def run_graph(dot):
""" Runs graphviz to see if the syntax is good. """
graph = AGraph()
graph = graph.from_string(dot)
extension = 'png'
graph.draw(path='output.png', prog='dot', format=extension)
sys.exit(0)
def networkx(self):
d = self.graph()
# FIXME deduplicate
from pygraphviz import AGraph
import networkx as nx
dot = AGraph(strict=True, directed=True)
def rec(nodes, parent):
for d in nodes:
if not isinstance(d, dict):
if '(dirty)' in d:
d = d.replace('(dirty)', '')
dot.add_node(d, label=d, color='red')
dot.add_edge(d, parent, color='red')
else:
dot.add_node(d, label=d)
dot.add_edge(d, parent)
else:
for k in d:
if '(dirty)' in k:
k = k.replace('(dirty)', '')
dot.add_node(k, label=k, color='red')
rec(d[k], k)
dot.add_edge(k, parent, color='red')
else:
dot.add_node(k, label=k)
rec(d[k], k)
dot.add_edge(k, parent)
for k in d:
dot.add_node(k, label=k)
rec(d[k], k)
return nx.nx_agraph.from_agraph(dot)
def gen_op_insts(rf_allocs: List[RFallocation], dfg: AGraph, fu: AGraph,
input_map: Dict[str, int]) -> List[ATAI]:
assembly = []
instructions: List[Instruction] = []
for instruction in fu.nodes():
instructions.append(parse_instruction(instruction))
for instruction in instructions:
n = dfg.get_node(instruction.name)
nodes = dfg.predecessors(n)
input_type0 = inst_input_type(rf_allocs, fu, nodes[0])
if len(nodes) > 1:
input_type1 = inst_input_type(rf_allocs, fu, nodes[1])
else:
input_type1 = input_type0
# This should never occur but we check for it anyways
if input_type0 == OpInput and input_type1 == OpInput:
if nodes[0] != nodes[1]:
raise DoubleUnidenticalOPInputException
# TODO: find scheduling for fetch ops might need to be swapped to fit?
if input_type0 == RFInput:
# If the data is in the RF we need to generate fetch instructions
assembly.append(
generate_fetch(rf_allocs, instruction, nodes[0],
ATAFetch.REG.REG0))
input0 = RFInput()
elif input_type0 == OpInput:
input0 = OpInput()
else:
n = input_map[nodes[0].get_name()]
if n is None:
raise FUinputException(
'Cannot find FU from which predecessing node originates in map'
)
input0 = FUinput(n)
if input_type1 == RFInput:
assembly.append(
generate_fetch(rf_allocs, instruction, nodes[1],
ATAFetch.REG.REG1))
input1 = RFInput()
elif input_type1 == OpInput:
input1 = OpInput()
else:
n = input_map[nodes[1].get_name()]
if n is None:
raise FUinputException(
'Cannot find FU from which predecessing node originates in map'
)
input1 = FUinput(n)
assembly.append(ATAOp(input0, input1, instruction.cycle))
return assembly
def __init__(self):
self.evolution = [] # List[str]
self._evaluating = None
# Dict[Candidate, Set[Requirement]]
self._dependencies = defaultdict(set)
# Dict[Candidate.name, Counter[Requirement]]
self._active_requirements = defaultdict(Counter)
self._node_names = {}
self._counter = count()
self.graph = AGraph(
directed=True,
rankdir="LR",
labelloc="top",
labeljust="center",
nodesep="0",
concentrate="true",
)
self.graph.add_node("root", label=":root:", shape="Mdiamond")
self._node_names[self._key(None)] = "root"
del self.graph.node_attr["label"]
self.graph.edge_attr.update({
"arrowhead": "empty",
"style": "dashed",
"color": "#808080"
})
def get_graphviz(self, triple_args_function=None,
ignore_properties=VIS_IGNORE_PROPERTIES):
"""
Create a pygraphviz graph from the tree
"""
def _id(node):
return node.uri.split("/")[-1]
g = AGraph(directed=True)
triples = list(self.get_triples())
nodeset = set(chain.from_iterable((t.subject, t.object)
for t in triples))
for n in nodeset:
label = "%s: %s" % (n.id, n.word)
for k, v in n.__dict__.iteritems():
if k not in ignore_properties:
label += "\\n%s: %s" % (k, v)
g.add_node(_id(n), label=label)
# create edges
for triple in triples:
kargs = (triple_args_function(triple)
if triple_args_function else {})
if 'label' not in kargs:
kargs['label'] = triple.predicate
g.add_edge(_id(triple.subject), _id(triple.object), **kargs)
# some theme options
g.graph_attr["rankdir"] = "BT"
g.node_attr["shape"] = "rect"
g.edge_attr["edgesize"] = 10
g.node_attr["fontsize"] = 10
g.edge_attr["fontsize"] = 10
return g
def toSVG(B, name):
if B:
graph = AGraph(toDot(B))
layout = graph.layout(prog="dot")
draw = graph.draw("{}.svg".format(name))
else:
print("Give me a better tree")
def draw(self):
tree = self.to_tree()
A = AGraph(tree)
if not self.filename:
self.filename = input('Please input a filename:')
A.draw('temp/{}.jpg'.format(self.filename),
format='jpg', prog='fdp')
def __init__(self, filename):
self.G = AGraph(filename)
xs = [(nodo, nodo.attr.get("initial", None))
for nodo in self.G.iternodes()]
xs = [x for x in xs if x[1]]
if len(xs) == 0:
raise BadInputGraph("Missing 'initial' node")
elif len(xs) > 1:
raise BadInputGraph("Cannot have two initial nodes")
if not any(nodo.attr.get("goal", None) for nodo in self.G.iternodes()):
raise BadInputGraph("Missing a goal state '[goal=\"1\"]'")
super(DotGraphSearchProblem, self).__init__(xs[0][0])
self.initial_state.attr["shape"] = "doublecircle"
for node in self.G.iternodes():
if self.is_goal(node):
node.attr["shape"] = "hexagon"
node.attr["color"] = "blue"
self.seen = set()
self.visit(self.initial_state)
for edge in self.G.iteredges():
edge.attr["style"] = "dotted"
x = edge.attr.get("weight", None)
if x:
x = int(x)
else:
x = 1
edge.attr["weight"] = x
edge.attr["label"] = x
def graphviz_to_firebase(dirname,filename):
"""
since several chars must be escaped from firebase keys,
(see #http://stackoverflow.com/questions/19132867/adding-firebase-data-dots-and-forward-slashes
we can't directly use them as keys so:
- we use integer i as key,
- "nodes" dict maps node name to i to preserve edges coherency
- node name is kept as default node label
"""
f=os.path.join(dirname, filename)
graph=filename.split('.')[0]
print('processing %s'%f),
agraph=AGraph(f)
nodes={}
for i,node in enumerate(agraph.iternodes()):
nodes[node]=i
attrs={}
attrs.update(agraph.node_attr)
attrs['label']=node #default label is node id
attrs.update(node.attr)
key='%s/node/%d'%(graph,i)
ref.patch(key,attrs)
print('.'),
for i,edge in enumerate(agraph.iteredges()):
attrs={}
attrs.update(agraph.edge_attr)
attrs.update(edge.attr)
attrs['source']=nodes[edge[0]]
attrs['target']=nodes[edge[1]]
#edges are added as attributes of their destination node
key='%s/edge/%d'%(graph,i)
ref.patch(key,attrs)
print('-'),
logging.info('ok')
def convert(graph_to_convert, layout_prog="dot"):
if isinstance(graph_to_convert, AGraph):
graph = graph_to_convert
else:
try:
graph = AGraph(graph_to_convert)
except BaseException as e:
raise ValueError(
"graph_to_convert must be one of a string, file, or AGraph object"
) from e
graph_edges = {
e[0] + "->" + e[1]: list37(e.attr.iteritems())
for e in list37(graph.edges_iter())
}
graph_nodes = {
n: list37(n.attr.iteritems())
for n in list37(graph.nodes_iter())
}
svg_graph = graph.draw(prog=layout_prog, format="svg")
nodes, edges = SvgParser(svg_graph).get_nodes_and_edges()
[e.enrich_from_graph(graph_edges[e.gid]) for e in edges]
[n.enrich_from_graph(graph_nodes[n.gid]) for n in nodes.values()]
mx_graph = MxGraph(nodes, edges)
return mx_graph.value()
def render(self, filename):
g = AGraph(strict=False, directed=True)
# create nodes
for frame_id, node in self.callers.items():
label = "{ %s }" % node
g.add_node(frame_id, shape='Mrecord', label=label,
fontsize=13, labelfontsize=13)
# create edges
for frame_id, node in self.callers.items():
child_nodes = []
for child_id in node.child_methods:
child_nodes.append(child_id)
g.add_edge(frame_id, child_id)
# order edges l to r
if len(child_nodes) > 1:
sg = g.add_subgraph(child_nodes, rank='same')
sg.graph_attr['rank'] = 'same'
prev_node = None
for child_node in child_nodes:
if prev_node:
sg.add_edge(prev_node, child_node, color="#ffffff")
prev_node = child_node
g.layout()
g.draw(path=filename, prog='dot')
print("callviz: rendered to %s" % filename)
self.clear()
def build_graph(ts):
g = AGraph(directed=True)
g.add_edges_from(ts.ts.todok().keys())
g.graph_attr['overlap'] = 'scalexy'
for n, s in zip(g.nodes(), ts._pwa.states):
n.attr['label'] = s
return g
def user_trace(graph: pgv.AGraph, quantities: List[Quantity]):
def request_value(quantity: Quantity) -> Tuple[str,str]:
print('Values for {}:'.format(quantity.name))
mag = input("Magnitude? (out of [{}])\n".format(','.join(quantity.magnitude._member_names_)))
if mag == "":
mag = quantity.magnitude._member_names_[0]
drv = input("Derivative? (out of [{}])\n".format(','.join(quantity.derivative._member_names_)))
if drv == "":
drv = quantity.derivative._member_names_[1]
return (mag,drv)
print('Enter start node for trace:')
start = str(tuple(request_value(q) for q in quantities))
if not graph.has_node(start):
print('START NODE NOT IN GRAPH')
return
print('\n\nEnter end node for trace:')
end = str(tuple(request_value(q) for q in quantities))
if not graph.has_node(end):
print('END NODE NOT IN GRAPH')
return
shgraph = trace(graph, start, end)
shgraph.draw('trace.pdf', prog='dot')
def run_graph(dot):
""" Runs graphviz to see if the syntax is good. """
graph = AGraph()
graph = graph.from_string(dot)
extension = 'png'
graph.draw(path='output.png', prog='dot', format=extension)
sys.exit(0)
def path_graph(nodes):
graph = AGraph(directed=True)
for node in nodes:
graph.add_node(node, shape='rectangle')
graph.add_path(nodes)
return graph
def plan_library_to_graphviz(planlibrary):
"""Converts a plan library into a graphviz data structure"""
G = AGraph()
for a in planlibrary:
G.add_edge(a.path[0], a.path[1])
return G
def __init__(self, finite_states):
self.states = finite_states
nodes = {
state : []
for state in finite_states
}
self.graph = AGraph(nodes, directed=True, strict=False)
self.edgesize = len(nodes) / 5.0
def draw(diagram: 'Diagram', output_file: 'str') -> None:
G = AGraph(**GRAPH_OPTIONS)
for node in diagram.components.values():
G.add_node(node.name, label=node.render(), **COMPONENT_OPTIONS)
for node in diagram.sections.values():
G.add_node(node.name, label=node.render(), **SECTION_OPTIONS)
add_edges(G, diagram)
G.write()
G.draw(output_file, prog=LAYOUT)
def __init__(self):
logging.basicConfig()
self.graph = AGraph(directed=True, strict=False)
self.graph.node_attr['shape'] = 'record'
self.graph.graph_attr['fontsize'] = '8'
self.graph.graph_attr['fontname'] = "Bitstream Vera Sans"
self.graph.graph_attr['label'] = ""
self.connected_nodes = set()
self.described_nodes = set()
def processLines(self):
if len(self.lines) == 0:
return
self.identifier = self.lines[0][2:]
s = '\n'.join(self.lines)
A = AGraph()
G = A.from_string(s)
self.processGraph(G)
def dot_to_plan_library(filename):
G = AGraph()
G.read(filename)
planlib = set([])
for edge in G.edges():
a = Action(list(edge))
planlib.add(a)
log.info("Loaded graph: " + str(planlib))
return planlib
def processLines(self):
if len(self.lines) == 0:
return
self.identifier = self.lines[0][2:]
s = '\n'.join(self.lines)
A = AGraph()
G = A.from_string(s)
self.processGraph(G)
def dot_to_graph(dot, output_path):
"""
Render by calling graphviz the figure on the output path.
:param dot: str with the
:param output_path:
:return:
"""
from pygraphviz import AGraph
graph = AGraph().from_string(dot)
graph.draw(path=output_path, prog='dot')
def from_agraph(cls, A: AGraph, lambdas):
""" Construct a ProgramAnalysisGraph from an AGraph """
self = cls(nx.DiGraph())
for n in A.nodes():
if n.attr["node_type"] in ("LoopVariableNode", "FuncVariableNode"):
self.add_variable_node(n)
for n in A.nodes():
if n.attr["node_type"] == "ActionNode":
self.add_action_node(A, lambdas, n)
for n in self.nodes(data=True):
n_preds = len(n[1]["pred_fns"])
if n_preds == 0:
del n[1]["pred_fns"]
elif n_preds == 1:
n[1]["update_fn"], = n[1].pop("pred_fns")
else:
n[1]["choice_fns"] = n[1].pop("pred_fns")
def update_fn(n, **kwargs):
cond_fn = n[1]["condition_fn"]
sig = signature(cond_fn)
ind = 0 if cond_fn(**kwargs) else 1
return n[1]["choice_fns"][ind](**kwargs)
n[1]["update_fn"] = partial(update_fn, n)
isolated_nodes = [
n
for n in self.nodes()
if len(list(self.predecessors(n)))
== len(list(self.successors(n)))
== 0
]
for n in isolated_nodes:
self.remove_node(n)
# Create lists of all input function and all input variables
self.input_variables = list()
self.input_functions = list()
for n in self.nodes():
if self.nodes[n].get("init_fn") is not None:
self.input_functions.append(n)
if (
self.nodes[n]["node_type"]
in ("LoopVariableNode", "FuncVariableNode")
and len(list(self.predecessors(n))) == 0
):
self.input_variables.append(n)
return self
def add_graph(g: AGraph, layer_graph: tx.Graph, cluster):
for node in layer_graph.nodes:
# HTML for record nodes https://graphviz.org/doc/info/shapes.html#top
g.add_node(f"{cluster}_{node.name}",
shape="none",
margin=0,
label=tx.utils.vizstyle(node))
for node in layer_graph.nodes:
for other_node in layer_graph.edges_out[node]:
g.add_edge(f"{cluster}_{node.name}",
f"{cluster}_{other_node.name}")
def startGraph():
# We maintain this globally to make it accessible, pylint: disable=global-statement
global graph
if Options.shallCreateGraph():
try:
from pygraphviz import AGraph # pylint: disable=I0021,import-error
graph = AGraph(name = "Optimization", directed = True)
graph.layout()
except ImportError:
warning("Cannot import pygraphviz module, no graphing capability.")
def gen_add_input2(
dfg: AGraph, fu: AGraph,
input_map: Dict[str, int]) -> Tuple[List[Input], List[Output]]:
outputs: List[Output] = []
inputs: List[Input] = []
nodes: List[Instruction] = []
for node in fu.nodes():
nodes.append(parse_instruction(node))
nodes.sort()
prev_o = 0
for node in nodes:
preds = dfg.predecessors(node.name)
parent0 = parse_instruction(preds[0])
parent1 = parse_instruction(preds[1])
if parent0.name in input_map:
label = dfg.get_node(parent0.name).attr['label']
if 'mul' in label:
latency = 2
else:
latency = 1
i0 = prev_o + 1
inputs.append(
Input(i0, input_map[parent0.name], parent0.cycle + latency))
else:
for output in outputs:
if output.cycle == parent0.cycle + 1:
i0 = output.val
break
if parent1.name in input_map:
label = dfg.get_node(parent1.name).attr['label']
if 'mul' in label:
latency = 2
else:
latency = 1
i1 = prev_o + 1
inputs.append(
Input(i1, input_map[parent1.name], parent1.cycle + latency))
else:
for output in outputs:
if output.cycle == parent1.cycle + 1:
i1 = output.val
break
expected = i0 + i1
prev_o = expected
outputs.append(Output(expected, node.cycle + 1))
inputs.sort()
return inputs, outputs
def _render(self, costs=False, word_probs=False, highlight_best=False):
from pygraphviz import AGraph
graph = AGraph(directed=True)
for node_id, node_label in self.nodes.iteritems():
attributes = self._node_attr(node_id, costs=costs, word_probs=word_probs)
graph.add_node(node_id, **attributes)
for (parent_node_id, child_node_id) in self.edges:
graph.add_edge(parent_node_id, child_node_id)
self.graph = graph
if highlight_best:
self._highlight_best()
def remove_bad_edges(graph: AGraph, collections: Iterable[Iterable[str]]):
for from_node, to_node in graph.edges():
from_group = None
to_group = None
for i, group in enumerate(collections):
if from_node in group:
from_group = i
if to_node in group:
to_group = i
if from_group is None or to_group is None or from_group < to_group:
graph.delete_edge(from_node, to_node)
def __call__(self):
self.request.response.setHeader('Content-Type', 'image/svg+xml')
self.request.response.setHeader('Content-Disposition',
'inline; filename=%s.svg' % \
self.context.getId())
tfile = tempfile.NamedTemporaryFile(suffix='.svg')
gv = generate_gv(self.context)
ag = AGraph(string=gv)
ag.layout()
ag.draw(path=tfile, format='svg', prog='dot')
tfile.seek(0)
return tfile.read()
def startGraph():
# We maintain this globally to make it accessible, pylint: disable=global-statement
global graph
if Options.shallCreateGraph():
try:
from pygraphviz import AGraph # pylint: disable=I0021,import-error
graph = AGraph(name="Optimization", directed=True)
graph.layout()
except ImportError:
warning("Cannot import pygraphviz module, no graphing capability.")
def draw_workflow(filename, workflow):
dot = AGraph(directed=True) # (comment="Computing scheme")
for i, n in workflow.nodes.items():
dot.add_node(i, label="{0} \n {1}".format(
n.foo.__name__, _format_arg_list(n.bound_args.args, None)))
for i in workflow.links:
for j in workflow.links[i]:
dot.add_edge(i, j[0])
dot.layout(prog='dot')
dot.draw(filename)
def render_local(self, filename):
"""Renders the OBST image locally using pygraphviz."""
# Get the graph information
node_list, edge_list = self.__generate_image()
# Generate the graph
from pygraphviz import AGraph
G=AGraph(strict=True,directed=True) # Create a graph
for node in node_list:
G.add_node(node)
for edge in edge_list:
G.add_edge(edge[0], edge[1])
G.layout('dot') # Set hierarchical layout
G.draw(filename) # Save the image.
def trace(graph: pgv.AGraph, start: str, end: str) -> pgv.AGraph:
nxgraph = nx.nx_agraph.from_agraph(graph)
assert(start in nxgraph and end in nxgraph)
shortest = nx.shortest_path(nxgraph, start, end)
shgraph = pgv.AGraph(directed=True,overlap=False,rankdir='LR')
for e in range(len(shortest)-1):
label = graph.get_edge(shortest[e], shortest[e+1]).attr['label']
shgraph.add_edge(shortest[e], shortest[e+1], label=label)
for n in shgraph.nodes_iter():
n.attr['label'] = graph.get_node(n).attr['label']
n.attr['style'] = graph.get_node(n).attr['style']
n.attr['fillcolor'] = graph.get_node(n).attr['fillcolor']
return shgraph
def to_dot(self, filename, edges):
from pygraphviz import AGraph
dot = AGraph(directed=True)
for n in edges.keys():
dot.add_node(str(n))
if lib.qcgc_arena_get_blocktype(ffi.cast("cell_t *", n)) not in [
lib.BLOCK_BLACK, lib.BLOCK_WHITE]:
node = dot.get_node(str(n))
node.attr['color'] = 'red'
for n in edges.keys():
if edges[n] is not None:
dot.add_edge(str(n), str(edges[n]))
dot.layout(prog='dot')
dot.draw(filename)
def __init__(self):
"""
Constructor
"""
QMainWindow.__init__(self)
self.ui = graphio.Ui_MainWindow()
self.ui.setupUi(self)
self.scene_graph = QGraphicsScene()
self.ui.graphicsView.setScene(self.scene_graph)
self.ui.graphicsView.update()
self.graph = AGraph(strict=True, directed=True)
self.graph.layout(prog='dot')
def _construct_graph(graph: gz.AGraph, state):
graph.add_node(
state.id_nr,
label=_state_to_node(state),
shape="record",
)
for move, next_state in state.next_states.items():
if next_state:
_construct_graph(graph, next_state)
graph.add_edge(u=state.id_nr,
v=next_state.id_nr,
key="l",
label=str(move))
def draw_workflow(filename, workflow):
dot = AGraph(directed=True, strict=False) # (comment="Computing scheme")
for i, n in workflow.nodes.items():
dot.add_node(i, label="{0} \n {1}".format(n.foo.__name__, _format_arg_list(n.bound_args.args, None)))
for i in workflow.links:
for j in workflow.links[i]:
dot.add_edge(i, j[0], j[1].name) # , headlabel=j[1].name, labeldistance=1.8)
dot.layout(prog="dot")
dot.draw(filename)
def crear_grafo_invocaciones(datos_csv):
'''[Autor: Ivan Litteri]
[Ayuda: crea grafo.svg y grafo.png]'''
g = AGraph(directed=True, rankdir='LR')
for funcion in datos:
g.add_node(funcion)
for i in datos[funcion]["invocaciones"]:
g.add_edge((funcion, i))
g.layout(prog='dot')
g.draw('grafo.svg')
g.draw('grafo.png')
def draw_finite_state_machine(finite_state_machine: FiniteStateMachine,
path: str):
"""Creates a directed non-strict multi graph image representation of the FSM."""
from pygraphviz import AGraph
graph = AGraph(strict=False, directed=True)
graph.add_nodes_from(finite_state_machine.state_set)
for initial_state in finite_state_machine.initial_states:
graph.get_node(initial_state).attr["color"] = "green"
for element, transitions in finite_state_machine.transitions.items():
for from_state, to_states in transitions.items():
for to_state in to_states:
graph.add_edge(from_state, to_state, label=element)
for final_state in finite_state_machine.final_states:
graph.get_node(final_state).attr["color"] = "red"
graph.draw(path, prog="dot")
def jupyter_draw(ppdot_str, format='png', prog='dot'):
from pygraphviz import AGraph
from IPython.display import Image
# convert ppdot to dot format
dot_str = process_string(ppdot_str)
# create graph and render image
graph = AGraph(string=dot_str)
data = graph.draw(format=format, prog=prog)
# pass image to IPython/Jupyter
image = Image(data=data)
return image
def run(self):
options = self.options
filename = self.arguments[0]
if self.content:
content = u'\n'.join(self.content)
ofilename = filename + '.' + self.outputformat
else:
content = open(filename).read().decode(options.get('encoding','utf-8'))
ofilename = os.path.splitext(filename)[0] + '.' + self.outputformat
g = AGraph(string=content)
g.layout(prog='dot')
opath = os.path.join(OUTPUT_DIR, ofilename)
g.draw(opath, 'png')
self.arguments[0] = opath
return super(GraphvizBlock, self).run()
def main():
"""
The entrypoint for the program.
"""
global _MESHINERY_GRAPH
global _MESHINERY_ARGS
# Register the keyboard interrupt and SIGTERM handler
signal.signal(signal.SIGINT, handle_sigint)
signal.signal(signal.SIGTERM, handle_sigint)
args = docopt(USAGE)
_MESHINERY_ARGS = args
if args['--verbose']:
logging.basicConfig(level=logging.DEBUG)
else:
logging.basicConfig(level=logging.INFO)
logging.info('Starting')
logging.debug('Args:\n{}'.format(pformat(args)))
agraph = AGraph(args['DOT_GRAPH_FILE'])
graph = nx.Graph(agraph)
_MESHINERY_GRAPH = graph # We intentionally don't take a fresh copy
if args['--clean']:
clean(graph,
dry_run=args['--dry-run'],
instance_id=args['--id'],
strays=args['--strays'])
if args['clean']:
return
# Arrange network namespaces and crate veth bridges
prepare_namespaces(graph,
dry_run=args['--dry-run'],
instance_id=args['--id'])
# Run commands associated with each node
try:
graph = execute(graph,
dry_run=args['--dry-run'],
instance_id=args['--id'])
_MESHINERY_GRAPH = graph
except Exception as e:
logging.error('Per-node command execution failed, cleaning up...')
logging.debug('Caught exception {} in main(): {}'.format(type(e), e))
clean(graph, dry_run=args['--dry-run'], instance_id=args['--id'])
sys.exit(1)
logging.info("Meshinery is ready. Press any key to clean up and exit.")
input()
clean(graph,
dry_run=args['--dry-run'],
instance_id=args['--id'],
strays=args['--strays'])
logging.info('Bye!')
def process_nodes(g: pgv.AGraph) -> Tuple[Node, bool]:
nodes = {str(gvnode): from_label(gvnode) for gvnode in g.nodes()}
root_node = None
for gvn, ndata in nodes.items():
if 'this/RootNode' in ndata[1]:
root_node = gvn
break
else:
print("Error: cannot find root node\n")
sys.exit(-1)
def walk(rn: pgv.Node) -> Tuple[Node, bool]:
args_dict = {}
correctness_holds = True
for n in g.successors(rn):
e = pgv.Edge(g, rn, n)
m = re.match('^args\\s+\\[(\\d+)\\]$', e.attr['label'])
assert m
arg_idx = int(m.group(1))
assert arg_idx not in args_dict
args_dict[arg_idx], have_correctness = walk(n)
if not have_correctness:
correctness_holds = False
args = [args_dict[idx] for idx in range(len(args_dict))]
new_node = Node(*nodes[rn], args=args)
if correctness_holds:
correctness_holds = 'this/CorrectnessHolds' in new_node.sets
return new_node, correctness_holds
return walk(root_node)
def __init__(self, filename):
self.G = AGraph(filename)
xs = [(nodo, nodo.attr.get("initial", None))
for nodo in self.G.iternodes()]
xs = [x for x in xs if x[1]]
if len(xs) == 0:
raise BadInputGraph("Missing 'initial' node")
elif len(xs) > 1:
raise BadInputGraph("Cannot have two initial nodes")
if not any(nodo.attr.get("goal", None) for nodo in self.G.iternodes()):
raise BadInputGraph("Missing a goal state '[goal=\"1\"]'")
super(DotGraphSearchProblem, self).__init__(xs[0][0])
self.initial_state.attr["shape"] = "doublecircle"
for node in self.G.iternodes():
if self.is_goal(node):
node.attr["shape"] = "hexagon"
node.attr["color"] = "blue"
self.seen = set()
self.visit(self.initial_state)
for edge in self.G.iteredges():
edge.attr["style"] = "dotted"
x = edge.attr.get("weight", None)
if x:
x = int(x)
else:
x = 1
edge.attr["weight"] = x
edge.attr["label"] = x
def graph(self, filename, reachable=True):
from pygraphviz import AGraph # NOTE - LIS machines do not have pygraphviz
graph = AGraph(strict=True, directed=True)
for vertex in self.vertices.values():
for connector in vertex.connectors:
if not reachable or (vertex.reachable and connector.reachable):
graphviz_connect(graph, vertex, connector)
for connector in self.connectors.values():
for edge in connector.edges:
if not reachable or (connector.reachable and edge.reachable):
graphviz_connect(graph, connector, edge)
for edge in self.edges.values():
for _, sink_vertex in edge.mappings:
if not reachable or (edge.reachable and sink_vertex.reachable):
graphviz_connect(graph, edge, sink_vertex)
graph.draw(filename, prog='dot')
def build_graph(score):
corpus= create_corpus(score)
calc_tf_idf(corpus, log_tf, log_idf)
#corpus= group_corpus(corpus, log_tf, log_idf)
g= AGraph(strict=False)
for i, d1 in enumerate(corpus):
d1_name= str(d1)
edges= [(d2, d2.similarity(d1)) for d2 in corpus[i+1:]]
edges.sort(key=lambda x:x[1], reverse=True)
edges= edges[:5]
for d2, weight in edges:
d2_name= str(d2)
g.add_edge(d1_name, d2_name)
e= g.get_edge(d1_name, d2_name)
e.attr['label']= str(weight)[:5]
#import ipdb;ipdb.set_trace()
return g
def __init__(self):
logging.basicConfig()
self.graph = AGraph(directed=True, strict=False)
self.graph.node_attr["shape"] = "record"
self.graph.graph_attr["fontsize"] = "8"
self.graph.graph_attr["fontname"] = "Bitstream Vera Sans"
self.graph.graph_attr["label"] = ""
self.connected_nodes = set()
self.described_nodes = set()
def __init__(self, title="System"):
self.schematic = AGraph(
directed=True,
label=title,
rankdir='LR',
splines='true'
)
self.nodes = []
self.edges = []
self.outputs = {}
self.ip_outputs = {}
def render_image(self, filename):
"""Renders the graph image locally using pygraphviz."""
# Create a graph
G=AGraph(directed=False)
# Add nodes
for node in self.nodes:
G.add_node(node)
# Add edges
for edge in self.edges:
G.add_edge(edge[0], edge[1], color='blue')
# Give layout and draw.
G.layout('circo')
G.draw(filename) # Save the image.
# Display the output image.
os.system("gwenview %s&" % filename)
class DotRenderer(GraphRenderer):
"""Renderer fox dot."""
"""The AGraph used for rendering."""
_graph = None
def __init__(self, settings, reporter):
GraphRenderer.__init__(self, settings, reporter)
if not pygraphvizAvail:
self.reporter.severe("Can not render dot format because module `pygraphviz` cannot be loaded")
def prepare(self):
self._graph = AGraph(strict=False, directed=True,
name=self._visitor.sourceName)
def finish(self):
# TODO The ordering of nodes seems to be rather random in the output;
# however, the node ordering is used for the layout of the graph
# at least by `dot` and by `neato`; there should be a way to
# determine the ordering
r = self._graph.string()
self._graph = None
return r
def renderAnchor(self, anchor):
self._graph.add_node(anchor.id(), label=anchor.name())
def renderReference(self, reference):
if reference.fromAnchor is None:
# No anchor to start edge from
# TODO Should result in a warning
return
fromId = reference.fromAnchor.id()
toId = reference.toAnchor.id()
if self._doReverse:
(fromId, toId) = (toId, fromId)
self._graph.add_edge(fromId, toId)
def render_image(node_list, edge_list):
# Generate the graph
from pygraphviz import AGraph
G=AGraph(strict=False,directed=True) # Create a graph
for node in node_list:
G.add_node(node)
for edge in edge_list:
G.add_edge(edge[0], edge[1])
G.layout('dot') # Set hierarchical layout
filename = str(time())
postfix = 0
while exists(filename+str(postfix)+".png"):
postfix+=1
filename += str(postfix) + ".png"
G.draw(filename) # Save the image.
with open(filename, "rb") as handle:
return xmlrpclib.Binary(handle.read())
def write_graph(probs, path):
graph = AGraph(directed=True)
next_label = 0
labels = {}
for from_state, to_states in probs.iteritems():
if from_state not in labels:
labels[from_state] = next_label
next_label += 1
for to_state in to_states:
if to_state not in labels:
labels[to_state] = next_label
next_label += 1
for label in xrange(next_label):
graph.add_node(label, fillcolor="blue", label="", style="filled")
for from_state, to_states in probs.iteritems():
for to_state, prob in to_states.iteritems():
graph.add_edge(labels[from_state], labels[to_state], label="%.2g" % prob)
# prog: neato (default), dot, twopi, circo, fdp or nop.
graph.layout()
graph.draw(path)
def igraph_from_dot(file):
"""numbered_graph(file) -> graph
Input:
file: the name of the dot-file
Output:
graph: igraph.Graph object. Verticies has the attribute
"name".
"""
print("Step 1/3: Reading from dot.")
a=AGraph(file)
vertices = a.nodes()
edges = a.edges()
numbered_edges = []
print("Step 2/3: To numbered graph. Be patient...")
for x, y in edges:
xx = vertices.index(x)
yy = vertices.index(y)
numbered_edges.append((xx,yy))
print("Step 3/3: To igraph.")
g=igraph.Graph(len(vertices), numbered_edges)
g.vs["name"]=vertices
return g
def as_graph(self, to=None):
from pygraphviz import AGraph
g = AGraph(directed=True)
for a in self.activities.values():
g.add_node(a.title, label=a.title)
for t in self.transitions.values():
g.add_edge(t.input.title, t.output.title, label=t.name)
if to:
g.write(to)
else:
return str(g)
def get_dot(self, labeller=None):
self.labeller = labeller
a_graph = AGraph(directed=True)
nx_graph = self.graph.nx_graph
# TODO: Add some default stuff?
# a_graph.graph_attr.update(N.graph.get('graph',{}))
# a_graph.node_attr.update(N.graph.get('node',{}))
# a_graph.edge_attr.update(N.graph.get('edge',{}))
structural_nodes = []
output_nodes = []
input_nodes = []
# First, add nodes
for node in nx_graph.nodes():
name, attrs = self.get_node_attributes(node)
if self.graph.is_input(node):
input_nodes.append(name)
elif self.graph.is_structural(node):
structural_nodes.append(name)
elif self.graph.is_output(node):
output_nodes.append(name)
# Keep a reference to the original node
a_graph.add_node(name, **attrs)
# We need to add subgraphs to cluster stuff on rank
sub = a_graph.add_subgraph(input_nodes, name='input')
sub.graph_attr['rank'] = 'source'
sub = a_graph.add_subgraph(structural_nodes, name='structural')
sub.graph_attr['rank'] = 'same'
sub = a_graph.add_subgraph(output_nodes, name='output')
sub.graph_attr['rank'] = 'sink'
# Now add edges
for u, v, edgedata in nx_graph.edges_iter(data=True):
attrs = {}
a_graph.add_edge(self.graph.node_to_name(u),
self.graph.node_to_name(v),
**attrs)
return a_graph
def cm_json_to_graph(im_json):
"""Return pygraphviz Agraph from Kappy's contact map JSON.
Parameters
----------
im_json : dict
A JSON dict which contains a contact map generated by Kappy.
Returns
-------
graph : pygraphviz.Agraph
A graph representing the contact map.
"""
cmap_data = im_json['contact map']['map']
# Initialize the graph
graph = AGraph()
# In this loop we add sites as nodes and clusters around sites to the
# graph. We also collect edges to be added between sites later.
edges = []
for node_idx, node in enumerate(cmap_data):
sites_in_node = []
for site_idx, site in enumerate(node['node_sites']):
# We map the unique ID of the site to its name
site_key = (node_idx, site_idx)
sites_in_node.append(site_key)
graph.add_node(site_key, label=site['site_name'], style='filled',
shape='ellipse')
# Each port link is an edge from the current site to the
# specified site
if not site['site_type'] or not site['site_type'][0] == 'port':
continue
for port_link in site['site_type'][1]['port_links']:
edge = (site_key, tuple(port_link))
edges.append(edge)
graph.add_subgraph(sites_in_node,
name='cluster_%s' % node['node_type'],
label=node['node_type'])
# Finally we add the edges between the sites
for source, target in edges:
graph.add_edge(source, target)
return graph