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Commit aa38e9f0 authored by Tiago Peixoto's avatar Tiago Peixoto
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Ditch graphviz python module in favor of libgvc + ctypes 

By using directly the C bindings to graphviz, we are able to return the
drawed graph as a string buffer in whatever format, which was not
possible with the SWIGified python interface.

Returning the drawed graph as a buffer is useful in doing animations,
among other things.
parent 7bedab86
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src/graph_tool/draw/__init__.py
View file @ aa38e9f0
......@@ -36,41 +36,77 @@ Contents
++++++++
"""
import sys, os, os.path, time, warnings, tempfile
import sys
import os
import os.path
import time
import warnings
import ctypes
import ctypes.util
from .. import _degree, _prop, PropertyMap, _check_prop_vector,\
_check_prop_scalar, _check_prop_writable, group_vector_property,\
ungroup_vector_property
from .. decorators import _limit_args
import numpy.random
from numpy import *
import copy
from .. dl_import import dl_import
dl_import("import libgraph_tool_layout")
try:
import gv
except ImportError:
warnings.warn("error importing gv module... graph_draw() will not work.",
ImportWarning)
try:
import matplotlib.cm
import matplotlib.colors
from pylab import imread
except ImportError:
warnings.warn("error importing matplotlib module... " + \
"graph_draw() will not work.", ImportWarning)
try:
libname = ctypes.util.find_library("c")
libc = ctypes.CDLL(libname)
libc.open_memstream.restype = ctypes.POINTER(ctypes.c_char)
except OSError:
pass
try:
libname = ctypes.util.find_library("gvc")
if libname is None:
raise OSError()
libgv = ctypes.CDLL(libname)
# properly set the return types of certain functions
ptype = ctypes.POINTER(ctypes.c_char)
libgv.gvContext.restype = ptype
libgv.agopen.restype = ptype
libgv.agnode.restype = ptype
libgv.agedge.restype = ptype
libgv.agget.restype = ptype
# create a context to use the whole time (if we keep freeing and recreating
# it, we will hit a memory leak in graphviz)
gvc = libgv.gvContext()
except OSError:
warnings.warn("error importing graphviz C library (libgvc)... " + \
"graph_draw() will not work.", ImportWarning)
__all__ = ["graph_draw", "arf_layout", "random_layout"]
def aset(elem, attr, value):
v = str(value)
libgv.agsafeset(elem, str(attr), v, v)
def aget(elem, attr):
return ctypes.string_at(libgv.agget(elem, str(attr)))
def graph_draw(g, pos=None, size=(15, 15), pin=False, layout=None, maxiter=None,
ratio="fill", overlap="prism", sep=None, splines=False,
vsize=0.105, penwidth=1.0, elen=None, gprops={}, vprops={},
eprops={}, vcolor="#a40000", ecolor="#2e3436",
vcmap=None, vnorm=True, ecmap=None,
enorm=True, vorder=None, eorder=None, output="",
output_format="auto", returngv=False, fork=False,
return_bitmap=False, seed=0):
eprops={}, vcolor="#a40000", ecolor="#2e3436", vcmap=None,
vnorm=True, ecmap=None, enorm=True, vorder=None, eorder=None,
output="", output_format="auto", fork=False,
return_string=False, seed=0):
r"""Draw a graph using graphviz.
Parameters
......@@ -198,16 +234,14 @@ def graph_draw(g, pos=None, size=(15, 15), pin=False, layout=None, maxiter=None,
"cmapx". If the value is "auto", the format is guessed from the 'output'
parameter, or 'xlib' if it is empty. If the value is None, no output is
produced.
returngv : bool (default: False)
Return the graph object used internally with the gv module.
fork : bool (default: False)
If True, the program is forked before drawing. This is used as a
work-around for a bug in graphviz, where the exit() function is called,
which would cause the calling program to end. This is always assumed
'True', if output_format = 'xlib'.
return_bitmap : bool (default: False)
If True, a bitmap (:class:`~numpy.ndarray`) of the rendered graph is
returned.
return_string : bool (default: False)
If True, a string containing the rendered graph as binary data is
returned (defaults to png format).
Returns
-------
......@@ -264,234 +298,237 @@ def graph_draw(g, pos=None, size=(15, 15), pin=False, layout=None, maxiter=None,
not os.access(os.path.dirname(output), os.W_OK):
raise IOError("cannot write to " + os.path.dirname(output))
if g.is_directed():
gvg = gv.digraph("G")
else:
gvg = gv.graph("G")
if layout is None:
layout = "neato" if g.num_vertices() <= 1000 else "sfdp"
if layout == "arf":
layout = "neato"
pos = arf_layout(g, pos=pos)
pin = True
if pos != None:
# copy user-supplied property
if isinstance(pos, PropertyMap):
pos = ungroup_vector_property(pos, [0, 1])
else:
pos = (g.copy_property(pos[0]), g.copy_property(pos[1]))
if type(vsize) == tuple:
s = g.new_vertex_property("double")
g.copy_property(vsize[0], s)
s.a *= vsize[1]
vsize = s
if type(penwidth) == tuple:
s = g.new_edge_property("double")
g.copy_property(penwidth[0], s)
s.a *= penwidth[1]
penwidth = s
# main graph properties
gv.setv(gvg, "outputorder", "edgesfirst")
gv.setv(gvg, "mode", "major")
if overlap == False:
overlap = "false"
else:
overlap = "true"
if isinstance(overlap, str):
gv.setv(gvg, "overlap", overlap)
if sep != None:
gv.setv(gvg, "sep", str(sep))
if splines:
gv.setv(gvg, "splines", "true")
gv.setv(gvg, "ratio", str(ratio))
# size is in centimeters... convert to inches
gv.setv(gvg, "size", "%f,%f" % (size[0] / 2.54, size[1] / 2.54))
if maxiter != None:
gv.setv(gvg, "maxiter", str(maxiter))
seed = numpy.random.randint(sys.maxint)
gv.setv(gvg, "start", "%d" % seed)
# apply all user supplied graph properties
for k, val in gprops.iteritems():
if isinstance(val, PropertyMap):
gv.setv(gvg, k, str(val[g]))
else:
gv.setv(gvg, k, str(val))
# normalize color properties
if vcolor != None and not isinstance(vcolor, str):
minmax = [float("inf"), -float("inf")]
for v in g.vertices():
c = vcolor[v]
minmax[0] = min(c, minmax[0])
minmax[1] = max(c, minmax[1])
if minmax[0] == minmax[1]:
minmax[1] += 1
if vnorm:
vnorm = matplotlib.colors.normalize(vmin=minmax[0], vmax=minmax[1])
else:
vnorm = lambda x: x
if ecolor != None and not isinstance(ecolor, str):
minmax = [float("inf"), -float("inf")]
for e in g.edges():
c = ecolor[e]
minmax[0] = min(c, minmax[0])
minmax[1] = max(c, minmax[1])
if minmax[0] == minmax[1]:
minmax[1] += 1
if enorm:
enorm = matplotlib.colors.normalize(vmin=minmax[0], vmax=minmax[1])
else:
enorm = lambda x: x
if vcmap is None:
vcmap = matplotlib.cm.jet
if ecmap is None:
ecmap = matplotlib.cm.jet
has_layout = False
try:
gvg = libgv.agopen("G", 1 if g.is_directed() else 0)
nodes = {}
if layout is None:
layout = "neato" if g.num_vertices() <= 1000 else "sfdp"
# add nodes
if vorder != None:
vertices = sorted(g.vertices(), lambda a, b: cmp(vorder[a], vorder[b]))
else:
vertices = g.vertices()
for v in vertices:
n = gv.node(gvg, str(g.vertex_index[v]))
if layout == "arf":
layout = "neato"
pos = arf_layout(g, pos=pos)
pin = True
if type(vsize) == PropertyMap:
vw = vh = vsize[v]
else:
vw = vh = vsize
gv.setv(n, "shape", "circle")
gv.setv(n, "width", "%g" % vw)
gv.setv(n, "height", "%g" % vh)
gv.setv(n, "style", "filled")
gv.setv(n, "color", ecolor if isinstance(ecolor, str) else "#2e3436")
# apply color
if isinstance(vcolor, str):
gv.setv(n, "fillcolor", vcolor)
else:
color = tuple([int(c * 255.0) for c in vcmap(vnorm(vcolor[v]))])
gv.setv(n, "fillcolor", "#%.2x%.2x%.2x%.2x" % color)
gv.setv(n, "label", "")
# user supplied position
if pos != None:
gv.setv(n, "pos", "%f,%f" % (pos[0][v], pos[1][v]))
gv.setv(n, "pin", str(pin))
# apply all user supplied properties
for k, val in vprops.iteritems():
if isinstance(val, PropertyMap):
gv.setv(n, k, str(val[v]))
# copy user-supplied property
if isinstance(pos, PropertyMap):
pos = ungroup_vector_property(pos, [0, 1])
else:
gv.setv(n, k, str(val))
nodes[v] = n
# add edges
if eorder != None:
edges = sorted(g.edges(), lambda a, b: cmp(eorder[a], eorder[b]))
else:
edges = g.edges()
for e in edges:
ge = gv.edge(nodes[e.source()],
nodes[e.target()])
gv.setv(ge, "arrowsize", "0.3")
if g.is_directed():
gv.setv(ge, "arrowhead", "vee")
# apply color
if isinstance(ecolor, str):
gv.setv(ge, "color", ecolor)
pos = (g.copy_property(pos[0]), g.copy_property(pos[1]))
if type(vsize) == tuple:
s = g.new_vertex_property("double")
g.copy_property(vsize[0], s)
s.a *= vsize[1]
vsize = s
if type(penwidth) == tuple:
s = g.new_edge_property("double")
g.copy_property(penwidth[0], s)
s.a *= penwidth[1]
penwidth = s
# main graph properties
aset(gvg, "outputorder", "edgesfirst")
aset(gvg, "mode", "major")
if overlap == False:
overlap = "false"
else:
color = tuple([int(c * 255.0) for c in ecmap(enorm(ecolor[e]))])
gv.setv(ge, "color", "#%.2x%.2x%.2x%.2x" % color)
# apply edge length
if elen != None:
if isinstance(elen, PropertyMap):
gv.setv(ge, "len", str(elen[e]))
overlap = "true"
if isinstance(overlap, str):
aset(gvg, "overlap", overlap)
if sep != None:
aset(gvg, "sep", sep)
if splines:
aset(gvg, "splines", "true")
aset(gvg, "ratio", ratio)
# size is in centimeters... convert to inches
aset(gvg, "size", "%f,%f" % (size[0] / 2.54, size[1] / 2.54))
if maxiter != None:
aset(gvg, "maxiter", maxiter)
seed = numpy.random.randint(sys.maxint)
aset(gvg, "start", "%d" % seed)
# apply all user supplied graph properties
for k, val in gprops.iteritems():
if isinstance(val, PropertyMap):
aset(gvg, k, val[g])
else:
gv.setv(ge, "len", str(elen))
# apply width
if penwidth != None:
if isinstance(penwidth, PropertyMap):
gv.setv(ge, "penwidth", str(penwidth[e]))
aset(gvg, k, val)
# normalize color properties
if vcolor != None and not isinstance(vcolor, str):
minmax = [float("inf"), -float("inf")]
for v in g.vertices():
c = vcolor[v]
minmax[0] = min(c, minmax[0])
minmax[1] = max(c, minmax[1])
if minmax[0] == minmax[1]:
minmax[1] += 1
if vnorm:
vnorm = matplotlib.colors.normalize(vmin=minmax[0], vmax=minmax[1])
else:
gv.setv(ge, "penwidth", str(penwidth))
# apply all user supplied properties
for k, v in eprops.iteritems():
if isinstance(v, PropertyMap):
gv.setv(ge, k, str(v[e]))
vnorm = lambda x: x
if ecolor != None and not isinstance(ecolor, str):
minmax = [float("inf"), -float("inf")]
for e in g.edges():
c = ecolor[e]
minmax[0] = min(c, minmax[0])
minmax[1] = max(c, minmax[1])
if minmax[0] == minmax[1]:
minmax[1] += 1
if enorm:
enorm = matplotlib.colors.normalize(vmin=minmax[0],
vmax=minmax[1])
else:
gv.setv(ge, k, str(v))
gv.layout(gvg, layout)
gv.render(gvg, "dot", "/dev/null") # retrieve positions
enorm = lambda x: x
if pos == None:
pos = (g.new_vertex_property("double"), g.new_vertex_property("double"))
for n, n_gv in nodes.iteritems():
p = gv.getv(n_gv, "pos")
p = p.split(",")
pos[0][n] = float(p[0])
pos[1][n] = float(p[1])
if vcmap is None:
vcmap = matplotlib.cm.jet
# I don't get this, but it seems necessary
pos[0].a /= 100
pos[1].a /= 100
if ecmap is None:
ecmap = matplotlib.cm.jet
pos = group_vector_property(pos)
# add nodes
if vorder != None:
vertices = sorted(g.vertices(), lambda a, b: cmp(vorder[a], vorder[b]))
else:
vertices = g.vertices()
for v in vertices:
n = libgv.agnode(gvg, str(int(v)))
if return_bitmap:
# This is a not-so-nice hack which obtains an image buffer from a png
# file. It is a pity that graphviz does not give access to its internal
# buffers.
tmp = tempfile.mkstemp(suffix=".png")[1]
gv.render(gvg, "png", tmp)
img = imread(tmp)
os.remove(tmp)
else:
if output_format == "auto":
if output == "":
output_format = "xlib"
if type(vsize) == PropertyMap:
vw = vh = vsize[v]
else:
vw = vh = vsize
aset(n, "shape", "circle")
aset(n, "width", "%g" % vw)
aset(n, "height", "%g" % vh)
aset(n, "style", "filled")
aset(n, "color", ecolor if isinstance(ecolor, str) else "#2e3436")
# apply color
if isinstance(vcolor, str):
aset(n, "fillcolor", vcolor)
else:
color = tuple([int(c * 255.0) for c in vcmap(vnorm(vcolor[v]))])
aset(n, "fillcolor", "#%.2x%.2x%.2x%.2x" % color)
aset(n, "label", "")
# user supplied position
if pos != None:
aset(n, "pos", "%f,%f" % (pos[0][v], pos[1][v]))
aset(n, "pin", pin)
# apply all user supplied properties
for k, val in vprops.iteritems():
if isinstance(val, PropertyMap):
aset(n, k, val[v])
else:
aset(n, k, val)
# add edges
if eorder != None:
edges = sorted(g.edges(), lambda a, b: cmp(eorder[a], eorder[b]))
else:
edges = g.edges()
for e in edges:
ge = libgv.agedge(gvg,
libgv.agnode(gvg, str(int(e.source()))),
libgv.agnode(gvg, str(int(e.target()))))
aset(ge, "arrowsize", "0.3")
if g.is_directed():
aset(ge, "arrowhead", "vee")
# apply color
if isinstance(ecolor, str):
aset(ge, "color", ecolor)
else:
color = tuple([int(c * 255.0) for c in ecmap(enorm(ecolor[e]))])
aset(ge, "color", "#%.2x%.2x%.2x%.2x" % color)
# apply edge length
if elen != None:
if isinstance(elen, PropertyMap):
aset(ge, "len", elen[e])
else:
aset(ge, "len", elen)
# apply width
if penwidth != None:
if isinstance(penwidth, PropertyMap):
aset(ge, "penwidth", penwidth[e])
else:
aset(ge, "penwidth", penwidth)
# apply all user supplied properties
for k, v in eprops.iteritems():
if isinstance(v, PropertyMap):
aset(ge, k, v[e])
else:
aset(ge, k, v)
libgv.gvLayout(gvc, gvg, layout)
has_layout = True
retv = libgv.gvRender(gvc, gvg, "dot", None) # retrieve positions only
if pos == None:
pos = (g.new_vertex_property("double"),
g.new_vertex_property("double"))
for v in g.vertices():
n = libgv.agnode(gvg, str(int(v)))
p = aget(n, "pos")
p = p.split(",")
pos[0][v] = float(p[0])
pos[1][v] = float(p[1])
# I don't get this, but it seems necessary
pos[0].a /= 100
pos[1].a /= 100
pos = group_vector_property(pos)
if return_string:
if output_format == "auto":
output_format = "png"
buf = ctypes.c_char_p()
buf_len = ctypes.c_size_t()
fstream = libc.open_memstream(ctypes.byref(buf),
ctypes.byref(buf_len))
libgv.gvRender(gvc, gvg, output_format, fstream)
libc.fclose(fstream)
data = copy.copy(ctypes.string_at(buf, buf_len.value))
libc.free(buf)
else:
if output_format == "auto":
if output == "":
output_format = "xlib"
elif output != None:
output_format = output.split(".")[-1]
# if using xlib we need to fork the process, otherwise good ol'
# graphviz will call exit() when the window is closed
if output_format == "xlib" or fork:
pid = os.fork()
if pid == 0:
libgv.gvRenderFilename(gvc, gvg, output_format, output)
os._exit(0) # since we forked, it's good to be sure
if output_format != "xlib":
os.wait()
elif output != None:
output_format = output.split(".")[-1]
# if using xlib we need to fork the process, otherwise good ol' graphviz
# will call exit() when the window is closed
if output_format == "xlib" or fork:
pid = os.fork()
if pid == 0:
gv.render(gvg, output_format, output)
os._exit(0) # since we forked, it's good to be sure
if output_format != "xlib":
os.wait()
elif output != None:
gv.render(gvg, output_format, output)
ret = [pos]
if return_bitmap:
ret.append(img)
if returngv:
ret.append(gv)
else:
gv.rm(gvg)
del gvg
libgv.gvRenderFilename(gvc, gvg, output_format, output)
ret = [pos]
if return_string:
ret.append(data)
finally:
if has_layout:
libgv.gvFreeLayout(gvc, gvg)
libgv.agclose(gvg)
if len(ret) > 1:
return tuple(ret)
......
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