def write_graphs_to_dots(self):
assert self.build_graph
self._load_packages()
from pygraph.readwrite import dot
base = self.output_dir
with open(join(base, 'digraph.dot'), 'w') as f:
data = dot.write(self.digraph)
f.write(data)
with open(join(base, 'bfs.dot'), 'w') as f:
(st, order) = breadth_first_search(self.digraph)
bfs = digraph()
bfs.add_spanning_tree(st)
data = dot.write(bfs)
f.write(data)
with open(join(base, 'dfs.dot'), 'w') as f:
(st, pre, post) = depth_first_search(self.digraph)
dfs = digraph()
dfs.add_spanning_tree(st)
data = dot.write(dfs)
f.write(data)
def write_graphs_to_dots(self):
assert self.build_graph
self._load_packages()
from pygraph.readwrite import dot
base = self.output_dir
with open(join(base, 'digraph.dot'), 'w') as f:
data = dot.write(self.digraph)
f.write(data)
with open(join(base, 'bfs.dot'), 'w') as f:
(st, order) = breadth_first_search(self.digraph)
bfs = digraph()
bfs.add_spanning_tree(st)
data = dot.write(bfs)
f.write(data)
with open(join(base, 'dfs.dot'), 'w') as f:
(st, pre, post) = depth_first_search(self.digraph)
dfs = digraph()
dfs.add_spanning_tree(st)
data = dot.write(dfs)
f.write(data)
def handle(self, **options):
gr = graph()
cats_by_id = dict((c.id, c) for c in Category.objects.all())
# Add nodes
dups = count()
for c in cats_by_id.itervalues():
try:
gr.add_node(c)
except AdditionError:
dups.next()
parent = cats_by_id.get(c.parent_id)
print 'WARNING: duplicate node :: <Category %i | %s>' % (c.id,
c)
print '\twith parent ' + '<Category %i | %s>' % (
parent.id, parent) if parent else 'None'
if dups.next() > 0: return
# Add edges
# gr.add_edge((CONCRETE_NODE, ROOT_NODE))
for c in cats_by_id.itervalues():
parent = cats_by_id.get(c.parent_id)
if parent:
gr.add_edge((c, parent))
# import ipdb; ipdb.set_trace()
# The whole tree from the root
st, order = breadth_first_search(
gr, root=Category.objects.get(title="Abstract"))
gst = digraph()
gst.add_spanning_tree(st)
dot = write(gst)
gvv = gv.readstring(dot)
gv.layout(gvv, 'dot')
gv.render(gvv, 'pdf', os.path.join(output_dir, 'abstract.pdf'))
st, order = breadth_first_search(
gr, root=Category.objects.get(title="Concrete"))
gst = digraph()
gst.add_spanning_tree(st)
dot = write(gst)
gvv = gv.readstring(dot)
gv.layout(gvv, 'dot')
gv.render(gvv, 'pdf', os.path.join(output_dir, 'concrete.pdf'))
def _build_graph(self):
"""Build a graph representing the communication cost within that
machine.
The cost of communication for each pair of cores is the
send_cost + receive_cost on that link. This is set as edge
weight and used by the schedulers when sorting
edges.
"""
_c_list = self.get_cores()
# Add all cores to the graph
gr = digraph()
gr.add_nodes(_c_list)
for snd in _c_list:
for rcv in _c_list:
if snd!=rcv:
snd_cost = self.get_send_cost(snd, rcv)
rcv_cost = self.get_receive_cost(snd, rcv)
gr.add_edge((snd, rcv), rcv_cost + snd_cost)
return gr
def test_complete_digraph(self):
gr = digraph()
gr.add_nodes(range(10))
gr.complete()
for i in range(10):
for j in range(10):
self.assertTrue((i, j) in gr.edges() or i == j)
def author_centrality(titles_to_authors):
"""
Identifies the centrality of an author
:param titles_to_authors: a dict keying title strings to the authors associated
:type titles_to_authors: dict
:return: a dict matching author to centrality
:rtype: dict
"""
author_graph = digraph()
author_graph.add_nodes(map(lambda x: u"title_%s" % x, titles_to_authors.keys()))
author_graph.add_nodes(list(set([u'author_%s' % author[u'user']
for authors in titles_to_authors.values()
for author in authors])))
for title in titles_to_authors:
for author in titles_to_authors[title]:
try:
author_graph.add_edge((u'title_%s' % title, u'author_%s' % author[u'user']))
except AdditionError:
pass
centralities = dict([('_'.join(item[0].split('_')[1:]), item[1])
for item in pagerank(author_graph).items() if item[0].startswith(u'author_')])
centrality_scaler = MinMaxScaler(centralities.values())
return dict([(cent_author, centrality_scaler.scale(cent_val))
for cent_author, cent_val in centralities.items()])
def __init__(self, robot, viewer = False):
self.robot = robot
self.env = robot.GetEnv ()
self.grasping_locations_cache = {}
self.viewMode = viewer
self.tray_stack = []
self.unMovableObjects = {self.env.GetKinBody('table')}
self.objSequenceInPlan = []
self.handled_objs = set()
self.object_mover = ObjectMover(self.env, use_ros, self.unMovableObjects)
self.obstruction_digraph = digraph()
v = self.robot.GetActiveDOFValues()
v[self.robot.GetJoint('torso_lift_joint').GetDOFIndex()]=1.0
self.robot.SetDOFValues(v)
if use_ros:
self.pr2robot = PR2Robot(self.env)
self.pr2robot.robot = self.robot
self.arm_mover = PR2MoveArm()
#loading the IK models
utils.pr2_tuck_arm(robot)
robot.SetActiveManipulator('leftarm')
ikmodel = openravepy.databases.inversekinematics.InverseKinematicsModel(
robot,iktype=openravepy.IkParameterization.Type.Transform6D)
if not ikmodel.load():
ikmodel.autogenerate()
robot.SetActiveManipulator('rightarm')
ikmodel = openravepy.databases.inversekinematics.InverseKinematicsModel(
robot,iktype=openravepy.IkParameterization.Type.Transform6D)
if not ikmodel.load():
ikmodel.autogenerate()
def pygraphCrit(edgePairs, nameMap, timeMap, allEdts, allEvts, mainGuid):
G = digraph()
srcs = []
dsts = []
for i in range(len(edgePairs)):
srcs.append(edgePairs[i][0])
dsts.append(edgePairs[i][1])
allNodes = set(srcs + dsts)
for i in allNodes:
if i == mainGuid:
continue
else:
G.add_node(str(i))
for i in range(len(edgePairs)):
curTime = 0
curSrc = str(edgePairs[i][0])
curDst = str(edgePairs[i][1])
if curSrc == mainGuid or curDst == mainGuid:
continue
if getNodeType(curSrc, allEdts, allEvts) == 'Event':
curTime = 1
else:
curTime = edtGuidToTime(curSrc, timeMap)
G.add_edge((curSrc, curDst), curTime)
if len(critical_path(G)) == 0:
print 'Cycle Detected, exiting; Please check that the OCR conifiguration file uses GUID type of COUNTED_MAP, and the application has no cycles.'
print 'Dumping cycle below.'
print find_cycle(G)
os.remove(HTML_FILE_NAME)
sys.exit(0)
return critical_path(G)
def condorcet_completion_method(self):
# Initialize the candidate graph
self.rounds = []
graph = digraph()
graph.add_nodes(self.candidates)
# Loop until we've considered all possible pairs
remaining_strong_pairs = deepcopy(self.strong_pairs)
while len(remaining_strong_pairs) > 0:
r = {}
# Find the strongest pair
largest_strength = max(remaining_strong_pairs.values())
strongest_pairs = matching_keys(remaining_strong_pairs, largest_strength)
if len(strongest_pairs) > 1:
r["tied_pairs"] = strongest_pairs
strongest_pair = self.break_ties(strongest_pairs)
else:
strongest_pair = list(strongest_pairs)[0]
r["pair"] = strongest_pair
# If the pair would add a cycle, skip it
graph.add_edge(strongest_pair)
if len(find_cycle(graph)) > 0:
r["action"] = "skipped"
graph.del_edge(strongest_pair)
else:
r["action"] = "added"
del remaining_strong_pairs[strongest_pair]
self.rounds.append(r)
self.old_graph = self.graph
self.graph = graph
self.graph_winner()
def _build_tree(self, g):
"""
We build a bad tree by inverting all edge weights and running
an MST algorithm on the resulting graph.
"""
# Build graph with inverted edges
g_inv = algorithms.invert_weights(g)
# Run binary tree algorithm
mst_inv = minimal_spanning_tree(g_inv, self.get_root_node())
# Build a new graph
badtree = digraph()
# Add nodes
for n in g.nodes():
badtree.add_node(n)
# Add edges, copy weights from non-inverted graph
for (e,s) in mst_inv.items():
if s != None:
badtree.add_edge((s, e), g.edge_weight((s, e)))
return badtree
def test_add_spanning_tree(self):
gr = digraph()
st = {0: None, 1: 0, 2: 0, 3: 1, 4: 2, 5: 3}
gr.add_spanning_tree(st)
for each in st:
self.assertTrue((st[each], each) in gr.edges()
or (each, st[each]) == (0, None))
def create_dtg_graph(sas):
# TODO -- create DTGs graph
gr = digraph()
for var in sas.variables:
gr.add_node(var.get_label())
for cg in sas.causal_graphs:
if cg.variable.is_always and not INCLUDE_ALWAYS:
'''skip "always" variable'''
elif cg.variable.isderived() and not INCLUDE_DERIVED_VARIABLE:
''' skip '''
else:
'''if not cg.variable.isderived():
print(str(cg.variable.index) + ": " + cg.variable.name + " => " + str(cg.variable.isderived()))'''
for causal in cg.causals:
if causal[0].is_always and not INCLUDE_ALWAYS:
''' skip '''
elif causal[0].isderived() and not INCLUDE_DERIVED_VARIABLE:
''' skip '''
else:
#gr.add_edge((causal[0].get_label(), cg.variable.get_label()))
gr.add_edge(
(cg.variable.get_label(), causal[0].get_label()))
return gr
def drawGraph(self, inputs):
fileName = 'planetModel.png'
gr = graph()
self.addGraphNode(1, gr, inputs)
# Draw as PNG
#with open("./planetModel.viz", 'wb') as f:
#dot = write(gr,f)
#f.write(dot)
#gvv = gv.readstring(dot)
#gv.layout(gvv,'dot')
#gv.render(gvv,'png', fileName)
#f.close()
gst = digraph()
self.addGraphNode(1, gst, inputs)
with open("./planetModel.viz", 'wb') as f:
#st, order = breadth_first_search(gst, root=1)
#gst2 = digraph()
#gst2.add_spanning_tree(gst.nodes())
#gst2.(1, 'post')
dot = write(gst, f)
f.write(dot)
gvv = gv.readstring(dot)
gv.layout(gvv, 'dot')
gv.render(gvv, 'png', fileName)
f.close()
return fileName
def __init__(self, **kwargs): # pylint:disable=super-init-not-called
"""Initialization."""
self.graph = digraph()
self.nodestatus = {}
self.nodeexceptions = {}
self.noderesults = {}
self._run_phase = 0
self._retry = {} # retries left, sleep time, etc
self._default_tries = None # num of tries for Jobs that set no value
self._default_delay = None # default delay between Job retries
self._default_retry_delay = None # min delay between retries of a Job
self._args = [] # Args for Check/Run methods
self._kwargs = {} # KWArgs for Check/Run methods
self._root = None # Root Job
self._checknrun_cwd = None
self._checknrun_storage = None
self._classmap = {} # map of name: actual_class_obj
self._cleanup = True # Should we automatically do a cleanup
self._verbose = False
self._debug = False
self._no_act = False
self._deps = {}
self._objsrun = [] # which objects ran, for triggering Cleanup
self._log = logging.getLogger('DoJobber')
logtarget = logging.StreamHandler()
logtarget.setFormatter(
logging.Formatter('DoJobber %(levelname)-19s: %(message)s')
)
if kwargs.get('dojobber_loglevel'):
self._log.setLevel(kwargs['dojobber_loglevel'])
else:
self._log.setLevel(logging.CRITICAL)
self._log.addHandler(logtarget)
def test_digraph_equality_attributes(self):
"""
Digraph equality test. This one checks node equality.
"""
gr = digraph()
gr.add_nodes([0, 1, 2])
gr.add_edge((0, 1))
gr.add_node_attribute(1, ('a', 'x'))
gr.add_node_attribute(2, ('b', 'y'))
gr.add_edge_attribute((0, 1), ('c', 'z'))
gr2 = deepcopy(gr)
gr3 = deepcopy(gr)
gr3.del_edge((0, 1))
gr3.add_edge((0, 1))
gr4 = deepcopy(gr)
gr4.del_edge((0, 1))
gr4.add_edge((0, 1))
gr4.add_edge_attribute((0, 1), ('d', 'k'))
gr5 = deepcopy(gr)
gr5.del_node(2)
gr5.add_node(2)
gr5.add_node_attribute(0, ('d', 'k'))
assert gr == gr2
assert gr2 == gr
assert gr != gr3
assert gr3 != gr
assert gr != gr4
assert gr4 != gr
assert gr != gr5
assert gr5 != gr
def test_digraph_equality_labels(self):
"""
Digraph equality test. This one checks node equality.
"""
gr = digraph()
gr.add_nodes([0, 1, 2])
gr.add_edge((0, 1), label="l1")
gr.add_edge((1, 2), label="l2")
gr2 = deepcopy(gr)
gr3 = deepcopy(gr)
gr3.del_edge((0, 1))
gr3.add_edge((0, 1))
gr4 = deepcopy(gr)
gr4.del_edge((0, 1))
gr4.add_edge((0, 1), label="l3")
assert gr == gr2
assert gr2 == gr
assert gr != gr3
assert gr3 != gr
assert gr != gr4
assert gr4 != gr
def test_a_b_c_d_square(self):
depgraph = digraph()
add_action(depgraph, "a#ta")
add_action(depgraph, "b#tb")
add_action(depgraph, "c#tc")
add_action(depgraph, "d#td")
depgraph.add_edge(("a#ta", "b#tb"))
depgraph.add_edge(("a#ta", "d#td"))
depgraph.add_edge(("c#tc", "b#tb"))
depgraph.add_edge(("c#tc", "d#td"))
(ise_model, xml, error) = self.order(depgraph)
self.assertActionsNb(ise_model, 4)
instructions = ise_model.instructions
self.assertNotEquals(instructions, None)
self.assertEquals(len(instructions), 1)
seq = instructions.pop()
instructions = self.assertSequence(seq, nb=2)
par = instructions[0]
actions = self.assertParallel(par, nb=2)
self.assertContainsAction(actions, "b#tb/Rule")
self.assertContainsAction(actions, "d#td/Rule")
par = instructions[1]
actions = self.assertParallel(par, nb=2)
self.assertContainsAction(actions, "a#ta/Rule")
self.assertContainsAction(actions, "c#tc/Rule")
def graphize(self):
try:
self.graph = pygraph.digraph()
except (NameError, AttributeError):
self.graph = digraph()
modules = [self.topModule] + self.moduleList
# first, we must add all the nodes. Only then can we add all the edges
self.graph.add_nodes(modules)
# here we have a strictly directed graph, so we need only insert directed edges
for module in modules:
def checkParent(child):
if module.name == child.parent:
return True
else:
return False
children = filter(checkParent, modules)
for child in children:
# due to compatibility issues, we need these try catch to pick the
# right function prototype.
try:
self.graph.add_edge(module, child)
except TypeError:
self.graph.add_edge((module, child))
def test_complete_digraph(self):
gr = digraph()
gr.add_nodes(range(10))
gr.complete()
for i in range(10):
for j in range(10):
self.assertTrue((i, j) in gr.edges() or i == j)
def test_add_empty_digraph(self):
gr1 = testlib.new_digraph()
gr1c = copy(gr1)
gr2 = digraph()
gr1.add_graph(gr2)
self.assertTrue(gr1.nodes() == gr1c.nodes())
self.assertTrue(gr1.edges() == gr1c.edges())
def build_bayes_graph(im,labels,sigma=1e2,kappa=2):
""" Build a graph from 4-neighborhood of pixels.
Foreground and background is determined from
labels (1 for foreground, -1 for background, 0 otherwise)
and is modeled with Gaussian Naive Bayes classifiers."""
m,n = im.shape[:2]
# RGB vector version (one pixel per row)
vim = im.reshape((-1,3))
# RGB for foreground and background
foreground = im[labels==1].reshape((-1,3))
background = im[labels==-1].reshape((-1,3))
train_data = [foreground,background]
print train_data
# train naive Bayes classifier
bc = bayes.BayesClassifier()
bc.train(train_data)
# get probabilities for all pixels
bc_lables,prob = bc.classify(vim)
prob_fg = prob[0]
prob_bg = prob[1]
# create graph with m*n+2 nodes
gr = digraph()
gr.add_nodes(range(m*n+2))
source = m*n # second to last is source
sink = m*n+1 # last node is sink
# normalize
for i in range(vim.shape[0]):
vim[i] = vim[i] / linalg.norm(vim[i])
# go through all nodes and add edges
for i in range(m*n):
# add edge from source
gr.add_edge((source,i), wt=(prob_fg[i]/(prob_fg[i]+prob_bg[i])))
# add edge to sink
gr.add_edge((i,sink), wt=(prob_bg[i]/(prob_fg[i]+prob_bg[i])))
# add edges to neighbors
if i%n != 0: # left exists
edge_wt = kappa*exp(-1.0*sum((vim[i]-vim[i-1])**2)/sigma)
gr.add_edge((i,i-1), wt=edge_wt)
if (i+1)%n != 0: # right exists
edge_wt = kappa*exp(-1.0*sum((vim[i]-vim[i+1])**2)/sigma)
gr.add_edge((i,i+1), wt=edge_wt)
if i//n != 0: # up exists
edge_wt = kappa*exp(-1.0*sum((vim[i]-vim[i-n])**2)/sigma)
gr.add_edge((i,i-n), wt=edge_wt)
if i//n != m-1: # down exists
edge_wt = kappa*exp(-1.0*sum((vim[i]-vim[i+n])**2)/sigma)
gr.add_edge((i,i+n), wt=edge_wt)
return gr
def _parse(self, file):
max_x = self._parse_int(file.readline())
max_y = self._parse_int(file.readline())
if max_x < max_y:
raise ValueError("Map must be horizontal: max_x >= max_y")
edge_count = self._parse_int(file.readline())
graph = digraph()
for i in range(0, (max_x + 1) * (max_y + 1)):
graph.add_node(i)
for _ in range(0, edge_count):
edge = file.readline().split()
if len(edge) != 4:
raise ValueError(
"Edge must be represented by 4 numbers: x1 y1 x2 y2")
x1 = self._parse_int(edge[0])
y1 = self._parse_int(edge[1])
x2 = self._parse_int(edge[2])
y2 = self._parse_int(edge[3])
graph.add_edge((y1 * (max_x + 1) + x1, y2 * (max_x + 1) + x2))
self._specification = MapSpecification(graph, max_x, max_y)
def graphizeSynth(self):
try:
self.graphSynth = pygraph.digraph()
except (NameError, AttributeError):
self.graphSynth = digraph()
modulesUnfiltered = [self.topModule] + self.moduleList
# first, we must add all the nodes. Only then can we add all the edges
# filter by synthesis boundaries
modules = filter(checkSynth, modulesUnfiltered)
self.graphSynth.add_nodes(modules)
# here we have a strictly directed graph, so we need only insert directed edges
for module in modules:
def checkParent(child):
if module.name == child.synthParent:
return True
else:
return False
children = filter(checkParent, modules)
for child in children:
#print "Adding p: " + module.name + " c: " + child.name
try:
self.graphSynth.add_edge(module, child)
except TypeError:
self.graphSynth.add_edge((module, child))
def drawGraph(self, inputs):
fileName = 'planetModel.png'
gr = graph()
self.addGraphNode(1,gr, inputs)
# Draw as PNG
#with open("./planetModel.viz", 'wb') as f:
#dot = write(gr,f)
#f.write(dot)
#gvv = gv.readstring(dot)
#gv.layout(gvv,'dot')
#gv.render(gvv,'png', fileName)
#f.close()
gst = digraph()
self.addGraphNode(1,gst, inputs)
with open("./planetModel.viz", 'wb') as f:
#st, order = breadth_first_search(gst, root=1)
#gst2 = digraph()
#gst2.add_spanning_tree(gst.nodes())
#gst2.(1, 'post')
dot = write(gst,f)
f.write(dot)
gvv = gv.readstring(dot)
gv.layout(gvv,'dot')
gv.render(gvv,'png', fileName)
f.close()
return fileName
def pygraphCrit(edgePairs, nameMap, timeMap, allEdts, allEvts, mainGuid):
G = digraph()
srcs = []
dsts = []
for i in range(len(edgePairs)):
srcs.append(edgePairs[i][0])
dsts.append(edgePairs[i][1])
allNodes = set(srcs+dsts)
for i in allNodes:
if i == mainGuid:
continue
else:
G.add_node(str(i))
for i in range(len(edgePairs)):
curTime = 0
curSrc = str(edgePairs[i][0])
curDst = str(edgePairs[i][1])
if curSrc == mainGuid or curDst == mainGuid:
continue
if getNodeType(curSrc, allEdts, allEvts) == 'Event':
curTime = 1
else:
curTime = edtGuidToTime(curSrc, timeMap)
G.add_edge((curSrc, curDst), curTime)
if len(critical_path(G)) == 0:
print 'Cycle Detected, exiting; Please check that the OCR conifiguration file uses GUID type of COUNTED_MAP, and the application has no cycles.'
print 'Dumping cycle below.'
print find_cycle(G)
os.remove(HTML_FILE_NAME)
sys.exit(0)
return critical_path(G)
def switchgraph(switchaddrs, outfile):
gr = digraph()
nodes = {}
edges = {}
for addr in switchaddrs:
print >> sys.stderr, "Querying %s..." % addr
try:
sysmac = switchquery(addr, PROCURVE_OIDS["system-mac"])
except SnmpError, err:
print >> sys.stderr, unicode(err)
continue
nodes[sysmac] = addr
cdpneigh = switchquery(addr, PROCURVE_OIDS["cdp-neigh"])
if not cdpneigh:
print >> sys.stderr, "%s didn't return any data!" % addr
continue
for port in cdpneigh[6]:
if 1 in cdpneigh[6][port]:
othermac = cdpneigh[6][port][1][0]
else:
continue
if othermac not in nodes:
nodes[othermac] = "%s\n%s" % (othermac,
cdpneigh[8][port][1][0][:20])
if (sysmac, othermac) not in edges and (othermac,
sysmac) not in edges:
edges[(sysmac, othermac)] = (port, cdpneigh[7][port][1][0])
def draw(self, filename):
print "initial state:", self.initial_state
print "final states", self.final_state
print "transition table:", self.transition_table
vertexes = self.transition_table.keys()
edges = self._edges()
gr = digraph()
#gr.add_nodes([str(vertex) for vertex in vertexes])
for vertex in vertexes:
attrs = []
if ((isinstance(self.final_state, list)
and vertex in self.final_state)
or (isinstance(self.final_state, int)
and vertex == self.final_state)):
attrs.append('final')
gr.add_node(str(vertex), attrs=attrs)
for edge, label in edges.items():
label = ', '.join(label)
gr.add_edge(edge=edge, label=label)
dot = write(gr)
gvv = gv.readstring(dot)
gv.layout(gvv, 'dot')
gv.render(gvv, 'png', '%s.png' % filename)
def test_a_b_c_d_square(self):
depgraph = digraph()
add_action(depgraph, "a#ta")
add_action(depgraph, "b#tb")
add_action(depgraph, "c#tc")
add_action(depgraph, "d#td")
depgraph.add_edge(("a#ta", "b#tb"))
depgraph.add_edge(("a#ta", "d#td"))
depgraph.add_edge(("c#tc", "b#tb"))
depgraph.add_edge(("c#tc", "d#td"))
(ise_model, xml, error) = self.order(depgraph)
self.assertActionsNb(ise_model, 4)
instructions = ise_model.instructions
self.assertNotEquals(instructions, None)
self.assertEquals(len(instructions), 1)
par = instructions.pop()
actions = self.assertParallel(par, nb=4)
a = self.assertContainsAction(actions, "a#ta/Rule")
b = self.assertContainsAction(actions, "b#tb/Rule")
c = self.assertContainsAction(actions, "c#tc/Rule")
d = self.assertContainsAction(actions, "d#td/Rule")
self.assertAction(a, id="a#ta/Rule", deps=set(['b#tb/Rule', 'd#td/Rule']))
self.assertAction(b, id="b#tb/Rule", deps=set())
self.assertAction(c, id="c#tc/Rule", deps=set(['b#tb/Rule', 'd#td/Rule']))
self.assertAction(d, id="d#td/Rule", deps=set())
def main(argv):
try:
opts, args = getopt.getopt(argv, '')
except getopt.GetoptError:
print('test.py <dir> <dir>')
sys.exit(2)
assert (len(args) == 2)
dirs = args
graphs = [
printDot(dirs[0] + '/graph.txt', '0'),
printDot(dirs[1] + '/graph.txt', '0')
]
types = [
parseTypes(dirs[0] + '/types.txt'),
parseTypes(dirs[1] + '/types.txt')
]
newG = digraph()
startN = ('0', '0')
newG.add_node(startN)
oneToOne(newG, graphs, types, startN)
printGraph(newG, ('0', '0'))
def __init__(self, var_lines):
try:
from pygraph.classes.digraph import digraph
except:
print(
"Error: pygraph not available. Advanced SAS+ reasoning will not work."
)
return None
# Parse the info
assert 'begin_variable' == var_lines.pop(0)
self.name = var_lines.pop(0)
self.axiom_layer = int(var_lines.pop(0))
domain_size = int(var_lines.pop(0))
# Create the graph
# Node: int corresponding to the value of the SAS+ variable
# Edge: label that indicates the operators that affect it
self.graph = digraph()
self.graph.name = self.name
self.transition_lookup = {}
# Add a node for each value in the domain
for i in range(domain_size):
self.graph.add_node(i, [('fluent', var_lines.pop(0))])
assert 'end_variable' == var_lines.pop(0)
# Create the accepting states
self.goal_vals = set([])
self.init_val = 0
def parse_generated_world(self, index, lines, data):
""" Parse the generated world and store its data
into the created data structure.
"""
# Skip the line ======== Generated World =========
index += 1
vertices = []
gr = digraph()
node_lines = []
edges = []
cur = ""
while index < len(lines) and "Weight" not in lines[index]:
line = lines[index].strip()
if "<-" in line:
words = line.split()
node = words[1]
for line in node_lines:
if node in line:
e = (line, cur)
if e not in edges:
#print "adding edge " + str(e)
gr.add_edge(e)
edges.append(e)
break
elif "=" in line:
#print "adding node: " + str(line)
gr.add_nodes([line])
node_lines.append(line)
cur = line
index += 1
return gr, index
def handle_recursive_calls(tpl_name, content):
# create the call graph as a directed graph
call_graph = digraph()
# visited_templates items will look like this:
# [("tpl1", "extends", "tpl2"), ...]
visited_templates = [(tpl_name, "", "")]
call_graph.add_node(tpl_name)
i = 0
while i < len(visited_templates):
name = visited_templates[i][0]
try:
tpl_content = content if i == 0 else Template.objects.get(name=name).content
except:
i += 1
continue
called_tpls = get_called_templates(tpl_content, name)
update_call_graph(call_graph, called_tpls)
# raises InfiniteRecursivityError in case of a cycle
cycle_test(call_graph, called_tpls)
visited_templates.extend(called_tpls)
i += 1
def run(self):
#print "save graph in dir"
gr = digraph()
for x in self.nodes:
gr.add_node(x.name)
for x in self.nodes:
x.addEdges(gr)
dirLck.acquire()
if not os.path.isdir(self.dir):
if -1 == os.getcwd().find(self.dir):
os.mkdir(self.dir)
dirLck.release()
if -1 == os.getcwd().find(self.dir):
os.chdir(self.dir)
dot = write(gr)
f = open(self.filename, 'w')
f.write(dot)
f.close()
proc = subprocess.Popen('dot -Tjpg ' + self.filename +' -o ' + self.filename + '.jpg', shell=True, stdout=subprocess.PIPE,)
r = proc.communicate()[0]
print ""
def merge_graphs(g1, g2):
"""
Merge two graphs to a new graph (V, E) with V = g1.nodes \union g2.nodes
and Edge e \in g1 or e \in g2 -> e \in E.
"""
if g1.DIRECTED or g2.DIRECTED:
g = digraph()
else:
g = graph()
for n in g1.nodes():
g.add_node(n)
for n in g2.nodes():
if not n in g.nodes():
g.add_node(n)
for e in g1.edges():
try:
g.add_edge(e, g1.edge_weight(e))
except:
logging.info("merge_graphs: adding edge %d %d failed" % (e[0], e[1]))
for e in g2.edges():
try:
g.add_edge(e, g2.edge_weight(e))
except:
logging.info("merge_graphs: adding edge %d %d failed" % (e[0], e[1]))
return g
def calculate_results(self):
# Don't bother if everyone's going to win
super(SchulzeSTV, self).calculate_results()
if hasattr(self, 'winners'):
return
# Generate the list of patterns we need to complete
self.generate_completed_patterns()
self.generate_vote_management_graph()
# Build the graph of possible winners
self.graph = digraph()
for candidate_set in itertools.combinations(self.candidates, self.required_winners):
self.graph.add_nodes([tuple(sorted(list(candidate_set)))])
# Generate the edges between nodes
for candidate_set in itertools.combinations(self.candidates, self.required_winners + 1):
for candidate in candidate_set:
other_candidates = sorted(set(candidate_set) - set([candidate]))
completed = self.proportional_completion(candidate, other_candidates)
weight = self.strength_of_vote_management(completed)
if weight > 0:
for subset in itertools.combinations(other_candidates, len(other_candidates) - 1):
self.graph.add_edge((tuple(other_candidates), tuple(sorted(list(subset) + [candidate]))), weight)
# Determine the winner through the Schwartz set heuristic
self.graph_winner()
# Split the "winner" into its candidate components
self.winners = set(self.winner)
del self.winner
def connect_graphs(g1, g2, connecting_edge, weight=1):
"""
Build a new graph out of the two given graphs.
Every node e in g1 will be represented as 1_e in the new graph and
every node e' in g2 as 2_e'.
@param connecting_edge: An edge (e_src, e_dst), where e_src is in
g1 and e_dst is in g2. This edge will connect g1 with g2.
@param weight: Weight of the connecting edge.
"""
g = digraph()
# Add nodes and edges
for (index, gr) in [(1, g1), (2, g2)]:
for n in gr.nodes():
g.add_node('%d_%d' % (index, n))
for (src, dst) in gr.edges():
g.add_edge(('%d_%d' % (index, src),
'%d_%d' % (index, dst)),
g.edge_weight((src, dst)))
# Connect subgraphs
conn_src, conn_dst = connecting_edge
g.add_edge(('%d_%d' % (1, conn_src),
'%d_%d' % (2, conn_dst)))
g.add_edge(('%d_%d' % (2, conn_dst),
'%d_%d' % (1, conn_src)))
return g
def friendly_rename(graph, name_prefix=""):
"""
Builds a new weighted digraph, based on the provided weighted digraph (which isn't modified),
which discards all names in favor of alphanumeric node identifiers.
"""
nextLetter = ord('A')
nextNumber = 1
identifierMap = {}
newGraph = digraph()
for node in graph.nodes():
if not graph.incidents(node):
identifier = name_prefix + chr(nextLetter)
nextLetter += 1
else:
identifier = "@" + name_prefix + str(nextNumber)
nextNumber += 1
newGraph.add_node(identifier, graph.node_attributes(node))
identifierMap[node] = identifier
for edge in graph.edges():
weight = graph.edge_weight(edge)
label = graph.edge_label(edge)
src = identifierMap[edge[0]]
dest = identifierMap[edge[1]]
new_edge = (src, dest)
attrs = graph.edge_attributes(edge)
newGraph.add_edge(new_edge, weight, label, attrs)
return newGraph
def sequential(m, nodes, coordinator):
"""
Construct a simple two-level tree. The coordinator is the root, and all
the other nodes are its children.
The weights of edges are taken from m.
@type m: graph
@param m: The machine model. The weights for the edges in the binary_tree
will be extracted from the model.
@type nodes: list
@param nodes: list of nodes to build a tree for. If list is
empty, it will default to m.nodes()
@type coordinator: number
@param coordinator: This node will be the root of the tree
@return digraph
"""
assert(len(m.nodes())>0) # graph has nodes
g = digraph()
g.add_node(coordinator)
for n in nodes:
if n != coordinator:
g.add_node(n)
g.add_edge((coordinator, n), \
m.edge_weight((n, coordinator)))
return g
def test_add_empty_digraph(self):
gr1 = testlib.new_digraph()
gr1c = copy(gr1)
gr2 = digraph()
gr1.add_graph(gr2)
self.assertTrue(gr1.nodes() == gr1c.nodes())
self.assertTrue(gr1.edges() == gr1c.edges())
def invert_weights(g):
"""
Invert the weights of the given graph.
The most expensive links will then be the cheapest and vice versa.
"""
assert isinstance(g, digraph)
# Determine the most expensive edge
w = 0
for (s,d) in g.edges():
w = max(w, g.edge_weight((s,d)))
print 'Maximum edge weight is %d' % w
w += 1 # Make sure the most expensive edge will have a cost of 1 afterwards
g_inv = digraph()
for n in g.nodes():
g_inv.add_node(n)
for (s,d) in g.edges():
assert g.edge_weight((s,d))<w
w_inv = w-g.edge_weight((s,d))
assert w_inv>0
try:
g_inv.add_edge((s,d), w_inv)
except:
assert g_inv.edge_weight((s,d)) == w_inv # This one fails
print "Edge %d %d already in graph, ignoring .. " % (s,d)
return g_inv
def author_centrality(titles_to_authors):
author_graph = digraph()
author_graph.add_nodes(map(lambda x: u"title_%s" % x,
titles_to_authors.keys()))
author_graph.add_nodes(list(set(
[u'author_%s' % author[u'user'] for authors in
titles_to_authors.values() for author in authors])))
for title in titles_to_authors:
log.debug(u"Working on title: %s" % title)
for author in titles_to_authors[title]:
try:
author_graph.add_edge(
(u'title_%s' % title, u'author_%s' % author[u'user']))
except AdditionError:
pass
centralities = dict([
('_'.join(item[0].split('_')[1:]), item[1]) for item in
pagerank(author_graph).items() if item[0].startswith(u'author_')])
centrality_scaler = MinMaxScaler(centralities.values())
return dict([(cent_author, centrality_scaler.scale(cent_val))
for cent_author, cent_val in centralities.items()])
def referergraph(self, refererlist, drawpath):
"""
Draw the graph of referers
"""
gr = digraph()
attr = list([('style', 'filled'), ('fillcolor', 'green'), ('shape', 'doublecircle')])
#first add all referer
for ref in refererlist:
try:
gr.add_node(ref.altname, attr)
except pygraph.classes.exceptions.AdditionError as e:
print e
print "=========================="
#now add the url that have the referer previously added
for ref in refererlist:
for url in ref.getlist:
print url
try:
gr.add_node(url[0])
except pygraph.classes.exceptions.AdditionError as e:
print "From url: " + str(e)
try:
gr.add_edge((ref.altname, url[0]),1,url[1])
except pygraph.classes.exceptions.AdditionError as e:
print "Edge addition: " + str(e)
return self.export(gr, drawpath, "referer")
def parse_generated_world(self, index, lines, data):
""" Parse the generated world and store its data
into the created data structure.
"""
# Skip the line ======== Generated World =========
index += 1
vertices = []
gr = digraph()
node_lines = []
edges = []
cur = ""
while index < len(lines) and "Weight" not in lines[index]:
line = lines[index].strip()
if "<-" in line:
words = line.split()
node = words[1]
for line in node_lines:
if node in line:
e = (line, cur)
if e not in edges:
#print "adding edge " + str(e)
gr.add_edge(e)
edges.append(e)
break
elif "=" in line:
#print "adding node: " + str(line)
gr.add_nodes([line])
node_lines.append(line)
cur = line
index += 1
return gr, index
def system_of_different_constraints():
"""
x1 - x2 <= 0
x1 - x5 <= -1
x2 - x5 <= 1
x3 - x1 <= 5
x4 - x1 <= 4
x4 - x3 <= -1
x5 - x3 <= -3
x5 - x4 <= -3
"""
m = int(input("Enter the number of limited conditions ->"))
n = int(input("Enter the number of variables ->"))
g = digraph()
for i in range(0, n + 1):
node = 'x' + str(i)
g.add_node(node)
if i > 0:
g.add_edge(('x0', node), 0)
print(g.nodes())
print(g.edges())
print("Enter the conditions: ")
for i in range(m):
print("The %d-th condition:" % (i + 1))
v1 = input("First variable: ")
v2 = input("Second variable: ")
b = int(input("Biase: "))
g.add_edge((v2, v1), b)
print(g.edges())
previous, dist = bellman_fold_notCLRS(g, 'x0')
print(previous, dist)
"""
def init_graph():
global g
if(g):
return g
g = digraph()
deps = []
for cls, lst in manifest.declarations.iteritems():
for declaration_id, dec in lst.iteritems():
log.debug('adding node %r' % declaration_id)
g.add_node(declaration_id)
reqs = getattr(dec, 'require', [])
if not(isinstance(reqs, (list, tuple))):
reqs = [reqs]
d = []
for req in reqs:
d.append([req.declaration_id, declaration_id])
if(d):
deps.append(d)
for dep in deps:
log.debug('adding edge %r' % dep)
g.add_edge(*dep)
return g
def fix_orphan_nodes(commit_graph, release):
new_graph = digraph()
new_graph.add_nodes(commit_graph.nodes())
[new_graph.add_edge(edge) for edge in commit_graph.edges()]
orphan_nodes = [node for node in new_graph.nodes() if not new_graph.incidents(node)]
[new_graph.add_edge((release, node)) for node in orphan_nodes if node != release]
return new_graph
def test_pagerank(self):
#Test example from wikipedia: http://en.wikipedia.org/wiki/File:Linkstruct3.svg
G = digraph()
G.add_nodes([1, 2, 3, 4, 5, 6, 7])
G.add_edge((1, 2))
G.add_edge((1, 3))
G.add_edge((1, 4))
G.add_edge((1, 5))
G.add_edge((1, 7))
G.add_edge((2, 1))
G.add_edge((3, 1))
G.add_edge((3, 2))
G.add_edge((4, 2))
G.add_edge((4, 3))
G.add_edge((4, 5))
G.add_edge((5, 1))
G.add_edge((5, 3))
G.add_edge((5, 4))
G.add_edge((5, 6))
G.add_edge((6, 1))
G.add_edge((6, 5))
G.add_edge((7, 5))
expected_pagerank = {
1: 0.280,
2: 0.159,
3: 0.139,
4: 0.108,
5: 0.184,
6: 0.061,
7: 0.069,
}
pr = pagerank(G)
for k in pr:
self.assertAlmostEqual(pr[k], expected_pagerank[k], places=3)
def graphizeSynth(self):
try:
self.graphSynth = pygraph.digraph()
except (NameError, AttributeError):
self.graphSynth = digraph()
modulesUnfiltered = [self.topModule] + self.moduleList
# first, we must add all the nodes. Only then can we add all the edges
# filter by synthesis boundaries
modules = filter(checkSynth, modulesUnfiltered)
self.graphSynth.add_nodes(modules)
# here we have a strictly directed graph, so we need only insert directed edges
for module in modules:
def checkParent(child):
if module.name == child.synthParent:
return True
else:
return False
children = filter(checkParent, modules)
for child in children:
#print "Adding p: " + module.name + " c: " + child.name
try:
self.graphSynth.add_edge(module,child)
except TypeError:
self.graphSynth.add_edge((module,child))
def create_object_graph(objects):
# create dict to map objectname to file object
mapped_objects = {}
for o in objects:
mapped_objects[o.get_object_name()] = o
object_graph = digraph()
object_graph.add_nodes([o.get_object_name() for o in objects])
# Create relationship list
successors = [(i.get_object_name(), [] if i.get_successors() is None else [mapped_objects[j] for j in i.get_successors()] ) for i in objects]
#
for obj, suc in successors:
for s in suc:
object_graph.add_edge((obj, s.get_object_name()))
object_names = [o.get_object_name() for o in objects]
for o in objects:
# Bind objects to previous release
predecessors = o.get_predecessors()
if predecessors is not None:
for p in predecessors:
if p not in object_names:
if not object_graph.has_node(p):
object_graph.add_node(p)
object_graph.add_edge((p,o.get_object_name()))
return object_graph
def createCircularDiGraph(self, polygon_tup, rates):
"""
Takes a polygon tuple and creates a circular directed graph
of the tuple.
returns the directed graph
"""
# Creating a digraph - directed graph - from rates dictionary
#rates_digraph = convertDictToDiGraph(rates)
dg = digraph()
dg.add_nodes(polygon_tup)
for i in range(len(polygon_tup)):
if i < len(polygon_tup) - 1:
#polygon_tup[i]
weight = rates[polygon_tup[i]][polygon_tup[i + 1]]
dg.add_edge((polygon_tup[i], polygon_tup[i + 1]),
wt=float(weight),
label=str(weight))
elif i == len(polygon_tup) - 1:
weight = rates[polygon_tup[-1]][polygon_tup[0]]
dg.add_edge((polygon_tup[-1], polygon_tup[0]),
wt=float(weight),
label=str(weight))
#self.createImageFromDiGraph(dg, 'best_polygon_solution_digraph.png')
return dg
def graphize(self):
try:
self.graph = pygraph.digraph()
except (NameError, AttributeError):
self.graph = digraph()
modules = [self.topModule] + self.moduleList
# first, we must add all the nodes. Only then can we add all the edges
self.graph.add_nodes(modules)
# here we have a strictly directed graph, so we need only insert directed edges
for module in modules:
def checkParent(child):
if module.name == child.parent:
return True
else:
return False
children = filter(checkParent, modules)
for child in children:
# due to compatibility issues, we need these try catch to pick the
# right function prototype.
try:
self.graph.add_edge(module,child)
except TypeError:
self.graph.add_edge((module,child))
def __init__(self, name='', preamble='', postamble=''):
"""Initializes SDF graph class
"""
# SDF related attributes
self.graph = digraph() # graph representation
self.name = name # name of sdf function
self.preamble = preamble # C-code for preamble
self.postamble = postamble # C-code for postamble
self.no_code = False # Error state for parsing
self.index_ctr = 0
# node related attributes
self.node_index = {} # index of node to order parallel nodes properly
self.node_type = {} # node type generic or splitter/joiner
self.node_param = {} # parameters of actors
self.repetition = {} # repetition vector
self.actor_code = {} # code of actor for actor firing
self.comm_code = {}
self.state = {} # state variables of actors
self.init = {} # initialization for state variables
self.exec_time = {
} # execution times of a single invocation for each actors
self.allocation = {}
# edge related attributes
self.consumption = {} # consumption rate
self.production = {} # production rate
self.delay = {} # number of delay tokens (i.e., init tokens)
self.token_type = {} # data type of token
self.source_tokens = {} # tokens for producer
self.target_tokens = {} # tokens for consumer
self.peek_tokens = {} # tokens for peeking
self.delay_tokens = {} # delay tokens on the edge
def test_par_a_b_n_actions(self):
depgraph = digraph()
na = random.randint(5, 10)
actions = []
for i in range(0, na):
actions.append(("Rule"+str(i), "Cmd"+str(i)))
add_action(depgraph, "a#ta", actions)
nb = random.randint(5, 10)
actions = []
for i in range(0, nb):
actions.append(("Rule"+str(i), "Cmd"+str(i)))
add_action(depgraph, "b#tb", actions)
(ise_model, xml, error) = self.order(depgraph)
self.assertActionsNb(ise_model, na+nb)
instructions = ise_model.instructions
self.assertNotEquals(instructions, None)
self.assertEquals(len(instructions), 1)
par = instructions.pop()
seqs = self.assertParallel(par, 2)
seqa = self.assertSequence(seqs[0], na)
for i in range(0, na):
self.assertAction(seqa[i], id="a#ta/Rule"+str(i),
cs="a#ta", cmd="Cmd"+str(i))
seqb = self.assertSequence(seqs[1], nb)
for i in range(0, nb):
self.assertAction(seqb[i], id="b#tb/Rule"+str(i),
cs="b#tb", cmd="Cmd"+str(i))
def test_seq_a_b_n_actions(self):
depgraph = digraph()
na = random.randint(5, 10)
actions = []
for i in range(0, na):
actions.append(("Rule"+str(i), "Cmd"+str(i)))
add_action(depgraph, "a#ta", actions)
nb = random.randint(5, 10)
actions = []
for i in range(0, nb):
actions.append(("Rule"+str(i), "Cmd"+str(i)))
add_action(depgraph, "b#tb", actions)
depgraph.add_edge(("a#ta", "b#tb"))
(ise_model, xml, error) = self.order(depgraph)
self.assertActionsNb(ise_model, na+nb)
instructions = ise_model.instructions
self.assertNotEquals(instructions, None)
self.assertEquals(len(instructions), 1)
seq = instructions.pop()
actions = self.assertSequence(seq, na+nb)
for i in range(0, nb):
self.assertAction(actions[i], id="b#tb/Rule"+str(i),
cs="b#tb", cmd="Cmd"+str(i))
for i in range(0, na):
self.assertAction(actions[nb+i], id="a#ta/Rule"+str(i),
cs="a#ta", cmd="Cmd"+str(i))
def calculate_results(self):
# Don't bother if everyone's going to win
super(SchulzeSTV, self).calculate_results()
if hasattr(self, 'winners'):
return
# Generate the list of patterns we need to complete
self.generate_completed_patterns()
self.generate_vote_management_graph()
# Build the graph of possible winners
self.graph = digraph()
for candidate_set in itertools.combinations(self.candidates, self.required_winners):
self.graph.add_nodes([tuple(sorted(list(candidate_set)))])
# Generate the edges between nodes
for candidate_set in itertools.combinations(self.candidates, self.required_winners + 1):
for candidate in candidate_set:
other_candidates = sorted(set(candidate_set) - set([candidate]))
completed = self.proportional_completion(candidate, other_candidates)
weight = self.strength_of_vote_management(completed)
if weight > 0:
for subset in itertools.combinations(other_candidates, len(other_candidates) - 1):
self.graph.add_edge((tuple(other_candidates), tuple(sorted(list(subset) + [candidate]))), weight)
# Determine the winner through the Schwartz set heuristic
self.graph_winner()
# Split the "winner" into its candidate components
self.winners = set(self.winner)
del self.winner
def build_bayes_graph(im, labels, sigma=1e2, kappa=2):
### """从像素四邻域建立一个图，前景和背景(前景用 1 标记，背景用 -1 标记，
### 其他的用 0 标记)由 labels 决定，并用朴素贝叶斯分类器建模 """
m, n = im.shape[:2]
# 每行是一个像素的 RGB 向量
vim = im.reshape((-1, 3))
# 前景和背景(RGB)
foreground = im[labels == 1].reshape((-1, 3))
background = im[labels == -1].reshape((-1, 3))
train_data = [foreground, background]
# 训练朴素贝叶斯分类器
bc = bayes.BayesClassifier()
bc.train(train_data)
# 获取所有像素的概率
bc_lables, prob = bc.classify(vim)
prob_fg = prob[0]
prob_bg = prob[1]
# 用m*n+2 个节点创建图
gr = digraph()
gr.add_nodes(range(m * n + 2))
source = m * n # 倒数第二个是源点
sink = m * n + 1 # 最后一个节点是汇点
# 归一化
for i in range(vim.shape[0]):
vim[i] = vim[i] / linalg.norm(vim[i])
# 遍历所有的节点，并添加边
for i in range(m * n):
# 从源点添加边
gr.add_edge((source, i), wt=(prob_fg[i] / (prob_fg[i] + prob_bg[i])))
# 向汇点添加边
gr.add_edge((i, sink), wt=(prob_bg[i] / (prob_fg[i] + prob_bg[i])))
# 向相邻节点添加边
if i % n != 0: #左边存在
edge_wt = kappa * np.exp(-1.0 * np.sum(
(vim[i] - vim[i - 1])**2) / sigma)
gr.add_edge((i, i - 1), wt=edge_wt)
if (i + 1) % n != 0: # 如果右边存在
edge_wt = kappa * np.exp(-1.0 * np.sum(
(vim[i] - vim[i + 1])**2) / sigma)
gr.add_edge((i, i + 1), wt=edge_wt)
if i // n != 0: #如果上方存在
edge_wt = kappa * np.exp(-1.0 * np.sum(
(vim[i] - vim[i - n])**2) / sigma)
gr.add_edge((i, i - n), wt=edge_wt)
if i // n != m - 1: # 如果下方存在
edge_wt = kappa * np.exp(-1.0 * np.sum(
(vim[i] - vim[i + n])**2) / sigma)
gr.add_edge((i, i + n), wt=edge_wt)
return gr
def build_bayes_graph(im,labels,sigma=1e2,kappa=1):
""" Build a graph from 4-neighborhood of pixels.
Foreground and background is determined from
labels (1 for foreground, -1 for background, 0 otherwise)
and is modeled with naive Bayes classifiers."""
m,n = im.shape[:2]
# RGB vector version (one pixel per row)
vim = im.reshape((-1,3))
# RGB for foreground and background
foreground = im[labels==1].reshape((-1,3))
background = im[labels==-1].reshape((-1,3))
train_data = [foreground,background]
# train naive Bayes classifier
bc = bayes.BayesClassifier()
bc.train(train_data)
# get probabilities for all pixels
bc_lables,prob = bc.classify(vim)
prob_fg = prob[0]
prob_bg = prob[1]
# create graph with m*n+2 nodes
gr = digraph()
gr.add_nodes(range(m*n+2))
source = m*n # second to last is source
sink = m*n+1 # last node is sink
# normalize
for i in range(vim.shape[0]):
vim[i] = vim[i] / (linalg.norm(vim[i]) + 1e-9)
# go through all nodes and add edges
for i in range(m*n):
# add edge from source
gr.add_edge((source,i), wt=(prob_fg[i]/(prob_fg[i]+prob_bg[i])))
# add edge to sink
gr.add_edge((i,sink), wt=(prob_bg[i]/(prob_fg[i]+prob_bg[i])))
# add edges to neighbors
if i%n != 0: # left exists
edge_wt = kappa*exp(-1.0*sum((vim[i]-vim[i-1])**2)/sigma)
gr.add_edge((i,i-1), wt=edge_wt)
if (i+1)%n != 0: # right exists
edge_wt = kappa*exp(-1.0*sum((vim[i]-vim[i+1])**2)/sigma)
gr.add_edge((i,i+1), wt=edge_wt)
if i//n != 0: # up exists
edge_wt = kappa*exp(-1.0*sum((vim[i]-vim[i-n])**2)/sigma)
gr.add_edge((i,i-n), wt=edge_wt)
if i//n != m-1: # down exists
edge_wt = kappa*exp(-1.0*sum((vim[i]-vim[i+n])**2)/sigma)
gr.add_edge((i,i+n), wt=edge_wt)
return gr
def calculate_results(self):
remaining_candidates = self.candidates.copy()
self.order = []
self.rounds = []
if self.winner_threshold is None:
winner_threshold = len(self.candidates)
else:
winner_threshold = min(len(self.candidates),
self.winner_threshold + 1)
for self.required_winners in range(1, winner_threshold):
# Generate the list of patterns we need to complete
self.generate_completed_patterns()
self.generate_vote_management_graph()
# Generate the edges between nodes
self.graph = digraph()
self.graph.add_nodes(remaining_candidates)
self.winners = set([])
self.tied_winners = set([])
# Generate the edges between nodes
for candidate_from in remaining_candidates:
other_candidates = sorted(
list(remaining_candidates - set([candidate_from])))
for candidate_to in other_candidates:
completed = self.proportional_completion(
candidate_from,
set([candidate_to]) | set(self.order))
weight = self.strength_of_vote_management(completed)
if weight > 0:
self.graph.add_edge((candidate_to, candidate_from),
weight)
# Determine the round winner through the Schwartz set heuristic
self.schwartz_set_heuristic()
# Extract the winner and adjust the remaining candidates list
self.order.append(self.winner)
round = {"winner": self.winner}
if len(self.tied_winners) > 0:
round["tied_winners"] = self.tied_winners
self.rounds.append(round)
remaining_candidates -= set([self.winner])
del self.winner
del self.actions
if hasattr(self, "tied_winners"):
del self.tied_winners
# Attach the last candidate as the sole winner if necessary
if self.winner_threshold is None or self.winner_threshold == len(
self.candidates):
self.rounds.append({"winner": list(remaining_candidates)[0]})
self.order.append(list(remaining_candidates)[0])
del self.winner_threshold
def _get_instrs_graph(self):
#initialize graph
igraph = digraph()
igraph.add_nodes(self.code.itervalues())
for ins in self.code.itervalues():
for suc in ins.succ:
igraph.add_edge((ins, self.code[suc]))
return igraph