def visualize(args, epoch, model, inference, data_loader, writer):
def save_image(image, tag):
image -= image.min()
image /= image.max()
grid = torchvision.utils.make_grid(image, nrow=4, pad_value=1)
writer.add_image(tag, grid, epoch)
model.eval()
with torch.no_grad():
for iter, data in enumerate(data_loader):
output, target = inference(model, data, device=args.device)
# HACK to make images look good in tensorboard
output, mean_o, std_o = transforms.normalize_instance(output)
output = output.clamp(-6, 6)
output = transforms.unnormalize(output, mean_o, std_o)
target, mean_t, std_t = transforms.normalize_instance(target)
target = target.clamp(-6, 6)
target = transforms.unnormalize(target, mean_t, std_t)
output = output.unsqueeze(1) # [batch_sz, h, w] --> [batch_sz, 1, h, w]
target = target.unsqueeze(1) # [batch_sz, h, w] --> [batch_sz, 1, h, w]
if isinstance(output, dict):
for k, output_val in output.items():
# save_image(input, 'Input_{}'.format(k))
save_image(target, 'Target_{}'.format(k))
save_image(output, 'Reconstruction_{}'.format(k))
save_image(torch.abs(target - output), 'Error_{}'.format(k))
else:
# save_image(input, 'Input')
save_image(target, 'Target')
save_image(output, 'Reconstruction')
save_image(torch.abs(target - output), 'Error')
break
def evaluate(args):
args.target_path = f'/home/tomerweiss/Datasets/singlecoil_{args.data_split}'
args.predictions_path = f'/home/liyon/PILOT/summary/{args.test_name}/rec'
print('/home/liyon/PILOT/summary/' + args.test_name + '/rec')
print("args: {}".format(args))
metrics = Metrics(METRIC_FUNCS)
for tgt_file in pathlib.Path(args.target_path).iterdir():
if tgt_file.is_dir():
continue
with h5py.File(tgt_file) as target, h5py.File(args.predictions_path +
'/' +
tgt_file.name) as recons:
if args.acquisition and args.acquisition == target.attrs[
'acquisition']:
continue
recons = recons['reconstruction'].value.squeeze(0)
target = target['reconstruction_esc'].value
target = transforms.to_tensor(target[:])
target = torch.nn.functional.avg_pool2d(target,
args.resolution_degrading)
target = center_crop_3d(target, recons.shape)
target, mean, std = transforms.normalize_instance(target,
eps=1e-11)
recons, meanr, stdr = transforms.normalize_instance(recons,
eps=1e-11)
target = target.numpy()
metrics.push(target, recons)
return metrics
def mnormalize(masked_kspace):
#getting image from masked data
image = transforms.ifft2(masked_kspace)
#normalizing the image
nimage, mean, std = transforms.normalize_instance(image, eps=1e-11)
#getting kspace data from normalized image
maksed_kspace_fni = transforms.ifftshift(nimage, dim=(-3, -2))
maksed_kspace_fni = torch.fft(maksed_kspace_fni, 2)
maksed_kspace_fni = transforms.fftshift(maksed_kspace_fni, dim=(-3, -2))
maksed_kspace_fni, mean, std = transforms.normalize_instance(masked_kspace,
eps=1e-11)
return maksed_kspace_fni, mean, std
def __call__(self, kspace, target, attrs, fname, slice):
"""
Args:
kspace (numpy.array): Input k-space of shape (num_coils, rows, cols, 2) for multi-coil
data or (rows, cols, 2) for single coil data.
target (numpy.array): Target image
attrs (dict): Acquisition related information stored in the HDF5 object.
fname (str): File name
slice (int): Serial number of the slice.
Returns:
(tuple): tuple containing:
image (torch.Tensor): Zero-filled input image.
target (torch.Tensor): Target image converted to a torch Tensor.
mean (float): Mean value used for normalization.
std (float): Standard deviation value used for normalization.
norm (float): L2 norm of the entire volume.
"""
target_inference = transforms.to_tensor(target)
kspace = transforms.to_tensor(kspace)
target = transforms.ifft2(kspace)
# Apply mask
seed = None if not self.use_seed else tuple(map(ord, fname))
if self.use_mask:
mask = transforms.get_mask(kspace, self.mask_func, seed)
masked_kspace = mask * kspace
else:
masked_kspace = kspace
image = transforms.ifft2(masked_kspace)
image_crop = transforms.complex_center_crop(
image, (self.resolution, self.resolution))
_, mean, std = transforms.normalize_instance_complex(image_crop,
eps=1e-11)
image_abs = transforms.complex_abs(image_crop)
image_abs, mean_abs, std_abs = transforms.normalize_instance(image_abs,
eps=1e-11)
image = transforms.normalize(image, mean, std)
target_image_complex_norm = transforms.normalize(target, mean, std)
target_kspace_train = transforms.fft2(target_image_complex_norm)
target = transforms.complex_center_crop(target, (320, 320))
target = transforms.complex_abs(target)
target_train = target
if RENORM:
target_train = transforms.normalize(target_train, mean_abs,
std_abs)
if CLAMP:
image = image.clamp(-6, 6)
target_train = target_train.clamp(-6, 6)
return image, target_train, target_kspace_train, mean, std, mask, mean_abs, std_abs, target_inference, attrs[
'max'], attrs['norm'].astype(np.float32)
def __call__(self, k_space, mask, target, attrs, f_name, slice):
"""
Args:
kspace (numpy.array): Input k-space of shape (num_coils, rows, cols, 2) for multi-coil
data or (rows, cols, 2) for single coil data.
mask (numpy.array): Mask from the test dataset
target (numpy.array): Target image
attrs (dict): Acquisition related information stored in the HDF5 object.
fname (str): File name
slice (int): Serial number of the slice.
Returns:
(tuple): tuple containing:
k_space (torch.Tensor): k-space(resolution x resolution x 2)
target (torch.Tensor): Target image converted to a torch Tensor.
fname (str): File name
slice (int): Serial number of the slice.
"""
k_space = transforms.to_tensor(k_space)
full_image = transforms.ifft2(k_space)
cropped_image = transforms.complex_center_crop(
full_image, (self.resolution, self.resolution))
k_space = transforms.fft2(cropped_image)
# Normalize input
cropped_image, mean, std = transforms.normalize_instance(cropped_image,
eps=1e-11)
cropped_image = cropped_image.clamp(-6, 6)
# Normalize target
target = transforms.to_tensor(target)
target = transforms.center_crop(target,
(self.resolution, self.resolution))
target = transforms.normalize(target, mean, std, eps=1e-11)
target = target.clamp(-6, 6)
return k_space, target, f_name, slice
def __call__(self, image, target, attrs, fname, slice):
"""
Args:
kspace (numpy.array): Input k-space of shape (num_coils, rows, cols, 2) for multi-coil
data or (rows, cols, 2) for single coil data.
target (numpy.array): Target image
attrs (dict): Acquisition related information stored in the HDF5 object.
fname (str): File name
slice (int): Serial number of the slice.
Returns:
(tuple): tuple containing:
image (torch.Tensor): Zero-filled input image.
target (torch.Tensor): Target image converted to a torch Tensor.
mean (float): Mean value used for normalization.
std (float): Standard deviation value used for normalization.
norm (float): L2 norm of the entire volume.
"""
image = transforms.to_tensor(image)
image, mean, std = transforms.normalize_instance(image, eps=1e-11)
image = image.clamp(-6, 6)
target = transforms.to_tensor(target)
# Normalize target
target = transforms.normalize(target, mean, std, eps=1e-11)
target = target.clamp(-6, 6)
return image, target, mean, std, fname, slice
def __call__(self, img, fname, slice):
image = transforms.to_tensor(img)
image = transforms.center_crop(image.permute(2,0,1), (self.resolution, self.resolution))
image, mean, std = transforms.normalize_instance(image, eps=1e-11)
image = image.clamp(-6, 6)
return image, mean, std, fname
def __call__(self, kspace, target, challenge, fname, slice_index):
original_kspace = transforms.to_tensor(kspace)
if self.reduce:
original_kspace = reducedimension(original_kspace, self.resolution)
# Apply mask
seed = None if not self.use_seed else tuple(map(ord, fname))
masked_kspace, mask = transforms.apply_mask(original_kspace,
self.mask_func, seed)
# Inverse Fourier Transform to get zero filled solution
image = transforms.ifft2(masked_kspace)
# Crop input image
image = transforms.complex_center_crop(
image, (self.resolution, self.resolution))
# Absolute value
image = transforms.complex_abs(image)
# Apply Root-Sum-of-Squares if multicoil data
if challenge == 'multicoil':
image = transforms.root_sum_of_squares(image)
# Normalize input
image, mean, std = transforms.normalize_instance(image, eps=1e-11)
target = transforms.to_tensor(target)
# Normalize target
target = transforms.normalize(target, mean, std, eps=1e-11)
target = target.clamp(-6, 6)
if self.polar:
original_kspace = cartesianToPolar(original_kspace)
masked_kspace = cartesianToPolar(masked_kspace)
return original_kspace, masked_kspace, mask, target, fname, slice_index
def __call__(self, kspace, target, attrs, fname, slice):
kspace = transforms.to_tensor(kspace)
image = transforms.ifft2_regular(kspace)
image = transforms.complex_center_crop(image, (self.resolution, self.resolution))
# image = transforms.complex_abs(image)
image, mean, std = transforms.normalize_instance(image, eps=1e-11)
# image, mean, std = transforms.normalize_instance_per_channel(image, eps=1e-11)
# image = image.clamp(-6, 6)
# kspace = transforms.fft2(image)
target = transforms.to_tensor(target)
target, mean, std = transforms.normalize_instance(target, eps=1e-11)
# # target = transforms.normalize(target, mean, std)
# target = target.clamp(-6, 6)
mean = std = 0
return image, target, mean, std, attrs['norm'].astype(np.float32)
def resize(hparams, image, target):
smallest_width = min(hparams.resolution, image.shape[-2])
smallest_height = min(hparams.resolution, image.shape[-3])
if target is not None:
smallest_width = min(smallest_width, target.shape[-1])
smallest_height = min(smallest_height, target.shape[-2])
crop_size = (smallest_height, smallest_width)
image = transforms.complex_center_crop(image, crop_size)
# Absolute value
image_abs = transforms.complex_abs(image)
# Apply Root-Sum-of-Squares if multicoil data
if hparams.challenge == "multicoil":
image_abs = transforms.root_sum_of_squares(image_abs)
# Normalize input
image_abs, mean, std = transforms.normalize_instance(image_abs, eps=1e-11)
image_abs = image_abs.clamp(-6, 6)
# Normalize target
if target is not None:
target = transforms.to_tensor(target)
target = transforms.center_crop(target, crop_size)
target = transforms.normalize(target, mean, std, eps=1e-11)
target = target.clamp(-6, 6)
else:
target = torch.Tensor([0])
return image, image_abs, target, mean, std
def __call__(self, kspace, target, attrs, fname, slice):
"""
Args:
kspace (numpy.Array): k-space measurements
target (numpy.Array): Target image
attrs (dict): Acquisition related information stored in the HDF5 object
fname (pathlib.Path): Path to the input file
slice (int): Serial number of the slice
Returns:
(tuple): tuple containing:
image (torch.Tensor): Normalized zero-filled input image
mean (float): Mean of the zero-filled image
std (float): Standard deviation of the zero-filled image
fname (pathlib.Path): Path to the input file
slice (int): Serial number of the slice
"""
kspace = transforms.to_tensor(kspace)
image = transforms.ifft2(kspace)
image = transforms.complex_center_crop(
image, (self.resolution, self.resolution))
# Apply Root-Sum-of-Squares if multicoil data
if self.which_challenge == 'multicoil':
image = transforms.root_sum_of_squares(image)
image = transforms.complex_abs(image)
image, mean, std = transforms.normalize_instance(image, eps=1e-11)
image = image.clamp(-6, 6)
kspace = transforms.rfft2(image)
return kspace, mean, std, fname, slice
def __call__(self, kspace, target, attrs, fname, slice):
"""
Args:
kspace (numpy.array): Input k-space of shape (num_coils, rows, cols, 2) for multi-coil
data or (rows, cols, 2) for single coil data.
target (numpy.array): Target image
attrs (dict): Acquisition related information stored in the HDF5 object.
fname (str): File name
slice (int): Serial number of the slice.
Returns:
(tuple): tuple containing:
image (torch.Tensor): Zero-filled input image.
target (torch.Tensor): Target image converted to a torch Tensor.
mean (float): Mean value used for normalization.
std (float): Standard deviation value used for normalization.
norm (float): L2 norm of the entire volume.
"""
kspace = transforms.to_tensor(kspace)
# Apply mask
seed = None if not self.use_seed else tuple(map(ord, fname))
if self.use_mask:
mask = transforms.get_mask(kspace, self.mask_func, seed)
masked_kspace = mask * kspace
else:
masked_kspace = kspace
image = transforms.ifft2(masked_kspace)
_, mean_image, std_image = transforms.normalize_instance(image, eps=1e-11)
masked_kspace, mean, std = transforms.normalize_instance_complex(masked_kspace)
kspace = transforms.normalize(kspace, mean, std)
return masked_kspace, kspace, mean, std, mean_image, std_image, mask
def __call__(self, kspace, target, attrs, fname, slice):
"""
Args:
kspace (numpy.Array): k-space measurements
target (numpy.Array): Target image
attrs (dict): Acquisition related information stored in the HDF5 object
fname (pathlib.Path): Path to the input file
slice (int): Serial number of the slice
Returns:
(tuple): tuple containing:
image (torch.Tensor): Normalized zero-filled input image
mean (float): Mean of the zero-filled image
std (float): Standard deviation of the zero-filled image
fname (pathlib.Path): Path to the input file
slice (int): Serial number of the slice
"""
kspace = transforms.to_tensor(kspace)
if self.mask_func is not None:
seed = tuple(map(ord, fname))
masked_kspace, _ = transforms.apply_mask(kspace, self.mask_func, seed)
else:
masked_kspace = kspace
# Inverse Fourier Transform to get zero filled solution
image = transforms.ifft2(masked_kspace)
# Crop input image
image = transforms.complex_center_crop(image, (self.resolution, self.resolution))
# Absolute value
image = transforms.complex_abs(image)
# Apply Root-Sum-of-Squares if multicoil data
if self.which_challenge == 'multicoil':
image = transforms.root_sum_of_squares(image)
# Normalize input
image, mean, std = transforms.normalize_instance(image)
image = image.clamp(-6, 6)
return image, mean, std, fname, slice
def __call__(self, image):
"""
Args:
image (numpy.array): DICOM image
Returns:
image (torch.Tensor): Zero-filled input image.
"""
# image = np.rot90(image, axes=(0, 1)).copy()
image = np.flip(image, 0)
# if image.shape[0] < self.resolution or image.shape[1] < self.resolution:
# return None
# # Crop center
# image = transforms.center_crop(image, (self.resolution, self.resolution))
res_crop = min(image.shape[0], image.shape[1])
image = transforms.center_crop(image, (res_crop, res_crop))
image = cv2.resize(image, dsize=(self.resolution, self.resolution), interpolation=cv2.INTER_CUBIC)
# Normalize input
image = transforms.to_tensor(image)
image, mean, std = transforms.normalize_instance(image, eps=1e-11)
image = image.clamp(-6, 6)
return image
def evaluate(args):
args.target_path = f'Datasets/brainT1/{args.data_split}'
args.predictions_path = f'/summary/{args.test_name}/rec'
print('summary/' + args.test_name + '/rec')
print("args: {}".format(args))
metrics = Metrics(METRIC_FUNCS)
for tgt_file in pathlib.Path(args.target_path).iterdir():
if tgt_file.is_dir():
continue
with h5py.File(tgt_file) as target, h5py.File(args.predictions_path +
'/' +
tgt_file.name) as recons:
if args.acquisition and args.acquisition == target.attrs[
'acquisition']:
continue
recons = recons['reconstruction'].value.squeeze(0)
target = target['data'].value
target = transforms.to_tensor(target[:])
if recons.shape[0] == recons.shape[2]:
# This means we look at the 3d resolution
min_to_crop = min(target.shape[0], target.shape[1],
target.shape[2])
min_to_crop -= min_to_crop % 2
target = pytorch_nufft.transforms.center_crop_3d(
target, (min_to_crop, min_to_crop, min_to_crop))
target = ndimage.zoom(target, recons.shape[0] / min_to_crop)
target = torch.from_numpy(target).float()
else:
target = torch.nn.functional.avg_pool2d(
target, args.resolution_degrading)
args.resolution = min(
target.shape[0] // args.resolution_degrading,
recons.shape[0])
target = pytorch_nufft.transforms.center_crop_3d(
target, recons.shape)
target, mean, std = transforms.normalize_instance(target,
eps=1e-11)
recons, meanr, stdr = transforms.normalize_instance(recons,
eps=1e-11)
target = target.numpy()
metrics.push(target, recons)
return metrics
def test_normalize_instance(shape):
input = create_input(shape)
output, mean, stddev = transforms.normalize_instance(input)
output = output.numpy()
assert np.isclose(input.numpy().mean(), mean, rtol=1e-2)
assert np.isclose(input.numpy().std(), stddev, rtol=1e-2)
assert np.isclose(output.mean(), 0, rtol=1e-2, atol=1e-3)
assert np.isclose(output.std(), 1, rtol=1e-2, atol=1e-3)
def __call__(self, ds_slice, gt_slice, attrs, file_name, s_idx, acc_fac):
assert gt_slice is None
with torch.autograd.no_grad():
ds_slice, mean, std = normalize_instance(to_tensor(ds_slice))
ds_slice = ds_slice.clamp(min=-6, max=6).unsqueeze(dim=0)
assert isinstance(file_name, str) and isinstance(s_idx, int), 'Incorrect types!'
extra_params = dict(mean=mean, std=std, acc_fac=acc_fac, attrs=attrs)
return ds_slice, file_name, s_idx, extra_params
def __call__(self, kspace, mask, target, attrs, fname, slice):
"""
Args:
kspace (numpy.array): Input k-space of shape (num_coils, rows, cols, 2) for multi-coil
data or (rows, cols, 2) for single coil data.
mask (numpy.array): Mask from the test dataset
target (numpy.array): Target image
attrs (dict): Acquisition related information stored in the HDF5 object.
fname (str): File name
slice (int): Serial number of the slice.
Returns:
(tuple): tuple containing:
image (torch.Tensor): Zero-filled input image.
target (torch.Tensor): Target image converted to a torch Tensor.
mean (float): Mean value used for normalization.
std (float): Standard deviation value used for normalization.
"""
kspace = transforms.to_tensor(kspace)
# Apply mask
if self.mask_func:
seed = None if not self.use_seed else tuple(map(ord, fname))
masked_kspace, mask = transforms.apply_mask(
kspace, self.mask_func, seed)
else:
masked_kspace = kspace
# Inverse Fourier Transform to get zero filled solution
image = transforms.ifft2(masked_kspace)
# Crop input image to given resolution if larger
smallest_width = min(self.resolution, image.shape[-2])
smallest_height = min(self.resolution, image.shape[-3])
if target is not None:
smallest_width = min(smallest_width, target.shape[-1])
smallest_height = min(smallest_height, target.shape[-2])
crop_size = (smallest_height, smallest_width)
image = transforms.complex_center_crop(image, crop_size)
# Absolute value
image = transforms.complex_abs(image)
# Apply Root-Sum-of-Squares if multicoil data
if self.which_challenge == 'multicoil':
image = transforms.root_sum_of_squares(image)
# Normalize input
image, mean, std = transforms.normalize_instance(image, eps=1e-11)
image = image.clamp(-6, 6)
# Normalize target
if target is not None:
target = transforms.to_tensor(target)
target = transforms.center_crop(target, crop_size)
target = transforms.normalize(target, mean, std, eps=1e-11)
target = target.clamp(-6, 6)
else:
target = torch.Tensor([0])
return image, target, mean, std, fname, slice
def __call__(self, kspace, target, attrs, fname, slice):
kspace_rect = transforms.to_tensor(kspace) ##rectangular kspace
image_rect = transforms.ifft2(kspace_rect) ##rectangular FS image
image_square = transforms.complex_center_crop(
image_rect,
(self.resolution, self.resolution)) ##cropped to FS square image
kspace_square = self.c3object.apply(
transforms.fft2(image_square)) #* 10000 ##kspace of square iamge
if self.augmentation:
kspace_square = self.augmentation.apply(kspace_square)
image_square = ifft_c3(kspace_square)
# Apply mask
seed = None if not self.use_seed else tuple(map(ord, fname))
masked_kspace_square, mask = transforms.apply_mask(
kspace_square, self.mask_func, seed) ##ZF square kspace
# Inverse Fourier Transform to get zero filled solution
# image = transforms.ifft2(masked_kspace)
image_square_us = ifft_c3(
masked_kspace_square) ## US square complex image
# Crop input image
# image = transforms.complex_center_crop(image, (self.resolution, self.resolution))
# Absolute value
# image = transforms.complex_abs(image)
image_square_abs = transforms.complex_abs(
image_square_us) ## US square real image
# Apply Root-Sum-of-Squares if multicoil data
# if self.which_challenge == 'multicoil':
# image = transforms.root_sum_of_squares(image)
# Normalize input
# image, mean, std = transforms.normalize_instance(image, eps=1e-11)
_, mean, std = transforms.normalize_instance(image_square_abs,
eps=1e-11)
# image = image.clamp(-6, 6)
# target = transforms.to_tensor(target)
target = image_square.permute(2, 0, 1)
# Normalize target
# target = transforms.normalize(target, mean, std, eps=1e-11)
# target = target.clamp(-6, 6)
# return image, target, mean, std, attrs['norm'].astype(np.float32)
# return masked_kspace_square.permute((2,0,1)), image, image_square.permute(2,0,1), mean, std, attrs['norm'].astype(np.float32)
# ksp, zf, target, me, st, nor
return masked_kspace_square.permute((2,0,1)), image_square_us.permute((2,0,1)), \
target, \
mean, std, attrs['norm'].astype(np.float32)
def __call__(self, ds_slice, gt_slice, attrs, file_name, s_idx, acc_fac):
with torch.autograd.no_grad():
ds_slice, mean, std = normalize_instance(to_tensor(ds_slice))
gt_slice = normalize(to_tensor(gt_slice), mean, std)
ds_slice = ds_slice.clamp(min=-6, max=6).unsqueeze(dim=0)
gt_slice = gt_slice.clamp(min=-6, max=6).unsqueeze(dim=0)
ds_slice, gt_slice = self.augment_data(ds_slice, gt_slice)
return ds_slice, gt_slice, 0
def __call__(self, kspace, target, attrs, fname, slice):
kspace = transforms.to_tensor(kspace)
image = transforms.ifft2_regular(kspace)
image = transforms.complex_center_crop(
image, (self.resolution, self.resolution))
# image = transforms.complex_abs(image)
image, mean, std = transforms.normalize_instance(image, eps=1e-11)
image = image.clamp(-6, 6)
kspace = transforms.fft2(image)
return image, mean, std, fname, slice
def train_step(model, data, device):
input, target, mean, std, norm, _, image_updated = data
# input, mean, std = transforms.normalize_instance(input, eps=1e-11)
target, _, _ = transforms.normalize_instance(target, eps=1e-11)
if CLAMP:
target = target.clamp(-6, 6)
if len(image_updated) != 0:
input = image_updated
input, mean, std = transforms.normalize_instance(input, eps=1e-11)
if CLAMP:
input = input.clamp(-6, 6)
input = input.unsqueeze(0).unsqueeze(1).to(device)
target = target.to(device)
output = model(input).squeeze(1).squeeze(0)
if SMOOTH:
loss = F.smooth_l1_loss(output, target)
else:
loss = F.l1_loss(output, target)
return loss
def __call__(self, kspace, target, attrs, fname):
target = transforms.to_tensor(target[:])
target = torch.nn.functional.avg_pool2d(target,self.resolution_degrading)
self.resolution=min(320//self.resolution_degrading,self.resolution)
target = pytorch_nufft.transforms.center_crop_3d(target, (self.depth, self.resolution, self.resolution))
target, mean, std = transforms.normalize_instance(target, eps=1e-11)
target = target.clamp(-6, 6)
kspace = pytorch_nufft.transforms.rfft3_regular(target)
return kspace, target, mean, std
def __call__(self, kspace, target, attrs, fname, slice):
"""
Args:
kspace (numpy.array): Input k-space of shape (num_coils, rows, cols, 2) for multi-coil
data or (rows, cols, 2) for single coil data.
target (numpy.array): Target image
attrs (dict): Acquisition related information stored in the HDF5 object.
fname (str): File name
slice (int): Serial number of the slice.
Returns:
(tuple): tuple containing:
image (torch.Tensor): Zero-filled input image.
target (torch.Tensor): Target image converted to a torch Tensor.
mean (float): Mean value used for normalization.
std (float): Standard deviation value used for normalization.
norm (float): L2 norm of the entire volume.
"""
kspace = transforms.to_tensor(kspace)
# Apply mask
seed = None if not self.use_seed else tuple(map(ord, fname))
if self.use_mask:
mask = transforms.get_mask(kspace, self.mask_func, seed)
masked_kspace = mask * kspace
else:
masked_kspace = kspace
# Inverse Fourier Transform to get zero filled solution
image = transforms.ifft2(masked_kspace)
# Crop input image
image = transforms.complex_center_crop(
image, (self.resolution, self.resolution))
# Absolute value
image = transforms.complex_abs(image)
# Apply Root-Sum-of-Squares if multicoil data
if self.which_challenge == 'multicoil':
image = transforms.root_sum_of_squares(image)
# Normalize input
image, mean, std = transforms.normalize_instance(image, eps=1e-11)
if CLAMP:
image = image.clamp(-6, 6)
# Normalize target
target = transforms.to_tensor(target)
target_train = transforms.normalize(target, mean, std, eps=1e-11)
if CLAMP:
target_train = target_train.clamp(
-6,
6) # Return target (for viz) and target_clamped (for training)
return image, target_train, mean, std, attrs['norm'].astype(
np.float32), target
def data_transform(kspace, mask_function, target, data_attributes, filename,
slice_num):
"""
Perform preprocessing of the kspace image, in order to get a proper input for the net. Should be invoked from
the SliceData class.
Args:
- kspace: complete sampled kspace image
- mask_func: masking function to apply mask to kspace (TODO not working: we are passing from outside)
- target: the target image to be reconstructed from the kspace
- data_attributes: attributes of the whole HDF5 file
Returns:
- normalized_masked_image: original kspace with mask applied and cropped to 320 x 320
- mask: mask generated by masking function
- normalized_target: normalized target
- max_value: highest entry in target tensor (for SSIM loss)
"""
kspace_t = transforms.to_tensor(kspace)
kspace_t = transforms.normalize_instance(kspace_t)[0]
masked_kspace, mask = transforms.apply_mask(
data=kspace_t, mask_func=mask_func
) # apply mask: returns masked space and generated mask
masked_image = fastmri.ifft2c(
masked_kspace
) # Apply Inverse Fourier Transform to get the complex image
masked_image = transforms.complex_center_crop(
masked_image, (320, 320)) # center crop masked image
masked_image = masked_image.permute(
2, 0, 1) # permuting the masked image fot pytorch n x c x h x w format
masked_image = transforms.normalize_instance(masked_image)[0] # normalize
target = transforms.to_tensor(target)
target = transforms.normalize_instance(target)[0] # normalize
target = torch.unsqueeze(target, 0) # add dimension
return kspace_t, masked_image, target, mask, data_attributes[
'max'], slice_num
def __call__(self, kspace, target, attrs, fname, slice):
"""
Args:
kspace (numpy.Array): k-space measurements
target (numpy.Array): Target image
attrs (dict): Acquisition related information stored in the HDF5 object
fname (pathlib.Path): Path to the input file
slice (int): Serial number of the slice
Returns:
(tuple): tuple containing:
image (torch.Tensor): Normalized zero-filled input image
mean (float): Mean of the zero-filled image
std (float): Standard deviation of the zero-filled image
fname (pathlib.Path): Path to the input file
slice (int): Serial number of the slice
"""
kspace = transforms.to_tensor(kspace)
if self.mask_func is not None:
seed = tuple(map(ord, fname))
masked_kspace, _ = transforms.apply_mask(kspace, self.mask_func, seed)
else:
masked_kspace = kspace
# Inverse Fourier Transform to get zero filled solution
image = transforms.ifft2(masked_kspace)
# Crop input image
image = transforms.complex_center_crop(image, (self.resolution, self.resolution))
# Absolute value
image = transforms.complex_abs(image)
# Apply Root-Sum-of-Squares if multicoil data
if self.which_challenge == 'multicoil':
image = transforms.root_sum_of_squares(image)
# Normalize input
image, mean, std = transforms.normalize_instance(image)
image = image.clamp(-6, 6)
# difference between kspace actual and target dim
extra = int(masked_kspace.shape[1] - self.kspace_x)
# clip kspace at input dim
if extra > 0:
masked_kspace = masked_kspace[:, (extra//2):-(extra//2), :]
# zero pad if necessary
elif extra < 0:
empty_kspace = torch.zeros((masked_kspace.shape[0], self.kspace_x, masked_kspace.shape[2]))
empty_kspace[:, -(extra//2):(extra//2), :] = masked_kspace
masked_kspace = empty_kspace
#TODO return mask as well for exclusive updates
return masked_kspace, image, mean, std, fname, slice
def inference(model, data, device):
input, target, mean, std, norm, unnormalized_target, image_updated = data
if len(target) != 0:
target, _, _ = transforms.normalize_instance(target, eps=1e-11)
if len(image_updated) != 0:
input = image_updated
input, mean, std = transforms.normalize_instance(input, eps=1e-11)
if CLAMP:
input = input.clamp(-6, 6)
input = input.unsqueeze(0).unsqueeze(1).to(device)
if len(unnormalized_target) != 0:
unnormalized_target = unnormalized_target.to(device)
output = model(input).squeeze(1).squeeze(0)
mean = mean.unsqueeze(0).unsqueeze(1).unsqueeze(2).to(device)
std = std.unsqueeze(0).unsqueeze(1).unsqueeze(2).to(device)
output = transforms.unnormalize(output, mean, std)
# if len(target) != 0:
# target = transforms.unnormalize(target, mean, std)
# if len(target) != 0:
# target = target * std + mean
return output, unnormalized_target
def to_spatial(self, kspace, resolution):
'''
k space: pytorch tensor post enchancement
'''
# Inverse Fourier Transform to get interpolated solution
image = transforms.ifft2(kspace)
# Crop input image
image = transforms.complex_center_crop(image, (resolution, resolution))
# Absolute value
image = transforms.complex_abs(image)
# Normalize input
image, mean, std = transforms.normalize_instance(image, eps=1e-11)
image = image.clamp(-6, 6)
return image
def kspacetoimage(kspace, args):
# Inverse Fourier Transform to get zero filled solution
image = transforms.ifft2(kspace)
# Crop input image
image = transforms.complex_center_crop(image,
(args.resolution, args.resolution))
# Absolute value
image = transforms.complex_abs(image)
# Apply Root-Sum-of-Squares if multicoil data
if args.challenge == 'multicoil':
image = transforms.root_sum_of_squares(image)
# Normalize input
image, mean, std = transforms.normalize_instance(image, eps=1e-11)
image = image.clamp(-6, 6)
return image
def nkspacetoimage(args, kspace_fni, mean, std, eps=1e-11):
#nkspace to image
assert kspace_fni.size(-1) == 2
image = transforms.ifftshift(kspace_fni, dim=(-3, -2))
image = torch.ifft(image, 2)
image = transforms.fftshift(image, dim=(-3, -2))
#denormalizing the nimage
image = (image * std) + mean
image = image[0]
image = transforms.complex_center_crop(image,
(args.resolution, args.resolution))
# Absolute value
image = transforms.complex_abs(image)
# Normalize input
image, mean, std = transforms.normalize_instance(image, eps=1e-11)
image = image.clamp(-6, 6)
return image
