def prepare_regions( self ):
"""
Partition the phase space into disjoint, recurrent regions.
Must have initialized self with index_map matrix and
region2gen dictionary, or used one of the load_from_* methods
to initialize these values.
"""
# returns a DiGraph
self.map_on_regions = utils.index_map_to_region_map( self.index_map,
self.region2gen )
# graph_mis from graphs.algorithms
scc_list, scc_components, recurrent_regions = graph_mis( self.map_on_regions,
return_rsccs=True )
nbunch = [ scc_components[i] for i in recurrent_regions ]
self.recurrent_subgraphs = []
# the actual partition of phase space in graph format
for n in nbunch:
# ignore disjoint regions/nodes that have self-loops => no
# entropy
if len( n ) == 1:
continue
G = DiGraph()
G.graph = self.map_on_regions.graph.subgraph( n )
self.recurrent_subgraphs.append( G )
# construct IndexMapProcessor for each disjoint region
# assign entropies of -1 to each recurrent region.
for region in self.recurrent_subgraphs:
self.phase_space.append( [ IndexMapProcessor( self.index_map,
self.region2gen,
region,
debug=self.debug,
verbose=self.verbose ),
-1 # initial entropy for region
] )
1 : [2],
2 : [3,4]
}
symbols = numpy.matrix( [[0,1,1],
[1,0,0],
[0,1,1]]
)
map_on_regions = DiGraph()
map_on_regions.from_numpy_matrix( symbols )
if 1:
hom_matrix = utils.load_matlab_matrix( 'henon_index.mat', 'hom_matrix' )
region2gen = utils.convert_matlab_gens( 'henon_gens.mat' )
map_on_regions = utils.index_map_to_region_map( hom_matrix, region2gen, shift=-1)
if 0:
hom_matrix = utils.load_matlab_matrix( 'leslie_index.mat', 'hom_matrix' )
region2gen = utils.convert_matlab_gens( 'leslie_gens.mat' )
map_on_regions = utils.index_map_to_region_map( hom_matrix, region2gen, shift=-1)
########################
#
# APPEARS THAT BAD EDGE SETS ARE BEING THROWN INTO ONE (1) SET. CHECK THIS!!
#
########################
debug = True
verbose = False
