def __call__(self, kspace, target, attrs, file_name, slice_num):
"""
Args:
kspace (numpy.Array): k-space measurements
target (numpy.Array): Target image
attrs (dict): Acquisition related information stored in the HDF5 object
file_name (str): File name
slice_num (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
file_name (str): File name
slice_num (int): Serial number of the slice
"""
kspace = to_tensor(kspace)
if self.mask_func is not None: # Validation set
seed = tuple(map(ord, file_name))
masked_kspace, _ = apply_mask(kspace, self.mask_func, seed)
else: # Test set
masked_kspace = kspace
data = k_slice_to_chw(masked_kspace)
pad = (self.divisor - (data.shape[-1] % self.divisor)) // 2
pad = [pad, pad]
data = F.pad(data, pad=pad,
value=0) # This pads at the last dimension of a tensor.
return data
def __call__(self, k_slice, target, attrs, file_name, slice_num):
if k_slice.ndim == 2: # For singlecoil. Makes data processing later on much easier.
k_slice = np.expand_dims(k_slice, axis=0)
elif k_slice.ndim != 3: # Prevents possible errors.
raise TypeError('Invalid slice dimensions.')
# I hope that async copy works for passing between processes but I am not sure.
kspace_target = to_tensor(k_slice).to(device=self.device,
non_blocking=True)
# Necessary since None cannot pass the default collate function.
# Target must be sent to GPU for evaluation with outputs.
target = 0 if target is None else to_tensor(target).to(
device=self.device, non_blocking=True)
return kspace_target, target, attrs, file_name, slice_num
def __call__(self, k_slice, target, attrs, file_name, slice_num):
"""
Args:
k_slice (numpy.array): Input k-space of shape (num_coils, height, width) for multi-coil
data or (rows, cols) for single coil data.
target (numpy.array): Target (320x320) image. May be None.
attrs (dict): Acquisition related information stored in the HDF5 object.
file_name (str): File name
slice_num (int): Serial number of the slice.
Returns:
(tuple): tuple containing:
data (torch.Tensor): kspace data converted to CHW format for CNNs, where C=(2*num_coils).
Also has padding in the width axis for auto-encoders, which have down-sampling regions.
This requires the data to be divisible by some number (usually 2**num_pooling_layers).
Otherwise, concatenation will not work in the decoder due to different sizes.
Only the width dimension is padded in this case due to the nature of the dataset.
The height is fixed at 640, while the width is variable.
labels (torch.Tensor): Coil-wise ground truth images. Shape=(num_coils, H, W)
"""
assert np.iscomplexobj(k_slice), 'kspace must be complex.'
assert k_slice.shape[-1] % 2 == 0, 'k-space data width must be even.'
if k_slice.ndim == 2: # For singlecoil. Makes data processing later on much easier.
k_slice = np.expand_dims(k_slice, axis=0)
elif k_slice.ndim != 3: # Prevents possible errors.
raise TypeError('Invalid slice type')
with torch.no_grad(): # Remove unnecessary gradient calculations.
# Now a Tensor of (num_coils, height, width, 2), where 2 is (real, imag).
# The data is in the GPU and has been amplified by the amplification factor.
k_slice = to_tensor(k_slice).to(device=self.device) * self.amp_fac
# k_slice = to_tensor(k_slice).cuda(self.device) * self.amp_fac
target_slice = complex_abs(ifft2(k_slice)) # I need cuda here!
# Apply mask
seed = None if not self.use_seed else tuple(map(ord, file_name))
masked_kspace, mask = apply_mask(k_slice, self.mask_func, seed)
data_slice = k_slice_to_chw(masked_kspace)
# assert data_slice.size(-1) % 2 == 0
margin = (data_slice.shape[-1] % self.divisor)
if margin > 0:
pad = [(self.divisor - margin) // 2,
(1 + self.divisor - margin) // 2]
else: # This is a temporary fix.
pad = [0, 0]
# right_pad = self.divisor - left_pad
# pad = [pad, pad]
data_slice = F.pad(
data_slice, pad=pad,
value=0) # This pads at the last dimension of a tensor.
# Using the data acquisition method (fat suppression) may be useful later on.
# print(1, data_slice.size())
# print(2, target_slice.size())
return data_slice, target_slice
def __call__(self, k_slice, target, attrs, file_name, slice_num):
assert np.iscomplexobj(k_slice), 'kspace must be complex.'
if k_slice.ndim == 2: # For singlecoil. Makes data processing later on much easier.
k_slice = np.expand_dims(k_slice, axis=0)
elif k_slice.ndim != 3: # Prevents possible errors.
raise RuntimeError(
'Invalid slice shape. Please check input shape.')
with torch.no_grad(): # Remove unnecessary gradient calculations.
# Now a Tensor of (num_coils, height, width, 2), where 2 is (real, imag).
kspace_target = to_tensor(k_slice).to(device=self.device)
# Apply mask
seed = None if not self.use_seed else tuple(map(ord, file_name))
masked_kspace, mask = apply_mask(kspace_target, self.mask_func,
seed)
# Multiplying the whole tensor by 1/scaling is faster than dividing the whole tensor by scaling.
# Maybe call this scaling k_scale or something. Using scaling every time is confusing.
k_scale = torch.std(
masked_kspace) # Pseudo-standard deviation for normalization.
masked_kspace *= (torch.as_tensor(1) / k_scale
) # Standardization of CNN inputs.
# Performing log weighting for smoother inputs. It can be before padding since 0 will be 0 after weighting.
masked_kspace = log_weighting(k_slice_to_chw(masked_kspace),
scale=self.log_amp_scale)
margin = masked_kspace.size(-1) % self.divisor
if margin > 0:
pad = [(self.divisor - margin) // 2,
(1 + self.divisor - margin) // 2]
else: # This is a temporary fix to prevent padding by half the divisor when margin=0.
pad = [0, 0]
# This pads at the last dimension of a tensor with 0.
masked_kspace = F.pad(masked_kspace, pad=pad, value=0)
return masked_kspace, kspace_target, (k_scale, mask)
def __call__(self, k_slice, target, attrs, file_name, slice_num):
assert np.iscomplexobj(k_slice), 'kspace must be complex.'
# assert k_slice.shape[-1] % 2 == 0, 'k-space data width must be even.'
if k_slice.ndim == 2: # For singlecoil. Makes data processing later on much easier.
k_slice = np.expand_dims(k_slice, axis=0)
elif k_slice.ndim != 3: # Prevents possible errors.
raise RuntimeError(
'Invalid slice shape. Please check input shape.')
with torch.no_grad(): # Remove unnecessary gradient calculations.
# Now a Tensor of (num_coils, height, width, 2), where 2 is (real, imag).
k_slice = to_tensor(k_slice).to(device=self.device)
scaling = torch.std(
k_slice) # Pseudo-standard deviation for normalization.
target_slice = complex_abs(
ifft2(k_slice)) # Labels are not standardized.
k_slice *= (torch.ones(
()) / scaling) # Standardization of CNN inputs.
# Using weird multiplication because multiplication is much faster than division.
# Multiplying the whole tensor by 1/scaling is faster than dividing the whole tensor by scaling.
# Apply mask
seed = None if not self.use_seed else tuple(map(ord, file_name))
masked_kspace, mask = apply_mask(k_slice, self.mask_func, seed)
data_slice = k_slice_to_chw(masked_kspace)
margin = data_slice.size(-1) % self.divisor
if margin > 0:
pad = [(self.divisor - margin) // 2,
(1 + self.divisor - margin) // 2]
else: # This is a temporary fix to prevent padding by half the divisor when margin=0.
pad = [0, 0]
data_slice = F.pad(
data_slice, pad=pad,
value=0) # This pads at the last dimension of a tensor with 0.
return data_slice, target_slice, scaling # This has a different output API.
def __call__(self, k_slice, target, attrs, file_name, slice_num):
assert np.iscomplexobj(k_slice), 'kspace must be complex.'
if k_slice.ndim == 2: # For singlecoil. Makes data processing later on much easier.
k_slice = np.expand_dims(k_slice, axis=0)
elif k_slice.ndim != 3: # Prevents possible errors.
raise RuntimeError(
'Invalid slice shape. Please check input shape.')
with torch.no_grad(): # Remove unnecessary gradient calculations.
# Now a Tensor of (num_coils, height, width, 2), where 2 is (real, imag).
kspace_target = to_tensor(k_slice).to(device=self.device)
c_img_target = k_slice_to_chw(
ifft2(kspace_target)) # Assumes only C2C will be calculated.
# Apply mask
seed = None if not self.use_seed else tuple(map(ord, file_name))
masked_kspace, mask = apply_mask(kspace_target, self.mask_func,
seed)
c_img_input = k_slice_to_chw(ifft2(masked_kspace))
c_scale = torch.std(c_img_input)
c_img_input *= (torch.tensor(1) / c_scale)
c_bias = torch.mean(c_img_input)
c_img_input -= c_bias
margin = c_img_input.size(-1) % self.divisor
if margin > 0: # Cut off instead of adding padding.
left = margin // 2
right = (margin + 1) // 2
assert c_img_input.size() == c_img_target.size()
c_img_input = c_img_input[..., left:-right]
c_img_target = c_img_target[..., left:-right]
assert c_img_input.size() == c_img_target.size()
return c_img_input, c_img_target, (c_scale, c_bias)
from data.data_transforms import kspace_to_nchw, nchw_to_kspace, to_tensor, k_slice_to_chw
import numpy as np
import torch
from time import time
k1 = np.random.uniform(size=(32, 15, 640, 328))
k2 = np.random.uniform(size=(32, 15, 640, 328))
k = k1 + k2 * 1j
kt = to_tensor(k)
tic = time()
ncwh = kspace_to_nchw(kt)
mid = kt.shape[1]
for idx, kts in enumerate(kt):
temp = k_slice_to_chw(kts)
print(idx, torch.eq(ncwh[idx], temp).all())
chan = 17
ri = chan % 2
sli = chan // 2
print(
torch.eq(torch.squeeze(ncwh[3, chan, ...]),
torch.squeeze(kt[3, sli, ..., ri])).all())
kspace = nchw_to_kspace(ncwh)
toc = time() - tic
print(torch.eq(kt, kspace).all(), toc)
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))
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))