def process_file(filename, treatment, rat, session):
"""prints out a variety of statistics for each zone"""
zone_g, between_zone_g = zone_graphs("zone-graph.txt")
baseline = uniform_zone_entropy(zone_g)
between_zone_baseline = uniform_zone_entropy(between_zone_g)
allzones = zones(filename)
bigram_counts = remove_terminal_transitions(bigrams(allzones))
bigram_probs = probs_bigrams(bigram_counts)
between_zone_bigram_counts = remove_self_transitions(bigram_counts)
between_zone_bigram_probs = probs_bigrams(between_zone_bigram_counts)
#print filename
for (zone, p) in bigram_probs.iteritems():
zone_destinations = zone_g[zone].keys()
#impossible_transitions = [(zone, z2, pr) for (z2, pr) in p.iteritems() if z2 not in zone_destinations]
impossible_transitions = find_impossible_transitions(zone_g, zone, p)
#if len(impossible_transitions) > 0:
#print "impossible transitions: " , treatment, rat, session, impossible_transitions
entropy = h(p.values())
count = sum(bigram_counts[zone].values())
bz_p = between_zone_bigram_probs[zone]
bz_entropy = h(bz_p.values())
bz_count = sum(between_zone_bigram_counts[zone].values())
#details = ' '.join([ "%4s:%f" % pair for pair in p.iteritems()])
#print "\t%4s : %4d * %f -> %4s" % (zone, count, entropy, details)
print ','.join([str(x) for x in
[treatment, rat, session, zone,
entropy, baseline[zone], baseline[zone]-entropy,
bz_entropy, between_zone_baseline[zone], between_zone_baseline[zone]-bz_entropy,
count, bz_count]])
def distance_matrix(filename, distance_finder, print_dicts=False):
allforays = [f for f in forays(zones(filename))]
nf = len(allforays)
if print_dicts:
print "%s: %d forays" % (filename, nf)
#for f in allforays:
#print '-'.join(f)
distances = numpy.zeros((nf, nf))
for i in range(0,nf-1):
for j in range(i+1,nf):
distances[i,j] = distance_finder.distance(allforays[i], allforays[j], False)
if print_dicts:
print type(distance_finder).__name__
print distances
return distances
