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import math
from typing import List, Tuple
try:
from typing import Literal
except ImportError:
from typing_extensions import Literal
from monai.transforms import Compose, OneOf
from monai.transforms import RandGaussianNoiseD, RandAdjustContrastD, RandGaussianSmoothD
from monai.transforms import RandFlipD, Rand3DElasticD, RandRotateD, RandZoomD, RandAffineD
def intensity_transform(hparams, loaded_keys) -> Tuple[Compose, List[str]]:
assert len(loaded_keys) > 0
image_key = loaded_keys[0]
return OneOf([
RandGaussianNoiseD(keys=image_key),
RandAdjustContrastD(
keys=image_key,
gamma=1.5
),
RandGaussianSmoothD(
# gaussian smoothing is also applied to mask
keys=loaded_keys,
sigma_x=(0.25, 0.75),
sigma_y=(0.25, 0.75),
sigma_z=(0.25, 0.75)
),
]), loaded_keys
def robustness_transform(hparams, loaded_keys) -> Tuple[Compose, List[str]]:
keys_to_transform = [key for key in loaded_keys if key != "coordinates"]
return Compose([
RandAffineD(
keys=keys_to_transform,
translate_range=(((-20, 10), 5, 5)), # permits keypoint misplacing as well as minor centering deviations
padding_mode="zeros",
prob=1 # elevated probability
),
RandRotateD(
keys=keys_to_transform,
range_x=math.radians(7), # spine roll, patient is not lying perfectly flat on their back
range_y=math.radians(5), # spine yaw, patient position is slightly skewed
range_z=math.radians(20), # spine pitch, strong deviation permitted
prob=1 # elevated probability
),
]), loaded_keys
def spatial_transform(hparams, loaded_keys, mode: Literal['simple', 'default'] = "default") -> Tuple[Compose, List[str]]:
keys_to_transform = [key for key in loaded_keys if key != "coordinates"]
transforms = [
RandFlipD(
keys=keys_to_transform,
spatial_axis=2 # only flip the vertebrae
),
RandRotateD(
keys=keys_to_transform,
range_x=math.radians(7), # spine roll, patient is not lying perfectly flat on their back
range_y=math.radians(5), # spine yaw, patient position is slightly skewed
range_z=math.radians(2), # spine pitch, patient's spine has a slight slope
# (may simulate kyphosis but resulting images are questionable
# for larger rotation angles)
prob=0.1 if not "robustness" in hparams.transforms else 0 # prevent attempts to re-rotate
),
RandZoomD(
keys=keys_to_transform,
mode='nearest',#['area', 'nearest'],
min_zoom=0.9, max_zoom=1.1,
),
]
if mode == 'simple':
transforms.append(
Rand3DElasticD(
sigma_range=(1, 2),
magnitude_range=(2, 8),
keys=keys_to_transform
)
)
return Compose(transforms), loaded_keys |