def test_groups():
avec = [34, 34, 5, 11, 5, 5433]
truth_clustering = [[0, 1], [2, 4], [3], [5]]
clustering = query.groups(avec, sort=False)
assert_equals(len(clustering), len(np.unique(avec)))
assert_equals(set(map(frozenset, truth_clustering)),
set(map(frozenset, clustering)))
clustering = query.groups(avec, sort=True)
assert_equals(map(len, clustering),
sorted(map(len, truth_clustering), reverse=True))
def infinite_relational_model(corr_matrix, lag_matrix, threshold, sampled_coords, window_size):
import numpy as np
import math
import json
import time
import itertools as it
from multiprocessing import cpu_count
from microscopes.common.rng import rng
from microscopes.common.relation.dataview import numpy_dataview
from microscopes.models import bb as beta_bernoulli
from microscopes.irm.definition import model_definition
from microscopes.irm import model, runner, query
from microscopes.kernels import parallel
from microscopes.common.query import groups, zmatrix_heuristic_block_ordering, zmatrix_reorder
cluster_matrix = []
graph = []
# calculate graph
for row in corr_matrix:
graph_row = []
for corr in row:
if corr < threshold:
graph_row.append(False)
else:
graph_row.append(True)
graph.append(graph_row)
graph = np.array(graph, dtype=np.bool)
graph_size = len(graph)
# conduct Infinite Relational Model
defn = model_definition([graph_size], [((0, 0), beta_bernoulli)])
views = [numpy_dataview(graph)]
prng = rng()
nchains = cpu_count()
latents = [model.initialize(defn, views, r=prng, cluster_hps=[{'alpha':1e-3}]) for _ in xrange(nchains)]
kc = runner.default_assign_kernel_config(defn)
runners = [runner.runner(defn, views, latent, kc) for latent in latents]
r = parallel.runner(runners)
start = time.time()
# r.run(r=prng, niters=1000)
# r.run(r=prng, niters=100)
r.run(r=prng, niters=20)
print ("inference took", time.time() - start, "seconds")
infers = r.get_latents()
clusters = groups(infers[0].assignments(0), sort=True)
ordering = list(it.chain.from_iterable(clusters))
z = graph.copy()
z = z[ordering]
z = z[:,ordering]
corr_matrix = corr_matrix[ordering]
corr_matrix = corr_matrix[:,ordering]
lag_matrix = lag_matrix[ordering]
lag_matrix = lag_matrix[:,ordering]
cluster_sampled_coords = np.array(sampled_coords)
cluster_sampled_coords = cluster_sampled_coords[ordering]
response_msg = {
'corrMatrix': corr_matrix.tolist(),
'lagMatrix': lag_matrix.tolist(),
'clusterMatrix': z.tolist(),
'clusterSampledCoords': cluster_sampled_coords.tolist(),
'nClusterList': [len(cluster) for cluster in clusters],
'ordering': ordering,
}
f = open("./expdata/clustermatrix-" + str(window_size) + ".json", "w")
json.dump(response_msg, f)
f.close()
return response_msg
# ##From here, we can finally run each chain of the sampler 1000 times
# In[ ]:
start = time.time()
r.run(r=prng, niters=1000)
print "inference took {} seconds".format(time.time() - start)
# ##Now that we have learned our model let's get our cluster assignments
# In[ ]:
infers = r.get_latents()
clusters = groups(infers[0].assignments(0), sort=True)
ordering = list(it.chain.from_iterable(clusters))
# ##Let's sort the communications matrix to highlight our inferred clusters
# In[ ]:
z = communications_relation.copy()
z = z[ordering]
z = z[:,ordering]
sizes = map(len, clusters)
boundaries = np.cumsum(sizes)[:-1]
def cluster_with_name(clusters, name, payload=None):
ident = namemap[name]
r = parallel.runner(runners)
# ##From here, we can finally run each chain of the sampler 1000 times
# In[ ]:
start = time.time()
r.run(r=prng, niters=1000)
print "inference took {} seconds".format(time.time() - start)
# ##Now that we have learned our model let's get our cluster assignments
# In[ ]:
infers = r.get_latents()
clusters = groups(infers[0].assignments(0), sort=True)
ordering = list(it.chain.from_iterable(clusters))
# ##Let's sort the communications matrix to highlight our inferred clusters
# In[ ]:
z = communications_relation.copy()
z = z[ordering]
z = z[:, ordering]
sizes = map(len, clusters)
boundaries = np.cumsum(sizes)[:-1]
def cluster_with_name(clusters, name, payload=None):
ident = namemap[name]