def _transform_zca(self, x, fit=False):
if self._to_zca:
if fit:
self._zca_class = preprocessing.ZCA(store_inverse=True)
self._zca_class.fit(x)
x = self._zca_class.transform(x)
return x
def main():
data_dir = string.preprocess('${PYLEARN2_DATA_PATH}/stl10')
print('Loading STL10-10 unlabeled and train datasets...')
downsampled_dir = data_dir + '/stl10_32x32'
data = serial.load(downsampled_dir + '/unlabeled.pkl')
supplement = serial.load(downsampled_dir + '/train.pkl')
print('Concatenating datasets...')
data.set_design_matrix(np.concatenate((data.X, supplement.X), axis=0))
del supplement
print("Preparing output directory...")
patch_dir = data_dir + '/stl10_patches_8x8'
serial.mkdir(patch_dir)
README = open(patch_dir + '/README', 'w')
README.write(textwrap.dedent("""
The .pkl files in this directory may be opened in python using
cPickle, pickle, or pylearn2.serial.load.
data.pkl contains a pylearn2 Dataset object defining an unlabeled
dataset of 2 million 6x6 approximately whitened, contrast-normalized
patches drawn uniformly at random from a downsampled (to 32x32)
version of the STL-10 train and unlabeled datasets.
preprocessor.pkl contains a pylearn2 Pipeline object that was used
to extract the patches and approximately whiten / contrast normalize
them. This object is necessary when extracting features for
supervised learning or test set classification, because the
extracted features must be computed using inputs that have been
whitened with the ZCA matrix learned and stored by this Pipeline.
They were created with the pylearn2 script make_stl10_patches.py.
All other files in this directory, including this README, were
created by the same script and are necessary for the other files
to function correctly.
"""))
README.close()
print("Preprocessing the data...")
pipeline = preprocessing.Pipeline()
pipeline.items.append(preprocessing.ExtractPatches(patch_shape=(8, 8),
num_patches=2*1000*1000))
pipeline.items.append(
preprocessing.GlobalContrastNormalization(sqrt_bias=10., use_std=True))
pipeline.items.append(preprocessing.ZCA())
data.apply_preprocessor(preprocessor=pipeline, can_fit=True)
data.use_design_loc(patch_dir + '/data.npy')
serial.save(patch_dir + '/data.pkl', data)
serial.save(patch_dir + '/preprocessor.pkl', pipeline)
def main():
data_dir = string_utils.preprocess('${PYLEARN2_DATA_PATH}/cifar100')
print('Loading CIFAR-100 train dataset...')
train = CIFAR100(which_set='train', gcn=55.)
print("Preparing output directory...")
output_dir = data_dir + '/pylearn2_gcn_whitened'
serial.mkdir(output_dir)
README = open(output_dir + '/README', 'w')
README.write(
textwrap.dedent("""
The .pkl files in this directory may be opened in python using
cPickle, pickle, or pylearn2.serial.load.
train.pkl, and test.pkl each contain
a pylearn2 Dataset object defining a labeled
dataset of a 32x32 contrast normalized,
approximately whitened version of the CIFAR-100 dataset.
train.pkl contains labeled train examples.
test.pkl contains labeled test examples.
preprocessor.pkl contains a pylearn2 ZCA object that was used
to approximately whiten the images. You may want to use this
object later to preprocess other images.
They were created with the pylearn2 script make_cifar100_gcn_whitened.py.
All other files in this directory, including this README, were
created by the same script and are necessary for the other files
to function correctly.
"""))
README.close()
print("Learning the preprocessor \
and preprocessing the unsupervised train data...")
preprocessor = preprocessing.ZCA()
train.apply_preprocessor(preprocessor=preprocessor, can_fit=True)
print('Saving the training data')
train.use_design_loc(output_dir + '/train.npy')
serial.save(output_dir + '/train.pkl', train)
print("Loading the test data")
test = CIFAR100(which_set='test', gcn=55.)
print("Preprocessing the test data")
test.apply_preprocessor(preprocessor=preprocessor, can_fit=False)
print("Saving the test data")
test.use_design_loc(output_dir + '/test.npy')
serial.save(output_dir + '/test.pkl', test)
serial.save(output_dir + '/preprocessor.pkl', preprocessor)
def main():
data_dir = string_utils.preprocess('${PYLEARN2_DATA_PATH}')
print('Loading CIFAR-100 train dataset...')
data = CIFAR100(which_set='train')
print("Preparing output directory...")
patch_dir = data_dir + '/cifar100/cifar100_patches'
serial.mkdir(patch_dir)
README = open(patch_dir + '/README', 'w')
README.write(
textwrap.dedent("""
The .pkl files in this directory may be opened in python using
cPickle, pickle, or pylearn2.serial.load.
data.pkl contains a pylearn2 Dataset object defining an unlabeled
dataset of 2 million 6x6 approximately whitened, contrast-normalized
patches drawn uniformly at random from the CIFAR-100 train set.
preprocessor.pkl contains a pylearn2 Pipeline object that was used
to extract the patches and approximately whiten / contrast normalize
them. This object is necessary when extracting features for
supervised learning or test set classification, because the
extracted features must be computed using inputs that have been
whitened with the ZCA matrix learned and stored by this Pipeline.
They were created with the pylearn2 script make_cifar100_patches.py.
All other files in this directory, including this README, were
created by the same script and are necessary for the other files
to function correctly.
"""))
README.close()
print("Preprocessing the data...")
pipeline = preprocessing.Pipeline()
pipeline.items.append(
preprocessing.ExtractPatches(patch_shape=(6, 6),
num_patches=2 * 1000 * 1000))
pipeline.items.append(
preprocessing.GlobalContrastNormalization(sqrt_bias=10., use_std=True))
pipeline.items.append(preprocessing.ZCA())
data.apply_preprocessor(preprocessor=pipeline, can_fit=True)
data.use_design_loc(patch_dir + '/data.npy')
serial.save(patch_dir + '/data.pkl', data)
serial.save(patch_dir + '/preprocessor.pkl', pipeline)
def get_preprocess_zca(self, preprocess_id):
row = self.db.executeSQL(
"""
SELECT n_components, n_drop_components, filter_bias
FROM hps3.preprocess_zca
WHERE preprocess_id = %s
""", (preprocess_id, ), self.db.FETCH_ONE)
if not row or row is None:
raise HPSData("No zca preprocess for preprocess_id="\
+str(preprocess_id))
(n_components, n_drop_components, filter_bias) = row
return pp.ZCA(n_components=n_components,
filter_bias=filter_bias,
n_drop_components=n_drop_components)
def get_dataset_cifar10():
"""
The orginal pipeline on cifar10 from pylearn2. Please refer to
pylearn2/scripts/train_example/make_dataset.py for details.
"""
train_path = 'cifar10_preprocessed_train.pkl'
test_path = 'cifar10_preprocessed_test.pkl'
if os.path.exists(train_path) and \
os.path.exists(test_path):
print 'loading preprocessed data'
trainset = serial.load(train_path)
testset = serial.load(test_path)
else:
print 'loading raw data...'
trainset = cifar10.CIFAR10(w5B5B5B5Bhich_set="train")
testset = cifar10.CIFAR10(which_set="test")
print 'preprocessing data...'
pipeline = preprocessing.Pipeline()
pipeline.items.append(
preprocessing.ExtractPatches(patch_shape=(8, 8), num_patches=150000))
pipeline.items.append(preprocessing.GlobalContrastNormalization())
pipeline.items.append(preprocessing.ZCA())
trainset.apply_preprocessor(preprocessor=pipeline, can_fit=True)
trainset.use_design_loc('train_design.npy')
testset.apply_preprocessor(preprocessor=pipeline, can_fit=True)
testset.use_design_loc('test_design.npy')
print 'saving preprocessed data...'
serial.save('cifar10_preprocessed_train.pkl', trainset)
serial.save('cifar10_preprocessed_test.pkl', testset)
trainset.yaml_src = '!pkl: "%s"' % train_path
testset.yaml_src = '!pkl: "%s"' % test_path
# this path will be used for visualizing weights after training is done
#global YAML
return trainset, testset
def generate_patches():
datasets = OrderedDict()
datasets['train'] = GenderWrite.gwdata.GWData(which_set='train',
start=1,
stop=201)
datasets['valid'] = GenderWrite.gwdata.GWData(which_set='train',
start=201,
stop=283)
datasets['test'] = GenderWrite.gwdata.GWData(which_set='test')
datasets['tottrain'] = GenderWrite.gwdata.GWData(which_set='train')
# preprocess patches
pipeline = preprocessing.Pipeline()
pipeline.items.append(preprocessing.GlobalContrastNormalization())
pipeline.items.append(preprocessing.ZCA())
for dstr, dset in datasets.iteritems():
print dstr
# only fit on train data
trainbool = dstr == 'train' or dstr == 'tottrain'
dset.apply_preprocessor(preprocessor=pipeline, can_fit=trainbool)
# save
dset.use_design_loc(DATA_DIR + dstr + '_design.npy')
serial.save(DATA_DIR + 'gw_preprocessed_' + dstr + '.pkl', dset)
preprocessor.pkl contains a pylearn2 ZCA object that was used to approximately whiten the images. You may want to use this object later to preprocess other images. They were created with the pylearn2 script make_cifar100_gcn_whitened.py. All other files in this directory, including this README, were created by the same script and are necessary for the other files to function correctly. """) README.close() print "Learning the preprocessor and preprocessing the unsupervised train data..." preprocessor = preprocessing.ZCA() train.apply_preprocessor(preprocessor = preprocessor, can_fit = True) print 'Saving the unsupervised data' train.use_design_loc(output_dir+'/train.npy') serial.save(output_dir + '/train.pkl', train) print "Loading the test data" test = CIFAR100(which_set = 'test', gcn = 55.) print "Preprocessing the test data" test.apply_preprocessor(preprocessor = preprocessor, can_fit = False) print "Saving the test data" test.use_design_loc(output_dir+'/test.npy') serial.save(output_dir+'/test.pkl', test)
to extract the patches and approximately whiten / contrast normalize
them. This object is necessary when extracting features for
supervised learning or test set classification, because the
extracted features must be computed using inputs that have been
whitened with the ZCA matrix learned and stored by this Pipeline.
They were created with the pylearn2 script make_cifar100_patches.py.
All other files in this directory, including this README, were
created by the same script and are necessary for the other files
to function correctly.
""")
README.close()
print("Preprocessing the data...")
pipeline = preprocessing.Pipeline()
pipeline.items.append(
preprocessing.ExtractPatches(patch_shape=(8, 8),
num_patches=2 * 1000 * 1000))
pipeline.items.append(
preprocessing.GlobalContrastNormalization(sqrt_bias=10., use_std=True))
pipeline.items.append(preprocessing.ZCA())
data.apply_preprocessor(preprocessor=pipeline, can_fit=True)
data.use_design_loc(patch_dir + '/data.npy')
serial.save(patch_dir + '/data.pkl', data)
serial.save(patch_dir + '/preprocessor.pkl', pipeline)
def main():
data_dir = string.preprocess('${PYLEARN2_DATA_PATH}/stl10')
print('Loading STL-10 unlabeled and train datasets...')
downsampled_dir = data_dir + '/stl10_32x32'
data = serial.load(downsampled_dir + '/unlabeled.pkl')
supplement = serial.load(downsampled_dir + '/train.pkl')
print('Concatenating datasets...')
data.set_design_matrix(np.concatenate((data.X, supplement.X), axis=0))
print("Preparing output directory...")
output_dir = data_dir + '/stl10_32x32_whitened'
serial.mkdir(output_dir)
README = open(output_dir + '/README', 'w')
README.write(
textwrap.dedent("""
The .pkl files in this directory may be opened in python using
cPickle, pickle, or pylearn2.serial.load.
unsupervised.pkl, unlabeled.pkl, train.pkl, and test.pkl each contain
a pylearn2 Dataset object defining an unlabeled
dataset of a 32x32 approximately whitened version of the STL-10
dataset. unlabeled.pkl contains unlabeled train examples. train.pkl
contains labeled train examples. unsupervised.pkl contains the union
of these (without any labels). test.pkl contains the labeled test
examples.
preprocessor.pkl contains a pylearn2 ZCA object that was used
to approximately whiten the images. You may want to use this
object later to preprocess other images.
They were created with the pylearn2 script make_stl10_whitened.py.
All other files in this directory, including this README, were
created by the same script and are necessary for the other files
to function correctly.
"""))
README.close()
print("Learning the preprocessor \
and preprocessing the unsupervised train data...")
preprocessor = preprocessing.ZCA()
data.apply_preprocessor(preprocessor=preprocessor, can_fit=True)
print('Saving the unsupervised data')
data.use_design_loc(output_dir + '/unsupervised.npy')
serial.save(output_dir + '/unsupervised.pkl', data)
X = data.X
unlabeled = X[0:100 * 1000, :]
labeled = X[100 * 1000:, :]
del X
print("Saving the unlabeled data")
data.X = unlabeled
data.use_design_loc(output_dir + '/unlabeled.npy')
serial.save(output_dir + '/unlabeled.pkl', data)
del data
del unlabeled
print("Saving the labeled train data")
supplement.X = labeled
supplement.use_design_loc(output_dir + '/train.npy')
serial.save(output_dir + '/train.pkl', supplement)
del supplement
del labeled
print("Loading the test data")
test = serial.load(downsampled_dir + '/test.pkl')
print("Preprocessing the test data")
test.apply_preprocessor(preprocessor=preprocessor, can_fit=False)
print("Saving the test data")
test.use_design_loc(output_dir + '/test.npy')
serial.save(output_dir + '/test.pkl', test)
serial.save(output_dir + '/preprocessor.pkl', preprocessor)
def get_dataset(tot=False, preprocessor='normal'):
if not os.path.exists(DATA_DIR+'train.npy') or \
not os.path.exists(DATA_DIR+'test.npy') or \
not os.path.exists(DATA_DIR+'targets.npy'):
initial_read()
train_path = DATA_DIR+'train_'+preprocessor+'_preprocessed.pkl'
valid_path = DATA_DIR+'valid_'+preprocessor+'_preprocessed.pkl'
tottrain_path = DATA_DIR+'tottrain_'+preprocessor+'_preprocessed.pkl'
test_path = DATA_DIR+'test_'+preprocessor+'_preprocessed.pkl'
if os.path.exists(train_path) and os.path.exists(valid_path) and os.path.exists(test_path):
print 'loading preprocessed data'
trainset = serial.load(train_path)
validset = serial.load(valid_path)
if tot:
tottrainset = serial.load(tottrain_path)
testset = serial.load(test_path)
else:
print 'loading raw data...'
trainset = Digits(which_set='train', start=0, stop=34000)
validset = Digits(which_set='train', start=34000, stop=42000)
tottrainset = Digits(which_set='train')
testset = Digits(which_set='test')
print 'preprocessing data...'
pipeline = preprocessing.Pipeline()
pipeline.items.append(preprocessing.GlobalContrastNormalization(sqrt_bias=10., use_std=True))
if preprocessor != 'nozca':
# ZCA = zero-phase component analysis
# very similar to PCA, but preserves the look of the original image better
pipeline.items.append(preprocessing.ZCA())
# note the can_fit=False's: no sharing between train and valid data
trainset.apply_preprocessor(preprocessor=pipeline, can_fit=True)
validset.apply_preprocessor(preprocessor=pipeline, can_fit=False)
tottrainset.apply_preprocessor(preprocessor=pipeline, can_fit=True)
testset.apply_preprocessor(preprocessor=pipeline, can_fit=False)
if preprocessor not in ('normal','nozca'):
for data in (trainset, validset, tottrainset, testset):
for ii in range(data.X.shape[0]):
# normalize to [0,1]
dmax = np.max(data.X[ii,:])
dmin = np.min(data.X[ii,:])
dnorm = (data.X[ii,:] - dmin) / (dmax - dmin)
# and convert to PIL image
img = Image.fromarray(dnorm.reshape(28, 28) * 255.).convert('L')
# apply preprocessor
if preprocessor == 'rotate':
rot = rng.randint(-40, 41)
img = img.rotate(rot, Image.BILINEAR)
elif preprocessor == 'emboss':
img = emboss(img)
elif preprocessor == 'hshear':
# coef = 0 means unsheared
coef = -1 + np.random.rand()*2
# note: image is moved with (coef/2)*28 to center it after shearing
img = img.transform((28,28), Image.AFFINE, (1,coef,-(coef/2)*28,0,1,0), Image.BILINEAR)
elif preprocessor == 'vshear':
coef = -1 + np.random.rand()*2
img = img.transform((28,28), Image.AFFINE, (1,0,0,coef,1,-(coef/2)*28), Image.BILINEAR)
elif preprocessor == 'patch':
# negative values are not possible in PIL, so do a zoom only transform then
x1 = np.random.randint(0, 5)
y1 = np.random.randint(0, 5)
x2 = np.random.randint(0, 5)
y2 = np.random.randint(0, 5)
img = img.transform((28,28), Image.EXTENT, (x1, y1, 28-x2, 28-y2), Image.BILINEAR)
# convert back to numpy array
data.X[ii,:] = np.array(img.getdata()) / 255.
if preprocessor == 'noisy':
# add noise
data.X[ii,:] += np.random.randn(28*28) * 0.1
# bound between [0,1]
data.X[ii,:] = np.minimum(np.ones(28*28), np.maximum(np.zeros(28*28), data.X[ii,:]))
# this uses numpy format for storage instead of pickle, for memory reasons
trainset.use_design_loc(DATA_DIR+'train_'+preprocessor+'_design.npy')
validset.use_design_loc(DATA_DIR+'valid_'+preprocessor+'_design.npy')
tottrainset.use_design_loc(DATA_DIR+'tottrain_'+preprocessor+'_design.npy')
testset.use_design_loc(DATA_DIR+'test_'+preprocessor+'_design.npy')
# this path can be used for visualizing weights after training is done
trainset.yaml_src = '!pkl: "%s"' % train_path
validset.yaml_src = '!pkl: "%s"' % valid_path
tottrainset.yaml_src = '!pkl: "%s"' % tottrain_path
testset.yaml_src = '!pkl: "%s"' % test_path
print 'saving preprocessed data...'
serial.save(train_path, trainset)
serial.save(valid_path, validset)
serial.save(tottrain_path, tottrainset)
serial.save(test_path, testset)
if tot:
return tottrainset, validset, testset
else:
return trainset, validset, testset
def get_data(tot=True, flatgrey=False):
tottrain_path = DATA_DIR+'gz_preprocessed_tottrain' + str(SUBMODEL) + '_64x.pkl'
test_path = DATA_DIR+'gz_preprocessed_test' + str(SUBMODEL) + '_64x.pkl'
if os.path.exists(test_path):
print 'loading preprocessed data'
datasets = OrderedDict()
# datasets['train'] = serial.load(train_path)
# datasets['valid'] = serial.load(valid_path)
if tot:
datasets['tottrain'] = serial.load(tottrain_path)
datasets['test'] = serial.load(test_path)
if tot:
return datasets['tottrain'], datasets['test']
else:
return datasets['train'], datasets['test']
else:
print 'preprocessing data...'
pipeline = preprocessing.Pipeline()
pipeline.items.append(preprocessing.GlobalContrastNormalization(use_std=True))
pipeline.items.append(preprocessing.ZCA())
# print 'traindata'
# data = GalaxyZoo.gzdeepdata.GZData(which_set='training', start=0, stop=39999)
# data.apply_preprocessor(preprocessor=pipeline, can_fit=True)
# # this path can be used for visualizing weights after training is done
# data.yaml_src = '!pkl: "%s"' % data
# # save
# data.use_design_loc(DATA_DIR+'train_design' + str(SUBMODEL) + '.npy')
# serial.save(DATA_DIR+'gz_preprocessed_train'+str(SUBMODEL) + '.pkl', data)
# print 'validdata'
# data = GalaxyZoo.gzdeepdata.GZData(which_set='training', start=40000, stop=61577)
# data.apply_preprocessor(preprocessor=pipeline, can_fit=False)
# # this path can be used for visualizing weights after training is done
# data.yaml_src = '!pkl: "%s"' % data
# # save
# data.use_design_loc(DATA_DIR+'valid_design' + str(SUBMODEL) + '.npy')
# serial.save(DATA_DIR+'gz_preprocessed_valid'+str(SUBMODEL) + '.pkl', data)
print 'tottraindata'
data = GalaxyZoo.gzdeepdata.GZData(which_set='training', flatgrey=flatgrey)
data.apply_preprocessor(preprocessor=pipeline, can_fit=True)
# this path can be used for visualizing weights after training is done
data.yaml_src = '!pkl: "%s"' % data
# save
data.use_design_loc(DATA_DIR + 'tottrain_design' + str(SUBMODEL) + '_64x.npy')
serial.save(DATA_DIR + 'gz_preprocessed_tottrain' + str(SUBMODEL) + '_64x.pkl', data)
print 'testdata'
data = GalaxyZoo.gzdeepdata.GZData(which_set='test', flatgrey=flatgrey)
data.apply_preprocessor(preprocessor=pipeline, can_fit=False)
# this path can be used for visualizing weights after training is done
data.yaml_src = '!pkl: "%s"' % data
# save
data.use_design_loc(DATA_DIR + 'test_design' + str(SUBMODEL) + '_64x.npy')
serial.save(DATA_DIR + 'gz_preprocessed_test' + str(SUBMODEL) + '_64x.pkl', data)
print 'Finished, now re-run for running model on GPU'
return None, None
def get_dataset(which_data, tot=False):
train_path = DATA_DIR + 'train' + which_data + '_preprocessed.pkl'
valid_path = DATA_DIR + 'valid' + which_data + '_preprocessed.pkl'
tottrain_path = DATA_DIR + 'tottrain' + which_data + '_preprocessed.pkl'
test_path = DATA_DIR + 'test' + which_data + '_preprocessed.pkl'
if os.path.exists(train_path) and os.path.exists(
valid_path) and os.path.exists(test_path):
print 'loading preprocessed data'
trainset = serial.load(train_path)
validset = serial.load(valid_path)
if tot:
tottrainset = serial.load(tottrain_path)
testset = serial.load(test_path)
else:
print 'loading raw data...'
trainset = Whales(which_set="train",
which_data=which_data,
start=0,
stop=56671)
validset = Whales(which_set="train",
which_data=which_data,
start=56671,
stop=66671)
tottrainset = Whales(which_set="train", which_data=which_data)
testset = Whales(which_set="test", which_data=which_data)
print 'preprocessing data...'
pipeline = preprocessing.Pipeline()
if which_data == 'melspectrum':
pipeline.items.append(
preprocessing.Standardize(global_mean=True, global_std=True))
# ZCA = zero-phase component analysis
# very similar to PCA, but preserves the look of the original image better
pipeline.items.append(preprocessing.ZCA())
else:
# global_mean/std=False voor per-feature standardization
pipeline.items.append(
preprocessing.Standardize(global_mean=False, global_std=False))
trainset.apply_preprocessor(preprocessor=pipeline, can_fit=True)
# this uses numpy format for storage instead of pickle, for memory reasons
trainset.use_design_loc(DATA_DIR + 'train_' + which_data +
'_design.npy')
# note the can_fit=False: no sharing between train and test data
validset.apply_preprocessor(preprocessor=pipeline, can_fit=False)
validset.use_design_loc(DATA_DIR + 'valid_' + which_data +
'_design.npy')
tottrainset.apply_preprocessor(preprocessor=pipeline, can_fit=True)
tottrainset.use_design_loc(DATA_DIR + 'tottrain_' + which_data +
'_design.npy')
# note the can_fit=False: no sharing between train and test data
testset.apply_preprocessor(preprocessor=pipeline, can_fit=False)
testset.use_design_loc(DATA_DIR + 'test_' + which_data + '_design.npy')
# this path can be used for visualizing weights after training is done
trainset.yaml_src = '!pkl: "%s"' % train_path
validset.yaml_src = '!pkl: "%s"' % valid_path
tottrainset.yaml_src = '!pkl: "%s"' % tottrain_path
testset.yaml_src = '!pkl: "%s"' % test_path
print 'saving preprocessed data...'
serial.save(DATA_DIR + 'train' + which_data + '_preprocessed.pkl',
trainset)
serial.save(DATA_DIR + 'valid' + which_data + '_preprocessed.pkl',
validset)
serial.save(DATA_DIR + 'tottrain' + which_data + '_preprocessed.pkl',
tottrainset)
serial.save(DATA_DIR + 'test' + which_data + '_preprocessed.pkl',
testset)
if tot:
return tottrainset, validset, testset
else:
return trainset, validset, testset
from pylearn2.utils import serial
from pylearn2.datasets import preprocessing
from pylearn2.datasets.tfd import TFD
train = TFD(which_set='train')
preprocessor = preprocessing.Pipeline()
preprocessor.items.append(preprocessing.GlobalContrastNormalization())
preprocessor.items.append(preprocessing.ZCA())
preprocessor.apply(train, can_fit=True)
serial.save('tfd_gcn_whitener.pkl', preprocessor)
def main():
data_name, model, pretrain, test, filter_channel, \
filter_size, activation, sparse_coeff, is_tied_weights, \
is_linear, do_zca, do_scale, do_maxpoool, n_epochs, batch_size = ProcessCommandLine()
print '... Loading data and parameters'
print 'dataset: ', data_name
print 'filter_channel=', filter_channel
print 'filter_size=', filter_size
print 'activation=', activation
print 'sparsity coefficient=', sparse_coeff
print 'Max pooling=', do_maxpoool
print 'tied weight=', is_tied_weights
print 'linear CAE=', is_linear
print 'ZCA whitening=', do_zca
print 'Scale image=', do_scale
print 'Batch size=', batch_size
print 'number of epoch=', n_epochs
# batch_size = 100 # number of images in each batch
n_epochs = 100 # number of experiment epochs
learning_rate = 0.1 # learning rate of SGD
# filter_channel = 16 # number of feature maps in ConvAE
# dataset = 'data/mnist.pkl.gz' # address of data
# rng = np.random.RandomState(23455) # random generator
# filter_size = 11
# n_images = 20
# sparse_coeff = 1
if sparse_coeff == 0:
model_type = 'cae'
else:
model_type = 'spcae'
model_save_name = model_type+'_'+data_name+'_'+ \
'[fn=%d,fs=%d,sp=%.3f,maxpool=%s,tied=%s,act=%s,linear=%s,ZCA=%s,scale=%s]' \
% (filter_channel, filter_size, sparse_coeff, do_maxpoool, is_tied_weights,
activation, is_linear, do_zca, do_scale)
results_dir = model_save_name + '/'
# results_dir = data_name+'_'+model_name+'/'
if not os.path.isdir(results_dir):
os.mkdir(results_dir)
if data_name == 'smallNORB':
### load smallNORB train set ###
# norb = SmallNORB('train', True)
# data_x = norb.adjust_for_viewer(norb.X)
# data_y = norb.y
# pickle.dump((data_x, data_y),open('smallNORB.pkl','wb'), -1)
# results_dir = 'smallNORB_scae/'
# results_dir = 'smallNORB_'+model_name+'/'
# if not os.path.isdir(results_dir):
# os.mkdir(results_dir)
# f = open('smallNORB.pkl', 'r')
# data, data_y = pickle.load(f)
# _, feat = data.shape
# f.close()
# train = NORB(which_norb='small', which_set='train')
# ipdb.set_trace()
# window = preprocessing.CentralWindow(window_shape=(64,64))
# train.apply_preprocessor(preprocessor=window)
# train.X = train.X.astype('float32')
# zca = preprocessing.ZCA()
# train.apply_preprocessor(preprocessor=zca, can_fit=True)
# _, feat = train.X.shape
# data_x = train.X[:, :feat/2]
norb = sio.loadmat('smallNORB_matlab/smallNORB_train_32x32.mat')
train_x = norb['trainData'].transpose(1, 0)
if do_zca:
zca = zca_whitening.ZCA()
zca.fit(train_x)
train_x = zca.transform(train_x)
if do_scale:
min_max_scaler = MinMaxScaler()
train_x_T = min_max_scaler.fit_transform(train_x.T)
train_x = train_x_T.T
data_x = train_x
idx = random.shuffle(range(data_x.shape[0]))
data_x = data_x[idx, :][0, :, :]
# ipdb.set_trace()
im_channel = 1
im_height = 32
im_width = 32
elif data_name == 'cifar':
### load cifar10 ###
# results_dir = 'cifar'+model_name+'/'
# data_x = pickle.load(open('cifar10.pkl', 'r'))
train = CIFAR10('train', gcn=55.)
im_channel = 3
im_height = 32
im_width = 32
# min_max_scaler = MinMaxScaler()
# data_x = min_max_scaler.fit_transform(data_x)
# data_x = cifar10.X
# elif data_name == 'cifarw':
# ### load cifar10 ###
# # results_dir = 'cifar'+model_name+'/'
# # data_x = pickle.load(open('cifar10_whitened.pkl', 'r'))
# train = CIFAR10('train', gcn=55.)
# # zca = preprocessing.ZCA()
# # cifar10.apply_preprocessor(preprocessor=zca, can_fit=True)
# im_channel = 3
# im_height = 32
# im_width = 32
# min_max_scaler = MinMaxScaler()
# data_x = min_max_scaler.fit_transform(cifar10.X)
# data_x = cifar10.X
# ipdb.set_trace()
elif data_name == 'svhn':
f = open('svhn.pkl', 'r')
svhn = pickle.load(f)
f.close()
im_channel = 3
im_height = 32
im_width = 32
train_x, train_y = svhn[0]
test_x, test_y = svhn[1]
extra_x, extra_y = svhn[2]
train_x = train_x.transpose([3, 2, 0, 1])
test_x = test_x.transpose([3, 2, 0, 1])
extra_x = extra_x.transpose([3, 2, 0, 1])
# Scale to [0,1]
channel_scale_factor = train_x.max(axis=(2, 3)).astype('float32')
train_x_scaled = train_x / channel_scale_factor.reshape(
channel_scale_factor.shape[0], im_channel, 1, 1)
data_x = train_x_scaled.reshape(train_x.shape[0],
im_channel * im_height * im_width)
elif data_name == 'mnist':
# f = open('mnist.pkl', 'r')
# mnist = pickle.load(f)
# f.close()
# train_x, train_y = mnist[0]
# valid_x, valid_y = mnist[1]
# test_x, test_y = mnist[2]
# data_x = train_x
train = MNIST('train')
# zca = preprocessing.ZCA()
# train.apply_preprocessor(preprocessor=zca, can_fit=True)
# ipdb.set_trace()
# min_max_scaler = MinMaxScaler()
# data_x = min_max_scaler.fit_transform(train.X)
# data_x = train.X
# data_y = train.y
im_channel = 1
im_height = 28
im_width = 28
elif data_name == 'bmnist':
train = BinarizedMNIST(which_set='train')
# zca = preprocessing.ZCA()
# train.apply_preprocessor(preprocessor=zca, can_fit=True)
# ipdb.set_trace()
# min_max_scaler = MinMaxScaler()
# data_x = min_max_scaler.fit_transform(train.X)
# data_x = train.X
# data_y = train.y
im_channel = 1
im_height = 28
im_width = 28
if do_zca and data_name not in ['smallNORB', 'svhn']:
zca = preprocessing.ZCA()
train.apply_preprocessor(preprocessor=zca, can_fit=True)
data_x = train.X
pass
if do_scale and data_name not in ['smallNORB', 'svhn']:
min_max_scaler = MinMaxScaler()
data_x_T = min_max_scaler.fit_transform(train.X.T)
data_x = data_x_T.T
pass
if not do_zca and not do_scale and data_name not in ['smallNORB', 'svhn']:
data_x = train.X
# if data_name not in ['smallNORB']:
# data_x = train.X
n_samples, n_feat = data_x.shape
data_x = data_x.reshape((n_samples, im_channel, im_height, im_width))
if data_name == 'mnist':
data_x = data_x.transpose(0, 1, 3, 2)
train_set_x = theano.shared(np.asarray(data_x, dtype=np.float32),
borrow=True)
# image_shp = (batch_size, im_channel, data_x.shape[2], data_x.shape[3])
image_shp = (batch_size, im_channel, im_height, im_width)
filter_shp = (filter_channel, im_channel, filter_size, filter_size)
print 'building model'
cae1 = CAE(image_shape=image_shp,
data=train_set_x,
filter_shape=filter_shp,
poolsize=(2, 2),
sparse_coeff=sparse_coeff,
activation=activation,
do_max_pool=do_maxpoool,
tied_weight=is_tied_weights,
is_linear=is_linear)
print 'model built'
sys.stdout.flush()
if model:
cae1.load(model)
pass
if pretrain:
do_pretraining_cae(data_name=data_name,
model=cae1,
save_name=model_save_name,
image_shape=image_shp,
result_dir=results_dir,
max_epoch=n_epochs)
elif test:
do_visualize(data_name=data_name, model=cae1, result_dir=results_dir)
