pytomography 3.1.4__tar.gz → 3.2.2__tar.gz

{pytomography-3.1.4 → pytomography-3.2.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: pytomography
-Version: 3.1.4
+Version: 3.2.2
 Summary: Package to perform tomographic image reconstruction
 Project-URL: Homepage, https://github.com/qurit/PyTomography
 Project-URL: Bug Tracker, https://github.com/qurit/PyTomography/issues
@@ -30,6 +30,7 @@ Requires-Dist: myst-parser; extra == 'doc'
 Requires-Dist: nbsphinx; extra == 'doc'
 Requires-Dist: pydata-sphinx-theme; extra == 'doc'
 Requires-Dist: sphinx-autoapi~=3.0.0; extra == 'doc'
+Requires-Dist: sphinx-design; extra == 'doc'
 Requires-Dist: sphinx~=6.2.1; extra == 'doc'
 Requires-Dist: toml; extra == 'doc'
 Description-Content-Type: text/markdown

{pytomography-3.1.4 → pytomography-3.2.2}/docs/source/autoapi/index.rst

@@ -7,5 +7,6 @@ This page contains auto-generated API reference documentation [#f1]_.
    :titlesonly:
 
    /autoapi/pytomography/index
+   /autoapi/test_multi_bed_recon/index
 
 .. [#f1] Created with `sphinx-autoapi <https://github.com/readthedocs/sphinx-autoapi>`_

{pytomography-3.1.4 → pytomography-3.2.2}/docs/source/autoapi/pytomography/io/SPECT/dicom/index.rst

@@ -85,7 +85,7 @@ Functions
    :rtype: float
 
 
-.. py:function:: get_energy_window_scatter_estimate(file, index_peak, index_lower, index_upper = None, weighting_lower = 0.5, weighting_upper = 0.5, return_scatter_variance_estimate = False)
+.. py:function:: get_energy_window_scatter_estimate(file, index_peak, index_lower, index_upper = None, weighting_lower = 0.5, weighting_upper = 0.5, proj_meta=None, sigma_theta = 0, sigma_r = 0, sigma_z = 0, N_sigmas = 3, return_scatter_variance_estimate = False)
 
    Gets an estimate of scatter projection data from a DICOM file using either the dual energy window (`index_upper=None`) or triple energy window method.
 
@@ -108,7 +108,7 @@ Functions
    :rtype: torch.Tensor[Ltheta,Lr,Lz]
 
 
-.. py:function:: get_energy_window_scatter_estimate_projections(file, projections, index_peak, index_lower, index_upper = None, weighting_lower = 0.5, weighting_upper = 0.5, return_scatter_variance_estimate = False)
+.. py:function:: get_energy_window_scatter_estimate_projections(file, projections, index_peak, index_lower, index_upper = None, weighting_lower = 0.5, weighting_upper = 0.5, proj_meta=None, sigma_theta = 0, sigma_r = 0, sigma_z = 0, N_sigmas = 3, return_scatter_variance_estimate = False)
 
    Gets an estimate of scatter projection data from a DICOM file using either the dual energy window (`index_upper=None`) or triple energy window method. This is seperate from ``get_energy_window_scatter_estimate`` as it allows a user to input projecitons that are already loaded/modified. This is useful for when projection data gets mixed for reconstructing multiple bed positions.
 
@@ -144,7 +144,7 @@ Functions
    :rtype: torch.Tensor
 
 
-.. py:function:: get_psfmeta_from_scanner_params(collimator_name, energy_keV, min_sigmas = 3, material = 'lead', intrinsic_resolution = 0)
+.. py:function:: get_psfmeta_from_scanner_params(collimator_name, energy_keV, min_sigmas = 3, material = 'lead', intrinsic_resolution = 0, intrinsic_resolution_140keV = None)
 
    Obtains SPECT PSF metadata given a unique collimator code and photopeak energy of radionuclide. For more information on collimator codes, see the "external data" section of the readthedocs page.
 
@@ -156,14 +156,16 @@ Functions
    :type min_sigmas: float
    :param material: Material of the collimator.
    :type material: str
-   :param intrinsic_resolution: Intrinsic resolution (FWHM) of the scintillator crystals. Defaults to 0.
+   :param intrinsic_resolution: Intrinsic resolution (FWHM) of the scintillator crystals. Note that most scanners provide the intrinsic resolution at 140keV only; if you only have access to this, you should use the ``intrinsic_resolution_140keV`` argument of this function. Defaults to 0.
    :type intrinsic_resolution: float
+   :param intrinsic_resolution_140keV: Intrinsic resolution (FWHM) of the scintillator crystals at an energy of 140keV. The true intrinsic resolution is calculated assuming the resolution is proportional to E^(-1/2). If provided, then ``intrinsic_resolution`` is ignored. Defaults to None.
+   :type intrinsic_resolution_140keV: float | None
 
    :returns: PSF metadata.
    :rtype: SPECTPSFMeta
 
 
-.. py:function:: CT_to_mumap(CT, files_CT, file_NM, index_peak = 0, technique = 'from_table')
+.. py:function:: CT_to_mumap(CT, files_CT, file_NM, index_peak = 0, technique = 'from_table', E_SPECT = None)
 
    Converts a CT image to a mu-map given SPECT projection data. The CT data must be aligned with the projection data already; this is a helper function for ``get_attenuation_map_from_CT_slices``.
 
@@ -177,6 +179,8 @@ Functions
    :type index_peak: int, optional
    :param technique: Technique to convert HU to attenuation coefficients. The default, 'from_table', uses a table of coefficients for bilinear curves obtained for a variety of common radionuclides. The technique 'from_cortical_bone_fit' looks for a cortical bone peak in the scan and uses that to obtain the bilinear coefficients. For phantom scans where the attenuation coefficient is always significantly less than bone, the cortical bone technique will still work, since the first part of the bilinear curve (in the air to water range) does not depend on the cortical bone fit. Alternatively, one can provide an arbitrary function here which takes in a 3D scan with units of HU and converts to mu.
    :type technique: str, optional
+   :param E_SPECT: Energy of the photopeak in SPECT scan; this overrides the energy in the DICOM file, so should only be used if the DICOM file is incorrect. If None, then the energy is obtained from the DICOM file.
+   :type E_SPECT: float
 
    :returns: Attenuation map in units of 1/cm
    :rtype: torch.tensor
@@ -216,7 +220,7 @@ Functions
    :rtype: function
 
 
-.. py:function:: get_attenuation_map_from_CT_slices(files_CT, file_NM = None, index_peak = 0, mode = 'constant', HU2mu_technique = 'from_table')
+.. py:function:: get_attenuation_map_from_CT_slices(files_CT, file_NM = None, index_peak = 0, mode = 'constant', HU2mu_technique = 'from_table', E_SPECT = None)
 
    Converts a sequence of DICOM CT files (corresponding to a single scan) into a torch.Tensor object usable as an attenuation map in PyTomography.
 
@@ -230,6 +234,8 @@ Functions
    :type mode: str
    :param HU2mu_technique: Technique to convert HU to attenuation coefficients. The default, 'from_table', uses a table of coefficients for bilinear curves obtained for a variety of common radionuclides. The technique 'from_cortical_bone_fit' looks for a cortical bone peak in the scan and uses that to obtain the bilinear coefficients. For phantom scans where the attenuation coefficient is always significantly less than bone, the cortical bone technique will still work, since the first part of the bilinear curve (in the air to water range) does not depend on the cortical bone fit. Alternatively, one can provide an arbitrary function here which takes in a 3D scan with units of HU and converts to mu.
    :type HU2mu_technique: str
+   :param E_SPECT: Energy of the photopeak in SPECT scan; this overrides the energy in the DICOM file, so should only be used if the DICOM file is incorrect. Defaults to None.
+   :type E_SPECT: float
 
    :returns: Tensor of shape [Lx, Ly, Lz] corresponding to attenuation map.
    :rtype: torch.Tensor

{pytomography-3.1.4 → pytomography-3.2.2}/docs/source/autoapi/pytomography/io/SPECT/index.rst

@@ -78,7 +78,7 @@ Functions
    :rtype: torch.Tensor
 
 
-.. py:function:: get_attenuation_map_from_CT_slices(files_CT, file_NM = None, index_peak = 0, mode = 'constant', HU2mu_technique = 'from_table')
+.. py:function:: get_attenuation_map_from_CT_slices(files_CT, file_NM = None, index_peak = 0, mode = 'constant', HU2mu_technique = 'from_table', E_SPECT = None)
 
    Converts a sequence of DICOM CT files (corresponding to a single scan) into a torch.Tensor object usable as an attenuation map in PyTomography.
 
@@ -92,12 +92,14 @@ Functions
    :type mode: str
    :param HU2mu_technique: Technique to convert HU to attenuation coefficients. The default, 'from_table', uses a table of coefficients for bilinear curves obtained for a variety of common radionuclides. The technique 'from_cortical_bone_fit' looks for a cortical bone peak in the scan and uses that to obtain the bilinear coefficients. For phantom scans where the attenuation coefficient is always significantly less than bone, the cortical bone technique will still work, since the first part of the bilinear curve (in the air to water range) does not depend on the cortical bone fit. Alternatively, one can provide an arbitrary function here which takes in a 3D scan with units of HU and converts to mu.
    :type HU2mu_technique: str
+   :param E_SPECT: Energy of the photopeak in SPECT scan; this overrides the energy in the DICOM file, so should only be used if the DICOM file is incorrect. Defaults to None.
+   :type E_SPECT: float
 
    :returns: Tensor of shape [Lx, Ly, Lz] corresponding to attenuation map.
    :rtype: torch.Tensor
 
 
-.. py:function:: get_energy_window_scatter_estimate(file, index_peak, index_lower, index_upper = None, weighting_lower = 0.5, weighting_upper = 0.5, return_scatter_variance_estimate = False)
+.. py:function:: get_energy_window_scatter_estimate(file, index_peak, index_lower, index_upper = None, weighting_lower = 0.5, weighting_upper = 0.5, proj_meta=None, sigma_theta = 0, sigma_r = 0, sigma_z = 0, N_sigmas = 3, return_scatter_variance_estimate = False)
 
    Gets an estimate of scatter projection data from a DICOM file using either the dual energy window (`index_upper=None`) or triple energy window method.
 
@@ -120,7 +122,7 @@ Functions
    :rtype: torch.Tensor[Ltheta,Lr,Lz]
 
 
-.. py:function:: get_psfmeta_from_scanner_params(collimator_name, energy_keV, min_sigmas = 3, material = 'lead', intrinsic_resolution = 0)
+.. py:function:: get_psfmeta_from_scanner_params(collimator_name, energy_keV, min_sigmas = 3, material = 'lead', intrinsic_resolution = 0, intrinsic_resolution_140keV = None)
 
    Obtains SPECT PSF metadata given a unique collimator code and photopeak energy of radionuclide. For more information on collimator codes, see the "external data" section of the readthedocs page.
 
@@ -132,14 +134,16 @@ Functions
    :type min_sigmas: float
    :param material: Material of the collimator.
    :type material: str
-   :param intrinsic_resolution: Intrinsic resolution (FWHM) of the scintillator crystals. Defaults to 0.
+   :param intrinsic_resolution: Intrinsic resolution (FWHM) of the scintillator crystals. Note that most scanners provide the intrinsic resolution at 140keV only; if you only have access to this, you should use the ``intrinsic_resolution_140keV`` argument of this function. Defaults to 0.
    :type intrinsic_resolution: float
+   :param intrinsic_resolution_140keV: Intrinsic resolution (FWHM) of the scintillator crystals at an energy of 140keV. The true intrinsic resolution is calculated assuming the resolution is proportional to E^(-1/2). If provided, then ``intrinsic_resolution`` is ignored. Defaults to None.
+   :type intrinsic_resolution_140keV: float | None
 
    :returns: PSF metadata.
    :rtype: SPECTPSFMeta
 
 
-.. py:function:: CT_to_mumap(CT, files_CT, file_NM, index_peak = 0, technique = 'from_table')
+.. py:function:: CT_to_mumap(CT, files_CT, file_NM, index_peak = 0, technique = 'from_table', E_SPECT = None)
 
    Converts a CT image to a mu-map given SPECT projection data. The CT data must be aligned with the projection data already; this is a helper function for ``get_attenuation_map_from_CT_slices``.
 
@@ -153,6 +157,8 @@ Functions
    :type index_peak: int, optional
    :param technique: Technique to convert HU to attenuation coefficients. The default, 'from_table', uses a table of coefficients for bilinear curves obtained for a variety of common radionuclides. The technique 'from_cortical_bone_fit' looks for a cortical bone peak in the scan and uses that to obtain the bilinear coefficients. For phantom scans where the attenuation coefficient is always significantly less than bone, the cortical bone technique will still work, since the first part of the bilinear curve (in the air to water range) does not depend on the cortical bone fit. Alternatively, one can provide an arbitrary function here which takes in a 3D scan with units of HU and converts to mu.
    :type technique: str, optional
+   :param E_SPECT: Energy of the photopeak in SPECT scan; this overrides the energy in the DICOM file, so should only be used if the DICOM file is incorrect. If None, then the energy is obtained from the DICOM file.
+   :type E_SPECT: float
 
    :returns: Attenuation map in units of 1/cm
    :rtype: torch.tensor

{pytomography-3.1.4 → pytomography-3.2.2}/docs/source/autoapi/pytomography/io/SPECT/simind/index.rst

@@ -111,7 +111,7 @@ Attributes
    :rtype: torch.Tensor[batch_size, Lx, Ly, Lz]
 
 
-.. py:function:: get_psfmeta_from_header(headerfile)
+.. py:function:: get_psfmeta_from_header(headerfile, min_sigmas=3)
 
    Obtains the SPECTPSFMeta data corresponding to a SIMIND simulation scan from the headerfile
 

{pytomography-3.1.4 → pytomography-3.2.2}/docs/source/autoapi/pytomography/likelihoods/index.rst

@@ -74,8 +74,8 @@ Classes
    :type projections: torch.Tensor | None
    :param additive_term: Additional term added after forward projection by the system matrix. This term might include things like scatter and randoms. Defaults to None.
    :type additive_term: torch.Tensor, optional
-   :param additive_term_variance_estimate: Variance estimate of the additive term. If none, then uncertainty estimation does not include contribution from the additive term. Defaults to None.
-   :type additive_term_variance_estimate: torch.tensor, optional
+   :param additive_term_variance_estimate: Operator for variance estimate of additive term. If none, then uncertainty estimation does not include contribution from the additive term. Defaults to None.
+   :type additive_term_variance_estimate: Callable, optional
 
    .. py:method:: compute_gradient(object, subset_idx = None, norm_BP_subset_method = 'subset_specific')
 
@@ -177,8 +177,8 @@ Classes
    :type projections: torch.Tensor | None
    :param additive_term: Additional term added after forward projection by the system matrix. This term might include things like scatter and randoms. Defaults to None.
    :type additive_term: torch.Tensor, optional
-   :param additive_term_variance_estimate: Variance estimate of the additive term. If none, then uncertainty estimation does not include contribution from the additive term. Defaults to None.
-   :type additive_term_variance_estimate: torch.tensor, optional
+   :param additive_term_variance_estimate: Operator for variance estimate of additive term. If none, then uncertainty estimation does not include contribution from the additive term. Defaults to None.
+   :type additive_term_variance_estimate: Callable, optional
 
    .. py:method:: _set_n_subsets(n_subsets)
 

{pytomography-3.1.4 → pytomography-3.2.2}/docs/source/autoapi/pytomography/likelihoods/likelihood/index.rst

@@ -27,8 +27,8 @@ Classes
    :type projections: torch.Tensor | None
    :param additive_term: Additional term added after forward projection by the system matrix. This term might include things like scatter and randoms. Defaults to None.
    :type additive_term: torch.Tensor, optional
-   :param additive_term_variance_estimate: Variance estimate of the additive term. If none, then uncertainty estimation does not include contribution from the additive term. Defaults to None.
-   :type additive_term_variance_estimate: torch.tensor, optional
+   :param additive_term_variance_estimate: Operator for variance estimate of additive term. If none, then uncertainty estimation does not include contribution from the additive term. Defaults to None.
+   :type additive_term_variance_estimate: Callable, optional
 
    .. py:method:: _set_n_subsets(n_subsets)
 

{pytomography-3.1.4 → pytomography-3.2.2}/docs/source/autoapi/pytomography/likelihoods/mse_objective/index.rst

@@ -61,8 +61,8 @@ Classes
    :type projections: torch.Tensor | None
    :param additive_term: Additional term added after forward projection by the system matrix. This term might include things like scatter and randoms. Defaults to None.
    :type additive_term: torch.Tensor, optional
-   :param additive_term_variance_estimate: Variance estimate of the additive term. If none, then uncertainty estimation does not include contribution from the additive term. Defaults to None.
-   :type additive_term_variance_estimate: torch.tensor, optional
+   :param additive_term_variance_estimate: Operator for variance estimate of additive term. If none, then uncertainty estimation does not include contribution from the additive term. Defaults to None.
+   :type additive_term_variance_estimate: Callable, optional
 
    .. py:method:: compute_gradient(object, subset_idx = None, norm_BP_subset_method = 'subset_specific')
 

{pytomography-3.1.4 → pytomography-3.2.2}/docs/source/autoapi/pytomography/projectors/PET/index.rst

@@ -36,7 +36,7 @@ Functions
 
 
 
-.. py:class:: PETLMSystemMatrix(object_meta, proj_meta, obj2obj_transforms = [], attenuation_map = None, scale_projection_by_sensitivity = False, N_splits = 1, device = pytomography.device)
+.. py:class:: PETLMSystemMatrix(object_meta, proj_meta, obj2obj_transforms = [], attenuation_map = None, scale_projection_by_sensitivity = False, N_splits = 1, FOV_scale_enabled = True, device = pytomography.device)
 
    Bases: :py:obj:`pytomography.projectors.SystemMatrix`
 

{pytomography-3.1.4 → pytomography-3.2.2}/docs/source/autoapi/pytomography/projectors/PET/petlm_system_matrix/index.rst

@@ -17,7 +17,7 @@ Classes
 
 
 
-.. py:class:: PETLMSystemMatrix(object_meta, proj_meta, obj2obj_transforms = [], attenuation_map = None, scale_projection_by_sensitivity = False, N_splits = 1, device = pytomography.device)
+.. py:class:: PETLMSystemMatrix(object_meta, proj_meta, obj2obj_transforms = [], attenuation_map = None, scale_projection_by_sensitivity = False, N_splits = 1, FOV_scale_enabled = True, device = pytomography.device)
 
    Bases: :py:obj:`pytomography.projectors.SystemMatrix`
 

{pytomography-3.1.4 → pytomography-3.2.2}/docs/source/autoapi/pytomography/transforms/SPECT/index.rst

@@ -87,18 +87,18 @@ Classes
 
 
 
-.. py:class:: SPECTPSFTransform(psf_meta = None, kernel_f = None, psf_net = None, assume_padded = True)
+.. py:class:: SPECTPSFTransform(psf_meta = None, psf_operator = None, assume_padded = True)
 
    Bases: :py:obj:`pytomography.transforms.Transform`
 
-   obj2obj transform used to model the effects of PSF blurring in SPECT. The smoothing kernel used to apply PSF modeling uses a Gaussian kernel with width :math:`\sigma` dependent on the distance of the point to the detector; that information is specified in the ``SPECTPSFMeta`` parameter. There are a few potential arguments to initialize this transform (i) `psf_meta`, which contains relevant collimator information to obtain a Gaussian PSF model that works for low/medium energy SPECT (ii) `kernel_f`, an callable function that gives the kernel at any source-detector distance :math:`d`, or (iii) `psf_net`, a network configured to automatically apply full PSF modeling to a given object :math:`f` at all source-detector distances. Only one of the arguments should be given.
+   obj2obj transform used to model the effects of PSF blurring in SPECT. The smoothing kernel used to apply PSF modeling uses a Gaussian kernel with width :math:`\sigma` dependent on the distance of the point to the detector; that information is specified in the ``SPECTPSFMeta`` parameter. There are a few potential arguments to initialize this transform (i) `psf_meta`, which contains relevant collimator information to obtain a Gaussian PSF model that works for low/medium energy SPECT (ii) `kernel_f`, an callable function that gives the kernel at any source-detector distance :math:`d`, or (iii) `psf_operator`, a network configured to automatically apply full PSF modeling to a given object :math:`f` at all source-detector distances. Only one of the arguments should be given.
 
    :param psf_meta: Metadata corresponding to the parameters of PSF blurring. In most cases (low/medium energy SPECT), this should be the only given argument.
    :type psf_meta: SPECTPSFMeta
    :param kernel_f: Function :math:`PSF(x,y,d)` that gives PSF at every source-detector distance :math:`d`. It should be able to take in 1D numpy arrays as its first two arguments, and a single argument for the final argument :math:`d`. The function should return a corresponding 2D PSF kernel.
    :type kernel_f: Callable
-   :param psf_net: Network that takes in an object :math:`f` and applies all necessary PSF correction to return a new object :math:`\tilde{f}` that is PSF corrected, such that subsequent summation along the x-axis accurately models the collimator detector response.
-   :type psf_net: Callable
+   :param psf_operator: Network that takes in an object :math:`f` and applies all necessary PSF correction to return a new object :math:`\tilde{f}` that is PSF corrected, such that subsequent summation along the x-axis accurately models the collimator detector response.
+   :type psf_operator: Callable
 
    .. py:method:: _configure_gaussian_model()
 
@@ -106,15 +106,9 @@ Classes
 
 
 
-   .. py:method:: _configure_kernel_model()
-
-      Internal function to configure arbitrary kernel modeling. This is called when `kernel_f` is given in initialization
-
-
-
    .. py:method:: _configure_manual_net()
 
-      Internal function to configure the PSF net. This is called when `psf_net` is given in initialization
+      Internal function to configure the PSF net. This is called when `psf_operator` is given in initialization
 
 
 

{pytomography-3.1.4 → pytomography-3.2.2}/docs/source/autoapi/pytomography/transforms/SPECT/psf/index.rst

@@ -13,7 +13,7 @@ Classes
 .. autoapisummary::
 
    pytomography.transforms.SPECT.psf.GaussianBlurNet
-   pytomography.transforms.SPECT.psf.ArbitraryPSFNet
+   pytomography.transforms.SPECT.psf.PSF2D
    pytomography.transforms.SPECT.psf.SPECTPSFTransform
 
 
@@ -50,30 +50,9 @@ Functions
 
 
 
-.. py:class:: ArbitraryPSFNet(kernel_f, distances, kernel_size, dr)
+.. py:class:: PSF2D(psf_operator, distances, kernel_size, dr)
 
-   Bases: :py:obj:`torch.nn.Module`
-
-   Network used to apply an arbitrary PSF based on the `kernel_f` function, which should be a function of parallel directions :math:`x` and :math:`y` and perpendicular direction :math:`d` to the detector head
-
-   :param kernel_f: PSF kernel
-   :type kernel_f: Callable
-   :param distances: Distances corresponding to each plane parallel to the detector
-   :type distances: Sequence[float]
-   :param kernel_size: Size of kernel used for blurring. Should be large enough to encapsulate the entire PSF at all distances
-   :type kernel_size: int
-   :param dr: The :math:`x` and :math:`y` voxel spacing in the object
-   :type dr: Sequence[float]
-
-   .. py:method:: forward(input)
-
-      Applies PSF blurring to `input`. Each X-plane gets a different blurring kernel applied, depending on detector distance.
-
-      :param input: Object to apply blurring to
-      :type input: torch.tensor
-
-      :returns: Blurred object, adjusted such that subsequent summation along the x-axis models the CDR
-      :rtype: torch.tensor
+   .. py:method:: __call__(input)
 
 
 
@@ -90,18 +69,18 @@ Functions
    :rtype: torch.nn.Conv2d
 
 
-.. py:class:: SPECTPSFTransform(psf_meta = None, kernel_f = None, psf_net = None, assume_padded = True)
+.. py:class:: SPECTPSFTransform(psf_meta = None, psf_operator = None, assume_padded = True)
 
    Bases: :py:obj:`pytomography.transforms.Transform`
 
-   obj2obj transform used to model the effects of PSF blurring in SPECT. The smoothing kernel used to apply PSF modeling uses a Gaussian kernel with width :math:`\sigma` dependent on the distance of the point to the detector; that information is specified in the ``SPECTPSFMeta`` parameter. There are a few potential arguments to initialize this transform (i) `psf_meta`, which contains relevant collimator information to obtain a Gaussian PSF model that works for low/medium energy SPECT (ii) `kernel_f`, an callable function that gives the kernel at any source-detector distance :math:`d`, or (iii) `psf_net`, a network configured to automatically apply full PSF modeling to a given object :math:`f` at all source-detector distances. Only one of the arguments should be given.
+   obj2obj transform used to model the effects of PSF blurring in SPECT. The smoothing kernel used to apply PSF modeling uses a Gaussian kernel with width :math:`\sigma` dependent on the distance of the point to the detector; that information is specified in the ``SPECTPSFMeta`` parameter. There are a few potential arguments to initialize this transform (i) `psf_meta`, which contains relevant collimator information to obtain a Gaussian PSF model that works for low/medium energy SPECT (ii) `kernel_f`, an callable function that gives the kernel at any source-detector distance :math:`d`, or (iii) `psf_operator`, a network configured to automatically apply full PSF modeling to a given object :math:`f` at all source-detector distances. Only one of the arguments should be given.
 
    :param psf_meta: Metadata corresponding to the parameters of PSF blurring. In most cases (low/medium energy SPECT), this should be the only given argument.
    :type psf_meta: SPECTPSFMeta
    :param kernel_f: Function :math:`PSF(x,y,d)` that gives PSF at every source-detector distance :math:`d`. It should be able to take in 1D numpy arrays as its first two arguments, and a single argument for the final argument :math:`d`. The function should return a corresponding 2D PSF kernel.
    :type kernel_f: Callable
-   :param psf_net: Network that takes in an object :math:`f` and applies all necessary PSF correction to return a new object :math:`\tilde{f}` that is PSF corrected, such that subsequent summation along the x-axis accurately models the collimator detector response.
-   :type psf_net: Callable
+   :param psf_operator: Network that takes in an object :math:`f` and applies all necessary PSF correction to return a new object :math:`\tilde{f}` that is PSF corrected, such that subsequent summation along the x-axis accurately models the collimator detector response.
+   :type psf_operator: Callable
 
    .. py:method:: _configure_gaussian_model()
 
@@ -109,15 +88,9 @@ Functions
 
 
 
-   .. py:method:: _configure_kernel_model()
-
-      Internal function to configure arbitrary kernel modeling. This is called when `kernel_f` is given in initialization
-
-
-
    .. py:method:: _configure_manual_net()
 
-      Internal function to configure the PSF net. This is called when `psf_net` is given in initialization
+      Internal function to configure the PSF net. This is called when `psf_operator` is given in initialization
 
 
 

{pytomography-3.1.4 → pytomography-3.2.2}/docs/source/autoapi/pytomography/utils/index.rst

@@ -291,7 +291,7 @@ Functions
    :rtype: np.array
 
 
-.. py:function:: compute_EW_scatter(projection_lower, projection_upper, width_lower, width_upper, width_peak, weighting_lower = 0.5, weighting_upper = 0.5, return_scatter_variance_estimate = False)
+.. py:function:: compute_EW_scatter(projection_lower, projection_upper, width_lower, width_upper, width_peak, weighting_lower = 0.5, weighting_upper = 0.5, proj_meta=None, sigma_theta = 0, sigma_r = 0, sigma_z = 0, N_sigmas = 3, return_scatter_variance_estimate = False)
 
    Computes triple energy window estimate from lower and upper scatter projections as well as window widths
 

{pytomography-3.1.4 → pytomography-3.2.2}/docs/source/autoapi/pytomography/utils/scatter/index.rst

@@ -13,11 +13,33 @@ Functions
 
 .. autoapisummary::
 
+   pytomography.utils.scatter.get_smoothed_scatter
    pytomography.utils.scatter.compute_EW_scatter
 
 
 
-.. py:function:: compute_EW_scatter(projection_lower, projection_upper, width_lower, width_upper, width_peak, weighting_lower = 0.5, weighting_upper = 0.5, return_scatter_variance_estimate = False)
+.. py:function:: get_smoothed_scatter(scatter, proj_meta, sigma_theta = 0, sigma_r = 0, sigma_z = 0, N_sigmas = 3)
+
+   Smooths SPECT projection metadata
+
+   :param scatter: Input projection data
+   :type scatter: torch.Tensor
+   :param proj_meta: Projection metadata
+   :type proj_meta: ProjMeta
+   :param sigma_theta: Smoothing in theta (specified in degrees). Defaults to 0.
+   :type sigma_theta: float, optional
+   :param sigma_r: Smoothing in r (specified in cm). Defaults to 0.
+   :type sigma_r: float, optional
+   :param sigma_z: Smoothing in z (specified in cm). Defaults to 0.
+   :type sigma_z: float, optional
+   :param N_sigmas: Number of sigmas to include in the smoothing kernel. Defaults to 3.
+   :type N_sigmas: int, optional
+
+   :returns: Smoothed projections
+   :rtype: torch.Tensor
+
+
+.. py:function:: compute_EW_scatter(projection_lower, projection_upper, width_lower, width_upper, width_peak, weighting_lower = 0.5, weighting_upper = 0.5, proj_meta=None, sigma_theta = 0, sigma_r = 0, sigma_z = 0, N_sigmas = 3, return_scatter_variance_estimate = False)
 
    Computes triple energy window estimate from lower and upper scatter projections as well as window widths
 

pytomography-3.2.2/docs/source/autoapi/test_multi_bed_recon/index.rst

@@ -0,0 +1,44 @@
+:py:mod:`test_multi_bed_recon`
+==============================
+
+.. py:module:: test_multi_bed_recon
+
+.. autoapi-nested-parse::
+
+   regression test for multi bed recon
+
+
+
+Module Contents
+---------------
+
+
+Functions
+~~~~~~~~~
+
+.. autoapisummary::
+
+   test_multi_bed_recon.test_multi_bed_recon
+   test_multi_bed_recon.reconstruct_singlebed
+
+
+
+Attributes
+~~~~~~~~~~
+
+.. autoapisummary::
+
+   test_multi_bed_recon.files_NM
+
+
+.. py:data:: files_NM
+   :value: []
+
+   
+
+.. py:function:: test_multi_bed_recon()
+
+
+.. py:function:: reconstruct_singlebed(i, projectionss, files_NM, files_CT)
+
+

{pytomography-3.1.4 → pytomography-3.2.2}/docs/source/conf.py

@@ -71,4 +71,16 @@ html_static_path = ['_static']
 
 # typehints
 autodoc_typehints = "description"
-autodoc_inherit_docstrings=True
+autodoc_inherit_docstrings=True
+
+# Add link to github
+html_theme_options = {
+    "icon_links": [
+        {
+            "name": "GitHub",
+            "url": "https://github.com/qurit/PyTomography",
+            "icon": "fa-brands fa-github",
+            "type": "fontawesome",
+        },
+    ],
+}

pytomography-3.2.2/docs/source/notebooks/run_all_notebooks.py

@@ -0,0 +1,29 @@
+import papermill as pm
+import os
+
+os.environ['PYDEVD_DISABLE_FILE_VALIDATION'] = '1'
+
+tutorials = [
+    #'t_siminddata.ipynb',
+    #'t_dicomdata.ipynb',
+    #'t_dicommultibed.ipynb',
+    #'t_uncertainty_spect.ipynb',
+    #'t_ac225_dicom_recon.ipynb',
+    't_ac225_simind_recon.ipynb',
+    #'t_PETGATE_scat_sino.ipynb',
+    't_PETGATE_scat_sinoTOF.ipynb',
+    #'t_PETGATE_scat_lm.ipynb',
+    #'t_PETGATE_scat_lmTOF.ipynb',
+    #'t_PETGATE_DIP.ipynb',
+    #'t_GE_HDF5.ipynb',
+    #'t_CT_GEN3.ipynb',
+    't_examplesystemmatrix.ipynb'
+]
+
+for tutorial in tutorials:
+    print(f"Running {tutorial}...")
+    try:
+        pm.execute_notebook(tutorial, tutorial)
+        print(f"{tutorial} ran successfully.")
+    except pm.PapermillExecutionError as e:
+        print(f"{tutorial} failed")