def edge_labels(graph_render):
source = graph_render.edge_renderer.data_source
xcoord = bkm.CustomJSTransform(v_func=EDGE_JS_CODE % "0",
args=dict(
provider=graph_render.layout_provider,
source=source))
ycoord = bkm.CustomJSTransform(v_func=EDGE_JS_CODE % "1",
args=dict(
provider=graph_render.layout_provider,
source=source))
source.data['labels'] = [
str(datum) if not pd.isnull(datum) else ''
for datum in source.data['relative_allocation']
]
# Use the transforms to supply coords to a LabelSet
labels = bkm.LabelSet(x=bkt.transform('start', xcoord),
y=bkt.transform('start', ycoord),
text='labels',
text_font_size="12px",
x_offset=0,
y_offset=0,
source=source,
render_mode='canvas')
return labels
def node_labels(graph_render):
source = graph_render.node_renderer.data_source
xcoord = bkm.CustomJSTransform(
v_func=NODE_JS_CODE % "0",
args=dict(provider=graph_render.layout_provider))
ycoord = bkm.CustomJSTransform(
v_func=NODE_JS_CODE % "1",
args=dict(provider=graph_render.layout_provider))
# Use the transforms to supply coords to a LabelSet
labels = bkm.LabelSet(x=bkt.transform('index', xcoord),
y=bkt.transform('index', ycoord),
text='index',
text_font_size="10px",
x_offset=0,
y_offset=-5,
source=source,
render_mode='canvas',
text_align='center')
return labels
def execute_callback(event) -> None:
nonlocal render
nonlocal dependency_source
np.random.seed(0)
all_pathes = nx.all_simple_paths(
graph,
source=f"{source_text.value}",
target=f"{target_text.value}",
cutoff=int(f"{cutoff_text.value}"),
)
pathes: Set = set()
for path in all_pathes:
pathes |= set(path)
subgraph = graph.subgraph(pathes)
render = bkgraphs.from_networkx(subgraph,
nx.spring_layout,
scale=1,
center=(0, 0))
render.node_renderer.glyph = bkmodels.Circle(
size=8, fill_color=bkpalettes.Spectral4[0])
p.renderers.clear()
p.renderers.append(render)
data_table.source = render.node_renderer.data_source
x, y = zip(*render.layout_provider.graph_layout.values())
render.node_renderer.data_source.data["x"] = x
render.node_renderer.data_source.data["y"] = y
labels = bkmodels.LabelSet(x="x",
y="y",
text="index",
source=render.node_renderer.data_source)
p.renderers.append(labels)
dependency_df = df[df["name"].isin(pathes)
& df["parent"].isin(pathes)].drop_duplicates(
subset=["name", "parent"])
dependency_source = bkmodels.ColumnDataSource(dependency_df)
dependency_table.source = dependency_source
def plot_task_communication(trace_events, workers, show_communication=False):
"""
Plots individual tasks on workers into a grid chart (one chart per worker).
:param show_communication: Merge all worker charts into one and plot communication edges.
"""
from bokeh import models, plotting
from bokeh.layouts import gridplot
from pandas import DataFrame
end_time = math.ceil(max([e.time for e in trace_events]))
plots = []
if show_communication:
plot = plotting.figure(plot_width=1200,
plot_height=850,
x_range=(0, end_time),
title='CPU schedules')
plot.yaxis.axis_label = 'Worker'
plot.xaxis.axis_label = 'Time'
plots.append(plot)
def get_worker_plot():
if show_communication:
return plot
else:
p = plotting.figure(plot_width=600,
plot_height=300,
x_range=(0, end_time),
title='Worker task execution')
p.yaxis.axis_label = 'Task'
p.xaxis.axis_label = 'Time'
plots.append(p)
return p
task_to_loc = {}
# render task rectangles
for index, worker in enumerate(workers):
locations = list(build_task_locations(trace_events, worker))
def normalize_height(height):
if show_communication:
return height / (worker.cpus * 2) + index
return height
worker_plot = get_worker_plot()
rectangles = [(rect[0], rect[1], normalize_height(rect[2]),
normalize_height(rect[3]))
for (task, rect) in locations]
render_rectangles(worker_plot, rectangles)
for i, (task, _) in enumerate(locations):
task_to_loc[task] = rectangles[i]
frame = DataFrame()
frame["label"] = [t[0].name for t in locations]
frame["bottom"] = [normalize_height(t[1][2]) for t in locations]
frame["left"] = [t[1][0] for t in locations]
source = models.ColumnDataSource(frame)
labels = models.LabelSet(x='left',
y='bottom',
x_offset=2,
y_offset=2,
text='label',
source=source,
text_color="white",
render_mode='canvas')
worker_plot.add_layout(labels)
if show_communication:
frame = DataFrame(
merge_trace_events(
trace_events,
lambda e: isinstance(e, FetchStartTraceEvent),
lambda e: isinstance(e, FetchEndTraceEvent),
lambda e: (e.output, e.target_worker, e.source_worker),
end_map=lambda e1, e2:
(workers.index(e1.source_worker), e1.time,
workers.index(e2.target_worker), e2.time, "{}/{:.2f}".
format(e1.output.parent.name, e1.output.size), e1.output)),
columns=["worker", "start", "worker2", "end", "label", "output"])
frame["src_task_y"] = frame["output"].map(lambda o: (task_to_loc[
o.parent][2] + task_to_loc[o.parent][3]) / 2)
plot = plots[-1]
source = models.ColumnDataSource(frame.drop(columns=["output"]))
plot.segment(y0='src_task_y',
x0='start',
y1='worker2',
x1='end',
source=source,
line_color="black",
line_width=2)
plot.circle(y="worker2",
x="end",
source=source,
size=15,
color="black")
labels = models.LabelSet(x='end',
y='worker2',
text='label',
x_offset=-10,
source=source,
text_color="black",
text_align="right",
render_mode='canvas')
plot.add_layout(labels)
return gridplot(plots, ncols=2)
'field': value_to_draw,
'transform': color_mapper
},
line_color='black',
line_width=1.0,
source=plot_df)
color_bar = bm.ColorBar(color_mapper=color_mapper,
ticker=bm.LogTicker(),
label_standoff=12,
border_line_color=None,
location=(0, 0))
p.add_layout(color_bar, 'right')
p.add_tools(bm.WheelZoomTool())
labels = bm.LabelSet(
x='x',
y='y',
text='text',
source=plot_df,
text_align='center',
text_color='#FFFFFF',
text_font_size={'value': '10px'},
render_mode='canvas',
)
p.add_layout(labels)
bio.show(p)
try:
bio.export_png(p, filename="{}.png".format(value_to_draw))
except:
pass
def plot_network(network,
layout_algorithm=None,
scale=1.0,
threshold=0.0,
node_description=None,
node_proportions=None,
weight_scale=5.0,
normalize_weights=True,
node_opts=None,
line_opts=None,
element_id='nx_id3',
figsize=(900, 900)):
if threshold > 0:
values = nx.get_edge_attributes(network, 'weight').values()
max_weight = max(1.0, max(values))
print('Max weigth: {}'.format(max_weight))
print('Mean weigth: {}'.format(sum(values) / len(values)))
filter_edges = [(u, v) for u, v, d in network.edges(data=True) \
if d['weight'] >= (threshold * max_weight)]
sub_network = network.edge_subgraph(filter_edges)
else:
sub_network = network
args = PlotNetworkUtility.layout_args(layout_algorithm, sub_network,
scale)
layout = (PlotNetworkUtility.get_layout_algorithm(layout_algorithm))(
sub_network, **args)
lines_source = NetworkUtility.get_edges_source(
sub_network,
layout,
scale=weight_scale,
normalize=normalize_weights)
nodes_source = NetworkUtility.create_nodes_data_source(
sub_network, layout)
nodes_community = NetworkMetricHelper.compute_partition(sub_network)
community_colors = NetworkMetricHelper.partition_colors(
nodes_community, bokeh.palettes.Category20[20])
nodes_source.add(nodes_community, 'community')
nodes_source.add(community_colors, 'community_color')
nodes_size = 5
if node_proportions is not None:
# NOTE!!! By pd index - not iloc!!
nodes_weight = node_proportions.loc[list(sub_network.nodes)]
nodes_weight = PlotNetworkUtility.project_series_to_range(
nodes_weight, 20, 60)
nodes_size = 'size'
nodes_source.add(nodes_weight, nodes_size)
node_opts = extend(DFLT_NODE_OPTS, node_opts or {})
line_opts = extend(DFLT_EDGE_OPTS, line_opts or {})
p = figure(plot_width=figsize[0],
plot_height=figsize[1],
x_axis_type=None,
y_axis_type=None)
#node_size = 'size' if node_proportions is not None else 5
r_lines = p.multi_line('xs',
'ys',
line_width='weights',
source=lines_source,
**line_opts)
r_nodes = p.circle('x',
'y',
size=nodes_size,
source=nodes_source,
**node_opts)
p.add_tools(bm.HoverTool(renderers=[r_nodes], tooltips=None, callback=WidgetUtility.\
glyph_hover_callback(nodes_source, 'node_id', text_ids=node_description.index, \
text=node_description, element_id=element_id))
)
text_opts = dict(x='x',
y='y',
text='name',
level='overlay',
text_align='center',
text_baseline='middle')
r_nodes.glyph.fill_color = 'lightgreen' # 'community_color'
p.add_layout(
bm.LabelSet(source=nodes_source, text_color='black', **text_opts))
return p
def plot_bipartite_network(
network: nx.Graph,
layout_data: nu.NodesLayout,
scale: float = 1.0,
titles: pd.DataFrame = None,
highlight_topic_ids=None,
element_id: str = 'nx_id1',
plot_width: int = 1000,
plot_height: int = 600,
) -> bp.Figure:
"""Plot a bipartite network. Return bokeh.Figure"""
tools: str = 'pan,wheel_zoom,box_zoom,reset,hover,save'
source_nodes, target_nodes = nu.get_bipartite_node_set(network, bipartite=0)
color_map: dict = (
{x: 'brown' if x in highlight_topic_ids else 'skyblue' for x in target_nodes}
if highlight_topic_ids is not None
else None
)
color_specifier: str = 'colors' if highlight_topic_ids is not None else 'skyblue'
source_source: bm.ColumnDataSource = layout_source.create_nodes_subset_data_source(
network, layout_data, source_nodes
)
target_source: bm.ColumnDataSource = layout_source.create_nodes_subset_data_source(
network, layout_data, target_nodes, color_map=color_map
)
lines_source: bm.ColumnDataSource = layout_source.create_edges_layout_data_source(
network, layout_data, scale=6.0, normalize=False
)
edges_alphas: List[float] = metrics.compute_alpha_vector(lines_source.data['weights'])
lines_source.add(edges_alphas, 'alphas')
p: bp.Figure = bp.figure(
plot_width=plot_width, plot_height=plot_height, x_axis_type=None, y_axis_type=None, tools=tools
)
_ = p.multi_line(
xs='xs', ys='ys', line_width='weights', level='underlay', alpha='alphas', color='black', source=lines_source
)
_ = p.circle(x='x', y='y', size=40, source=source_source, color='lightgreen', line_width=1, alpha=1.0)
r_targets: bm.GlyphRenderer = p.circle(
x='x', y='y', size=25, source=target_source, color=color_specifier, alpha=1.0
)
p.add_tools(
bm.HoverTool(
renderers=[r_targets],
tooltips=None,
callback=wu.glyph_hover_callback2(
glyph_source=target_source,
glyph_id='node_id',
text_ids=titles.index,
text=titles,
element_id=element_id,
),
)
)
text_opts: dict = dict(x='x', y='y', text='name', level='overlay', x_offset=0, y_offset=0, text_font_size='8pt')
p.add_layout(
bm.LabelSet(source=source_source, text_color='black', text_align='center', text_baseline='middle', **text_opts)
)
target_source.data['name'] = [str(x) for x in target_source.data['name']] # pylint: disable=unsubscriptable-object
p.add_layout(
bm.LabelSet(source=target_source, text_color='black', text_align='center', text_baseline='middle', **text_opts)
)
return p
def _plot_network(
network: nx.Graph,
layout_algorithm: str = None,
scale: float = 1.0,
threshold: float = 0.0,
node_description: pd.Series = None,
node_proportions: Union[int, str] = None,
weight_name: str = 'weight',
weight_scale: float = 5.0,
normalize_weights: bool = True,
node_opts=None,
line_opts=None,
element_id: str = 'nx_id3',
figsize: Tuple[int, int] = (900, 900),
node_range: Tuple[int, int] = (20, 60),
edge_range: Tuple[int, int] = (1.0, 5.0),
):
if threshold > 0:
values = nx.get_edge_attributes(network, weight_name).values()
max_weight = max(1.0, max(values))
print('Max weigth: {}'.format(max_weight))
print('Mean weigth: {}'.format(sum(values) / len(values)))
filter_edges = [(u, v) for u, v, d in network.edges(data=True)
if d[weight_name] >= (threshold * max_weight)]
sub_network = network.edge_subgraph(filter_edges)
else:
sub_network = network
args = _layout_args(layout_algorithm, sub_network, scale)
layout = (_get_layout_algorithm(layout_algorithm))(sub_network, **args)
lines_source = layout_source.create_edges_layout_data_source(
sub_network,
layout,
weight=weight_name,
scale=weight_scale,
normalize=normalize_weights,
project_range=edge_range,
)
nodes_source = layout_source.create_nodes_data_source(sub_network, layout)
nodes_community = metrics.compute_partition(sub_network)
community_colors = metrics.partition_colors(nodes_community,
bokeh.palettes.Category20[20])
nodes_source.add(nodes_community, 'community')
nodes_source.add(community_colors, 'community_color')
nodes_size = 5
if node_proportions is not None:
if isinstance(node_proportions, int):
nodes_size = node_proportions
else:
nodes_size = 'size'
nodes_weight = project_values_to_range(
[node_proportions[n] for n in sub_network.nodes], *node_range)
nodes_source.add(nodes_weight, nodes_size)
node_opts = extend(dict(color='green', alpha=1.0), node_opts or {})
line_opts = extend(dict(color='black', alpha=0.4), line_opts or {})
p = figure(plot_width=figsize[0],
plot_height=figsize[1],
x_axis_type=None,
y_axis_type=None)
_ = p.multi_line('xs',
'ys',
line_width='weights',
level='underlay',
source=lines_source,
**line_opts)
r_nodes = p.circle('x',
'y',
size=nodes_size,
source=nodes_source,
**node_opts)
p.add_tools(
bokeh.models.HoverTool(
renderers=[r_nodes],
tooltips=None,
callback=wu.glyph_hover_callback2(nodes_source,
'node_id',
text_ids=node_description.index,
text=node_description,
element_id=element_id),
))
text_opts = dict(x='x',
y='y',
text='name',
level='overlay',
x_offset=0,
y_offset=0,
text_font_size='12pt')
r_nodes.glyph.fill_color = 'lightgreen' # 'community_color'
nodes_source.data['name'] = [str(x) for x in nodes_source.data['name']] # pylint: disable=unsubscriptable-object
p.add_layout(
bm.LabelSet(source=nodes_source,
text_align='center',
text_baseline='middle',
text_color='black',
**text_opts))
return p
