Author: ruschein
Date: 2009-12-21 10:43:33 -0800 (Mon, 21 Dec 2009)
New Revision: 18797
Modified:
cytoscape/trunk/testData/NNFData/generate_multi_level_networks
Log:
Fixed and tested.
Modified: cytoscape/trunk/testData/NNFData/generate_multi_level_networks
===================================================================
--- cytoscape/trunk/testData/NNFData/generate_multi_level_networks
2009-12-19 01:00:03 UTC (rev 18796)
+++ cytoscape/trunk/testData/NNFData/generate_multi_level_networks
2009-12-21 18:43:33 UTC (rev 18797)
@@ -2,7 +2,7 @@
"""
Program for generating multi-level nested network files.
"""
-from sets import Set
+#from sets import Set
from random import randint
import sys, os, math
@@ -38,23 +38,25 @@
# Returns the approx. no of nodes per network.
-def CalcApproxNetworkSize(levels, object_count):
- def f(x):
- return math.pow(x, levels + 1) - (object_count + 1) * x + object_count
- def f_prime(x):
- return (levels + 1) * math.pow(x, levels) - object_count - 1
- def root(k, x):
+def CalcApproxNetworkSize(levels, link_factor, object_count):
+ def f(n):
+ return (1.0 + link_factor) * math.pow(n, levels + 1.0) - (1.0 +
link_factor + object_count) * n + object_count
+ def f_prime(n):
+ return (1.0 + link_factor) * (levels + 1.0) * math.pow(n, levels) -
1.0 - link_factor - object_count
+ def root(k, x): # k-th root of x
return math.pow(x, 1.0 / k)
# Use Newton-Raphson to find the root of f()
- x = root(levels, object_count) # initial approximation
+ no_of_nodes_per_network = root(levels, object_count) # initial
approximation
iteration_count = 10
- for i in range(0, iteration_count):
- x = x - f(x) / f_prime(x)
+ max_rel_error = 1.0e-10
+ while True:
+ old_no_of_nodes_per_network = no_of_nodes_per_network
+ no_of_nodes_per_network = no_of_nodes_per_network -
f(no_of_nodes_per_network) / f_prime(no_of_nodes_per_network)
+ if math.fabs(old_no_of_nodes_per_network - no_of_nodes_per_network) <
max_rel_error:
+ return no_of_nodes_per_network
- return x
-
# Command-line argument processing. Returns the triple (levels, object_count,
link_factor).
def ProcessArgs(argv):
if len(argv) != 4:
@@ -78,8 +80,7 @@
(levels, object_count, link_factor) = ProcessArgs(sys.argv)
-approx_total_node_count = object_count / (1.0 + link_factor)
-nodes_per_network = CalcApproxNetworkSize(levels,
approx_total_node_count)
+nodes_per_network = CalcApproxNetworkSize(levels, link_factor,
object_count)
edges_per_network = nodes_per_network * link_factor
nodes_per_network = int(nodes_per_network + 0.5) # Round to nearest
integer.
edges_per_network = int(edges_per_network + 0.5) # Round to nearest
integer.
@@ -98,13 +99,13 @@
if level > 1:
print # Output a blank line.
- print "# Starting level " + str(level)
+# print "# Starting level " + str(level)
network_name_prefix = "L" + str(level) + "_"
for network in range(1, no_of_networks + 1):
network_name = network_name_prefix + str(network)
node_name_prefix = "L" + str(level + 1) + "_"
- GenerateNetwork(network_name, node_name_prefix, nodes_per_network,
edges_per_network)
+# GenerateNetwork(network_name, node_name_prefix, nodes_per_network,
edges_per_network)
actual_object_count += nodes_per_network + edges_per_network
no_of_networks *= nodes_per_network
--
You received this message because you are subscribed to the Google Groups
"cytoscape-cvs" group.
To post to this group, send email to [email protected].
To unsubscribe from this group, send email to
[email protected].
For more options, visit this group at
http://groups.google.com/group/cytoscape-cvs?hl=en.
