def __call__(self, input_image):
"""
Transforms an image by first shifting and scaling, and then optionally clamps the values.
:param input_image:
:param shift:
:param scale:
:param clamp_min:
:param clamp_max:
:return:
"""
output_image = input_image
if self.shift is not None or self.scale is not None:
output_image = rescale(output_image,
shift=self.shift,
scale=self.scale)
if self.random_shift is not None or self.random_scale is not None:
current_random_shift = random.float_uniform(
-self.random_shift, self.random_shift)
current_random_scale = 1 + random.float_uniform(
-self.random_scale, self.random_scale)
output_image = rescale(output_image,
shift=current_random_shift,
scale=current_random_scale)
if self.clamp_min is not None or self.clamp_max is not None:
output_image = clamp(output_image,
clamp_min=self.clamp_min,
clamp_max=self.clamp_max)
return output_image
def get(self, **kwargs):
"""
Apply random scaling, in each dimension. The scale factor will be computed from a random uniform
distribution 1+[-random_scale, random_scale].
:param input_image: ITK image
:param random_scale: float, list of floats
ranges for uniform random scaling in each dimension
:param kwargs:
chain: if True returns the transform instead of the output image (default=False)
:return:
"""
# scale by individual factor in each dimension
if isinstance(self.random_scale, list) or isinstance(
self.random_scale, tuple):
current_scale = [
1.0 +
float_uniform(-self.random_scale[i], self.random_scale[i])
for i in range(len(self.random_scale))
]
else:
current_scale = 1.0 + float_uniform(-self.random_scale,
self.random_scale)
return self.get_scale_transform(current_scale)
def get_deformation_transform(dim,
grid_nodes,
origin,
physical_dimensions,
spline_order,
deformation_value):
"""
Returns the sitk transform based on the given parameters.
:param dim: The dimension.
:param grid_nodes: The number of grid nodes in each dimension.
:param origin: The domain origin.
:param physical_dimensions: The domain physical size.
:param spline_order: The spline order.
:param deformation_value: The maximum deformation value.
:return: The sitk.BSplineTransform() with the specified parameters.
"""
mesh_size = [grid_node - spline_order for grid_node in grid_nodes]
t = sitk.BSplineTransform(dim, spline_order)
t.SetTransformDomainOrigin(origin)
t.SetTransformDomainMeshSize(mesh_size)
t.SetTransformDomainPhysicalDimensions(physical_dimensions)
t.SetTransformDomainDirection(np.eye(dim).flatten())
if isinstance(deformation_value, list) or isinstance(deformation_value, tuple):
deform_params = []
for v in deformation_value:
for i in range(int(np.prod(grid_nodes))):
deform_params.append(float_uniform(-v, v))
else:
deform_params = [float_uniform(-deformation_value, deformation_value)
for _ in t.GetParameters()]
t.SetParameters(deform_params)
return t
def shift_scale_clamp(input_image,
shift=None,
scale=None,
clamp_min=None,
clamp_max=None,
random_shift=None,
random_scale=None):
"""
Transforms an image by first shifting and scaling, and then optionally clamps the values.
Order of operations:
image += shift
image *= scale
image += random.float_uniform(-random_shift, random_shift)
image *= 1 + random.float_uniform(-random_scale, random_scale)
image = np.clip(image, clamp_min, clamp_max)
:param input_image: The sitk image.
:param shift: The intensity shift (added) value (image += shift).
:param scale: The intensity scale (multiplied) value (image *= scale).
:param clamp_min: The minimum value to clamp (image = np.clip(image, clamp_min, clamp_max)).
:param clamp_max: The maximum value to clamp (image = np.clip(image, clamp_min, clamp_max)).
:param random_shift: The random shift (image += random.float_uniform(-random_shift, random_shift)).
:param random_scale: The additional random scale (image *= 1 + random.float_uniform(-random_scale, random_scale)).
:return: The transformed sitk image.
"""
output_image = input_image
if shift is not None or scale is not None:
output_image = shift_scale(output_image, shift=shift, scale=scale)
if random_shift is not None or random_scale is not None:
current_random_shift = random.float_uniform(-random_shift, random_shift)
current_random_scale = 1 + random.float_uniform(-random_scale, random_scale)
output_image = shift_scale(output_image, shift=current_random_shift, scale=current_random_scale)
if clamp_min is not None or clamp_max is not None:
output_image = clamp(output_image, clamp_min=clamp_min, clamp_max=clamp_max)
return output_image
def __call__(self, input_image):
"""
Transforms an image by first shifting and scaling, and then optionally clamps the values.
Order of operations:
image += shift
image *= scale
image += random.float_uniform(-random_shift, random_shift)
image *= 1 + random.float_uniform(-random_scale, random_scale)
image = np.clip(image, clamp_min, clamp_max)
:param input_image: np input image
:return: np processed image
"""
output_image = input_image
if self.shift is not None:
output_image += self.shift
if self.scale is not None:
output_image *= self.scale
if self.random_shift is not None:
current_random_shift = random.float_uniform(
-self.random_shift, self.random_shift)
output_image += current_random_shift
if self.random_scale is not None:
current_random_scale = 1 + random.float_uniform(
-self.random_scale, self.random_scale)
output_image *= current_random_scale
if self.clamp_min is not None or self.clamp_max is not None:
output_image = np.clip(output_image, self.clamp_min,
self.clamp_max)
return output_image
def get(self, **kwargs):
"""
Returns the sitk transform based on the given parameters.
:param kwargs: Must contain either 'image', or 'input_size' and 'input_spacing', which define the input image physical space.
:return: The sitk.AffineTransform().
"""
# TODO check, if direction or origin are really needed
input_size, input_spacing, input_direction, input_origin = self.get_image_size_spacing_direction_origin(
**kwargs)
assert np.allclose(
input_direction,
np.eye(self.dim).flatten()
), 'this transformation only works for eye direction, is: ' + input_direction
assert np.allclose(
input_origin, np.zeros(self.dim)
), 'this transformation only works for zeros origin, is: ' + input_origin
max_translation = [
input_size[i] * input_spacing[i] - self.remove_border[i]
for i in range(self.dim)
]
current_offset = [
max_translation[i] *
float_uniform(-self.random_factor[i], self.random_factor[i])
for i in range(len(self.random_factor))
]
return self.get_translate_transform(self.dim, current_offset)
def get_random_move(self, image):
"""
Calculates a list of x/y offsets for a given image.
:param image: The image.
:return: List of x/y offset tuples.
"""
random_move_x = float_uniform(-self.image_size[0] * self.random_move, self.image_size[0] * self.random_move)
random_move_y = float_uniform(-self.image_size[1] * self.random_move, self.image_size[1] * self.random_move)
frame_axis = self.video_frame_stack_axis
random_moves = []
for i in range(image.shape[frame_axis]):
displacement_x = (i / image.shape[frame_axis]) * random_move_x
displacement_y = (i / image.shape[frame_axis]) * random_move_y
displacement_x += float_uniform(-self.image_size[0] * self.random_jiggle, self.image_size[0] * self.random_jiggle)
displacement_y += float_uniform(-self.image_size[1] * self.random_jiggle, self.image_size[1] * self.random_jiggle)
random_moves.append((int(displacement_x), int(displacement_y)))
return random_moves
def get(self, **kwargs):
"""
Returns the sitk transform based on the given parameters.
:param kwargs: Not used.
:return: The sitk.AffineTransform().
"""
current_offset = [float_uniform(-self.random_offset[i], self.random_offset[i])
for i in range(len(self.random_offset))]
return self.get_translate_transform(self.dim, current_offset)
def get(self, **kwargs):
"""
Returns the sitk transform based on the given parameters.
:param kwargs: Not used.
:return: The sitk.AffineTransform().
"""
if self.dim == 2:
self.current_angles = [float_uniform(-self.random_angles[0], self.random_angles[0])]
elif self.dim == 3:
# rotate by same random angle in each dimension
if len(self.random_angles) == 1:
angle = float_uniform(-self.random_angles[0], self.random_angles[0])
self.current_angles = [angle] * self.dim
else:
# rotate by individual angle in each dimension
self.current_angles = [float_uniform(-self.random_angles[i], self.random_angles[i])
for i in range(self.dim)]
return self.get_rotation_transform(self.dim, self.current_angles)
def intensity_postprocessing_mr_random(self, image):
"""
Intensity postprocessing for MR input. Random augmentation version.
:param image: The np input image.
:return: The processed image.
"""
image = change_gamma_unnormalized(image, float_uniform(0.5, 1.5))
image = normalize_robust(image, consideration_factors=(0.1, 0.1))
return ShiftScaleClamp(random_shift=0.6,
random_scale=0.6,
clamp_min=-1.0)(image)
def intensity_postprocessing_ct_random(self, image):
"""
Intensity postprocessing for CT input. Random augmentation version.
:param image: The np input image.
:return: The processed image.
"""
if not self.normalize_zero_mean_unit_variance:
random_lambda = float_uniform(0.9, 1.1)
image = change_gamma_unnormalized(image, random_lambda)
output = ShiftScaleClamp(shift=0,
scale=1 / 2048,
random_shift=self.random_intensity_shift,
random_scale=self.random_intensity_scale,
clamp_min=-1.0,
clamp_max=1.0)(image)
else:
random_lambda = float_uniform(0.9, 1.1)
image = change_gamma_unnormalized(image, random_lambda)
output = normalize_zero_mean_unit_variance(image)
return output
def all_generators_post_processing_random_np(self, generators_dict):
"""
Randomly augments images in the generators_dict according to the parameters.
:param generators_dict: The generators_dict of np arrays.
:return: The generators_dict with randomly moved np arrays.
"""
image = generators_dict['image']
frame_axis = self.video_frame_stack_axis
random_move_x = float_uniform(-self.image_size[0] * self.random_move,
self.image_size[0] * self.random_move)
random_move_y = float_uniform(-self.image_size[1] * self.random_move,
self.image_size[1] * self.random_move)
for i in range(image.shape[frame_axis]):
displacement_x = (i / image.shape[frame_axis]) * random_move_x
displacement_y = (i / image.shape[frame_axis]) * random_move_y
displacement_x += float_uniform(
-self.image_size[0] * self.random_jiggle,
self.image_size[0] * self.random_jiggle)
displacement_y += float_uniform(
-self.image_size[1] * self.random_jiggle,
self.image_size[1] * self.random_jiggle)
displacement_x = int(displacement_x)
displacement_y = int(displacement_y)
if displacement_x == 0 and displacement_y == 0:
continue
for key in generators_dict.keys():
if len(generators_dict[key].shape) == 4:
if key == 'image':
generators_dict[key][:, i:i + 1, :, :] = roll_with_pad(
generators_dict[key][:, i:i + 1, :, :],
[0, 0, displacement_y, displacement_x],
mode='reflect')
else:
generators_dict[key][:, i:i + 1, :, :] = roll_with_pad(
generators_dict[key][:, i:i + 1, :, :],
[0, 0, displacement_y, displacement_x],
mode='constant')
return generators_dict
def get(self, **kwargs):
"""
Returns the sitk transform based on the given parameters.
:param kwargs: Must contain either 'image', or 'input_size' and 'input_spacing', which define the input image physical space.
:return: The sitk.AffineTransform().
"""
input_size, input_spacing = self.get_image_size_spacing(**kwargs)
remove_border = self.remove_border
if remove_border is None:
remove_border = [0] * self.dim
current_offset = [(input_size[i] * input_spacing[i] - remove_border[i]) * float_uniform(-self.random_factor[i], self.random_factor[i])
for i in range(len(self.random_factor))]
return self.get_translate_transform(self.dim, current_offset)
def get(self, **kwargs):
"""
Returns the sitk transform based on the given parameters.
:param kwargs: Not used.
:return: The sitk.AffineTransform().
"""
scale = 1.0 + float_uniform(-self.random_scale, self.random_scale)
current_scale = []
for i in range(self.dim):
if i in self.ignore_dim:
current_scale.append(1.0)
else:
current_scale.append(scale)
return self.get_scale_transform(self.dim, current_scale)
def get(self, **kwargs):
"""
Apply a random rotation transform to an input image.
:param input_image: ITK image
the input image
:param random_angles: float, list of float
random rotation angle ranges (in radians) for each dimension
:param kwargs:
chain: if True returns the transform instead of the output image (default=False)
:return:
"""
if self.dim == 2:
self.current_angles = [float_uniform(-self.random_angles[0], self.random_angles[0])]
elif self.dim == 3:
# rotate by same random angle in each dimension
if len(self.random_angles) == 1:
angle = float_uniform(-self.random_angles[0], self.random_angles[0])
self.current_angles = [angle] * self.dim
else:
# rotate by individual angle in each dimension
self.current_angles = [float_uniform(-self.random_angles[i], self.random_angles[i])
for i in range(self.dim)]
return self.get_rotation_transform(self.current_angles)
def get(self, **kwargs):
"""
Returns the sitk transform based on the given parameters.
:param kwargs: Must contain either 'image', or 'input_size' and 'input_spacing', which define the input image physical space.
:return: The sitk.AffineTransform().
"""
# TODO check, if direction or origin are needed
# TODO right now it only works when direction is np.eye and origin is np.zeros
input_size, input_spacing, input_direction, input_origin = self.get_image_size_spacing_direction_origin(
**kwargs)
current_offset = [
(input_size[i] * input_spacing[i] - self.remove_border[i]) *
float_uniform(-self.random_factor[i], self.random_factor[i])
for i in range(len(self.random_factor))
]
return self.get_translate_transform(self.dim, current_offset)
def postprocessing_random(self, image):
"""
Performs random augmentations of a grayscale image. Augmentation consists of random gamma correction,
random intensity shift/scale per video and per frame.
:param image: The grayscale image to augment.
:return: The augmented grayscale image.
"""
random_lambda = float_uniform(0.6, 1.4)
image = change_gamma_unnormalized(image, random_lambda)
image = ShiftScaleClamp(random_shift=0.65, random_scale=0.65)(image)
if len(image.shape) == 4:
for i in range(image.shape[self.video_frame_stack_axis]):
current_slice = [slice(None), slice(None)]
current_slice.insert(self.video_frame_stack_axis, slice(i, i + 1))
image[tuple(current_slice)] = ShiftScaleClamp(random_shift=0.1, random_scale=0.1)(image[tuple(current_slice)])
return image
def get(self, **kwargs):
"""
Deform the image randomly with a given set of parameters using ITK's BSplineTransform.
:param input_image: ITK image
the input image
:param grid_nodes: list of ints
the number of nodes per dimension on the output space
:param deform_range: float, list of floats
random deformation ranges (in mm)
:param spline_order: int, default is same as image dimension
the order of the b-spline
:param output_size: list
the output size of the image (required to compute transformations)
:param direction: list
the output direction of the image (transform matrix)
:param kwargs:
chain: if True returns the transform instead of the output image (default=False)
:return:
"""
input_image = kwargs.get('image')
input_size = input_image.GetSize()
input_spacing = input_image.GetSpacing()
origin = [
-input_size[i] * input_spacing[i] * 0.5 for i in range(self.dim)
]
physical_dimensions = [
input_size[i] * input_spacing[i] for i in range(self.dim)
]
# get the transform params
current_transformation = self.get_deformation_transform(
self.grid_nodes, origin, physical_dimensions, self.spline_order)
# define the displacement range in mm per control point
# modify the parameters
deform_params = [
float_uniform(-self.deformation_value, self.deformation_value)
for _ in current_transformation.GetParameters()
]
# set them back to the transform
current_transformation.SetParameters(deform_params)
# output spacing is input spacing: --> assumed (1, 1[, 1])!
return current_transformation
def get(self, **kwargs):
"""
Apply a random translation, in each dimension specified in the random offset.
The offset will be computed a uniform distribution 1+[-random_offset, random_offset].
:param input_image: ITK image
:param random_offset: float, list of floats
ranges for uniform random offset in each dimension
:param kwargs:
chain: if True returns the transform instead of the output image (default=False)
:return:
"""
# translate by individual offset in each dimension
current_offset = [
1.0 + float_uniform(-self.random_offset[i], self.random_offset[i])
for i in range(len(self.random_offset))
]
return self.get_translate_transform(current_offset)
def get(self, **kwargs):
"""
Returns the sitk transform based on the given parameters.
:param kwargs: Must contain 'start' and 'extent' which define the bounding box in physical coordinates.
:return: The sitk.AffineTransform().
"""
output_size = kwargs.get('output_size', self.output_size)
output_spacing = kwargs.get('output_spacing', self.output_spacing)
extent = kwargs.get('extent', self.output_spacing)
max_translation = [
extent[i] - output_size[i] * output_spacing[i]
for i in range(self.dim)
]
current_offset = [
np.maximum(0.0, max_translation[i]) * float_uniform(-0.5, 0.5)
for i in range(self.dim)
]
return self.get_translate_transform(self.dim, current_offset)
def get(self, **kwargs):
"""
Returns the sitk transform based on the given parameters.
:param kwargs: Must contain either 'image', or 'input_size' and 'input_spacing', which define the input image physical space.
:return: The sitk.AffineTransform().
"""
output_size = kwargs.get('output_size', self.output_size)
output_spacing = kwargs.get('output_spacing', self.output_spacing)
# TODO check, if direction or origin are really needed
input_size, input_spacing, input_direction, input_origin = self.get_image_size_spacing_direction_origin(
**kwargs)
assert np.allclose(
input_direction,
np.eye(self.dim).flatten()
), 'this transformation only works for eye direction, is: ' + input_direction
max_translation = [
input_size[i] * input_spacing[i] -
output_size[i] * output_spacing[i] for i in range(self.dim)
]
current_offset = [
np.maximum(0.0, max_translation[i]) * float_uniform(-0.5, 0.5)
for i in range(self.dim)
]
return self.get_translate_transform(self.dim, current_offset)
def update(self, **kwargs):
if self.random_shift is not None:
self.current_random_shift = random.float_uniform(-self.random_shift, self.random_shift)
if self.random_scale is not None:
self.current_random_scale = 1 + random.float_uniform(-self.random_scale, self.random_scale)
def rotate_all_random(self):
for i in range(self.dim):
for j in range(i + 1, self.dim):
plane = Plane(i, j, float_uniform(0, 2 * math.pi))
self.planes.append(plane)
def data_generators(self, iterator, datasources, transformation,
image_post_processing,
random_translation_single_landmark, image_size):
"""
Returns the data generators that process one input. See datasources() for dict values.
:param datasources: datasources dict.
:param transformation: transformation.
:param image_post_processing: The np postprocessing function for the image data generator.
:return: A dict of data generators.
"""
generators_dict = {}
generators_dict['image'] = ImageGenerator(
self.dim,
image_size,
self.image_spacing,
interpolator='linear',
post_processing_np=image_post_processing,
data_format=self.data_format,
resample_default_pixel_value=self.image_default_pixel_value,
name='image',
parents=[datasources['image'], transformation])
if self.generate_landmark_mask:
generators_dict['landmark_mask'] = ImageGenerator(
self.dim,
image_size,
self.image_spacing,
interpolator='nearest',
data_format=self.data_format,
resample_default_pixel_value=0,
name='landmark_mask',
parents=[datasources['landmark_mask'], transformation])
if self.generate_labels or self.generate_single_vertebrae:
generators_dict['labels'] = ImageGenerator(
self.dim,
image_size,
self.image_spacing,
interpolator='nearest',
post_processing_np=self.split_labels,
data_format=self.data_format,
name='labels',
parents=[datasources['labels'], transformation])
if self.generate_heatmaps or self.generate_spine_heatmap:
generators_dict['heatmaps'] = LandmarkGeneratorHeatmap(
self.dim,
image_size,
self.image_spacing,
sigma=self.heatmap_sigma,
scale_factor=1.0,
normalize_center=True,
data_format=self.data_format,
name='heatmaps',
parents=[datasources['landmarks'], transformation])
if self.generate_landmarks:
generators_dict['landmarks'] = LandmarkGenerator(
self.dim,
image_size,
self.image_spacing,
data_format=self.data_format,
name='landmarks',
parents=[datasources['landmarks'], transformation])
if self.generate_single_vertebrae_heatmap:
single_landmark = LambdaNode(
lambda id_dict, landmarks: landmarks[int(id_dict[
'landmark_id']):int(id_dict['landmark_id']) + 1],
name='single_landmark',
parents=[iterator, datasources['landmarks']])
if random_translation_single_landmark:
single_landmark = LambdaNode(
lambda l: [
Landmark(
l[0].coords + float_uniform(
-self.random_translation_single_landmark, self.
random_translation_single_landmark, [self.dim
]), True)
],
name='single_landmark_translation',
parents=[single_landmark])
generators_dict['single_heatmap'] = LandmarkGeneratorHeatmap(
self.dim,
image_size,
self.image_spacing,
sigma=self.heatmap_sigma,
scale_factor=1.0,
normalize_center=True,
data_format=self.data_format,
name='single_heatmap',
parents=[single_landmark, transformation])
if self.generate_single_vertebrae:
if self.data_format == 'channels_first':
generators_dict['single_label'] = LambdaNode(
lambda id_dict, images: images[int(id_dict[
'landmark_id']) + 1:int(id_dict['landmark_id']) + 2,
...],
name='single_label',
parents=[iterator, generators_dict['labels']])
else:
generators_dict['single_label'] = LambdaNode(
lambda id_dict, images: images[...,
int(id_dict['landmark_id'])
+ 1:int(id_dict[
'landmark_id']) + 2],
name='single_label',
parents=[iterator, generators_dict['labels']])
if self.generate_spine_heatmap:
generators_dict['spine_heatmap'] = LambdaNode(
lambda images: gaussian(np.sum(images,
axis=0 if self.data_format ==
'channels_first' else -1,
keepdims=True),
sigma=self.spine_heatmap_sigma),
name='spine_heatmap',
parents=[generators_dict['heatmaps']])
return generators_dict
def data_generators(self, iterator, datasources, transformation, image_post_processing, random_translation_single_landmark, image_size, crop=False):
"""
Returns the data generators that process one input. See datasources() for dict values.
:param datasources: datasources dict.
:param transformation: transformation.
:param image_post_processing: The np postprocessing function for the image data generator.
:return: A dict of data generators.
"""
generators_dict = {}
kwparents = {'output_size': image_size}
image_datasource = datasources['image'] if not crop else LambdaNode(self.landmark_based_crop, name='image_cropped', kwparents={'image': datasources['image'], 'landmarks': datasources['landmarks']})
generators_dict['image'] = ImageGenerator(self.dim,
None,
self.image_spacing,
interpolator='linear',
post_processing_np=image_post_processing,
data_format=self.data_format,
resample_default_pixel_value=self.image_default_pixel_value,
np_pixel_type=self.output_image_type,
name='image',
parents=[image_datasource, transformation],
kwparents=kwparents)
# generators_dict['image'] = ImageGenerator(self.dim,
# None,
# self.image_spacing,
# interpolator='linear',
# post_processing_np=image_post_processing,
# data_format=self.data_format,
# resample_default_pixel_value=self.image_default_pixel_value,
# np_pixel_type=self.output_image_type,
# name='image_cropped',
# parents=[LambdaNode(self.landmark_based_crop, name='image_cropped', kwparents={'image': datasources['image'], 'landmarks': datasources['landmarks']}), transformation],
# kwparents=kwparents)
if self.generate_landmark_mask:
generators_dict['landmark_mask'] = ImageGenerator(self.dim,
None,
self.image_spacing,
interpolator='nearest',
data_format=self.data_format,
resample_default_pixel_value=0,
name='landmark_mask',
parents=[datasources['landmark_mask'], transformation],
kwparents=kwparents)
if self.generate_labels:
generators_dict['labels'] = ImageGenerator(self.dim,
None,
self.image_spacing,
interpolator='nearest',
post_processing_np=self.split_labels,
data_format=self.data_format,
name='labels',
parents=[datasources['labels'], transformation],
kwparents=kwparents)
if self.generate_heatmaps or self.generate_spine_heatmap:
generators_dict['heatmaps'] = LandmarkGeneratorHeatmap(self.dim,
None,
self.image_spacing,
sigma=self.heatmap_sigma,
scale_factor=1.0,
normalize_center=True,
data_format=self.data_format,
name='heatmaps',
parents=[datasources['landmarks'], transformation],
kwparents=kwparents)
if self.generate_landmarks:
generators_dict['landmarks'] = LandmarkGenerator(self.dim,
None,
self.image_spacing,
data_format=self.data_format,
name='landmarks',
parents=[datasources['landmarks'], transformation],
kwparents=kwparents)
if self.generate_single_vertebrae_heatmap:
single_landmark = LambdaNode(lambda id_dict, landmarks: landmarks[int(id_dict['landmark_id']):int(id_dict['landmark_id']) + 1],
name='single_landmark',
parents=[iterator, datasources['landmarks']])
if random_translation_single_landmark:
single_landmark = LambdaNode(lambda l: [Landmark(l[0].coords + float_uniform(-self.random_translation_single_landmark, self.random_translation_single_landmark, [self.dim]), True)],
name='single_landmark_translation',
parents=[single_landmark])
generators_dict['single_heatmap'] = LandmarkGeneratorHeatmap(self.dim,
None,
self.image_spacing,
sigma=self.single_heatmap_sigma,
scale_factor=1.0,
normalize_center=True,
data_format=self.data_format,
np_pixel_type=self.output_image_type,
name='single_heatmap',
parents=[single_landmark, transformation],
kwparents=kwparents)
if self.generate_single_vertebrae:
if self.generate_labels:
if self.data_format == 'channels_first':
generators_dict['single_label'] = LambdaNode(lambda id_dict, images: images[int(id_dict['landmark_id']) + 1:int(id_dict['landmark_id']) + 2, ...],
name='single_label',
parents=[iterator, generators_dict['labels']])
else:
generators_dict['single_label'] = LambdaNode(lambda id_dict, images: images[..., int(id_dict['landmark_id']) + 1:int(id_dict['landmark_id']) + 2],
name='single_label',
parents=[iterator, generators_dict['labels']])
else:
labels_unsmoothed = ImageGenerator(self.dim,
None,
self.image_spacing,
interpolator='nearest',
post_processing_np=None,
data_format=self.data_format,
name='labels_unsmoothed',
parents=[datasources['labels'], transformation],
kwparents=kwparents)
generators_dict['single_label'] = LambdaNode(lambda id_dict, labels: self.split_and_smooth_single_label(labels, int(id_dict['landmark_id'])),
name='single_label',
parents=[iterator, labels_unsmoothed])
if self.generate_spine_heatmap:
generators_dict['spine_heatmap'] = LambdaNode(lambda images: normalize(gaussian(np.sum(images, axis=0 if self.data_format == 'channels_first' else -1, keepdims=True), sigma=self.spine_heatmap_sigma), out_range=(0, 1)),
name='spine_heatmap',
parents=[generators_dict['heatmaps']])
return generators_dict
