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to_gda.py
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to_gda.py
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__author__ = 'lisette.espin'
#############################################################################
# DEPENDENCIES
#############################################################################
import sys
import os
from scipy.io import loadmat
import networkx as nx
import numpy as np
import pandas as pd
#############################################################################
# CONSTANTS
#############################################################################
MISSINGVALUECODE = '?'
#############################################################################
# FUNCTIONS
#############################################################################
def load_mat(fn,classname,missingvaluecode):
obj = loadmat(fn)
graph = nx.from_scipy_sparse_matrix(obj['A'])
# renaming nodes
mapping = {n:'node{}'.format(n + 1) for n in graph.nodes()}
graph = nx.relabel_nodes(graph, mapping)
# attributes
attribute_names = ['status', 'gender', 'major', '2major', 'dorm', 'year', 'highschool']
nodes = pd.DataFrame(np.array(obj['local_info']), index=graph.nodes(), columns=attribute_names)
nodes.index.name = 'Name'
# missing values as ?
nodes.replace(missingvaluecode,MISSINGVALUECODE,inplace=True)
# class goes as last column
cols = list(attribute_names)
del(cols[cols.index(classname)])
cols.append(classname)
nodes = nodes[cols]
# removing nodes with missing values in class
try:
toremove = nodes[nodes[classname] == '?'].index
nodes = nodes.drop(toremove)
graph.remove_nodes_from(toremove.values)
except:
pass
# removing singletons
toremove = [n for n in graph.nodes() if graph.degree(n)==0]
graph.remove_nodes_from(toremove)
print(nx.info(graph))
return nodes,graph
def write_nodes(nodes,classname,networkfn,output):
fn = networkfn.split('/')[-1].split('.')[0]
fn = os.path.join(output,'{}-{}-nodes.gda'.format(fn,classname))
nodes.to_csv(fn,header=True)
def write_edges(graph,classname,networkfn,output):
fn = networkfn.split('/')[-1].split('.')[0]
fn = os.path.join(output, '{}-{}-edges.gda'.format(fn,classname))
edges = ['link{},{}'.format(edge_id+1,node) for edge_id, edge in enumerate(graph.edges()) for node in edge]
with open(fn,'w') as f:
f.write('link,entity\n')
f.write('\n'.join(edges))
#############################################################################
# MAIN
#############################################################################
if __name__ == '__main__':
fn = sys.argv[1]
classname = sys.argv[2]
missingvaluecode = sys.argv[3]
output = sys.argv[4]
nodes = None
graph = None
if os.path.exists(fn):
ext = fn.endswith('.mat')
if ext:
nodes,graph = load_mat(fn,classname,missingvaluecode)
else:
print('{} NOT supported.'.format(ext))
if nodes is not None and graph is not None:
print('graph succesfully loaded!')
write_nodes(nodes,classname,fn,output)
print('nodes saved!')
write_edges(graph,classname,fn,output)
print('edges saved!')