def train_epoch(model, optimizer, train_loader):
model.train()
avg_loss = 0.
start_epoch = start_iter = time.perf_counter()
for iteration, sample in enumerate(train_loader):
img_gt, img_und, rawdata_und, masks, norm = sample
# Extract input and ground truth image
input_img = T.complex_abs(img_und).squeeze()
input_img = T.center_crop(input_img, [320, 320])
input_img = input_img[None,None,:,:].cuda()
target_img = T.complex_abs(img_gt).squeeze()
target_img = T.center_crop(target_img, [320, 320])
target_img = target_img[None,None,:,:].cuda()
output = model(input_img)
loss = F.l1_loss(output, target_img)
#loss = ssim(target_img, output)
optimizer.zero_grad()
loss.backward()
optimizer.step()
avg_loss = 0.99 * avg_loss + 0.01 * loss.item() if iteration > 0 else loss.item()
return avg_loss, time.perf_counter() - start_epoch
def get_epoch_batch(subject_id, acc, center_fract, is_undersampled, use_seed=True):
''' random select a few slices (batch_size) from each volume'''
fname, rawdata_name, slice = subject_id
with h5py.File(rawdata_name, 'r') as data:
if(is_undersampled):
rawdata = data['kspace_8af'][slice]
else:
rawdata = data['kspace'][slice]
slice_kspace = T.to_tensor(rawdata).unsqueeze(0)
S, Ny, Nx, ps = slice_kspace.shape
# apply random mask
shape = np.array(slice_kspace.shape)
mask_func = MaskFunc(center_fractions=[center_fract], accelerations=[acc])
seed = None if not use_seed else tuple(map(ord, fname))
mask = mask_func(shape, seed)
# undersample
masked_kspace = torch.where(mask == 0, torch.Tensor([0]), slice_kspace)
masks = mask.repeat(S, Ny, 1, ps)
img_gt, img_und = T.ifft2(slice_kspace), T.ifft2(masked_kspace)
# perform data normalization which is important for network to learn useful features
# during inference there is no ground truth image so use the zero-filled recon to normalize
norm = T.complex_abs(img_und).max()
if norm < 1e-6: norm = 1e-6
# normalized data
img_gt, img_und, rawdata_und = img_gt/norm, img_und/norm, masked_kspace/norm
return img_gt.squeeze(0), img_und.squeeze(0), rawdata_und.squeeze(0), masks.squeeze(0), norm
def get_epoch_batch(subject_id, acc, center_fract, use_seed=True):
''' randomly select a few slices (batch_size) from each volume'''
fname, rawdata_name, slice = subject_id
with h5py.File(rawdata_name, 'r') as data:
rawdata = data['kspace'][slice]
slice_kspace = T.to_tensor(rawdata).unsqueeze(0)
S, Ny, Nx, ps = slice_kspace.shape
# apply random mask
shape = np.array(slice_kspace.shape)
mask_func = MaskFunc(center_fractions=[center_fract], accelerations=[acc])
seed = None if not use_seed else tuple(map(ord, fname))
mask = mask_func(shape, seed)
# undersample
masked_kspace = torch.where(mask == 0, torch.Tensor([0]), slice_kspace)
masks = mask.repeat(S, Ny, 1, ps)
# normalise data
img_gt, img_und = T.ifft2(slice_kspace), T.ifft2(masked_kspace)
norm = T.complex_abs(img_und).max()
if norm < 1e-6: norm = 1e-6
img_gt, img_und, rawdata_und = img_gt / norm, img_und / norm, masked_kspace / norm
return img_gt.squeeze(0), img_und.squeeze(0), rawdata_und.squeeze(
0), masks.squeeze(0), norm
def val_epoch(model, test_loader):
#Setting model to evaluation mode
model.eval()
start_epoch = start_iter = time.perf_counter()
losses = []
for iteration, sample in enumerate(test_loader):
img_gt, img_und, rawdata_und, masks, norm = sample
# Extract input and ground truth image
input_img = T.complex_abs(img_und).squeeze()
input_img = T.center_crop(input_img, [320, 320])
input_img = input_img[None,None,:,:].cuda()
target_img = T.complex_abs(img_gt).squeeze()
target_img = T.center_crop(target_img, [320, 320])
target_img = target_img[None,None,:,:].cuda()
output = model(input_img)
loss = F.l1_loss(output, target_img)
losses.append(loss.item())
return np.mean(losses), time.perf_counter() - start_epoch
def eval_model(model):
#Testing the trained model on test set - 20%
data_path = '/data/local/NC2019MRI/train/'
all_files = sorted(os.listdir(data_path))
#Using 20% of data as test set
all_files = all_files[round(len(all_files)*0.8):]
#acc and cent_fract should be (8, 0.04) or (4, 0.08)
acc = 8
cen_fract = 0.04
# random masks for each slice
seed = False
# data loading is faster using a bigger number for num_workers. 0 means using one cpu to load data
num_workers = 12
all_losses = []
for file in all_files:
# first load all file names, paths and slices.
data_list = load_test_data_path(data_path, file)
#Create a dataloader containing all slices for particular slice
test_dataset = MRIDataset(data_list['test'], acceleration=acc, center_fraction=cen_fract, use_seed=seed,is_undersampled=False)
test_loader = DataLoader(test_dataset, shuffle=False, batch_size=1, num_workers=num_workers)
#Call model over all slices. pred_vol is a list of volume slices (in correct order)
pred_vol,test_time = test_epoch(model, test_loader)
#3d Volume achieved by stacking slices
pred = torch.stack(pred_vol, dim=0)
#Loading Ground Truth
with h5py.File(data_path + file, "r") as hf:
volume_kspace = hf['kspace'][()]
#Transform k-space to real valued image
volume_kspace2 = T.to_tensor(volume_kspace)
# Apply Inverse Fourier Transform to get the complex image
volume_image = T.ifft2(volume_kspace2)
volume_image_abs = T.complex_abs(volume_image)
volume_image_abs = volume_image_abs[5:, :, :]
real_gt = T.center_crop(volume_image_abs, [320, 320])
#visualize predicted and gt slices
show_slices(pred, [5, 10, 20, pred.shape[0]-1], cmap='gray')
show_slices(real_gt, [5, 10, 20, pred.shape[0]-1], cmap='gray')
#calculate ssim score between volumes
ssim_score = ssim(real_gt.numpy(), pred.numpy())
all_losses.append(ssim_score)
average_ssim = sum(all_losses) / len(all_losses)
return average_ssim
def test_epoch(model, test_loader):
model.eval()
start_epoch = start_iter = time.perf_counter()
losses = []
output_vol = []
gt_vol = []
for iteration, sample in enumerate(test_loader):
img_gt, img_und, rawdata_und, masks, norm = sample
# Extract input and ground truth image
input_img = T.complex_abs(img_und).squeeze()
input_img = T.center_crop(input_img, [320, 320])
input_img = input_img[None,None,:,:].cuda()
output = model(input_img)
output = output[0,0,:,:].cpu().detach()
output_vol.append(output*norm)
#return np.mean(losses), time.perf_counter() - start_epoch
return output_vol, time.perf_counter() - start_epoch
fig = plt.figure(figsize=(15,10))
for i, num in enumerate(slice_nums):
plt.subplot(1, len(slice_nums), i + 1)
plt.imshow(data[num], cmap=cmap)
plt.axis('off')
plt.show()
show_slices(np.log(np.abs(volume_kspace) + 1e-9), [0, 10, 20, 30], cmap='gray')
# Show slices in the sample as real images
from functions import transforms as T
volume_kspace2 = T.to_tensor(volume_kspace)
volume_image = T.ifft2(volume_kspace2)
volume_image_abs = T.complex_abs(volume_image)
show_slices(volume_image_abs, [0, 10, 20, 30], cmap='gray')
##
## Simulate under-sample data
##
import torch
from functions.subsample import MaskFunc
# Initiate MaskFunc() for 2 AF respectively
mask_func0 = MaskFunc(center_fractions=[0.08], accelerations=[4])
mask_func1 = MaskFunc(center_fractions=[0.04], accelerations=[8])
# See subsample.py for detailed annotation for class MaskFunc().
acc = 8
cen_fract = 0.04
seed = False # random masks for each slice
num_workers = 12 # data loading workers
# create data loader for training set/ validation set
train_dataset = MRIDataset(data_list['train'],
acceleration=acc,
center_fraction=cen_fract,
use_seed=seed)
train_loader = DataLoader(train_dataset,
shuffle=True,
batch_size=1,
num_workers=num_workers)
for iteration, sample in enumerate(train_loader):
img_gt, img_und, rawdata_und, masks, norm = sample
# stack different slices into a volume for visualisation
A = masks[..., 0].squeeze()
B = torch.log(T.complex_abs(rawdata_und) + 1e-9).squeeze()
C = T.complex_abs(img_und).squeeze()
D = T.complex_abs(img_gt).squeeze()
all_imgs = torch.stack([A, B, C, D], dim=0)
# mask, masked space, undersampled image, ground truth
show_slices(all_imgs, [0, 1, 2, 3], cmap='gray')
plt.pause(1)
if iteration >= 3: break # to show 4 random slices