def setUp(self):
self._sample_number = 1000
self._dim = 32
self._patchsize = 6
mat = np.random.rand(100, self._dim, self._dim, 3)
mat_sc = np.random.rand(100, self._dim, self._dim)
mat_mc = np.random.rand(100, self._dim, self._dim, 6)
self.data = datasets.NdarraySet(mat)
self.data_sc = datasets.NdarraySet(mat_sc)
self.data_mc = datasets.NdarraySet(mat_mc)
self.extractor = pipeline.PatchExtractor(self._patchsize, 1)
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)
if mpi.is_root():
logging.getLogger().setLevel(logging.DEBUG)
# Parameters of the script
ROOT = '/u/vis/farrell/datasets/CUB_200_2011/'
CONVOLUTION_OUTPUT = '/u/vis/ttmp/jiayq/birds/conv/'
CONVOLUTION_FILE = '/u/vis/ttmp/jiayq/birds/conv/convolution.pickle'
CROP = 1.5
MIRRORED = True
SUBSET = None
TARGET_SIZE = [128, 128]
CONV = pipeline.ConvLayer([
pipeline.PatchExtractor([5, 5], 1),
pipeline.MeanvarNormalizer({'reg': 10}),
pipeline.LinearEncoder({}, trainer=pipeline.ZcaTrainer({'reg': 0.1})),
pipeline.ReLUEncoder({'twoside': False},
trainer=pipeline.NormalizedKmeansTrainer({
'k':
200,
'max_iter':
100
})),
#pipeline.PyramidPooler({'level': 2, 'method': 'ave'})
pipeline.FixedSizePooler({
'size': '5',
'method': 'max'
})
])
# local import
import birdtax
import treereg
########
# Settings
########
ROOT = "/u/vis/x1/common/CUB_200_2011/"
FEATDIR = "/u/vis/ttmp/jiayq/birds/"
CROP = 1.2
MIRRORED = True
TARGET_SIZE = [128,128]
CONV = pipeline.ConvLayer(
[pipeline.PatchExtractor([5,5], 1),
pipeline.MeanvarNormalizer({'reg': 10}),
pipeline.LinearEncoder({},
trainer = pipeline.ZcaTrainer({'reg': 0.1})),
pipeline.ThresholdEncoder({},
trainer = pipeline.OMPTrainer({'k':1024, 'max_iter':100})),
pipeline.PyramidPooler({'level': 3, 'method': 'max'})
], fixed_size = True)
#FLAT_REG = [0.0001] # tuned parameter
#HIER_REG = [0.01] # tuned parameter
#TREE_REG = [0.0001]
########
# Main script
########
gflags.DEFINE_bool("extract", False,
if mpi.is_root():
logging.getLogger().setLevel(logging.DEBUG)
logging.info('Loading cifar data...')
cifar = visiondata.CifarDataset('/u/vis/x1/common/CIFAR/cifar-10-batches-py', \
is_training=True)
cifar_test = visiondata.CifarDataset(
'/u/vis/x1/common/CIFAR/cifar-10-batches-py', \
is_training=False)
try:
conv = pickle.load(open('cifar_conv.pickle'))
logging.info('Skipping first layer training')
except Exception, e:
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})), # Does whitening
pipeline.ThresholdEncoder({
'alpha': 0.0,
'twoside': False
},
trainer=pipeline.NormalizedKmeansTrainer({
'k':
1600,
'max_iter':
100
})), # does encoding
pipeline.SpatialPooler({
'grid': (2, 2),
import cPickle as pickle
import logging
from matplotlib import pyplot
from iceberk import mpi, visiondata, pipeline, datasets, mathutil, visualize
import numpy as np
mpi.root_log_level(logging.DEBUG)
# compute the features
bird = visiondata.CUBDataset('/u/vis/x1/common/CUB_200_2011',
is_training=True,
crop=1.2,
prefetch=True,
target_size=[256, 256])
logging.info("Generating the data...")
regions = pipeline.PatchExtractor([5, 5], 1).sample(bird, 400000)
normalizer = pipeline.MeanvarNormalizer({'reg': 10})
whitener = pipeline.LinearEncoder({},
trainer=pipeline.ZcaTrainer({'reg': 0.1}))
encoder = pipeline.ReLUEncoder({'twoside': False},
trainer=pipeline.OMPTrainer({
'k': 1600,
'max_iter': 100
}))
regions_n = normalizer.process(regions)
whitener.train(regions_n)
regions_w = whitener.process(regions_n)
encoder.train(regions_w)
regions_e = encoder.process(regions_w)
dictionary = encoder.dictionary
def bird_demo():
logging.info('Loading data...')
bird = visiondata.CUBDataset(FLAGS.root,
is_training=True,
crop=FLAGS.crop,
version=FLAGS.version,
prefetch=True,
target_size=TARGET_SIZE)
bird_test = visiondata.CUBDataset(FLAGS.root,
is_training=False,
crop=FLAGS.crop,
version=FLAGS.version,
prefetch=True,
target_size=TARGET_SIZE)
if FLAGS.mirrored:
bird = datasets.MirrorSet(bird)
conv = pipeline.ConvLayer(
[
pipeline.PatchExtractor([FLAGS.patch, FLAGS.patch],
1), # extracts patches
pipeline.MeanvarNormalizer({'reg': 10}), # normalizes the patches
pipeline.LinearEncoder({},
trainer=pipeline.ZcaTrainer({'reg': 0.1})),
pipeline.ThresholdEncoder({
'alpha': 0.25,
'twoside': True
},
trainer=pipeline.OMPTrainer(
{
'k': FLAGS.k,
'max_iter': 100
})),
pipeline.SpatialPooler({
'grid': 4,
'method': 'max'
})
],
fixed_size=True)
logging.info('Training the pipeline...')
conv.train(bird, 400000, exhaustive=True)
logging.info('Extracting features...')
Xtrain = conv.process_dataset(bird, as_2d=True)
Ytrain = bird.labels().astype(np.int)
Xtest = conv.process_dataset(bird_test, as_2d=True)
Ytest = bird_test.labels().astype(np.int)
# normalization
m, std = classifier.feature_meanstd(Xtrain, reg=0.01)
# to match Adam Coates' pipeline
Xtrain -= m
Xtrain /= std
Xtest -= m
Xtest /= std
w, b = classifier.l2svm_onevsall(Xtrain,
Ytrain,
0.005,
fminargs={'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)
mpi.root_pickle((m, std, w, b, conv[-2].dictionary),
'debug_features.pickle')
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})), # Does whitening
pipeline.ThresholdEncoder({
'alpha': 0.25,
'twoside': True
},
trainer=pipeline.OMPTrainer({
'k': 800,
'max_iter': 100
})), # does encoding
pipeline.SpatialPooler({
'grid': (2, 2),
'method': 'ave'
}) # average pool
])
logging.info('Training the pipeline...')
conv.train(cifar, 50000)
logging.info('Dumping the pipeline...')
if mpi.is_root():
with open(os.path.join(FLAGS.output_dir, FLAGS.model_file),
'w') as fid:
pickle.dump(conv, fid)
fid.close()
with open(os.path.join(FLAGS.output_dir, FLAGS.model_file), 'r') as fid:
conv = pickle.load(fid)
logging.info('Extracting features...')
Xtrain = conv.process_dataset(cifar, as_2d=True)
mpi.dump_matrix_multi(
Xtrain, os.path.join(FLAGS.output_dir, FLAGS.feature_file + '_train'))
Ytrain = cifar.labels().astype(np.int)
Xtest = conv.process_dataset(cifar_test, as_2d=True)
mpi.dump_matrix_multi(
Xtest, os.path.join(FLAGS.output_dir, FLAGS.feature_file + '_test'))
Ytest = cifar_test.labels().astype(np.int)
# normalization
m, std = classifier.feature_meanstd(Xtrain)
Xtrain -= m
Xtrain /= std
Xtest -= m
Xtest /= std
w, b = classifier.l2svm_onevsall(Xtrain, Ytrain, 0.01)
if mpi.is_root():
with open(os.path.join(FLAGS.output_dir, FLAGS.svm_file), 'w') as fid:
pickle.dump({'m': m, 'std': std, 'w': w, 'b': b}, fid)
accu = np.sum(Ytrain == (np.dot(Xtrain,w)+b).argmax(axis=1)) \
/ float(len(Ytrain))
accu_test = np.sum(Ytest == (np.dot(Xtest,w)+b).argmax(axis=1)) \
/ float(len(Ytest))
logging.info('Training accuracy: %f' % accu)
logging.info('Testing accuracy: %f' % accu_test)
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
import numpy as np
mpi.root_log_level(logging.DEBUG)
try:
conv = pickle.load(open('conv.pickle'))
regions_pooled = mpi.load_matrix_multi(\
'/tscratch/tmp/jiayq/pooled_lda/regions_pooled', N = 10)
except IOError:
# compute the features
logging.info("Generating the data...")
bird = visiondata.CUBDataset('/u/vis/x1/common/CUB_200_2011',
is_training=True,
crop=1.2,
prefetch=True,
target_size=[256, 256])
regions = pipeline.PatchExtractor([25, 25], 1).sample(bird, 100000)
regions.resize((regions.shape[0], ) + (25, 25, 3))
regions_data = datasets.NdarraySet(regions)
try:
conv = pickle.load(open('conv.pickle'))
except IOError:
logging.info("Training the feature extraction pipeline...")
conv = pipeline.ConvLayer([
pipeline.PatchExtractor([5, 5], 1), # extracts patches
pipeline.MeanvarNormalizer({'reg': 10}), # normalizes the patches
pipeline.LinearEncoder({},
trainer = pipeline.ZcaTrainer({'reg': 0.1})),
#pipeline.SpatialMeanNormalizer({'channels': 3}),
pipeline.ThresholdEncoder({'alpha': 0.25, 'twoside': False},
trainer = pipeline.OMPTrainer(
{'k': 3200, 'max_iter':100})),
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