def forward(self, img_output, targets, extra_params):
if img_output.size(0) > 1:
raise NotImplementedError('Only one at a time for now.')
img_target = targets['img_targets']
# For removing width dimension padding. Recall that complex number form has 2 as last dim size.
left = (img_output.size(-1) - img_target.size(-1)) // 2
right = left + img_target.size(-1)
# Cropping width dimension by pad.
img_recon = F.relu(
img_output[..., left:right]
) # Removing values below 0, which are impossible anyway.
assert img_recon.shape == img_target.shape, 'Reconstruction and target sizes are different.'
recons = {'img_recons': img_recon}
if self.challenge == 'multicoil':
rss_recon = center_crop(img_recon, (
self.resolution, self.resolution)) * extra_params['img_scales']
rss_recon = root_sum_of_squares(rss_recon, dim=1).squeeze()
recons['rss_recons'] = rss_recon
return recons # recons are not rescaled except rss_recons.
def forward(self, cmg_output, targets, extra_params):
if cmg_output.size(0) > 1:
raise NotImplementedError('Only one at a time for now.')
cmg_target = targets['cmg_targets']
cmg_recon = nchw_to_kspace(cmg_output)
assert cmg_recon.shape == cmg_target.shape, 'Reconstruction and target sizes are different.'
assert (cmg_recon.size(-3) % 2 == 0) and (cmg_recon.size(-2) % 2 == 0), \
'Not impossible but not expected to have sides with odd lengths.'
if self.residual_acs: # Adding the semi-k-space of the ACS as a residual. Necessary due to complex cropping.
raise NotImplementedError('Not ready yet.')
# cmg_acs = targets['cmg_acss']
# cmg_recon = cmg_recon + cmg_acs
kspace_recon = fft2(cmg_recon)
img_recon = complex_abs(cmg_recon)
recons = {
'kspace_recons': kspace_recon,
'cmg_recons': cmg_recon,
'img_recons': img_recon
}
if self.challenge == 'multicoil':
rss_recon = center_crop(img_recon, (
self.resolution, self.resolution)) * extra_params['cmg_scales']
rss_recon = root_sum_of_squares(rss_recon, dim=1).squeeze()
recons['rss_recons'] = rss_recon
return recons # recons are not rescaled except rss_recons.
def forward(self, outputs, targets, extra_params):
img_recon, phase_recon = outputs
if img_recon.size(0) > 1:
raise NotImplementedError('Only one at a time for now.')
img_target = targets['img_targets']
img_recon = F.relu(img_recon) # img_recons must be positive numbers.
assert img_recon.shape == img_target.shape, 'Reconstruction and target sizes are different.'
# Input transform had addition of pi as pre-processing.
phase_recon = phase_recon - math.pi # No clamping implemented since the loss is MSE.
cmg_recon = torch.stack([
img_recon * torch.cos(phase_recon),
img_recon * torch.sin(phase_recon)
],
dim=-1)
kspace_recon = fft2(cmg_recon)
recons = {
'img_recons': img_recon,
'phase_recons': phase_recon,
'cmg_recons': cmg_recon,
'kspace_recons': kspace_recon
}
if self.challenge == 'multicoil':
rss_recon = center_crop(
img_recon,
shape=(self.resolution,
self.resolution)) * extra_params['img_scales']
rss_recon = root_sum_of_squares(rss_recon, dim=1).squeeze()
recons['rss_recons'] = rss_recon
return recons # recons are not rescaled except rss_recons.
def __call__(self, masked_kspace, target, attrs, file_name, slice_num):
assert isinstance(
masked_kspace, torch.Tensor
), 'k-space target was expected to be a Pytorch Tensor.'
if masked_kspace.dim(
) == 3: # If the collate function does not expand dimensions for single-coil.
masked_kspace = masked_kspace.expand(1, 1, -1, -1, -1)
elif masked_kspace.dim(
) == 4: # If the collate function does not expand dimensions for multi-coil.
masked_kspace = masked_kspace.expand(1, -1, -1, -1, -1)
elif masked_kspace.dim(
) != 5: # Expanded k-space should have 5 dimensions.
raise RuntimeError('k-space target has invalid shape!')
if masked_kspace.size(0) != 1:
raise NotImplementedError('Batch size should be 1 for now.')
with torch.no_grad():
input_image = complex_abs(ifft2(masked_kspace))
# Cropping is mandatory if RSS means the 320 version. Not so if a larger image is used.
# However, I think that removing target processing is worth the loss of flexibility.
input_image = center_crop(input_image,
shape=(self.resolution, self.resolution))
img_scale = torch.std(input_image)
input_image /= img_scale
extra_params = {'img_scales': img_scale}
extra_params.update(attrs)
# Use plurals as keys to reduce confusion.
input_rss = root_sum_of_squares(input_image, dim=1).squeeze()
targets = {'img_inputs': input_image, 'rss_inputs': input_rss}
return input_image, targets, extra_params
def forward(self, semi_kspace_outputs, targets, extra_params):
if semi_kspace_outputs.size(0) > 1:
raise NotImplementedError('Only one at a time for now.')
semi_kspace_targets = targets['semi_kspace_targets']
# For removing width dimension padding. Recall that k-space form has 2 as last dim size.
left = (semi_kspace_outputs.size(-1) -
semi_kspace_targets.size(-2)) // 2
right = left + semi_kspace_targets.size(-2)
# Cropping width dimension by pad.
semi_kspace_recons = nchw_to_kspace(semi_kspace_outputs[...,
left:right])
assert semi_kspace_recons.shape == semi_kspace_targets.shape, 'Reconstruction and target sizes are different.'
assert (semi_kspace_recons.size(-3) % 2 == 0) and (semi_kspace_recons.size(-2) % 2 == 0), \
'Not impossible but not expected to have sides with odd lengths.'
# Removing weighting.
if self.weighted:
weighting = extra_params['weightings']
semi_kspace_recons = semi_kspace_recons / weighting
if self.residual_acs:
num_low_freqs = extra_params['num_low_frequency']
acs_mask = find_acs_mask(semi_kspace_recons, num_low_freqs)
semi_kspace_recons = semi_kspace_recons + acs_mask * semi_kspace_targets
if self.replace:
mask = extra_params['masks']
semi_kspace_recons = semi_kspace_recons * (
1 - mask) + semi_kspace_targets * mask
kspace_recons = fft1(semi_kspace_recons, direction='height')
cmg_recons = ifft1(semi_kspace_recons, direction='width')
img_recons = complex_abs(cmg_recons)
recons = {
'semi_kspace_recons': semi_kspace_recons,
'kspace_recons': kspace_recons,
'cmg_recons': cmg_recons,
'img_recons': img_recons
}
if self.challenge == 'multicoil':
rss_recons = center_crop(img_recons,
(self.resolution, self.resolution))
rss_recons = root_sum_of_squares(rss_recons, dim=1).squeeze()
rss_recons *= extra_params[
'sk_scales'] # This value was divided in the inputs. It is thus multiplied here.
recons['rss_recons'] = rss_recons
return recons # Returning scaled reconstructions. Not rescaled. RSS images are rescaled.
def forward(self, img_output, targets, extra_params):
if img_output.size(0) > 1:
raise NotImplementedError('Only one at a time for now.')
# Removing values below 0, which are impossible anyway.
img_recon = F.relu(
center_crop(img_output, shape=(self.resolution, self.resolution)))
img_recon *= extra_params['img_scales']
if self.challenge == 'multicoil':
img_recon = root_sum_of_squares(img_recon, dim=1)
return img_recon.squeeze()
def forward(self, kspace_outputs, targets, extra_params):
if kspace_outputs.size(0) > 1:
raise NotImplementedError('Only one slice at a time for now.')
kspace_targets = targets['kspace_targets']
# For removing width dimension padding. Recall that k-space form has 2 as last dim size.
left = (kspace_outputs.size(-1) - kspace_targets.size(-2)) // 2
right = left + kspace_targets.size(-2)
# Cropping width dimension by pad.
kspace_recons = nchw_to_kspace(kspace_outputs[..., left:right])
assert kspace_recons.shape == kspace_targets.shape, 'Reconstruction and target sizes are different.'
assert (kspace_recons.size(-3) % 2 == 0) and (kspace_recons.size(-2) % 2 == 0), \
'Not impossible but not expected to have sides with odd lengths.'
# Removing weighting.
if self.weighted:
weighting = extra_params['weightings']
kspace_recons = kspace_recons / weighting
if self.residual_acs:
num_low_freqs = extra_params['num_low_frequency']
acs_mask = find_acs_mask(kspace_recons, num_low_freqs)
kspace_recons = kspace_recons + acs_mask * kspace_targets
if self.replace: # Replace with original k-space if replace=True
mask = extra_params['masks']
kspace_recons = kspace_recons * (1 - mask) + kspace_targets * mask
cmg_recons = ifft2(kspace_recons)
img_recons = complex_abs(cmg_recons)
recons = {
'kspace_recons': kspace_recons,
'cmg_recons': cmg_recons,
'img_recons': img_recons
}
if img_recons.size(1) == 15:
top = (img_recons.size(-2) - self.resolution) // 2
left = (img_recons.size(-1) - self.resolution) // 2
rss_recon = img_recons[:, :, top:top + self.resolution,
left:left + self.resolution]
rss_recon = root_sum_of_squares(
rss_recon, dim=1).squeeze() # rss_recon is in 2D
recons['rss_recons'] = rss_recon
return recons # Returning scaled reconstructions. Not rescaled.
def forward(self, semi_kspace_output: Tensor, targets: dict,
extra_params: dict):
assert semi_kspace_output.dim() == 5 and semi_kspace_output.size(
1) == 2, 'Invalid shape!'
if semi_kspace_output.size(0) > 1:
raise NotImplementedError('Only one at a time for now.')
semi_kspace_target = targets['semi_kspace_targets']
semi_kspace_recon = semi_kspace_output.permute(
dims=(0, 2, 3, 4, 1)) # Convert back into NCHW2
if semi_kspace_recon.shape != semi_kspace_target.shape: # Cropping recon left-right.
left = (semi_kspace_recon.size(-2) -
semi_kspace_target.size(-2)) // 2
semi_kspace_recon = semi_kspace_recon[
..., left:left + semi_kspace_target.size(-2), :]
assert semi_kspace_recon.shape == semi_kspace_target.shape, 'Reconstruction and target sizes are different.'
assert (semi_kspace_recon.size(-3) % 2 == 0) and (semi_kspace_recon.size(-2) % 2 == 0), \
'Not impossible but not expected to have sides with odd lengths.'
if self.weighted:
semi_kspace_recon = semi_kspace_recon / extra_params['weightings']
if self.replace:
mask = extra_params['masks']
semi_kspace_recon = semi_kspace_target * mask + (
1 - mask) * semi_kspace_recon
# kspace_recon = fft1(semi_kspace_recon, direction='height')
cmg_recon = ifft1(semi_kspace_recon, direction='width')
img_recon = complex_abs(cmg_recon)
recons = {
'semi_kspace_recons': semi_kspace_recon,
'cmg_recons': cmg_recon,
'img_recons': img_recon
}
if self.challenge == 'multicoil':
rss_recon = center_crop(
img_recon,
(self.resolution, self.resolution)) * extra_params['sk_scales']
rss_recon = root_sum_of_squares(rss_recon, dim=1).squeeze()
recons['rss_recons'] = rss_recon
return recons # recons are not rescaled except rss_recons.
def make_rss_slice(image, dim=1, resolution=320):
assert image.dim() == 4, 'Real-valued images are expected.'
if image.size(0) > 1:
raise NotImplementedError('Batch size is expected to be 1.')
top = (image.size(-2) - resolution) // 2
left = (image.size(-1) - resolution) // 2
image = image.detach()[:, :, top:top + resolution, left:left + resolution]
if image.size(1) == 1: # Single-coil
return image.squeeze().to(device='cpu', non_blocking=True)
elif image.size(1) != 15:
raise ValueError('Invalid number of coils for this dataset.')
rss = root_sum_of_squares(image, dim=dim).squeeze()
return rss.to(device='cpu', non_blocking=True)
def forward(self, output, targets, extra_params):
if output.size(0) > 1:
raise NotImplementedError('Batch size is expected to be 1.')
if self.output_mode == 'cmg':
recons = self._cmg_output(output, targets, extra_params)
elif self.output_mode == 'img':
recons = self._img_output(output, targets, extra_params)
else:
raise NotImplementedError('Invalid output mode.')
if self.challenge == 'multicoil':
rss_recon = center_crop(recons['img_recons'],
shape=(self.resolution, self.resolution))
rss_recon *= extra_params['cmg_scales']
rss_recon = root_sum_of_squares(rss_recon, dim=1).squeeze()
recons['rss_recons'] = rss_recon
return recons
def forward(self, semi_kspace_outputs, targets, extra_params):
if semi_kspace_outputs.size(0) > 1:
raise NotImplementedError('Only one at a time for now.')
semi_kspace_recons = nchw_to_kspace(semi_kspace_outputs)
semi_kspace_targets = targets['semi_kspace_targets']
assert semi_kspace_recons.shape == semi_kspace_targets.shape, 'Reconstruction and target sizes are different.'
assert (semi_kspace_recons.size(-3) % 2 == 0) and (semi_kspace_recons.size(-2) % 2 == 0), \
'Not impossible but not expected to have sides with odd lengths.'
# Removing weighting.
if self.weighted:
weighting = extra_params['weightings']
semi_kspace_recons = semi_kspace_recons / weighting
if self.residual_acs: # Adding the semi-k-space of the ACS as a residual. Necessary due to complex cropping.
semi_kspace_acs = targets['semi_kspace_acss']
semi_kspace_recons = semi_kspace_recons + semi_kspace_acs
kspace_recons = fft1(semi_kspace_recons, direction='height')
cmg_recons = ifft1(semi_kspace_recons, direction='width')
img_recons = complex_abs(cmg_recons)
recons = {
'semi_kspace_recons': semi_kspace_recons,
'kspace_recons': kspace_recons,
'cmg_recons': cmg_recons,
'img_recons': img_recons
}
if self.challenge == 'multicoil':
rss_recons = root_sum_of_squares(img_recons, dim=1).squeeze()
rss_recons *= extra_params['sk_scales']
recons['rss_recons'] = rss_recons
return recons # Returning scaled reconstructions. Not rescaled. RSS images are rescaled.
def test_root_sum_of_squares(shape, dim):
tensor = create_tensor(shape)
out_torch = data_transforms.root_sum_of_squares(tensor, dim).numpy()
out_numpy = np.sqrt(np.sum(tensor.numpy()**2, dim))
assert np.allclose(out_torch, out_numpy)
def __call__(self, kspace_target, target, attrs, file_name, slice_num):
assert isinstance(
kspace_target, torch.Tensor
), 'k-space target was expected to be a Pytorch Tensor.'
if kspace_target.dim(
) == 3: # If the collate function does not expand dimensions for single-coil.
kspace_target = kspace_target.expand(1, 1, -1, -1, -1)
elif kspace_target.dim(
) == 4: # If the collate function does not expand dimensions for multi-coil.
kspace_target = kspace_target.expand(1, -1, -1, -1, -1)
elif kspace_target.dim(
) != 5: # Expanded k-space should have 5 dimensions.
raise RuntimeError('k-space target has invalid shape!')
if kspace_target.size(0) != 1:
raise NotImplementedError('Batch size should be 1 for now.')
with torch.no_grad():
# Apply mask
seed = None if not self.use_seed else tuple(map(ord, file_name))
masked_kspace, mask, info = apply_info_mask(
kspace_target, self.mask_func, seed)
input_image = complex_abs(ifft2(masked_kspace))
# Cropping is mandatory if RSS means the 320 version. Not so if a larger image is used.
# However, I think that removing target processing is worth the loss of flexibility.
input_image = center_crop(input_image,
shape=(self.resolution, self.resolution))
img_scale = torch.std(input_image)
input_image /= img_scale
# No subtraction by the mean. I do not know if this is a good idea or not.
if self.use_patch:
assert self.resolution == 320
left = torch.randint(low=0,
high=self.resolution - self.patch_size,
size=(1, )).squeeze()
top = torch.randint(low=0,
high=self.resolution - self.patch_size,
size=(1, )).squeeze()
input_image = input_image[:, :, top:top + self.patch_size,
left:left + self.patch_size]
target = target[top:top + self.patch_size,
left:left + self.patch_size]
extra_params = {'img_scales': img_scale, 'masks': mask}
extra_params.update(info)
extra_params.update(attrs)
# Data augmentation by flipping images up-down and left-right.
if self.augment_data:
flip_lr = torch.rand(()) < 0.5
flip_ud = torch.rand(()) < 0.5
if flip_lr and flip_ud:
input_image = torch.flip(input_image, dims=(-2, -1))
target = torch.flip(target, dims=(-2, -1))
elif flip_ud:
input_image = torch.flip(input_image, dims=(-2, ))
target = torch.flip(target, dims=(-2, ))
elif flip_lr:
input_image = torch.flip(input_image, dims=(-1, ))
target = torch.flip(target, dims=(-1, ))
# Use plurals as keys to reduce confusion.
input_rss = root_sum_of_squares(input_image, dim=1).squeeze()
targets = {
'img_inputs': input_image,
'rss_targets': target,
'rss_inputs': input_rss
}
return input_image, targets, extra_params
import torch
import h5py
from data.data_transforms import ifft2, to_tensor, root_sum_of_squares, center_crop, complex_center_crop, complex_abs
file = '/media/veritas/D/FastMRI/multicoil_val/file1001798.h5'
sdx = 10
with h5py.File(file, mode='r') as hf:
kspace = hf['kspace'][sdx]
target = hf['reconstruction_rss'][sdx]
cmg_scale = 2E-5
recon = complex_center_crop(ifft2(to_tensor(kspace) / cmg_scale),
shape=(320, 320)) * cmg_scale
recon = root_sum_of_squares(complex_abs(recon))
target = to_tensor(target)
print(torch.allclose(recon, target))
def __call__(self, kspace_target, target, attrs, file_name, slice_num):
assert isinstance(
kspace_target, torch.Tensor
), 'k-space target was expected to be a Pytorch Tensor.'
if kspace_target.dim(
) == 3: # If the collate function does not expand dimensions for single-coil.
kspace_target = kspace_target.expand(1, 1, -1, -1, -1)
elif kspace_target.dim(
) == 4: # If the collate function does not expand dimensions for multi-coil.
kspace_target = kspace_target.expand(1, -1, -1, -1, -1)
elif kspace_target.dim(
) != 5: # Expanded k-space should have 5 dimensions.
raise RuntimeError('k-space target has invalid shape!')
if kspace_target.size(0) != 1:
raise NotImplementedError('Batch size should be 1 for now.')
with torch.no_grad():
# Apply mask
seed = None if not self.use_seed else tuple(map(ord, file_name))
masked_kspace, mask, info = apply_info_mask(
kspace_target, self.mask_func, seed)
input_image = complex_abs(ifft2(masked_kspace))
# Cropping is mandatory if RSS means the 320 version. Not so if a larger image is used.
# However, I think that removing target processing is worth the loss of flexibility.
input_image = center_crop(input_image,
shape=(self.resolution, self.resolution))
img_scale = torch.std(input_image)
input_image /= img_scale
extra_params = {'img_scales': img_scale, 'masks': mask}
extra_params.update(info)
extra_params.update(attrs)
if target is 0:
target = center_crop(
root_sum_of_squares(complex_abs(ifft2(kspace_target)),
dim=1),
shape=(self.resolution, self.resolution)).squeeze()
# Data augmentation by flipping images up-down and left-right.
if self.augment_data:
flip_lr = torch.rand(()) < 0.5
flip_ud = torch.rand(()) < 0.5
if flip_lr and flip_ud:
input_image = torch.flip(input_image, dims=(-2, -1))
target = torch.flip(target, dims=(-2, -1))
elif flip_ud:
input_image = torch.flip(input_image, dims=(-2, ))
target = torch.flip(target, dims=(-2, ))
elif flip_lr:
input_image = torch.flip(input_image, dims=(-1, ))
target = torch.flip(target, dims=(-1, ))
# Use plurals as keys to reduce confusion.
input_rss = root_sum_of_squares(input_image, dim=1).squeeze()
targets = {
'img_inputs': input_image,
'rss_targets': target,
'rss_inputs': input_rss
}
if self.fat_info:
fat_supp = extra_params[
'acquisition'] == 'CORPDFS_FBK' # Fat suppressed acquisition.
batch, _, height, width = input_image.shape
fat_info = torch.ones(size=(batch, 1, height, width),
device=self.device) * fat_supp
input_image = torch.cat([input_image, fat_info], dim=1)
return input_image, targets, extra_params
import torch
import h5py
import numpy as np
from data.data_transforms import root_sum_of_squares, center_crop, ifft2, to_tensor, complex_abs
file = '/media/veritas/D/FastMRI/multicoil_val/file1000229.h5'
with h5py.File(file, 'r') as hf:
kspace = hf['kspace'][()]
rss = hf['reconstruction_rss'][()]
kspace = to_tensor(kspace)
image = center_crop(root_sum_of_squares(complex_abs(ifft2(kspace)), dim=1),
shape=(320, 320)).squeeze().numpy()
print(np.allclose(image, rss))
