerate(in_dot.get_nodes(), 1)}
    svg_io = BytesIO(in_dot.create_svg())
    doc = minidom.parse(svg_io)  # parseString also exists
    node_dict = {node_mapping[p.getAttribute('id')]: (c_text.firstChild.data,
                                        float(c_text.getAttribute('x')),
                                        float(c_text.getAttribute('y')))

                 for p in doc.getElementsByTagName("g") if "node" == p.getAttribute('class').lower()
                 for c_text in p.getElementsByTagName('text')
                 }
    doc.unlink()
    return node_dict

Answer 6

To directly access the results from the Graphviz rendering command (e.g. dot) as binary data string from within Python instead of writing to a file, use the pipe()-method of your Graph or Digraph object:

h = Graph('hello', format='svg')

h.edge('Hello', 'World')

print(h.pipe().decode('utf-8'))

Answer 7

I struggled with this recently, and the answers here were some help but not quite there. The suggestions about networkx are on the right track. Networkx uses pygraphviz to interface with graphviz, and so you can instead use pygraphviz directly if you wish:

import pygraphviz as pgv
G = pgv.AGraph(strict=False,directed=True)
# add nodes and edges
G.add_edge(1,2)
G.add_edge(2,1)
# generate a layout--this creates `pos` attributes for both nodes and edges
G.layout(prog="dot") 
#change something about the graph that would change the layout, e.g.,
edge = G.get_edge("1", "2")
edge.attr["label"] = "test label"
# create the graph using the layout already generated; note, do not provide `prog`
G.draw("test.pdf")
# compare it to a newly generated layout
G.draw("test2.pdf", prog="dot")

The important part is to not provide prog to the draw command if you want to use the node and edge positions already generated by the layout command. I see now this is stated in the pygraphviz docstring for draw. BTW, it is does the same as prog="neato" with the -n2 argument. Looking at the sources, pygraphviz calls graphviz to generate the layout.