def intranode_distance():
#choose a random leaf
print('process the graph')
elected = soma
while elected.out_degree() != 0:
elected = random.choice(list(tree.vertices()))
#measure distance for all the resting leaves
for node in tree.vertices():
if node.out_degree() == 0:
distanceNode[node] = distance(name[elected], name[node])
else:
distanceNode[node] = 1
#diffuse tubuline demand proportional respect the elected leaf distance
tubuline.a = 2**(0.01 * distanceNode.a)
cent_order.a = 1000 / (cent_order.a + 1)
size = draw.prop_to_size(cent_order)
#plot it to understand
pos = draw.sfdp_layout(tree)
draw.graph_draw(tree,
pos=pos,
vertex_fill_color=tubuline,
vertex_size=size)
draw.graph_draw(tree,
pos=pos,
vertex_fill_color=tubuline,
vertex_text=distanceNode)
def plot_graph(G,node_color={},node_shape={},edge_width={},ax=None,name="graph",save=False):
nodes = G.nodes()
nN = len(nodes)
index = {nodes[i]:i for i in range(nN)}
#graph for plotting
G0 = gt.Graph(directed=False)
v_id = G0.new_vertex_property("int") #node ID
v_co = G0.new_vertex_property("int") #node color
if node_color == {}:
color = {n:0 for n in nodes}
else:
color = node_color
v_sh = G0.new_vertex_property("int") #node shape
if node_shape == {}:
shape = {n:0 for n in nodes}
else:
shape = node_shape
vlist = []
e_w = G0.new_edge_property("float") #edge weight
if edge_width == {}:
width = {e:1 for e in G.edges()}
else:
width = edge_width
for n in nodes:
v = G0.add_vertex()
v_id[v] = n
v_co[v] = color[n]
v_sh[v] = shape[n]
vlist.append(v)
for n,p in G.edges():
i,j = index[n],index[p]
e = G0.add_edge(vlist[i],vlist[j])
e_w[e] = width[(n,p)]
# G0.vertex_properties["ID"] = v_id
# G0.vertex_properties["Shape"] = v_ta
# G0.vertex_properties["Color"] = v_gp
# G0.edge_properties["Weight"] = e_w
if save:
G0.save(name+".xml.gz")
#plot graph
pos = sfdp_layout(G0,eweight=e_w)
if ax == None:
graph_draw(G0,pos,output_size=(1000,1000),
vertex_fill_color=v_co,
vertex_shape=v_sh,
vertex_size=15,
edge_pen_width=e_w,
bg_color=[1., 1., 1., 1.],
output=name+".png"
)
else:
graph_draw(G0,pos,output_size=(1000,1000),
vertex_fill_color=v_co,
vertex_shape=v_sh,
vertex_size=15,
edge_pen_width=e_w,
bg_color=[1., 1., 1., 1.],
mplfig=ax
)
def draw_similarity_graph(g):
state = minimize_blockmodel_dl(g)
b = state.b
pos = sfdp_layout(g, eweight=g.edge_properties['sim'])
graph_draw(g, pos, output_size=(1000, 1000), vertex_color=[1, 1, 1, 0],
vertex_size=g.vertex_properties['freq'], edge_pen_width=1.2,
vcmap=matplotlib.cm.gist_heat_r, output="word_similarity.png")
state = minimize_blockmodel_dl(g)
graph_draw(g, pos=pos, vertex_fill_color=b, vertex_shape=b, output="blocks_mdl.png")
def init_graph_viz(self):
pos = sfdp_layout(self.g)
if 'pos' in self.graph_viz_params:
pos = self.graph_viz_params['pos']
self.graph_viz_params.__delitem__('pos')
self.win = GraphWindow(self.g, pos, **self.graph_viz_params)
self.win.connect("delete_event", Gtk.main_quit)
GObject.idle_add(self.simulate)
self.win.show_all()
def draw_game_flow(self, model: GameModel):
self.log.debug('drawing game flow for model {0}'.format(model.name))
TMPUTILS.clear_container(self.game_flow_panel)
all_phases = [
phase for pt in [model.table_type] + model.player_types
for phase in pt.phases
]
phase_phase = {}
for phase in all_phases:
phase_phase[phase] = list(TMPUTILS.end_phases(phase))
graph = Graph()
graph.vp.name = graph.new_vertex_property('string')
graph.vp.color = graph.new_vertex_property('string')
graph.vp.text_pos = graph.new_vertex_property('float')
graph.vp.text_off = graph.new_vertex_property('vector<float>')
phase_vertex = {}
for phase in all_phases:
vertex = graph.add_vertex()
phase_vertex[phase] = vertex
text = phase.name
graph.vp.name[vertex] = text
if phase is model.start_phase:
color = self.config.start_game_color()
elif phase is model.end_phase:
color = self.config.end_game_color()
elif phase in model.table_type.phases:
color = self.config.table_color()
else:
number = model.player_types.index(
model.get_player_type_for_phase(phase))
color = self.config.player_color(number)
graph.vp.color[vertex] = color
graph.vp.text_pos[vertex] = 0
graph.vp.text_off[vertex] = [0, 0]
for phase in all_phases:
for other in phase_phase[phase]:
graph.add_edge(phase_vertex[phase], phase_vertex[other])
pos = sfdp_layout(graph)
vprops = {
'text': graph.vp.name,
'fill_color': graph.vp.color,
'text_position': graph.vp.text_pos,
'text_offset': graph.vp.text_off
}
graph_widget = GraphWidget(graph, pos, vprops=vprops, vertex_size=50)
self.game_flow_panel.pack_start(Gtk.Label('gameflow'), False, False, 0)
self.game_flow_panel.pack_start(graph_widget, True, True, 0)
self.show_all()
def create_graph_visualizations(self, dur='week'):
gc = Graph_Creator(dur)
d = 'weekly'
if dur == 'day':
d = 'daily'
graphs = gc.create_culumative_graphs()
sorted_dates = sorted(graphs.iterkeys())
for i, date in enumerate(sorted_dates):
pos = gtdraw.sfdp_layout(graphs[date])
gtdraw.graph_draw(graphs[date],
pos=pos,
output=project_folder + 'outputs/' + d + '/' +
str(i) + '.png')
def plot_graph(self,
fname,
g=None,
size=1000,
fsize=16,
vsize=8,
ptype="pdf",
method='arf'):
"""
plot the grap (needs more tuning options
:Parameter:
- fname : filename (will write filename.pdf)
- size : outputsize will be (size, size) in px [default 800]
- fsize : font size [default 10]
- method : placement method to draw graph, can be one of
arf
frucht
radtree
sfdp
random
"""
if g:
draw_g = g
else:
draw_g = self.molg
import graph_tool.draw
import graph_tool.draw as gt
g = draw_g
if method == 'arf':
pos = graph_tool.draw.arf_layout(draw_g, max_iter=0)
elif method == 'frucht':
pos = graph_tool.draw.fruchterman_reingold_layout(draw_g,
n_iter=1000)
elif method == 'radtree':
pos = gt.radial_tree_layout(g, g.vertex(0))
elif method == 'sfdp':
pos = gt.sfdp_layout(g)
elif method == 'sfdp':
pos = gt.random_layout(g)
else:
pos = None
from graph_tool.draw import graph_draw
graph_draw(draw_g,pos=pos, vertex_text=draw_g.vp.type, vertex_font_size=fsize, vertex_size=vsize, \
output_size=(size, size), output=fname+"."+ptype, bg_color=[1,1,1,1])
return
def draw_clustering(graph, filename=None, pos=None, vmore=None,
emore=None, show_filling=False, curved=False,
cluster_index_name='cluster', osize=800):
# graph.set_edge_filter(graph.ep['fake'], inverted=True)
pos = pos or gtdraw.sfdp_layout(graph)
vertex_options = {'pen_width': 0}
vertex_options.update(add_cluster_name_and_color(graph,
cluster_index_name))
name = graph.new_vertex_property('string')
for i, v in enumerate(graph.vertices()):
name[v] = str(i)
if np.unique(graph.vp[cluster_index_name].a).size < 2:
vertex_options['text'] = name
if vmore:
vertex_options.update(vmore)
# d = count_disagreements(graph, alt_index=cluster_index_name)
# if not show_filling:
# graph.set_edge_filter(graph.ep['fake'], inverted=True)
# print(str(d.a.sum().ravel()[0]) + ' disagreements')
if not show_filling:
edge_options = {'pen_width': 2}
else:
edge_width = graph.new_edge_property('float')
for e in graph.edges():
if not graph.ep['fake'][e]:
edge_width[e] = 6
else:
edge_width[e] = 3 # if graph.ep['sign'][e] else 1
edge_options = {'pen_width': edge_width}
edge_options.update(add_edge_sign_color(graph))
# edge_options.update(add_edge_disagreement_size(graph, d))
if emore:
edge_options.update(emore)
more_opts = {}
if curved:
from math import sqrt
control = graph.new_edge_property("vector<double>")
for e in graph.edges():
d = sqrt(sum((pos[e.source()].a - pos[e.target()].a) ** 2)) / 5
control[e] = [0.3, d, 0.7, .5*d]
more_opts['edge_control_points'] = control
gtdraw.graph_draw(graph, pos=pos, vprops=vertex_options,
eprops=edge_options, output=filename, fit_view=True,
output_size=(osize, int(0.7*osize)), inline=True,
**more_opts)
def planted_clusters(ball_size=12, nb_balls=5, pos=False, p=0.07):
new_graph()
true_cluster = {}
balls = [make_ball(true_cluster, ball_size) for _ in range(nb_balls-1)]
filling = int(1.1*ball_size*nb_balls) - len(redensify.G)
if filling > 0:
balls.append(make_ball(true_cluster, filling, exact=True))
if pos:
from graph_tool import draw as gtdraw
redensify.EDGES_ORIG = list(redensify.EDGES_SIGN.keys())
redensify.N = len(redensify.G)
k = to_graph_tool()
pos = gtdraw.sfdp_layout(k).get_2d_array([0, 1])
for b1, b2 in combinations(balls, 2):
link_balls(b1, b2)
flip_random_edges(p)
finalize_graph()
return true_cluster, pos
def visualize(self, graph_view, outfile, drawing_props):
g = graph_view
props = self.process_drawing_properties(g, drawing_props)
out = os.path.join(
self.results_path, 'sfdp_' + drawing_props['props_type'] + '_' +
outfile + '.' + props['fmt'])
os.makedirs(os.path.dirname(out), exist_ok=True)
pos = sfdp_layout(g)
try:
if len(list(g.vertices())) > 0:
graph_draw(g,
pos,
vprops=props['vprops'],
eprops=props['eprops'],
output_size=(props['output_width'],
props['output_height']),
output=out)
except Exception as e:
print(e)
def build_model(vkapi: vk.API, user_for_analyse: dict):
friend_list, friend_links = __prepare_data(vkapi, user_for_analyse)
graph = Graph(directed=False)
vmap = graph.add_edge_list(friend_links.values, hashed=True)
state = minimize_blockmodel_dl(graph)
layout = sfdp_layout(graph, groups=state.b)
state.draw(pos=layout,
vertex_text=vmap,
vertex_font_size=3,
vertex_size=3,
vertex_color=[128, 128, 128, 1],
output_size=(2000, 2000),
output="graph.svg")
with open("graph.svg", 'r') as source:
graph_image = source.read()
os.remove("graph.svg")
return graph_image
def draw_similarity_graph(g):
state = minimize_blockmodel_dl(g)
b = state.b
pos = sfdp_layout(g, eweight=g.edge_properties['sim'])
graph_draw(g,
pos,
output_size=(1000, 1000),
vertex_color=[1, 1, 1, 0],
vertex_size=g.vertex_properties['freq'],
edge_pen_width=1.2,
vcmap=matplotlib.cm.gist_heat_r,
output="word_similarity.png")
state = minimize_blockmodel_dl(g)
graph_draw(g,
pos=pos,
vertex_fill_color=b,
vertex_shape=b,
output="blocks_mdl.png")
def plot(self, output_file_with_extension: Optional[str] = None):
"""
To return a graph image
:param output_file_with_extension: the output file name with extension
:return: str
"""
self._logger.info("Graph to image")
pos = sfdp_layout(self)
graph_draw(
self,
pos=pos,
vertex_shape="circle",
vertex_size=3,
vertex_anchor=0,
vertex_color="white",
vertex_fill_color=(0, 0, 0, 1), # normalized values
vertex_pen_width=1,
edge_color=(1, 0, 0, 1),
bg_color=(0, 0, 0, 1),
output_size=[1024, 1024],
output=output_file_with_extension,
)
def plotg(g, layout='sfdp', pos=True):
gg = lg2gt(g)
if not pos:
if layout == 'fr':
pos = gtd.fruchterman_reingold_layout(gg)
else:
pos = gtd.sfdp_layout(gg)
else:
pos = gg.new_vertex_property("vector<double>")
n = gg.num_vertices()
s = 2.0 * np.pi / n
for v in range(gg.num_vertices()):
idx = int(gg.vertex_properties['label'][gg.vertex(v)]) - 1
pos[gg.vertex(v)] = (n * np.cos(s * idx), n * np.sin(s * idx))
gtd.graph_draw(gg,
pos,
vertex_text=gg.vertex_properties['label'],
vertex_font_size=32,
edge_pen_width=1,
edge_marker_size=15,
vertex_pen_width=1,
vertex_fill_color=[0.62109375, 0.875, 0.23828125, 1])
def step_layout(self, dt):
sfdp_layout(self.G,
pos=self.G.vp.pos,
pin=self.G.vp.pinned,
**SFDP_SETTINGS)
def main():
options = parse_arguments()
clusters_enabled = options["mapping_location"] is not None
if options["should_merge"] and not clusters_enabled:
raise "You need to provide a mapping to use merged view.`"
# Get the string containing the input matrix form a file/pipe
if options["matrix_location"] is not None:
with open(options["matrix_location"], 'r') as file:
matrix_string = file.read().strip().split("\n")
else:
matrix_string = sys.stdin
# Parse the input matrix string
height, width, matrix = parse_matrix(matrix_string, options["has_size"])
# Get the string containing the mapping if specified
if clusters_enabled:
with open(options["mapping_location"], 'r') as file:
mapping_string = file.read().strip()
mapping = parse_mapping(mapping_string, options["has_size"])
else:
mapping = None
if options["should_merge"]:
height, width, matrix, mapping = merge_clusters(matrix, mapping)
graph = Graph()
graph.add_vertex(height + width)
shape = graph.new_vertex_property("string")
color = graph.new_vertex_property("string")
index = graph.new_vertex_property("string")
for i in range(height):
v = graph.vertex(i)
shape[v] = "square"
color[v] = "red"
index[v] = str(i)
for i in range(width):
v = graph.vertex(height + i)
shape[v] = "circle"
if clusters_enabled:
color[v] = COLORS[mapping[i] % len(COLORS)]
else:
color[v] = COLORS[0]
index[v] = str(i)
for i in range(height):
for j in range(width):
if abs(matrix[i][j]) < EPSILON:
continue
graph.add_edge(graph.vertex(i), graph.vertex(height + j))
graph.set_directed(False)
if clusters_enabled:
groups = graph.new_vertex_property("int")
for i in range(width):
v = graph.vertex(height + i)
groups[v] = mapping[i]
position = sfdp_layout(graph, groups=groups)
else:
position = None
graph_draw(graph,
pos=position,
vertex_text=index,
vertex_shape=shape,
vertex_fill_color=color,
vertex_pen_width=1.2,
vertex_color="black",
edge_pen_width=3.4,
fit_view=True,
bg_color=(255, 255, 255, 1),
output=options["output_file"])
def draw_for(self, phase: Phase, model: GameModel):
self.log.debug('drawing phase flow {0}'.format(phase.name))
TMPUTILS.clear_container(self.main_panel)
top = Gtk.HBox()
name = Gtk.Label(phase.name)
top.pack_start(name, True, True, 0)
refresh_button = Gtk.Button('Refresh')
refresh_button.connect('clicked', lambda w: self.draw_for(phase, model))
top.pack_start(refresh_button, True, True, 0)
self.main_panel.pack_start(top, False, False, 0)
#TMPUTILS.start_rule_color = TMPUTILS.rule_color
#start = phase.rules[0]
#start = Rule('Początek {0}'.format(phase.name))
start = Rule('Start {0}'.format(phase.name))
start.next = phase.rules
phase.rules = [start]
rules_set = phase.all_rules_set()
phase.rules = start.next
graph = Graph()
graph.vp.name = graph.new_vertex_property('string')
graph.vp.fullname = graph.new_vertex_property('string')
graph.vp.color = graph.new_vertex_property('string')
graph.vp.shape = graph.new_vertex_property('string')
graph.vp.rotation = graph.new_vertex_property('float')
graph.vp.text_pos = graph.new_vertex_property('float')
graph.vp.text_rotation = graph.new_vertex_property('float')
graph.ep.text = graph.new_edge_property('string')
graph.ep.text_color = graph.new_edge_property('string')
rule_vertex = {}
self.vertex_rule = {}
for rule in rules_set:
vertex = graph.add_vertex()
rule_vertex[rule] = vertex
self.vertex_rule[vertex] = rule
graph.vp.name[vertex] = rule.verticle_name()
graph.vp.fullname[vertex] = rule.name
if rule is start:
color = self.config.start_rule_color()
elif issubclass(rule.__class__, ChangePhase):
color = TMPUTILS.end_rule_color(rule, model)
elif len([r for k, v in rule.rules_dict().items() for r in v]) == 0:
color = self.config.wrong_rule_color()
else:
color = TMPUTILS.rule_color()
graph.vp.color[vertex] = color
#graph.vp.shape[vertex] = 'square' if issubclass(rule.__class__, If) else 'circle'
graph.vp.shape[vertex] = self.config.rule_shape(rule)
#graph.vp.rotation[vertex] = pi / 4 if issubclass(rule.__class__, If) else 0
graph.vp.rotation[vertex] = self.config.rule_rotation(rule)
graph.vp.text_pos[vertex] = 0
#graph.vp.text_rotation[vertex] = - pi / 4 if issubclass(rule.__class__, If) else 0
graph.vp.text_rotation[vertex] = self.config.rule_text_rotation(rule)
for rule in rules_set:
for next_text, next_rule_list in rule.rules_dict().items():
for next_rule in next_rule_list:
edge = graph.add_edge(rule_vertex[rule], rule_vertex[next_rule])
#as_polish = {'No': "Nie", 'Yes': "Tak"}
#graph.ep.text[edge] = as_polish[next_text] if next_text in as_polish else next_text
graph.ep.text[edge] = next_text
graph.ep.text_color[edge] = TMPUTILS.text_color(next_text)
pos = sfdp_layout(graph)
vprops = {
'text': graph.vp.name,
'fill_color': graph.vp.color,
'shape': graph.vp.shape,
'rotation': graph.vp.rotation,
'text_position': graph.vp.text_pos,
'text_rotation': graph.vp.text_rotation
}
eprops = {
'text': graph.ep.text,
'text_color': graph.ep.text_color
}
self.graph_widget = GraphWidget(graph, pos, display_props=[graph.vp.fullname], vprops=vprops, eprops=eprops,
vertex_size=50)
#jest cos takiego jak GraphWidget.key_press_callback ale u mnie nie dziala...
self.graph_widget.connect('button-release-event', self.on_vertex_clicked)
self.main_panel.pack_start(self.graph_widget, True, True, 0)
self.show_all()
def draw_for(self, sender, model: GameModel):
self.log.debug('drawing place map for model {0}'.format(model.name))
TMPUTILS.clear_container(self.main_panel)
refresh_button = Gtk.Button('Refresh')
refresh_button.connect('clicked',
lambda w: self.draw_for(sender, model))
self.main_panel.pack_start(refresh_button, False, False, 0)
all_places = set()
for player_type in model.player_types + [model.table_type]:
for place in player_type.places:
all_places.add(place)
place_vertex = {}
graph = Graph()
graph.vp.name = graph.new_vertex_property('string')
graph.vp.color = graph.new_vertex_property('string')
graph.vp.text_pos = graph.new_vertex_property('float')
graph.ep.color = graph.new_edge_property('vector<float>')
for place in all_places:
vertex = graph.add_vertex()
place_vertex[place] = vertex
graph.vp.name[vertex] = place.name
graph.vp.color[vertex] = TMPUTILS.table_color(
) if place in model.table_type.places else TMPUTILS.player_color()
graph.vp.text_pos[vertex] = 0
self.graph = graph
self.place_vertex = place_vertex
self.rule_edge = {}
for phase in model.all_phases():
for source, target, rule in self.edge_info_for_phase(phase):
edge = graph.add_edge(place_vertex[source],
place_vertex[target])
if rule not in self.rule_edge:
self.rule_edge[rule] = []
self.rule_edge[rule].append(edge)
graph.ep.color[edge] = [0.179, 0.203, 0.210, 0.8]
pos = sfdp_layout(graph)
vprops = {
'text': graph.vp.name,
'fill_color': graph.vp.color,
'text_position': graph.vp.text_pos,
}
eprops = {'color': graph.ep.color}
self.graph_widget = GraphWidget(graph,
pos,
vprops=vprops,
eprops=eprops,
vertex_size=50)
self.main_panel.pack_start(self.graph_widget, True, True, 0)
self.show_all()
def render_graph(g, path='graph/{}.pdf'):
# the simplest way
arg_map = dict(
g = g,
output = path.format('1-1-random-simplest'),
)
graph_draw(**arg_map)
# use constants
arg_map.update(dict(
output = path.format('1-2-random-constant'),
output_size = (SIZE, SIZE),
vertex_size = MA_V_SIZE,
edge_pen_width = MA_E_PWIDTH,
))
graph_draw(**arg_map)
# use prop_to_size
v_count_p = g.vp['count']
e_count_p = g.ep['count']
v_size_by_count_p = prop_to_size(v_count_p, MI_V_SIZE, MA_V_SIZE)
e_pwidth_by_count_p = prop_to_size(e_count_p, MI_E_PWIDTH, MA_E_PWIDTH)
arg_map.update(dict(
output = path.format('1-3-random-size'),
vertex_size = v_size_by_count_p,
edge_pen_width = e_pwidth_by_count_p,
))
graph_draw(**arg_map)
# use fill_color
debug('v_count_p.a : {}', v_count_p.a)
v_color_by_count_p = prop_to_size(v_count_p, 0, 1)
debug('v_color_by_count_p.a: {}', v_color_by_count_p.a)
arg_map.update(dict(
output = path.format('1-4-random-color'),
vertex_fill_color = v_color_by_count_p,
))
graph_draw(**arg_map)
# use closeness
v_closeness_p = g.vp['closeness']
v_color_by_closeness_p = prop_to_size(v_closeness_p, 0, 1)
#closeness_arg_map = arg_map.copy()
#closeness_arg_map.update(dict(
# output = path.format('1-5-random-closeness'),
# vertex_fill_color = v_color_by_closeness_p,
#))
arg_map.update(dict(
output = path.format('1-5-random-closeness'),
vertex_fill_color = v_color_by_closeness_p,
))
graph_draw(**arg_map)
# sfdp_layout
arg_map.update(dict(
output = path.format('2-1-sfdp'),
pos = sfdp_layout(g),
))
graph_draw(**arg_map)
# sfdp_layout with only edge's weight
arg_map.update(dict(
output = path.format('2-2-sfdp-edge-weight'),
pos = sfdp_layout(g, eweight=e_count_p),
))
graph_draw(**arg_map)
# sfdp_layout with both edge and vertex's weight
arg_map.update(dict(
output = path.format('2-3-sfdp-both-weight'),
pos = sfdp_layout(g, eweight=e_count_p, vweight=v_count_p),
))
graph_draw(**arg_map)
# fruchterman_reingold_layout
arg_map.update(dict(
output = path.format('3-1-fr'),
pos = fruchterman_reingold_layout(g),
))
graph_draw(**arg_map)
# fruchterman_reingold_layout with edge's weight
arg_map.update(dict(
output = path.format('3-2-fp-edge-weight'),
pos = fruchterman_reingold_layout(g, weight=e_count_p),
))
graph_draw(**arg_map)
# arf_layout
arg_map.update(dict(
output = path.format('4-1-arf'),
pos = arf_layout(g),
))
graph_draw(**arg_map)
# arf_layout with edge's weight
arg_map.update(dict(
output = path.format('4-2-arf-edge-weight'),
pos = arf_layout(g, weight=e_count_p),
))
graph_draw(**arg_map)
def visualisation(g, subtree_height=2):
from cc_pivot import draw_clustering
import draw_utils as du
from graph_tool import draw as gdraw
import graph_tool as gt
import numpy as np
import seaborn as sns
G, E = cexp.redensify.G, cexp.redensify.EDGES_SIGN
root = 16
Gbfs, parents, tree = initial_spanning_tree(G, root)
ecol, esize = du.color_graph(g, tree)
tmap = du.map_from_list_of_edges(g, tree)
g.set_edge_filter(tmap)
tpos = gdraw.sfdp_layout(g)
g.set_edge_filter(None)
ecol, esize = du.color_graph(g, tree)
g_halo = g.new_vertex_property('bool')
g_halo.a[root] = True
draw_clustering(g, pos=tpos, vmore={'size': 22, 'halo': g_halo},
emore={'pen_width': esize, 'color': ecol, }, osize=900)
Bparent = deepcopy(parents)
Bg = deepcopy(Gbfs)
for u in Bg:
p = Bparent[u]
Bg[u].discard(p)
dtree, height, strees = dfs_of_a_tree(Bg, root, Bparent, subtree_height)
cols = sns.color_palette('rainbow', len(strees))
random.shuffle(cols)
ecol, esize = du.color_graph(g, tree)
for e in tree:
ge = g.edge(*e)
ecol[ge] = du.light_gray # [.25,.25,.25,.8]
esize[ge] = 1.5
for st, c in zip(strees, cols):
for u, v in ((u, v) for u, v in st.items() if v is not None):
ge = g.edge(u, v)
ecol[ge] = c
esize[ge] = 3
draw_clustering(g, pos=tpos, vmore={'size': 22},
emore={'pen_width': esize, 'color': ecol}, osize=900)
tree_membership = {u: i for i, st in enumerate(strees) for u in st}
tree_root = [[k for k, v in t.items() if v is None][0] for t in strees]
support_tree = []
for st in strees:
support_tree.append({(u, v) if u < v else (v, u)
for u, v in st.items() if v is not None})
within_tree, across_trees = bipartition_edges(E, strees, tree_membership, support_tree)
Gt = {i: set() for i, u in enumerate(strees)}
Et = {e: random.choice(list(candidates))
for e, candidates in across_trees.items()}
for e, n in Et.items():
add_edge(Gt, *e)
k = gt.Graph(directed=False)
k.add_vertex(len(strees))
names = k.new_vertex_property('string')
vcols = k.new_vertex_property('vector<double>')
etext = k.new_edge_property('string')
prev_pos = tpos.get_2d_array((0, 1))
new_pos = np.zeros((2, len(strees)))
stpos = k.new_vertex_property('vector<double>')
for i, (stree_prt, root) in enumerate(zip(strees, tree_root)):
v = k.vertex(i)
members = sorted(stree_prt.keys())
mpos = prev_pos[:, members]
new_pos[:, i] = mpos.mean(1)
stpos[v] = prev_pos[:, root] # mpos.mean(1)
names[v] = str(root)
vcols[v] = list(cols[i]) + [.9, ]
for e, n in Et.items():
ke = k.add_edge(*e)
etext[ke] = str(n)
gdraw.graph_draw(k, stpos, eprops={'text': etext}, output_size=(800, 800),
vprops={'pen_width': 0, 'text': names, 'fill_color': vcols, 'size': 24})
stars, _, star_membership = extract_stars(Gt)
within_star, across_stars = bipartition_edges(Et, stars, star_membership)
scols, ssize = k.new_edge_property('vector<double>'), k.new_edge_property('double')
cols_s = sns.color_palette('Set1', len(stars))
star_halo = k.new_vertex_property('bool')
star_halo.a = np.zeros(k.num_vertices())
for s in stars:
star_halo[g.vertex(s.center)] = True
for e in k.edges():
u, v = int(e.source()), int(e.target())
su, sv = star_membership[u], star_membership[v]
if su == sv and stars[su].center in [u, v]:
scols[e], ssize[e] = list(cols_s[su]) + [.9, ], 3
else:
scols[e], ssize[e] = [.2, .2, .2, .8], 1
stext = k.new_edge_property('string')
vs_cols = k.new_vertex_property('vector<double>')
for u in k.vertices():
vs_cols[u] = list(cols_s[star_membership[int(u)]]) + [.9]
for candidates in across_stars.values():
chosen = sorted(candidates)[0]
ke = k.edge(*chosen)
ssize[ke] = 3
stext[ke] = str(Et[chosen])
scols[ke] = du.black
gdraw.graph_draw(k, stpos, vprops={'pen_width': 0, 'text': names, 'fill_color': vs_cols, 'size': 24, 'halo': star_halo},
eprops={'pen_width': ssize, 'color': scols, 'text': stext}, output_size=(800, 800))
def draw_network(network,
nsize="total-degree",
ncolor="group",
nshape="o",
nborder_color="k",
nborder_width=0.5,
esize=1.,
ecolor="k",
spatial=True,
size=(600, 600),
dpi=75):
'''
Draw a given graph/network.
Parameters
----------
network : :class:`~nngt.Graph` or subclass
The graph/network to plot.
nsize : float, array of floats or string, optional (default: "total-degree")
Size of the nodes; if a number, percentage of the canvas length,
otherwize a string that correlates the size to a node attribute among
"in/out/total-degree", "betweenness".
ncolor : float, array of floats or string, optional (default: 0.5)
Color of the nodes; if a float in [0, 1], position of the color in the
current palette, otherwise a string that correlates the color to a node
attribute among "in/out/total-degree", "betweenness" or "group".
nshape : char or array of chars, optional (default: "o")
Shape of the nodes (see `Matplotlib markers <http://matplotlib.org/api/markers_api.html?highlight=marker#module-matplotlib.markers>`_).
nborder_color : char, array of char, float or array of float, optional (default: "k")
Color of the node's border using predefined `Matplotlib colors <http://matplotlib.org/api/colors_api.html?highlight=color#module-matplotlib.colors>`_).
or floats in [0, 1] defining the position in the palette.
nborder_width : float or array of floats, optional (default: 0.5)
Width of the border in percent of canvas size.
esize : float or array of floats, optional (default: 0.5)
Width of the edges in percent of canvas size.
ecolor : char, array of char, float or array of float, optional (default: "k")
Edge color.
spatial : bool, optional (default: True)
If True, use the neurons' positions to draw them.
size : tuple of ints, optional (default: (600,600))
(width, height) tuple for the canvas size (in px).
dpi : int, optional (default: 75)
Resolution (dot per inch).
'''
pos, layout = None, None
n = network.node_nb()
e = network.edge_nb()
# compute properties
if issubclass(str, nsize.__class__):
if e:
nsize = _node_size(network, nsize)
nsize.a *= 0.01 * size[0]
elif issubclass(float, nsize.__class__):
nsize = np.repeat(nsize, n)
if issubclass(str, esize.__class__):
if e:
esize = _edge_size(network, esize)
esize.a *= 0.01 * size[0]
elif issubclass(float, esize.__class__):
esize = np.repeat(esize, e)
esize = network.new_edge_property("double", esize)
ncolor = _node_color(network, ncolor)
if issubclass(float, nborder_color.__class__):
nborder_color = np.repeat(nborder_color, n)
if issubclass(float, ecolor.__class__):
ecolor = np.repeat(ecolor, e)
# draw
pos = np.zeros((n, 2))
if not e:
nsize = 0.02 * size[0]
esize = 0.01 * size[0]
if spatial and network.is_spatial():
pos = network[POS]
else:
pos[:, 0] = size[0] * (np.random.uniform(size=n) - 0.5)
pos[:, 1] = size[1] * (np.random.uniform(size=n) - 0.5)
elif spatial and network.is_spatial():
pos = network.position.T
pos = network.new_vertex_property("vector<double>", pos)
else:
ebetw = network.betweenness_list(as_prop=True)[1]
pos = gplot.sfdp_layout(network, eweight=ebetw)
if not e:
size_inches = (size[0] / float(dpi), size[1] / float(dpi))
fig = plt.figure(facecolor='white', figsize=size_inches, dpi=dpi)
ax = fig.add_subplot(111, frameon=0, aspect=1)
fig.facecolor = "white"
fig.figsize = size
ax.set_axis_off()
if hasattr(network, "population"):
for group in network.population.itervalues():
idx = group.id_list
ax.scatter(pos[idx, 0],
pos[idx, 1],
s=nsize,
color=palette(ncolor[idx[0]]))
else:
ax.scatter(pos[:, 0], pos[:, 1], s=nsize)
ax.set_xlim([-0.51 * size[0], 0.51 * size[0]])
ax.set_ylim([-0.51 * size[1], 0.51 * size[1]])
plt.show()
elif spatial and network.is_spatial():
gplot.graph_draw(network,
pos=pos,
vertex_color=nborder_color,
vertex_fill_color=ncolor,
vertex_size=nsize,
edge_color=ecolor,
edge_pen_width=esize,
output_size=size)
else:
gplot.graph_draw(network,
pos=pos,
vertex_color=nborder_color,
vertex_fill_color=ncolor,
vertex_size=nsize,
edge_color=ecolor,
edge_pen_width=esize,
output_size=size)
def _test():
import numpy as np
import ClearMap.Tests.Files as tf
import ClearMap.Analysis.Graphs.GraphProcessing as gp
#reload(gp)
skeleton = tf.source('skeleton');
#import ClearMap.Visualization.Plot3d as p3d
#p3d.plot(skeleton)
#reload(gp)
g = gp.graph_from_skeleton(skeleton)
g.vertex_coordinates()
s = gp.graph_to_skeleton(g)
assert np.all(s==skeleton)
gc = gp.clean_graph(g, verbose=True)
gr = gp.reduce_graph(gc, verbose=True)
gr2 = gr.copy();
gr2.set_edge_geometry_type('edge')
l = gr.edge_geometry_lengths();
print(l)
g = gp.ggt.Graph(n_vertices=10);
g.add_edge(np.array([[7,8],[7,9],[1,2],[2,3],[3,1],[1,4],[4,5],[2,6],[6,7]]));
g.set_vertex_coordinates(np.array([[10,10,10],[0,0,0],[1,1,1],[1,1,0],[5,0,0],[8,0,1],[0,7,1],[0,10,2],[0,12,3],[3,7,7]], dtype=float));
import ClearMap.Visualization.Plot3d as p3d
p3d.plot_graph_line(g)
gc = gp.clean_graph(g, verbose=True);
p3d.plot_graph_line(gc)
gr = gp.reduce_graph(gc, edge_geometry=True, verbose=True)
#gr.set_edge_geometry(0.1*np.ones(gr.edge_geometry(as_list=False).shape[0]), 'radii')
import ClearMap.Visualization.Plot3d as p3d
vertex_colors = np.random.rand(g.n_vertices, 4);
vertex_colors[:,3] = 1;
p3d.plot_graph_mesh(gr, default_radius=1, vertex_colors=vertex_colors)
eg = gr.edge_geometry(as_list=False);
egs = 0.5 * eg;
gr.set_edge_geometry(name='coordinates', values=egs)
#tracing
import numpy as np
import ClearMap.Visualization.Plot3d as p3d
import ClearMap.Analysis.Graphs.GraphProcessing as gp
g = gp.ggt.Graph(n_vertices=10);
g.add_edge(np.array([[0,1],[1,2],[2,3],[3,4],[4,0],[0,5],[5,6],[6,7],[0,8],[8,9],[9,0]]));
g.set_vertex_coordinates(np.array([[0,0,0],[1,0,0],[2,0,0],[2,2,0],[0,1,0],[0,0,1],[0,0,2],[0,0,3],[0,-1,0],[0,-1,-1]], dtype=float));
g.set_vertex_radii(np.array([10,6,4,6,7,4,2,2,5,5]) * 0.02)
vertex_colors = np.array([g.vertex_radii()]*4).T; vertex_colors = vertex_colors / vertex_colors.max(); vertex_colors[:,3] = 1;
p3d.plot_graph_mesh(g, default_radius=1, vertex_colors=vertex_colors)
def condition(graph, vertex):
r = graph.vertex_radii(vertex=vertex);
print('condition, vertex=%d, radius=%r' % (vertex,r))
return r >= 5 * 0.02;
label = np.zeros(g.n_vertices, dtype=bool);
label[0] = True;
traced = gp.trace_vertex_label(g, label, condition=condition, steps=1)
print(traced)
vertex_colors = np.array([[1,0,0,1],[1,1,1,1]])[np.asarray(traced, dtype=int)]
p3d.plot_graph_mesh(g, default_radius=1, vertex_colors=vertex_colors)
from importlib import reload;
reload(gp)
# edge tracing
import ClearMap.Analysis.Graphs.GraphGt as ggt
edges = [[0,1],[1,2],[2,3],[4,5],[5,6],[1,7]];
g = ggt.Graph(edges=edges)
l,m = g.edge_graph(return_edge_map=True);
import numpy as np
label = np.zeros(len(edges), dtype=bool);
label[1] = True;
import ClearMap.Analysis.Graphs.GraphProcessing as gp
def condition(graph, edge):
print('condition, edge=%d' % (edge,))
return True;
traced = gp.trace_edge_label(g, label, condition=condition);
print(traced)
# expansion of edge lengths
import numpy as np
import ClearMap.Tests.Files as tf
import ClearMap.Analysis.Graphs.GraphProcessing as gp
graph = gp.ggt.Graph(n_vertices=5);
graph.add_edge([[0,1],[0,2],[0,3],[2,3],[2,1],[0,4]]);
graph.add_edge_property('length', np.array([0,1,2,3,4,5])+2);
e, m = gp.expand_graph_length(graph, 'length', True)
import graph_tool.draw as gd
pos = gp.ggt.vertex_property_map_to_python(gd.sfdp_layout(e.base))
import matplotlib.pyplot as plt
plt.figure(1); plt.clf();
import matplotlib.collections as mc
import ClearMap.Visualization.Color as col
colors = np.array([col.color(c) for c in ['red', 'blue', 'green', 'black', 'purple', 'orange']])
ec = e.edge_connectivity();
lines = pos[ec];
cols = colors[m];
lc = mc.LineCollection(lines, linewidths=1, color=cols);
ax = plt.gca();
ax.add_collection(lc)
ax.autoscale()
ax.margins(0.1)
plt.scatter(pos[:,0], pos[:,1])
p =pos[:graph.n_vertices]
plt.scatter(p[:,0],p[:,1], color='red')
gtg = g.return_gt_graph()
g.v['deg'] = gtg.degree_property_map('total').a
# how many "actors" are there per layer?
g.v[g.v.deg != 0].groupby('layer').size()
# In[12]:
# create graph_tool graph for layout
import graph_tool.draw as gtd
gtg = g.return_gt_graph()
gtg.set_directed(False)
# get sfdp layout postitions
pos = gtd.sfdp_layout(gtg, gamma=.5)
pos = pos.get_2d_array([0, 1])
g.v['x'] = pos[0]
g.v['y'] = pos[1]
# configure nodes
kwds_scatter = {'s': 1,
'c': 'k'}
# configure edges
kwds_quiver = {'headwidth': 1,
'alpha': .3,
'cmap': 'prism'}
# color by type
C = g.e.groupby('type').grouper.group_info[0]
from Orange.data import Table
matplotlib.use('Agg')
from graph_tool.draw import sfdp_layout, graph_draw
from induce_graph import induce_graph, cutoff
iris = Table('iris')
graph = induce_graph(iris)
graph_1 = cutoff(graph, 0.1)
graph_2 = cutoff(graph, 0.2)
graph_3 = cutoff(graph, 0.3)
vertex_layout = sfdp_layout(graph_2)
rgb_colors = ([[70, 190, 250]] * 50) + ([[237, 70, 47]] *
50) + ([[170, 242, 43]] * 50)
rgb_colors = [[r / 255, g / 255, b / 255] for r, g, b in rgb_colors]
colors = graph_1.new_vertex_property('vector<double>')
for node, color in zip(graph_1.vertices(), rgb_colors):
colors[node] = color
graph_draw(graph_1,
vertex_layout,
vertex_fill_color=colors,
output='iris_threshold_01.png',
output_size=(600, 400))
graph_draw(graph_2,
'''
Plot the graph
'''
if nngt.get_config("with_plot"):
import matplotlib.pyplot as plt
colors = np.zeros(num_nodes)
colors[500:] = 1
if nngt.get_config("backend") == "graph-tool":
from graph_tool.draw import graph_draw, prop_to_size, sfdp_layout
pm = net.new_vertex_property("int", colors)
size = net.new_vertex_property("double", val=5.)
pos = sfdp_layout(net, groups=pm, C=1., K=20, gamma=5, mu=20)
graph_draw(net, pos=pos, vertex_fill_color=pm, vertex_color=pm,
vertex_size=size, nodesfirst=True,
edge_color=[0.179, 0.203,0.210, 0.3])
elif nngt.get_config("backend") == "networkx":
import networkx as nx
plt.figure()
init_pos = {i: np.random.uniform(-1000., -900, 2) for i in range(500)}
init_pos.update(
{i: np.random.uniform(900., 1000, 2) for i in range(500, 1000)})
layout = nx.spring_layout(net, k=20, pos=init_pos)
nx.draw(net, pos=layout, node_color=colors, node_size=20)
elif nngt.get_config("backend") == "igraph":
import igraph as ig
colors = [(1, 0, 0) for _ in range(500)]
colors.extend([(0, 0, 1) for _ in range(500)])
def mydraw():
pos = draw.sfdp_layout(tree)
draw.graph_draw(tree, pos=pos, vertex_fill_color=tubuline)
draw.graph_hist, bins = np.histogram(samples, bins=50)
# append degree
gtg = g.return_gt_graph()
g.v['deg'] = gtg.degree_property_map('total').a
# how many "actors" are there per layer?
g.v[g.v.deg != 0].groupby('layer').size()
# In[12]:
# create graph_tool graph for layout
import graph_tool.draw as gtd
gtg = g.return_gt_graph()
gtg.set_directed(False)
# get sfdp layout postitions
pos = gtd.sfdp_layout(gtg, gamma=.5)
pos = pos.get_2d_array([0, 1])
g.v['x'] = pos[0]
g.v['y'] = pos[1]
# configure nodes
kwds_scatter = {'s': 1, 'c': 'k'}
# configure edges
kwds_quiver = {'headwidth': 1, 'alpha': .3, 'cmap': 'prism'}
# color by type
C = g.e.groupby('type').grouper.group_info[0]
# plot
fig, ax = plt.subplots(1, 2, figsize=(15, 7))
g.plot_2d('x',
def draw_network(network, nsize="total-degree", ncolor="group", nshape="o",
nborder_color="k", nborder_width=0.5, esize=1., ecolor="k",
spatial=True, size=(600,600), dpi=75):
'''
Draw a given graph/network.
Parameters
----------
network : :class:`~nngt.Graph` or subclass
The graph/network to plot.
nsize : float, array of floats or string, optional (default: "total-degree")
Size of the nodes; if a number, percentage of the canvas length,
otherwize a string that correlates the size to a node attribute among
"in/out/total-degree", "betweenness".
ncolor : float, array of floats or string, optional (default: 0.5)
Color of the nodes; if a float in [0, 1], position of the color in the
current palette, otherwise a string that correlates the color to a node
attribute among "in/out/total-degree", "betweenness" or "group".
nshape : char or array of chars, optional (default: "o")
Shape of the nodes (see `Matplotlib markers <http://matplotlib.org/api/markers_api.html?highlight=marker#module-matplotlib.markers>`_).
nborder_color : char, array of char, float or array of float, optional (default: "k")
Color of the node's border using predefined `Matplotlib colors <http://matplotlib.org/api/colors_api.html?highlight=color#module-matplotlib.colors>`_).
or floats in [0, 1] defining the position in the palette.
nborder_width : float or array of floats, optional (default: 0.5)
Width of the border in percent of canvas size.
esize : float or array of floats, optional (default: 0.5)
Width of the edges in percent of canvas size.
ecolor : char, array of char, float or array of float, optional (default: "k")
Edge color.
spatial : bool, optional (default: True)
If True, use the neurons' positions to draw them.
size : tuple of ints, optional (default: (600,600))
(width, height) tuple for the canvas size (in px).
dpi : int, optional (default: 75)
Resolution (dot per inch).
'''
pos,layout = None,None
n = network.node_nb()
e = network.edge_nb()
# compute properties
if issubclass(str,nsize.__class__):
if e:
nsize = _node_size(network, nsize)
nsize.a *= 0.01*size[0]
elif issubclass(float, nsize.__class__):
nsize = np.repeat(nsize, n)
if issubclass(str,esize.__class__):
if e:
esize = _edge_size(network, esize)
esize.a *= 0.01*size[0]
elif issubclass(float, esize.__class__):
esize = np.repeat(esize, e)
esize = network.graph.new_edge_property("double",esize)
ncolor = _node_color(network, ncolor)
if issubclass(float, nborder_color.__class__):
nborder_color = np.repeat(nborder_color, n)
if issubclass(float, ecolor.__class__):
ecolor = np.repeat(ecolor, e)
# draw
pos = np.zeros((n,2))
if not e:
nsize = 0.02*size[0]
esize = 0.01*size[0]
if spatial and network.is_spatial():
pos = network[POS]
else:
pos[:,0] = size[0]*(np.random.uniform(size=n)-0.5)
pos[:,1] = size[1]*(np.random.uniform(size=n)-0.5)
elif spatial and network.is_spatial():
pos = network[POS]
pos = network.graph.new_vertex_property("vector<double>",pos)
else:
ebetw = network.graph.betweenness_list(as_prop=True)[1]
pos = gplot.sfdp_layout(network.graph, eweight=ebetw)
if not e:
size_inches = (size[0]/float(dpi),size[1]/float(dpi))
fig = plt.figure(facecolor='white', figsize=size_inches, dpi=dpi)
ax = fig.add_subplot(111, frameon=0, aspect=1)
fig.facecolor = "white"
fig.figsize=size
ax.set_axis_off()
if hasattr(network, "population"):
for group in network.population.itervalues():
idx = group.id_list
ax.scatter(pos[idx,0], pos[idx,1], s=nsize,
color=palette(ncolor[idx[0]]))
else:
ax.scatter(pos[:,0], pos[:,1], s=nsize)
ax.set_xlim([-0.51*size[0],0.51*size[0]])
ax.set_ylim([-0.51*size[1],0.51*size[1]])
plt.show()
elif spatial and network.is_spatial():
gplot.graph_draw(network.graph, pos=pos, vertex_color=nborder_color,
vertex_fill_color=ncolor, vertex_size=nsize, edge_color=ecolor,
edge_pen_width=esize, output_size=size)
else:
gplot.graph_draw(network.graph, pos=pos, vertex_color=nborder_color,
vertex_fill_color=ncolor, vertex_size=nsize, edge_color=ecolor,
edge_pen_width=esize, output_size=size)