def __init__(self,
reader,
data_param,
batch_size,
spatial_window_size=(),
window_border=(),
queue_length=10):
self.batch_size = batch_size
self.reader = reader
Layer.__init__(self, name='input_buffer')
InputBatchQueueRunner.__init__(
self,
capacity=queue_length,
shuffle=False)
tf.logging.info('reading size of preprocessed inputs')
self.window = ImageWindow.from_data_reader_properties(
self.reader.input_sources,
self.reader.shapes,
self.reader.tf_dtypes,
data_param)
if spatial_window_size:
# override all spatial window defined in input
# modalities sections
# this is useful when do inference with a spatial window
# which is different from the training specifications
self.window.set_spatial_shape(spatial_window_size)
self.border_size = window_border
tf.logging.info('initialised window instance')
self._create_queue_and_ops(self.window,
enqueue_size=1,
dequeue_size=batch_size)
tf.logging.info("initialised sampler output %s", self.window.shapes)
def __init__(self,
reader,
data_param,
batch_size=10,
n_interpolations=10,
queue_length=10,
name='linear_interpolation_sampler'):
self.n_interpolations = n_interpolations
self.reader = reader
Layer.__init__(self, name=name)
InputBatchQueueRunner.__init__(self,
capacity=queue_length,
shuffle=False)
tf.logging.info('reading size of preprocessed images')
self.window = ImageWindow.from_data_reader_properties(
self.reader.input_sources, self.reader.shapes,
self.reader.tf_dtypes, data_param)
# only try to use the first spatial shape available
image_spatial_shape = list(self.reader.shapes.values())[0][:3]
self.window.set_spatial_shape(image_spatial_shape)
tf.logging.info('initialised window instance')
self._create_queue_and_ops(self.window,
enqueue_size=self.n_interpolations,
dequeue_size=batch_size)
tf.logging.info("initialised sampler output %s ", self.window.shapes)
assert not self.window.has_dynamic_shapes, \
"dynamic shapes not supported, please specify " \
"spatial_window_size = (1, 1, 1)"
def __init__(self,
names=('vector',),
vector_size=(100,),
batch_size=10,
n_interpolations=10,
mean=0.0,
stddev=1.0,
repeat=1,
queue_length=10):
self.n_interpolations = max(n_interpolations, 1)
self.mean = mean
self.stddev = stddev
self.repeat = repeat
Layer.__init__(self, name='input_buffer')
InputBatchQueueRunner.__init__(
self,
capacity=queue_length,
shuffle=False)
tf.logging.info('reading size of preprocessed images')
self.names = names
vector_shapes = {names[0]: vector_size}
vector_dtypes = {names[0]: tf.float32}
self.window = ImageWindow(names=tuple(vector_shapes),
shapes=vector_shapes,
dtypes=vector_dtypes)
tf.logging.info('initialised window instance')
self._create_queue_and_ops(self.window,
enqueue_size=self.n_interpolations,
dequeue_size=batch_size)
tf.logging.info("initialised sampler output %s ", self.window.shapes)
def __init__(self,
reader,
data_param,
batch_size,
windows_per_image,
queue_length=10):
self.reader = reader
Layer.__init__(self, name='input_buffer')
InputBatchQueueRunner.__init__(self,
capacity=queue_length,
shuffle=True)
tf.logging.info('reading size of preprocessed images')
self.window = ImageWindow.from_data_reader_properties(
self.reader.input_sources, self.reader.shapes,
self.reader.tf_dtypes, data_param)
tf.logging.info('initialised window instance')
self._create_queue_and_ops(self.window,
enqueue_size=windows_per_image,
dequeue_size=batch_size)
tf.logging.info(
"initialised sampler output %s "
" [-1 for dynamic size]", self.window.shapes)
self.spatial_coordinates_generator = rand_spatial_coordinates
def __init__(self,
reader,
data_param,
batch_size,
spatial_window_size=None,
window_border=None,
queue_length=10,
name='grid_sampler'):
self.batch_size = batch_size
self.border_size = window_border or (0, 0, 0)
self.reader = reader
Layer.__init__(self, name=name)
InputBatchQueueRunner.__init__(self,
capacity=queue_length,
shuffle=False)
tf.logging.info('reading size of preprocessed inputs')
# override all spatial window defined in input
# modalities sections
# this is useful when do inference with a spatial window
# which is different from the training specifications
self.window = ImageWindow.from_data_reader_properties(
self.reader.input_sources, self.reader.shapes,
self.reader.tf_dtypes, spatial_window_size or data_param)
tf.logging.info('initialised window instance')
self._create_queue_and_ops(self.window,
enqueue_size=1,
dequeue_size=batch_size)
tf.logging.info("initialised sampler output %s", self.window.shapes)
def __init__(self,
reader=None,
window_sizes=None,
batch_size=1,
windows_per_image=1,
queue_length=10,
shuffle=True,
epoch=-1,
name='image_dataset'):
Layer.__init__(self, name=name)
self.dataset = None
self.iterator = None
self.reader = reader
self.batch_size = batch_size
self.queue_length = queue_length
self.n_subjects = 1
self.from_generator = inspect.isgeneratorfunction(self.layer_op)
self.shuffle = shuffle
self.epoch = epoch
self.window = None
if reader is not None:
self.window = ImageWindow.from_data_reader_properties(
reader.input_sources,
reader.shapes,
reader.tf_dtypes,
window_sizes or (-1, -1, -1))
self.n_subjects = reader.num_subjects
self.window.n_samples = \
1 if self.from_generator else windows_per_image
def __init__(self,
reader,
data_param,
batch_size=10,
n_interpolations=10,
queue_length=10):
self.n_interpolations = n_interpolations
self.reader = reader
Layer.__init__(self, name='input_buffer')
InputBatchQueueRunner.__init__(
self,
capacity=queue_length,
shuffle=False)
tf.logging.info('reading size of preprocessed images')
self.window = ImageWindow.from_data_reader_properties(
self.reader.input_sources,
self.reader.shapes,
self.reader.tf_dtypes,
data_param)
# only try to use the first spatial shape available
image_spatial_shape = list(self.reader.shapes.values())[0][:3]
self.window.set_spatial_shape(image_spatial_shape)
tf.logging.info('initialised window instance')
self._create_queue_and_ops(self.window,
enqueue_size=self.n_interpolations,
dequeue_size=batch_size)
tf.logging.info("initialised sampler output %s ", self.window.shapes)
assert not self.window.has_dynamic_shapes, \
"dynamic shapes not supported, please specify " \
"spatial_window_size = (1, 1, 1)"
def __init__(self,
reader,
data_param,
batch_size,
spatial_window_size=(),
windows_per_image=1,
shuffle_buffer=True,
queue_length=10,
name='resize_sampler'):
self.reader = reader
self.windows_per_image = windows_per_image
self.shuffle = bool(shuffle_buffer)
Layer.__init__(self, name=name)
InputBatchQueueRunner.__init__(self,
capacity=queue_length,
shuffle=self.shuffle)
tf.logging.info('reading size of preprocessed images')
self.window = ImageWindow.from_data_reader_properties(
self.reader.input_sources, self.reader.shapes,
self.reader.tf_dtypes, data_param)
if spatial_window_size:
# override all spatial window defined in input
# modalities sections
# this is useful when do inference with a spatial window
# which is different from the training specifications
self.window.set_spatial_shape(spatial_window_size)
tf.logging.info('initialised window instance')
self._create_queue_and_ops(self.window,
enqueue_size=1,
dequeue_size=batch_size)
tf.logging.info("initialised sampler output %s ", self.window.shapes)
def __init__(self,
reader=None,
window_sizes=None,
batch_size=1,
windows_per_image=1,
queue_length=10,
shuffle=True,
epoch=-1,
name='image_dataset'):
Layer.__init__(self, name=name)
self.dataset = None
self.iterator = None
self.reader = reader
self.batch_size = batch_size
self.queue_length = queue_length
self.n_subjects = 1
self.from_generator = inspect.isgeneratorfunction(self.layer_op)
self.shuffle = shuffle
self.epoch = epoch
self.window = None
if reader is not None:
self.window = ImageWindow.from_data_reader_properties(
reader.input_sources, reader.shapes, reader.tf_dtypes,
window_sizes or (-1, -1, -1))
self.n_subjects = reader.num_subjects
self.window.n_samples = \
1 if self.from_generator else windows_per_image
def __init__(self,
names=('vector', ),
vector_size=(100, ),
batch_size=10,
n_interpolations=10,
mean=0.0,
stddev=1.0,
repeat=1,
queue_length=10,
name='random_vector_sampler'):
# repeat=None for infinite loops
Layer.__init__(self, name=name)
self.n_interpolations = max(n_interpolations, 1)
self.mean = mean
self.stddev = stddev
self.repeat = repeat
InputBatchQueueRunner.__init__(self,
capacity=queue_length,
shuffle=False)
tf.logging.info('reading size of preprocessed images')
vector_shapes = {names[0]: vector_size}
vector_dtypes = {names[0]: tf.float32}
self.window = ImageWindow(shapes=vector_shapes, dtypes=vector_dtypes)
tf.logging.info('initialised window instance')
self._create_queue_and_ops(self.window,
enqueue_size=self.n_interpolations,
dequeue_size=batch_size)
tf.logging.info("initialised sampler output %s ", self.window.shapes)
def __init__(self,
spatial_axis=0,
do_cropping=True,
name='spatial_gradient'):
Layer.__init__(self, name=name)
self.spatial_axis = int(spatial_axis)
self.do_cropping = do_cropping
def __init__(self,
reader_0,
reader_1,
data_param,
batch_size=1):
Layer.__init__(self, name='pairwise_sampler_resize')
# reader for the fixed images
self.reader_0 = reader_0
# reader for the moving images
self.reader_1 = reader_1
# TODO:
# 0) check the readers should have the same length file list
# 1) detect window shape mismatches or defaulting
# windows to the fixed image reader properties
# 2) reshape images to (supporting multi-modal data)
# [batch, x, y, channel] or [batch, x, y, z, channels]
# 3) infer spatial rank
# 4) make ``label`` optional
self.batch_size = int(batch_size)
assert self.batch_size > 0, "batch size must be greater than 0"
self.spatial_rank = 3
self.window = ImageWindow.from_data_reader_properties(
self.reader_0.input_sources,
self.reader_0.shapes,
self.reader_0.tf_dtypes,
data_param)
if self.window.has_dynamic_shapes:
tf.logging.fatal('Dynamic shapes not supported.\nPlease specify '
'all spatial dims of the input data, for the '
'spatial_window_size parameter.')
raise NotImplementedError
# TODO: check spatial dims the same across input modalities
self.image_shape = \
self.reader_0.shapes['fixed_image'][:self.spatial_rank]
self.moving_image_shape = \
self.reader_1.shapes['moving_image'][:self.spatial_rank]
self.window_size = self.window.shapes['fixed_image'][1:]
# initialise a dataset prefetching pairs of image and label volumes
n_subjects = len(self.reader_0.output_list)
int_seq = list(range(n_subjects))
# make the list of sequence divisible by batch size
while len(int_seq) > 0 and len(int_seq) % self.batch_size != 0:
int_seq.append(int_seq[-1])
image_dataset = tf.data.Dataset.from_tensor_slices(int_seq)
# mapping random integer id to 4 volumes moving/fixed x image/label
# tf.py_func wrapper of ``get_pairwise_inputs``
image_dataset = image_dataset.map(
lambda image_id: tuple(tf.py_func(
self.get_pairwise_inputs, [image_id],
[tf.int32, tf.float32, tf.float32, tf.int32, tf.int32])),
num_parallel_calls=4) # supported by tf 1.4?
# todo: sequential and no repeatition
image_dataset = image_dataset.batch(self.batch_size)
self.iterator = image_dataset.make_initializable_iterator()
def __init__(self, sigma=1, truncate=3.0, type_str='gaussian'):
"""
:param sigma: standard deviation
:param truncate: Truncate the filter at this many standard deviations
:param type_str: type of kernels
"""
Layer.__init__(self, name='approximated_smoothing')
self.kernel_func = look_up_operations(
type_str.lower(), SUPPORTED_KERNELS)
self.sigma = sigma
self.truncate = truncate
def __init__(self, reader_0, reader_1, data_param, batch_size=1):
Layer.__init__(self, name='pairwise_sampler_uniform')
# reader for the fixed images
self.reader_0 = reader_0
# reader for the moving images
self.reader_1 = reader_1
# TODO:
# 0) check the readers should have the same length file list
# 1) detect window shape mismatches or defaulting
# windows to the fixed image reader properties
# 2) reshape images to (supporting multi-modal data)
# [batch, x, y, channel] or [batch, x, y, z, channels]
# 3) infer spatial rank
# 4) make ``label`` optional
self.batch_size = batch_size
self.spatial_rank = 3
self.window = ImageWindow.from_data_reader_properties(
self.reader_0.input_sources, self.reader_0.shapes,
self.reader_0.tf_dtypes, data_param)
if self.window.has_dynamic_shapes:
tf.logging.fatal('Dynamic shapes not supported.\nPlease specify '
'all spatial dims of the input data, for the '
'spatial_window_size parameter.')
raise NotImplementedError
# TODO: check spatial dims the same across input modalities
self.image_shape = \
self.reader_0.shapes['fixed_image'][:self.spatial_rank]
self.moving_image_shape = \
self.reader_1.shapes['moving_image'][:self.spatial_rank]
self.window_size = self.window.shapes['fixed_image']
# initialise a dataset prefetching pairs of image and label volumes
n_subjects = len(self.reader_0.output_list)
rand_ints = np.random.randint(n_subjects, size=[n_subjects])
image_dataset = Dataset.from_tensor_slices(rand_ints)
# mapping random integer id to 4 volumes moving/fixed x image/label
# tf.py_func wrapper of ``get_pairwise_inputs``
image_dataset = image_dataset.map(
lambda image_id: tuple(
tf.py_func(self.get_pairwise_inputs, [image_id], [
tf.int64, tf.float32, tf.float32, tf.int32, tf.int32
])),
num_threads=4) # supported by tf 1.4?
image_dataset = image_dataset.repeat() # num_epochs can be param
image_dataset = image_dataset.shuffle(buffer_size=self.batch_size * 20)
image_dataset = image_dataset.batch(self.batch_size)
self.iterator = image_dataset.make_initializable_iterator()
def __init__(self,
reader=None,
window_sizes=None,
batch_size=1,
windows_per_image=1,
queue_length=10,
shuffle=True,
epoch=-1,
smaller_final_batch_mode='pad',
seed=None,
name='image_dataset'):
Layer.__init__(self, name=name)
self._num_threads = 1
self._enqueuer = None
self._seed = seed
self.dataset = None
self.iterator = None
self.reader = reader
self.batch_size = batch_size
self.queue_length = int(max(queue_length, round(batch_size * 5.0)))
if self.queue_length > queue_length:
tf.logging.warning(
'sampler queue_length should be larger than batch_size, '
'defaulting to batch_size * 5.0 (%s).', self.queue_length)
self.from_generator = inspect.isgeneratorfunction(self.layer_op)
self.shuffle = shuffle
self.epoch = 1 if self.from_generator else epoch
self.smaller_final_batch_mode = look_up_operations(
smaller_final_batch_mode.lower(), SMALLER_FINAL_BATCH_MODE)
self.n_subjects = 1
self.window = None
if reader is not None:
self.window = ImageWindow.from_data_reader_properties(
reader.input_sources,
reader.shapes,
reader.tf_dtypes,
window_sizes or (-1, -1, -1))
self.n_subjects = reader.num_subjects
self.window.n_samples = windows_per_image
def __init__(self,
scale,
interpolation='linear',
boundary='zero',
transform=None,
name='AffineAugmentation'):
"""
:param scale: how extreme the perturbation is, with 0. meaning
no perturbation and 1.0 giving largest perturbations.
:param interpolation: the image value interpolation used by
the resampling.
:param boundary: the boundary handling used by the resampling
:param name: string name of the layer.
"""
Layer.__init__(self, name=name)
self.scale = min(max(float(scale), 0.0), 1.0)
self.interpolation = interpolation
self.boundary = boundary
self._transform = None
if transform is not None:
self._transform = transform
def __init__(self, name='crop_concat'):
Layer.__init__(self, name=name)
def __init__(self, name='crop_concat'):
Layer.__init__(self, name=name)
