def get_landmark_transform(config):
return transforms.Compose([
# WrapImageLandmarksSOLT(),
slc.Stream([
slt.RandomFlip(p=0.5, axis=1),
slt.RandomScale(range_x=(0.8, 1.2), p=1),
slt.RandomRotate(rotation_range=(-180, 180), p=0.2),
slt.RandomProjection(affine_transforms=slc.Stream([
slt.RandomScale(range_x=(0.8, 1.3), p=1),
slt.RandomRotate(rotation_range=(-180, 180), p=1),
slt.RandomShear(range_x=(-0.1, 0.1), range_y=(0, 0), p=0.5),
slt.RandomShear(range_y=(-0.1, 0.1), range_x=(0, 0), p=0.5),
]), v_range=(1e-5, 2e-3), p=0.8),
slt.PadTransform(int(config.dataset.crop_size * 1.4), padding='z'),
slt.CropTransform(config.dataset.crop_size, crop_mode='r'),
slc.SelectiveStream([
slt.ImageSaltAndPepper(p=1, gain_range=0.01),
slt.ImageBlur(p=1, blur_type='g', k_size=(3, 5)),
slt.ImageBlur(p=1, blur_type='m', k_size=(3, 5)),
slt.ImageAdditiveGaussianNoise(p=1, gain_range=0.5),
slc.Stream([
slt.ImageSaltAndPepper(p=1, gain_range=0.05),
slt.ImageBlur(p=0.5, blur_type='m', k_size=(3, 5)),
]),
slc.Stream([
slt.ImageBlur(p=0.5, blur_type='m', k_size=(3, 5)),
slt.ImageSaltAndPepper(p=1, gain_range=0.01),
]),
slc.Stream()
]),
slt.ImageGammaCorrection(p=1, gamma_range=(0.5, 1.5))
]),
SOLTtoHourGlassGSinput(downsample=4, sigma=3),
ApplyTransformByIndex(transform=dwutils.npg2tens, ids=[0, 1]),
])
def get_landmark_transform_kneel(config):
cutout = slt.ImageCutOut(
cutout_size=(int(config.dataset.cutout *
config.dataset.augs.crop.crop_x),
int(config.dataset.cutout *
config.dataset.augs.crop.crop_y)),
p=0.5)
ppl = transforms.Compose([
slc.Stream(),
slc.SelectiveStream(
[
slc.Stream([
slt.RandomFlip(p=0.5, axis=1),
slt.RandomProjection(affine_transforms=slc.Stream([
slt.RandomScale(range_x=(0.9, 1.1), p=1),
slt.RandomRotate(rotation_range=(-90, 90), p=1),
slt.RandomShear(
range_x=(-0.1, 0.1), range_y=(-0.1, 0.1), p=0.5),
slt.RandomShear(
range_x=(-0.1, 0.1), range_y=(-0.1, 0.1), p=0.5),
]),
v_range=(1e-5, 2e-3),
p=0.5),
# slt.RandomScale(range_x=(0.5, 2.5), p=0.5),
]),
slc.Stream()
],
probs=[0.7, 0.3]),
slc.Stream([
slt.PadTransform(
(config.dataset.augs.pad.pad_x, config.dataset.augs.pad.pad_y),
padding='z'),
slt.CropTransform((config.dataset.augs.crop.crop_x,
config.dataset.augs.crop.crop_y),
crop_mode='r'),
]),
slc.SelectiveStream([
slt.ImageSaltAndPepper(p=1, gain_range=0.01),
slt.ImageBlur(p=1, blur_type='g', k_size=(3, 5)),
slt.ImageBlur(p=1, blur_type='m', k_size=(3, 5)),
slt.ImageAdditiveGaussianNoise(p=1, gain_range=0.5),
slc.Stream([
slt.ImageSaltAndPepper(p=1, gain_range=0.05),
slt.ImageBlur(p=0.5, blur_type='m', k_size=(3, 5)),
]),
slc.Stream([
slt.ImageBlur(p=0.5, blur_type='m', k_size=(3, 5)),
slt.ImageSaltAndPepper(p=1, gain_range=0.01),
]),
slc.Stream()
],
n=1),
slt.ImageGammaCorrection(p=0.5, gamma_range=(0.5, 1.5)),
cutout if config.dataset.use_cutout else slc.Stream(),
DataToFunction(solt_to_img_target),
ApplyByIndex(transforms.ToTensor(), 0)
])
return ppl
def init_augs():
kvs = GlobalKVS()
args = kvs['args']
cutout = slt.ImageCutOut(cutout_size=(int(args.cutout * args.crop_x),
int(args.cutout * args.crop_y)),
p=0.5)
# plus-minus 1.3 pixels
jitter = slt.KeypointsJitter(dx_range=(-0.003, 0.003),
dy_range=(-0.003, 0.003))
ppl = tvt.Compose([
jitter if args.use_target_jitter else slc.Stream(),
slc.SelectiveStream([
slc.Stream([
slt.RandomFlip(p=0.5, axis=1),
slt.RandomProjection(affine_transforms=slc.Stream([
slt.RandomScale(range_x=(0.8, 1.3), p=1),
slt.RandomRotate(rotation_range=(-90, 90), p=1),
slt.RandomShear(
range_x=(-0.1, 0.1), range_y=(-0.1, 0.1), p=0.5),
]),
v_range=(1e-5, 2e-3),
p=0.5),
slt.RandomScale(range_x=(0.5, 2.5), p=0.5),
]),
slc.Stream()
],
probs=[0.7, 0.3]),
slc.Stream([
slt.PadTransform((args.pad_x, args.pad_y), padding='z'),
slt.CropTransform((args.crop_x, args.crop_y), crop_mode='r'),
]),
slc.SelectiveStream([
slt.ImageSaltAndPepper(p=1, gain_range=0.01),
slt.ImageBlur(p=1, blur_type='g', k_size=(3, 5)),
slt.ImageBlur(p=1, blur_type='m', k_size=(3, 5)),
slt.ImageAdditiveGaussianNoise(p=1, gain_range=0.5),
slc.Stream([
slt.ImageSaltAndPepper(p=1, gain_range=0.05),
slt.ImageBlur(p=0.5, blur_type='m', k_size=(3, 5)),
]),
slc.Stream([
slt.ImageBlur(p=0.5, blur_type='m', k_size=(3, 5)),
slt.ImageSaltAndPepper(p=1, gain_range=0.01),
]),
slc.Stream()
],
n=1),
slt.ImageGammaCorrection(p=0.5, gamma_range=(0.5, 1.5)),
cutout if args.use_cutout else slc.Stream(),
partial(solt2torchhm, downsample=None, sigma=None),
])
kvs.update('train_trf', ppl)
def get_landmark_transform_kneel(config):
cutout = slt.ImageCutOut(cutout_size=(int(config.dataset.cutout * config.dataset.augs.crop.crop_x),
int(config.dataset.cutout * config.dataset.augs.crop.crop_y)),
p=0.5)
# plus-minus 1.3 pixels
jitter = slt.KeypointsJitter(dx_range=(-0.003, 0.003), dy_range=(-0.003, 0.003))
ppl = transforms.Compose([
ColorPaddingWithSide(p=0.05, pad_size=10, side=SIDES.RANDOM, color=(50,100)),
TriangularMask(p=0.025, arm_lengths=(100, 50), side=SIDES.RANDOM, color=(50,100)),
TriangularMask(p=0.025, arm_lengths=(50, 100), side=SIDES.RANDOM, color=(50,100)),
LowVisibilityTransform(p=0.05, alpha=0.15, bgcolor=(50,100)),
SubSampleUpScale(p=0.01),
jitter if config.dataset.augs.use_target_jitter else slc.Stream(),
slc.SelectiveStream([
slc.Stream([
slt.RandomFlip(p=0.5, axis=1),
slt.RandomProjection(affine_transforms=slc.Stream([
slt.RandomScale(range_x=(0.9, 1.1), p=1),
slt.RandomRotate(rotation_range=(-90, 90), p=1),
slt.RandomShear(range_x=(-0.1, 0.1), range_y=(-0.1, 0.1), p=0.5),
]), v_range=(1e-5, 2e-3), p=0.5),
# slt.RandomScale(range_x=(0.5, 2.5), p=0.5),
]),
slc.Stream()
], probs=[0.7, 0.3]),
slc.Stream([
slt.PadTransform((config.dataset.augs.pad.pad_x, config.dataset.augs.pad.pad_y), padding='z'),
slt.CropTransform((config.dataset.augs.crop.crop_x, config.dataset.augs.crop.crop_y), crop_mode='r'),
]),
slc.SelectiveStream([
slt.ImageSaltAndPepper(p=1, gain_range=0.01),
slt.ImageBlur(p=1, blur_type='g', k_size=(3, 5)),
slt.ImageBlur(p=1, blur_type='m', k_size=(3, 5)),
slt.ImageAdditiveGaussianNoise(p=1, gain_range=0.5),
slc.Stream([
slt.ImageSaltAndPepper(p=1, gain_range=0.05),
slt.ImageBlur(p=0.5, blur_type='m', k_size=(3, 5)),
]),
slc.Stream([
slt.ImageBlur(p=0.5, blur_type='m', k_size=(3, 5)),
slt.ImageSaltAndPepper(p=1, gain_range=0.01),
]),
slc.Stream()
], n=1),
slt.ImageGammaCorrection(p=0.5, gamma_range=(0.5, 1.5)),
cutout if config.dataset.use_cutout else slc.Stream(),
partial(solt2torchhm, downsample=None, sigma=None),
])
return ppl
def get_wrist_fracture_transformation(crop_size):
return transforms.Compose([
SplitDataToFunction(wrap_img_target_solt),
slc.Stream([
slt.RandomFlip(p=1, axis=1),
slt.RandomProjection(affine_transforms=slc.Stream([
slt.RandomScale(range_x=(0.8, 1.2), p=1),
slt.RandomShear(range_x=(-0.1, 0.1), p=0.5),
slt.RandomShear(range_y=(-0.1, 0.1), p=0.5),
slt.RandomRotate(rotation_range=(-10, 10), p=1),
]),
v_range=(1e-5, 5e-4),
p=0.8),
slt.PadTransform(pad_to=(256, 256), padding='z'),
slt.CropTransform(crop_size, crop_mode='r'),
slc.SelectiveStream([
slc.SelectiveStream([
slt.ImageSaltAndPepper(p=1, gain_range=0.01),
slt.ImageBlur(p=0.5, blur_type='m', k_size=(11, )),
]),
slt.ImageAdditiveGaussianNoise(p=1, gain_range=0.5),
]),
slt.ImageGammaCorrection(p=1, gamma_range=(0.5, 1.5)),
]),
DataToFunction(solt_to_img_target),
ApplyByIndex(transforms.ToTensor(), 0)
])
def test_blur_samples_correctly(blur_t, k_size, sigma):
trf = slt.ImageBlur(blur_type=blur_t, k_size=k_size, gaussian_sigma=sigma)
trf.sample_transform()
if isinstance(k_size, int):
k_size = (k_size, )
if sigma is None:
sigma = 1
assert trf.state_dict['k_size'] in k_size
assert trf.state_dict['sigma'] == sigma
def test_blur_arguments(blur_t, k_size, sigma, to_catch):
with pytest.raises(to_catch):
slt.ImageBlur(blur_type=blur_t, k_size=k_size, gaussian_sigma=sigma)
def train_test_transforms(conf, mean=None, std=None):
trf = conf['training']
prob = trf['transform_probability']
crop_size = tuple(trf['crop_size'])
# Training transforms
if trf['uCT']:
train_transforms = [
slt.RandomProjection(slc.Stream([
slt.RandomRotate(rotation_range=tuple(trf['rotation_range']),
p=prob),
slt.RandomScale(range_x=tuple(trf['scale_range']),
range_y=tuple(trf['scale_range']),
same=False,
p=prob),
slt.RandomShear(range_x=tuple(trf['shear_range']),
range_y=tuple(trf['shear_range']),
p=prob),
slt.RandomTranslate(range_x=trf['translation_range'],
range_y=trf['translation_range'],
p=prob)
]),
v_range=tuple(trf['v_range'])),
# Spatial
slt.RandomFlip(p=prob),
slt.PadTransform(pad_to=crop_size),
slt.CropTransform(crop_mode='r', crop_size=crop_size),
# Intensity
#slt.ImageGammaCorrection(gamma_range=tuple(trf['gamma_range']), p=prob),
#slt.ImageRandomHSV(h_range=tuple(trf['hsv_range']),
# s_range=tuple(trf['hsv_range']),
# v_range=tuple(trf['hsv_range']), p=prob),
# Brightness/contrast
slc.SelectiveStream([
slt.ImageRandomBrightness(brightness_range=tuple(
trf['brightness_range']),
p=prob),
slt.ImageRandomContrast(contrast_range=trf['contrast_range'],
p=prob)
]),
# Noise
slc.SelectiveStream([
slt.ImageSaltAndPepper(p=prob,
gain_range=trf['gain_range_sp']),
slt.ImageAdditiveGaussianNoise(
p=prob, gain_range=trf['gain_range_gn']),
slc.SelectiveStream([
slt.ImageBlur(p=prob,
blur_type='g',
k_size=(3, 7, 11),
gaussian_sigma=tuple(trf['sigma'])),
slt.ImageBlur(p=prob,
blur_type='m',
k_size=(3, 7, 11),
gaussian_sigma=tuple(trf['sigma']))
])
])
]
else:
train_transforms = [
# Projection
slt.RandomProjection(
slc.Stream([
slt.RandomRotate(rotation_range=tuple(
trf['rotation_range']),
p=prob),
slt.RandomScale(range_x=tuple(trf['scale_range']),
range_y=tuple(trf['scale_range']),
same=False,
p=prob),
#slt.RandomShear(range_x=tuple(trf['shear_range']),
# range_y=tuple(trf['shear_range']), p=prob),
#slt.RandomTranslate(range_x=trf['translation_range'], range_y=trf['translation_range'], p=prob)
]),
v_range=tuple(trf['v_range'])),
# Spatial
slt.RandomFlip(p=prob),
slt.PadTransform(pad_to=crop_size[1]),
slt.CropTransform(crop_mode='r', crop_size=crop_size),
# Intensity
# Add an empty stream
#slc.SelectiveStream([]),
slc.SelectiveStream([
slt.ImageGammaCorrection(gamma_range=tuple(trf['gamma_range']),
p=prob),
slt.ImageRandomHSV(h_range=tuple(trf['hsv_range']),
s_range=tuple(trf['hsv_range']),
v_range=tuple(trf['hsv_range']),
p=prob)
]),
slc.SelectiveStream([
slt.ImageRandomBrightness(brightness_range=tuple(
trf['brightness_range']),
p=prob),
slt.ImageRandomContrast(contrast_range=trf['contrast_range'],
p=prob)
]),
slc.SelectiveStream([
slt.ImageSaltAndPepper(p=prob,
gain_range=trf['gain_range_sp']),
slt.ImageAdditiveGaussianNoise(
p=prob, gain_range=trf['gain_range_gn']),
slc.SelectiveStream([
slt.ImageBlur(p=prob,
blur_type='g',
k_size=(3, 7, 11),
gaussian_sigma=tuple(trf['sigma'])),
slt.ImageBlur(p=prob,
blur_type='m',
k_size=(3, 7, 11),
gaussian_sigma=tuple(trf['sigma']))
])
])
]
train_trf = [
wrap_solt,
#slc.Stream(train_transforms),
slc.Stream([
slt.PadTransform(pad_to=crop_size[1]),
slt.CropTransform(crop_mode='r', crop_size=crop_size)
]),
unwrap_solt,
ApplyTransform(numpy2tens, (0, 1, 2))
]
# Validation transforms
val_trf = [
wrap_solt,
slc.Stream([
slt.PadTransform(pad_to=crop_size[1]),
slt.CropTransform(crop_mode='r', crop_size=crop_size)
]), unwrap_solt,
ApplyTransform(numpy2tens, idx=(0, 1, 2))
]
# Test transforms
test_trf = [unwrap_solt, ApplyTransform(numpy2tens, idx=(0, 1, 2))]
# Use normalize_channel_wise if mean and std not calculated
if mean is not None and std is not None:
train_trf.append(
ApplyTransform(partial(normalize_channel_wise, mean=mean,
std=std)))
if mean is not None and std is not None:
val_trf.append(
ApplyTransform(partial(normalize_channel_wise, mean=mean,
std=std)))
# Compose transforms
train_trf_cmp = Compose(train_trf)
val_trf_cmp = Compose(val_trf)
test_trf_cmp = Compose(test_trf)
return {
'train': train_trf_cmp,
'val': val_trf_cmp,
'test': test_trf_cmp,
'train_list': train_trf,
'val_list': val_trf,
'test_list': test_trf
}
def train_test_transforms(conf, mean=None, std=None, crop_size=(512, 1024)):
"""
Compiles the different image augmentations that are used for input images.
:param conf: Transformation parameters
:param mean: Dataset image mean
:param std: Dataset image std
:param crop_size: Image size for the segmentation model
:return: Compiled transformation objects, and lists of the used transforms
"""
trf = conf['training']
prob = trf['transform_probability']
# Training transforms
# 3D transforms
if trf['experiment'] == '3D':
train_transforms = [
slc.SelectiveStream([
slc.Stream([
slt.RandomProjection(
slc.Stream([
slt.RandomRotate(rotation_range=tuple(
trf['rotation_range']),
p=prob),
slt.RandomScale(range_x=tuple(trf['scale_range']),
range_y=tuple(trf['scale_range']),
same=False,
p=prob),
#slt.RandomShear(range_x=tuple(trf['shear_range']),
# range_y=tuple(trf['shear_range']), p=prob),
slt.RandomTranslate(
range_x=trf['translation_range'],
range_y=trf['translation_range'],
p=prob)
]),
v_range=None #tuple(trf['v_range'])
),
# Spatial
slt.RandomFlip(p=prob),
slt.PadTransform(pad_to=crop_size),
slt.CropTransform(crop_mode='r', crop_size=crop_size),
# Intensity
# Brightness/contrast
slc.SelectiveStream([
slt.ImageRandomBrightness(brightness_range=tuple(
trf['brightness_range']),
p=prob),
slt.ImageRandomContrast(
contrast_range=trf['contrast_range'], p=prob)
]),
# Noise
slc.SelectiveStream([
slt.ImageSaltAndPepper(
p=prob, gain_range=trf['gain_range_sp']),
slt.ImageAdditiveGaussianNoise(
p=prob, gain_range=trf['gain_range_gn']),
slc.SelectiveStream([
slt.ImageBlur(p=prob,
blur_type='g',
k_size=(3, 7, 11),
gaussian_sigma=tuple(trf['sigma'])),
slt.ImageBlur(p=prob,
blur_type='m',
k_size=(3, 7, 11),
gaussian_sigma=tuple(trf['sigma']))
])
])
]),
# Empty stream
slc.Stream([
slt.PadTransform(pad_to=crop_size),
slt.CropTransform(crop_mode='r', crop_size=crop_size)
])
])
]
# 2D transforms
else:
train_transforms = [
slc.SelectiveStream([
slc.Stream([
# Projection
slt.RandomProjection(
slc.Stream([
slt.RandomRotate(rotation_range=tuple(
trf['rotation_range']),
p=prob),
slt.RandomScale(range_x=tuple(trf['scale_range']),
range_y=tuple(trf['scale_range']),
same=False,
p=prob),
# slt.RandomShear(range_x=tuple(trf['shear_range']),
# range_y=tuple(trf['shear_range']), p=prob),
slt.RandomTranslate(
range_x=trf['translation_range'],
range_y=trf['translation_range'],
p=prob)
]),
v_range=tuple(trf['v_range'])),
# Spatial
slt.RandomFlip(p=prob),
slt.PadTransform(pad_to=crop_size),
slt.CropTransform(crop_mode='r', crop_size=crop_size),
# Intensity
slc.SelectiveStream([
slt.ImageGammaCorrection(gamma_range=tuple(
trf['gamma_range']),
p=prob),
slt.ImageRandomHSV(h_range=tuple(trf['hsv_range']),
s_range=tuple(trf['hsv_range']),
v_range=tuple(trf['hsv_range']),
p=prob)
]),
slc.SelectiveStream([
slt.ImageRandomBrightness(brightness_range=tuple(
trf['brightness_range']),
p=prob),
slt.ImageRandomContrast(
contrast_range=trf['contrast_range'], p=prob)
]),
slc.SelectiveStream([
slt.ImageSaltAndPepper(
p=prob, gain_range=trf['gain_range_sp']),
slt.ImageAdditiveGaussianNoise(
p=prob, gain_range=trf['gain_range_gn']),
slc.SelectiveStream([
slt.ImageBlur(p=prob,
blur_type='g',
k_size=(3, 7, 11),
gaussian_sigma=tuple(trf['sigma'])),
slt.ImageBlur(p=prob,
blur_type='m',
k_size=(3, 7, 11),
gaussian_sigma=tuple(trf['sigma']))
])
])
]),
# Empty stream
slc.Stream([
slt.PadTransform(pad_to=crop_size),
slt.CropTransform(crop_mode='r', crop_size=crop_size)
])
])
]
# Compile training transforms
train_trf = [
# Move to SOLT format
wrap_solt,
# Transforms
slc.Stream(train_transforms),
# Extract image
unwrap_solt,
# Move to tensor
ApplyTransform(numpy2tens, (0, 1, 2))
]
# Validation transforms
val_trf = [
wrap_solt,
slc.Stream([
slt.PadTransform(pad_to=crop_size[1]),
slt.CropTransform(crop_mode='r', crop_size=crop_size)
]), unwrap_solt,
ApplyTransform(numpy2tens, idx=(0, 1, 2))
]
# Test transforms
test_trf = [unwrap_solt, ApplyTransform(numpy2tens, idx=(0, 1, 2))]
# Normalize train and val images if mean and std are given
if mean is not None and std is not None:
train_trf.append(
ApplyTransform(partial(normalize_channel_wise, mean=mean,
std=std)))
if mean is not None and std is not None:
val_trf.append(
ApplyTransform(partial(normalize_channel_wise, mean=mean,
std=std)))
# Compose transforms
train_trf_cmp = Compose(train_trf)
val_trf_cmp = Compose(val_trf)
test_trf_cmp = Compose(test_trf)
return {
'train': train_trf_cmp,
'val': val_trf_cmp,
'test': test_trf_cmp,
'train_list': train_trf,
'val_list': val_trf,
'test_list': test_trf
}
slt.RandomRotate(rotation_range=(-90, 90), p=1),
slt.RandomShear(range_x=(-0.2, 0.2), range_y=None, p=0.7),
]),
v_range=(1e-6, 3e-4),
p=1),
# Various cropping and padding tricks
slt.PadTransform(1000, 'z'),
slt.CropTransform(1000, crop_mode='c'),
slt.CropTransform(950, crop_mode='r'),
slt.PadTransform(1000, 'z'),
# Intensity augmentations
slt.ImageGammaCorrection(p=1, gamma_range=(0.5, 3)),
slc.SelectiveStream([
slc.SelectiveStream([
slt.ImageSaltAndPepper(p=1, gain_range=0.01),
slt.ImageBlur(p=0.5, blur_type='m', k_size=(11, )),
]),
slt.ImageAdditiveGaussianNoise(p=1, gain_range=0.5),
]),
])
for i in range(10):
res = stream(dc)
img_res, kp_c, lbl_c = res.data
fig = plt.figure(figsize=(10, 10))
ax = fig.add_subplot(1, 1, 1)
ax.imshow(img_res, cmap=plt.cm.Greys_r)
for pts, cls in zip([kp_c.data], ['Cardiomegaly']):
text_bbox = dict(facecolor='red', alpha=0.7, lw=0)