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))
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)
image = image.clamp(-6, 6)
return image, mean, std, fname, slice
def __call__(self, kspace, target, attrs, fname, slice):
kspace_square = transforms.to_tensor(kspace) ##kspace
image_square = ifft_c3(kspace_square)
seed = None if not self.use_seed else tuple(map(ord, fname))
masked_kspace_square, mask = transforms.apply_mask2(
kspace_square, self.mask_func, seed) ##ZF square kspace
image_square_us = ifft_c3(
masked_kspace_square) ## US square complex imagea
sz = kspace_square.size
stacked_kspace_square = kspace_square.permute((0, 3, 1, 2)).reshape(
(-1, sz(-3), sz(-2)))
stacked_masked_kspace_square = masked_kspace_square.permute(
(0, 3, 1, 2)).reshape((-1, sz(-3), sz(-2)))
stacked_image_square = image_square.permute((0, 3, 1, 2)).reshape(
(-1, sz(-3), sz(-2)))
us_image_square_rss = torch.sqrt(
torch.sum(image_square_us**2, dim=(0, -1)))
image_square_rss = torch.sqrt(torch.sum(image_square**2, dim=(0, -1)))
return stacked_kspace_square,stacked_masked_kspace_square , stacked_image_square , \
us_image_square_rss , \
image_square_rss
mode = 'validation'
data_list = load_traindata_path(dataset_dir, name)
save_dir = '/media/htic/NewVolume3/Balamurali/knee_mri_vsnet/coronal_dp_h5/{}'.format(
mode)
#center_fract = 0.08
#acc = 4
#shape = [1,640,368,2]
#mask_func = MaskFunc(center_fractions=[center_fract], accelerations=[acc])
#mask = mask_func(shape) ##
#mask = T.ifftshift(mask)
mask_path = '/media/htic/NewVolume3/Balamurali/knee_mri_vsnet/coronal_pd/masks/random4_masks_640_368.mat'
mask = loadmat(mask_path)['mask']
maskT = T.to_tensor(mask)
for rawdata_name, coil_name, folder_name, file_name in tqdm(data_list[mode]):
rawdata = np.complex64(loadmat(rawdata_name)['rawdata']).transpose(2, 0, 1)
sensitivity = np.complex64(loadmat(coil_name)['sensitivities'])
rawdata2 = T.to_tensor(rawdata)
sensitivity2 = T.to_tensor(sensitivity.transpose(2, 0, 1))
img_und, img_gt, img_und_kspace, rawdata_und, masks, sensitivity = data_for_training(
rawdata2, sensitivity2, maskT)
#print (img_und.shape,img_gt.shape,img_und_kspace.shape,rawdata_und.shape,masks.shape,sensitivity.shape)
img_und_np = img_und.numpy()
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))
mask = transforms.get_mask(kspace, self.mask_func, seed)
masked_kspace = mask * kspace
# Inverse Fourier Transform to get zero filled solution
image_precrop = transforms.ifft2(masked_kspace)
masked_kspace, _, _ = transforms.normalize_instance_complex(
masked_kspace, eps=1e-11)
kspace, _, _ = transforms.normalize_instance_complex(kspace, eps=1e-11)
# Crop input image
image = transforms.complex_center_crop(
image_precrop, (self.resolution, self.resolution))
image_abs = transforms.complex_abs(image)
_, mean_abs, std_abs = transforms.normalize_instance(image_abs,
eps=1e-11)
# Normalize input
image, mean, std = transforms.normalize_instance_complex(image,
eps=1e-11)
image = image.clamp(-6, 6)
target = transforms.to_tensor(target)
target_train = target
if not TRAIN_COMPLEX:
# Normalize target
if RENORM:
target_train = transforms.normalize(target,
mean_abs,
std_abs,
eps=1e-11)
target_train = target_train.clamp(
-6, 6
) # Return target (for viz) and target_clamped (for training)
else:
target_train = transforms.ifft2(kspace)
target_train = transforms.complex_center_crop(
target_train, (self.resolution, self.resolution))
if RENORM:
target_train = transforms.normalize(target_train,
mean,
std,
eps=1e-11)
return image, target_train, mean, std, attrs['norm'].astype(
np.float32
), target, mean_abs, std_abs, kspace, masked_kspace, image_precrop
def find_unmask(mask):
unmask = np.where(mask == 1.0, 0.0, 1.0)
unmask = transforms.to_tensor(unmask)
unmask = unmask.float()
return unmask
def apply(self, ksp_torch):
ksp_npy = ksp_torch[:, :, 0].numpy() + 1j * ksp_torch[:, :, 1].numpy()
return transforms.to_tensor(randomflip(ksp_npy) *
self.translation()).float()
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_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 = transforms.fft2(image_square) ##kspace of square iamge
if self.augmentation:
kspace_square = self.augmentation.apply(kspace_square)
image_square = transforms.ifft2(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 = transforms.ifft2(
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, 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
image_square2 = ifft_c3(kspace_square) ##for training domain_transform
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)
us_image_square = 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)
us_image_square_abs = transforms.complex_abs(
us_image_square) ## US square real image
us_image_square_rss = transforms.root_sum_of_squares(
us_image_square_abs, dim=0)
stacked_kspace_square = []
for i in (range(len(kspace_square[:, 0, 0, 0]))):
stacked_kspace_square.append(kspace_square[i, :, :, 0])
stacked_kspace_square.append(kspace_square[i, :, :, 1])
stacked_kspace_square = torch.stack(stacked_kspace_square)
stacked_masked_kspace_square = []
# masked_kspace_square = transforms.to_tensor(masked_kspace_square)
# for i in range(len(masked_kspace_square[:,0,0,0])):
# stacked_masked_kspace_square.stack(masked_kspace_square[i,:,:,0],masked_kspace_square[i,:,:,1])
for i in (range(len(masked_kspace_square[:, 0, 0, 0]))):
stacked_masked_kspace_square.append(masked_kspace_square[i, :, :,
0])
stacked_masked_kspace_square.append(masked_kspace_square[i, :, :,
1])
stacked_masked_kspace_square = torch.stack(
stacked_masked_kspace_square)
stacked_image_square = []
for i in (range(len(image_square[:, 0, 0, 0]))):
stacked_image_square.append(image_square2[i, :, :, 0])
stacked_image_square.append(image_square2[i, :, :, 1])
stacked_image_square = torch.stack(stacked_image_square)
return stacked_kspace_square,stacked_masked_kspace_square , stacked_image_square , \
us_image_square_rss , \
target *10000 \
#mean, std, attrs['norm'].astype(np.float32)
'''
datadir = '../multicoil_val/multicoil_val/'
outdir = datadir+'/../multicoil_val2/'
completed = []
for fi in glob.glob(datadir+'/*.h5'):
with h5py.File(fi,'r') as h5:
print(fi)
volume_ksp = h5['kspace']
print(volume_ksp.shape,volume_ksp.dtype)
nslice,nch, ht, wd = volume_ksp.shape
if wd < shp[1]:
continue
for sl in range(2,nslice-2):
ksp = T.to_tensor(volume_ksp[sl])
sq = tosquare(ksp,shp)
with h5py.File('%s/%s-%.2d.h5' % (outdir,os.path.basename(fi)[:-3],sl),'w') as hw:
hw['kspace']=sq.numpy()
completed.append(fi)
if len(completed)%3==0:
for rfi in completed:
if os.path.exists(rfi):
os.unlink(rfi)
# break
def __call__(self, ksp_cmplx, fname, sensitivity, acceleration):
"""
Args:
kspace (numpy.array): Input k-space of the multi-coil data
fname (str): File name
sensitivity maps (numpy.array): ENLIVE sensitivity maps
acceleartion: whether to train for 5x US ksp or 10x US kspace
"""
sens_t = T.to_tensor(sensitivity)
ksp_t = T.to_tensor(ksp_cmplx)
ksp_t = ksp_t.permute(2, 0, 1, 3)
img_gt = T.ifft2(ksp_t)
img_gt_sens = T.combine_all_coils(img_gt, sens_t)
img_gt_np = T.zero_filled_reconstruction(ksp_cmplx)
if acceleration == 5:
if ksp_t.shape[2] == 170:
sp_r5 = np.load(
"/media/student1/NewVolume/MR_Reconstruction/midl/MC-MRRec-challenge/Data/poisson_sampling/R5_218x170.npy"
)
elif ksp_t.shape[2] == 174:
sp_r5 = np.load(
"/media/student1/NewVolume/MR_Reconstruction/midl/MC-MRRec-challenge/Data/poisson_sampling/R5_218x174.npy"
)
elif ksp_t.shape[2] == 180:
sp_r5 = np.load(
"/media/student1/NewVolume/MR_Reconstruction/midl/MC-MRRec-challenge/Data/poisson_sampling/R5_218x180.npy"
)
elif acceleration == 10:
if ksp_t.shape[2] == 170:
sp_r5 = np.load(
"/media/student1/NewVolume/MR_Reconstruction/midl/MC-MRRec-challenge/Data/poisson_sampling/R10_218x170.npy"
)
elif ksp_t.shape[2] == 174:
sp_r5 = np.load(
"/media/student1/NewVolume/MR_Reconstruction/midl/MC-MRRec-challenge/Data/poisson_sampling/R10_218x174.npy"
)
elif ksp_t.shape[2] == 180:
sp_r5 = np.load(
"/media/student1/NewVolume/MR_Reconstruction/midl/MC-MRRec-challenge/Data/poisson_sampling/R10_218x180.npy"
)
randint = random.randint(0, 99) #to get a random mask everytime !
mask = sp_r5[randint]
mask = torch.from_numpy(mask)
mask = (torch.stack((mask, mask), dim=-1)).float()
ksp_us = torch.where(mask == 0, torch.Tensor([0]), ksp_t)
img_us = T.ifft2(ksp_us)
img_us_sens = T.combine_all_coils(img_us, sens_t)
ksp_us_np = ksp_us.numpy()
ksp_us_cmplx = ksp_us_np[:, :, :, 0] + 1j * ksp_us_np[:, :, :, 1]
ksp_us_cmplx = ksp_us_cmplx.transpose(1, 2, 0)
img_us_np = T.zero_filled_reconstruction(ksp_us_cmplx)
pha_gt = T.phase(img_gt_sens)
pha_us = T.phase(img_us_sens)
pha_gt = pha_gt + 3.1415927410125732
pha_us = pha_us + 3.1415927410125732
mag_gt = T.complex_abs(img_gt_sens)
mag_us = T.complex_abs(img_us_sens)
mag_gt_pad = T.pad(mag_gt, [256, 256])
mag_us_pad = T.pad(mag_us, [256, 256])
pha_gt_pad = T.pad(pha_gt, [256, 256])
pha_us_pad = T.pad(pha_us, [256, 256])
return mag_us_pad / mag_us_pad.max(), mag_gt_pad / mag_us_pad.max(
), pha_us_pad, pha_gt_pad, ksp_us / mag_us_pad.max(
), img_us_sens / mag_us_pad.max(), img_gt_sens / mag_us_pad.max(
), img_us_np / img_us_np.max(), img_gt_np / img_us_np.max(
), sens_t, mask, img_us_np.max(), fname
file = '../fastMRIData/singlecoil_val/file1000000.h5'
hf = h5py.File(file)
print('Keys:', list(hf.keys()))
print('Attrs:', dict(hf.attrs))
volume_kspace = hf['kspace'][()]
print(volume_kspace.dtype)
print(volume_kspace.shape)
slice_kspace = volume_kspace # Choosing the 20-th slice of this volume
show_slices(np.log(np.abs(slice_kspace) + 1e-9), [0, 5, 10])
# In[9]:
slice_kspace2 = T.to_tensor(
slice_kspace) # Convert from numpy array to pytorch tensor
slice_image = T.ifft2(
slice_kspace2) # Apply Inverse Fourier Transform to get the complex image
slice_image_abs = T.complex_abs(
slice_image) # Compute absolute value to get a real image
# In[10]:
show_slices(slice_image_abs, [0, 5, 10], cmap='gray')
# As we can see, each slice in a multi-coil MRI scan focusses on a different region of the image. These slices can be combined into the full image using the Root-Sum-of-Squares (RSS) transform.
# In[11]:
slice_image_rss = T.root_sum_of_squares(slice_image_abs, dim=0)
def get_attack_loss_new(model, ori_target, loss_f=torch.nn.MSELoss(reduction='none'),
xs=np.random.randint(low=100, high=320-100, size=(16,)),
ys=np.random.randint(low=100, high=320-100, size=(16,)),
shape=(320, 320), n_pixel_range=(10, 11), train=False, optimizer=None):
input_o = ori_target.unsqueeze(1).to(args.device)
input_o = input_o.clone()
#input_o = transforms.complex_abs(ori_input.clone())
#input_o, mean, std = transforms.normalize_instance(ori_target.unsqueeze(1).clone())
#input_o = torch.clamp(input_o, -6, 6)
#perturb_noise = perturb_noise_init(x=x, y=y, shape=shape, n_pixel_range=n_pixel_range)
p_max = input_o.max().cpu()
#p_min = (p_max - input.min()) / 2
#p_min = (p_max - input_o.min())
p_min = input_o.min().cpu()
perturb_noise = [perturb_noise_init(x=x, y=y, shape=shape, n_pixel_range=n_pixel_range, pixel_value_range=(p_min, p_max)) for x, y in zip(xs, ys)]
perturb_noise = np.stack(perturb_noise)
# perturb the target to get the perturbed image
#perturb_noise = np.expand_dims(perturb_noise, axis=0)
#perturb_noise = np.stack((perturb_noise,)*ori_target.shape(0), -1)
seed = np.random.randint(999999999)
perturb_noise = transforms.to_tensor(perturb_noise).unsqueeze(1).to(args.device)
if not args.fnaf_eval_control:
input_o += perturb_noise
target = input_o.clone()
#print(input_o.shape)
input_o = np.complex64(input_o.cpu().numpy())
input_o = transforms.to_tensor(input_o)
input_o = transforms.fft2(input_o)
input_o, mask = transforms.apply_mask(input_o, mask_f, seed)
input_o = transforms.ifft2(input_o)
image = transforms.complex_abs(input_o).to(args.device)
image, mean, std = transforms.normalize_instance(image, eps=1e-11)
image = image.clamp(-6, 6)
target = transforms.normalize(target, mean, std, eps=1e-11)
target = target.clamp(-6, 6)
#information_loss = loss_f(og_image.squeeze(1), image.squeeze(1)).mean(-1).mean(-1).cpu().numpy()
#information_loss = np.array([0]*len(xs))
# apply the perturbed image to the model to get the loss
if train:
output = model(image).squeeze(1)
else:
with torch.no_grad():
output = model(image).squeeze(1)
#perturb_noise_tensor = transforms.to_tensor(perturb_noise).to(args.device, dtype=torch.double)
perturb_noise = perturb_noise.squeeze(1)
perturb_noise_tensor = perturb_noise
perturb_noise = perturb_noise.cpu().numpy()
mask = adjusted_mask((perturb_noise > 0).astype(np.double))
#mask = (perturb_noise > 0).astype(np.double)
target = target.squeeze(1)
mask_0 = transforms.to_tensor(mask).to(args.device)
loss = loss_f((output*mask_0), (target*mask_0))
if train:
b_loss = loss.sum() / mask_0.sum() * 1 + loss_f(output, target).mean()
b_loss.backward()
optimizer.step()
loss = loss.detach()
loss = loss.mean(-1).mean(-1).cpu().numpy()
#loss = loss.mean(-1).mean(-1).numpy()
# information_loss_list.append(information_loss)
# xs_list.append(xs)
# ys_list.append(ys)
return loss
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 = transforms.to_tensor(target)
kspace = transforms.to_tensor(kspace)
# Apply mask
seed = None if not self.use_seed else tuple(map(ord, fname))
fn_image = 0
if args.fn_train:
#fn_image_kspace = kspace.clone()
fn_image = transforms.ifft2(kspace).clone()
# Crop input image to given resolution if larger
smallest_width = min(min(args.resolution, fn_image.shape[-2]), target.shape[-1])
smallest_height = min(min(args.resolution, fn_image.shape[-3]), target.shape[-2])
crop_size = (smallest_height, smallest_width)
fn_image = transforms.complex_center_crop(fn_image, crop_size)
# Absolute value
fn_image = transforms.complex_abs(fn_image)
# Apply Root-Sum-of-Squares if multicoil data
if self.which_challenge == 'multicoil':
fn_image = transforms.root_sum_of_squares(fn_image)
masked_kspace, mask = transforms.apply_mask(kspace, self.mask_func, seed)
# Inverse Fourier Transform to get zero filled solution
image = transforms.ifft2(masked_kspace)
# Crop input image to given resolution if larger
smallest_width = min(min(args.resolution, image.shape[-2]), target.shape[-1])
smallest_height = min(min(args.resolution, image.shape[-3]), target.shape[-2])
crop_size = (smallest_height, smallest_width)
image = transforms.complex_center_crop(image, crop_size)
target = transforms.center_crop(target, 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
target = transforms.normalize(target, mean, std, eps=1e-11)
target = target.clamp(-6, 6)
item = image, target, mean, std, attrs['norm'].astype(np.float32)
if args.fn_train:
item = image, target, mean, std, attrs['norm'].astype(np.float32), fn_image
return item
def to_k_space(image):
#image = image.numpy()
image = np.complex64(image)
image = transforms.to_tensor(image)
return transforms.fft2(image)
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
if self.normalize:
image, mean, std = transforms.normalize_instance(image, eps=1e-11)
if CLAMP:
image = image.clamp(-6, 6)
else:
mean = -1.0
std = -1.0
# Normalize target
if target is not None:
target = transforms.to_tensor(target)
target_train = target
if self.normalize:
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)
norm = attrs['norm'].astype(np.float32)
else:
target_train = []
target = []
norm = -1.0
image_updated = []
if os.path.exists(
'/home/manivasagam/code/fastMRIPrivate/models/unet_volumes/reconstructions_train/'
+ fname):
updated_fname = '/home/manivasagam/code/fastMRIPrivate/models/unet_volumes/reconstructions_train/' + fname
with h5py.File(updated_fname, 'r') as data:
image_updated = data['reconstruction'][slice]
image_updated = transforms.to_tensor(image_updated)
elif os.path.exists(
'/home/manivasagam/code/fastMRIPrivate/models/unet_volumes/reconstructions_val/'
+ fname):
updated_fname = '/home/manivasagam/code/fastMRIPrivate/models/unet_volumes/reconstructions_val/' + fname
with h5py.File(updated_fname, 'r') as data:
image_updated = data['reconstruction'][slice]
image_updated = transforms.to_tensor(image_updated)
elif os.path.exists(
'/home/manivasagam/code/fastMRIPrivate/models/unet_volumes/reconstructions_test/'
+ fname):
updated_fname = '/home/manivasagam/code/fastMRIPrivate/models/unet_volumes/reconstructions_test/' + fname
with h5py.File(updated_fname, 'r') as data:
image_updated = data['reconstruction'][slice]
image_updated = transforms.to_tensor(image_updated)
return image, target_train, mean, std, norm, target, image_updated
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)
gt = transforms.ifft2(kspace)
gt = transforms.complex_center_crop(gt, (self.resolution, self.resolution))
kspace = transforms.fft2(gt)
# Apply mask
seed = None if not self.use_seed else tuple(map(ord, fname))
masked_kspace, mask = transforms.apply_mask(kspace, self.mask_func, seed)
# Inverse Fourier Transform to get zero filled solution
image = transforms.ifft2(masked_kspace)
masked_kspace = transforms.fft2_nshift(image)
# Crop input image
image = transforms.complex_center_crop(image, (self.resolution, self.resolution))
# Absolute value
image_mod = transforms.complex_abs(image).max()
image_r = image[:, :, 0]*6.0/image_mod
image_i = image[:, :, 1]*6.0/image_mod
# image_r = image[:, :, 0]
# image_i = image[:, :, 1]
# Apply Root-Sum-of-Squares if multicoil data
if self.which_challenge == 'multicoil':
image = transforms.root_sum_of_squares(image)
# Normalize input
image = np.stack((image_r, image_i), axis=-1)
image = image.transpose((2, 0, 1))
image = transforms.to_tensor(image)
target = transforms.ifft2(kspace)
target = transforms.complex_center_crop(target, (self.resolution, self.resolution))
# Normalize target
target_r = target[:, :, 0]*6.0/image_mod
target_i = target[:, :, 1]*6.0/image_mod
# target_r = target[:, :, 0]
# target_i = target[:, :, 1]
target = np.stack((target_r, target_i), axis=-1)
target = target.transpose((2, 0, 1))
target = transforms.to_tensor(target)
image_mod = np.stack((image_mod, image_mod), axis=0)
image_mod = transforms.to_tensor(image_mod)
norm = attrs['norm'].astype(np.float32)
norm = np.stack((norm, norm), axis=-1)
norm = transforms.to_tensor(norm)
mask = mask.expand(kspace.shape)
mask = mask.transpose(0, 2).transpose(1, 2)
mask = transforms.ifftshift(mask)
masked_kspace = masked_kspace.transpose(0, 2).transpose(1, 2)
return image, target
