def _make_npz(path, urls):
x_url, y_url = urls
x_path = download.cached_download(x_url)
y_path = download.cached_download(y_url)
with gzip.open(x_path, 'rb') as imgpath, gzip.open(y_path,
'rb') as lblpath:
labels = numpy.frombuffer(lblpath.read(), dtype=numpy.uint8, offset=8)
images = numpy.frombuffer(imgpath.read(), dtype=numpy.uint8,
offset=16).reshape(len(labels), 784)
numpy.savez_compressed(path, x=images, y=labels)
return {'x': images, 'y': labels}
def download(base_path, name, url, img_type):
cache_root = "{0}/{1}/cache".format(base_path, name)
print("Caching to {0}".format(cache_root))
set_cache(cache_root)
archive_path = dl.cached_download(url)
fileOb = zipfile.ZipFile(archive_path, mode='r')
names = fileOb.namelist()
try:
os.makedirs(cache_root)
except OSError:
if not os.path.isdir(cache_root):
raise
data, label = [], []
try:
for name in names:
path = cache_root + name
if bool(re.search('obj', name)):
obj = fileOb.extract(name, path=path)
img = imreadBGR(obj, img_type)
data.append(img)
label.append(int(name.split("__")[0].split("/obj")[1]))
finally:
print("processed {0} images".format(len(names)))
#shutil.rmtree(cache_root)
#data = np.stack(data, axis=0).transpose([0, 3, 1, 2])
label = np.array(label).astype(np.uint8)
return data, label
def download_and_extract_qm9(save_filepath):
logger = getLogger(__name__)
logger.warning('Extracting QM9 dataset, it takes time...')
download_file_path = download.cached_download(download_url)
tf = tarfile.open(download_file_path, 'r')
temp_dir = tempfile.mkdtemp()
tf.extractall(temp_dir)
file_re = os.path.join(temp_dir, '*.xyz')
file_pathes = glob.glob(file_re)
# Make sure the order is sorted
file_pathes.sort()
ls = []
for path in tqdm(file_pathes):
with open(path, 'r') as f:
data = [line.strip() for line in f]
num_atom = int(data[0])
properties = list(map(float, data[1].split('\t')[1:]))
smiles = data[3 + num_atom].split('\t')
new_ls = smiles + properties
ls.append(new_ls)
df = pandas.DataFrame(ls, columns=_smiles_column_names + _label_names)
df.to_csv(save_filepath)
shutil.rmtree(temp_dir)
return True
def creator(path):
archive_path = download.cached_download(url)
train_x = numpy.empty((5, 10000, 3072), dtype=numpy.uint8)
train_y = numpy.empty((5, 10000), dtype=numpy.uint8)
test_y = numpy.empty(10000, dtype=numpy.uint8)
dir_name = '{}-batches-py'.format(name)
with tarfile.open(archive_path, 'r:gz') as archive:
# training set
for i in range(5):
file_name = '{}/data_batch_{}'.format(dir_name, i + 1)
d = pickle.load(archive.extractfile(file_name))
train_x[i] = d['data']
train_y[i] = d['labels']
# test set
file_name = '{}/test_batch'.format(dir_name)
d = pickle.load(archive.extractfile(file_name))
test_x = d['data']
test_y[...] = d['labels'] # copy to array
train_x = train_x.reshape(50000, 3072)
train_y = train_y.reshape(50000)
numpy.savez_compressed(path, train_x=train_x, train_y=train_y,
test_x=test_x, test_y=test_y)
return {'train_x': train_x, 'train_y': train_y,
'test_x': test_x, 'test_y': test_y}
def creator(cache_path):
data_path = download.cached_download(data_url)
shutil.copy(data_path, cache_path)
global task_names
assays, smiles, task_names = _load(data_path)
return create_dataset(assays, smiles, smiles2fp)
def __init__(self, pretrained_model='auto'):
super(HyperFaceModel, self).__init__(
conv1 = L.Convolution2D(3, 96, 11, stride=4, pad=0),
conv1a = L.Convolution2D(96, 256, 4, stride=4, pad=0),
conv2 = L.Convolution2D(96, 256, 5, stride=1, pad=2),
conv3 = L.Convolution2D(256, 384, 3, stride=1, pad=1),
conv3a = L.Convolution2D(384, 256, 2, stride=2, pad=0),
conv4 = L.Convolution2D(384, 384, 3, stride=1, pad=1),
conv5 = L.Convolution2D(384, 256, 3, stride=1, pad=1),
conv_all = L.Convolution2D(768, 192, 1, stride=1, pad=0),
fc_full = L.Linear(6 * 6 * 192, 3072),
fc_detection1 = L.Linear(3072, 512),
fc_detection2 = L.Linear(512, 2),
fc_landmarks1 = L.Linear(3072, 512),
fc_landmarks2 = L.Linear(512, 42),
fc_visibility1 = L.Linear(3072, 512),
fc_visibility2 = L.Linear(512, 21),
fc_pose1 = L.Linear(3072, 512),
fc_pose2 = L.Linear(512, 3),
fc_gender1 = L.Linear(3072, 512),
fc_gender2 = L.Linear(512, 2),
)
# download pretrained weights
if pretrained_model == 'auto':
rospy.loginfo("Loading pretrained model. (This may take some minutes.)")
url = 'https://jsk-ros-pkg.s3.amazonaws.com/chainer/hyperface_model_epoch_190.npz'
load_npz(download.cached_download(url), self)
rospy.loginfo("Model loaded")
elif pretrained_model:
rospy.loginfo("Loading pretrained model: %s" % pretrained_model)
load_npz(pretrained_model, self)
rospy.loginfo("Model loaded")
else:
rospy.logwarn("No pretrained model is loaded.")
def download_and_extract_qm9(save_filepath):
logger = getLogger(__name__)
logger.warning('Extracting QM9 dataset, it takes time...')
download_file_path = download.cached_download(download_url)
tf = tarfile.open(download_file_path, 'r')
temp_dir = tempfile.mkdtemp()
tf.extractall(temp_dir)
file_re = os.path.join(temp_dir, '*.xyz')
file_pathes = glob.glob(file_re)
# Make sure the order is sorted
file_pathes.sort()
ls = []
for path in tqdm(file_pathes):
with open(path, 'r') as f:
data = [line.strip() for line in f]
num_atom = int(data[0])
properties = list(map(float, data[1].split('\t')[1:]))
smiles = data[3 + num_atom].split('\t')
new_ls = smiles + properties
ls.append(new_ls)
df = pandas.DataFrame(ls, columns=_smiles_column_names + _label_names)
df.to_csv(save_filepath)
shutil.rmtree(temp_dir)
return True
def creator(path):
archive_path = download.cached_download(url)
train_x = numpy.empty((5, 10000, 3072), dtype=numpy.uint8)
train_y = numpy.empty((5, 10000), dtype=numpy.uint8)
test_y = numpy.empty(10000, dtype=numpy.uint8)
dir_name = '{}-batches-py/'.format(name)
with tarfile.open(archive_path, 'r:gz') as archive:
# training set
for i in range(5):
file_name = '{}/data_batch_{}'.format(dir_name, i + 1)
d = pickle.load(archive.extractfile(file_name))
train_x[i] = d['data']
train_y[i] = d['labels']
# test set
file_name = '{}/test_batch'.format(dir_name)
d = pickle.load(archive.extractfile(file_name))
test_x = d['data']
test_y[...] = d['labels'] # copy to array
train_x = train_x.reshape(50000, 3072)
train_y = train_y.reshape(50000)
numpy.savez_compressed(path, x=train_x, y=train_y)
return {'train_x': train_x, 'train_y': train_y,
'test_x': test_x, 'test_y': test_y}
def _make_npz(path, url):
_path = download.cached_download(url)
raw = io.loadmat(_path)
images = raw["X"].astype(numpy.uint8)
labels = raw["y"].astype(numpy.uint8)
numpy.savez_compressed(path, x=images, y=labels)
return {'x': images, 'y': labels}
def _make_npz(path, url):
_path = download.cached_download(url)
raw = io.loadmat(_path)
images = raw["X"].astype(numpy.uint8)
labels = raw["y"].astype(numpy.uint8)
numpy.savez_compressed(path, x=images, y=labels)
return {'x': images, 'y': labels}
def _creator(cached_file_path, sdffile, url):
download_file_path = download.cached_download(url)
with zipfile.ZipFile(download_file_path, 'r') as z:
z.extract(sdffile)
mol_supplier = Chem.SDMolSupplier(sdffile)
shutil.move(sdffile, cached_file_path)
return mol_supplier
def download_and_extract_reddit(save_dirpath):
# type: (str) -> bool
print('downloading reddit dataset...')
download_file_path = download.cached_download(download_url)
print('extracting reddit dataset...')
zip = ZipFile(download_file_path, 'r')
zip.extractall(save_dirpath)
return True
def _make_npz(path_npz, url, model):
path_caffemodel = download.cached_download(url)
sys.stderr.write(
'Now loading caffemodel (usually it may take few minutes)\n')
sys.stderr.flush()
GoogLeNet.convert_caffemodel_to_npz(path_caffemodel, path_npz)
npz.load_npz(path_npz, model)
return model
def _make_npz(path_npz, url, model):
path_caffemodel = download.cached_download(url)
sys.stderr.write(
'Now loading caffemodel (usually it may take few minutes)\n')
sys.stderr.flush()
VGGLayers.convert_caffemodel_to_npz(path_caffemodel, path_npz)
npz.load_npz(path_npz, model)
return model
def download_and_extract_cora(save_dirpath):
# type: (str) -> bool
print('downloading cora dataset...')
download_file_path = download.cached_download(download_url)
print('extracting cora dataset...')
tf = tarfile.open(download_file_path, 'r')
tf.extractall(os.path.dirname(save_dirpath))
return True
def _load_words(url):
path = download.cached_download(url)
words = []
with open(path) as words_file:
for line in words_file:
if line:
words += line.strip().split()
words.append('<eos>')
return words
def _load_words(url):
path = download.cached_download(url)
words = []
with open(path) as words_file:
for line in words_file:
if line:
words += line.strip().split()
words.append('<eos>')
return words
def download_and_extract_zinc250k(save_filepath):
logger = getLogger(__name__)
logger.info('Extracting ZINC250k dataset...')
download_file_path = download.cached_download(download_url)
df = pandas.read_csv(download_file_path)
# 'smiles' column contains '\n', need to remove it.
df['smiles'] = df['smiles'].apply(_remove_new_line)
df.to_csv(save_filepath, columns=_smiles_column_names + _label_names)
return True
def download_and_extract_zinc250k(save_filepath):
logger = getLogger(__name__)
logger.info('Extracting ZINC250k dataset...')
download_file_path = download.cached_download(download_url)
df = pandas.read_csv(download_file_path)
# 'smiles' column contains '\n', need to remove it.
df['smiles'] = df['smiles'].apply(_remove_new_line)
df.to_csv(save_filepath, columns=_smiles_column_names + _label_names)
return True
def __init__(self, n_layers):
root = download.get_dataset_directory('pfnet/chainer/models/')
caffemodel_path = os.path.join(
root, 'ResNet-{}-model.caffemodel'.format(n_layers))
if not os.path.exists(caffemodel_path):
if n_layers == 50:
cache_path = download.cached_download(self.URLS['resnet50'])
elif n_layers == 101:
cache_path = download.cached_download(self.URLS['resnet101'])
elif n_layers == 152:
cache_path = download.cached_download(self.URLS['resnet152'])
shutil.move(cache_path, caffemodel_path)
super(ResNet, self).__init__(os.path.basename(caffemodel_path),
n_layers=n_layers)
self._children.remove('fc6')
del self.fc6
del self.functions['fc6']
del self.functions['prob']
self.train = True
def __init__(self, n_layers):
root = download.get_dataset_directory('pfnet/chainer/models/')
caffemodel_path = os.path.join(
root, 'ResNet-{}-model.caffemodel'.format(n_layers))
if not os.path.exists(caffemodel_path):
if n_layers == 50:
cache_path = download.cached_download(self.URLS['resnet50'])
elif n_layers == 101:
cache_path = download.cached_download(self.URLS['resnet101'])
elif n_layers == 152:
cache_path = download.cached_download(self.URLS['resnet152'])
shutil.move(cache_path, caffemodel_path)
super(ResNet, self).__init__(
os.path.basename(caffemodel_path), n_layers=n_layers)
self._children.remove('fc6')
del self.fc6
del self.functions['fc6']
del self.functions['prob']
self.train = True
def download_pdbbind_time(url, save_filepath):
"""Download and caches PDBBind year table.
Args:
url(str): URL of year table
save_filepath(str): filepath for year table
Returns(bool): If success downloading, returning `True`.
"""
download_file_path = download.cached_download(url)
shutil.move(download_file_path, save_filepath)
return True
def download_pdbbind_time(url, save_filepath):
"""Download and caches PDBBind year table.
Args:
url(str): URL of year table
save_filepath(str): filepath for year table
Returns(bool): If success downloading, returning `True`.
"""
download_file_path = download.cached_download(url)
shutil.move(download_file_path, save_filepath)
return True
def _make_npz(path, urls):
x_url, y_url = urls
x_path = download.cached_download(x_url)
y_path = download.cached_download(y_url)
with gzip.open(x_path, 'rb') as fx, gzip.open(y_path, 'rb') as fy:
fx.read(4)
fy.read(4)
N, = struct.unpack('>i', fx.read(4))
if N != struct.unpack('>i', fy.read(4))[0]:
raise RuntimeError('wrong pair of MNIST images and labels')
fx.read(8)
x = numpy.empty((N, 784), dtype=numpy.uint8)
y = numpy.empty(N, dtype=numpy.uint8)
for i in six.moves.range(N):
y[i] = ord(fy.read(1))
for j in six.moves.range(784):
x[i, j] = ord(fx.read(1))
numpy.savez_compressed(path, x=x, y=y)
return {'x': x, 'y': y}
def download_model(url, subdir_name=None, root_dir_name='ronekko'):
root_dir_path = get_dataset_directory(root_dir_name)
basename = os.path.basename(url)
if subdir_name is None:
subdir_name = ''
save_dir_path = os.path.join(root_dir_path, subdir_name)
save_file_path = os.path.join(save_dir_path, basename)
if not os.path.exists(save_file_path):
cache_path = cached_download(url)
if not os.path.exists(save_dir_path):
os.mkdir(save_dir_path)
os.rename(cache_path, save_file_path)
return save_file_path
def _make_npz(path, urls):
x_url, y_url = urls
x_path = download.cached_download(x_url)
y_path = download.cached_download(y_url)
with gzip.open(x_path, 'rb') as fx, gzip.open(y_path, 'rb') as fy:
fx.read(4)
fy.read(4)
N, = struct.unpack('>i', fx.read(4))
if N != struct.unpack('>i', fy.read(4))[0]:
raise RuntimeError('wrong pair of MNIST images and labels')
fx.read(8)
x = numpy.empty((N, 784), dtype=numpy.uint8)
y = numpy.empty(N, dtype=numpy.uint8)
for i in six.moves.range(N):
y[i] = ord(fy.read(1))
for j in six.moves.range(784):
x[i, j] = ord(fx.read(1))
numpy.savez_compressed(path, x=x, y=y)
return {'x': x, 'y': y}
def creator(path):
archive_path = download.cached_download(url)
if name == 'cifar-10':
train_x = numpy.empty((5, 10000, 3072), dtype=numpy.uint8)
train_y = numpy.empty((5, 10000), dtype=numpy.uint8)
test_y = numpy.empty(10000, dtype=numpy.uint8)
dir_name = '{}-batches-py'.format(name)
with tarfile.open(archive_path, 'r:gz') as archive:
# training set
for i in range(5):
file_name = '{}/data_batch_{}'.format(dir_name, i + 1)
d = _pickle_load(archive.extractfile(file_name))
train_x[i] = d['data']
train_y[i] = d['labels']
# test set
file_name = '{}/test_batch'.format(dir_name)
d = _pickle_load(archive.extractfile(file_name))
test_x = d['data']
test_y[...] = d['labels'] # copy to array
train_x = train_x.reshape(50000, 3072)
train_y = train_y.reshape(50000)
else:
# name == 'cifar-100'
def load(archive, file_name):
d = _pickle_load(archive.extractfile(file_name))
x = d['data'].reshape((-1, 3072))
y = numpy.array(d['fine_labels'], dtype=numpy.uint8)
return x, y
with tarfile.open(archive_path, 'r:gz') as archive:
train_x, train_y = load(archive, 'cifar-100-python/train')
test_x, test_y = load(archive, 'cifar-100-python/test')
numpy.savez_compressed(path,
train_x=train_x,
train_y=train_y,
test_x=test_x,
test_y=test_y)
return {
'train_x': train_x,
'train_y': train_y,
'test_x': test_x,
'test_y': test_y
}
def download(dataset_type='normal'):
if dataset_type == 'normal':
url = 'https://github.com/brendenlake/omniglot/blob/master/python/images_background.zip'
elif dataset_type == 'small1':
url = 'https://github.com/brendenlake/omniglot/blob/master/python/images_background_small1.zip'
elif dataset_type == 'small2':
url = 'https://github.com/brendenlake/omniglot/blob/master/python/images_background_small2.zip'
elif dataset_type == 'evaluation':
url = 'https://github.com/brendenlake/omniglot/blob/master/python/images_evaluation.zip'
archive_path = dl.cached_download(url)
with tarfile.open(archive_path, 'r:gz') as archive:
names = archive.getnames()
for name in names:
print(name)
def _download_and_extract_tox21(config_name, save_filepath):
is_successful = False
c = _config[config_name]
url = c['url']
sdffile = c['filename']
# Download tox21 dataset
download_file_path = download.cached_download(url)
# Extract zipfile to get sdffile
with zipfile.ZipFile(download_file_path, 'r') as z:
z.extract(sdffile)
shutil.move(sdffile, save_filepath)
is_successful = True
return is_successful
def download(dataset_type='normal'): if dataset_type=='normal': url = 'https://github.com/brendenlake/omniglot/blob/master/python/images_background.zip' elif dataset_type=='small1': url = 'https://github.com/brendenlake/omniglot/blob/master/python/images_background_small1.zip' elif dataset_type=='small2': url = 'https://github.com/brendenlake/omniglot/blob/master/python/images_background_small2.zip' elif dataset_type=='evaluation': url = 'https://github.com/brendenlake/omniglot/blob/master/python/images_evaluation.zip' archive_path = dl.cached_download(url) with tarfile.open(archive_path, 'r:gz') as archive: names = archive.getnames() for name in names: print(name)
def creator(path):
def load(archive, file_name):
d = _pickle_load(archive.extractfile(file_name))
x = d['data'].reshape((-1, 3072))
y = numpy.array(d['fine_labels'], dtype=numpy.uint8)
return x, y
archive_path = download.cached_download(url)
with tarfile.open(archive_path, 'r:gz') as archive:
train_x, train_y = load(archive, 'cifar-100-python/train')
test_x, test_y = load(archive, 'cifar-100-python/test')
numpy.savez_compressed(path, train_x=train_x, train_y=train_y,
test_x=test_x, test_y=test_y)
return {'train_x': train_x, 'train_y': train_y,
'test_x': test_x, 'test_y': test_y}
def download_dataset(dataset_url, save_filepath):
"""Download and caches MoleculeNet Dataset
Args:
dataset_url (str): URL of dataset
save_filepath (str): filepath for dataset
Returns (bool): If success downloading, returning `True`.
"""
logger = getLogger(__name__)
logger.warning('Downloading {} dataset, it takes time...'.format(
dataset_url.split('/')[-1]))
download_file_path = download.cached_download(dataset_url)
shutil.move(download_file_path, save_filepath)
# pandas can load gzipped or tarball csv file
return True
def creator(path):
def load(archive, file_name):
d = _pickle_load(archive.extractfile(file_name))
x = d['data'].reshape((-1, 3072))
y = numpy.array(d['fine_labels'], dtype=numpy.uint8)
return x, y
archive_path = download.cached_download(url)
with tarfile.open(archive_path, 'r:gz') as archive:
train_x, train_y = load(archive, 'cifar-100-python/train')
test_x, test_y = load(archive, 'cifar-100-python/test')
numpy.savez_compressed(path, train_x=train_x, train_y=train_y,
test_x=test_x, test_y=test_y)
return {'train_x': train_x, 'train_y': train_y,
'test_x': test_x, 'test_y': test_y}
def download():
url = "http://people.csail.mit.edu/rgrosse/intrinsic/intrinsic-data.tar.gz"
archive_path = dl.cached_download(url)
with tarfile.open(archive_path, 'r:gz') as archive:
names = archive.getnames()
key_set = set()
object_set = set()
for path in names:
if bool(re.search("png", path)):
key = os.path.split(path)[1].split(".")[0]
key_set.add(key)
object_name = os.path.split(os.path.split(path)[0])[1]
# print(object_name)
object_set.add(object_name)
print(key_set, object_set)
def download_dataset(dataset_url, save_filepath):
"""Download and caches MoleculeNet Dataset
Args:
dataset_url (str): URL of dataset
save_filepath (str): filepath for dataset
Returns (bool): If success downloading, returning `True`.
"""
logger = getLogger(__name__)
logger.warning('Downloading {} dataset, it takes time...'
.format(dataset_url.split('/')[-1]))
download_file_path = download.cached_download(dataset_url)
shutil.move(download_file_path, save_filepath)
# pandas can load gzipped or tarball csv file
return True
def load_model(model_name, n_class):
archs = {'nin': NIN, 'vgg16': VGG16BatchNormalization}
model = archs[model_name](n_class=n_class)
if model_name == 'nin':
pass
elif model_name == 'vgg16':
rospack = rospkg.RosPack()
model_path = osp.join(rospack.get_path('decopin_hand'), 'scripts',
'vgg16', 'VGG_ILSVRC_16_layers.npz')
if not osp.exists(model_path):
from chainer.dataset import download
from chainer.links.caffe.caffe_function import CaffeFunction
path_caffemodel = download.cached_download(
'http://www.robots.ox.ac.uk/%7Evgg/software/very_deep/caffe/VGG_ILSVRC_19_layers.caffemodel'
)
caffemodel = CaffeFunction(path_caffemodel)
npz.save_npz(model_path, caffemodel, compression=False)
vgg16 = VGG16Layers(
pretrained_model=model_path) # original VGG16 model
print('Load model from {}'.format(model_path))
for l in model.children():
if l.name.startswith('conv'):
# l.disable_update() # Comment-in for transfer learning, comment-out for fine tuning
l1 = getattr(vgg16, l.name)
l2 = getattr(model, l.name)
assert l1.W.shape == l2.W.shape
assert l1.b.shape == l2.b.shape
l2.W.data[...] = l1.W.data[...]
l2.b.data[...] = l1.b.data[...]
elif l.name in ['fc6', 'fc7']:
l1 = getattr(vgg16, l.name)
l2 = getattr(model, l.name)
assert l1.W.size == l2.W.size
assert l1.b.size == l2.b.size
l2.W.data[...] = l1.W.data.reshape(l2.W.shape)[...]
l2.b.data[...] = l1.b.data.reshape(l2.b.shape)[...]
else:
print('Model type {} is invalid.'.format(model_name))
exit()
return model
def creator(path):
archive_path = download.cached_download(url)
if name == 'cifar-10':
train_x = numpy.empty((5, 10000, 3072), dtype=numpy.uint8)
train_y = numpy.empty((5, 10000), dtype=numpy.uint8)
test_y = numpy.empty(10000, dtype=numpy.uint8)
dir_name = '{}-batches-py'.format(name)
with tarfile.open(archive_path, 'r:gz') as archive:
# training set
for i in range(5):
file_name = '{}/data_batch_{}'.format(dir_name, i + 1)
d = _pickle_load(archive.extractfile(file_name))
train_x[i] = d['data']
train_y[i] = d['labels']
# test set
file_name = '{}/test_batch'.format(dir_name)
d = _pickle_load(archive.extractfile(file_name))
test_x = d['data']
test_y[...] = d['labels'] # copy to array
train_x = train_x.reshape(50000, 3072)
train_y = train_y.reshape(50000)
else:
# name == 'cifar-100'
def load(archive, file_name):
d = _pickle_load(archive.extractfile(file_name))
x = d['data'].reshape((-1, 3072))
y = numpy.array(d['fine_labels'], dtype=numpy.uint8)
return x, y
with tarfile.open(archive_path, 'r:gz') as archive:
train_x, train_y = load(archive, 'cifar-100-python/train')
test_x, test_y = load(archive, 'cifar-100-python/test')
numpy.savez_compressed(path, train_x=train_x, train_y=train_y,
test_x=test_x, test_y=test_y)
return {'train_x': train_x, 'train_y': train_y,
'test_x': test_x, 'test_y': test_y}
def creator(path):
dump_path = download.cached_download(url)
tmp_dir = tempfile.mkdtemp()
# WikiExtractor needs .bz2 extension to function well
dump_sym = os.path.join(tmp_dir, 'dump.bz2')
os.symlink(dump_path, dump_sym)
print "Extracting dump..."
extract_dir = os.path.join(tmp_dir,'extracts')
extract_dump(dump_sym, extract_dir, quiet=True)
print "Building vocabulary and sequence array.."
seq,voc = _build_dataset(extract_dir, path,max,th)
# clean up temp file:
print "Removing dump"
shutil.rmtree(extract_dir)
return seq, voc
def get_atom_init_json_filepath(download_if_not_exist=True):
"""Construct a filepath which stores atom_init_json
This method check whether the file exist or not, and downloaded it if
necessary.
Args:
download_if_not_exist (bool): If `True` download dataset
if it is not downloaded yet.
Returns (str): file path for atom_init_json
"""
cache_root = download.get_dataset_directory(_root)
cache_path = os.path.join(cache_root, file_name_atom_init_json)
if not os.path.exists(cache_path) and download_if_not_exist:
logger = getLogger(__name__)
logger.info('Downloading atom_init.json...')
download_file_path = download.cached_download(download_url)
shutil.copy(download_file_path, cache_path)
return cache_path
def creator(path):
archive_path = download.cached_download(url)
images = []
labels = []
with zipfile.ZipFile(archive_path, 'r') as archive:
for i in range(1, 378 + 1):
image_name = 'base/cmp_b{:04d}.jpg'.format(i)
label_name = 'base/cmp_b{:04d}.png'.format(i)
image = Image.open(io.BytesIO(archive.read(image_name)))
image = np.asarray(image)
images.append(image)
label = Image.open(io.BytesIO(archive.read(label_name)))
label = np.asarray(label)
labels.append(label)
np.savez_compressed(path, images=images, labels=labels)
return {'images': images, 'labels': labels}
def download():
url = "http://www.eecs.berkeley.edu/Research/Projects/CS/vision/grouping/BSR/BSR_bsds500.tgz"
archive_path = dl.cached_download(url)
with tarfile.open(archive_path, 'r:gz') as archive:
names = archive.getnames()
cache_root = "./temp/"
try:
os.makedirs(cache_root)
except OSError:
if not os.path.isdir(cache_root):
raise
cache_path = tempfile.mkdtemp(dir=cache_root)
data = []
try:
for name in names:
if bool(re.search("BSR/BSDS500/data/images/train/",
name)) and bool(re.search("jpg", name)):
path = cache_path
archive.extract(name, path)
img = imreadBGR(path + "/" + name)
lead = img.shape[0]
#for bsds500, imgs are of shape 481*321*3
if lead != 481:
img = img.transpose([1, 0, 2])
lead = img.shape[0]
if lead != 481:
raise ValueError(
"img shape not to be 481*321*3, but: {}".format(
img.shape))
data.append(img)
finally:
shutil.rmtree(cache_root)
data = np.stack(data, axis=0)
data = data.transpose([0, 3, 1, 2])
return data
def download():
url = "http://www.eecs.berkeley.edu/Research/Projects/CS/vision/grouping/BSR/BSR_bsds500.tgz"
archive_path = dl.cached_download(url)
with tarfile.open(archive_path, 'r:gz') as archive:
names = archive.getnames()
cache_root = "./temp/"
try:
os.makedirs(cache_root)
except OSError:
if not os.path.isdir(cache_root):
raise
cache_path = tempfile.mkdtemp(dir=cache_root)
data = []
try:
for name in names:
if bool(re.search("BSR/BSDS500/data/images/train/", name)) and bool(re.search("jpg", name)):
path = cache_path
archive.extract(name, path)
img = imreadBGR(path+"/"+name)
lead = img.shape[0]
#for bsds500, imgs are of shape 481*321*3
if lead!=481:
img = img.transpose([1,0,2])
lead = img.shape[0]
if lead!=481:
raise ValueError("img shape not to be 481*321*3, but: {}".format(img.shape))
data.append(img)
finally:
shutil.rmtree(cache_root)
data = np.stack(data, axis=0)
data = data.transpose([0,3,1,2])
return data
def download(dataset_type='unprocessed'):
if dataset_type == 'unprocessed':
url = "http://www.cs.columbia.edu/CAVE/databases/SLAM_coil-20_coil-100/coil-20/coil-20-unproc.zip"
elif dataset_type == 'processed':
url = 'http://www.cs.columbia.edu/CAVE/databases/SLAM_coil-20_coil-100/coil-20/coil-20-proc.zip'
else:
raise ValueError(
"dataset_type should be either unprocessed or processed")
archive_path = dl.cached_download(url)
fileOb = zipfile.ZipFile(archive_path, mode='r')
names = fileOb.namelist()
cache_root = "./temp/"
try:
os.makedirs(cache_root)
except OSError:
if not os.path.isdir(cache_root):
raise
cache_path = tempfile.mkdtemp(dir=cache_root)
data, label = [], []
try:
for name in names:
path = cache_path + name
if bool(re.search('obj', name)):
img = imreadBGR(fileOb.extract(name, path=path))
data.append(img)
label.append(int(name.split("__")[0].split("/obj")[1]))
finally:
shutil.rmtree(cache_root)
data = np.stack(data, axis=0).transpose([0, 3, 1, 2])
label = np.array(label).astype(np.uint8)
data = np.reshape(data, (data.shape[0], -1))
return data, label
def download(dataset_type='unprocessed'):
if dataset_type=='unprocessed':
url = "http://www.cs.columbia.edu/CAVE/databases/SLAM_coil-20_coil-100/coil-20/coil-20-unproc.zip"
elif dataset_type=='processed':
url = 'http://www.cs.columbia.edu/CAVE/databases/SLAM_coil-20_coil-100/coil-20/coil-20-proc.zip'
else:
raise ValueError("dataset_type should be either unprocessed or processed")
archive_path = dl.cached_download(url)
fileOb = zipfile.ZipFile(archive_path, mode='r')
names = fileOb.namelist()
cache_root = "./temp/"
try:
os.makedirs(cache_root)
except OSError:
if not os.path.isdir(cache_root):
raise
cache_path = tempfile.mkdtemp(dir=cache_root)
data, label = [], []
try:
for name in names:
path = cache_path+name
if bool(re.search('obj', name)):
img = imreadBGR(fileOb.extract(name, path=path))
data.append(img)
label.append(int(name.split("__")[0].split("/obj")[1]))
finally:
shutil.rmtree(cache_root)
data = np.stack(data, axis=0).transpose([0, 3, 1, 2])
label = np.array(label).astype(np.uint8)
return data, label
def _make_npz(path_npz, url, model):
path_caffemodel = download.cached_download(url)
print('Now loading caffemodel (usually it may take few minutes)')
GoogLeNet.convert_caffemodel_to_npz(path_caffemodel, path_npz)
npz.load_npz(path_npz, model)
return model
def _make_npz(path_npz, url, model):
path_caffemodel = download.cached_download(url)
print('Now loading caffemodel (usually it may take few minutes)')
VGG16Layers.convert_caffemodel_to_npz(path_caffemodel, path_npz)
npz.load_npz(path_npz, model)
return model
