def full_steady_state_calc(G,nodes_list,init_dID,desired_dID):
""" run through full steady state calculation from stochastic transition matrix
to find the probability of being in each attractor during steady state """
state_trans_dict = create_state_transitions_dict(G)
deterministic_transition_graph = time_evol.net_state_transition(G, nodes_list) # deterministic transition graph
attractors = time_evol.find_attractor_old(deterministic_transition_graph) # this must only print out cycles for a subset of the graph...
attractor_list = make_attractor_list(attractors)
T = create_transition_matrix(state_trans_dict)
attractor_dict, prob_desired_dID = find_steady_state(T,attractor_list,init_dID,desired_dID)
return attractor_dict, prob_desired_dID
def main():
print "updating_rule module is the main code."
edge_file = '../data/inputs/edges-init.dat'
#############################
## Read in anterior nodes
#############################
node_file = '../data/inputs/ant-nodes-init.dat'
desired_node_file = '../data/inputs/ant-nodes-final.dat'
G = inet.read_network_from_file(edge_file, node_file)
nodes_list = G.nodes()
node_dict = nx.get_node_attributes(G,'state')
init_dID = time_evol.binary_to_decimal(nodes_list, node_dict)
#############################
## Read in posterior nodes
#############################
post_node_file = '../data/inputs/post-nodes-init.dat'
post_desired_node_file = '../data/inputs/post-nodes-final.dat'
G_post = inet.read_network_from_file(edge_file, post_node_file)
post_nodes_list = G_post.nodes()
post_node_dict = nx.get_node_attributes(G_post,'state')
post_init_dID = time_evol.binary_to_decimal(post_nodes_list, post_node_dict)
#############################
# print G.nodes()
# print G.edges()
# prev_state = nx.get_node_attributes(G,'state') # dict of key=node, value=state of network G
# print "network state @ prev step", OrderedDict(sorted(prev_state.items(), key=lambda t: t[0]))
# curr_state = boolean_updating(G)
# print "network state @ curr step", OrderedDict(sorted(curr_state.items(), key=lambda t: t[0]))
# print prev_state
# print curr_state
###### calc steady state probabilities #####################################################
# init_dID,desired_dID = 0, 43
init_dID,desired_dID = 20, 980
attractor_dict, prob_desired_dID = full_steady_state_calc(G,nodes_list,init_dID,desired_dID)
print attractor_dict
print prob_desired_dID
exit()
#############################################################################################
## Create deterministic transition graph
state_trans_dict = create_state_transitions_dict(G)
G_state_trans = create_graph_from_transitions(state_trans_dict) # stochastic transition graph
## Calculate in and out degrees of transition graph
out_deg_dict = G_state_trans.out_degree(G_state_trans.nodes())
sorted_out_deg_dict = sorted(out_deg_dict.items(), key=operator.itemgetter(1))
in_deg_dict = G_state_trans.in_degree(G_state_trans.nodes())
sorted_in_deg_dict = sorted(in_deg_dict.items(), key=operator.itemgetter(1))
largest = max(nx.strongly_connected_components(G_state_trans), key=len)
# print len(largest) # this shows that graph of stochastic state transitions is strongly connected
# attractors = time_evol.find_attractor_old(G_state_trans)
create_transition_matrix(state_trans_dict)
deterministic_transition_graph = time_evol.net_state_transition(G, nodes_list) # deterministic transition graph
attractors = time_evol.find_attractor_old(deterministic_transition_graph) # this must only print out cycles for a subset of the graph...
#############################
## Find control kernals
#############################
attractor_ID = 980
# print find_len_1_control_kernals(deterministic_transition_graph, nodes_list, attractor_ID)
# print find_len_2_control_kernals(deterministic_transition_graph, nodes_list, attractor_ID)
print find_len_2_control_kernals_fo_real(deterministic_transition_graph, nodes_list, attractor_ID)
exit()
#############################
## Desired node states
## Anterior
G_desired = inet.read_network_from_file(edge_file, desired_node_file)
desired_nodes_list = G_desired.nodes()
desired_node_dict = nx.get_node_attributes(G_desired,'state')
desired_dID = time_evol.binary_to_decimal(desired_nodes_list,desired_node_dict)
print "desired_node_dict:", desired_node_dict
print "desired dID:", desired_dID
## Posterior
G_desired_post = inet.read_network_from_file(edge_file, post_desired_node_file)
post_desired_nodes_list = G_desired_post.nodes()
post_desired_node_dict = nx.get_node_attributes(G_desired_post,'state')
post_desired_dID = time_evol.binary_to_decimal(post_desired_nodes_list,post_desired_node_dict)
print "post_desired_node_dict:", post_desired_node_dict
print "desired dID:", post_desired_dID
## Check if path between desired init state and final state
print nx.has_path(deterministic_transition_graph,init_dID,desired_dID)
## Print binary version of attractors
print "attractors:"
print attractors
## Network 980 is the steady state network, let's see if this is correct based on rules
# steady_state_network =
print "end_ant:", desired_node_dict
print "beg_ant:", node_dict
print "end_ant_dID:", desired_dID
print "beg_ant_dID:", init_dID
print "end_post:", post_desired_node_dict
print "beg_post:", post_node_dict
print "end_post_dID:", post_desired_dID
print "beg_post_dID:", post_init_dID
# print attractors
# print G_state_trans.edges()
# for line in nx.generate_edgelist(G_state_trans, data=False):
# print line
# nx.draw(G_state_trans)
# nx.write_graphml(G_state_trans,'g_state_trans.xml')
# plt.show()
# for graph in list(nx.weakly_connected_component_subgraphs(deterministic_transition_graph)):
# if 43 in graph.nodes():
# print [time_evol.decimal_to_binary(nodes_list, dID) for dID in graph.nodes()]
# print " 0:", time_evol.decimal_to_binary(nodes_list, 0)
# print "683:", time_evol.decimal_to_binary(nodes_list, 683)
# nx.draw(deterministic_transition_graph)
# nx.write_graphml(deterministic_transition_graph,'deterministic_transition_graph.xml')
# plt.show()
exit()
