def build_A_tables_for_lanes(sumo_network, lanes=None):
"""Returns dict of dataframes for different lane adjacency matrices"""
if lanes is None:
lanes = sumo_network.lanes_with_detectors()
A_dfs = {}
A_dfs['A_downstream'] = nx.to_pandas_adjacency(
sumo_network.graph, nodelist=lanes).astype('bool')
A_dfs['A_upstream'] = nx.to_pandas_adjacency(sumo_network.graph.reverse(),
nodelist=lanes).astype('bool')
A_dfs['A_neighbors'] = nx.to_pandas_adjacency(
sumo_network.get_lane_graph_for_neighboring_lanes(
include_self_adjacency=False),
nodelist=lanes).astype('bool')
A_dfs['A_turn_movements'] = nx.to_pandas_adjacency(
sumo_network.get_lane_graph_for_turn_movements(),
nodelist=lanes).astype('bool')
A_dfs['A_through_movements'] = nx.to_pandas_adjacency(
sumo_network.get_lane_graph_for_thru_movements(),
nodelist=lanes).astype('bool')
return A_dfs
def compare_interactions_df(G, node_a=str, node_b=str, method="ratio"):
import networkx as nx
import pandas as pd
import numpy as np
Gs = split_graph(G)
interaction_dict_i = dict()
for node in G.nodes():
ratio_dict = dict()
for interaction in Gs:
if method == "ratio":
df = nx.to_pandas_adjacency(Gs[interaction],
weight="log_score")
a = df[node_a][node]
b = df[node_b][node]
ratio = a - b # calculate the ratio of interaction scores (using log values log(a)-log(b) = log(a/b))
# This bypass divition with 0 issues as in a/b, b might be 0
if method == "difference":
df = nx.to_pandas_adjacency(Gs[interaction], weight="score")
a = df[node_a][node]
b = df[node_b][node]
ratio = a - b # Calulate the difference in interaction score
if method == "specificity":
df = nx.to_pandas_adjacency(Gs[interaction],
weight="specificity")
a = df[node_a][node]
b = df[node_b][node]
ratio = a - b # Calulate the difference in specificity
ratio_dict[interaction] = ratio
interaction_dict_i[node] = ratio_dict
df_i = pd.DataFrame(interaction_dict_i)
interaction_dict_o = dict()
for node in G.nodes():
ratio_dict = dict()
for interaction in Gs:
if method == "ratio":
df = nx.to_pandas_adjacency(Gs[interaction],
weight="log_score")
a = df[node][node_a]
b = df[node][node_b]
ratio = a - b # calculate the ratio of interaction scores (using log values log(a)-log(b) = log(a/b))
# This bypass divition with 0 issues as in a/b, b might be 0
if method == "difference":
df = nx.to_pandas_adjacency(Gs[interaction], weight="score")
a = df[node][node_a]
b = df[node][node_b]
ratio = a - b # Calulate the difference in interaction score
ratio_dict[interaction] = ratio
interaction_dict_o[node] = ratio_dict
df_o = pd.DataFrame(interaction_dict_o)
return df_i, df_o
def test_normalize_graph(self):
matrix = pd.DataFrame([[0,4,2,0,0],[1,0,2,0,0],[1,0,0,0,0], [0,0,1,0,5],[0,0,0,5,0]])
graph = nx.from_pandas_adjacency(matrix, create_using= nx.DiGraph)
print(matrix)
print(nx.to_pandas_adjacency(graph))
calculate_total_node_volume(graph)
normalize_directional_graph(graph)
print(nx.to_pandas_adjacency(graph))
def load_everything(
graph_type,
version="2019-09-18-v2",
return_keys=None,
return_df=False,
return_ids=False,
):
"""Function to load an adjacency matrix and optionally return some associated
metadata
Parameters
----------
graph_type : str
Which version of the graph to load
version : str, optional
Date/version descriptor for which dataset to use, by default "2019-09-18-v2"
return_df : bool, optional
Whether to return a Pandas DataFrame representation of the adjacency,
by default False
return_ids : bool, optional
Whether to return the cell ids (skeleton ids), by default False
Returns
-------
[type]
[description]
Raises
------
ValueError
[description]
"""
graph = load_networkx(graph_type, version=version)
nx_ids = np.array(list(graph.nodes()), dtype=int)
df_adj = nx.to_pandas_adjacency(graph)
df_ids = df_adj.index.values.astype(int)
if not np.array_equal(nx_ids, df_ids):
raise ValueError(
"Networkx indexing is inconsistent with Pandas adjacency")
adj = nx.to_pandas_adjacency(graph).values
outs = [adj]
if return_keys is not None:
if not isinstance(return_keys, list):
return_keys = [return_keys]
for k in return_keys:
labels = meta_to_array(graph, k)
outs.append(labels)
if return_df:
outs.append(df_adj)
if return_ids:
outs.append(df_ids)
if len(outs) > 1:
outs = tuple(outs)
return outs
else:
return adj
def getGraphFromFile(file_path):
file = open(file_path, "r")
graph = nx.Graph()
content = file.read()
# dictionary with coordinates of nodes
coords = {}
cities = []
#
# turninig on options to see all information in DataFrame
#pd.set_option('display.max_rows', None)
#pd.set_option('display.max_columns', None)
# extract node section
node_section = content[content.find("NODES"):content.find("LINK")]
# extract nodes only
node_section = node_section[node_section.find("(") +
1:node_section.rfind(")")]
# split into single nodes
nodes = node_section.split('\n')[1:-1]
for node in nodes:
# get list with name on 0 index and two coordinates
node = node.replace('(', '').replace(')', '').split(' ')[2:-1]
node.pop(1)
cities.append(node[0])
coords[node[0]] = {"x": node[1], "y": node[2]}
graph.add_node(node[0])
# extract link section
link_section = content[content.find("LINKS"):content.find("DEMAND")]
link_section = link_section[link_section.find("(") +
1:link_section.rfind(")")]
links = link_section.split('\n')[1:-1]
#print(links)
for link in links:
link = link[link.find("(") + 1:link.find(")")].split(' ')[1:-1]
lon1 = float(coords[link[0]]["x"]) # lon
lat1 = float(coords[link[0]]["y"]) # lat
lon2 = float(coords[link[1]]["x"])
lat2 = float(coords[link[1]]["y"])
edge_real_distance = geodesic((lat1, lon1), (lat2, lon2)).kilometers
graph.add_edge(link[0], link[1])
graph[link[0]][link[1]]['weight'] = edge_real_distance
graph[link[0]][link[1]]['pheromone'] = 1
#
# distance dataframe
df = nx.to_pandas_adjacency(graph, weight='weight', nonedge=np.inf)
# beginnine pheromone amount for each city in dataframe
pheromone = nx.to_pandas_adjacency(graph, weight='pheromone', nonedge=0)
#
# beginning eta amount for each citi in dataframe
eta = 1 / df
return graph, df, pheromone, eta, cities
def test_from_adjacency(self):
nodelist = [1, 2]
dftrue = pd.DataFrame([[1, 1], [1, 0]], dtype=int,
index=nodelist, columns=nodelist)
G = nx.Graph([(1, 1), (1, 2)])
df = nx.to_pandas_adjacency(G, dtype=int)
pd.testing.assert_frame_equal(df, dftrue)
def prunedDF(dataFrame, saveAsGraph, file=''):
if isinstance(dataFrame, pd.DataFrame):
graph = nx.from_pandas_adjacency(dataFrame)
graph.remove_nodes_from(list(nx.isolates(graph)))
if saveAsGraph:
saveGraph(graph, file)
return nx.to_pandas_adjacency(graph)
def PPICompute(graph,proteinNodes,trueP,falseP):
#print('PPI - starting subgraph')
subPROTEIN = graph.subgraph(proteinNodes) # did the PPI filter out some proteins?
#subPROTEIN = subPROTEIN.subgraph( set(subPROTEIN.nodes) - set(nx.isolates(subPROTEIN)) )
trues = set()
neighborSet = set()
#print('PPI - making neighborSet')
for protein in trueP:
if protein in set(proteinNodes):
trues.add(protein)
neighborSet = neighborSet | set(nx.all_neighbors(subPROTEIN, protein))
nodesList = trues | neighborSet
finalGraph = subPROTEIN.subgraph(nodesList)
#print('PPI - making adj subgraph') # this is slow
adjIt = nx.to_pandas_adjacency(finalGraph,weight='combined_score')
# this does our PPI computations with the values we want
#print('PPI - matrix and loop')
RR = completePPI(finalGraph,trues,nodesList,adjIt)
#print('PPI - done with these computations')
return RR
def calculatePhi(graph, k):
path = 'graphs/'
file = [graph]
edgelist = pd.read_csv(path + file[0],
delimiter=' ',
skiprows=1,
header=None)
G = nx.from_pandas_edgelist(edgelist,
source=0,
target=1,
create_using=nx.Graph())
adj_matr = nx.to_pandas_adjacency(G, dtype=np.float64)
laplacian = sparse.csgraph.laplacian(adj_matr.values, normed=True)
laplacian = normalize(laplacian)
eigenvalues, eigenvectors = np.linalg.eig(laplacian)
kmeans = KMeans(n_clusters=k,
max_iter=3000).fit(eigenvectors.astype(np.float64))
cut_edges = 0
for i in range(edgelist.shape[0]):
if (kmeans.labels_[edgelist[0][i]] != kmeans.labels_[edgelist[1][i]]):
cut_edges += 1
counter = collections.Counter(kmeans.labels_)
smallest = math.inf
for key, value in counter.items():
if (value < smallest):
smallest = value
phi = cut_edges / smallest
return phi
def get_adjacency(self, *, weight_col=None, norm_type=None):
"""
Creates edge graph in the matrix format. Row indeces are event_col values,
from which the transition occured, and columns are events, to
which the transition occured. The values are weights of the edges defined
with weight_col and norm_type parameters.
Parameters
----------
weight_col: str (optional, default=None)
Aggregation column for transitions weighting. To calculate weights
as number of transion events use None. To calculate number
of unique users passed through given transition 'user_id'.
For any other aggreagtion, like number of sessions, pass the column name.
norm_type: {None, 'full', 'node'} (optional, default=None)
Type of normalization. If None return raw number of transtions
or other selected aggregation column. 'full' - normalized over
entire dataset. 'node' weight for edge A --> B normalized over
user in A
Returns
-------
Dataframe with number of columns and rows equal to unique number of
event_col values.
Return type
-----------
pd.DataFrame
"""
agg = self.get_edgelist(weight_col=weight_col, norm_type=norm_type)
graph = nx.DiGraph()
graph.add_weighted_edges_from(agg.values)
return nx.to_pandas_adjacency(graph)
def step(self):
# collect knowledge, attitude, and belief valence data
# loop through each agent and only store agent info if necessary
for i in range(len(self.all_agents)):
a = self.all_agents[i]
# for sensitivity analysis, only collect knowledge information
# collect knowledge flows
if ((a.timeKnowledge == a.currentStep - 1) and
(np.isnan(a.receivedKnowledge) == False)) or (
(a.timeKnowledge == 0) and (a.currentStep == 0)):
kn = {
'CurrentStep': a.currentStep,
'MyAgentID': a.agent_number,
'OtherAgentID': a.receivedKnowledge,
'TimeKnowledgeReceived': a.timeKnowledge,
'HasKnowledge': a.hasKnowledge,
'Model': self.cognitivePhase,
'NumInitialKnowledgeAgents': self.numRandomKnowledgeAgents,
'NumberAgentsSeeded': self.numSeeds,
'SuccessProbability': self.probSuccess,
'RateOfLogisticCurve': self.a,
'SensitivityAnalysis': self.sensitivityAnalysis,
'Subgraph': self.subgraph
}
kn = pd.DataFrame(data=kn, index=np.arange(0, 1))
self.knowledge_table = self.knowledge_table.append(kn)
if self.sensitivityAnalysis == False:
# collect attitude values if agent's attitude has changed
if ((a.timeNewAttitude == a.currentStep - 1)
or (a.currentStep == 0)):
at = {
'CurrentStep': a.currentStep,
'TimeNewAttitude': a.timeNewAttitude,
'MyAgentID': a.agent_number,
'Attitude': a.attitude
}
at = pd.DataFrame(data=at, index=np.arange(0, 1))
self.attitude_table = self.attitude_table.append(at)
# collect contact network, social network, and interaction times
if self.step_number % 1440 == 0:
print("current step: ", self.step_number)
if self.networkPhase != 1:
# create table with social network
#sn=nx.to_pandas_dataframe(self.socialNetwork)
sn = nx.to_pandas_adjacency(self.socialNetwork)
sn['Step'] = self.step_number
sn['contactWeight'] = self.beta1
sn['attWeight'] = self.beta2
sn['roleWeight'] = self.beta3
self.social_table = self.social_table.append(sn)
self.step_number = self.step_number + 1
self.schedule.step()
def BuildAM(par, t, data_type):
k = par["k"]
path = par["path"]
os.chdir(path)
if(t == "cg"):
G = nx.complete_graph(10)
am = nx.to_pandas_adjacency(G)
elif(t == "half"):
am = pd.read_table("C:\\Users\\Administrator\\Desktop\\causal_compare\\data_e\\inter_" + str(k) + ".txt", header=None)
am = CreatPesudoAM(am)
elif(t == "mmhc"):
am = pd.read_csv("C:\\Users\\Administrator\\Desktop\\causal_compare\\beem_e\\" + par["i"] + "_" + par["j"] + "\\mmhc\\"+ data_type+ "_adjacent_matrix_" + str(k) + ".csv", index_col=0)
elif(t == "sparcc"):
p = pd.read_table("C:\\Users\\Administrator\\Desktop\\causal_compare\\data_e\\" + par["i"] + "_" + par["j"] + "\\SparCC\\p_" + str(k) + ".txt", index_col=0)
am = pd.DataFrame(np.zeros([p.shape[0], p.shape[0]]))
am.columns = ["sp" + str(i) for i in range(p.shape[0])]
am.index = ["sp" + str(i) for i in range(p.shape[0])]
for s in range(p.shape[0]):
for t in range(p.shape[1]):
if(p.ix[s, t] <= 0.05):
am.ix[s, t] = 1
elif(t == "true"):
am = pd.read_table("C:\\Users\\Administrator\\Desktop\\causal_compare\\data_e\\inter_" + str(k) + ".txt", header=None)
label = ["sp" + str(i) for i in range(len(am))]
am.index = label; am.columns = label
#am = pd.DataFrame(am, index=label, columns=label)
return am
def test_roundtrip(self):
# edgelist
Gtrue = nx.Graph([(1, 1), (1, 2)])
df = nx.to_pandas_edgelist(Gtrue)
G = nx.from_pandas_edgelist(df)
assert_graphs_equal(Gtrue, G)
# adjacency
Gtrue = nx.Graph(({
1: {
1: {
'weight': 1
},
2: {
'weight': 1
}
},
2: {
1: {
'weight': 1
}
}
}))
df = nx.to_pandas_adjacency(Gtrue, dtype=int)
G = nx.from_pandas_adjacency(df)
assert_graphs_equal(Gtrue, G)
def Crear_Grafos(nombre, size, int_distancia):
G = nx.Graph()
nodes = []
for i in range(size):
nodes.append(i)
print(nodes)
for i in nodes:
idx = nodes.index(i) + 1
print(idx)
for j in nodes[idx:len(nodes)]:
if rnd.randint(0, 80) == 1:
G.add_edge(i, j, distancia=rnd.randint(1, int_distancia))
print(G.edges)
df = pd.DataFrame()
df = nx.to_pandas_adjacency(G, dtype=int, weight='distancia')
df.to_csv(nombre + ".csv", index=None, header=None)
plt.figure(figsize=(15, 15))
position = nx.spring_layout(G, scale=5, iterations=200)
nx.draw_networkx_nodes(G,
position,
node_size=50,
node_color="#de8919",
node_shape="<")
nx.draw_networkx_edges(G, position, width=0.5, edge_color='black')
plt.axis("off")
plt.savefig(nombre + ".png", bbox_inches='tight')
plt.savefig(nombre + ".eps", bbox_inches='tight')
plt.show(G)
def convert_to_csv(graph,
c_obj,
c_nodes,
output_path=config.path,
adj_mat=False):
if adj_mat:
df_matrix = nx.to_pandas_adjacency(graph, dtype=np.uint8)
df_matrix.to_csv(output_path + 'Adj_matrix_bbike_map.csv', index=False)
adj_list = list(nx.generate_adjlist(graph))
df_list = pd.DataFrame(adj_list, columns=['row'])
df_list = pd.DataFrame(df_list.row.str.split(' ').tolist())
df_list = df_list.rename(columns={0: 'Source'})
df_list.to_csv(output_path + 'Adj_list_bbike_map.csv', index=False)
df_nodes = pd.DataFrame(dict(graph.nodes(data=True))).T
df_nodes.to_csv(output_path + 'All.csv', index=False)
to_dict_nodes = df_nodes.loc[df_nodes['osmid'].isin(c_nodes)]
to_dict_nodes.to_csv(output_path + 'Nodes_bbike_map.csv', index=False)
to_dict_objects = df_nodes.loc[df_nodes['osmid'].isin(c_obj)]
to_dict_objects.to_csv(output_path + 'Objects_bbike_map.csv', index=False)
adj_list = pd.read_csv(output_path + 'Adj_list_bbike_map.csv')
df_graph = df_nodes.merge(adj_list, left_on='osmid', right_on='Source')
adj = df_graph.iloc[:, 6:].to_numpy()
adj = [node[~pd.isnull(node)] for node in adj]
df_graph['adj'] = adj
df_graph = df_graph[['osmid', 'x', 'y', 'weight',
'adj']].set_index('osmid')
with open(output_path + 'Chel_simp.pickle', 'wb') as f:
pickle.dump(graph, f)
return df_graph
def from_json(
self,
jsonstr,
func=nf.MJ_func, # default mechanism for all nodes
SpN=2):
self.graph = self.node_lut = self.tpm = None
jdict = json.loads(jsonstr)
edges = jdict.get('edges', [])
i, j = zip(*edges)
n_list = sorted(set(i + j))
nodes = [Node(**nd) for nd in jdict.get('nodes', [])]
for n in nodes:
n.func = nf.funcLUT[n.func]
self.graph = nx.DiGraph(edges)
self.node_lut = dict((n.label, n) for n in nodes)
S = nx.DiGraph(jdict.get('tpm', []))
#self.tpm = sbs2sbn(nx.to_pandas_adjacency(S))
s2s_df = nx.to_pandas_adjacency(S)
df = pd.DataFrame(index=s2s_df.index, columns=self.node_lut.keys())
for istate in s2s_df.index:
for outstate in s2s_df.columns:
if s2s_df.loc[istate, outstate] == 0:
continue
ns = nodes_state(outstate, self.node_lut.keys())
print(f'DBG: istate={istate} ns={ns}')
df.loc[istate] = list(ns.values())
self.tpm = df
def graph_contrast_heatmap(G, H):
fig, ax = plt.subplots(figsize=(10, 10))
# same network, return empty plot
if G.edges == H.edges:
return plt
# grab set of nodes from all graphs
nodelist = set()
for g in [
G,
H,
]:
for node in g.nodes:
nodelist.add(node)
g = nx.to_pandas_adjacency(G, nodelist=nodelist)
h = nx.to_pandas_adjacency(H, nodelist=nodelist)
h.replace(1, 2, inplace=True)
a = g + h
# drop zeros from resulting dataframe
a = a.loc[(a != 0).any(1)]
a = a.loc[:, (a != 0).any(axis=0)]
ax = seaborn.heatmap(a,
cbar=False,
square=True,
linewidths=1.5,
cmap=['white', 'red', 'blue', 'purple'])
ax.set_xticklabels(labels=list(a.columns),
rotation=45,
rotation_mode="anchor",
ha="right",
fontsize=7)
ax.set_yticklabels(labels=list(a.index), fontsize=7)
plt.xlabel("target")
plt.ylabel("source")
fig.tight_layout()
return plt
def wrapper(self, *args, **kwargs):
before = nx.to_pandas_adjacency(self._dg)
func(self, *args, **kwargs)
after = nx.to_pandas_adjacency(self._dg)
idx_union = before.index.union(after.index)
before = before.reindex(idx_union)
after = after.reindex(idx_union)
diff = after.subtract(before)
# Find symmetric difference. This is what I would use to do CRUD on relational db.
df = diff.unstack().to_frame()
df.index = df.index.rename(['child', 'parent'])
df.columns = ['diff']
df = df[df['diff'] != 0]
df['changed'] = df['diff'].map(lambda x: 'Added'
if x > 0 else 'Removed')
print('Symmetric diff:\n', df)
def na():
pr_sorted = sorted(pr.items(), key=operator.itemgetter(1), reverse=True)
# test graph
edges = {"to": [0, 1, 2, 2], "from": [2, 0, 1, 1]}
df = pd.DataFrame(edges)
G = nx.from_pandas_edgelist(df, "to", "from", create_using=nx.MultiDiGraph)
print(nx.to_pandas_adjacency(G))
def build_adjacency_matrix_from_graph(graph,
attribute_name,
all_nodes=None,
distribution=False):
"""
Building a adjacency matrix for a condensed graph.
Args:
graph: the condensed graph that is described by the produced adjacency matrix.
attribute_name: the name of the attribute to use as names in the matrix
all_nodes: list of nodes to be considered in the adjacency matrix,
should be according to the requested attribute.
distribution: if false all the values are {0,1}, else the number number of adjacent nodes normalized.
Returns: the adjacency matrix.
"""
AdjacencyGraphBuilder._validate_attribute_is_unique(
graph, attribute_name)
graph = graph.copy()
# The condensed nodes attributes.
node_attribute_value = nx.get_node_attributes(graph, attribute_name)
# The index / columns of the adjacency matrix will be returned with the attribute value.
rename_dict = {k: v.value for k, v in node_attribute_value.items()}
existing_nodes = rename_dict.values()
if all_nodes is not None:
for node in set(all_nodes) - set(existing_nodes):
node_name = 'dummy {}'.format(node)
graph.add_node(node_name, **{attribute_name: node})
rename_dict[node_name] = node
# The adjacency matrix of the condensed graph.
condensed_graph_df = nx.to_pandas_adjacency(graph)
# Renaming the index/columns to the appropriate name.
condensed_graph_df = condensed_graph_df.rename(columns=rename_dict,
index=rename_dict)
# Condensing the matrix.
condensed_graph_df = condensed_graph_df.groupby(
condensed_graph_df.index).sum().T
condensed_graph_df = condensed_graph_df.groupby(
condensed_graph_df.index).sum()
# If a distribution is desired then the number of adjacent nodes is normalized
if distribution:
condensed_graph_df = (condensed_graph_df /
condensed_graph_df.sum()).fillna(0)
# if not it is updated to {0/1}
else:
condensed_graph_df = (condensed_graph_df /
condensed_graph_df).fillna(0)
return condensed_graph_df
def test_to_pandas_adjacency_with_nodelist():
G = nx.complete_graph(5)
nodelist = [1, 4]
expected = pd.DataFrame([[0, 1], [1, 0]],
dtype=int,
index=nodelist,
columns=nodelist)
pd.testing.assert_frame_equal(
expected, nx.to_pandas_adjacency(G, nodelist, dtype=int))
def test_from_adjacency(self):
nodelist = [1, 2]
dftrue = pd.DataFrame([[1, 1], [1, 0]], dtype=int, index=nodelist, columns=nodelist)
G = nx.Graph([(1, 1), (1, 2)])
df = nx.to_pandas_adjacency(G, dtype=int)
pd.testing.assert_frame_equal(df, dftrue)
# deprecated
df = nx.to_pandas_dataframe(G, dtype=int)
pd.testing.assert_frame_equal(df, dftrue)
def test_from_adjacency_named(self):
# example from issue #3105
data = {"A": {"A": 0, "B": 0, "C": 0},
"B": {"A": 1, "B": 0, "C": 0},
"C": {"A": 0, "B": 1, "C": 0}}
dftrue = pd.DataFrame(data)
df = dftrue[["A", "C", "B"]]
G = nx.from_pandas_adjacency(df, create_using=nx.DiGraph())
df = nx.to_pandas_adjacency(G, dtype=int)
pd.testing.assert_frame_equal(df, dftrue)
def clip_to_table(self, clip, nodelist=None):
"""
This method recieves a networkx graph and return its dataframe
"""
if nodelist == None:
df_nodelist = sorted(clip.nodes())
Table_clip = nx.to_pandas_adjacency(clip, nodelist=df_nodelist)
return Table_clip
def test_from_adjacency_named(self):
# example from issue #3105
data = {"A": {"A": 0, "B": 0, "C": 0},
"B": {"A": 1, "B": 0, "C": 0},
"C": {"A": 0, "B": 1, "C": 0}}
dftrue = pd.DataFrame(data)
df = dftrue[["A", "C", "B"]]
G = nx.from_pandas_adjacency(df, create_using=nx.DiGraph())
df = nx.to_pandas_adjacency(G, dtype=int)
pd.testing.assert_frame_equal(df, dftrue)
def test_roundtrip(self):
# edgelist
Gtrue = nx.Graph([(1, 1), (1, 2)])
df = nx.to_pandas_edgelist(Gtrue)
G = nx.from_pandas_edgelist(df)
assert_graphs_equal(Gtrue, G)
# adjacency
Gtrue = nx.Graph(({1: {1: {'weight': 1}, 2: {'weight': 1}}, 2: {1: {'weight': 1}}}))
df = nx.to_pandas_adjacency(Gtrue, dtype=int)
G = nx.from_pandas_adjacency(df)
assert_graphs_equal(Gtrue, G)
def load_adjacency(graph_type="G",
nodelist=None,
output="numpy",
path=None,
version=None):
g = load_networkx(graph_type=graph_type, path=path, version=version)
if output == "numpy":
adj = nx.to_numpy_array(g, nodelist=nodelist)
elif output == "pandas":
adj = nx.to_pandas_adjacency(g, nodelist=nodelist)
return adj
def GenerateGraph(nameToSave,Smin,Smax,max_weight,numberOfGraphs):
for h in range(numberOfGraphs):
G=nx.Graph()
size=rdm.randint(Smin,Smax)
for i in range(size):
for j in range(i, size):
if rdm.randint(0,int(size/20))==0:
G.add_edge(i,j, weight=rdm.randint(1,max_weight))
df = pd.DataFrame()
df = nx.to_pandas_adjacency(G, dtype=int, weight='weight')
df.to_csv(nameToSave+str(h)+".csv")
def occurence(data,document): #生成共现矩阵
empty1=[];empty2=[];empty3=[]
for a in data:
for b in data:
count = 0
for x in document:
if [a in i for i in x].count(True) >0 and [b in i for i in x].count(True) >0:
count += 1
empty1.append(a);empty2.append(b);empty3.append(count)
df=pd.DataFrame({'from':empty1,'to':empty2,'weight':empty3})
G=nx.from_pandas_edgelist(df, 'from', 'to', 'weight')
return (nx.to_pandas_adjacency(G, dtype=int))
def test_roundtrip(self, graph):
# edgelist
Gtrue = graph([(1, 1), (1, 2)])
df = nx.to_pandas_edgelist(Gtrue)
G = nx.from_pandas_edgelist(df, create_using=graph)
assert_graphs_equal(Gtrue, G)
# adjacency
adj = {1: {1: {"weight": 1}, 2: {"weight": 1}}, 2: {1: {"weight": 1}}}
Gtrue = graph(adj)
df = nx.to_pandas_adjacency(Gtrue, dtype=int)
G = nx.from_pandas_adjacency(df, create_using=graph)
assert_graphs_equal(Gtrue, G)
def make_directed_graph(nodes, edges, normalize=True):
#nodes,edges = make_traded_volume_matrix(input_path, cutoff)
graph = nx.DiGraph() #Rows are the active agent
graph.add_nodes_from(nodes)
graph.add_weighted_edges_from(edges)
if normalize == True:
adjacency_df = nx.to_pandas_adjacency(graph)
graph = nx.from_pandas_adjacency(
adjacency_df.div(adjacency_df.sum(axis=1), axis=0).fillna(
0)) # We can end up dividing with zero so we need to fill that
return graph
def networks(corr_list, indexname, stockyear, show_networks=False):
"""
Creates the correlation network from correlation matrices.
:param corr_list: List of correlation matrices from incremented data
:param indexname: Name of index being referenced (labeling purposes)
:param stockyear: Start year of data being used (labeling purposes)
:param show_networks: Indicates whether to display the correlation networks
The pseudocode goes as follows:
for each correlation matrix:
links = pd.DataFrame(var1, var2, value)
links(var1,var2) = stock1, stock2
links(value) = correlation
links_filtered = links[correlation above predetermined threshold]
G = graph(edges from links_filtered)
if show_networks:
display network
:Returns:
none
Saves adjacency matrices to external files (for later use)
Optionally displays the graphs using networkx
"""
for i in range(len(corr_list)):
# creates the filtered links for each correlation set, threshold at 0.5 somewhat arbitrarily
corr_df = corr_list[i]
links = corr_df.stack().reset_index()
links.columns = ['var1', 'var2', 'value']
mean = np.mean(links['value'])
std = np.std(links['value'])
links_filtered = links.loc[(links['value'] > mean - std)
& (links['var1'] != links['var2'])]
G = nx.from_pandas_edgelist(links_filtered, 'var1', 'var2')
G_df = nx.to_pandas_adjacency(G)
G_df.to_csv('Graphs/{}_{}/adjacency_matrix/range_{}.csv'.format(
indexname, stockyear, i))
if show_networks:
plt.figure(i)
nx.draw_spring(G,
with_labels=True,
node_color='orange',
node_size=400,
edge_color='black',
linewidths=1,
font_size=9)
if show_networks:
plt.show()
def graph_contrast_report(G, H):
# same network, return empty plot
if G.edges == H.edges:
return "same graph"
# grab set of nodes from all graphs
nodelist = set()
for g in [
G,
H,
]:
for node in g.nodes:
nodelist.add(node)
g = nx.to_pandas_adjacency(G, nodelist=nodelist)
h = nx.to_pandas_adjacency(H, nodelist=nodelist)
h.replace(1, 2, inplace=True)
a = g + h
# drop zeros from resulting dataframe
a = a.loc[(a != 0).any(1)]
a = a.loc[:, (a != 0).any(axis=0)]
no_change = 0
deletion = 0
insertion = 0
purple = 0
for r in a.to_numpy():
row = list(r)
no_change += row.count(0)
deletion += row.count(1)
insertion += row.count(2)
purple += row.count(3)
return (no_change, deletion, insertion, purple)