def iterator(self,
mode=None,
batch_size=None,
num_batches=None,
topo=None,
targets=None,
rng=None):
"""
Method inherited from the Dataset.
"""
self.mode = mode
self.batch_size = batch_size
self._targets = targets
self.cur_idx = -1
if mode == 'sequential':
self.subset_iterator = SequentialSubsetIterator(
self.data_n_rows,
batch_size=1,
num_batches=num_batches,
rng=None)
return self
else:
raise NotImplementedError(
'other iteration scheme not supported for now!')
def test_correct_sequential_slices():
iterator = SequentialSubsetIterator(10, 3, 4)
sl = iterator.next()
assert sl.start == 0
assert sl.stop == 3
assert sl.step is None
sl = iterator.next()
assert sl.start == 3
assert sl.stop == 6
assert sl.step is None
sl = iterator.next()
assert sl.start == 6
assert sl.stop == 9
assert sl.step is None
sl = iterator.next()
assert sl.start == 9
assert sl.stop == 10
assert sl.step is None
def iterator(self, mode=None, batch_size=None, num_batches=None,
topo=None, targets=None, rng=None):
"""
method inherited from Dataset
"""
self.mode = mode
self.batch_size = batch_size
self._targets = targets
if mode == 'sequential':
self.subset_iterator = SequentialSubsetIterator(self.data_n_rows,
batch_size, num_batches, rng=None)
return self
else:
raise NotImplementedError('other iteration scheme not supported for now!')
def test_misc_exceptions():
raised = False
try:
SubsetIterator.__new__(SubsetIterator).next()
except NotImplementedError:
raised = True
assert raised
raised = False
try:
SubsetIterator(1, 2, 3)
except NotImplementedError:
raised = True
assert raised
raised = False
try:
SequentialSubsetIterator(10, 3, 3, rng=0)
except ValueError:
raised = True
assert raised
def test_correct_sequential_slices():
iterator = SequentialSubsetIterator(10, 3, 4)
sl = iterator.next()
assert sl.start == 0
assert sl.stop == 3
assert sl.step is None
sl = iterator.next()
assert sl.start == 3
assert sl.stop == 6
assert sl.step is None
sl = iterator.next()
assert sl.start == 6
assert sl.stop == 9
assert sl.step is None
sl = iterator.next()
assert sl.start == 9
assert sl.stop == 10
assert sl.step is None
def test_sequential_num_batches_and_batch_size():
try:
# This should be fine, we have enough examples for 4 batches
# (with one under-sized batch).
iterator = SequentialSubsetIterator(10, 3, 4)
for i in range(4):
iterator.next()
except Exception as e:
assert False
raised = False
try:
iterator.next()
except StopIteration:
raised = True
assert raised
try:
# This should be fine, we have enough examples for 4 batches
# (with one to spare).
iterator = SequentialSubsetIterator(10, 3, 3)
for i in range(3):
iterator.next()
except Exception:
assert False
raised = False
try:
iterator.next()
except StopIteration:
raised = True
assert raised
try:
# This should fail, since you can't make 5 batches of 3 from 10.
iterator = SequentialSubsetIterator(10, 3, 5)
except ValueError:
return
assert False
def test_sequential_num_batches_and_batch_size():
try:
# This should be fine, we have enough examples for 4 batches
# (with one under-sized batch).
iterator = SequentialSubsetIterator(10, 3, 4)
for i in range(4):
iterator.next()
except Exception as e:
assert False
raised = False
try:
iterator.next()
except StopIteration:
raised = True
assert raised
try:
# This should be fine, we have enough examples for 4 batches
# (with one to spare).
iterator = SequentialSubsetIterator(10, 3, 3)
for i in range(3):
iterator.next()
except Exception:
assert False
raised = False
try:
iterator.next()
except StopIteration:
raised = True
assert raised
try:
# This should fail, since you can't make 5 batches of 3 from 10.
iterator = SequentialSubsetIterator(10, 3, 5)
except ValueError:
return
assert False
class SparseDataset(Dataset):
"""
SparseDataset is by itself an iterator.
"""
def __init__(self,
load_path=None,
from_scipy_sparse_dataset=None,
zipped_npy=True):
self.load_path = load_path
if self.load_path != None:
if zipped_npy == True:
print '... loading sparse data set from a zip npy file'
self.sparse_matrix = scipy.sparse.csr_matrix(numpy.load(
gzip.open(load_path)),
dtype=floatX)
else:
print '... loading sparse data set from a npy file'
self.sparse_matrix = scipy.sparse.csr_matrix(
numpy.load(load_path).item(), dtype=floatX)
else:
print '... building from given sparse dataset'
self.sparse_matrix = from_scipy_sparse_dataset
self.data_n_rows = self.sparse_matrix.shape[0]
self.num_examples = self.data_n_rows
def get_design_matrix(self):
return self.sparse_matrix
def get_batch_design(self, batch_size, include_labels=False):
"""
method inherited from Dataset
"""
self.iterator(mode='sequential',
batch_size=batch_size,
num_batches=None,
topo=None)
return self.next()
def get_batch_topo(self, batch_size):
"""
method inherited from Dataset
"""
raise NotImplementedError('Not implemented for sparse dataset')
def iterator(self,
mode=None,
batch_size=None,
num_batches=None,
topo=None,
targets=None,
rng=None):
"""
method inherited from Dataset
"""
self.mode = mode
self.batch_size = batch_size
self._targets = targets
if mode == 'sequential':
self.subset_iterator = SequentialSubsetIterator(self.data_n_rows,
batch_size,
num_batches,
rng=None)
return self
else:
raise NotImplementedError(
'other iteration scheme not supported for now!')
def __iter__(self):
return self
def next(self):
indx = self.subset_iterator.next()
try:
mini_batch = self.sparse_matrix[indx]
except IndexError:
# the ind of minibatch goes beyond the boundary
import ipdb
ipdb.set_trace()
return mini_batch
class SparseDataset(Dataset):
"""
SparseDataset is by itself an iterator.
"""
def __init__(self, load_path=None, from_scipy_sparse_dataset=None, zipped_npy=True):
self.load_path = load_path
if self.load_path != None:
if zipped_npy == True:
print '... loading sparse data set from a zip npy file'
self.sparse_matrix = scipy.sparse.csr_matrix(
numpy.load(gzip.open(load_path)), dtype=floatX)
else:
print '... loading sparse data set from a npy file'
self.sparse_matrix = scipy.sparse.csr_matrix(
numpy.load(load_path).item(), dtype=floatX)
else:
print '... building from given sparse dataset'
self.sparse_matrix = from_scipy_sparse_dataset
self.data_n_rows = self.sparse_matrix.shape[0]
self.num_examples = self.data_n_rows
def get_design_matrix(self):
return self.sparse_matrix
def get_batch_design(self, batch_size, include_labels=False):
"""
method inherited from Dataset
"""
self.iterator(mode='sequential', batch_size=batch_size, num_batches=None, topo=None)
return self.next()
def get_batch_topo(self, batch_size):
"""
method inherited from Dataset
"""
raise NotImplementedError('Not implemented for sparse dataset')
def iterator(self, mode=None, batch_size=None, num_batches=None,
topo=None, targets=None, rng=None):
"""
method inherited from Dataset
"""
self.mode = mode
self.batch_size = batch_size
self._targets = targets
if mode == 'sequential':
self.subset_iterator = SequentialSubsetIterator(self.data_n_rows,
batch_size, num_batches, rng=None)
return self
else:
raise NotImplementedError('other iteration scheme not supported for now!')
def __iter__(self):
return self
def next(self):
indx = self.subset_iterator.next()
try:
mini_batch = self.sparse_matrix[indx]
except IndexError:
# the ind of minibatch goes beyond the boundary
import ipdb; ipdb.set_trace()
return mini_batch
class CroppedPatchesDataset(Dataset):
"""
CroppedPatchesDataset is by itself an iterator.
"""
def __init__(self,
img_shape,
iter_mode="fprop",
h5_file=None,
start=None,
stop=None,
mode=None):
self.__dict__.update(locals())
self.img_shape = img_shape
if self.self is not None:
del self.self
if mode is not None:
self.mode = mode
elif start is not None or stop is not None:
self.mode = "r+"
else:
self.mode = "r"
if not os.path.isfile(h5_file):
raise ValueError("Please enter a valid file path.")
self.initialize_dataset(h5_file)
def initialize_dataset(self, h5_file):
"""
Set the files and the patches,...etc.
"""
self.h5file = tables.openFile(h5_file, mode=self.mode)
self.dataset = self.h5file.root
self.X = self.dataset.Data.Pt
self.Y = self.dataset.Data.Tgt
self.imgnos = self.dataset.Data.Ino
self.plocs = self.dataset.Data.Ploc
self.data_n_rows = self.targets.shape[0]
def set_iter_mode(self, r_mode):
self.iter_mode = r_mode
def get_design_matrix(self):
"""
Return the patches as a dense design matrix.
"""
return self.patches
def get_batch_design(self, batch_size, include_labels=False):
"""
Method inherited from the Dataset.
"""
self.iterator(mode='sequential',
batch_size=batch_size,
num_batches=None,
topo=None)
return self.next()
def get_batch_topo(self, batch_size):
"""
Method inherited from the Dataset.
"""
raise NotImplementedError('Not implemented for sparse dataset')
def iterator(self,
mode=None,
batch_size=None,
num_batches=None,
topo=None,
targets=None,
rng=None):
"""
Method inherited from the Dataset.
"""
self.mode = mode
self.batch_size = batch_size
self._targets = targets
self.cur_idx = -1
if mode == 'sequential':
self.subset_iterator = SequentialSubsetIterator(
self.data_n_rows,
batch_size=1,
num_batches=num_batches,
rng=None)
return self
else:
raise NotImplementedError(
'other iteration scheme not supported for now!')
def __iter__(self):
return self
def next(self):
"""
Method for the getting the next indices from the minibatch.
"""
if self.cur_idx == -1:
batch_start_indx = self.subset_iterator.next()
else:
batch_start_indx = self.cur_idx
begining_img_no = self.imgnos[batch_start_indx]
mini_batch_patches = []
mini_batch_plocs = []
mini_batch_imgnos = []
mini_batch_targets = []
indx = batch_start_indx
while indx is not None:
if (mini_batch_targets[-1] is not None) and (mini_batch_imgnos[-1]
!= begining_img_no):
self.cur_idx = indx
break
try:
mini_batch_patches.append(self.X[indx.start])
mini_batch_targets.append(self.Y[indx.start])
mini_batch_imgnos.append(self.imgnos[indx.start])
mini_batch_plocs.append(self.plocs[indx.start])
except IndexError:
print "The index of minibatch goes beyond the boundary."
import ipdb
ipdb.set_trace()
indx = self.subset_iterator.next()
if self.iter_mode == "train":
return (mini_batch_patches, mini_batch_targets)
else:
return (mini_batch_patches, mini_batch_targets, mini_batch_imgnos,
mini_batch_plocs)
class CroppedPatchesDataset(Dataset):
"""
CroppedPatchesDataset is by itself an iterator.
"""
def __init__(self,
img_shape,
iter_mode="fprop",
h5_file=None,
start=None,
stop=None,
mode=None):
self.__dict__.update(locals())
self.img_shape = img_shape
if self.self is not None:
del self.self
if mode is not None:
self.mode = mode
elif start is not None or stop is not None:
self.mode = "r+"
else:
self.mode = "r"
if not os.path.isfile(h5_file):
raise ValueError("Please enter a valid file path.")
self.initialize_dataset(h5_file)
def initialize_dataset(self, h5_file):
"""
Set the files and the patches,...etc.
"""
self.h5file = tables.openFile(h5_file, mode=self.mode)
self.dataset = self.h5file.root
self.X = self.dataset.Data.Pt
self.Y = self.dataset.Data.Tgt
self.imgnos = self.dataset.Data.Ino
self.plocs = self.dataset.Data.Ploc
self.data_n_rows = self.targets.shape[0]
def set_iter_mode(self, r_mode):
self.iter_mode = r_mode
def get_design_matrix(self):
"""
Return the patches as a dense design matrix.
"""
return self.patches
def get_batch_design(self, batch_size, include_labels=False):
"""
Method inherited from the Dataset.
"""
self.iterator(mode='sequential', batch_size=batch_size, num_batches=None, topo=None)
return self.next()
def get_batch_topo(self, batch_size):
"""
Method inherited from the Dataset.
"""
raise NotImplementedError('Not implemented for sparse dataset')
def iterator(self,
mode=None,
batch_size=None,
num_batches=None,
topo=None,
targets=None,
rng=None):
"""
Method inherited from the Dataset.
"""
self.mode = mode
self.batch_size = batch_size
self._targets = targets
self.cur_idx = -1
if mode == 'sequential':
self.subset_iterator = SequentialSubsetIterator(self.data_n_rows,
batch_size=1, num_batches=num_batches, rng=None)
return self
else:
raise NotImplementedError('other iteration scheme not supported for now!')
def __iter__(self):
return self
def next(self):
"""
Method for the getting the next indices from the minibatch.
"""
if self.cur_idx == -1:
batch_start_indx = self.subset_iterator.next()
else:
batch_start_indx = self.cur_idx
begining_img_no = self.imgnos[batch_start_indx]
mini_batch_patches = []
mini_batch_plocs = []
mini_batch_imgnos = []
mini_batch_targets = []
indx = batch_start_indx
while indx is not None:
if (mini_batch_targets[-1] is not None) and (mini_batch_imgnos[-1] != begining_img_no):
self.cur_idx = indx
break
try:
mini_batch_patches.append(self.X[indx.start])
mini_batch_targets.append(self.Y[indx.start])
mini_batch_imgnos.append(self.imgnos[indx.start])
mini_batch_plocs.append(self.plocs[indx.start])
except IndexError:
print "The index of minibatch goes beyond the boundary."
import ipdb; ipdb.set_trace()
indx = self.subset_iterator.next()
if self.iter_mode == "train":
return (mini_batch_patches, mini_batch_targets)
else:
return (mini_batch_patches, mini_batch_targets, mini_batch_imgnos, mini_batch_plocs)