def test_centered_fft2_forward_normalization(shape):
"""
Test centered 2D Fast Fourier Transform with forward normalization.
Args:
shape: shape of the input
Returns:
None
"""
shape = shape + [2]
x = create_input(shape)
out_torch = fft2(x,
centered=True,
normalization="forward",
spatial_dims=[-2, -1]).numpy()
out_torch = out_torch[..., 0] + 1j * out_torch[..., 1]
input_numpy = tensor_to_complex_np(x)
input_numpy = np.fft.ifftshift(input_numpy, (-2, -1))
out_numpy = np.fft.fft2(input_numpy, norm="forward")
out_numpy = np.fft.fftshift(out_numpy, (-2, -1))
if not np.allclose(out_torch, out_numpy):
raise AssertionError
def test_tensor_to_complex_np(x):
"""
Test if the tensor_to_complex_np function works as expected.
Args:
x: The input array.
Returns:
None
"""
x = tensor_to_complex_np(x)
if x.ndim != 3:
raise AssertionError
if x.shape[-1] == 2:
raise AssertionError
def test_complex_abs(shape):
"""
Test complex absolute value.
Args:
shape: shape of the input
Returns:
None
"""
shape = shape + [2]
x = create_input(shape)
out_torch = complex_abs(x).numpy()
input_numpy = tensor_to_complex_np(x)
out_numpy = np.abs(input_numpy)
if not np.allclose(out_torch, out_numpy):
raise AssertionError
def test_non_centered_fft2(shape):
"""
Test non-centered 2D Fast Fourier Transform.
Args:
shape: shape of the input
Returns:
None
"""
shape = shape + [2]
x = create_input(shape)
out_torch = fft2(x,
centered=False,
normalization="ortho",
spatial_dims=[-2, -1]).numpy()
out_torch = out_torch[..., 0] + 1j * out_torch[..., 1]
input_numpy = tensor_to_complex_np(x)
out_numpy = np.fft.fft2(input_numpy, norm="ortho")
if not np.allclose(out_torch, out_numpy):
raise AssertionError
def evaluate(
arguments,
reconstruction_key,
mask_background,
output_path,
method,
acc,
no_params,
slice_start,
slice_end,
coil_dim,
):
"""
Evaluates the reconstructions.
Parameters
----------
arguments: The CLI arguments.
reconstruction_key: The key of the reconstruction to evaluate.
mask_background: The background mask.
output_path: The output path.
method: The reconstruction method.
acc: The acceleration factor.
no_params: The number of parameters.
slice_start: The start slice. (optional)
slice_end: The end slice. (optional)
coil_dim: The coil dimension. (optional)
Returns
-------
dict: A dict where the keys are metric names and the values are the mean of the metric.
"""
_metrics = Metrics(METRIC_FUNCS, output_path,
method) if arguments.type == "mean_std" else {}
for tgt_file in tqdm(arguments.target_path.iterdir()):
if exists(arguments.predictions_path / tgt_file.name):
with h5py.File(tgt_file, "r") as target, h5py.File(
arguments.predictions_path / tgt_file.name, "r") as recons:
kspace = target["kspace"][()]
if arguments.sense_path is not None:
sense = h5py.File(arguments.sense_path / tgt_file.name,
"r")["sensitivity_map"][()]
elif "sensitivity_map" in target:
sense = target["sensitivity_map"][()]
sense = sense.squeeze().astype(np.complex64)
if sense.shape != kspace.shape:
sense = np.transpose(sense, (0, 3, 1, 2))
target = np.abs(
tensor_to_complex_np(
torch.sum(
complex_mul(
ifft2(to_tensor(kspace),
centered="fastmri"
in str(arguments.sense_path).lower()),
complex_conj(to_tensor(sense)),
),
coil_dim,
)))
recons = recons[reconstruction_key][()]
if recons.ndim == 4:
recons = recons.squeeze(coil_dim)
if arguments.crop_size is not None:
crop_size = arguments.crop_size
crop_size[0] = min(target.shape[-2], int(crop_size[0]))
crop_size[1] = min(target.shape[-1], int(crop_size[1]))
crop_size[0] = min(recons.shape[-2], int(crop_size[0]))
crop_size[1] = min(recons.shape[-1], int(crop_size[1]))
target = center_crop(target, crop_size)
recons = center_crop(recons, crop_size)
if mask_background:
for sl in range(target.shape[0]):
mask = convex_hull_image(
np.where(
np.abs(target[sl]) > threshold_otsu(
np.abs(target[sl])), 1, 0) # type: ignore
)
target[sl] = target[sl] * mask
recons[sl] = recons[sl] * mask
if slice_start is not None:
target = target[slice_start:]
recons = recons[slice_start:]
if slice_end is not None:
target = target[:slice_end]
recons = recons[:slice_end]
for sl in range(target.shape[0]):
target[sl] = target[sl] / np.max(np.abs(target[sl]))
recons[sl] = recons[sl] / np.max(np.abs(recons[sl]))
target = np.abs(target)
recons = np.abs(recons)
if arguments.type == "mean_std":
_metrics.push(target, recons)
else:
_target = np.expand_dims(target, coil_dim)
_recons = np.expand_dims(recons, coil_dim)
for sl in range(target.shape[0]):
_metrics["FNAME"] = tgt_file.name
_metrics["SLICE"] = sl
_metrics["ACC"] = acc
_metrics["METHOD"] = method
_metrics["MSE"] = [mse(target[sl], recons[sl])]
_metrics["NMSE"] = [nmse(target[sl], recons[sl])]
_metrics["PSNR"] = [psnr(target[sl], recons[sl])]
_metrics["SSIM"] = [ssim(_target[sl], _recons[sl])]
_metrics["PARAMS"] = no_params
if not exists(arguments.output_path):
pd.DataFrame(columns=_metrics.keys()).to_csv(
arguments.output_path, index=False, mode="w")
pd.DataFrame(_metrics).to_csv(arguments.output_path,
index=False,
header=False,
mode="a")
return _metrics