Index

A

add_regularizer() (mumott.optimization.loss_functions.HuberLoss method) (mumott.optimization.loss_functions.SquaredLoss method) add_source() (mumott.core.simulator.Simulator method) adjoint() (mumott.methods.projectors.SAXSProjector method) (mumott.methods.projectors.SAXSProjectorCUDA method)

append() (mumott.core.geometry.Geometry method) (mumott.core.projection_stack.ProjectionStack method) (mumott.data_handling.DataContainer method) attach_to_stack() (mumott.core.projection_stack.Projection method) attached (mumott.core.projection_stack.Projection property) azimuthal_zero (mumott.core.spherical_harmonic_mapper.SphericalHarmonicMapper property)

B

Background

basis_set (mumott.core.simulator.Simulator property) Bibliography

C

calculate_sph_coefficients_rotated_around_z() (in module mumott.core.wigner_d_utilities) calculate_sph_coefficients_rotated_around_z_derived_wrt_the_angle() (in module mumott.core.wigner_d_utilities) calculate_sph_coefficients_rotated_by_90_degrees_around_negative_x() (in module mumott.core.wigner_d_utilities) calculate_sph_coefficients_rotated_by_90_degrees_around_positive_x() (in module mumott.core.wigner_d_utilities) calculate_sph_coefficients_rotated_by_euler_angles() (in module mumott.core.wigner_d_utilities) CG change_projection() (mumott.output_handling.ProjectionViewer method) channels (mumott.methods.basis_sets.TrivialBasis property) coefficients (mumott.methods.residual_calculators.GradientResidualCalculator property) (mumott.methods.residual_calculators.ZHTTResidualCalculator property) colormap (mumott.output_handling.OrientationImageMapper property) coordinates (mumott.core.spherical_harmonic_mapper.SphericalHarmonicMapper property) correct_for_transmission() (mumott.data_handling.DataContainer method) csr_representation (mumott.methods.basis_sets.GaussianKernels property) (mumott.methods.basis_sets.NearestNeighbor property) (mumott.methods.basis_sets.SphericalHarmonics property) (mumott.methods.basis_sets.TrivialBasis property)

cuda_difference() (in module mumott.core.cuda_kernels) cuda_framewise_contraction() (in module mumott.core.cuda_kernels) cuda_framewise_contraction_adjoint() (in module mumott.core.cuda_kernels) cuda_l1_gradient() (in module mumott.core.cuda_kernels) cuda_lower_bound() (in module mumott.core.cuda_kernels) cuda_rescale() (in module mumott.core.cuda_kernels) cuda_rescale_array() (in module mumott.core.cuda_kernels) cuda_scaled_difference() (in module mumott.core.cuda_kernels) cuda_sum() (in module mumott.core.cuda_kernels) cuda_tv_gradient() (in module mumott.core.cuda_kernels) cuda_weighted_difference() (in module mumott.core.cuda_kernels) cuda_weighted_sign() (in module mumott.core.cuda_kernels)

D

data (mumott.core.projection_stack.Projection property) (mumott.core.projection_stack.ProjectionStack property) (mumott.data_handling.DataContainer property) DataContainer (class in mumott.data_handling) DD degree_of_symmetry_map() (in module mumott.methods.utilities.fiber_fit) delete_projections() (mumott.core.geometry.Geometry method) detach_from_stack() (mumott.core.projection_stack.Projection method) detector_angles (mumott.core.geometry.Geometry property) detector_direction_origin (mumott.core.geometry.Geometry property)

detector_direction_positive_90 (mumott.core.geometry.Geometry property) diode (mumott.core.projection_stack.Projection property) (mumott.core.projection_stack.ProjectionStack property) (mumott.data_handling.DataContainer property) directions (mumott.methods.residual_calculators.ZHTTResidualCalculator property) distance_radius (mumott.core.simulator.Simulator property) dtype (mumott.methods.projectors.SAXSProjector property) (mumott.methods.projectors.SAXSProjectorCUDA property) (mumott.methods.residual_calculators.GradientResidualCalculator property) (mumott.methods.residual_calculators.ZHTTResidualCalculator property)

E

ell_indices (mumott.core.spherical_harmonic_mapper.SphericalHarmonicMapper property) (mumott.methods.basis_sets.SphericalHarmonics property) ell_max (mumott.core.spherical_harmonic_mapper.SphericalHarmonicMapper property) (mumott.methods.basis_sets.SphericalHarmonics property) (mumott.methods.residual_calculators.ZHTTResidualCalculator property)

emm_indices (mumott.core.spherical_harmonic_mapper.SphericalHarmonicMapper property) (mumott.methods.basis_sets.SphericalHarmonics property) enforce_friedel_symmetry (mumott.methods.basis_sets.GaussianKernels property) (mumott.methods.basis_sets.NearestNeighbor property)

F

find_approximate_symmetry_axis() (in module mumott.methods.utilities.fiber_fit) find_nearest_neighbor_index() (mumott.methods.basis_sets.NearestNeighbor method) forward() (mumott.methods.basis_sets.GaussianKernels method) (mumott.methods.basis_sets.NearestNeighbor method) (mumott.methods.basis_sets.SphericalHarmonics method) (mumott.methods.basis_sets.TrivialBasis method) (mumott.methods.projectors.SAXSProjector method) (mumott.methods.projectors.SAXSProjectorCUDA method)

framewise_contraction() (in module mumott.methods.utilities.tensor_operations) framewise_contraction_transpose() (in module mumott.methods.utilities.tensor_operations) full_circle_covered (mumott.core.geometry.Geometry property)

G

GaussianKernels (class in mumott.methods.basis_sets) generate_map() (mumott.methods.basis_sets.GaussianKernels method) (mumott.methods.basis_sets.NearestNeighbor method) (mumott.methods.basis_sets.SphericalHarmonics method) (mumott.methods.basis_sets.TrivialBasis method) Geometry (class in mumott.core.geometry) geometry (mumott.core.projection_stack.Projection property) (mumott.core.projection_stack.ProjectionStack property) (mumott.data_handling.DataContainer property) GeometryTuple (class in mumott.core.geometry) get_absorbances() (in module mumott.data_handling.utilities) get_alignment_geometry() (in module mumott.pipelines.utilities.alignment_geometry) get_amplitudes() (mumott.core.spherical_harmonic_mapper.SphericalHarmonicMapper method) (mumott.methods.basis_sets.GaussianKernels method) (mumott.methods.basis_sets.NearestNeighbor method) get_covariances() (mumott.methods.basis_sets.SphericalHarmonics method) get_estimate_of_lifschitz_constant() (mumott.optimization.loss_functions.SquaredLoss method) get_estimate_of_matrix_norm() (mumott.methods.residual_calculators.GradientResidualCalculator method) (mumott.methods.residual_calculators.ZHTTResidualCalculator method) get_filtered_projections() (in module mumott.pipelines.fbp_utilities) get_function_values() (mumott.methods.basis_sets.NearestNeighbor method) get_gradient() (mumott.methods.residual_calculators.ZHTTResidualCalculator method) get_gradient_from_residual_gradient() (mumott.methods.residual_calculators.GradientResidualCalculator method) get_harmonic_coefficients() (mumott.core.spherical_harmonic_mapper.SphericalHarmonicMapper method) get_inner_product() (mumott.methods.basis_sets.GaussianKernels method) (mumott.methods.basis_sets.SphericalHarmonics method) (mumott.methods.basis_sets.TrivialBasis method) get_largest_eigenvalue() (in module mumott.methods.utilities.preconditioning) get_loss() (mumott.optimization.loss_functions.HuberLoss method) (mumott.optimization.loss_functions.SquaredLoss method) get_output() (mumott.methods.basis_sets.GaussianKernels method) (mumott.methods.basis_sets.NearestNeighbor method) (mumott.methods.basis_sets.SphericalHarmonics method) (mumott.methods.basis_sets.TrivialBasis method)

get_regularization_norm() (mumott.optimization.loss_functions.HuberLoss method) (mumott.optimization.loss_functions.SquaredLoss method) (mumott.optimization.regularizers.GroupLasso method) (mumott.optimization.regularizers.HuberNorm method) (mumott.optimization.regularizers.L1Norm method) (mumott.optimization.regularizers.L2Norm method) (mumott.optimization.regularizers.Laplacian method) (mumott.optimization.regularizers.TotalVariation method) get_residual_norm() (mumott.optimization.loss_functions.HuberLoss method) (mumott.optimization.loss_functions.SquaredLoss method) get_residuals() (mumott.methods.residual_calculators.GradientResidualCalculator method) (mumott.methods.residual_calculators.ZHTTResidualCalculator method) get_second_moments() (mumott.methods.basis_sets.NearestNeighbor method) get_sirt_preconditioner() (in module mumott.methods.utilities.preconditioning) get_sirt_weights() (in module mumott.methods.utilities.preconditioning) get_spherical_harmonic_coefficients() (mumott.methods.basis_sets.GaussianKernels method) (mumott.methods.basis_sets.NearestNeighbor method) (mumott.methods.basis_sets.SphericalHarmonics method) (mumott.methods.basis_sets.TrivialBasis method) get_sub_geometry() (mumott.methods.basis_sets.NearestNeighbor method) get_tensor_sirt_preconditioner() (in module mumott.methods.utilities.preconditioning) get_tensor_sirt_weights() (in module mumott.methods.utilities.preconditioning) get_transmittivities() (in module mumott.data_handling.utilities) gradient() (mumott.methods.basis_sets.GaussianKernels method) (mumott.methods.basis_sets.NearestNeighbor method) (mumott.methods.basis_sets.SphericalHarmonics method) (mumott.methods.basis_sets.TrivialBasis method) GradientDescent (class in mumott.optimization.optimizers) GradientResidualCalculator (class in mumott.methods.residual_calculators) grid (mumott.methods.basis_sets.GaussianKernels property) (mumott.methods.basis_sets.NearestNeighbor property) grid_hash (mumott.methods.basis_sets.GaussianKernels property) (mumott.methods.basis_sets.NearestNeighbor property) grid_scale (mumott.methods.basis_sets.GaussianKernels property) GroupLasso (class in mumott.optimization.regularizers)

H

hash_data (mumott.core.projection_stack.Projection property) (mumott.core.projection_stack.ProjectionStack property) hash_diode (mumott.core.projection_stack.Projection property) (mumott.core.projection_stack.ProjectionStack property) hash_inner_angles (mumott.core.geometry.Geometry property) hash_inner_axes (mumott.core.geometry.Geometry property) hash_j_offsets (mumott.core.geometry.Geometry property)

hash_k_offsets (mumott.core.geometry.Geometry property) hash_outer_angles (mumott.core.geometry.Geometry property) hash_outer_axes (mumott.core.geometry.Geometry property) hash_rotations (mumott.core.geometry.Geometry property) hash_weights (mumott.core.projection_stack.Projection property) (mumott.core.projection_stack.ProjectionStack property) HuberLoss (class in mumott.optimization.loss_functions) HuberNorm (class in mumott.optimization.regularizers)

I

index_by_key() (mumott.core.projection_stack.ProjectionStack method) influences (mumott.core.simulator.Simulator property) initial_values (mumott.optimization.loss_functions.HuberLoss property) (mumott.optimization.loss_functions.SquaredLoss property) inner_angle (mumott.core.geometry.GeometryTuple attribute) (mumott.core.projection_stack.Projection property) inner_angles (mumott.core.geometry.Geometry property) inner_angles_as_array (mumott.core.geometry.Geometry property) inner_axes (mumott.core.geometry.Geometry property) inner_axes_as_array (mumott.core.geometry.Geometry property) inner_axis (mumott.core.geometry.GeometryTuple attribute) (mumott.core.projection_stack.Projection property) insert() (mumott.core.geometry.Geometry method) (mumott.core.projection_stack.ProjectionStack method)

integration_mode (mumott.methods.basis_sets.GaussianKernels property) (mumott.methods.basis_sets.NearestNeighbor property) (mumott.methods.basis_sets.SphericalHarmonics property) (mumott.methods.basis_sets.TrivialBasis property) is_dirty (mumott.methods.basis_sets.GaussianKernels property) (mumott.methods.basis_sets.NearestNeighbor property) (mumott.methods.basis_sets.TrivialBasis property) (mumott.methods.projectors.SAXSProjector property) (mumott.methods.projectors.SAXSProjectorCUDA property) (mumott.methods.residual_calculators.GradientResidualCalculator property) (mumott.methods.residual_calculators.ZHTTResidualCalculator property) ISTA

J

j_direction_0 (mumott.core.geometry.Geometry property) j_offset (mumott.core.geometry.GeometryTuple attribute) (mumott.core.projection_stack.Projection property) j_offsets (mumott.core.geometry.Geometry property) j_offsets_as_array (mumott.core.geometry.Geometry property) john_transform() (in module mumott.core.john_transform)

john_transform_adjoint() (in module mumott.core.john_transform) john_transform_adjoint_cuda() (in module mumott.core.john_transform_cuda) john_transform_adjoint_sparse_cuda() (in module mumott.core.john_transform_sparse_cuda) john_transform_cuda() (in module mumott.core.john_transform_cuda) john_transform_parameters (mumott.methods.projectors.SAXSProjector property) (mumott.methods.projectors.SAXSProjectorCUDA property) john_transform_sparse_cuda() (in module mumott.core.john_transform_sparse_cuda)

K

k_direction_0 (mumott.core.geometry.Geometry property) k_offset (mumott.core.geometry.GeometryTuple attribute) (mumott.core.projection_stack.Projection property)

k_offsets (mumott.core.geometry.Geometry property) k_offsets_as_array (mumott.core.geometry.Geometry property) kernel_scale_parameter (mumott.methods.basis_sets.GaussianKernels property)

L

L1Norm (class in mumott.optimization.regularizers) L2Norm (class in mumott.optimization.regularizers) Laplacian (class in mumott.optimization.regularizers)

LBFGS (class in mumott.optimization.optimizers) list_to_hash() (in module mumott.core.hashing) load_d_matrices() (in module mumott.core.wigner_d_utilities)

M

map (mumott.core.spherical_harmonic_mapper.SphericalHarmonicMapper property) MITRA module mumott.core.cuda_kernels mumott.core.hashing mumott.core.john_transform mumott.core.john_transform_cuda mumott.core.john_transform_sparse_cuda mumott.core.wigner_d_utilities mumott.data_handling.utilities mumott.methods.utilities.fiber_fit mumott.methods.utilities.preconditioning mumott.methods.utilities.tensor_operations MOTR mumott.core.cuda_kernels module mumott.core.hashing module

mumott.core.john_transform module mumott.core.john_transform_cuda module mumott.core.john_transform_sparse_cuda module mumott.core.wigner_d_utilities module mumott.data_handling.utilities module mumott.methods.utilities.fiber_fit module mumott.methods.utilities.preconditioning module mumott.methods.utilities.tensor_operations module

N

NearestNeighbor (class in mumott.methods.basis_sets) no_tqdm (mumott.optimization.optimizers.GradientDescent property) (mumott.optimization.optimizers.LBFGS property) (mumott.optimization.optimizers.ZHTTOptimizer property)

number_of_projections (mumott.methods.projectors.SAXSProjector property) (mumott.methods.projectors.SAXSProjectorCUDA property)

O

optimize() (mumott.core.simulator.Simulator method) (mumott.optimization.optimizers.GradientDescent method) (mumott.optimization.optimizers.LBFGS method) (mumott.optimization.optimizers.ZHTTOptimizer method) OrientationImageMapper (class in mumott.output_handling) outer_angle (mumott.core.geometry.GeometryTuple attribute) (mumott.core.projection_stack.Projection property)

outer_angles (mumott.core.geometry.Geometry property) outer_angles_as_array (mumott.core.geometry.Geometry property) outer_axes (mumott.core.geometry.Geometry property) outer_axes_as_array (mumott.core.geometry.Geometry property) outer_axis (mumott.core.geometry.GeometryTuple attribute) (mumott.core.projection_stack.Projection property)

P

p_direction_0 (mumott.core.geometry.Geometry property) phi (mumott.core.spherical_harmonic_mapper.SphericalHarmonicMapper property) polar_zero (mumott.core.spherical_harmonic_mapper.SphericalHarmonicMapper property) preconditioner (mumott.optimization.loss_functions.HuberLoss property) (mumott.optimization.loss_functions.SquaredLoss property) preconditioner_hash (mumott.optimization.loss_functions.HuberLoss property) (mumott.optimization.loss_functions.SquaredLoss property) probed_coordinates (mumott.core.geometry.Geometry property) (mumott.methods.basis_sets.GaussianKernels property) (mumott.methods.basis_sets.NearestNeighbor property) (mumott.methods.basis_sets.TrivialBasis property) (mumott.methods.residual_calculators.GradientResidualCalculator property) (mumott.methods.residual_calculators.ZHTTResidualCalculator property) ProbedCoordinates (class in mumott.core.probed_coordinates)

Projection (class in mumott.core.projection_stack) projection_matrix (mumott.methods.basis_sets.GaussianKernels property) (mumott.methods.basis_sets.NearestNeighbor property) (mumott.methods.basis_sets.SphericalHarmonics property) (mumott.methods.basis_sets.TrivialBasis property) projection_matrix_hash (mumott.methods.basis_sets.GaussianKernels property) (mumott.methods.basis_sets.NearestNeighbor property) projection_shape (mumott.core.geometry.Geometry property) (mumott.methods.projectors.SAXSProjector property) (mumott.methods.projectors.SAXSProjectorCUDA property) projections (mumott.data_handling.DataContainer property) ProjectionStack (class in mumott.core.projection_stack) ProjectionViewer (class in mumott.output_handling) proximal_operator() (mumott.optimization.regularizers.GroupLasso method)

R

RADTT read() (mumott.core.geometry.Geometry method) reconstruction_rotations (mumott.core.geometry.Geometry property) regularization_weights (mumott.optimization.loss_functions.HuberLoss property) (mumott.optimization.loss_functions.SquaredLoss property) regularizers (mumott.optimization.loss_functions.HuberLoss property) (mumott.optimization.loss_functions.SquaredLoss property) reset_simulation() (mumott.core.simulator.Simulator method) residual_norm_multiplier (mumott.optimization.loss_functions.HuberLoss property) (mumott.optimization.loss_functions.SquaredLoss property) rotate_reconstruction() (mumott.core.geometry.Geometry method) rotate_system_vectors() (mumott.core.geometry.Geometry method) rotated_coefficients (mumott.methods.residual_calculators.ZHTTResidualCalculator property) rotation (mumott.core.geometry.GeometryTuple attribute) (mumott.core.projection_stack.Projection property)

rotations (mumott.core.geometry.Geometry property) rotations_as_array (mumott.core.geometry.Geometry property) run_discrete_directions() (in module mumott.pipelines.reconstruction) run_fbp() (in module mumott.pipelines.filtered_back_projection) run_group_lasso() (in module mumott.pipelines.reconstruction) run_mitra() (in module mumott.pipelines.reconstruction) run_motr() (in module mumott.pipelines.async_pipelines) run_optical_flow_alignment() (in module mumott.pipelines.optical_flow_alignment) run_phase_matching_alignment() (in module mumott.pipelines.phase_matching_alignment) run_radtt() (in module mumott.pipelines.async_pipelines) run_sigtt() (in module mumott.pipelines.reconstruction) run_sirt() (in module mumott.pipelines.reconstruction) run_smotr() (in module mumott.pipelines.sparse_pipelines) run_spradtt() (in module mumott.pipelines.sparse_pipelines) run_stsirt() (in module mumott.pipelines.sparse_pipelines) run_tensor_sirt() (in module mumott.pipelines.async_pipelines)

S

SAXS SAXSProjector (class in mumott.methods.projectors) SAXSProjectorCUDA (class in mumott.methods.projectors) SAXSTT shape (mumott.core.simulator.Simulator property) shift_center_of_reconstruction() (in module mumott.pipelines.utilities.alignment_geometry) SIGTT simulation (mumott.core.simulator.Simulator property) Simulator (class in mumott.core.simulator)

SIRT SMOTR sources (mumott.core.simulator.Simulator property) SphericalHarmonicMapper (class in mumott.core.spherical_harmonic_mapper) SphericalHarmonics (class in mumott.methods.basis_sets) SPRADTT SquaredLoss (class in mumott.optimization.loss_functions) STSIRT symmetric_part_along_given_direction() (in module mumott.methods.utilities.fiber_fit) system_rotations (mumott.core.geometry.Geometry property)

T

theta (mumott.core.spherical_harmonic_mapper.SphericalHarmonicMapper property) to_spherical (mumott.core.probed_coordinates.ProbedCoordinates property) TotalVariation (class in mumott.optimization.regularizers)

TrivialBasis (class in mumott.methods.basis_sets) TV two_theta (mumott.core.geometry.Geometry property)

U

unit_vectors (mumott.core.spherical_harmonic_mapper.SphericalHarmonicMapper property) update_zeros() (mumott.core.spherical_harmonic_mapper.SphericalHarmonicMapper method) use_preconditioner_mask (mumott.optimization.loss_functions.HuberLoss property) (mumott.optimization.loss_functions.SquaredLoss property)

use_weights (mumott.optimization.loss_functions.HuberLoss property) (mumott.optimization.loss_functions.SquaredLoss property)

V

volume_mask (mumott.core.simulator.Simulator property) volume_shape (mumott.core.geometry.Geometry property) (mumott.methods.projectors.SAXSProjector property) (mumott.methods.projectors.SAXSProjectorCUDA property) (mumott.methods.residual_calculators.ZHTTResidualCalculator property)

W

WAXS weights (mumott.core.projection_stack.Projection property) (mumott.core.projection_stack.ProjectionStack property) (mumott.data_handling.DataContainer property)

wheel_properties (mumott.output_handling.OrientationImageMapper property) Workflow write() (mumott.core.geometry.Geometry method)

Z

ZHTTOptimizer (class in mumott.optimization.optimizers)

ZHTTResidualCalculator (class in mumott.methods.residual_calculators)