def main(argv=None):
if argv is None:
argv = sys.argv
# Setup vanilla CLI parsing and add custom arg(s).
parser = utils.setup_cli_parsing()
parser.add_option("",
"--codewords",
help="number of codewords.",
default=50,
type="int")
(options, args) = parser.parse_args()
# Setup logging
utils.setup_logging(options)
logger = logging.getLogger()
# Read graph file list and label file list
graph_file_list = utils.read_graph_file_list(options)
if not options.globalLabelFile is None:
label_file_list = [options.globalLabelFile] * len(graph_file_list)
else:
label_file_list = utils.read_label_file_list(options,
graph_file_list)
# Read class info and grouping info
class_info = utils.read_class_info(options)
group_info = utils.read_group_info(options)
assert (group_info.shape[0] ==
len(class_info) ==
len(graph_file_list) ==
len(label_file_list))
# Zip lists together
data = zip(graph_file_list,
label_file_list,
class_info)
# Run fine-structure analysis
fsa_res = fsa.run_fsa(data,
options.radii,
options.recompute,
options.writeAs,
options.skip,
options.omitDegenerate)
data_mat = fsa_res['data_mat']
data_idx = fsa_res['data_idx']
# Create cross-validation folds
# NOTE: random_state=0 should guarantee equal splits
n_graphs = len(class_info)
cv = ShuffleSplit(n_graphs,
n_iter=options.cvRuns,
test_size=0.2,
random_state=0)
# Try inplace feature normalization
if options.normalize:
logger.info("Running feature normalization ...")
scaler = preprocessing.StandardScaler(copy=False)
scaler.fit_transform(fsa_res['data_mat'])
scores = []
todisk = []
for cv_id, (trn, tst) in enumerate(cv):
# Compose training data
pos = []
for i in trn:
tmp = np.where(data_idx==i)[0]
pos.extend(list(tmp))
np_pos = np.array(pos)
# Learn a codebook from training data
codebook = fsa.learn_codebook(data_mat[np_pos,:],
options.codewords,
options.seed)
# Compute BoW histograms for training data
bow_trn_mat = np.zeros((len(trn), options.codewords))
for cnt, i in enumerate(trn):
np_pos = np.where(data_idx==i)[0]
bow_trn_mat[cnt,:] = np.asarray(fsa.bow(data_mat[np_pos,:],
codebook))
# Cross-validate (5-fold) SVM classifier and parameters
param_selection = [{'kernel': ['rbf'],
'gamma': np.logspace(-6,2,10),
'C': [1, 10, 100, 1000]},
{'kernel': ['linear'],
'C': [1, 10, 100, 1000]}]
clf = GridSearchCV(svm.SVC(C=1), param_selection, cv=5)
clf.fit(bow_trn_mat, np.asarray(class_info)[trn])
# Compute BoW histograms for testing data
bow_tst_mat = np.zeros((len(tst), options.codewords))
for cnt,i in enumerate(tst):
pos = np.where(data_idx==i)[0]
bow_tst_mat[cnt,:] = fsa.bow(data_mat[pos,:], codebook)
yhat = clf.predict(bow_tst_mat)
gold = np.asarray(class_info)[tst]
print "yhat : ", yhat
print "gold : ", gold
tmp = {"yhat" : list(yhat),
"gold" : list(gold)}
todisk.append(tmp)
# Score the classifier
score = clf.score(bow_tst_mat, np.asarray(class_info)[tst])
scores.append(score)
logger.info("Score (%.2d): %.2f" % (cv_id,100*score))
json_file = "%s.json" % options.writeAs
with open(json_file, 'w') as outfile:
json.dump(todisk, outfile)
utils.show_summary(scores)
def main(argv=None):
if argv is None:
argv = sys.argv
# Setup vanilla CLI parsing and add custom arg(s).
parser = utils.setup_cli_parsing()
parser.add_option("",
"--mixComp",
help="number of GMM components.",
default=3,
type="int")
(options, args) = parser.parse_args()
# Setup logging
utils.setup_logging(options)
logger = logging.getLogger()
# Read graph file list and label file list
graph_file_list = utils.read_graph_file_list(options)
label_file_list = utils.read_label_file_list(options, graph_file_list)
# Read class info and grouping info
class_info = utils.read_class_info(options)
group_info = utils.read_group_info(options)
assert (group_info.shape[0] == len(class_info) == len(graph_file_list) ==
len(label_file_list))
# Zip lists together
data = zip(graph_file_list, label_file_list, class_info)
# Run fine-structure analysis
fsa_res = fsa.run_fsa(data, options.radii, options.recompute,
options.writeAs, options.skip,
options.omitDegenerate)
data_mat = fsa_res['data_mat']
data_idx = fsa_res['data_idx']
# Create cross-validation folds (20% testing)
n_graphs = len(class_info)
cv = ShuffleSplit(n_graphs,
n_iter=options.cvRuns,
test_size=0.2,
random_state=0)
# Our unique class labels
label_set = np.unique(class_info)
if options.normalize:
logger.info("Running feature normalization ...")
scaler = preprocessing.StandardScaler(copy=False)
scaler.fit_transform(fsa_res['data_mat'])
scores = []
for cv_id, (trn, tst) in enumerate(cv):
models = []
for l in label_set:
l_idx = np.where(class_info == l)[0]
l_idx = np.asarray(l_idx).ravel()
l_trn = np.intersect1d(l_idx, trn)
pos = []
for i in l_trn:
tmp = np.where(fsa_res['data_idx'] == i)[0]
pos.extend(list(tmp))
np_pos = np.asarray(pos)
gmm_model = fsa.estimate_gm(data_mat[np_pos, :], options.mixComp)
models.append(gmm_model)
predict = []
for i in tst:
pos = np.where(data_idx == i)[0]
map_idx = fsa.pp_gmm(data_mat[pos, :], models, argmax=True)
predict.append(label_set[map_idx])
# Score the MAP classifier
truth = [class_info[i] for i in tst]
score = accuracy_score(truth, predict)
print "yhat :", predict
print "gold :", truth
logger.info("Score (%.2d): %.2f" % (cv_id, 100 * score))
scores.append(score)
utils.show_summary(scores)
def main(argv=None):
if argv is None:
argv = sys.argv
# Setup vanilla CLI parsing and add custom arg(s).
parser = utils.setup_cli_parsing()
parser.add_option("",
"--mixComp",
help="number of GMM components.",
default=3,
type="int")
(options, args) = parser.parse_args()
# Setup logging
utils.setup_logging(options)
logger = logging.getLogger()
# Read graph file list and label file list
graph_file_list = utils.read_graph_file_list(options)
label_file_list = utils.read_label_file_list(options, graph_file_list)
# Read class info and grouping info
class_info = utils.read_class_info(options)
group_info = utils.read_group_info(options)
assert (group_info.shape[0] ==
len(class_info) ==
len(graph_file_list) ==
len(label_file_list))
# Zip lists together
data = zip(graph_file_list,
label_file_list,
class_info)
# Run fine-structure analysis
fsa_res = fsa.run_fsa(data,
options.radii,
options.recompute,
options.writeAs,
options.skip,
options.omitDegenerate)
data_mat = fsa_res['data_mat']
data_idx = fsa_res['data_idx']
# Create cross-validation folds (20% testing)
n_graphs = len(class_info)
cv = ShuffleSplit(n_graphs,
n_iter=options.cvRuns,
test_size=0.2,
random_state=0)
# Our unique class labels
label_set = np.unique(class_info)
if options.normalize:
logger.info("Running feature normalization ...")
scaler = preprocessing.StandardScaler(copy=False)
scaler.fit_transform(fsa_res['data_mat'])
scores = []
for cv_id, (trn, tst) in enumerate(cv):
models = []
for l in label_set:
l_idx = np.where(class_info == l)[0]
l_idx = np.asarray(l_idx).ravel()
l_trn = np.intersect1d(l_idx, trn)
pos = []
for i in l_trn:
tmp = np.where(fsa_res['data_idx']==i)[0]
pos.extend(list(tmp))
np_pos = np.asarray(pos)
gmm_model = fsa.estimate_gm(data_mat[np_pos,:], options.mixComp)
models.append(gmm_model)
predict = []
for i in tst:
pos = np.where(data_idx==i)[0]
map_idx = fsa.pp_gmm(data_mat[pos,:], models, argmax=True)
predict.append(label_set[map_idx])
# Score the MAP classifier
truth = [class_info[i] for i in tst]
score = accuracy_score(truth, predict)
print "yhat :", predict
print "gold :", truth
logger.info("Score (%.2d): %.2f" % (cv_id, 100*score))
scores.append(score)
utils.show_summary(scores)
def main(argv=None):
if argv is None:
argv = sys.argv
# Setup vanilla CLI parsing and add custom arg(s).
parser = utils.setup_cli_parsing()
parser.add_option("",
"--codewords",
help="number of codewords.",
default=50,
type="int")
(options, args) = parser.parse_args()
# Setup logging
utils.setup_logging(options)
logger = logging.getLogger()
# Read graph file list and label file list
graph_file_list = utils.read_graph_file_list(options)
if not options.globalLabelFile is None:
label_file_list = [options.globalLabelFile] * len(graph_file_list)
else:
label_file_list = utils.read_label_file_list(options,
graph_file_list)
# Read class info and grouping info
class_info = utils.read_class_info(options)
group_info = utils.read_group_info(options)
assert (group_info.shape[0] ==
len(class_info) ==
len(graph_file_list) ==
len(label_file_list))
# Zip lists together
data = zip(graph_file_list,
label_file_list,
class_info)
# Run fine-structure analysis
fsa_res = fsa.run_fsa(data,
options.radii,
options.recompute,
options.writeAs,
options.skip,
options.omitDegenerate)
data_mat = fsa_res['data_mat']
data_idx = fsa_res['data_idx']
# Create cross-validation folds
n_graphs = len(class_info)
cv = ShuffleSplit(n_graphs,
n_iter=options.cvRuns,
test_size=0.2,
random_state=0)
# Try inplace feature normalization
if options.normalize:
logger.info("Running feature normalization ...")
scaler = preprocessing.StandardScaler(copy=False)
scaler.fit_transform(fsa_res['data_mat'])
scores = []
for cv_id, (trn, tst) in enumerate(cv):
# Compose training data
pos = []
for i in trn:
tmp = np.where(data_idx==i)[0]
pos.extend(list(tmp))
np_pos = np.array(pos)
# Learn a codebook from training data
codebook = fsa.learn_codebook(data_mat[np_pos,:],
options.codewords,
options.seed)
# Compute BoW histograms for training data
bow_trn_mat = np.zeros((len(trn), options.codewords))
for cnt, i in enumerate(trn):
np_pos = np.where(data_idx==i)[0]
bow_trn_mat[cnt,:] = np.asarray(fsa.bow(data_mat[np_pos,:],
codebook))
# Cross-validate (5-fold) SVM classifier and parameters
param_selection = [{'kernel': ['rbf'],
'gamma': np.logspace(-6,2,10),
'C': [1, 10, 100, 1000]},
{'kernel': ['linear'],
'C': [1, 10, 100, 1000]}]
clf = GridSearchCV(svm.SVC(C=1), param_selection)
clf.fit(bow_trn_mat, np.asarray(class_info)[trn], cv=5)
# Compute BoW histograms for testing data
bow_tst_mat = np.zeros((len(tst), options.codewords))
for cnt,i in enumerate(tst):
pos = np.where(data_idx==i)[0]
bow_tst_mat[cnt,:] = fsa.bow(data_mat[pos,:], codebook)
print "yhat : ", clf.predict(bow_tst_mat)
print "gold : ", np.asarray(class_info)[tst]
# Score the classifier
score = clf.score(bow_tst_mat, np.asarray(class_info)[tst])
scores.append(score)
logger.info("Score (%.2d): %.2f" % (cv_id,100*score))
utils.show_summary(scores)