pytomography.transforms.shared
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Submodules#
Package Contents#
Classes#
Object to object transform used to take in a coefficient image \(\alpha\) and return an image estimate \(f = K\alpha\). This transform implements the matrix \(K\). |
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Applies a Gaussian smoothing filter to the reconstructed object with the specified full-width-half-max (FWHM) |
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obj2obj transform used to rotate an object to angle \(\beta\) in the DICOM reference frame. (Note that an angle of ) |
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The parent class for all transforms used in reconstruction (obj2obj, im2im, obj2im). Subclasses must implement the |
- class pytomography.transforms.shared.KEMTransform(support_objects, support_kernels=None, support_kernels_params=None, distance_kernel=None, distance_kernel_params=None, size=5, top_N=None, kernel_on_gpu=False)[source]#
Bases:
pytomography.transforms.Transform
Object to object transform used to take in a coefficient image \(\alpha\) and return an image estimate \(f = K\alpha\). This transform implements the matrix \(K\).
- Parameters:
support_objects (Sequence[torch.tensor]) – Objects used for support when building each basis function. These may correspond to PET/CT/MRI images, for example.
support_kernels (Sequence[Callable], optional) – A list of functions corresponding to the support kernel of each support object. If none, defaults to \(k(v_i, v_j; \sigma) = \exp\left(-\frac{(v_i-v_j)^2}{2\sigma^2} \right)\) for each support object. Defaults to None.
support_kernels_params (Sequence[Sequence[float]], optional) – A list of lists, where each sublist contains the additional parameters corresponding to each support kernel (parameters that follow the semi-colon in the expression above). As an example, if using the default configuration for
support_kernels
for two different support objects (say CT and PET), one could givensupport_kernel_params=[[40],[5]]
If none then defaults to a list of N*[[1]] where N is the number of support objects. Defaults to None.distance_kernel (Callable, optional) – Kernel used to weight based on voxel-voxel distance. If none, defaults to :math:`k(x_i, x_j; sigma) = expleft(-frac{(x_i-x_j)^2}{2sigma^2} right) Defaults to None.
distance_kernel_params (_type_, optional) – A list of parameters corresponding to additional parameters for the
distance_kernel
(i.e. the parameters that follow the semi-colon in the expression above). If none, then defaults to \(\sigma=1\). Defaults to None.size (int, optional) – The size of each kernel. Defaults to 5.
top_N (int | None) –
kernel_on_gpu (bool) –
- configure(object_meta, proj_meta)[source]#
Function used to initalize the transform using corresponding object and projection metadata
- Parameters:
object_meta (SPECTObjectMeta) – Object metadata.
proj_meta (SPECTProjMeta) – Projections metadata.
- Return type:
None
- forward(object)[source]#
Forward transform corresponding to \(K\alpha\)
- Parameters:
object (torch.Tensor) – Coefficient image \(\alpha\)
- Returns:
Image \(K\alpha\)
- Return type:
torch.tensor
- backward(object, norm_constant=None)[source]#
Backward transform corresponding to \(K^T\alpha\). Since the matrix is symmetric, the implementation is the same as forward.
- Parameters:
object (torch.Tensor) – Coefficient image \(\alpha\)
norm_constant (torch.Tensor | None) –
- Returns:
Image \(K^T\alpha\)
- Return type:
torch.tensor
- class pytomography.transforms.shared.GaussianFilter(FWHM, n_sigmas=3)[source]#
Bases:
pytomography.transforms.Transform
Applies a Gaussian smoothing filter to the reconstructed object with the specified full-width-half-max (FWHM)
- Parameters:
FWHM (float) – Specifies the width of the gaussian
n_sigmas (float) – Number of sigmas to include before truncating the kernel.
- configure(object_meta, proj_meta)[source]#
Configures the transform to the object/proj metadata. This is done after creating the network so that it can be adjusted to the system matrix.
- Parameters:
object_meta (ObjectMeta) – Object metadata.
proj_meta (ProjMeta) – Projections metadata.
- Return type:
None
- forward(object)[source]#
Applies the Gaussian smoothing
- Parameters:
object (torch.tensor) – Object to smooth
- Returns:
Smoothed object
- Return type:
torch.tensor
- backward(object, norm_constant=None)[source]#
Applies Gaussian smoothing in back projection. Because the operation is symmetric, it is the same as the forward projection.
- Parameters:
object (torch.tensor) – Object to smooth
norm_constant (torch.tensor, optional) – Normalization constant used in iterative algorithms. Defaults to None.
- Returns:
Smoothed object
- Return type:
torch.tensor
- class pytomography.transforms.shared.RotationTransform(mode='bilinear')[source]#
Bases:
pytomography.transforms.Transform
obj2obj transform used to rotate an object to angle \(\beta\) in the DICOM reference frame. (Note that an angle of )
- Parameters:
mode (str) – Interpolation mode used in the rotation.
- forward(object, angles)[source]#
Rotates an object to angle \(\beta\) in the DICOM reference frame. Note that the scanner angle \(\beta\) is related to \(\phi\) (azimuthal angle) by \(\phi = 3\pi/2 - \beta\).
- Parameters:
object (torch.tensor) – Tensor of size [batch_size, Lx, Ly, Lz] being rotated.
angles (torch.Tensor) – Tensor of size [batch_size] corresponding to the rotation angles.
- Returns:
Tensor of size [batch_size, Lx, Ly, Lz] where each element in the batch dimension is rotated by the corresponding angle.
- Return type:
torch.tensor
- backward(object, angles)[source]#
Forward projection \(A:\mathbb{U} \to \mathbb{U}\) of attenuation correction.
- Parameters:
object (torch.tensor) – Tensor of size [batch_size, Lx, Ly, Lz] being rotated.
angles (torch.Tensor) – Tensor of size [batch_size] corresponding to the rotation angles.
- Returns:
Tensor of size [batch_size, Lx, Ly, Lz] where each element in the batch dimension is rotated by the corresponding angle.
- Return type:
torch.tensor
- class pytomography.transforms.shared.DVFMotionTransform(dvf_forward=None, dvf_backward=None)[source]#
Bases:
pytomography.transforms.Transform
The parent class for all transforms used in reconstruction (obj2obj, im2im, obj2im). Subclasses must implement the
__call__
method.- Parameters:
device (str) – Pytorch device used for computation
dvf_forward (torch.Tensor | None) –
dvf_backward (torch.Tensor | None) –
- _get_old_coordinates()[source]#
Obtain meshgrid of coordinates corresponding to the object
- Returns:
Tensor of coordinates corresponding to input object
- Return type:
torch.Tensor
- _get_new_coordinates(old_coordinates, DVF)[source]#
Obtain the new coordinates of each voxel based on the DVF.
- Parameters:
old_coordinates (torch.Tensor) – Old coordinates of each voxel
DVF (torch.Tensor) – Deformation vector field.
- Returns:
_description_
- Return type:
_type_
- _apply_dvf(DVF, vol_ratio, object_i)[source]#
Applies the deformation vector field to the object
- Parameters:
DVF (torch.Tensor) – Deformation vector field
object_i (torch.Tensor) – Old object.
- Returns:
Deformed object.
- Return type:
torch.Tensor