def main (k, m="means", init_type="random"):
# Starting clustering timer
start_cluster = timeit.default_timer()
# Initialize clusters
if init_type == "random":
initial_clusters = Initialize.random_centers(k)
else:
init_type = "kplusplus"
initial_clusters = Initialize.kmeans_plusplus(k, train_images_flat,\
dist_fn=Distance.sumsq)
# Run clustering algorithm
final_responsibilities, final_clusters = Kmeans.kmeans(k,train_images_flat,
initial_clusters, distfn = Distance.sumsq, method=m)
# Find and print clustering time
end_cluster = timeit.default_timer()
clustering_time = end_cluster - start_cluster
print "Time spent clustering : ", clustering_time
# Save representative images to file.
title = m + "_" + init_type + "_cluster" + str(k)
File.save_images(k, train_images, final_responsibilities,
final_clusters, title)
###########################################################################
# Calculate Accuracy #
###########################################################################
# Calculate final accuracy for clusters
final, cluster_set = Accuracy.final_accuracy(final_responsibilities,
train_labels, train_images_flat, final_clusters)
# Now see how well we can classify the dataset
start_cluster_test = timeit.default_timer()
predictions = ClassifyClusters.classify(cluster_set, test_images_flat,
test_labels, distfn = Distance.sumsq)
finish_cluster_test = timeit.default_timer()
# find time it took to test
testing_time = finish_cluster_test - start_cluster_test
print "Time spent testing : ", testing_time
###########################################################################
# Outputs #
###########################################################################
# k, prediction level, cluster_set,
results = {"k" : k, "prediction_accuracy" : predictions[1],
"cluster_means" : cluster_set, "cluster_stats" : final,
"clustering_time" : clustering_time, "testing_time" : testing_time}
with open('./results/' + title + '/' + title + '_results.json', 'w') as outfile:
json.dump(results, outfile, cls=File.NumpyEncoder)
def kmeans(k, training_data, initial_clusters, distfn = Distance.sumsq,
method = "means"):
n = len(training_data) # number of training instances
i = 0 # keep track of iteration
r = np.zeros((n,k)) # create empty array to store cluster assignments
# find and store k that minimize sum of square distance for each image
# in form of a vector of shape (n,)
newks = np.apply_along_axis(Distance.leastsquares, 1, training_data,
initial_clusters, distfn)
# Check if every cluster is represented within the cluster assignments;
# if not then re-initialize centers
while np.array_equal(np.unique(newks), np.array(range(k))) == False:
initial_clusters = Initialize.random_centers(k)
newks = np.apply_along_axis(Distance.leastsquares, 1, training_data,
initial_clusters, distfn)
# create one hot coded vector for each image to signify cluster assignment
r[range(n), newks] = 1
# create a "means" vector to store cluster centers as they are updated
means = initial_clusters
# Find new means
while True:
for smallk in range(k): # iterate through clusters
ones = np.where(r[:,smallk]==1)[0]
# The k-means method updates cluster centers to be the mean of each
# corresponding pixel of the datapoints that are contained in that
# cluster.
if method == "means":
means[smallk,:] = np.mean(training_data[list(ones),:], axis=0)
# The k-medoids method updates cluster centers to be the closest
# *datapoint* to the mean of the corresponding pixel of datapoints
# contained in that cluster.
elif method == "medoids":
dist_to_ctr = np.sum((training_data[list(ones),:]
- np.mean(training_data[list(ones),:], axis=0))**2,axis=1)
means[smallk,:]=training_data[list(ones),:]\
[np.argmin(dist_to_ctr)]
# The k-medians method updates cluster centeras to be the median of
# each corresponding pixel of the datapoints contained in that
# cluster.
elif method == "medians":
means[smallk,:] = np.median(training_data[list(ones),:],axis=0)
# If no proper value is chosen for method, then return error.
else:
raise ValueError("Not a valid method specification; must be \
'means','medoids', or 'medians'")
# update responsibilities by minimizing distance metric
r_new = np.zeros((n,k))
# stores indices of k's that minimize distance metric
newks = np.apply_along_axis(Distance.leastsquares, 1, training_data,
means, distfn)
r_new[range(n), newks] = 1
# if none of the responsibilities change, then we've reached the optimal
# cluster assignments
if np.all((r_new - r)==0):
return r, means
else:
r = r_new
# After each iteration, print iteration number and the number of images
# assigned to a given cluster.
print i, r.sum(axis=0)
i += 1
print 'finished'