# setup geoprocessor
GP = cm.gp_init()
# G: = \\nicknet.env.duke.edu\network\research\lel\GraphGroup
# G:\chapel_hill\network\full_lc\network_lc.txt
# easy_install -U networkx # got networkx-0.35.1
# E:\code\connmod\branches\ch\data\net2010\network_euc_na.txt
# get arguments
in_network_txt = sys.argv[1]
# initialize logging
log = '%s/log_centrality.txt' % os.path.dirname(in_network_txt)
cm.log_init(log)
cm.log('Reading network configuration')
F = cm.read_network(in_network_txt) # read in full network
nodes_shp = F.config[('shapefile', 'nodes')]
lcpaths_txt = F.config[('leastcostpaths', 'txt')]
G = NX.Graph() # create fresh graph
cm.log('Reading least-cost paths into fresh graph with only centroids')
rdr = csv.reader(open(lcpaths_txt, 'r'))
headers = rdr.next()
for row in rdr:
c1, c2, w = row[0:3]
G.add_edge(int(c1), int(c2), weight=int(w))
cm.log(
'Calculating centrality metrics (only works with NetworkX 0.35.1 and higher)'
)
# E:\code\connmod\branches\ch\data\net2010\network_trunc_lc.txt "Feature Set" "2010\truncated\edges - trunc lc"
# E:\code\connmod\branches\ch\data\net2010c\network_trunc_lc.txt "2010\truncated\edges - trunc lc"
import sys, string, os, arcgisscripting, csv, networkx as NX, cm
# Create the Geoprocessor object
GP = cm.gp_init()
log = '%s/log.txt' % os.path.dirname(sys.argv[0])
cm.log_init(log, 'debug')
# Script arguments...
network_txt = sys.argv[1]
edges_lyr = sys.argv[2]
# read in network
cm.log('Reading input network')
G = cm.read_network(network_txt)
edges_shp = G.config[('shapefile', 'edges')]
lc_txt = G.config[('leastcostpaths', 'txt')]
## debug
##edges_lyr = 'edges_lyr'; GP.MakeFeatureLayer(edges_shp, edges_lyr)
##GP.SelectLayerByAttribute_management(edges_lyr, "NEW_SELECTION", "\"EdgeID\" IN (6693)")
# get selected edges
cur = GP.SearchCursor(edges_lyr)
row = cur.Next()
e_selected = []
while row:
e_selected.append(row.GetValue('EdgeID'))
row = cur.Next()
# network derivative data files
network = os.path.splitext(network_txt)[0]
network_edgelist = network + '_edgelist.txt'
network_nodeattr = network + '_nodeattr.csv'
network_edgeattr = network + '_edgeattr.csv'
# initialize output folder
GP.CreateFolder_management(os.path.dirname(wd), os.path.basename(wd))
# logging
log = '%s/log.txt' % wd
cm.log_init(log, 'debug')
# NetworkX version report and check
cm.log('Using NetworkX %s' % NX.__version__)
if NX.__version__ < '1.0':
cm.log('MUST FIX: Need NetworkX version 1.0 or higher', type='error')
try:
cm.log('Creating folder and geodatabase')
if not GP.Exists(gdb):
GP.CreateFileGDB_management(os.path.dirname(gdb), os.path.basename(gdb))
GP.workspace = wd
cm.log('Copying patches')
GP.CopyFeatures(patches_in, patches)
flds = GP.ListFields(patches)
if 'PATCHID' in [f.Name.upper() for f in flds]:
cm.log('The PatchID field name is reserved. Please remove this field from the input patches.', type='error')
GP.AddField(patches, 'PatchID', 'LONG')
# setup geoprocessor
GP = cm.gp_init()
# Get arguments:
in_network_txt = sys.argv[1] # the textfile that locates all the graph stuff
wt_min = sys.argv[2] # minimum edge weight
wt_max = sys.argv[3] # max weight
wt_inc = sys.argv[4] # increment for thresholding sequence (loop)
out_csv = sys.argv[5] # output CSV file (generates a plot, not an Arc object)
# initialize logging
log = '%s/log_thresholding.txt' % os.path.dirname(in_network_txt)
cm.log_init(log)
cm.log('Reading network configuration')
F = cm.read_network(in_network_txt) # read in full network
#nodes_shp = F.config[('shapefile', 'nodes')]
lcpaths_txt = F.config[('leastcostpaths', 'txt')]
G = NX.XGraph() # create fresh graph
cm.log('Reading least-cost paths into fresh graph with only centroids')
rdr = csv.reader(open(lcpaths_txt,'r'))
headers = rdr.next()
for row in rdr:
c1,c2,w = row[0:3]
G.add_edge(int(c1), int(c2), int(w))
# Process and write output:
cm.log('Creating sequence of thresholded networks')
import sys, string, os, arcgisscripting
import networkx as NX
import cm
# Create the Geoprocessor object
GP = cm.gp_init()
log = '%s/log.txt' % os.path.dirname(sys.argv[0])
cm.log_init(log, 'debug')
# Script arguments...
network_txt = sys.argv[1]
pts_inx = sys.argv[2]
edges_lyr = sys.argv[3]
# read in network
cm.log('Reading input network')
G = cm.read_network(network_txt)
nodes_shp = G.config[('shapefile', 'nodes')]
edges_shp = G.config[('shapefile', 'edges')]
# Local variables...
centroids_near_pts = 'in_memory\\centroids_near_pts'
##centroids_near_pts = "E:\\code\\connmod\\branches\\ch\\data\\net2010\\centroids_near.dbf"
if GP.exists(centroids_near_pts):
GP.delete(centroids_near_pts)
#debug
#GP.CopyFeatures(pts_inx, r'C:\temp\connectivity\network_cost\geodb.gdb\pts_inx')
GP.MakeFeatureLayer(nodes_shp, 'nodes_lyr')
GP.SelectLayerByAttribute_management('nodes_lyr', 'NEW_SELECTION', "\"NodeType\" = 'centroid'")
# arguments in
in_network_txt = sys.argv[1]
out_network_fld = sys.argv[2]
out_network_txt = sys.argv[3]
# setup vars for out_network config
out_network = os.path.splitext(out_network_txt)[0]
out_edgelist = out_network + '_edgelist.txt'
out_nodeattr = out_network + '_nodeattr.csv'
out_edgeattr = out_network + '_edgeattr.csv'
# logging
log = '%s/log.txt' % os.path.dirname(out_network)
cm.log_init(log, 'debug')
cm.log('Reading input network')
G = cm.read_network(in_network_txt)
# PROBLEM: patches sharing same node, ie edge
#Identity_analysis full\nodes patches D:\code\connmod\branches\ch\data\network\full_2\nodes_identity.shp ALL "" KEEP_RELATIONSHIPS
cm.log('Removing existing internal nodes (%d) and edges (%d)' %
(len(G.nbytype['internal']), len(G.ebytype['internal'])))
H = G.copy()
H.delete_edges_from(G.ebytype['internal'])
H.delete_nodes_from(G.nbytype['internal'])
cm.copy_g_attr(G, H)
cm.log('Adding edges from centroids (%d) to perimeter nodes (%d)' %
(len(G.nbytype['centroid']), len(G.nbytype['perimeter'])))
centroids = G.nbytype['centroid']
else:
costthreshold = int(sys.argv[2].split()[0])
out_network_fld = sys.argv[3]
out_network_txt = sys.argv[4]
# setup vars for out_network config
out_network = os.path.splitext(out_network_txt)[0]
out_edgelist = out_network + '_edgelist.txt'
out_nodeattr = out_network + '_nodeattr.csv'
out_edgeattr = out_network + '_edgeattr.csv'
# logging
log = '%s/log.txt' % os.path.dirname(out_network)
cm.log_init(log, 'debug')
cm.log('Reading input network')
G = cm.read_network(in_network_txt)
cm.log('Trimming graph based on threshold cumulative cost %g' % costthreshold)
H = G.copy()
nlist = []
for n, z in G.nz.iteritems():
if z >= costthreshold:
H.remove_edges_from(G.edges(n))
H.remove_node(n)
edges = H.edges(data=True)
for (u, v, w) in edges:
if w['weight'] >= costthreshold:
H.remove_edge(u, v)
cm.log('Trimming isolated nodes with 1 or 0 neighbors')
2] == '#': # if no linear unit specified in optional eucthreshold parameter
eucthreshold = ''
else:
eucthreshold = int(sys.argv[2].split()[0])
out_network = os.path.splitext(out_network_txt)[0]
out_lcpaths = out_network + '_lcpaths.txt'
out_edgelist = out_network + '_edgelist.txt'
out_nodeattr = out_network + '_nodeattr.csv'
out_edgeattr = out_network + '_edgeattr.csv'
paths_tbl = '%s/geodb.gdb/paths_%s' % (os.path.dirname(in_network_txt), net)
log = '%s/log_%s.txt' % (os.path.dirname(wd), net)
cm.log_init(log)
cm.log('Reading in network')
G = cm.read_network(in_network_txt)
cm.log('Converting network edge weights to integer')
for (u, v, d) in G.edges_iter(data=True):
G.remove_edge(u, v)
G.add_edge(u, v, weight=int(d['weight']))
H = NX.Graph() # setup empty subgraph to populate with edges
cm.log(
'Building centroid-to-centroid paths restricted by component using bidirectional_dijkstra'
)
Cs = NX.connected_component_subgraphs(G)
nC = len(Cs)
paths = {}