def test_complex_center_crop(shape, target_shape):
shape = shape + [2]
input = create_input(shape)
out_torch = transforms.complex_center_crop(input, target_shape).numpy()
assert list(out_torch.shape) == target_shape + [
2,
]
def save_zero_filled(data_dir, out_dir, which_challenge):
reconstructions = {}
for fname in tqdm(list(data_dir.glob("*.h5"))):
with h5py.File(fname, "r") as hf:
et_root = etree.fromstring(hf["ismrmrd_header"][()])
masked_kspace = transforms.to_tensor(hf["kspace"][()])
# extract target image width, height from ismrmrd header
enc = ["encoding", "encodedSpace", "matrixSize"]
crop_size = (
int(et_query(et_root, enc + ["x"])),
int(et_query(et_root, enc + ["y"])),
)
# inverse Fourier Transform to get zero filled solution
image = fastmri.ifft2c(masked_kspace)
# check for FLAIR 203
if image.shape[-2] < crop_size[1]:
crop_size = (image.shape[-2], image.shape[-2])
# crop input image
image = transforms.complex_center_crop(image, crop_size)
# absolute value
image = fastmri.complex_abs(image)
# apply Root-Sum-of-Squares if multicoil data
if which_challenge == "multicoil":
image = fastmri.rss(image, dim=1)
reconstructions[fname.name] = image
fastmri.save_reconstructions(reconstructions, out_dir)
def to_cropped_image(masked_kspace, target, attrs):
# inverse Fourier transform to get zero filled solution
image = fastmri.ifft2c(masked_kspace)
# crop input to correct size
if target is not None:
crop_size = (target.shape[-2], target.shape[-1])
else:
crop_size = (attrs["recon_size"][0], attrs["recon_size"][1])
# check for FLAIR 203
if image.shape[-2] < crop_size[1]:
crop_size = (image.shape[-2], image.shape[-2])
image = T.complex_center_crop(image, crop_size)
# absolute value
image = fastmri.complex_abs(image)
# normalize input
image, mean, std = T.normalize_instance(image, eps=1e-11)
image = image.clamp(-6, 6)
# normalize target
if target is not None:
if isinstance(target, np.ndarray):
target = T.to_tensor(target)
target = T.center_crop(target, crop_size)
target = T.normalize(target, mean, std, eps=1e-11)
target = target.clamp(-6, 6)
else:
target = torch.Tensor([0])
return image, target
def save_zero_filled(data_dir, out_dir, which_challenge):
reconstructions = {}
for f in data_dir.iterdir():
with h5py.File(f, "r") as hf:
enc = ismrmrd.xsd.CreateFromDocument(hf["ismrmrd_header"][()]).encoding[0]
masked_kspace = transforms.to_tensor(hf["kspace"][()])
# extract target image width, height from ismrmrd header
crop_size = (enc.reconSpace.matrixSize.x, enc.reconSpace.matrixSize.y)
# inverse Fourier Transform to get zero filled solution
image = fastmri.ifft2c(masked_kspace)
# check for FLAIR 203
if image.shape[-2] < crop_size[1]:
crop_size = (image.shape[-2], image.shape[-2])
# crop input image
image = transforms.complex_center_crop(image, crop_size)
# absolute value
image = fastmri.complex_abs(image)
# apply Root-Sum-of-Squares if multicoil data
if which_challenge == "multicoil":
image = fastmri.rss(image, dim=1)
reconstructions[f.name] = image
fastmri.save_reconstructions(reconstructions, out_dir)
def load_data_from_pathlist(path):
file_num = len(path)
use_num = file_num // 3
total_target_list = []
total_sampled_image_list = []
for h5_num in range(use_num):
total_kspace, slices_num, target = load_dataset(path[h5_num])
image_list = []
slice_kspace_tensor_list = []
target_image_list = []
for i in range(slices_num):
slice_kspace = total_kspace[i]
#target_image = target[i]
slice_kspace_tensor = T.to_tensor(
slice_kspace) # convert numpy to tensor
slice_kspace_tensor = slice_kspace_tensor.float()
#print(slice_kspace_tensor.shape)
slice_kspace_tensor_list.append(
slice_kspace_tensor) # 35* torch[640, 368])
#target = target_image_list.append(target_image)
#image_list_tensor = torch.stack(image_list, dim=0) # torch.Size([35, 640, 368])
#total_image_list.append(image_list_tensor)
mask_func = RandomMaskFunc(
center_fractions=[0.08],
accelerations=[4]) # create the mask function object
sampled_image_list = []
target_list = []
for i in range(slices_num):
slice_kspace_tensor = slice_kspace_tensor_list[i]
masked_kspace, mask = T.apply_mask(slice_kspace_tensor, mask_func)
Ny, Nx, _ = slice_kspace_tensor.shape
mask = mask.repeat(Ny, 1, 1).squeeze()
# functions.show_slice(mask, cmap='gray')
# functions.show_slice(image_list[10], cmap='gray')
sampled_image = fastmri.ifft2c(
masked_kspace) # inverse fast FT to get the complex image
sampled_image = T.complex_center_crop(sampled_image, (320, 320))
sampled_image_abs = fastmri.complex_abs(sampled_image)
sampled_image_list.append(sampled_image_abs)
sampled_image_list_tensor = torch.stack(
sampled_image_list, dim=0) # torch.Size([35, 640, 368])
total_sampled_image_list.append(sampled_image_list_tensor)
target = T.to_tensor(target)
total_target_list.append(target)
#target_image_tensor = torch.cat(target_image_list, dim=0) # torch.Size([6965, 640, 368])
total_target = torch.cat(total_target_list, dim=0)
total_sampled_image_tensor = torch.cat(
total_sampled_image_list, dim=0) # torch.Size([6965, 640, 368])
total_sampled_image_tensor, mean, std = T.normalize_instance(
total_sampled_image_tensor, eps=1e-11)
total_sampled_image_tensor = total_sampled_image_tensor.clamp(-6, 6)
target_image_tensor = T.normalize(total_target, mean, std, eps=1e-11)
target_image_tensor = target_image_tensor.clamp(-6, 6)
# total_image_tensor = torch.stack(total_image_list, dim=0) # torch.Size([199, 35, 640, 368])
# total_sampled_image_tensor = torch.stack(total_sampled_image_list, dim=0) # torch.Size([199, 35, 640, 368])
#print(target_image_tensor.shape)
#print(total_sampled_image_tensor.shape)
return target_image_tensor, total_sampled_image_tensor
def _base_fastmri_unet_transform(
kspace,
mask,
ground_truth,
attrs,
which_challenge="singlecoil",
):
kspace = fastmri_transforms.to_tensor(kspace)
mask = mask[..., :kspace.shape[-2]] # accounting for variable size masks
masked_kspace = kspace * mask.unsqueeze(-1) + 0.0
# inverse Fourier transform to get zero filled solution
image = fastmri.ifft2c(masked_kspace)
# crop input to correct size
if ground_truth is not None:
crop_size = (ground_truth.shape[-2], ground_truth.shape[-1])
else:
crop_size = (attrs["recon_size"][0], attrs["recon_size"][1])
# check for FLAIR 203
if image.shape[-2] < crop_size[1]:
crop_size = (image.shape[-2], image.shape[-2])
# noinspection PyTypeChecker
image = fastmri_transforms.complex_center_crop(image, crop_size)
# absolute value
image = fastmri.complex_abs(image)
# apply Root-Sum-of-Squares if multicoil data
if which_challenge == "multicoil":
image = fastmri.rss(image)
# normalize input
image, mean, std = fastmri_transforms.normalize_instance(image, eps=1e-11)
image = image.clamp(-6, 6)
return image.unsqueeze(0), mean, std
def visualize_kspace(kspace, dim=None, crop=False, output_filepath=None):
kspace = fastmri.ifft2c(kspace)
if crop:
crop_size = (kspace.shape[-2], kspace.shape[-2])
kspace = T.complex_center_crop(kspace, crop_size)
kspace = fastmri.complex_abs(kspace)
kspace, _, _ = T.normalize_instance(kspace, eps=1e-11)
kspace = kspace.clamp(-6, 6)
else:
# Compute absolute value to get a real image
kspace = fastmri.complex_abs(kspace)
if dim is not None:
kspace = fastmri.rss(kspace, dim=dim)
img = np.abs(kspace.numpy())
if output_filepath is not None:
if not output_filepath.parent.exists():
output_filepath.parent.mkdir(parents=True)
plt.imshow(img, cmap='gray')
plt.axis("off")
plt.savefig(output_filepath, bbox_inches="tight", pad_inches=0)
else:
plt.imshow(img, cmap='gray')
plt.show()
def __call__(self, kspace, mask, target, attrs, fname, slice_num):
"""
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_num (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.
fname (str): File name.
slice_num (int): Serial number of the slice.
"""
kspace = transforms.to_tensor(kspace)
image = fastmri.ifft2c(kspace)
# crop input to correct size
if target is not None:
crop_size = (target.shape[-2], target.shape[-1])
else:
crop_size = (attrs["recon_size"][0], attrs["recon_size"][1])
# check for sFLAIR 203
if image.shape[-2] < crop_size[1]:
crop_size = (image.shape[-2], image.shape[-2])
image = transforms.complex_center_crop(image, crop_size)
#getLR
imgfft = fastmri.fft2c(image)
imgfft = transforms.complex_center_crop(imgfft,(160,160))
LR_image = fastmri.ifft2c(imgfft)
# absolute value
LR_image = fastmri.complex_abs(LR_image)
# normalize input
LR_image, mean, std = transforms.normalize_instance(LR_image, eps=1e-11)
LR_image = LR_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 LR_image, target, mean, std, fname, slice_num
dest_path = Path(dest_data_folder)
for fname in sorted(files):
print(fname)
orig = h5py.File(fname)
dest = h5py.File(dest_path / fname.name, 'a')
volume_kspace = orig['kspace'][()]
kspace_list = []
reconstruction_list = []
total_slices = volume_kspace.shape[0]
for i in range(total_slices // 2 - num_middle_slices // 2,
total_slices // 2 + num_middle_slices // 2 + 1):
slice_kspace = volume_kspace[i]
slice_kspace2 = to_tensor(
slice_kspace) # Convert from numpy array to pytorch tensor
kspace_crop = complex_center_crop(slice_kspace2, (size, size))
ift = fastmri.ifft2c(
kspace_crop
) # Apply Inverse Fourier Transform to get the complex image
reconstruction = fastmri.complex_abs(ift)
kspace_list.append(tensor_to_complex_np(kspace_crop))
reconstruction_list.append(reconstruction)
stacked_kspace = np.stack(kspace_list)
stacked_reconstruction_esc = np.stack(reconstruction_list)
dest['kspace'] = stacked_kspace
dest['reconstruction_esc'] = stacked_reconstruction_esc
dest['ismrmrd_header'] = orig['ismrmrd_header'][()]
dest.attrs['norm'] = np.linalg.norm(stacked_reconstruction_esc)
def __call__(self, kspace, mask, target, attrs, fname, slice_num):
"""
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_num (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.
fname (str): File name.
slice_num (int): Serial number of the slice.
"""
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 = fastmri.ifft2c(masked_kspace)
# crop input to correct size
if target is not None:
crop_size = (target.shape[-2], target.shape[-1])
else:
crop_size = (attrs["recon_size"][0], attrs["recon_size"][1])
# check for FLAIR 203
if image.shape[-2] < crop_size[1]:
crop_size = (image.shape[-2], image.shape[-2])
image = transforms.complex_center_crop(image, crop_size)
# absolute value
image = fastmri.complex_abs(image)
# apply Root-Sum-of-Squares if multicoil data
if self.which_challenge == "multicoil":
image = fastmri.rss(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_num
def __call__(
self,
kspace: np.ndarray,
mask: np.ndarray,
target: np.ndarray,
attrs: Dict,
fname: str,
slice_num: int,
) -> Tuple[torch.Tensor, torch.Tensor, torch.Tensor, torch.Tensor, str,
int, float]:
"""
Args:
kspace: Input k-space of shape (num_coils, rows, cols) for
multi-coil data or (rows, cols) for single coil data.
mask: Mask from the test dataset.
target: Target image.
attrs: Acquisition related information stored in the HDF5 object.
fname: File name.
slice_num: Serial number of the slice.
Returns:
tuple containing:
image: Zero-filled input image.
target: Target image converted to a torch.Tensor.
mean: Mean value used for normalization.
std: Standard deviation value used for normalization.
fname: File name.
slice_num: Serial number of the slice.
"""
kspace = T.to_tensor(kspace)
# check for max value
max_value = attrs["max"] if "max" in attrs.keys() else 0.0
# apply mask
if self.mask_func:
seed = None if not self.use_seed else tuple(map(ord, fname))
masked_kspace, mask = T.apply_mask(kspace, self.mask_func, seed)
else:
masked_kspace = kspace
# inverse Fourier transform to get zero filled solution
image = fastmri.ifft2c(masked_kspace)
if not self.test_mode:
# crop input to correct size
if target is not None:
crop_size = (target.shape[-2], target.shape[-1])
else:
crop_size = (attrs["recon_size"][0], attrs["recon_size"][1])
# check for FLAIR 203
if self.test_mode or image.shape[-2] < crop_size[1]:
crop_size = (image.shape[-2], image.shape[-2])
image = T.complex_center_crop(image, crop_size)
# absolute value
image = fastmri.complex_abs(image)
# apply Root-Sum-of-Squares if multicoil data
if self.which_challenge == "multicoil":
image = fastmri.rss(image)
# normalize input
image, mean, std = T.normalize_instance(image, eps=1e-11)
image = image.clamp(-6, 6)
# normalize target
if not self.test_mode and target is not None:
target = T.to_tensor(target)
target = T.center_crop(target, crop_size)
target = T.normalize(target, mean, std, eps=1e-11)
target = target.clamp(-6, 6)
else:
target = torch.Tensor([0])
return image, target, mean, std, fname, slice_num, max_value