LCPQ/quantum_package
10
0
Fork 0
mirror of https://github.com/LCPQ/quantum_package synced 2024-11-18 12:03:57 +01:00
Code Issues Releases Wiki Activity
8dc7ea8481
quantum_package/scripts/module/pydot.py

2126 lines
60 KiB
Python
Raw Normal View History

Add dot file to only_children_to_all_genealogy.py
2015-05-04 12:30:31 +02:00
# -*- coding: Latin-1 -*-
"""Graphviz's dot language Python interface.
This module provides with a full interface to create handle modify
and process graphs in Graphviz's dot language.
References:
pydot Homepage: http://code.google.com/p/pydot/
Graphviz: http://www.graphviz.org/
DOT Language: http://www.graphviz.org/doc/info/lang.html
Programmed and tested with Graphviz 2.26.3 and Python 2.6 on OSX 10.6.4
Copyright (c) 2005-2011 Ero Carrera <ero.carrera@gmail.com>
Distributed under MIT license [http://opensource.org/licenses/mit-license.html].
"""
__author__ = 'Ero Carrera'
__version__ = '1.0.*'
__license__ = 'MIT'
import os
import re
import subprocess
import tempfile
import copy
import sys
try:
import dot_parser
except Exception as e:
print >> sys.stderr, "Couldn't import dot_parser, loading of dot files will not be possible."
GRAPH_ATTRIBUTES = set(['Damping', 'K', 'URL', 'aspect', 'bb', 'bgcolor',
'center', 'charset', 'clusterrank', 'colorscheme', 'comment', 'compound',
'concentrate', 'defaultdist', 'dim', 'dimen', 'diredgeconstraints',
'dpi', 'epsilon', 'esep', 'fontcolor', 'fontname', 'fontnames',
'fontpath', 'fontsize', 'id', 'label', 'labeljust', 'labelloc',
'landscape', 'layers', 'layersep', 'layout', 'levels', 'levelsgap',
'lheight', 'lp', 'lwidth', 'margin', 'maxiter', 'mclimit', 'mindist',
'mode', 'model', 'mosek', 'nodesep', 'nojustify', 'normalize', 'nslimit',
'nslimit1', 'ordering', 'orientation', 'outputorder', 'overlap',
'overlap_scaling', 'pack', 'packmode', 'pad', 'page', 'pagedir',
'quadtree', 'quantum', 'rankdir', 'ranksep', 'ratio', 'remincross',
'repulsiveforce', 'resolution', 'root', 'rotate', 'searchsize', 'sep',
'showboxes', 'size', 'smoothing', 'sortv', 'splines', 'start',
'stylesheet', 'target', 'truecolor', 'viewport', 'voro_margin',
# for subgraphs
'rank'])
EDGE_ATTRIBUTES = set(['URL',
'arrowhead',
'arrowsize',
'arrowtail',
'color',
'colorscheme',
'comment',
'constraint',
'decorate',
'dir',
'edgeURL',
'edgehref',
'edgetarget',
'edgetooltip',
'fontcolor',
'fontname',
'fontsize',
'headURL',
'headclip',
'headhref',
'headlabel',
'headport',
'headtarget',
'headtooltip',
'href',
'id',
'label',
'labelURL',
'labelangle',
'labeldistance',
'labelfloat',
'labelfontcolor',
'labelfontname',
'labelfontsize',
'labelhref',
'labeltarget',
'labeltooltip',
'layer',
'len',
'lhead',
'lp',
'ltail',
'minlen',
'nojustify',
'penwidth',
'pos',
'samehead',
'sametail',
'showboxes',
'style',
'tailURL',
'tailclip',
'tailhref',
'taillabel',
'tailport',
'tailtarget',
'tailtooltip',
'target',
'tooltip',
'weight',
'rank'])
NODE_ATTRIBUTES = set(['URL', 'color', 'colorscheme', 'comment',
'distortion', 'fillcolor', 'fixedsize', 'fontcolor', 'fontname',
'fontsize', 'group', 'height', 'id', 'image', 'imagescale', 'label',
'labelloc', 'layer', 'margin', 'nojustify', 'orientation', 'penwidth',
'peripheries', 'pin', 'pos', 'rects', 'regular', 'root', 'samplepoints',
'shape', 'shapefile', 'showboxes', 'sides', 'skew', 'sortv', 'style',
'target', 'tooltip', 'vertices', 'width', 'z',
# The following are attributes dot2tex
'texlbl', 'texmode'])
CLUSTER_ATTRIBUTES = set(['K',
'URL',
'bgcolor',
'color',
'colorscheme',
'fillcolor',
'fontcolor',
'fontname',
'fontsize',
'label',
'labeljust',
'labelloc',
'lheight',
'lp',
'lwidth',
'nojustify',
'pencolor',
'penwidth',
'peripheries',
'sortv',
'style',
'target',
'tooltip'])
#
# Extented version of ASPN's Python Cookbook Recipe:
# Frozen dictionaries.
# http://aspn.activestate.com/ASPN/Cookbook/Python/Recipe/414283
#
# This version freezes dictionaries used as values within dictionaries.
#
class frozendict(dict):
def _blocked_attribute(obj):
raise AttributeError("A frozendict cannot be modified.")
_blocked_attribute = property(_blocked_attribute)
__delitem__ = __setitem__ = clear = _blocked_attribute
pop = popitem = setdefault = update = _blocked_attribute
def __new__(cls, *args, **kw):
new = dict.__new__(cls)
args_ = []
for arg in args:
if isinstance(arg, dict):
arg = copy.copy(arg)
for k, v in arg.iteritems():
if isinstance(v, frozendict):
arg[k] = v
elif isinstance(v, dict):
arg[k] = frozendict(v)
elif isinstance(v, list):
v_ = list()
for elm in v:
if isinstance(elm, dict):
v_.append(frozendict(elm))
else:
v_.append(elm)
arg[k] = tuple(v_)
args_.append(arg)
else:
args_.append(arg)
dict.__init__(new, *args_, **kw)
return new
def __init__(self, *args, **kw):
pass
def __hash__(self):
try:
return self._cached_hash
except AttributeError:
h = self._cached_hash = hash(tuple(sorted(self.iteritems())))
return h
def __repr__(self):
return "frozendict(%s)" % dict.__repr__(self)
dot_keywords = ['graph', 'subgraph', 'digraph', 'node', 'edge', 'strict']
id_re_alpha_nums = re.compile('^[_a-zA-Z][a-zA-Z0-9_,]*$', re.UNICODE)
id_re_alpha_nums_with_ports = re.compile(
'^[_a-zA-Z][a-zA-Z0-9_,:\"]*[a-zA-Z0-9_,\"]+$',
re.UNICODE)
id_re_num = re.compile('^[0-9,]+$', re.UNICODE)
id_re_with_port = re.compile('^([^:]*):([^:]*)$', re.UNICODE)
id_re_dbl_quoted = re.compile('^\".*\"$', re.S | re.UNICODE)
id_re_html = re.compile('^<.*>$', re.S | re.UNICODE)
def needs_quotes(s):
"""Checks whether a string is a dot language ID.
It will check whether the string is solely composed
by the characters allowed in an ID or not.
If the string is one of the reserved keywords it will
need quotes too but the user will need to add them
manually.
"""
# If the name is a reserved keyword it will need quotes but pydot
# can't tell when it's being used as a keyword or when it's simply
# a name. Hence the user needs to supply the quotes when an element
# would use a reserved keyword as name. This function will return
# false indicating that a keyword string, if provided as-is, won't
# need quotes.
if s in dot_keywords:
return False
chars = [ord(c) for c in s if ord(c) > 0x7f or ord(c) == 0]
if chars and not id_re_dbl_quoted.match(s) and not id_re_html.match(s):
return True
for test_re in [
id_re_alpha_nums,
id_re_num,
id_re_dbl_quoted,
id_re_html,
id_re_alpha_nums_with_ports]:
if test_re.match(s):
return False
m = id_re_with_port.match(s)
if m:
return needs_quotes(m.group(1)) or needs_quotes(m.group(2))
return True
def quote_if_necessary(s):
if isinstance(s, bool):
if s is True:
return 'True'
return 'False'
if not isinstance(s, basestring):
return s
if not s:
return s
if needs_quotes(s):
replace = {'"': r'\"',
"\n": r'\n',
"\r": r'\r'}
for (a, b) in replace.items():
s = s.replace(a, b)
return '"' + s + '"'
return s
def graph_from_dot_data(data):
"""Load graph as defined by data in DOT format.
The data is assumed to be in DOT format. It will
be parsed and a Dot class will be returned,
representing the graph.
"""
return dot_parser.parse_dot_data(data)
def graph_from_dot_file(path):
"""Load graph as defined by a DOT file.
The file is assumed to be in DOT format. It will
be loaded, parsed and a Dot class will be returned,
representing the graph.
"""
fd = file(path, 'rb')
data = fd.read()
fd.close()
return graph_from_dot_data(data)
def graph_from_edges(edge_list, node_prefix='', directed=False):
"""Creates a basic graph out of an edge list.
The edge list has to be a list of tuples representing
the nodes connected by the edge.
The values can be anything: bool, int, float, str.
If the graph is undirected by default, it is only
calculated from one of the symmetric halves of the matrix.
"""
if directed:
graph = Dot(graph_type='digraph')
else:
graph = Dot(graph_type='graph')
for edge in edge_list:
if isinstance(edge[0], str):
src = node_prefix + edge[0]
else:
src = node_prefix + str(edge[0])
if isinstance(edge[1], str):
dst = node_prefix + edge[1]
else:
dst = node_prefix + str(edge[1])
e = Edge(src, dst)
graph.add_edge(e)
return graph
def graph_from_adjacency_matrix(matrix, node_prefix=u'', directed=False):
"""Creates a basic graph out of an adjacency matrix.
The matrix has to be a list of rows of values
representing an adjacency matrix.
The values can be anything: bool, int, float, as long
as they can evaluate to True or False.
"""
node_orig = 1
if directed:
graph = Dot(graph_type='digraph')
else:
graph = Dot(graph_type='graph')
for row in matrix:
if not directed:
skip = matrix.index(row)
r = row[skip:]
else:
skip = 0
r = row
node_dest = skip + 1
for e in r:
if e:
graph.add_edge(
Edge(node_prefix + node_orig,
node_prefix + node_dest))
node_dest += 1
node_orig += 1
return graph
def graph_from_incidence_matrix(matrix, node_prefix='', directed=False):
"""Creates a basic graph out of an incidence matrix.
The matrix has to be a list of rows of values
representing an incidence matrix.
The values can be anything: bool, int, float, as long
as they can evaluate to True or False.
"""
node_orig = 1
if directed:
graph = Dot(graph_type='digraph')
else:
graph = Dot(graph_type='graph')
for row in matrix:
nodes = []
c = 1
for node in row:
if node:
nodes.append(c * node)
c += 1
nodes.sort()
if len(nodes) == 2:
graph.add_edge(
Edge(node_prefix + abs(nodes[0]),
node_prefix + nodes[1]))
if not directed:
graph.set_simplify(True)
return graph
def __find_executables(path):
"""Used by find_graphviz
path - single directory as a string
If any of the executables are found, it will return a dictionary
containing the program names as keys and their paths as values.
Otherwise returns None
"""
success = False
progs = {
'dot': '',
'twopi': '',
'neato': '',
'circo': '',
'fdp': '',
'sfdp': ''}
was_quoted = False
path = path.strip()
if path.startswith('"') and path.endswith('"'):
path = path[1:-1]
was_quoted = True
if os.path.isdir(path):
for prg in progs.iterkeys():
if progs[prg]:
continue
if os.path.exists(os.path.join(path, prg)):
if was_quoted:
progs[prg] = '"' + os.path.join(path, prg) + '"'
else:
progs[prg] = os.path.join(path, prg)
success = True
elif os.path.exists(os.path.join(path, prg + '.exe')):
if was_quoted:
progs[prg] = '"' + os.path.join(path, prg + '.exe') + '"'
else:
progs[prg] = os.path.join(path, prg + '.exe')
success = True
if success:
return progs
else:
return None
# The multi-platform version of this 'find_graphviz' function was
# contributed by Peter Cock
#
def find_graphviz():
"""Locate Graphviz's executables in the system.
Tries three methods:
First: Windows Registry (Windows only)
This requires Mark Hammond's pywin32 is installed.
Secondly: Search the path
It will look for 'dot', 'twopi' and 'neato' in all the directories
specified in the PATH environment variable.
Thirdly: Default install location (Windows only)
It will look for 'dot', 'twopi' and 'neato' in the default install
location under the "Program Files" directory.
It will return a dictionary containing the program names as keys
and their paths as values.
If this fails, it returns None.
"""
# Method 1 (Windows only)
#
if os.sys.platform == 'win32':
HKEY_LOCAL_MACHINE = 0x80000002
KEY_QUERY_VALUE = 0x0001
RegOpenKeyEx = None
RegQueryValueEx = None
RegCloseKey = None
try:
import win32api
import win32con
RegOpenKeyEx = win32api.RegOpenKeyEx
RegQueryValueEx = win32api.RegQueryValueEx
RegCloseKey = win32api.RegCloseKey
except ImportError:
# Print a messaged suggesting they install these?
#
pass
try:
import ctypes
def RegOpenKeyEx(key, subkey, opt, sam):
result = ctypes.c_uint(0)
ctypes.windll.advapi32.RegOpenKeyExA(
key,
subkey,
opt,
sam,
ctypes.byref(result))
return result.value
def RegQueryValueEx(hkey, valuename):
data_type = ctypes.c_uint(0)
data_len = ctypes.c_uint(1024)
data = ctypes.create_string_buffer(1024)
res = ctypes.windll.advapi32.RegQueryValueExA(
hkey,
valuename,
0,
ctypes.byref(data_type),
data,
ctypes.byref(data_len))
return data.value
RegCloseKey = ctypes.windll.advapi32.RegCloseKey
except ImportError:
# Print a messaged suggesting they install these?
#
pass
if RegOpenKeyEx is not None:
# Get the GraphViz install path from the registry
#
hkey = None
potentialKeys = [
"SOFTWARE\\ATT\\Graphviz",
"SOFTWARE\\AT&T Research Labs\\Graphviz",
]
for potentialKey in potentialKeys:
try:
hkey = RegOpenKeyEx(HKEY_LOCAL_MACHINE,
potentialKey, 0, KEY_QUERY_VALUE)
if hkey is not None:
path = RegQueryValueEx(hkey, "InstallPath")
RegCloseKey(hkey)
# The regitry variable might exist, left by old installations
# but with no value, in those cases we keep
# searching...
if not path:
continue
# Now append the "bin" subdirectory:
#
path = os.path.join(path, "bin")
progs = __find_executables(path)
if progs is not None:
# print "Used Windows registry"
return progs
except Exception as excp:
#raise excp
pass
else:
break
# Method 2 (Linux, Windows etc)
#
if 'PATH' in os.environ:
for path in os.environ['PATH'].split(os.pathsep):
progs = __find_executables(path)
if progs is not None:
# print "Used path"
return progs
# Method 3 (Windows only)
#
if os.sys.platform == 'win32':
# Try and work out the equivalent of "C:\Program Files" on this
# machine (might be on drive D:, or in a different language)
#
if 'PROGRAMFILES' in os.environ:
# Note, we could also use the win32api to get this
# information, but win32api may not be installed.
path = os.path.join(
os.environ['PROGRAMFILES'],
'ATT',
'GraphViz',
'bin')
else:
# Just in case, try the default...
path = r"C:\Program Files\att\Graphviz\bin"
progs = __find_executables(path)
if progs is not None:
# print "Used default install location"
return progs
for path in (
'/usr/bin', '/usr/local/bin',
'/opt/local/bin',
'/opt/bin', '/sw/bin', '/usr/share',
'/Applications/Graphviz.app/Contents/MacOS/'):
progs = __find_executables(path)
if progs is not None:
# print "Used path"
return progs
# Failed to find GraphViz
#
return None
class Common:
"""Common information to several classes.
Should not be directly used, several classes are derived from
this one.
"""
def __getstate__(self):
dict = copy.copy(self.obj_dict)
return dict
def __setstate__(self, state):
self.obj_dict = state
def __get_attribute__(self, attr):
"""Look for default attributes for this node"""
attr_val = self.obj_dict['attributes'].get(attr, None)
if attr_val is None:
# get the defaults for nodes/edges
default_node_name = self.obj_dict['type']
# The defaults for graphs are set on a node named 'graph'
if default_node_name in ('subgraph', 'digraph', 'cluster'):
default_node_name = 'graph'
g = self.get_parent_graph()
if g is not None:
defaults = g.get_node(default_node_name)
else:
return None
# Multiple defaults could be set by having repeated 'graph [...]'
# 'node [...]', 'edge [...]' statements. In such case, if the
# same attribute is set in different statements, only the first
# will be returned. In order to get all, one would call the
# get_*_defaults() methods and handle those. Or go node by node
# (of the ones specifying defaults) and modify the attributes
# individually.
#
if not isinstance(defaults, (list, tuple)):
defaults = [defaults]
for default in defaults:
attr_val = default.obj_dict['attributes'].get(attr, None)
if attr_val:
return attr_val
else:
return attr_val
return None
def set_parent_graph(self, parent_graph):
self.obj_dict['parent_graph'] = parent_graph
def get_parent_graph(self):
return self.obj_dict.get('parent_graph', None)
def set(self, name, value):
"""Set an attribute value by name.
Given an attribute 'name' it will set its value to 'value'.
There's always the possibility of using the methods:
set_'name'(value)
which are defined for all the existing attributes.
"""
self.obj_dict['attributes'][name] = value
def get(self, name):
"""Get an attribute value by name.
Given an attribute 'name' it will get its value.
There's always the possibility of using the methods:
get_'name'()
which are defined for all the existing attributes.
"""
return self.obj_dict['attributes'].get(name, None)
def get_attributes(self):
""""""
return self.obj_dict['attributes']
def set_sequence(self, seq):
self.obj_dict['sequence'] = seq
def get_sequence(self):
return self.obj_dict['sequence']
def create_attribute_methods(self, obj_attributes):
# for attr in self.obj_dict['attributes']:
for attr in obj_attributes:
# Generate all the Setter methods.
#
self.__setattr__(
'set_' +
attr,
lambda x,
a=attr: self.obj_dict['attributes'].__setitem__(
a,
x))
# Generate all the Getter methods.
#
self.__setattr__(
'get_' + attr,
lambda a=attr: self.__get_attribute__(a))
class Error(Exception):
"""General error handling class.
"""
def __init__(self, value):
self.value = value
def __str__(self):
return self.value
class InvocationException(Exception):
"""To indicate that a ploblem occurred while running any of the GraphViz executables.
"""
def __init__(self, value):
self.value = value
def __str__(self):
return self.value
class Node(object, Common):
"""A graph node.
This class represents a graph's node with all its attributes.
node(name, attribute=value, ...)
name: node's name
All the attributes defined in the Graphviz dot language should
be supported.
"""
def __init__(self, name='', obj_dict=None, **attrs):
#
# Nodes will take attributes of all other types because the defaults
# for any GraphViz object are dealt with as if they were Node definitions
#
if obj_dict is not None:
self.obj_dict = obj_dict
else:
self.obj_dict = dict()
# Copy the attributes
#
self.obj_dict['attributes'] = dict(attrs)
self.obj_dict['type'] = 'node'
self.obj_dict['parent_graph'] = None
self.obj_dict['parent_node_list'] = None
self.obj_dict['sequence'] = None
# Remove the compass point
#
port = None
if isinstance(name, basestring) and not name.startswith('"'):
idx = name.find(':')
if idx > 0 and idx + 1 < len(name):
name, port = name[:idx], name[idx:]
if isinstance(name, (long, int)):
name = str(name)
self.obj_dict['name'] = quote_if_necessary(name)
self.obj_dict['port'] = port
self.create_attribute_methods(NODE_ATTRIBUTES)
def set_name(self, node_name):
"""Set the node's name."""
self.obj_dict['name'] = node_name
def get_name(self):
"""Get the node's name."""
return self.obj_dict['name']
def get_port(self):
"""Get the node's port."""
return self.obj_dict['port']
def add_style(self, style):
styles = self.obj_dict['attributes'].get('style', None)
if not styles and style:
styles = [style]
else:
styles = styles.split(',')
styles.append(style)
self.obj_dict['attributes']['style'] = ','.join(styles)
def to_string(self):
"""Returns a string representation of the node in dot language.
"""
# RMF: special case defaults for node, edge and graph properties.
#
node = quote_if_necessary(self.obj_dict['name'])
node_attr = list()
for attr, value in self.obj_dict['attributes'].iteritems():
if value is not None:
node_attr.append('%s=%s' % (attr, quote_if_necessary(value)))
else:
node_attr.append(attr)
# No point in having nodes setting any defaults if the don't set
# any attributes...
#
if node in ('graph', 'node', 'edge') and len(node_attr) == 0:
return ''
node_attr = ', '.join(node_attr)
if node_attr:
node += ' [' + node_attr + ']'
return node + ';'
class Edge(object, Common):
"""A graph edge.
This class represents a graph's edge with all its attributes.
edge(src, dst, attribute=value, ...)
src: source node's name
dst: destination node's name
All the attributes defined in the Graphviz dot language should
be supported.
Attributes can be set through the dynamically generated methods:
set_[attribute name], i.e. set_label, set_fontname
or directly by using the instance's special dictionary:
Edge.obj_dict['attributes'][attribute name], i.e.
edge_instance.obj_dict['attributes']['label']
edge_instance.obj_dict['attributes']['fontname']
"""
def __init__(self, src='', dst='', obj_dict=None, **attrs):
if isinstance(src, (list, tuple)) and dst == '':
src, dst = src
if obj_dict is not None:
self.obj_dict = obj_dict
else:
self.obj_dict = dict()
# Copy the attributes
#
self.obj_dict['attributes'] = dict(attrs)
self.obj_dict['type'] = 'edge'
self.obj_dict['parent_graph'] = None
self.obj_dict['parent_edge_list'] = None
self.obj_dict['sequence'] = None
if isinstance(src, Node):
src = src.get_name()
if isinstance(dst, Node):
dst = dst.get_name()
points = (quote_if_necessary(src), quote_if_necessary(dst))
self.obj_dict['points'] = points
self.create_attribute_methods(EDGE_ATTRIBUTES)
def get_source(self):
"""Get the edges source node name."""
return self.obj_dict['points'][0]
def get_destination(self):
"""Get the edge's destination node name."""
return self.obj_dict['points'][1]
def __hash__(self):
return hash(hash(self.get_source()) + hash(self.get_destination()))
def __eq__(self, edge):
"""Compare two edges.
If the parent graph is directed, arcs linking
node A to B are considered equal and A->B != B->A
If the parent graph is undirected, any edge
connecting two nodes is equal to any other
edge connecting the same nodes, A->B == B->A
"""
if not isinstance(edge, Edge):
raise Error("Can't compare and edge to a non-edge object.")
if self.get_parent_graph().get_top_graph_type() == 'graph':
# If the graph is undirected, the edge has neither
# source nor destination.
#
if ((self.get_source() == edge.get_source() and self.get_destination() == edge.get_destination()) or (
edge.get_source() == self.get_destination() and edge.get_destination() == self.get_source())):
return True
else:
if self.get_source() == edge.get_source(
) and self.get_destination() == edge.get_destination():
return True
return False
def parse_node_ref(self, node_str):
if not isinstance(node_str, str):
return node_str
if node_str.startswith('"') and node_str.endswith('"'):
return node_str
node_port_idx = node_str.rfind(':')
if node_port_idx > 0 and node_str[0] == '"' and node_str[
node_port_idx -
1] == '"':
return node_str
if node_port_idx > 0:
a = node_str[:node_port_idx]
b = node_str[node_port_idx + 1:]
node = quote_if_necessary(a)
node += ':' + quote_if_necessary(b)
return node
return node_str
def to_string(self):
"""Returns a string representation of the edge in dot language.
"""
src = self.parse_node_ref(self.get_source())
dst = self.parse_node_ref(self.get_destination())
if isinstance(src, frozendict):
edge = [Subgraph(obj_dict=src).to_string()]
elif isinstance(src, (int, long)):
edge = [str(src)]
else:
edge = [src]
if (self.get_parent_graph() and
self.get_parent_graph().get_top_graph_type() and
self.get_parent_graph().get_top_graph_type() == 'digraph'):
edge.append('->')
else:
edge.append('--')
if isinstance(dst, frozendict):
edge.append(Subgraph(obj_dict=dst).to_string())
elif isinstance(dst, (int, long)):
edge.append(str(dst))
else:
edge.append(dst)
edge_attr = list()
for attr, value in self.obj_dict['attributes'].iteritems():
if value is not None:
edge_attr.append('%s=%s' % (attr, quote_if_necessary(value)))
else:
edge_attr.append(attr)
edge_attr = ', '.join(edge_attr)
if edge_attr:
edge.append(' [' + edge_attr + ']')
return ' '.join(edge) + ';'
class Graph(object, Common):
"""Class representing a graph in Graphviz's dot language.
This class implements the methods to work on a representation
of a graph in Graphviz's dot language.
graph( graph_name='G', graph_type='digraph',
strict=False, suppress_disconnected=False, attribute=value, ...)
graph_name:
the graph's name
graph_type:
can be 'graph' or 'digraph'
suppress_disconnected:
defaults to False, which will remove from the
graph any disconnected nodes.
simplify:
if True it will avoid displaying equal edges, i.e.
only one edge between two nodes. removing the
duplicated ones.
All the attributes defined in the Graphviz dot language should
be supported.
Attributes can be set through the dynamically generated methods:
set_[attribute name], i.e. set_size, set_fontname
or using the instance's attributes:
Graph.obj_dict['attributes'][attribute name], i.e.
graph_instance.obj_dict['attributes']['label']
graph_instance.obj_dict['attributes']['fontname']
"""
def __init__(
self,
graph_name='G',
obj_dict=None,
graph_type='digraph',
strict=False,
suppress_disconnected=False,
simplify=False,
**attrs):
if obj_dict is not None:
self.obj_dict = obj_dict
else:
self.obj_dict = dict()
self.obj_dict['attributes'] = dict(attrs)
if graph_type not in ['graph', 'digraph']:
raise Error(
'Invalid type "%s". Accepted graph types are: graph, digraph, subgraph' %
graph_type)
self.obj_dict['name'] = quote_if_necessary(graph_name)
self.obj_dict['type'] = graph_type
self.obj_dict['strict'] = strict
self.obj_dict['suppress_disconnected'] = suppress_disconnected
self.obj_dict['simplify'] = simplify
self.obj_dict['current_child_sequence'] = 1
self.obj_dict['nodes'] = dict()
self.obj_dict['edges'] = dict()
self.obj_dict['subgraphs'] = dict()
self.set_parent_graph(self)
self.create_attribute_methods(GRAPH_ATTRIBUTES)
def get_graph_type(self):
return self.obj_dict['type']
def get_top_graph_type(self):
parent = self
while True:
parent_ = parent.get_parent_graph()
if parent_ == parent:
break
parent = parent_
return parent.obj_dict['type']
def set_graph_defaults(self, **attrs):
self.add_node(Node('graph', **attrs))
def get_graph_defaults(self, **attrs):
graph_nodes = self.get_node('graph')
if isinstance(graph_nodes, (list, tuple)):
return [node.get_attributes() for node in graph_nodes]
return graph_nodes.get_attributes()
def set_node_defaults(self, **attrs):
self.add_node(Node('node', **attrs))
def get_node_defaults(self, **attrs):
graph_nodes = self.get_node('node')
if isinstance(graph_nodes, (list, tuple)):
return [node.get_attributes() for node in graph_nodes]
return graph_nodes.get_attributes()
def set_edge_defaults(self, **attrs):
self.add_node(Node('edge', **attrs))
def get_edge_defaults(self, **attrs):
graph_nodes = self.get_node('edge')
if isinstance(graph_nodes, (list, tuple)):
return [node.get_attributes() for node in graph_nodes]
return graph_nodes.get_attributes()
def set_simplify(self, simplify):
"""Set whether to simplify or not.
If True it will avoid displaying equal edges, i.e.
only one edge between two nodes. removing the
duplicated ones.
"""
self.obj_dict['simplify'] = simplify
def get_simplify(self):
"""Get whether to simplify or not.
Refer to set_simplify for more information.
"""
return self.obj_dict['simplify']
def set_type(self, graph_type):
"""Set the graph's type, 'graph' or 'digraph'."""
self.obj_dict['type'] = graph_type
def get_type(self):
"""Get the graph's type, 'graph' or 'digraph'."""
return self.obj_dict['type']
def set_name(self, graph_name):
"""Set the graph's name."""
self.obj_dict['name'] = graph_name
def get_name(self):
"""Get the graph's name."""
return self.obj_dict['name']
def set_strict(self, val):
"""Set graph to 'strict' mode.
This option is only valid for top level graphs.
"""
self.obj_dict['strict'] = val
def get_strict(self, val):
"""Get graph's 'strict' mode (True, False).
This option is only valid for top level graphs.
"""
return self.obj_dict['strict']
def set_suppress_disconnected(self, val):
"""Suppress disconnected nodes in the output graph.
This option will skip nodes in the graph with no incoming or outgoing
edges. This option works also for subgraphs and has effect only in the
current graph/subgraph.
"""
self.obj_dict['suppress_disconnected'] = val
def get_suppress_disconnected(self, val):
"""Get if suppress disconnected is set.
Refer to set_suppress_disconnected for more information.
"""
return self.obj_dict['suppress_disconnected']
def get_next_sequence_number(self):
seq = self.obj_dict['current_child_sequence']
self.obj_dict['current_child_sequence'] += 1
return seq
def add_node(self, graph_node):
"""Adds a node object to the graph.
It takes a node object as its only argument and returns
None.
"""
if not isinstance(graph_node, Node):
raise TypeError(
'add_node() received a non node class object: ' +
str(graph_node))
node = self.get_node(graph_node.get_name())
if not node:
self.obj_dict['nodes'][
graph_node.get_name()] = [
graph_node.obj_dict]
#self.node_dict[graph_node.get_name()] = graph_node.attributes
graph_node.set_parent_graph(self.get_parent_graph())
else:
self.obj_dict['nodes'][
graph_node.get_name()].append(
graph_node.obj_dict)
graph_node.set_sequence(self.get_next_sequence_number())
def del_node(self, name, index=None):
"""Delete a node from the graph.
Given a node's name all node(s) with that same name
will be deleted if 'index' is not specified or set
to None.
If there are several nodes with that same name and
'index' is given, only the node in that position
will be deleted.
'index' should be an integer specifying the position
of the node to delete. If index is larger than the
number of nodes with that name, no action is taken.
If nodes are deleted it returns True. If no action
is taken it returns False.
"""
if isinstance(name, Node):
name = name.get_name()
if name in self.obj_dict['nodes']:
if index is not None and index < len(self.obj_dict['nodes'][name]):
del self.obj_dict['nodes'][name][index]
return True
else:
del self.obj_dict['nodes'][name]
return True
return False
def get_node(self, name):
"""Retrieve a node from the graph.
Given a node's name the corresponding Node
instance will be returned.
If one or more nodes exist with that name a list of
Node instances is returned.
An empty list is returned otherwise.
"""
match = list()
if name in self.obj_dict['nodes']:
match.extend([Node(obj_dict=obj_dict)
for obj_dict in self.obj_dict['nodes'][name]])
return match
def get_nodes(self):
"""Get the list of Node instances."""
return self.get_node_list()
def get_node_list(self):
"""Get the list of Node instances.
This method returns the list of Node instances
composing the graph.
"""
node_objs = list()
for node, obj_dict_list in self.obj_dict['nodes'].iteritems():
node_objs.extend([Node(obj_dict=obj_d) for obj_d in obj_dict_list])
return node_objs
def add_edge(self, graph_edge):
"""Adds an edge object to the graph.
It takes a edge object as its only argument and returns
None.
"""
if not isinstance(graph_edge, Edge):
raise TypeError(
'add_edge() received a non edge class object: ' +
str(graph_edge))
edge_points = (graph_edge.get_source(), graph_edge.get_destination())
if edge_points in self.obj_dict['edges']:
edge_list = self.obj_dict['edges'][edge_points]
edge_list.append(graph_edge.obj_dict)
else:
self.obj_dict['edges'][edge_points] = [graph_edge.obj_dict]
graph_edge.set_sequence(self.get_next_sequence_number())
graph_edge.set_parent_graph(self.get_parent_graph())
def del_edge(self, src_or_list, dst=None, index=None):
"""Delete an edge from the graph.
Given an edge's (source, destination) node names all
matching edges(s) will be deleted if 'index' is not
specified or set to None.
If there are several matching edges and 'index' is
given, only the edge in that position will be deleted.
'index' should be an integer specifying the position
of the edge to delete. If index is larger than the
number of matching edges, no action is taken.
If edges are deleted it returns True. If no action
is taken it returns False.
"""
if isinstance(src_or_list, (list, tuple)):
if dst is not None and isinstance(dst, (int, long)):
index = dst
src, dst = src_or_list
else:
src, dst = src_or_list, dst
if isinstance(src, Node):
src = src.get_name()
if isinstance(dst, Node):
dst = dst.get_name()
if (src, dst) in self.obj_dict['edges']:
if index is not None and index < len(
self.obj_dict['edges'][
(src, dst)]):
del self.obj_dict['edges'][(src, dst)][index]
return True
else:
del self.obj_dict['edges'][(src, dst)]
return True
return False
def get_edge(self, src_or_list, dst=None):
"""Retrieved an edge from the graph.
Given an edge's source and destination the corresponding
Edge instance(s) will be returned.
If one or more edges exist with that source and destination
a list of Edge instances is returned.
An empty list is returned otherwise.
"""
if isinstance(src_or_list, (list, tuple)) and dst is None:
edge_points = tuple(src_or_list)
edge_points_reverse = (edge_points[1], edge_points[0])
else:
edge_points = (src_or_list, dst)
edge_points_reverse = (dst, src_or_list)
match = list()
if edge_points in self.obj_dict['edges'] or (
self.get_top_graph_type() == 'graph' and edge_points_reverse in self.obj_dict['edges']):
edges_obj_dict = self.obj_dict['edges'].get(
edge_points,
self.obj_dict['edges'].get(edge_points_reverse, None))
for edge_obj_dict in edges_obj_dict:
match.append(
Edge(
edge_points[0],
edge_points[1],
obj_dict=edge_obj_dict))
return match
def get_edges(self):
return self.get_edge_list()
def get_edge_list(self):
"""Get the list of Edge instances.
This method returns the list of Edge instances
composing the graph.
"""
edge_objs = list()
for edge, obj_dict_list in self.obj_dict['edges'].iteritems():
edge_objs.extend([Edge(obj_dict=obj_d) for obj_d in obj_dict_list])
return edge_objs
def add_subgraph(self, sgraph):
"""Adds an subgraph object to the graph.
It takes a subgraph object as its only argument and returns
None.
"""
if not isinstance(
sgraph,
Subgraph) and not isinstance(
sgraph,
Cluster):
raise TypeError(
'add_subgraph() received a non subgraph class object:' +
str(sgraph))
if sgraph.get_name() in self.obj_dict['subgraphs']:
sgraph_list = self.obj_dict['subgraphs'][sgraph.get_name()]
sgraph_list.append(sgraph.obj_dict)
else:
self.obj_dict['subgraphs'][sgraph.get_name()] = [sgraph.obj_dict]
sgraph.set_sequence(self.get_next_sequence_number())
sgraph.set_parent_graph(self.get_parent_graph())
def get_subgraph(self, name):
"""Retrieved a subgraph from the graph.
Given a subgraph's name the corresponding
Subgraph instance will be returned.
If one or more subgraphs exist with the same name, a list of
Subgraph instances is returned.
An empty list is returned otherwise.
"""
match = list()
if name in self.obj_dict['subgraphs']:
sgraphs_obj_dict = self.obj_dict['subgraphs'].get(name)
for obj_dict_list in sgraphs_obj_dict:
#match.extend( Subgraph( obj_dict = obj_d ) for obj_d in obj_dict_list )
match.append(Subgraph(obj_dict=obj_dict_list))
return match
def get_subgraphs(self):
return self.get_subgraph_list()
def get_subgraph_list(self):
"""Get the list of Subgraph instances.
This method returns the list of Subgraph instances
in the graph.
"""
sgraph_objs = list()
for sgraph, obj_dict_list in self.obj_dict['subgraphs'].iteritems():
sgraph_objs.extend([Subgraph(obj_dict=obj_d)
for obj_d in obj_dict_list])
return sgraph_objs
def set_parent_graph(self, parent_graph):
self.obj_dict['parent_graph'] = parent_graph
for obj_list in self.obj_dict['nodes'].itervalues():
for obj in obj_list:
obj['parent_graph'] = parent_graph
for obj_list in self.obj_dict['edges'].itervalues():
for obj in obj_list:
obj['parent_graph'] = parent_graph
for obj_list in self.obj_dict['subgraphs'].itervalues():
for obj in obj_list:
Graph(obj_dict=obj).set_parent_graph(parent_graph)
def to_string(self):
"""Returns a string representation of the graph in dot language.
It will return the graph and all its subelements in string from.
"""
graph = list()
if self.obj_dict.get('strict', None) is not None:
if self == self.get_parent_graph() and self.obj_dict['strict']:
graph.append('strict ')
if self.obj_dict['name'] == '':
if 'show_keyword' in self.obj_dict and self.obj_dict[
'show_keyword']:
graph.append('subgraph {\n')
else:
graph.append('{\n')
else:
graph.append(
'%s %s {\n' %
(self.obj_dict['type'], self.obj_dict['name']))
for attr in self.obj_dict['attributes'].iterkeys():
if self.obj_dict['attributes'].get(attr, None) is not None:
val = self.obj_dict['attributes'].get(attr)
if val is not None:
graph.append('%s=%s' % (attr, quote_if_necessary(val)))
else:
graph.append(attr)
graph.append(';\n')
edges_done = set()
edge_obj_dicts = list()
for e in self.obj_dict['edges'].itervalues():
edge_obj_dicts.extend(e)
if edge_obj_dicts:
edge_src_set, edge_dst_set = zip(
*[obj['points'] for obj in edge_obj_dicts])
edge_src_set, edge_dst_set = set(edge_src_set), set(edge_dst_set)
else:
edge_src_set, edge_dst_set = set(), set()
node_obj_dicts = list()
for e in self.obj_dict['nodes'].itervalues():
node_obj_dicts.extend(e)
sgraph_obj_dicts = list()
for sg in self.obj_dict['subgraphs'].itervalues():
sgraph_obj_dicts.extend(sg)
obj_list = sorted([(obj['sequence'], obj) for obj in (
edge_obj_dicts + node_obj_dicts + sgraph_obj_dicts)])
for idx, obj in obj_list:
if obj['type'] == 'node':
node = Node(obj_dict=obj)
if self.obj_dict.get('suppress_disconnected', False):
if (node.get_name() not in edge_src_set and
node.get_name() not in edge_dst_set):
continue
graph.append(node.to_string() + '\n')
elif obj['type'] == 'edge':
edge = Edge(obj_dict=obj)
if self.obj_dict.get('simplify', False) and edge in edges_done:
continue
graph.append(edge.to_string() + '\n')
edges_done.add(edge)
else:
sgraph = Subgraph(obj_dict=obj)
graph.append(sgraph.to_string() + '\n')
graph.append('}\n')
return ''.join(graph)
class Subgraph(Graph):
"""Class representing a subgraph in Graphviz's dot language.
This class implements the methods to work on a representation
of a subgraph in Graphviz's dot language.
subgraph(graph_name='subG', suppress_disconnected=False, attribute=value, ...)
graph_name:
the subgraph's name
suppress_disconnected:
defaults to false, which will remove from the
subgraph any disconnected nodes.
All the attributes defined in the Graphviz dot language should
be supported.
Attributes can be set through the dynamically generated methods:
set_[attribute name], i.e. set_size, set_fontname
or using the instance's attributes:
Subgraph.obj_dict['attributes'][attribute name], i.e.
subgraph_instance.obj_dict['attributes']['label']
subgraph_instance.obj_dict['attributes']['fontname']
"""
# RMF: subgraph should have all the attributes of graph so it can be passed
# as a graph to all methods
#
def __init__(
self,
graph_name='',
obj_dict=None,
suppress_disconnected=False,
simplify=False,
**attrs):
Graph.__init__(
self,
graph_name=graph_name,
obj_dict=obj_dict,
suppress_disconnected=suppress_disconnected,
simplify=simplify,
**attrs)
if obj_dict is None:
self.obj_dict['type'] = 'subgraph'
class Cluster(Graph):
"""Class representing a cluster in Graphviz's dot language.
This class implements the methods to work on a representation
of a cluster in Graphviz's dot language.
cluster(graph_name='subG', suppress_disconnected=False, attribute=value, ...)
graph_name:
the cluster's name (the string 'cluster' will be always prepended)
suppress_disconnected:
defaults to false, which will remove from the
cluster any disconnected nodes.
All the attributes defined in the Graphviz dot language should
be supported.
Attributes can be set through the dynamically generated methods:
set_[attribute name], i.e. set_color, set_fontname
or using the instance's attributes:
Cluster.obj_dict['attributes'][attribute name], i.e.
cluster_instance.obj_dict['attributes']['label']
cluster_instance.obj_dict['attributes']['fontname']
"""
def __init__(
self,
graph_name='subG',
obj_dict=None,
suppress_disconnected=False,
simplify=False,
**attrs):
Graph.__init__(
self,
graph_name=graph_name,
obj_dict=obj_dict,
suppress_disconnected=suppress_disconnected,
simplify=simplify,
**attrs)
if obj_dict is None:
self.obj_dict['type'] = 'subgraph'
self.obj_dict['name'] = 'cluster_' + graph_name
self.create_attribute_methods(CLUSTER_ATTRIBUTES)
class Dot(Graph):
"""A container for handling a dot language file.
This class implements methods to write and process
a dot language file. It is a derived class of
the base class 'Graph'.
"""
def __init__(self, *argsl, **argsd):
Graph.__init__(self, *argsl, **argsd)
self.shape_files = list()
self.progs = None
self.formats = [
'canon',
'cmap',
'cmapx',
'cmapx_np',
'dia',
'dot',
'fig',
'gd',
'gd2',
'gif',
'hpgl',
'imap',
'imap_np',
'ismap',
'jpe',
'jpeg',
'jpg',
'mif',
'mp',
'pcl',
'pdf',
'pic',
'plain',
'plain-ext',
'png',
'ps',
'ps2',
'svg',
'svgz',
'vml',
'vmlz',
'vrml',
'vtx',
'wbmp',
'xdot',
'xlib']
self.prog = 'dot'
# Automatically creates all the methods enabling the creation
# of output in any of the supported formats.
for frmt in self.formats:
self.__setattr__(
'create_' + frmt,
lambda f=frmt,
prog=self.prog: self.create(
format=f,
prog=prog))
f = self.__dict__['create_' + frmt]
f.__doc__ = '''Refer to the docstring accompanying the 'create' method for more information.'''
for frmt in self.formats + ['raw']:
self.__setattr__(
'write_' + frmt,
lambda path,
f=frmt,
prog=self.prog: self.write(
path,
format=f,
prog=prog))
f = self.__dict__['write_' + frmt]
f.__doc__ = '''Refer to the docstring accompanying the 'write' method for more information.'''
def __getstate__(self):
dict = copy.copy(self.obj_dict)
return dict
def __setstate__(self, state):
self.obj_dict = state
def set_shape_files(self, file_paths):
"""Add the paths of the required image files.
If the graph needs graphic objects to be used as shapes or otherwise
those need to be in the same folder as the graph is going to be rendered
from. Alternatively the absolute path to the files can be specified when
including the graphics in the graph.
The files in the location pointed to by the path(s) specified as arguments
to this method will be copied to the same temporary location where the
graph is going to be rendered.
"""
if isinstance(file_paths, basestring):
self.shape_files.append(file_paths)
if isinstance(file_paths, (list, tuple)):
self.shape_files.extend(file_paths)
def set_prog(self, prog):
"""Sets the default program.
Sets the default program in charge of processing
the dot file into a graph.
"""
self.prog = prog
def set_graphviz_executables(self, paths):
"""This method allows to manually specify the location of the GraphViz executables.
The argument to this method should be a dictionary where the keys are as follows:
{'dot': '', 'twopi': '', 'neato': '', 'circo': '', 'fdp': ''}
and the values are the paths to the corresponding executable, including the name
of the executable itself.
"""
self.progs = paths
def write(self, path, prog=None, format='raw'):
"""Writes a graph to a file.
Given a filename 'path' it will open/create and truncate
such file and write on it a representation of the graph
defined by the dot object and in the format specified by
'format'.
The format 'raw' is used to dump the string representation
of the Dot object, without further processing.
The output can be processed by any of graphviz tools, defined
in 'prog', which defaults to 'dot'
Returns True or False according to the success of the write
operation.
There's also the preferred possibility of using:
write_'format'(path, prog='program')
which are automatically defined for all the supported formats.
[write_ps(), write_gif(), write_dia(), ...]
"""
if prog is None:
prog = self.prog
dot_fd = file(path, "w+b")
if format == 'raw':
data = self.to_string()
if isinstance(data, basestring):
if not isinstance(data, unicode):
try:
data = unicode(data, 'utf-8')
except:
pass
try:
data = data.encode('utf-8')
except:
pass
dot_fd.write(data)
else:
dot_fd.write(self.create(prog, format))
dot_fd.close()
return True
def create(self, prog=None, format='ps'):
"""Creates and returns a Postscript representation of the graph.
create will write the graph to a temporary dot file and process
it with the program given by 'prog' (which defaults to 'twopi'),
reading the Postscript output and returning it as a string is the
operation is successful.
On failure None is returned.
There's also the preferred possibility of using:
create_'format'(prog='program')
which are automatically defined for all the supported formats.
[create_ps(), create_gif(), create_dia(), ...]
If 'prog' is a list instead of a string the fist item is expected
to be the program name, followed by any optional command-line
arguments for it:
[ 'twopi', '-Tdot', '-s10' ]
"""
if prog is None:
prog = self.prog
if isinstance(prog, (list, tuple)):
prog, args = prog[0], prog[1:]
else:
args = []
if self.progs is None:
self.progs = find_graphviz()
if self.progs is None:
raise InvocationException(
'GraphViz\'s executables not found')
if prog not in self.progs:
raise InvocationException(
'GraphViz\'s executable "%s" not found' % prog)
if not os.path.exists(
self.progs[prog]) or not os.path.isfile(
self.progs[prog]):
raise InvocationException(
'GraphViz\'s executable "%s" is not a file or doesn\'t exist' %
self.progs[prog])
tmp_fd, tmp_name = tempfile.mkstemp()
os.close(tmp_fd)
self.write(tmp_name)
tmp_dir = os.path.dirname(tmp_name)
# For each of the image files...
#
for img in self.shape_files:
# Get its data
#
f = file(img, 'rb')
f_data = f.read()
f.close()
# And copy it under a file with the same name in the temporary directory
#
f = file(os.path.join(tmp_dir, os.path.basename(img)), 'wb')
f.write(f_data)
f.close()
cmdline = [self.progs[prog], '-T' + format, tmp_name] + args
p = subprocess.Popen(
cmdline,
cwd=tmp_dir,
stderr=subprocess.PIPE, stdout=subprocess.PIPE)
stderr = p.stderr
stdout = p.stdout
stdout_output = list()
while True:
data = stdout.read()
if not data:
break
stdout_output.append(data)
stdout.close()
stdout_output = ''.join(stdout_output)
if not stderr.closed:
stderr_output = list()
while True:
data = stderr.read()
if not data:
break
stderr_output.append(data)
stderr.close()
if stderr_output:
stderr_output = ''.join(stderr_output)
#pid, status = os.waitpid(p.pid, 0)
status = p.wait()
if status != 0:
raise InvocationException(
'Program terminated with status: %d. stderr follows: %s' % (
status, stderr_output))
elif stderr_output:
print stderr_output
# For each of the image files...
#
for img in self.shape_files:
# remove it
#
os.unlink(os.path.join(tmp_dir, os.path.basename(img)))
os.unlink(tmp_name)
return stdout_output
Reference in New Issue Copy Permalink