def prune_conv(conv, dataset, num_patches, num_features):
if not isinstance(conv[-1], pipeline.Pooler):
raise TypeError, "The last layer should be a pooler."
if not isinstance(conv[-2], pipeline.FeatureEncoder):
raise TypeError, "The second last layer should be an encoder."
logging.debug('Randomly sampling pooled features...')
features = conv.sample(dataset, num_patches, True)
if features.shape[1] != conv[-2].dictionary.shape[0]:
raise ValueError, "Huh, I can't figure out the encoding method.\n"\
"Feature shape: %d, dictionary size: %d" % \
(features.shape[1], conv[-2].dictionary.shape[0])
logging.debug('Perform feature selection...')
covmat = mathutil.mpi_cov(features)
if mpi.is_root():
selected_idx = max_variance_feature_selection(covmat, num_features)
else:
selected_idx = None
selected_idx = mpi.COMM.bcast(selected_idx)
conv[-2].dictionary = conv[-2].dictionary[selected_idx]
return covmat
def prune_conv(conv, dataset, num_patches, num_features):
if not isinstance(conv[-1], pipeline.Pooler):
raise TypeError, "The last layer should be a pooler."
if not isinstance(conv[-2], pipeline.FeatureEncoder):
raise TypeError, "The second last layer should be an encoder."
logging.debug('Randomly sampling pooled features...')
features = conv.sample(dataset, num_patches, True)
if features.shape[1] != conv[-2].dictionary.shape[0]:
raise ValueError, "Huh, I can't figure out the encoding method.\n"\
"Feature shape: %d, dictionary size: %d" % \
(features.shape[1], conv[-2].dictionary.shape[0])
logging.debug('Perform feature selection...')
covmat = mathutil.mpi_cov(features)
if mpi.is_root():
selected_idx = max_variance_feature_selection(covmat, num_features)
else:
selected_idx = None
selected_idx = mpi.COMM.bcast(selected_idx)
conv[-2].dictionary = conv[-2].dictionary[selected_idx]
return covmat
def stl_demo():
"""Performs a demo classification on stl
"""
logging.info('Loading stl data...')
stl = visiondata.STL10Dataset(FLAGS.root, 'unlabeled', target_size=32)
stl_train = visiondata.STL10Dataset(FLAGS.root, 'train', target_size=32)
stl_test = visiondata.STL10Dataset(FLAGS.root, 'test', target_size=32)
conv = pipeline.ConvLayer([
pipeline.PatchExtractor([6, 6], 1), # extracts patches
pipeline.MeanvarNormalizer({'reg': 10}), # normalizes the patches
pipeline.LinearEncoder({},
trainer = pipeline.ZcaTrainer({'reg': 0.1})),
pipeline.ThresholdEncoder({'alpha': 0.25, 'twoside': False},
trainer = pipeline.NormalizedKmeansTrainer(
{'k': FLAGS.fromdim, 'max_iter':100})),
pipeline.SpatialPooler({'grid': (FLAGS.grid, FLAGS.grid), 'method': FLAGS.method}) # average pool
])
logging.info('Training the pipeline...')
conv.train(stl, 400000, exhaustive = True)
logging.info('Extracting features...')
X = conv.process_dataset(stl, as_2d = False)
Xtrain = conv.process_dataset(stl_train, as_2d = False)
Ytrain = stl_train.labels().astype(np.int)
Xtest = conv.process_dataset(stl_test, as_2d = False)
Ytest = stl_test.labels().astype(np.int)
# before we do feature computation, try to do dimensionality reduction
X.resize(np.prod(X.shape[:-1]), X.shape[-1])
Xtrain.resize(np.prod(Xtrain.shape[:-1]), Xtrain.shape[-1])
Xtest.resize(np.prod(Xtest.shape[:-1]), Xtest.shape[-1])
m, std = classifier.feature_meanstd(X, 0.01)
X -= m
X /= std
Xtrain -= m
Xtrain /= std
Xtest -= m
Xtest /= std
covmat = mathutil.mpi_cov(X)
current_dim = FLAGS.fromdim
if FLAGS.svd == 1:
eigval, eigvec = np.linalg.eigh(covmat)
while current_dim >= 100:
if current_dim < FLAGS.fromdim:
if FLAGS.svd == 1:
# directly do dimensionality reduction
U = eigvec[:, -current_dim:]
Xtrain_red = np.dot(Xtrain, U)
Xtest_red = np.dot(Xtest, U)
else:
# do subsampling
temp = code_ap.code_af(X, current_dim, tol=current_dim * 0.01)
logging.info("selected %d dims" % len(temp[0]))
sel = temp[0]
sel = mpi.COMM.bcast(sel)
Cpred = covmat[sel]
Csel = Cpred[:,sel]
W = np.linalg.solve(Csel, Cpred)
# perform svd
U, D, _ = np.linalg.svd(W, full_matrices = 0)
U *= D
Xtrain_red = np.dot(Xtrain[:, sel], U)
Xtest_red = np.dot(Xtest[:, sel], U)
Xtrain_red.resize(Ytrain.shape[0], Xtrain_red.size / Ytrain.shape[0])
Xtest_red.resize(Ytest.shape[0], Xtest_red.size / Ytest.shape[0])
else:
Xtrain_red = Xtrain.copy()
Xtest_red = Xtest.copy()
Xtrain_red.resize(Ytrain.shape[0], Xtrain_red.size / Ytrain.shape[0])
Xtest_red.resize(Ytest.shape[0], Xtest_red.size / Ytest.shape[0])
w, b = classifier.l2svm_onevsall(Xtrain_red, Ytrain, 0.005,
fminargs={'disp': 0, 'maxfun': 1000})
accu_train = classifier.Evaluator.accuracy(Ytrain, np.dot(Xtrain_red, w) + b)
accu_test = classifier.Evaluator.accuracy(Ytest, np.dot(Xtest_red, w) + b)
logging.info('%d - %d, Training accuracy: %f' % (FLAGS.fromdim, current_dim, accu_train))
logging.info('%d - %d, Testing accuracy: %f' % (FLAGS.fromdim, current_dim, accu_test))
current_dim /= 2
])
logging.info('Training the pipeline...')
conv.train(cifar, 400000, exhaustive = True)
"""
conv = pickle.load(open('cvpr_exemplar_centroids_conv.pickle'))
_, ap_result = pickle.load(open('cvpr_exemplar_centroids.pickle'))
logging.info('Extracting features...')
Xtrain = conv.process_dataset(cifar, as_2d = False)
# we simply use all the features to compute the covmat
Xtrain.resize(np.prod(Xtrain.shape[:-1]), Xtrain.shape[-1])
m, std = classifier.feature_meanstd(Xtrain, 0.01)
Xtrain -= m
Xtrain /= std
covmat = mathutil.mpi_cov(Xtrain)
# do subsampling
"""
ap_result = code_ap.code_af(Xtrain, todim)
"""
sel = ap_result[0]
sel = mpi.COMM.bcast(sel)
Cpred = covmat[sel]
Csel = Cpred[:,sel]
Crecon = np.dot(Cpred.T, np.dot(np.linalg.pinv(Csel), Cpred))
Crecon = (Crecon + Crecon.T) / 2
eigval = np.linalg.eigvals(covmat)
eigval_recon = np.linalg.eigvals(Crecon)
# random
def cifar_demo():
"""Performs a demo classification on cifar
"""
mpi.mkdir(FLAGS.output_dir)
logging.info('Loading cifar data...')
cifar = visiondata.CifarDataset(FLAGS.root, is_training=True)
cifar_test = visiondata.CifarDataset(FLAGS.root, is_training=False)
if FLAGS.trainer == "pink":
trainer = pinker.SpatialPinkTrainer({
'size': (FLAGS.patch, FLAGS.patch),
'reg': 0.1
})
else:
trainer = pipeline.ZcaTrainer({'reg': 0.1})
conv = pipeline.ConvLayer([
pipeline.PatchExtractor([FLAGS.patch, FLAGS.patch],
1), # extracts patches
pipeline.MeanvarNormalizer({'reg': 10}), # normalizes the patches
pipeline.LinearEncoder({}, trainer=trainer),
pipeline.ThresholdEncoder({
'alpha': 0.0,
'twoside': False
},
trainer=pipeline.OMPTrainer({
'k': FLAGS.fromdim,
'max_iter': 100
})),
pipeline.SpatialPooler({
'grid': (FLAGS.grid, FLAGS.grid),
'method': FLAGS.method
}) # average pool
])
logging.info('Training the pipeline...')
conv.train(cifar, 400000, exhaustive=True)
logging.info('Extracting features...')
Xtrain = conv.process_dataset(cifar, as_2d=False)
Ytrain = cifar.labels().astype(np.int)
Xtest = conv.process_dataset(cifar_test, as_2d=False)
Ytest = cifar_test.labels().astype(np.int)
# before we do feature computation, try to do dimensionality reduction
Xtrain.resize(np.prod(Xtrain.shape[:-1]), Xtrain.shape[-1])
Xtest.resize(np.prod(Xtest.shape[:-1]), Xtest.shape[-1])
m, std = classifier.feature_meanstd(Xtrain, 0.01)
Xtrain -= m
Xtrain /= std
Xtest -= m
Xtest /= std
covmat = mathutil.mpi_cov(Xtrain)
if False:
# directly do dimensionality reduction
eigval, eigvec = np.linalg.eigh(covmat)
U = eigvec[:, -FLAGS.todim:]
Xtrain = np.dot(Xtrain, U)
Xtest = np.dot(Xtest, U)
else:
# do subsampling
import code_ap
temp = code_ap.code_af(Xtrain, FLAGS.todim)
sel = temp[0]
sel = mpi.COMM.bcast(sel)
Cpred = covmat[sel]
Csel = Cpred[:, sel]
W = np.linalg.solve(Csel, Cpred)
# perform svd
U, D, _ = np.linalg.svd(W, full_matrices=0)
U *= D
Xtrain = np.dot(Xtrain[:, sel], U)
Xtest = np.dot(Xtest[:, sel], U)
Xtrain.resize(Ytrain.shape[0], Xtrain.size / Ytrain.shape[0])
Xtest.resize(Ytest.shape[0], Xtest.size / Ytest.shape[0])
"""
# This part is used to do post-pooling over all features nystrom subsampling
# normalization
Xtrain.resize(Xtrain.shape[0], np.prod(Xtrain.shape[1:]))
Xtest.resize(Xtest.shape[0], np.prod(Xtest.shape[1:]))
m, std = classifier.feature_meanstd(Xtrain, reg = 0.01)
# to match Adam Coates' pipeline
Xtrain -= m
Xtrain /= std
Xtest -= m
Xtest /= std
covmat = mathutil.mpi_cov(Xtrain)
eigval, eigvec = np.linalg.eigh(covmat)
U = eigvec[:, -(200*FLAGS.grid*FLAGS.grid):]
#U = eigvec[:,-400:] * np.sqrt(eigval[-400:])
Xtrain = np.dot(Xtrain, U)
Xtest = np.dot(Xtest, U)
"""
w, b = classifier.l2svm_onevsall(Xtrain,
Ytrain,
0.002,
fminargs={
'disp': 0,
'maxfun': 1000
})
accu_train = classifier.Evaluator.accuracy(Ytrain, np.dot(Xtrain, w) + b)
accu_test = classifier.Evaluator.accuracy(Ytest, np.dot(Xtest, w) + b)
logging.info('Training accuracy: %f' % accu_train)
logging.info('Testing accuracy: %f' % accu_test)
logging.info('Training the pipeline...')
conv.train(cifar, 400000, exhaustive=True)
mpi.root_pickle(conv, 'cifar_conv.pickle')
# do pruning
try:
selected_idx = pickle.load(open('cifar_selected_idx.pickle'))
logging.info('Skipping first layer pruning')
except Exception, e:
features = conv.sample(cifar, 200000, True)
mpi.dump_matrix_multi(features, '/u/vis/ttmp/jiayq/cifar/cifar_feature_pooled_sample')
m, std = mathutil.mpi_meanstd(features)
features -= m
features /= std
covmat = mathutil.mpi_cov(features, reg = 0.01)
if mpi.is_root():
selected_idx = pcfs.max_variance_feature_selection(covmat, 800)
else:
selected_idx = None
selected_idx = mpi.COMM.bcast(selected_idx)
mpi.root_pickle((m, std, covmat), 'cifar_squared_correlation.pickle')
mpi.root_pickle(selected_idx, 'cifar_selected_idx.pickle')
dictionary_all = conv[-2].dictionary
for i in [25,50,100,200,400,800,1600]:
logging.info('Training with dictionary size %d' % i)
#conv[-2].dictionary = np.ascontiguousarray(dictionary_all[selected_idx[:i]])
conv[-2].dictionary = np.ascontiguousarray(dictionary_all[:i])
logging.info('Training the pipeline...')
conv.train(cifar, 400000, exhaustive=True)
mpi.root_pickle(conv, 'cifar_conv.pickle')
# do pruning
try:
selected_idx = pickle.load(open('cifar_selected_idx.pickle'))
logging.info('Skipping first layer pruning')
except Exception, e:
features = conv.sample(cifar, 200000, True)
mpi.dump_matrix_multi(
features, '/u/vis/ttmp/jiayq/cifar/cifar_feature_pooled_sample')
m, std = mathutil.mpi_meanstd(features)
features -= m
features /= std
covmat = mathutil.mpi_cov(features, reg=0.01)
if mpi.is_root():
selected_idx = pcfs.max_variance_feature_selection(covmat, 800)
else:
selected_idx = None
selected_idx = mpi.COMM.bcast(selected_idx)
mpi.root_pickle((m, std, covmat), 'cifar_squared_correlation.pickle')
mpi.root_pickle(selected_idx, 'cifar_selected_idx.pickle')
dictionary_all = conv[-2].dictionary
for i in [25, 50, 100, 200, 400, 800, 1600]:
logging.info('Training with dictionary size %d' % i)
#conv[-2].dictionary = np.ascontiguousarray(dictionary_all[selected_idx[:i]])
conv[-2].dictionary = np.ascontiguousarray(dictionary_all[:i])
def apcluster_k(feature, num_centers, corr = True, tol = 0):
"""perform the affinity propagation algorithm for the input codes.
"""
logging.debug("ap: preparing similarity matrix")
covmat = mathutil.mpi_cov(feature)
std = np.diag(covmat)
# normalize
std = np.sqrt(std**2 + 0.01)
if corr:
# compute correlation. If corr is False, we will use the covariance
# directly
covmat /= std
covmat /= std[:, np.newaxis]
# compute the similarity matrix
norm = np.diag(covmat) / 2
covmat -= norm
covmat -= norm[:, np.newaxis]
# add a small noise to covmat
noise = (covmat + np.finfo(np.float64).eps) * \
np.random.rand(covmat.shape[0], covmat.shape[1])
mpi.COMM.Bcast(noise)
covmat += noise
# The remaining part can just be carried out on root
if mpi.is_root():
# set preference
pmax = covmat.max()
#af = AffinityPropagation().fit(covmat, pmax)
#num_max = len(af.cluster_centers_indices_)
# in fact, num_max would always be covmat.shape[0] so we don't really
# run ap
num_max = covmat.shape[0]
logging.debug("ap: pmax = %s, num = %d" % (pmax, num_max))
pmin = covmat.min()
af = AffinityPropagation().fit(covmat, pmin)
# num_min is the theoretical min, but the python code seem to raise bugs...
num_min = len(af.cluster_centers_indices_)
logging.debug("ap: pmin = %s, num = %d" % (pmin, num_min))
if num_centers < num_min:
logging.warning("num_centers too small, will return %d centers" % (num_min,))
return af.cluster_centers_indices_, af.labels_, covmat
if num_centers > num_max:
logging.warning("num_centers too large, will return everything.")
return np.arange(covmat.shape[0], dtype=np.int), \
np.arange(covmat.shape[0], dtype=np.int)
logging.debug("ap: start affinity propagation")
# We will simply use bisection search to find the right number of centroids.
for i in range(_AP_MAX_ITERATION):
pref = (pmax + pmin) / 2
af = AffinityPropagation().fit(covmat, pref)
num = len(af.cluster_centers_indices_)
logging.debug("ap try %d: pref = %s, num = %s" % (i + 1, pref, num))
if num >= num_centers - tol and num <= num_centers + tol:
break
elif num < num_centers:
pmin = pref
num_min = num
else:
pmax = pref
num_max = num
else:
af = None
mpi.barrier()
af = mpi.COMM.bcast(af)
return af.cluster_centers_indices_, af.labels_, covmat
def cifar_demo():
"""Performs a demo classification on cifar
"""
mpi.mkdir(FLAGS.output_dir)
logging.info('Loading cifar data...')
cifar = visiondata.CifarDataset(FLAGS.root, is_training=True)
cifar_test = visiondata.CifarDataset(FLAGS.root, is_training=False)
conv = pipeline.ConvLayer([
pipeline.PatchExtractor([6, 6], 1), # extracts patches
pipeline.MeanvarNormalizer({'reg': 10}), # normalizes the patches
pipeline.LinearEncoder({},
trainer = pipeline.ZcaTrainer({'reg': 0.1})),
pipeline.ThresholdEncoder({'alpha': 0.25, 'twoside': False},
trainer = pipeline.NormalizedKmeansTrainer(
{'k': FLAGS.fromdim, 'max_iter':100})),
pipeline.SpatialPooler({'grid': (FLAGS.grid, FLAGS.grid), 'method': FLAGS.method}) # average pool
])
logging.info('Training the pipeline...')
conv.train(cifar, 400000, exhaustive = True)
logging.info('Extracting features...')
Xtrain = conv.process_dataset(cifar, as_2d = False)
Ytrain = cifar.labels().astype(np.int)
Xtest = conv.process_dataset(cifar_test, as_2d = False)
Ytest = cifar_test.labels().astype(np.int)
# before we do feature computation, try to do dimensionality reduction
Xtrain.resize(np.prod(Xtrain.shape[:-1]), Xtrain.shape[-1])
Xtest.resize(np.prod(Xtest.shape[:-1]), Xtest.shape[-1])
m, std = classifier.feature_meanstd(Xtrain, 0.01)
Xtrain -= m
Xtrain /= std
Xtest -= m
Xtest /= std
covmat = mathutil.mpi_cov(Xtrain)
current_dim = FLAGS.fromdim
if FLAGS.svd == 1:
eigval, eigvec = np.linalg.eigh(covmat)
while current_dim >= 100:
if current_dim < FLAGS.fromdim:
if FLAGS.svd == 1:
# directly do dimensionality reduction
U = eigvec[:, -current_dim:]
Xtrain_red = np.dot(Xtrain, U)
Xtest_red = np.dot(Xtest, U)
else:
# do subsampling
temp = code_ap.code_af(Xtrain, current_dim)
logging.info("selected %d dims" % len(temp[0]))
sel = temp[0]
Xtrain_red = np.ascontiguousarray(Xtrain[:, sel])
Xtest_red = np.ascontiguousarray(Xtest[:, sel])
Xtrain_red.resize(Ytrain.shape[0], Xtrain_red.size / Ytrain.shape[0])
Xtest_red.resize(Ytest.shape[0], Xtest_red.size / Ytest.shape[0])
else:
Xtrain_red = Xtrain.copy()
Xtest_red = Xtest.copy()
Xtrain_red.resize(Ytrain.shape[0], Xtrain_red.size / Ytrain.shape[0])
Xtest_red.resize(Ytest.shape[0], Xtest_red.size / Ytest.shape[0])
w, b = classifier.l2svm_onevsall(Xtrain_red, Ytrain, 0.005,
fminargs={'disp': 0, 'maxfun': 1000})
accu_train = classifier.Evaluator.accuracy(Ytrain, np.dot(Xtrain_red, w) + b)
accu_test = classifier.Evaluator.accuracy(Ytest, np.dot(Xtest_red, w) + b)
logging.info('%d - %d, Training accuracy: %f' % (FLAGS.fromdim, current_dim, accu_train))
logging.info('%d - %d, Testing accuracy: %f' % (FLAGS.fromdim, current_dim, accu_test))
current_dim /= 2
def stl_demo():
"""Performs a demo classification on stl
"""
logging.info('Loading stl data...')
stl = visiondata.STL10Dataset(FLAGS.root, 'unlabeled', target_size=32)
stl_train = visiondata.STL10Dataset(FLAGS.root, 'train', target_size=32)
stl_test = visiondata.STL10Dataset(FLAGS.root, 'test', target_size=32)
conv = pipeline.ConvLayer([
pipeline.PatchExtractor([6, 6], 1), # extracts patches
pipeline.MeanvarNormalizer({'reg': 10}), # normalizes the patches
pipeline.LinearEncoder({}, trainer=pipeline.ZcaTrainer({'reg': 0.1})),
pipeline.ThresholdEncoder({
'alpha': 0.25,
'twoside': False
},
trainer=pipeline.NormalizedKmeansTrainer({
'k':
FLAGS.fromdim,
'max_iter':
100
})),
pipeline.SpatialPooler({
'grid': (FLAGS.grid, FLAGS.grid),
'method': FLAGS.method
}) # average pool
])
logging.info('Training the pipeline...')
conv.train(stl, 400000, exhaustive=True)
logging.info('Extracting features...')
X = conv.process_dataset(stl, as_2d=False)
Xtrain = conv.process_dataset(stl_train, as_2d=False)
Ytrain = stl_train.labels().astype(np.int)
Xtest = conv.process_dataset(stl_test, as_2d=False)
Ytest = stl_test.labels().astype(np.int)
# before we do feature computation, try to do dimensionality reduction
X.resize(np.prod(X.shape[:-1]), X.shape[-1])
Xtrain.resize(np.prod(Xtrain.shape[:-1]), Xtrain.shape[-1])
Xtest.resize(np.prod(Xtest.shape[:-1]), Xtest.shape[-1])
m, std = classifier.feature_meanstd(X, 0.01)
X -= m
X /= std
Xtrain -= m
Xtrain /= std
Xtest -= m
Xtest /= std
covmat = mathutil.mpi_cov(X)
current_dim = FLAGS.fromdim
if FLAGS.svd == 1:
eigval, eigvec = np.linalg.eigh(covmat)
while current_dim >= 100:
if current_dim < FLAGS.fromdim:
if FLAGS.svd == 1:
# directly do dimensionality reduction
U = eigvec[:, -current_dim:]
Xtrain_red = np.dot(Xtrain, U)
Xtest_red = np.dot(Xtest, U)
else:
# do subsampling
temp = code_ap.code_af(X, current_dim, tol=current_dim * 0.01)
logging.info("selected %d dims" % len(temp[0]))
sel = temp[0]
sel = mpi.COMM.bcast(sel)
Cpred = covmat[sel]
Csel = Cpred[:, sel]
W = np.linalg.solve(Csel, Cpred)
# perform svd
U, D, _ = np.linalg.svd(W, full_matrices=0)
U *= D
Xtrain_red = np.dot(Xtrain[:, sel], U)
Xtest_red = np.dot(Xtest[:, sel], U)
Xtrain_red.resize(Ytrain.shape[0],
Xtrain_red.size / Ytrain.shape[0])
Xtest_red.resize(Ytest.shape[0], Xtest_red.size / Ytest.shape[0])
else:
Xtrain_red = Xtrain.copy()
Xtest_red = Xtest.copy()
Xtrain_red.resize(Ytrain.shape[0],
Xtrain_red.size / Ytrain.shape[0])
Xtest_red.resize(Ytest.shape[0], Xtest_red.size / Ytest.shape[0])
w, b = classifier.l2svm_onevsall(Xtrain_red,
Ytrain,
0.005,
fminargs={
'disp': 0,
'maxfun': 1000
})
accu_train = classifier.Evaluator.accuracy(Ytrain,
np.dot(Xtrain_red, w) + b)
accu_test = classifier.Evaluator.accuracy(Ytest,
np.dot(Xtest_red, w) + b)
logging.info('%d - %d, Training accuracy: %f' %
(FLAGS.fromdim, current_dim, accu_train))
logging.info('%d - %d, Testing accuracy: %f' %
(FLAGS.fromdim, current_dim, accu_test))
current_dim /= 2
def apcluster_k(feature, num_centers, corr=True, tol=0):
"""perform the affinity propagation algorithm for the input codes.
"""
logging.debug("ap: preparing similarity matrix")
covmat = mathutil.mpi_cov(feature)
std = np.diag(covmat)
# normalize
std = np.sqrt(std**2 + 0.01)
if corr:
# compute correlation. If corr is False, we will use the covariance
# directly
covmat /= std
covmat /= std[:, np.newaxis]
# compute the similarity matrix
norm = np.diag(covmat) / 2
covmat -= norm
covmat -= norm[:, np.newaxis]
# add a small noise to covmat
noise = (covmat + np.finfo(np.float64).eps) * \
np.random.rand(covmat.shape[0], covmat.shape[1])
mpi.COMM.Bcast(noise)
covmat += noise
# The remaining part can just be carried out on root
if mpi.is_root():
# set preference
pmax = covmat.max()
#af = AffinityPropagation().fit(covmat, pmax)
#num_max = len(af.cluster_centers_indices_)
# in fact, num_max would always be covmat.shape[0] so we don't really
# run ap
num_max = covmat.shape[0]
logging.debug("ap: pmax = %s, num = %d" % (pmax, num_max))
pmin = covmat.min()
af = AffinityPropagation().fit(covmat, pmin)
# num_min is the theoretical min, but the python code seem to raise bugs...
num_min = len(af.cluster_centers_indices_)
logging.debug("ap: pmin = %s, num = %d" % (pmin, num_min))
if num_centers < num_min:
logging.warning("num_centers too small, will return %d centers" %
(num_min, ))
return af.cluster_centers_indices_, af.labels_, covmat
if num_centers > num_max:
logging.warning("num_centers too large, will return everything.")
return np.arange(covmat.shape[0], dtype=np.int), \
np.arange(covmat.shape[0], dtype=np.int)
logging.debug("ap: start affinity propagation")
# We will simply use bisection search to find the right number of centroids.
for i in range(_AP_MAX_ITERATION):
pref = (pmax + pmin) / 2
af = AffinityPropagation().fit(covmat, pref)
num = len(af.cluster_centers_indices_)
logging.debug("ap try %d: pref = %s, num = %s" %
(i + 1, pref, num))
if num >= num_centers - tol and num <= num_centers + tol:
break
elif num < num_centers:
pmin = pref
num_min = num
else:
pmax = pref
num_max = num
else:
af = None
mpi.barrier()
af = mpi.COMM.bcast(af)
return af.cluster_centers_indices_, af.labels_, covmat
fid = open(model_file_first, 'w')
pickle.dump(conv, fid)
fid.close()
mpi.barrier()
################################################################################
# Obtains statistics from the first layer
################################################################################
if os.path.exists(order_file):
logging.info('skipping the feature selection layer...')
order = np.load(order_file)
else:
# now, since we cannot possibly store the stl intermediate features, we do
# computation online and discard them on the fly
feat = conv.sample(stl, 400000)
covmat = mathutil.mpi_cov(feat)
if mpi.is_root():
# do greedy feature scoring
order = pcfs.principal_component_feature_selection(
covmat, feat.shape[1])
np.save(order_file, order)
np.save(covmat_file, covmat)
residual = [np.diag(pcfs.conditional_covariance(covmat, order[:i])).sum() \
for i in range(1, feat.shape[1], 10)]
try:
from matplotlib import pyplot
pyplot.plot(range(1, feat.shape[1], 10), residual)
pyplot.show()
except Exception, e:
pass
else:
def cifar_demo():
"""Performs a demo classification on cifar
"""
mpi.mkdir(FLAGS.output_dir)
logging.info('Loading cifar data...')
cifar = visiondata.CifarDataset(FLAGS.root, is_training=True)
cifar_test = visiondata.CifarDataset(FLAGS.root, is_training=False)
if FLAGS.trainer == "pink":
trainer = pinker.SpatialPinkTrainer({'size': (FLAGS.patch, FLAGS.patch), 'reg': 0.1})
else:
trainer = pipeline.ZcaTrainer({'reg': 0.1})
conv = pipeline.ConvLayer([
pipeline.PatchExtractor([FLAGS.patch, FLAGS.patch], 1), # extracts patches
pipeline.MeanvarNormalizer({'reg': 10}), # normalizes the patches
pipeline.LinearEncoder({},
trainer = trainer),
pipeline.ThresholdEncoder({'alpha': 0.0, 'twoside': False},
trainer = pipeline.OMPTrainer(
{'k': FLAGS.fromdim, 'max_iter':100})),
pipeline.SpatialPooler({'grid': (FLAGS.grid, FLAGS.grid), 'method': FLAGS.method}) # average pool
])
logging.info('Training the pipeline...')
conv.train(cifar, 400000, exhaustive = True)
logging.info('Extracting features...')
Xtrain = conv.process_dataset(cifar, as_2d = False)
Ytrain = cifar.labels().astype(np.int)
Xtest = conv.process_dataset(cifar_test, as_2d = False)
Ytest = cifar_test.labels().astype(np.int)
# before we do feature computation, try to do dimensionality reduction
Xtrain.resize(np.prod(Xtrain.shape[:-1]), Xtrain.shape[-1])
Xtest.resize(np.prod(Xtest.shape[:-1]), Xtest.shape[-1])
m, std = classifier.feature_meanstd(Xtrain, 0.01)
Xtrain -= m
Xtrain /= std
Xtest -= m
Xtest /= std
covmat = mathutil.mpi_cov(Xtrain)
if False:
# directly do dimensionality reduction
eigval, eigvec = np.linalg.eigh(covmat)
U = eigvec[:, -FLAGS.todim:]
Xtrain = np.dot(Xtrain, U)
Xtest = np.dot(Xtest, U)
else:
# do subsampling
import code_ap
temp = code_ap.code_af(Xtrain, FLAGS.todim)
sel = temp[0]
sel = mpi.COMM.bcast(sel)
Cpred = covmat[sel]
Csel = Cpred[:,sel]
W = np.linalg.solve(Csel, Cpred)
# perform svd
U, D, _ = np.linalg.svd(W, full_matrices = 0)
U *= D
Xtrain = np.dot(Xtrain[:, sel], U)
Xtest = np.dot(Xtest[:, sel], U)
Xtrain.resize(Ytrain.shape[0], Xtrain.size / Ytrain.shape[0])
Xtest.resize(Ytest.shape[0], Xtest.size / Ytest.shape[0])
"""
# This part is used to do post-pooling over all features nystrom subsampling
# normalization
Xtrain.resize(Xtrain.shape[0], np.prod(Xtrain.shape[1:]))
Xtest.resize(Xtest.shape[0], np.prod(Xtest.shape[1:]))
m, std = classifier.feature_meanstd(Xtrain, reg = 0.01)
# to match Adam Coates' pipeline
Xtrain -= m
Xtrain /= std
Xtest -= m
Xtest /= std
covmat = mathutil.mpi_cov(Xtrain)
eigval, eigvec = np.linalg.eigh(covmat)
U = eigvec[:, -(200*FLAGS.grid*FLAGS.grid):]
#U = eigvec[:,-400:] * np.sqrt(eigval[-400:])
Xtrain = np.dot(Xtrain, U)
Xtest = np.dot(Xtest, U)
"""
w, b = classifier.l2svm_onevsall(Xtrain, Ytrain, 0.002,
fminargs={'disp': 0, 'maxfun': 1000})
accu_train = classifier.Evaluator.accuracy(Ytrain, np.dot(Xtrain, w) + b)
accu_test = classifier.Evaluator.accuracy(Ytest, np.dot(Xtest, w) + b)
logging.info('Training accuracy: %f' % accu_train)
logging.info('Testing accuracy: %f' % accu_test)
def cifar_demo():
"""Performs a demo classification on cifar
"""
mpi.mkdir(FLAGS.output_dir)
logging.info('Loading cifar data...')
cifar = visiondata.CifarDataset(FLAGS.root, is_training=True)
cifar_test = visiondata.CifarDataset(FLAGS.root, is_training=False)
conv = pipeline.ConvLayer([
pipeline.PatchExtractor([6, 6], 1), # extracts patches
pipeline.MeanvarNormalizer({'reg': 10}), # normalizes the patches
pipeline.LinearEncoder({}, trainer=pipeline.ZcaTrainer({'reg': 0.1})),
pipeline.ThresholdEncoder({
'alpha': 0.25,
'twoside': False
},
trainer=pipeline.NormalizedKmeansTrainer({
'k':
FLAGS.fromdim,
'max_iter':
100
})),
pipeline.SpatialPooler({
'grid': (FLAGS.grid, FLAGS.grid),
'method': FLAGS.method
}) # average pool
])
logging.info('Training the pipeline...')
conv.train(cifar, 400000, exhaustive=True)
logging.info('Extracting features...')
Xtrain = conv.process_dataset(cifar, as_2d=False)
Ytrain = cifar.labels().astype(np.int)
Xtest = conv.process_dataset(cifar_test, as_2d=False)
Ytest = cifar_test.labels().astype(np.int)
# before we do feature computation, try to do dimensionality reduction
Xtrain.resize(np.prod(Xtrain.shape[:-1]), Xtrain.shape[-1])
Xtest.resize(np.prod(Xtest.shape[:-1]), Xtest.shape[-1])
m, std = classifier.feature_meanstd(Xtrain, 0.01)
Xtrain -= m
Xtrain /= std
Xtest -= m
Xtest /= std
covmat = mathutil.mpi_cov(Xtrain)
current_dim = FLAGS.fromdim
if FLAGS.svd == 1:
eigval, eigvec = np.linalg.eigh(covmat)
while current_dim >= 100:
if current_dim < FLAGS.fromdim:
if FLAGS.svd == 1:
# directly do dimensionality reduction
U = eigvec[:, -current_dim:]
Xtrain_red = np.dot(Xtrain, U)
Xtest_red = np.dot(Xtest, U)
else:
# do subsampling
temp = code_ap.code_af(Xtrain, current_dim)
logging.info("selected %d dims" % len(temp[0]))
sel = temp[0]
Xtrain_red = np.ascontiguousarray(Xtrain[:, sel])
Xtest_red = np.ascontiguousarray(Xtest[:, sel])
Xtrain_red.resize(Ytrain.shape[0],
Xtrain_red.size / Ytrain.shape[0])
Xtest_red.resize(Ytest.shape[0], Xtest_red.size / Ytest.shape[0])
else:
Xtrain_red = Xtrain.copy()
Xtest_red = Xtest.copy()
Xtrain_red.resize(Ytrain.shape[0],
Xtrain_red.size / Ytrain.shape[0])
Xtest_red.resize(Ytest.shape[0], Xtest_red.size / Ytest.shape[0])
w, b = classifier.l2svm_onevsall(Xtrain_red,
Ytrain,
0.005,
fminargs={
'disp': 0,
'maxfun': 1000
})
accu_train = classifier.Evaluator.accuracy(Ytrain,
np.dot(Xtrain_red, w) + b)
accu_test = classifier.Evaluator.accuracy(Ytest,
np.dot(Xtest_red, w) + b)
logging.info('%d - %d, Training accuracy: %f' %
(FLAGS.fromdim, current_dim, accu_train))
logging.info('%d - %d, Testing accuracy: %f' %
(FLAGS.fromdim, current_dim, accu_test))
current_dim /= 2
fid = open(model_file_first,'w')
pickle.dump(conv, fid)
fid.close()
mpi.barrier()
################################################################################
# Obtains statistics from the first layer
################################################################################
if os.path.exists(order_file):
logging.info('skipping the feature selection layer...')
order = np.load(order_file)
else:
# now, since we cannot possibly store the stl intermediate features, we do
# computation online and discard them on the fly
feat = conv.sample(stl, 400000)
covmat = mathutil.mpi_cov(feat)
if mpi.is_root():
# do greedy feature scoring
order = pcfs.principal_component_feature_selection(covmat, feat.shape[1])
np.save(order_file, order)
np.save(covmat_file, covmat)
residual = [np.diag(pcfs.conditional_covariance(covmat, order[:i])).sum() \
for i in range(1, feat.shape[1], 10)]
try:
from matplotlib import pyplot
pyplot.plot(range(1, feat.shape[1], 10), residual)
pyplot.show()
except Exception, e:
pass
else:
order = None