def render_graph_with_graphviz(g, filename):
"""manual hack to render graph because graphtool's graphviz rendering is broken"""
edgelist = []
for i in g.edges():
edgelist.append([g.vp.id[i.source()], g.vp.id[i.target()]])
dot = Digraph()
dot.engine = 'sfdp'
dot.node_attr = {'shape': "point"}
dot.edge_attr = {'arrowsize': "0.1", 'penwidth':'0.1'}
dot.graph_attr = {'outputorder':'edgesfirst', 'overlap':'false'}
size = g.degree_property_map('out')
label_size_scaler = graph_tool.draw.prop_to_size(size, mi=2, ma=6, log=False, power=0.5)
node_size_scaler = graph_tool.draw.prop_to_size(size, mi=0.005, ma=0.1, log=False, power=1)
# https://github.com/xflr6/graphviz/issues/85
for i in flatten_list(edgelist):
gt_node = graph_tool.util.find_vertex(g, g.vp.id, i)[0]
# gt_node = g_kld2.vertex(vd_kld2[i])
label_size =label_size_scaler[gt_node]
node_size = node_size_scaler[gt_node]
dot.node(i, xlabel=i, width=str(node_size), fontsize=str(label_size))
dot.edges(edgelist)
dot.render(filename = filename)
def recalc_layout_dot(self):
"""recalculate node positions with dot layout"""
logging.info('dot recalculating starting')
t1 = time()
# think i have to set it here as well, is defined in force calcs
# maybe move to get_node_text_dimensions?
# self.dim_ar = np.array([[self.g.nodes[i]['width'], self.g.nodes[i]['height']] for i in self.g.nodes])
# get node array
self.base_pos_ar = np.array([
(self.g.nodes[i]['x'], self.g.nodes[i]['y']) for i in self.g.nodes
])
dg = Digraph()
dg.graph_attr = {'rankdir': 'BT', 'dpi': '72'}
dg.edges([i for i in self.g.edges])
for i in self.g.nodes:
# dg.node(i) = {'width': self.g.nodes[i]['width']/96, 'height': self.g.nodes[i]['height']/96}
dg.node(i,
width=str(self.g.nodes[i]['width'] / 72),
height=str(self.g.nodes[i]['height'] / 72))
dg_gv_piped = dg.pipe(format='json')
dg_gv_parsed = json.loads(dg_gv_piped)
for i in dg_gv_parsed['objects']:
posx, posy = i['pos'].split(',')
self.g.nodes[i['name']]['x'] = float(posx) + 20
self.g.nodes[i['name']]['y'] = float(posy)
pos_nds = np.array([(self.g.nodes[i]['x'], self.g.nodes[i]['y'])
for i in self.g.nodes])
self.chng_ar = (pos_nds - self.base_pos_ar) / self.step
t2 = time()
logging.info('dot recalc done in ' + str(round(t2 - t1)) + ' seconds')
# function: smaller angle -> greater force
# no force if angle is pi
force_mult = np.pi - angle
# kinda would like to have some division for low angles because it really ups those forces
# minus just doesn't cut it
# more important than having 0 force (stuff will oscillate out anyways)
force_mult = 1/angle
# maybe have to multiply by constant?
disp_vec *= force_mult
from graphviz import Digraph
dg = Digraph()
dg.graph_attr = {'rankdir': 'BT', 'dpi': '72'}
dg.edge('a', 'b', label = 'kkk')
import json
dg_gv_piped = dg.pipe(format = 'json')
dg_gv_parsed = json.loads(dg_gv_piped)
27 86.997
27 36.026
27 47.808
27 63.439
27 76.842'
is lp?
ontology = getData(o)["ontology_tree"]
#
# the tree of networks
f = o_template % "tree"
print(f)
graph_attr = {}
graph_attr["nodesep"] = "1"
graph_attr["ranksep"] = "0.3"
# graph_attr.edge_attr["color"] = "blue"
graph_attr["splines"] = "false" # ""polyline"
edge_attr = {}
# edge_attr["tailport"] = "s"
# edge_attr["headport"] = "n"
simple_graph = Digraph("T", filename=f)
simple_graph.graph_attr = graph_attr
simple_graph.edge_attr = edge_attr
ontology_hierarchy = walkTreeOnly(ontology, "root", simple_graph)
print(ontology_hierarchy)
simple_graph.view() # generates pdf
os.remove(f)
#
# one node at the time starting with the root node in the network tree
behaviour_nodes = []
structure_nodes = []
graph_attr["rankdir"] = "LR"
edge_attr["tailport"] = "e"
edge_attr["headport"] = "w" # msg_box"
graph_attr["nodesep"] = "0.4"
def makeOntologyDotGraph(ontology_tree, ontology_name, show="write"):
"""
makes the ontology tree for each domain as a pdf and one pdf with all together
"""
import subprocess
ontology = ontology_tree
dot_path = os.path.join(DIRECTORIES["ontology_repository"], ontology_name, DIRECTORIES["ontology_graphs_location"],
"%s")
o_template = dot_path # + ".gv"
o = FILES["ontology_file"] % ontology_name
#
# the tree of networks
f = o_template % "tree"
print(f)
graph_attr = {}
graph_attr["nodesep"] = "1"
graph_attr["ranksep"] = "0.3"
# graph_attr.edge_attr["color"] = "blue"
graph_attr["splines"] = "false" # ""polyline"
edge_attr = {}
# edge_attr["tailport"] = "s"
# edge_attr["headport"] = "n"
simple_graph = Digraph("T", filename=f)
simple_graph.graph_attr = graph_attr
simple_graph.edge_attr = edge_attr
ontology_hierarchy = walkTreeOnly(ontology, "root", simple_graph)
print(ontology_hierarchy)
if show == "view":
simple_graph.view() # generates pdf
else:
simple_graph.render()
os.remove(f)
#
# one node at the time starting with the root node in the network tree
behaviour_nodes = []
structure_nodes = []
graph_attr["rankdir"] = "LR"
edge_attr["tailport"] = "e"
edge_attr["headport"] = "w" # msg_box"
graph_attr["nodesep"] = "0.4"
graph_attr["ranksep"] = "0.8"
node = "root"
n = str(node)
f = o_template % n
print(f)
node_graph = Digraph(n, filename=f, graph_attr=graph_attr)
node_graph.graph_attr = graph_attr
node_graph.edge_attr = edge_attr
ontology_hierarchy = singleNodeOnly(ontology, n, node_graph, behaviour_nodes, structure_nodes)
if show != "summary":
node_graph.view()
tree = ["root"]
makeTree(ontology, "root", tree)
for node in tree:
if node != "root":
n = str(node)
f = o_template % n
print(f)
node_graph = Digraph(n, filename=f, graph_attr=graph_attr)
ontology_hierarchy = singleNodeOnly(ontology, n, node_graph, behaviour_nodes, structure_nodes)
if show != "summary":
node_graph.view()
pdf_template = dot_path + ".pdf"
merger = PdfFileMerger()
pdf = pdf_template % "tree"
merger.append(open(pdf, 'rb'))
pdf = pdf_template % str("root")
merger.append(open(pdf, 'rb'))
for node in tree:
if node != "root":
pdf = pdf_template % str(node)
merger.append(open(pdf, 'rb'))
o_ = o_template % str(node)
if os.path.exists(o_):
os.remove(o_)
o = dot_path % "all_nodes" + ".pdf"
merger.write(o)
if show == "summary":
shell_file = FILES["latex_shell_ontology_view_exec"] % ontology_name
args = ['sh', shell_file, dot_path.replace("%s", "")]
# print('ARGS: ', args)
make_it = subprocess.Popen(
args,
# start_new_session=True,
# stdout=subprocess.PIPE,
# stderr=subprocess.PIPE
)
out, error = make_it.communicate()
print("file written to :", o)
def recalc_layout_dot(self):
"""recalculate node positions with dot layout"""
logging.info('dot recalculating starting')
t1 = time()
# think i have to set it here as well, is defined in force calcs
# maybe move to get_node_text_dimensions?
# self.dim_ar = np.array([[self.g.nodes[i]['width'], self.g.nodes[i]['height']] for i in self.g.nodes])
# get node array
self.base_pos_ar = np.array([(self.g.nodes[i]['x'],self.g.nodes[i]['y']) for i in self.g.nodes])
dg = Digraph()
dg.graph_attr = {'rankdir': 'BT', 'dpi': '72'}
if self.use_edge_labels != True:
dg.edges([i for i in self.g.edges])
for n in self.g.nodes:
# dg.node(i) = {'width': self.g.nodes[i]['width']/96, 'height': self.g.nodes[i]['height']/96}
if self.g.nodes[n]['nd_tp'] == 'nd':
dg.node(n, width = str(self.g.nodes[n]['width']/72), height = str(self.g.nodes[n]['height']/72))
# assumes now that every edge has a label over which the out/in-going nodes can be retrieved
if self.use_edge_labels == True:
dg_edges = []
for n in self.g.nodes:
if self.g.nodes[n]['nd_tp'] == 'lbl':
node_out = list(self.g.predecessors(n))[0]
node_in = list(self.g.successors(n))[0]
dg.edge(node_out, node_in, label = self.g.nodes[n]['title'])
logging.info(['graph:\n', str(dg)])
# logging.info(['graph:\n', dg])
dg_gv_piped = dg.pipe(format = 'json')
dg_gv_parsed = json.loads(dg_gv_piped)
# loop over edges? have to get get info somehow
if self.use_edge_labels == True:
for e in dg_gv_parsed['edges']:
lbl_text = e['label']
lbl_x, lbl_y = e['lp'].split(',')
head_id = e['tail']
tail_id = e['head']
head_name = dg_gv_parsed['objects'][head_id]['name']
tail_name = dg_gv_parsed['objects'][tail_id]['name']
elbl_nd_name = elbl_nd_name = "lbl_" + head_name + "_" + tail_name + "_" + lbl_text
self.g.nodes[elbl_nd_name]['x'] = float(lbl_x)
# self.g.nodes[elbl_nd_name]['x'] = float(lbl_x) + self.g.nodes[elbl_nd_name]['width']/2
self.g.nodes[elbl_nd_name]['y'] = float(lbl_y)
for i in dg_gv_parsed['objects']:
posx, posy = i['pos'].split(',')
self.g.nodes[i['name']]['x'] = float(posx) + 20 # tf is this +20 doing here
self.g.nodes[i['name']]['y'] = float(posy)
pos_nds = np.array([(self.g.nodes[i]['x'],self.g.nodes[i]['y']) for i in self.g.nodes])
logging.info(['pos_nds:\n', pos_nds])
self.chng_ar = (pos_nds - self.base_pos_ar)/self.step
t2 = time()
logging.info('dot recalc done in ' + str(round(t2-t1)) + ' seconds')