def __init__(
self,
image_size=IMAGE_SIZE,
acq_type='radial',
dcomp=True,
scale_factor=1e6,
traj=None,
crop_image_data=False,
**kwargs,
):
self.image_size = image_size
self.acq_type = acq_type
self.traj = traj
self._check_acq_type()
self.dcomp = dcomp
self.scale_factor = scale_factor
self.crop_image_data = crop_image_data
self.nufft_obj = KbNufftModule(
im_size=self.image_size,
grid_size=None,
norm='ortho',
)
super(NonCartesianFastMRIDatasetBuilder, self).__init__(
**kwargs,
)
if self.brain:
raise ValueError(
'Currently the non cartesian data works only with knee data.')
self._check_mode()
self._check_dcomp_multicoil()
def test_adjoint_and_gradients(im_size, batch_size):
tf.random.set_seed(0)
grid_size = tuple(np.array(im_size) * 2)
im_rank = len(im_size)
M = im_size[0] * 2**im_rank
nufft_ob = KbNufftModule(im_size=im_size,
grid_size=grid_size,
norm='ortho',
grad_traj=True)
# Generate Trajectory
ktraj_ori = tf.Variable(
tf.random.uniform(
(batch_size, im_rank, M), minval=-1 / 2, maxval=1 / 2) * 2 * np.pi)
# Have a random signal
signal = tf.Variable(
tf.cast(tf.random.uniform((batch_size, 1, *im_size)), tf.complex64))
kdata = tf.Variable(
kbnufft_forward(nufft_ob._extract_nufft_interpob())(signal, ktraj_ori))
Idata = tf.Variable(
kbnufft_adjoint(nufft_ob._extract_nufft_interpob())(kdata, ktraj_ori))
ktraj_noise = np.copy(ktraj_ori)
ktraj_noise += 0.01 * tf.Variable(
tf.random.uniform(
(batch_size, im_rank, M), minval=-1 / 2, maxval=1 / 2) * 2 * np.pi)
ktraj = tf.Variable(ktraj_noise)
with tf.GradientTape(persistent=True) as g:
I_nufft = kbnufft_adjoint(nufft_ob._extract_nufft_interpob())(kdata,
ktraj)
A = get_fourier_matrix(ktraj, im_size, im_rank, do_ifft=True)
I_ndft = tf.reshape(tf.transpose(tf.matmul(kdata, A), [0, 1, 2]),
(batch_size, 1, *im_size))
loss_nufft = tf.math.reduce_mean(tf.abs(Idata - I_nufft)**2)
loss_ndft = tf.math.reduce_mean(tf.abs(Idata - I_ndft)**2)
tf_test = tf.test.TestCase()
# Test if the NUFFT and NDFT operation is same
tf_test.assertAllClose(I_nufft, I_ndft, atol=2e-3)
# Test gradients with respect to kdata
gradient_ndft_kdata = g.gradient(I_ndft, kdata)[0]
gradient_nufft_kdata = g.gradient(I_nufft, kdata)[0]
tf_test.assertAllClose(gradient_ndft_kdata,
gradient_nufft_kdata,
atol=6e-3)
# Test gradients with respect to trajectory location
gradient_ndft_traj = g.gradient(I_ndft, ktraj)[0]
gradient_nufft_traj = g.gradient(I_nufft, ktraj)[0]
tf_test.assertAllClose(gradient_ndft_traj, gradient_nufft_traj, atol=6e-3)
# Test gradients in chain rule with respect to ktraj
gradient_ndft_loss = g.gradient(loss_ndft, ktraj)[0]
gradient_nufft_loss = g.gradient(loss_nufft, ktraj)[0]
tf_test.assertAllClose(gradient_ndft_loss, gradient_nufft_loss, atol=5e-4)
def __init__(self, multicoil=False, im_size=(640, 472), density_compensation=False, **kwargs):
super(NFFTBase, self).__init__(**kwargs)
self.multicoil = multicoil
self.im_size = im_size
self.nufft_ob = KbNufftModule(
im_size=im_size,
grid_size=None,
norm='ortho',
)
self.density_compensation = density_compensation
self.forward_op = kbnufft_forward(self.nufft_ob._extract_nufft_interpob())
self.backward_op = kbnufft_adjoint(self.nufft_ob._extract_nufft_interpob())
def test_adjoint_gradient():
traj = ktraj_function()
kspace = tf.zeros([1, 1, kspace_shape], dtype=tf.complex64)
nufft_ob = KbNufftModule(
im_size=(640, 400),
grid_size=None,
norm='ortho',
)
backward_op = kbnufft_adjoint(nufft_ob._extract_nufft_interpob())
with tf.GradientTape() as tape:
tape.watch(kspace)
res = backward_op(kspace, traj)
grad = tape.gradient(res, kspace)
tf_test = tf.test.TestCase()
tf_test.assertEqual(grad.shape, kspace.shape)
def test_forward_gradient():
traj = ktraj_function()
image = tf.zeros([1, 1, *image_shape], dtype=tf.complex64)
nufft_ob = KbNufftModule(
im_size=(640, 400),
grid_size=None,
norm='ortho',
)
forward_op = kbnufft_forward(nufft_ob._extract_nufft_interpob())
with tf.GradientTape() as tape:
tape.watch(image)
res = forward_op(image, traj)
grad = tape.gradient(res, image)
tf_test = tf.test.TestCase()
tf_test.assertEqual(grad.shape, image.shape)
def setup():
spokelength = 400
grid_size = (spokelength, spokelength)
nspokes = 10
ga = np.deg2rad(180 / ((1 + np.sqrt(5)) / 2))
kx = np.zeros(shape=(spokelength, nspokes))
ky = np.zeros(shape=(spokelength, nspokes))
ky[:, 0] = np.linspace(-np.pi, np.pi, spokelength)
for i in range(1, nspokes):
kx[:, i] = np.cos(ga) * kx[:, i - 1] - np.sin(ga) * ky[:, i - 1]
ky[:, i] = np.sin(ga) * kx[:, i - 1] + np.cos(ga) * ky[:, i - 1]
ky = np.transpose(ky)
kx = np.transpose(kx)
ktraj = np.stack((ky.flatten(), kx.flatten()), axis=0)
im_size = (200, 200)
nufft_ob = KbNufftModule(im_size=im_size,
grid_size=grid_size,
norm='ortho')
torch_forward = KbNufft(im_size=im_size, grid_size=grid_size, norm='ortho')
torch_backward = AdjKbNufft(im_size=im_size,
grid_size=grid_size,
norm='ortho')
return ktraj, nufft_ob, torch_forward, torch_backward
def profile_tfkbnufft(
image,
ktraj,
im_size,
device,
):
if device == 'CPU':
num_nuffts = 20
else:
num_nuffts = 50
print(f'Using {device}')
device_name = f'/{device}:0'
with tf.device(device_name):
image = tf.constant(image)
if device == 'GPU':
image = tf.cast(image, tf.complex64)
ktraj = tf.constant(ktraj)
nufft_ob = KbNufftModule(im_size=im_size, grid_size=None, norm='ortho')
forward_op = kbnufft_forward(nufft_ob._extract_nufft_interpob())
adjoint_op = kbnufft_adjoint(nufft_ob._extract_nufft_interpob())
# warm-up computation
for _ in range(2):
y = forward_op(image, ktraj)
start_time = time.perf_counter()
for _ in range(num_nuffts):
y = forward_op(image, ktraj)
end_time = time.perf_counter()
avg_time = (end_time - start_time) / num_nuffts
print('forward average time: {}'.format(avg_time))
# warm-up computation
for _ in range(2):
x = adjoint_op(y, ktraj)
# run the adjoint speed tests
start_time = time.perf_counter()
for _ in range(num_nuffts):
x = adjoint_op(y, ktraj)
end_time = time.perf_counter()
avg_time = (end_time - start_time) / num_nuffts
print('backward average time: {}'.format(avg_time))
def test_ncpdnet_init_and_call_3d(dcomp, volume_shape):
model = NCPDNet(
n_iter=1,
n_primal=2,
n_filters=2,
multicoil=False,
im_size=volume_shape,
three_d=True,
dcomp=dcomp,
fastmri=False,
)
af = 16
traj = get_stacks_of_radial_trajectory(volume_shape, af=af)
spokelength = volume_shape[-2]
nspokes = volume_shape[-1] // af
nstacks = volume_shape[0]
kspace_shape = nspokes * spokelength * nstacks
extra_args = (tf.constant([volume_shape]), )
if dcomp:
nufft_ob = KbNufftModule(
im_size=volume_shape,
grid_size=None,
norm='ortho',
)
interpob = nufft_ob._extract_nufft_interpob()
nufftob_forw = kbnufft_forward(interpob)
nufftob_back = kbnufft_adjoint(interpob)
dcomp = calculate_radial_dcomp_tf(
interpob,
nufftob_forw,
nufftob_back,
traj[0],
stacks=True,
)
dcomp = tf.ones([1, tf.shape(dcomp)[0]],
dtype=dcomp.dtype) * dcomp[None, :]
extra_args += (dcomp, )
res = model([
tf.zeros([1, 1, kspace_shape, 1], dtype=tf.complex64),
traj,
extra_args,
])
assert res.shape[1:4] == volume_shape
def generate_oasis_tf_records(
acq_type='radial_stacks',
af=4,
mode='train',
shard=0,
shard_size=3300,
slice_size=176,
):
tf.config.experimental_run_functions_eagerly(
True,
)
path = Path(OASIS_DATA_DIR) / mode
filenames = sorted(list(path.glob('*.nii.gz')))
filenames = filenames[shard*shard_size:(shard+1)*shard_size]
scale_factor = 1e-2
volume_size = (slice_size, 256, 256)
extension = get_extension_for_acq(
volume_size,
acq_type=acq_type,
compute_dcomp=True,
scale_factor=scale_factor,
af=af,
)
extension = extension + '.tfrecords'
nufft_ob = KbNufftModule(
im_size=volume_size,
grid_size=None,
norm='ortho',
)
volume_transform = non_cartesian_from_volume_to_nc_kspace_and_traj(
nufft_ob,
volume_size,
acq_type=acq_type,
scale_factor=scale_factor,
compute_dcomp=True,
af=af,
)
for filename in tqdm(filenames):
directory = filename.parent
filename_tfrecord = directory / (filename.stem + extension)
if filename_tfrecord.exists():
continue
volume = from_file_to_volume(filename)
if volume.shape[0] % 2 != 0:
continue
if volume.shape[0] == 36 or volume.shape[0] == 44:
continue
with tf.device('/gpu:0'):
volume = tf.constant(volume, dtype=tf.complex64)
model_inputs, model_outputs = volume_transform(volume)
with tf.io.TFRecordWriter(str(filename_tfrecord)) as writer:
example = encode_example(model_inputs, model_outputs, compute_dcomp=True)
writer.write(example)
def test_gridded_preprocessing():
image_size = (640, 400)
nfft_ob = KbNufftModule(im_size=image_size)
preproc_fun = non_cartesian_from_kspace_to_nc_kspace_and_traj(
nfft_ob,
image_size,
gridding=True,
af=20,
)
image = tf.random.normal([1, 320, 320])
kspace = tf.cast(tf.random.normal([1, 640, 320]), tf.complex64)
(kspace_masked, mask), image_out = preproc_fun(image, kspace)
assert tf.squeeze(kspace_masked).shape == image_size
def train_nc_kspace_dataset_from_indexable(
path,
volume_size=(256, 256, 256),
scale_factor=1,
n_samples=None,
acq_type='radial_stacks',
compute_dcomp=False,
shuffle=True,
**acq_kwargs,
):
files_ds = tf.data.Dataset.list_files(f'{path}*.nii.gz', shuffle=False)
# this makes sure the file selection is happening once when using less than
# all samples
if shuffle:
files_ds = files_ds.shuffle(
buffer_size=1000,
seed=0,
reshuffle_each_iteration=False,
)
volume_ds = files_ds.map(
_tf_filename_to_volume,
num_parallel_calls=3,
)
# filter flat volumes and uneven
volume_ds = volume_ds.filter(lambda x: tf.shape(x)[0] > 1)
volume_ds = volume_ds.filter(lambda x: tf.math.mod(tf.shape(x)[0], 2) == 0)
if n_samples is not None:
volume_ds = volume_ds.take(n_samples)
nufft_ob = KbNufftModule(
im_size=volume_size,
grid_size=None,
norm='ortho',
)
volume_ds = volume_ds.map(
non_cartesian_from_volume_to_nc_kspace_and_traj(
nufft_ob,
volume_size,
acq_type=acq_type,
scale_factor=scale_factor,
compute_dcomp=compute_dcomp,
**acq_kwargs,
),
num_parallel_calls=3,
).repeat().prefetch(buffer_size=3)
return volume_ds
def train_nc_kspace_dataset_from_indexable(
path,
image_size,
inner_slices=None,
rand=False,
scale_factor=1,
contrast=None,
n_samples=None,
acq_type='radial',
compute_dcomp=True, # for backwards compatibility
**acq_kwargs,
):
if not compute_dcomp:
raise NotImplementedError(
'Non-cartesian multicoil is not implemented without density compensation.'
)
selection = [{'inner_slices': inner_slices, 'rand': rand}]
def _tf_filename_to_image_and_kspace_and_contrast(filename):
def _from_train_file_to_image_and_kspace_and_contrast_tensor_to_tensor(
filename):
filename_str = filename.numpy()
image, kspace, contrast = from_multicoil_train_file_to_image_and_kspace_and_contrast(
filename_str,
selection=selection,
)
return tf.convert_to_tensor(image), tf.convert_to_tensor(
kspace), tf.convert_to_tensor(contrast)
[image, kspace, contrast] = tf.py_function(
_from_train_file_to_image_and_kspace_and_contrast_tensor_to_tensor,
[filename],
[tf.float32, tf.complex64, tf.string],
)
if rand:
n_slices = (1, )
else:
n_slices = (inner_slices, )
kspace_size = n_slices + (None, 640, None)
image_size = n_slices + (320, 320)
image.set_shape(image_size)
kspace.set_shape(kspace_size)
return image, kspace, contrast
files_ds = tf.data.Dataset.list_files(f'{path}*.h5', shuffle=False)
# this makes sure the file selection is happening once when using less than
# all samples
files_ds = files_ds.shuffle(
buffer_size=1000,
seed=0,
reshuffle_each_iteration=False,
)
image_and_kspace_and_contrast_ds = files_ds.map(
_tf_filename_to_image_and_kspace_and_contrast,
num_parallel_calls=tf.data.experimental.AUTOTUNE,
)
# contrast filtering
if contrast:
image_and_kspace_and_contrast_ds = image_and_kspace_and_contrast_ds.filter(
lambda image, kspace, tf_contrast: tf_contrast == contrast)
image_and_kspace_ds = image_and_kspace_and_contrast_ds.map(
lambda image, kspace, tf_contrast: (image, kspace),
num_parallel_calls=tf.data.experimental.AUTOTUNE,
)
if n_samples is not None:
image_and_kspace_ds = image_and_kspace_ds.take(n_samples)
nufft_ob = KbNufftModule(
im_size=image_size,
grid_size=None,
norm='ortho',
)
masked_kspace_ds = image_and_kspace_ds.map(
non_cartesian_from_kspace_to_nc_kspace_and_traj(
nufft_ob,
image_size,
acq_type=acq_type,
scale_factor=scale_factor,
**acq_kwargs,
),
num_parallel_calls=tf.data.experimental.AUTOTUNE
if rand or inner_slices is not None else None,
).repeat().prefetch(buffer_size=tf.data.experimental.AUTOTUNE)
return masked_kspace_ds
class NonCartesianFastMRIDatasetBuilder(FastMRIDatasetBuilder):
def __init__(
self,
image_size=IMAGE_SIZE,
acq_type='radial',
dcomp=True,
scale_factor=1e6,
traj=None,
crop_image_data=False,
**kwargs,
):
self.image_size = image_size
self.acq_type = acq_type
self.traj = traj
self._check_acq_type()
self.dcomp = dcomp
self.scale_factor = scale_factor
self.crop_image_data = crop_image_data
self.nufft_obj = KbNufftModule(
im_size=self.image_size,
grid_size=None,
norm='ortho',
)
super(NonCartesianFastMRIDatasetBuilder, self).__init__(
**kwargs,
)
if self.brain:
raise ValueError(
'Currently the non cartesian data works only with knee data.')
self._check_mode()
self._check_dcomp_multicoil()
def _check_acq_type(self,):
if self.acq_type not in ['spiral', 'radial', 'cartesian_debug', 'other']:
raise ValueError(
f'acq_type must be spiral, radial or cartesian_debug but is {self.acq_type}'
)
if self.acq_type == 'other' and self.traj is None:
raise ValueError(
f'Please provide a trajectory as input in case `acq_type` is `other`'
)
def _check_mode(self,):
if self.mode == 'test':
raise ValueError('NonCartesian dataset cannot be used in test mode')
def _check_dcomp_multicoil(self,):
if self.multicoil and not self.dcomp:
raise ValueError('You must use density compensation when in multicoil')
def generate_trajectory(self,):
if self.acq_type == 'radial':
traj = get_radial_trajectory(self.image_size, af=self.af)
elif self.acq_type == 'cartesian':
traj = get_debugging_cartesian_trajectory()
elif self.acq_type == 'spiral':
traj = get_spiral_trajectory(self.image_size, af=self.af)
elif self.acq_type == 'other':
traj = self.traj
return traj
def preprocessing(self, image, kspace):
traj = self.generate_trajectory()
interpob = self.nufft_obj._extract_nufft_interpob()
nufftob_forw = kbnufft_forward(interpob, multiprocessing=True)
nufftob_back = kbnufft_adjoint(interpob, multiprocessing=True)
if self.dcomp:
dcomp = calculate_density_compensator(
interpob,
nufftob_forw,
nufftob_back,
traj[0],
)
traj = tf.repeat(traj, tf.shape(image)[0], axis=0)
orig_image_channels = ortho_ifft2d(kspace)
if self.crop_image_data:
image = adjust_image_size(image, self.image_size)
nc_kspace = nufft(self.nufft_obj, orig_image_channels, traj, self.image_size, multicoil=self.multicoil)
nc_kspace, image = scale_tensors(nc_kspace, image, scale_factor=self.scale_factor)
image = image[..., None]
nc_kspaces_channeled = nc_kspace[..., None]
orig_shape = tf.ones([tf.shape(kspace)[0]], dtype=tf.int32) * self.image_size[-1]
if not self.crop_image_data:
output_shape = tf.shape(image)[1:][None, :]
output_shape = tf.tile(output_shape, [tf.shape(image)[0], 1])
extra_args = (orig_shape,)
if self.dcomp:
dcomp = tf.ones(
[tf.shape(kspace)[0], tf.shape(dcomp)[0]],
dtype=dcomp.dtype,
) * dcomp[None, :]
extra_args += (dcomp,)
model_inputs = (nc_kspaces_channeled, traj)
if self.multicoil:
smaps = non_cartesian_extract_smaps(nc_kspace, traj, dcomp, nufftob_back, self.image_size)
model_inputs += (smaps,)
if not self.crop_image_data:
model_inputs += (output_shape,)
model_inputs += (extra_args,)
return model_inputs, image
class NFFTBase(Layer):
def __init__(self,
multicoil=False,
im_size=(640, 472),
density_compensation=False,
**kwargs):
super(NFFTBase, self).__init__(**kwargs)
self.multicoil = multicoil
self.im_size = im_size
self.nufft_ob = KbNufftModule(
im_size=im_size,
grid_size=None,
norm='ortho',
)
self.density_compensation = density_compensation
self.forward_op = kbnufft_forward(
self.nufft_ob._extract_nufft_interpob())
self.backward_op = kbnufft_adjoint(
self.nufft_ob._extract_nufft_interpob())
def pad_for_nufft(self, image):
return _pad_for_nufft(image, self.im_size)
def crop_for_pad(self, image, shape):
return _crop_for_pad(image, shape, self.im_size)
def crop_for_nufft(self, image):
return _crop_for_nufft(image, self.im_size)
def op(self, inputs):
if self.multicoil:
image, ktraj, smaps = inputs
else:
image, ktraj = inputs
# for tfkbnufft we need a coil dimension even if there is none
image = image[:, None, ..., 0]
if self.multicoil:
image = image * smaps
kspace = nufft(self.nufft_ob, image, ktraj, image_size=self.im_size)
# TODO: get rid of shape return as not needed in the end.
# shape is computed once in the preprocessing and passed on as is.
shape = tf.ones([tf.shape(image)[0]],
dtype=tf.int32) * tf.shape(image)[-1]
return kspace[..., None], [shape]
def adj_op(self, inputs):
if self.multicoil:
if self.density_compensation:
kspace, ktraj, smaps, shape, dcomp, = inputs
else:
kspace, ktraj, smaps, shape = inputs
else:
if self.density_compensation:
kspace, ktraj, shape, dcomp = inputs
else:
kspace, ktraj, shape = inputs
if self.density_compensation:
kspace = tf.cast(dcomp, kspace.dtype) * kspace[..., 0]
else:
kspace = kspace[..., 0]
image = self.backward_op(kspace, ktraj)
## image resizing
if len(self.im_size) < 3:
# NOTE: for now very ugly way to deal with this condition
shape = tf.reshape(shape[0], [])
reshaping_condition = tf.math.less(shape, self.im_size[-1])
else:
shape = shape[0]
reshaping_condition = tf.reduce_any(
tf.math.less(shape, self.im_size))
image_reshaped = tf.cond(
pred=reshaping_condition,
true_fn=lambda: self.crop_for_pad(image, shape),
false_fn=lambda: image,
)
if self.multicoil:
image = tf.reduce_sum(image_reshaped * tf.math.conj(smaps), axis=1)
else:
image = image_reshaped[:, 0]
image = image[..., None]
return image
def generate_multicoil_nc_tf_records(
acq_type='radial',
af=4,
mode='train',
brain=False,
):
if brain:
path = Path(FASTMRI_DATA_DIR) / f'brain_multicoil_{mode}'
else:
path = Path(FASTMRI_DATA_DIR) / f'multicoil_{mode}'
filenames = sorted(list(path.glob('*.h5')))
scale_factor = 1e6
image_size = (640, 400)
nufft_ob = KbNufftModule(
im_size=image_size,
grid_size=None,
norm='ortho',
)
class PreProcModel(tf.keras.models.Model):
def __init__(self, **kwargs):
super().__init__(**kwargs)
interpob = nufft_ob._extract_nufft_interpob()
self.nufftob_back = kbnufft_adjoint(interpob,
multiprocessing=False)
self.nufftob_forw = kbnufft_forward(interpob,
multiprocessing=False)
if acq_type == 'radial':
self.traj = get_radial_trajectory(image_size, af=af)
elif acq_type == 'cartesian':
self.traj = get_debugging_cartesian_trajectory()
elif acq_type == 'spiral':
self.traj = get_spiral_trajectory(image_size, af=af)
else:
raise NotImplementedError(
f'{acq_type} dataset not implemented yet.')
self.dcomp = calculate_density_compensator(
interpob,
self.nufftob_forw,
self.nufftob_back,
self.traj[0],
)
if brain:
self.fft = FFTBase(False, multicoil=True, use_smaps=False)
def call(self, inputs):
images = inputs['image']
kspaces = inputs['kspace']
if brain:
complex_images = self.fft.adj_op([kspaces[..., None],
None])[..., 0]
complex_images_padded = adjust_image_size(
complex_images,
image_size,
multicoil=True,
)
kspaces = self.fft.op([complex_images_padded[..., None],
None])[..., 0]
traj = tf.repeat(self.traj, tf.shape(images)[0], axis=0)
orig_image_channels = tf_ortho_ifft2d(kspaces)
nc_kspace = nufft(nufft_ob,
orig_image_channels,
traj,
image_size,
multiprocessing=False)
nc_kspace_scaled = nc_kspace * scale_factor
images_scaled = images * scale_factor
images_channeled = images_scaled[..., None]
nc_kspaces_channeled = nc_kspace_scaled[..., None]
orig_shape = tf.ones([tf.shape(kspaces)[0]],
dtype=tf.int32) * tf.shape(kspaces)[-1]
dcomp = tf.ones([tf.shape(kspaces)[0],
tf.shape(self.dcomp)[0]],
dtype=self.dcomp.dtype) * self.dcomp[None, :]
extra_args = (orig_shape, dcomp)
smaps = non_cartesian_extract_smaps(nc_kspace, traj, dcomp,
self.nufftob_back, orig_shape)
model_inputs = (nc_kspaces_channeled, traj, smaps, extra_args)
if brain:
output_shape = tf.shape(images)[1:][None, :]
output_shape = tf.tile(output_shape, [tf.shape(images)[0], 1])
model_inputs += (output_shape, )
return model_inputs, images_channeled
extension = f'_nc_{acq_type}'
if af != 4:
extension += f'_af{af}'
extension += '.tfrecords'
selection = [
{
'inner_slices': None,
'rand': False
}, # slice selection
{
'rand': False,
'keep_dim': False
}, # coil selection
]
mirrored_strategy = tf.distribute.MirroredStrategy()
with mirrored_strategy.scope():
preproc_model = PreProcModel()
for filename in tqdm(filenames):
directory = filename.parent
filename_tfrecord = directory / (filename.stem + extension)
if filename_tfrecord.exists():
continue
image, kspace, _ = from_multicoil_train_file_to_image_and_kspace_and_contrast(
filename,
selection=selection,
)
data = tf.data.Dataset.zip({
'image':
tf.data.Dataset.from_tensor_slices(image),
'kspace':
tf.data.Dataset.from_tensor_slices(kspace),
})
data = data.batch(len(image))
options = tf.data.Options()
options.experimental_distribute.auto_shard_policy = tf.data.experimental.AutoShardPolicy.OFF
data = data.with_options(options)
model_inputs, model_outputs = preproc_model.predict(data)
with tf.io.TFRecordWriter(str(filename_tfrecord)) as writer:
example = encode_ncmc_example(model_inputs, [model_outputs])
writer.write(example)
def train_nc_kspace_dataset_from_indexable(
path,
image_size,
inner_slices=None,
rand=False,
scale_factor=1,
contrast=None,
n_samples=None,
acq_type='radial',
compute_dcomp=False,
**acq_kwargs,
):
r"""Non-cartesian dataset for the training/validation set of single coil fastMRI.
The undersampling is performed retrospectively on the fully-sampled kspace,
using spiral or radial trajectories. A uniform cartesian trajectory is also
available for debugging.
The non-uniform Fourier transform is implemented by tfkbnufft.
The output of the dataset is of the form:
```
(retrospectively_undersampled_nc_kspace, nc_trajectory, extra_args), ground_truth_reconstruction
```
where `extra_args` contains the original shape fo the image, and potentially
the density compensation factors.
Prefetching is performed, as well as parallel calls for preprocessing when
rand or inner_slices are active.
The ground truth reconstruction is read directly from the h5 file and not
obtained through the Fourier inversion of the kspace.
Arguments:
path (str): the path to the fastMRI files. Should end with a `/`.
image_size (tuple of int): the fixed image size to consider for the
non-uniform Fourier transform. It needs to be fixed to only use
a single plan. An image size of (640, 400) will lead to 99.5
percents of the dataset being only padded and not cropped.
inner_slices (int or None): the slices to consider in the volumes. The
slicing will be performed as `inner_slices//2:-inner_slices//2`.
If None, all slices are considered. Defaults to None.
rand (bool): whether or not to sample one slice randomly from the
considered slices of the volumes. If None, all slices are taken.
Defaults to None.
scale_factor (int or float): the multiplicative scale factor for both the
kspace and the target reconstruction. Typically, 1e6 is a good value
for fastMRI, because it sets the values in a range acceptable for
neural networks training. See [R2020] (3.4 Training) for more details
on this value. Defaults to 1.
contrast (str or None): the contrast to select for this dataset. If None,
all contrasts are considered. Available contrasts for fastMRI single
coil are typically `CORPD_FBK` (Proton density) and `CORPDFS_FBK`
(Proton density with fat suppression). Defaults to None.
n_samples (int or None): the number of samples to consider from this set.
If None, all samples are used. Defaults to None.
acq_type (str): the type of non-cartesian trajectory to use. Choices are
`radial`, `spiral` or `cartesian` (for debugging purposes). Defaults
to radial.
compute_dcomp (bool): whether to compute and return the density compensation
factors. See [P1999] for more on density compensation. Defaults to
False.
**acq_kwargs: keyword arguments for the non-cartesian trajectory. See
fastmri_recon/data/utils/non_cartesian.py for more info.
Returns:
tf.data.Dataset: the training/validation non-cartesian dataset.
"""
selection = [{'inner_slices': inner_slices, 'rand': rand}]
def _tf_filename_to_image_and_kspace_and_contrast(filename):
def _from_train_file_to_image_and_kspace_and_contrast_tensor_to_tensor(
filename):
filename_str = filename.numpy()
image, kspace, contrast = from_train_file_to_image_and_kspace_and_contrast(
filename_str,
selection=selection,
)
return tf.convert_to_tensor(image), tf.convert_to_tensor(
kspace), tf.convert_to_tensor(contrast)
[image, kspace, contrast] = tf.py_function(
_from_train_file_to_image_and_kspace_and_contrast_tensor_to_tensor,
[filename],
[tf.float32, tf.complex64, tf.string],
)
if rand:
n_slices = (1, )
else:
n_slices = (inner_slices, )
kspace_size = n_slices + (640, None)
image_size = n_slices + (320, 320)
image.set_shape(image_size)
kspace.set_shape(kspace_size)
return image, kspace, contrast
files_ds = tf.data.Dataset.list_files(f'{path}*.h5', shuffle=False)
# this makes sure the file selection is happening once when using less than
# all samples
files_ds = files_ds.shuffle(
buffer_size=1000,
seed=0,
reshuffle_each_iteration=False,
)
image_and_kspace_and_contrast_ds = files_ds.map(
_tf_filename_to_image_and_kspace_and_contrast,
num_parallel_calls=tf.data.experimental.AUTOTUNE,
)
# contrast filtering
if contrast:
image_and_kspace_and_contrast_ds = image_and_kspace_and_contrast_ds.filter(
lambda image, kspace, tf_contrast: tf_contrast == contrast)
image_and_kspace_ds = image_and_kspace_and_contrast_ds.map(
lambda image, kspace, tf_contrast: (image, kspace),
num_parallel_calls=tf.data.experimental.AUTOTUNE,
)
if n_samples is not None:
image_and_kspace_ds = image_and_kspace_ds.take(n_samples)
nufft_ob = KbNufftModule(
im_size=image_size,
grid_size=None,
norm='ortho',
)
masked_kspace_ds = image_and_kspace_ds.map(
non_cartesian_from_kspace_to_nc_kspace_and_traj(
nufft_ob,
image_size,
acq_type=acq_type,
scale_factor=scale_factor,
compute_dcomp=compute_dcomp,
**acq_kwargs,
),
num_parallel_calls=tf.data.experimental.AUTOTUNE
if rand or inner_slices is not None else None,
).repeat()
if rand or inner_slices is not None:
masked_kspace_ds = masked_kspace_ds.prefetch(
buffer_size=tf.data.experimental.AUTOTUNE)
return masked_kspace_ds
def generate_multicoil_nc_tf_records(
acq_type='radial',
af=4,
mode='train',
):
path = Path(FASTMRI_DATA_DIR) / f'multicoil_{mode}'
filenames = sorted(list(path.glob('*.h5')))
scale_factor = 1e6
image_size = (640, 400)
nufft_ob = KbNufftModule(
im_size=image_size,
grid_size=None,
norm='ortho',
)
class PreProcModel(tf.keras.models.Model):
def __init__(self, **kwargs):
super().__init__(**kwargs)
interpob = nufft_ob._extract_nufft_interpob()
self.nufftob_back = kbnufft_adjoint(interpob,
multiprocessing=False)
self.nufftob_forw = kbnufft_forward(interpob,
multiprocessing=False)
if acq_type == 'radial':
self.traj = get_radial_trajectory(image_size, af=af)
elif acq_type == 'cartesian':
self.traj = get_debugging_cartesian_trajectory()
elif acq_type == 'spiral':
self.traj = get_spiral_trajectory(image_size, af=af)
else:
raise NotImplementedError(
f'{acq_type} dataset not implemented yet.')
self.dcomp = calculate_density_compensator(
interpob,
self.nufftob_forw,
self.nufftob_back,
self.traj[0],
)
def call(self, inputs):
images, kspaces = inputs
traj = tf.repeat(self.traj, tf.shape(images)[0], axis=0)
orig_image_channels = tf_ortho_ifft2d(kspaces)
nc_kspace = nufft(nufft_ob,
orig_image_channels,
traj,
image_size,
multiprocessing=False)
nc_kspace_scaled = nc_kspace * scale_factor
images_scaled = images * scale_factor
images_channeled = images_scaled[..., None]
nc_kspaces_channeled = nc_kspace_scaled[..., None]
orig_shape = tf.ones([tf.shape(kspaces)[0]],
dtype=tf.int32) * tf.shape(kspaces)[-1]
dcomp = tf.ones([tf.shape(kspaces)[0],
tf.shape(self.dcomp)[0]],
dtype=self.dcomp.dtype) * self.dcomp[None, :]
extra_args = (orig_shape, dcomp)
smaps = non_cartesian_extract_smaps(nc_kspace, traj, dcomp,
self.nufftob_back, orig_shape)
return (nc_kspaces_channeled, traj, smaps,
extra_args), images_channeled
extension = f'_nc_{acq_type}.tfrecords'
selection = [
{
'inner_slices': None,
'rand': False
}, # slice selection
{
'rand': False,
'keep_dim': False
}, # coil selection
]
mirrored_strategy = tf.distribute.MirroredStrategy()
with mirrored_strategy.scope():
preproc_model = PreProcModel()
for filename in tqdm(filenames):
directory = filename.parent
filename_tfrecord = directory / (filename.stem + extension)
if filename_tfrecord.exists():
continue
image, kspace, _ = from_multicoil_train_file_to_image_and_kspace_and_contrast(
filename,
selection=selection,
)
model_inputs, model_outputs = preproc_model.predict([image, kspace])
with tf.io.TFRecordWriter(str(filename_tfrecord)) as writer:
example = encode_ncmc_example(model_inputs, [model_outputs])
writer.write(example)
class NFFTBase(Layer):
def __init__(self, multicoil=False, im_size=(640, 472), density_compensation=False, **kwargs):
super(NFFTBase, self).__init__(**kwargs)
self.multicoil = multicoil
self.im_size = im_size
self.nufft_ob = KbNufftModule(
im_size=im_size,
grid_size=None,
norm='ortho',
)
self.density_compensation = density_compensation
self.forward_op = kbnufft_forward(self.nufft_ob._extract_nufft_interpob())
self.backward_op = kbnufft_adjoint(self.nufft_ob._extract_nufft_interpob())
def pad_for_nufft(self, image):
return _pad_for_nufft(image, self.im_size)
def crop_for_pad(self, image, shape):
return _crop_for_pad(image, shape, self.im_size)
def crop_for_nufft(self, image):
return _crop_for_nufft(image, self.im_size)
def op(self, inputs):
if self.multicoil:
image, ktraj, smaps = inputs
else:
image, ktraj = inputs
# for tfkbnufft we need a coil dimension even if there is none
image = image[:, None, ..., 0]
if self.multicoil:
image = image * smaps
kspace = nufft(self.nufft_ob, image, ktraj, image_size=self.im_size)
shape = tf.ones([tf.shape(image)[0]], dtype=tf.int32) * tf.shape(image)[-1]
return kspace[..., None], [shape]
def adj_op(self, inputs):
if self.multicoil:
if self.density_compensation:
kspace, ktraj, smaps, shape, dcomp, = inputs
else:
kspace, ktraj, smaps, shape = inputs
else:
if self.density_compensation:
kspace, ktraj, shape, dcomp = inputs
else:
kspace, ktraj, shape = inputs
shape = tf.reshape(shape[0], [])
if self.density_compensation:
kspace = tf.cast(dcomp, kspace.dtype) * kspace[..., 0]
else:
kspace = kspace[..., 0]
image = self.backward_op(kspace, ktraj)
image_reshaped = tf.cond(
tf.math.greater_equal(shape, self.im_size[-1]),
lambda: image,
lambda: self.crop_for_pad(image, shape),
)
if self.multicoil:
image = tf.reduce_sum(image_reshaped * tf.math.conj(smaps), axis=1)
else:
image = image_reshaped[:, 0]
image = image[..., None]
return image