.. AUTO-GENERATED FILE -- DO NOT EDIT! :mod:`reconst` ============== .. automodule:: dipy.reconst .. currentmodule:: dipy.reconst .. autosummary:: bench test .. AUTO-GENERATED FILE -- DO NOT EDIT! Module: :mod:`reconst.base` --------------------------- .. automodule:: dipy.reconst.base .. currentmodule:: dipy.reconst.base .. autosummary:: ReconstFit ReconstModel .. AUTO-GENERATED FILE -- DO NOT EDIT! Module: :mod:`reconst.benchmarks` --------------------------------- .. automodule:: dipy.reconst.benchmarks .. currentmodule:: dipy.reconst.benchmarks .. autosummary:: .. AUTO-GENERATED FILE -- DO NOT EDIT! Module: :mod:`reconst.benchmarks.bench_bounding_box` ---------------------------------------------------- .. automodule:: dipy.reconst.benchmarks.bench_bounding_box .. currentmodule:: dipy.reconst.benchmarks.bench_bounding_box .. autosummary:: bench_bounding_box bounding_box measure .. AUTO-GENERATED FILE -- DO NOT EDIT! Module: :mod:`reconst.benchmarks.bench_csd` ------------------------------------------- .. automodule:: dipy.reconst.benchmarks.bench_csd .. currentmodule:: dipy.reconst.benchmarks.bench_csd .. autosummary:: ConstrainedSphericalDeconvModel GradientTable bench_csdeconv num_grad read_stanford_labels .. AUTO-GENERATED FILE -- DO NOT EDIT! Module: :mod:`reconst.benchmarks.bench_peaks` --------------------------------------------- .. automodule:: dipy.reconst.benchmarks.bench_peaks .. currentmodule:: dipy.reconst.benchmarks.bench_peaks .. autosummary:: bench_local_maxima local_maxima measure unique_edges .. AUTO-GENERATED FILE -- DO NOT EDIT! Module: :mod:`reconst.benchmarks.bench_squash` ---------------------------------------------- .. automodule:: dipy.reconst.benchmarks.bench_squash .. currentmodule:: dipy.reconst.benchmarks.bench_squash .. autosummary:: bench_quick_squash measure ndindex old_squash quick_squash reduce .. AUTO-GENERATED FILE -- DO NOT EDIT! Module: :mod:`reconst.benchmarks.bench_vec_val_sum` --------------------------------------------------- .. automodule:: dipy.reconst.benchmarks.bench_vec_val_sum .. currentmodule:: dipy.reconst.benchmarks.bench_vec_val_sum .. autosummary:: bench_vec_val_vect measure randn vec_val_vect with_einsum .. AUTO-GENERATED FILE -- DO NOT EDIT! Module: :mod:`reconst.cache` ---------------------------- .. automodule:: dipy.reconst.cache .. currentmodule:: dipy.reconst.cache .. autosummary:: Cache auto_attr .. AUTO-GENERATED FILE -- DO NOT EDIT! Module: :mod:`reconst.cross_validation` --------------------------------------- .. automodule:: dipy.reconst.cross_validation .. currentmodule:: dipy.reconst.cross_validation .. autosummary:: coeff_of_determination kfold_xval .. AUTO-GENERATED FILE -- DO NOT EDIT! Module: :mod:`reconst.csdeconv` ------------------------------- .. automodule:: dipy.reconst.csdeconv .. currentmodule:: dipy.reconst.csdeconv .. autosummary:: AxSymShResponse ConstrainedSDTModel ConstrainedSphericalDeconvModel SphHarmFit SphHarmModel TensorModel auto_response cart2sphere csdeconv estimate_response fa_inferior fa_superior fa_trace_to_lambdas forward_sdeconv_mat forward_sdt_deconv_mat fractional_anisotropy get_sphere lazy_index lpn multi_voxel_fit ndindex odf_deconv odf_sh_to_sharp peaks_from_model quad real_sph_harm real_sym_sh_basis recursive_response response_from_mask sh_to_rh single_tensor sph_harm_ind_list vec2vec_rotmat .. AUTO-GENERATED FILE -- DO NOT EDIT! Module: :mod:`reconst.dki` -------------------------- .. automodule:: dipy.reconst.dki .. currentmodule:: dipy.reconst.dki .. autosummary:: DiffusionKurtosisFit DiffusionKurtosisModel ReconstModel TensorFit Wcons Wrotate Wrotate_element apparent_kurtosis_coef axial_kurtosis carlson_rd carlson_rf cart2sphere check_multi_b decompose_tensor design_matrix directional_diffusion directional_diffusion_variance directional_kurtosis dki_prediction from_lower_triangular get_sphere kurtosis_maximum local_maxima lower_triangular mean_diffusivity mean_kurtosis ndindex ols_fit_dki radial_kurtosis sphere2cart split_dki_param vec_val_vect wls_fit_dki .. AUTO-GENERATED FILE -- DO NOT EDIT! Module: :mod:`reconst.dki_micro` -------------------------------- .. automodule:: dipy.reconst.dki_micro .. currentmodule:: dipy.reconst.dki_micro .. autosummary:: DiffusionKurtosisFit DiffusionKurtosisModel KurtosisMicrostructuralFit KurtosisMicrostructureModel axial_diffusivity axonal_water_fraction decompose_tensor diffusion_components directional_diffusion directional_kurtosis dkimicro_prediction dti_design_matrix from_lower_triangular get_sphere kurtosis_maximum lower_triangular mean_diffusivity ndindex radial_diffusivity split_dki_param tortuosity trace vec_val_vect .. AUTO-GENERATED FILE -- DO NOT EDIT! Module: :mod:`reconst.dsi` -------------------------- .. automodule:: dipy.reconst.dsi .. currentmodule:: dipy.reconst.dsi .. autosummary:: Cache DiffusionSpectrumDeconvFit DiffusionSpectrumDeconvModel DiffusionSpectrumFit DiffusionSpectrumModel OdfFit OdfModel LR_deconv create_qspace create_qtable fftn fftshift gen_PSF half_to_full_qspace hanning_filter ifftshift map_coordinates multi_voxel_fit pdf_interp_coords pdf_odf project_hemisph_bvecs threshold_propagator .. AUTO-GENERATED FILE -- DO NOT EDIT! Module: :mod:`reconst.dti` -------------------------- .. automodule:: dipy.reconst.dti .. currentmodule:: dipy.reconst.dti .. autosummary:: ReconstModel TensorFit TensorModel apparent_diffusion_coef auto_attr axial_diffusivity color_fa decompose_tensor design_matrix determinant deviatoric eig_from_lo_tri fractional_anisotropy from_lower_triangular geodesic_anisotropy get_sphere gradient_table isotropic iter_fit_tensor linearity lower_triangular mean_diffusivity mode nlls_fit_tensor norm ols_fit_tensor pinv planarity quantize_evecs radial_diffusivity restore_fit_tensor sphericity tensor_prediction trace vec_val_vect vector_norm wls_fit_tensor .. AUTO-GENERATED FILE -- DO NOT EDIT! Module: :mod:`reconst.forecast` ------------------------------- .. automodule:: dipy.reconst.forecast .. currentmodule:: dipy.reconst.forecast .. autosummary:: Cache ForecastFit ForecastModel OdfFit OdfModel cart2sphere csdeconv find_signal_means forecast_error_func forecast_matrix lb_forecast leastsq multi_voxel_fit optional_package psi_l real_sph_harm rho_matrix warn .. AUTO-GENERATED FILE -- DO NOT EDIT! Module: :mod:`reconst.fwdti` ---------------------------- .. automodule:: dipy.reconst.fwdti .. currentmodule:: dipy.reconst.fwdti .. autosummary:: FreeWaterTensorFit FreeWaterTensorModel ReconstModel TensorFit check_multi_b cholesky_to_lower_triangular decompose_tensor design_matrix from_lower_triangular fwdti_prediction lower_triangular lower_triangular_to_cholesky multi_voxel_fit ndindex nls_fit_tensor nls_iter vec_val_vect wls_fit_tensor wls_iter .. AUTO-GENERATED FILE -- DO NOT EDIT! Module: :mod:`reconst.gqi` -------------------------- .. automodule:: dipy.reconst.gqi .. currentmodule:: dipy.reconst.gqi .. autosummary:: Cache GeneralizedQSamplingFit GeneralizedQSamplingModel OdfFit OdfModel equatorial_maximum equatorial_zone_vertices gfa local_maxima multi_voxel_fit normalize_qa npa odf_sum patch_maximum patch_sum patch_vertices polar_zone_vertices remove_similar_vertices squared_radial_component triple_odf_maxima upper_hemi_map .. AUTO-GENERATED FILE -- DO NOT EDIT! Module: :mod:`reconst.ivim` --------------------------- .. automodule:: dipy.reconst.ivim .. currentmodule:: dipy.reconst.ivim .. autosummary:: IvimFit IvimModelTRR IvimModelVP ReconstModel IvimModel differential_evolution f_D_star_error f_D_star_prediction ivim_model_selector ivim_prediction least_squares multi_voxel_fit optional_package .. AUTO-GENERATED FILE -- DO NOT EDIT! Module: :mod:`reconst.mapmri` ----------------------------- .. automodule:: dipy.reconst.mapmri .. currentmodule:: dipy.reconst.mapmri .. autosummary:: Cache MapmriFit MapmriModel Optimizer ReconstFit ReconstModel b_mat b_mat_isotropic binomialfloat cart2sphere create_rspace delta factorial2 gcv_cost_function generalized_crossvalidation generalized_crossvalidation_array genlaguerre gradient_table hermite isotropic_scale_factor map_laplace_s map_laplace_t map_laplace_u mapmri_STU_reg_matrices mapmri_index_matrix mapmri_isotropic_K_mu_dependent mapmri_isotropic_K_mu_independent mapmri_isotropic_M_mu_dependent mapmri_isotropic_M_mu_independent mapmri_isotropic_index_matrix mapmri_isotropic_laplacian_reg_matrix mapmri_isotropic_laplacian_reg_matrix_from_index_matrix mapmri_isotropic_odf_matrix mapmri_isotropic_odf_sh_matrix mapmri_isotropic_phi_matrix mapmri_isotropic_psi_matrix mapmri_isotropic_radial_pdf_basis mapmri_isotropic_radial_signal_basis mapmri_laplacian_reg_matrix mapmri_odf_matrix mapmri_phi_1d mapmri_phi_matrix mapmri_psi_1d mapmri_psi_matrix mfactorial multi_voxel_fit optional_package real_sph_harm sfactorial sph_harm_ind_list warn .. AUTO-GENERATED FILE -- DO NOT EDIT! Module: :mod:`reconst.mcsd` --------------------------- .. automodule:: dipy.reconst.mcsd .. currentmodule:: dipy.reconst.mcsd .. autosummary:: MSDeconvFit MultiShellDeconvModel MultiShellResponse QpFitter multi_tissue_basis multi_voxel_fit optional_package solve_qp .. AUTO-GENERATED FILE -- DO NOT EDIT! Module: :mod:`reconst.msdki` ---------------------------- .. automodule:: dipy.reconst.msdki .. currentmodule:: dipy.reconst.msdki .. autosummary:: MeanDiffusionKurtosisFit MeanDiffusionKurtosisModel ReconstModel auto_attr check_multi_b design_matrix mean_signal_bvalue msdki_prediction ndindex round_bvals unique_bvals wls_fit_msdki .. AUTO-GENERATED FILE -- DO NOT EDIT! Module: :mod:`reconst.multi_voxel` ---------------------------------- .. automodule:: dipy.reconst.multi_voxel .. currentmodule:: dipy.reconst.multi_voxel .. autosummary:: CallableArray MultiVoxelFit ReconstFit as_strided multi_voxel_fit ndindex .. AUTO-GENERATED FILE -- DO NOT EDIT! Module: :mod:`reconst.odf` -------------------------- .. automodule:: dipy.reconst.odf .. currentmodule:: dipy.reconst.odf .. autosummary:: OdfFit OdfModel ReconstFit ReconstModel gfa minmax_normalize .. AUTO-GENERATED FILE -- DO NOT EDIT! Module: :mod:`reconst.qtdmri` ----------------------------- .. automodule:: dipy.reconst.qtdmri .. currentmodule:: dipy.reconst.qtdmri .. autosummary:: Cache QtdmriFit QtdmriModel GCV_cost_function H angular_basis_EAP_opt angular_basis_opt cart2sphere create_rt_space_grid design_matrix_spatial elastic_crossvalidation factorial factorial2 fmin_l_bfgs_b generalized_crossvalidation genlaguerre gradient_table_from_gradient_strength_bvecs l1_crossvalidation multi_voxel_fit optional_package part1_reg_matrix_tau part23_iso_reg_matrix_q part23_reg_matrix_q part23_reg_matrix_tau part4_iso_reg_matrix_q part4_reg_matrix_q part4_reg_matrix_tau qtdmri_anisotropic_scaling qtdmri_eap_matrix qtdmri_eap_matrix_ qtdmri_index_matrix qtdmri_isotropic_eap_matrix qtdmri_isotropic_eap_matrix_ qtdmri_isotropic_index_matrix qtdmri_isotropic_laplacian_reg_matrix qtdmri_isotropic_scaling qtdmri_isotropic_signal_matrix qtdmri_isotropic_signal_matrix_ qtdmri_isotropic_to_mapmri_matrix qtdmri_laplacian_reg_matrix qtdmri_mapmri_isotropic_normalization qtdmri_mapmri_normalization qtdmri_number_of_coefficients qtdmri_signal_matrix qtdmri_signal_matrix_ qtdmri_temporal_normalization qtdmri_to_mapmri_matrix radial_basis_EAP_opt radial_basis_opt real_sph_harm temporal_basis visualise_gradient_table_G_Delta_rainbow warn .. AUTO-GENERATED FILE -- DO NOT EDIT! Module: :mod:`reconst.sfm` -------------------------- .. automodule:: dipy.reconst.sfm .. currentmodule:: dipy.reconst.sfm .. autosummary:: Cache ExponentialIsotropicFit ExponentialIsotropicModel IsotropicFit IsotropicModel ReconstFit ReconstModel SparseFascicleFit SparseFascicleModel auto_attr nanmean optional_package sfm_design_matrix .. AUTO-GENERATED FILE -- DO NOT EDIT! Module: :mod:`reconst.shm` -------------------------- .. automodule:: dipy.reconst.shm .. currentmodule:: dipy.reconst.shm .. autosummary:: Cache CsaOdfModel LooseVersion OdfFit OdfModel OpdtModel QballBaseModel QballModel ResidualBootstrapWrapper SphHarmFit SphHarmModel anisotropic_power auto_attr bootstrap_data_array bootstrap_data_voxel calculate_max_order cart2sphere concatenate diag diff dot empty eye forward_sdeconv_mat gen_dirac hat lazy_index lcr_matrix lpn normalize_data order_from_ncoef pinv randint real_sph_harm real_sym_sh_basis real_sym_sh_mrtrix sf_to_sh sh_to_rh sh_to_sf sh_to_sf_matrix smooth_pinv sph_harm_ind_list spherical_harmonics svd unique .. AUTO-GENERATED FILE -- DO NOT EDIT! Module: :mod:`reconst.shore` ---------------------------- .. automodule:: dipy.reconst.shore .. currentmodule:: dipy.reconst.shore .. autosummary:: Cache ShoreFit ShoreModel cart2sphere create_rspace factorial genlaguerre l_shore multi_voxel_fit n_shore optional_package real_sph_harm shore_indices shore_matrix shore_matrix_odf shore_matrix_pdf shore_order warn .. AUTO-GENERATED FILE -- DO NOT EDIT! Module: :mod:`reconst.utils` ---------------------------- .. automodule:: dipy.reconst.utils .. currentmodule:: dipy.reconst.utils .. autosummary:: dki_design_matrix .. currentmodule:: dipy.reconst bench ~~~~~ .. autofunction:: bench test ~~~~ .. autofunction:: test .. currentmodule:: dipy.reconst.base :class:`ReconstFit` ~~~~~~~~~~~~~~~~~~~ .. autoclass:: ReconstFit :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`ReconstModel` ~~~~~~~~~~~~~~~~~~~~~ .. autoclass:: ReconstModel :members: :undoc-members: :show-inheritance: .. automethod:: __init__ .. currentmodule:: dipy.reconst.benchmarks .. currentmodule:: dipy.reconst.benchmarks.bench_bounding_box bench_bounding_box ~~~~~~~~~~~~~~~~~~ .. autofunction:: bench_bounding_box bounding_box ~~~~~~~~~~~~ .. autofunction:: bounding_box measure ~~~~~~~ .. autofunction:: measure .. currentmodule:: dipy.reconst.benchmarks.bench_csd :class:`ConstrainedSphericalDeconvModel` ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autoclass:: ConstrainedSphericalDeconvModel :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`GradientTable` ~~~~~~~~~~~~~~~~~~~~~~ .. autoclass:: GradientTable :members: :undoc-members: :show-inheritance: .. automethod:: __init__ bench_csdeconv ~~~~~~~~~~~~~~ .. autofunction:: bench_csdeconv num_grad ~~~~~~~~ .. autofunction:: num_grad read_stanford_labels ~~~~~~~~~~~~~~~~~~~~ .. autofunction:: read_stanford_labels .. currentmodule:: dipy.reconst.benchmarks.bench_peaks bench_local_maxima ~~~~~~~~~~~~~~~~~~ .. autofunction:: bench_local_maxima local_maxima ~~~~~~~~~~~~ .. autofunction:: local_maxima measure ~~~~~~~ .. autofunction:: measure unique_edges ~~~~~~~~~~~~ .. autofunction:: unique_edges .. currentmodule:: dipy.reconst.benchmarks.bench_squash bench_quick_squash ~~~~~~~~~~~~~~~~~~ .. autofunction:: bench_quick_squash measure ~~~~~~~ .. autofunction:: measure ndindex ~~~~~~~ .. autofunction:: ndindex old_squash ~~~~~~~~~~ .. autofunction:: old_squash quick_squash ~~~~~~~~~~~~ .. autofunction:: quick_squash reduce ~~~~~~ .. autofunction:: reduce .. currentmodule:: dipy.reconst.benchmarks.bench_vec_val_sum bench_vec_val_vect ~~~~~~~~~~~~~~~~~~ .. autofunction:: bench_vec_val_vect measure ~~~~~~~ .. autofunction:: measure randn ~~~~~ .. autofunction:: randn vec_val_vect ~~~~~~~~~~~~ .. autofunction:: vec_val_vect with_einsum ~~~~~~~~~~~ .. autofunction:: with_einsum .. currentmodule:: dipy.reconst.cache :class:`Cache` ~~~~~~~~~~~~~~ .. autoclass:: Cache :members: :undoc-members: :show-inheritance: .. automethod:: __init__ auto_attr ~~~~~~~~~ .. autofunction:: auto_attr .. currentmodule:: dipy.reconst.cross_validation coeff_of_determination ~~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: coeff_of_determination kfold_xval ~~~~~~~~~~ .. autofunction:: kfold_xval .. currentmodule:: dipy.reconst.csdeconv :class:`AxSymShResponse` ~~~~~~~~~~~~~~~~~~~~~~~~ .. autoclass:: AxSymShResponse :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`ConstrainedSDTModel` ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autoclass:: ConstrainedSDTModel :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`ConstrainedSphericalDeconvModel` ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autoclass:: ConstrainedSphericalDeconvModel :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`SphHarmFit` ~~~~~~~~~~~~~~~~~~~ .. autoclass:: SphHarmFit :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`SphHarmModel` ~~~~~~~~~~~~~~~~~~~~~ .. autoclass:: SphHarmModel :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`TensorModel` ~~~~~~~~~~~~~~~~~~~~ .. autoclass:: TensorModel :members: :undoc-members: :show-inheritance: .. automethod:: __init__ auto_response ~~~~~~~~~~~~~ .. autofunction:: auto_response cart2sphere ~~~~~~~~~~~ .. autofunction:: cart2sphere csdeconv ~~~~~~~~ .. autofunction:: csdeconv estimate_response ~~~~~~~~~~~~~~~~~ .. autofunction:: estimate_response fa_inferior ~~~~~~~~~~~ .. autofunction:: fa_inferior fa_superior ~~~~~~~~~~~ .. autofunction:: fa_superior fa_trace_to_lambdas ~~~~~~~~~~~~~~~~~~~ .. autofunction:: fa_trace_to_lambdas forward_sdeconv_mat ~~~~~~~~~~~~~~~~~~~ .. autofunction:: forward_sdeconv_mat forward_sdt_deconv_mat ~~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: forward_sdt_deconv_mat fractional_anisotropy ~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: fractional_anisotropy get_sphere ~~~~~~~~~~ .. autofunction:: get_sphere lazy_index ~~~~~~~~~~ .. autofunction:: lazy_index lpn ~~~ .. autofunction:: lpn multi_voxel_fit ~~~~~~~~~~~~~~~ .. autofunction:: multi_voxel_fit ndindex ~~~~~~~ .. autofunction:: ndindex odf_deconv ~~~~~~~~~~ .. autofunction:: odf_deconv odf_sh_to_sharp ~~~~~~~~~~~~~~~ .. autofunction:: odf_sh_to_sharp peaks_from_model ~~~~~~~~~~~~~~~~ .. autofunction:: peaks_from_model quad ~~~~ .. autofunction:: quad real_sph_harm ~~~~~~~~~~~~~ .. autofunction:: real_sph_harm real_sym_sh_basis ~~~~~~~~~~~~~~~~~ .. autofunction:: real_sym_sh_basis recursive_response ~~~~~~~~~~~~~~~~~~ .. autofunction:: recursive_response response_from_mask ~~~~~~~~~~~~~~~~~~ .. autofunction:: response_from_mask sh_to_rh ~~~~~~~~ .. autofunction:: sh_to_rh single_tensor ~~~~~~~~~~~~~ .. autofunction:: single_tensor sph_harm_ind_list ~~~~~~~~~~~~~~~~~ .. autofunction:: sph_harm_ind_list vec2vec_rotmat ~~~~~~~~~~~~~~ .. autofunction:: vec2vec_rotmat .. currentmodule:: dipy.reconst.dki :class:`DiffusionKurtosisFit` ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autoclass:: DiffusionKurtosisFit :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`DiffusionKurtosisModel` ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autoclass:: DiffusionKurtosisModel :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`ReconstModel` ~~~~~~~~~~~~~~~~~~~~~ .. autoclass:: ReconstModel :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`TensorFit` ~~~~~~~~~~~~~~~~~~ .. autoclass:: TensorFit :members: :undoc-members: :show-inheritance: .. automethod:: __init__ Wcons ~~~~~ .. autofunction:: Wcons Wrotate ~~~~~~~ .. autofunction:: Wrotate Wrotate_element ~~~~~~~~~~~~~~~ .. autofunction:: Wrotate_element apparent_kurtosis_coef ~~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: apparent_kurtosis_coef axial_kurtosis ~~~~~~~~~~~~~~ .. autofunction:: axial_kurtosis carlson_rd ~~~~~~~~~~ .. autofunction:: carlson_rd carlson_rf ~~~~~~~~~~ .. autofunction:: carlson_rf cart2sphere ~~~~~~~~~~~ .. autofunction:: cart2sphere check_multi_b ~~~~~~~~~~~~~ .. autofunction:: check_multi_b decompose_tensor ~~~~~~~~~~~~~~~~ .. autofunction:: decompose_tensor design_matrix ~~~~~~~~~~~~~ .. autofunction:: design_matrix directional_diffusion ~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: directional_diffusion directional_diffusion_variance ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: directional_diffusion_variance directional_kurtosis ~~~~~~~~~~~~~~~~~~~~ .. autofunction:: directional_kurtosis dki_prediction ~~~~~~~~~~~~~~ .. autofunction:: dki_prediction from_lower_triangular ~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: from_lower_triangular get_sphere ~~~~~~~~~~ .. autofunction:: get_sphere kurtosis_maximum ~~~~~~~~~~~~~~~~ .. autofunction:: kurtosis_maximum local_maxima ~~~~~~~~~~~~ .. autofunction:: local_maxima lower_triangular ~~~~~~~~~~~~~~~~ .. autofunction:: lower_triangular mean_diffusivity ~~~~~~~~~~~~~~~~ .. autofunction:: mean_diffusivity mean_kurtosis ~~~~~~~~~~~~~ .. autofunction:: mean_kurtosis ndindex ~~~~~~~ .. autofunction:: ndindex ols_fit_dki ~~~~~~~~~~~ .. autofunction:: ols_fit_dki radial_kurtosis ~~~~~~~~~~~~~~~ .. autofunction:: radial_kurtosis sphere2cart ~~~~~~~~~~~ .. autofunction:: sphere2cart split_dki_param ~~~~~~~~~~~~~~~ .. autofunction:: split_dki_param vec_val_vect ~~~~~~~~~~~~ .. autofunction:: vec_val_vect wls_fit_dki ~~~~~~~~~~~ .. autofunction:: wls_fit_dki .. currentmodule:: dipy.reconst.dki_micro :class:`DiffusionKurtosisFit` ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autoclass:: DiffusionKurtosisFit :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`DiffusionKurtosisModel` ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autoclass:: DiffusionKurtosisModel :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`KurtosisMicrostructuralFit` ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autoclass:: KurtosisMicrostructuralFit :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`KurtosisMicrostructureModel` ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autoclass:: KurtosisMicrostructureModel :members: :undoc-members: :show-inheritance: .. automethod:: __init__ axial_diffusivity ~~~~~~~~~~~~~~~~~ .. autofunction:: axial_diffusivity axonal_water_fraction ~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: axonal_water_fraction decompose_tensor ~~~~~~~~~~~~~~~~ .. autofunction:: decompose_tensor diffusion_components ~~~~~~~~~~~~~~~~~~~~ .. autofunction:: diffusion_components directional_diffusion ~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: directional_diffusion directional_kurtosis ~~~~~~~~~~~~~~~~~~~~ .. autofunction:: directional_kurtosis dkimicro_prediction ~~~~~~~~~~~~~~~~~~~ .. autofunction:: dkimicro_prediction dti_design_matrix ~~~~~~~~~~~~~~~~~ .. autofunction:: dti_design_matrix from_lower_triangular ~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: from_lower_triangular get_sphere ~~~~~~~~~~ .. autofunction:: get_sphere kurtosis_maximum ~~~~~~~~~~~~~~~~ .. autofunction:: kurtosis_maximum lower_triangular ~~~~~~~~~~~~~~~~ .. autofunction:: lower_triangular mean_diffusivity ~~~~~~~~~~~~~~~~ .. autofunction:: mean_diffusivity ndindex ~~~~~~~ .. autofunction:: ndindex radial_diffusivity ~~~~~~~~~~~~~~~~~~ .. autofunction:: radial_diffusivity split_dki_param ~~~~~~~~~~~~~~~ .. autofunction:: split_dki_param tortuosity ~~~~~~~~~~ .. autofunction:: tortuosity trace ~~~~~ .. autofunction:: trace vec_val_vect ~~~~~~~~~~~~ .. autofunction:: vec_val_vect .. currentmodule:: dipy.reconst.dsi :class:`Cache` ~~~~~~~~~~~~~~ .. autoclass:: Cache :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`DiffusionSpectrumDeconvFit` ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autoclass:: DiffusionSpectrumDeconvFit :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`DiffusionSpectrumDeconvModel` ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autoclass:: DiffusionSpectrumDeconvModel :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`DiffusionSpectrumFit` ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autoclass:: DiffusionSpectrumFit :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`DiffusionSpectrumModel` ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autoclass:: DiffusionSpectrumModel :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`OdfFit` ~~~~~~~~~~~~~~~ .. autoclass:: OdfFit :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`OdfModel` ~~~~~~~~~~~~~~~~~ .. autoclass:: OdfModel :members: :undoc-members: :show-inheritance: .. automethod:: __init__ LR_deconv ~~~~~~~~~ .. autofunction:: LR_deconv create_qspace ~~~~~~~~~~~~~ .. autofunction:: create_qspace create_qtable ~~~~~~~~~~~~~ .. autofunction:: create_qtable fftn ~~~~ .. autofunction:: fftn fftshift ~~~~~~~~ .. autofunction:: fftshift gen_PSF ~~~~~~~ .. autofunction:: gen_PSF half_to_full_qspace ~~~~~~~~~~~~~~~~~~~ .. autofunction:: half_to_full_qspace hanning_filter ~~~~~~~~~~~~~~ .. autofunction:: hanning_filter ifftshift ~~~~~~~~~ .. autofunction:: ifftshift map_coordinates ~~~~~~~~~~~~~~~ .. autofunction:: map_coordinates multi_voxel_fit ~~~~~~~~~~~~~~~ .. autofunction:: multi_voxel_fit pdf_interp_coords ~~~~~~~~~~~~~~~~~ .. autofunction:: pdf_interp_coords pdf_odf ~~~~~~~ .. autofunction:: pdf_odf project_hemisph_bvecs ~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: project_hemisph_bvecs threshold_propagator ~~~~~~~~~~~~~~~~~~~~ .. autofunction:: threshold_propagator .. currentmodule:: dipy.reconst.dti :class:`ReconstModel` ~~~~~~~~~~~~~~~~~~~~~ .. autoclass:: ReconstModel :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`TensorFit` ~~~~~~~~~~~~~~~~~~ .. autoclass:: TensorFit :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`TensorModel` ~~~~~~~~~~~~~~~~~~~~ .. autoclass:: TensorModel :members: :undoc-members: :show-inheritance: .. automethod:: __init__ apparent_diffusion_coef ~~~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: apparent_diffusion_coef auto_attr ~~~~~~~~~ .. autofunction:: auto_attr axial_diffusivity ~~~~~~~~~~~~~~~~~ .. autofunction:: axial_diffusivity color_fa ~~~~~~~~ .. autofunction:: color_fa decompose_tensor ~~~~~~~~~~~~~~~~ .. autofunction:: decompose_tensor design_matrix ~~~~~~~~~~~~~ .. autofunction:: design_matrix determinant ~~~~~~~~~~~ .. autofunction:: determinant deviatoric ~~~~~~~~~~ .. autofunction:: deviatoric eig_from_lo_tri ~~~~~~~~~~~~~~~ .. autofunction:: eig_from_lo_tri fractional_anisotropy ~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: fractional_anisotropy from_lower_triangular ~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: from_lower_triangular geodesic_anisotropy ~~~~~~~~~~~~~~~~~~~ .. autofunction:: geodesic_anisotropy get_sphere ~~~~~~~~~~ .. autofunction:: get_sphere gradient_table ~~~~~~~~~~~~~~ .. autofunction:: gradient_table isotropic ~~~~~~~~~ .. autofunction:: isotropic iter_fit_tensor ~~~~~~~~~~~~~~~ .. autofunction:: iter_fit_tensor linearity ~~~~~~~~~ .. autofunction:: linearity lower_triangular ~~~~~~~~~~~~~~~~ .. autofunction:: lower_triangular mean_diffusivity ~~~~~~~~~~~~~~~~ .. autofunction:: mean_diffusivity mode ~~~~ .. autofunction:: mode nlls_fit_tensor ~~~~~~~~~~~~~~~ .. autofunction:: nlls_fit_tensor norm ~~~~ .. autofunction:: norm ols_fit_tensor ~~~~~~~~~~~~~~ .. autofunction:: ols_fit_tensor pinv ~~~~ .. autofunction:: pinv planarity ~~~~~~~~~ .. autofunction:: planarity quantize_evecs ~~~~~~~~~~~~~~ .. autofunction:: quantize_evecs radial_diffusivity ~~~~~~~~~~~~~~~~~~ .. autofunction:: radial_diffusivity restore_fit_tensor ~~~~~~~~~~~~~~~~~~ .. autofunction:: restore_fit_tensor sphericity ~~~~~~~~~~ .. autofunction:: sphericity tensor_prediction ~~~~~~~~~~~~~~~~~ .. autofunction:: tensor_prediction trace ~~~~~ .. autofunction:: trace vec_val_vect ~~~~~~~~~~~~ .. autofunction:: vec_val_vect vector_norm ~~~~~~~~~~~ .. autofunction:: vector_norm wls_fit_tensor ~~~~~~~~~~~~~~ .. autofunction:: wls_fit_tensor .. currentmodule:: dipy.reconst.forecast :class:`Cache` ~~~~~~~~~~~~~~ .. autoclass:: Cache :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`ForecastFit` ~~~~~~~~~~~~~~~~~~~~ .. autoclass:: ForecastFit :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`ForecastModel` ~~~~~~~~~~~~~~~~~~~~~~ .. autoclass:: ForecastModel :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`OdfFit` ~~~~~~~~~~~~~~~ .. autoclass:: OdfFit :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`OdfModel` ~~~~~~~~~~~~~~~~~ .. autoclass:: OdfModel :members: :undoc-members: :show-inheritance: .. automethod:: __init__ cart2sphere ~~~~~~~~~~~ .. autofunction:: cart2sphere csdeconv ~~~~~~~~ .. autofunction:: csdeconv find_signal_means ~~~~~~~~~~~~~~~~~ .. autofunction:: find_signal_means forecast_error_func ~~~~~~~~~~~~~~~~~~~ .. autofunction:: forecast_error_func forecast_matrix ~~~~~~~~~~~~~~~ .. autofunction:: forecast_matrix lb_forecast ~~~~~~~~~~~ .. autofunction:: lb_forecast leastsq ~~~~~~~ .. autofunction:: leastsq multi_voxel_fit ~~~~~~~~~~~~~~~ .. autofunction:: multi_voxel_fit optional_package ~~~~~~~~~~~~~~~~ .. autofunction:: optional_package psi_l ~~~~~ .. autofunction:: psi_l real_sph_harm ~~~~~~~~~~~~~ .. autofunction:: real_sph_harm rho_matrix ~~~~~~~~~~ .. autofunction:: rho_matrix warn ~~~~ .. autofunction:: warn .. currentmodule:: dipy.reconst.fwdti :class:`FreeWaterTensorFit` ~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autoclass:: FreeWaterTensorFit :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`FreeWaterTensorModel` ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autoclass:: FreeWaterTensorModel :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`ReconstModel` ~~~~~~~~~~~~~~~~~~~~~ .. autoclass:: ReconstModel :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`TensorFit` ~~~~~~~~~~~~~~~~~~ .. autoclass:: TensorFit :members: :undoc-members: :show-inheritance: .. automethod:: __init__ check_multi_b ~~~~~~~~~~~~~ .. autofunction:: check_multi_b cholesky_to_lower_triangular ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: cholesky_to_lower_triangular decompose_tensor ~~~~~~~~~~~~~~~~ .. autofunction:: decompose_tensor design_matrix ~~~~~~~~~~~~~ .. autofunction:: design_matrix from_lower_triangular ~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: from_lower_triangular fwdti_prediction ~~~~~~~~~~~~~~~~ .. autofunction:: fwdti_prediction lower_triangular ~~~~~~~~~~~~~~~~ .. autofunction:: lower_triangular lower_triangular_to_cholesky ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: lower_triangular_to_cholesky multi_voxel_fit ~~~~~~~~~~~~~~~ .. autofunction:: multi_voxel_fit ndindex ~~~~~~~ .. autofunction:: ndindex nls_fit_tensor ~~~~~~~~~~~~~~ .. autofunction:: nls_fit_tensor nls_iter ~~~~~~~~ .. autofunction:: nls_iter vec_val_vect ~~~~~~~~~~~~ .. autofunction:: vec_val_vect wls_fit_tensor ~~~~~~~~~~~~~~ .. autofunction:: wls_fit_tensor wls_iter ~~~~~~~~ .. autofunction:: wls_iter .. currentmodule:: dipy.reconst.gqi :class:`Cache` ~~~~~~~~~~~~~~ .. autoclass:: Cache :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`GeneralizedQSamplingFit` ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autoclass:: GeneralizedQSamplingFit :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`GeneralizedQSamplingModel` ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autoclass:: GeneralizedQSamplingModel :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`OdfFit` ~~~~~~~~~~~~~~~ .. autoclass:: OdfFit :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`OdfModel` ~~~~~~~~~~~~~~~~~ .. autoclass:: OdfModel :members: :undoc-members: :show-inheritance: .. automethod:: __init__ equatorial_maximum ~~~~~~~~~~~~~~~~~~ .. autofunction:: equatorial_maximum equatorial_zone_vertices ~~~~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: equatorial_zone_vertices gfa ~~~ .. autofunction:: gfa local_maxima ~~~~~~~~~~~~ .. autofunction:: local_maxima multi_voxel_fit ~~~~~~~~~~~~~~~ .. autofunction:: multi_voxel_fit normalize_qa ~~~~~~~~~~~~ .. autofunction:: normalize_qa npa ~~~ .. autofunction:: npa odf_sum ~~~~~~~ .. autofunction:: odf_sum patch_maximum ~~~~~~~~~~~~~ .. autofunction:: patch_maximum patch_sum ~~~~~~~~~ .. autofunction:: patch_sum patch_vertices ~~~~~~~~~~~~~~ .. autofunction:: patch_vertices polar_zone_vertices ~~~~~~~~~~~~~~~~~~~ .. autofunction:: polar_zone_vertices remove_similar_vertices ~~~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: remove_similar_vertices squared_radial_component ~~~~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: squared_radial_component triple_odf_maxima ~~~~~~~~~~~~~~~~~ .. autofunction:: triple_odf_maxima upper_hemi_map ~~~~~~~~~~~~~~ .. autofunction:: upper_hemi_map .. currentmodule:: dipy.reconst.ivim :class:`IvimFit` ~~~~~~~~~~~~~~~~ .. autoclass:: IvimFit :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`IvimModelTRR` ~~~~~~~~~~~~~~~~~~~~~ .. autoclass:: IvimModelTRR :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`IvimModelVP` ~~~~~~~~~~~~~~~~~~~~ .. autoclass:: IvimModelVP :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`ReconstModel` ~~~~~~~~~~~~~~~~~~~~~ .. autoclass:: ReconstModel :members: :undoc-members: :show-inheritance: .. automethod:: __init__ IvimModel ~~~~~~~~~ .. autofunction:: IvimModel differential_evolution ~~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: differential_evolution f_D_star_error ~~~~~~~~~~~~~~ .. autofunction:: f_D_star_error f_D_star_prediction ~~~~~~~~~~~~~~~~~~~ .. autofunction:: f_D_star_prediction ivim_model_selector ~~~~~~~~~~~~~~~~~~~ .. autofunction:: ivim_model_selector ivim_prediction ~~~~~~~~~~~~~~~ .. autofunction:: ivim_prediction least_squares ~~~~~~~~~~~~~ .. autofunction:: least_squares multi_voxel_fit ~~~~~~~~~~~~~~~ .. autofunction:: multi_voxel_fit optional_package ~~~~~~~~~~~~~~~~ .. autofunction:: optional_package .. currentmodule:: dipy.reconst.mapmri :class:`Cache` ~~~~~~~~~~~~~~ .. autoclass:: Cache :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`MapmriFit` ~~~~~~~~~~~~~~~~~~ .. autoclass:: MapmriFit :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`MapmriModel` ~~~~~~~~~~~~~~~~~~~~ .. autoclass:: MapmriModel :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`Optimizer` ~~~~~~~~~~~~~~~~~~ .. autoclass:: Optimizer :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`ReconstFit` ~~~~~~~~~~~~~~~~~~~ .. autoclass:: ReconstFit :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`ReconstModel` ~~~~~~~~~~~~~~~~~~~~~ .. autoclass:: ReconstModel :members: :undoc-members: :show-inheritance: .. automethod:: __init__ b_mat ~~~~~ .. autofunction:: b_mat b_mat_isotropic ~~~~~~~~~~~~~~~ .. autofunction:: b_mat_isotropic binomialfloat ~~~~~~~~~~~~~ .. autofunction:: binomialfloat cart2sphere ~~~~~~~~~~~ .. autofunction:: cart2sphere create_rspace ~~~~~~~~~~~~~ .. autofunction:: create_rspace delta ~~~~~ .. autofunction:: delta factorial2 ~~~~~~~~~~ .. autofunction:: factorial2 gcv_cost_function ~~~~~~~~~~~~~~~~~ .. autofunction:: gcv_cost_function generalized_crossvalidation ~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: generalized_crossvalidation generalized_crossvalidation_array ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: generalized_crossvalidation_array genlaguerre ~~~~~~~~~~~ .. autofunction:: genlaguerre gradient_table ~~~~~~~~~~~~~~ .. autofunction:: gradient_table hermite ~~~~~~~ .. autofunction:: hermite isotropic_scale_factor ~~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: isotropic_scale_factor map_laplace_s ~~~~~~~~~~~~~ .. autofunction:: map_laplace_s map_laplace_t ~~~~~~~~~~~~~ .. autofunction:: map_laplace_t map_laplace_u ~~~~~~~~~~~~~ .. autofunction:: map_laplace_u mapmri_STU_reg_matrices ~~~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: mapmri_STU_reg_matrices mapmri_index_matrix ~~~~~~~~~~~~~~~~~~~ .. autofunction:: mapmri_index_matrix mapmri_isotropic_K_mu_dependent ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: mapmri_isotropic_K_mu_dependent mapmri_isotropic_K_mu_independent ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: mapmri_isotropic_K_mu_independent mapmri_isotropic_M_mu_dependent ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: mapmri_isotropic_M_mu_dependent mapmri_isotropic_M_mu_independent ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: mapmri_isotropic_M_mu_independent mapmri_isotropic_index_matrix ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: mapmri_isotropic_index_matrix mapmri_isotropic_laplacian_reg_matrix ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: mapmri_isotropic_laplacian_reg_matrix mapmri_isotropic_laplacian_reg_matrix_from_index_matrix ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: mapmri_isotropic_laplacian_reg_matrix_from_index_matrix mapmri_isotropic_odf_matrix ~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: mapmri_isotropic_odf_matrix mapmri_isotropic_odf_sh_matrix ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: mapmri_isotropic_odf_sh_matrix mapmri_isotropic_phi_matrix ~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: mapmri_isotropic_phi_matrix mapmri_isotropic_psi_matrix ~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: mapmri_isotropic_psi_matrix mapmri_isotropic_radial_pdf_basis ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: mapmri_isotropic_radial_pdf_basis mapmri_isotropic_radial_signal_basis ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: mapmri_isotropic_radial_signal_basis mapmri_laplacian_reg_matrix ~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: mapmri_laplacian_reg_matrix mapmri_odf_matrix ~~~~~~~~~~~~~~~~~ .. autofunction:: mapmri_odf_matrix mapmri_phi_1d ~~~~~~~~~~~~~ .. autofunction:: mapmri_phi_1d mapmri_phi_matrix ~~~~~~~~~~~~~~~~~ .. autofunction:: mapmri_phi_matrix mapmri_psi_1d ~~~~~~~~~~~~~ .. autofunction:: mapmri_psi_1d mapmri_psi_matrix ~~~~~~~~~~~~~~~~~ .. autofunction:: mapmri_psi_matrix mfactorial ~~~~~~~~~~ .. autofunction:: mfactorial multi_voxel_fit ~~~~~~~~~~~~~~~ .. autofunction:: multi_voxel_fit optional_package ~~~~~~~~~~~~~~~~ .. autofunction:: optional_package real_sph_harm ~~~~~~~~~~~~~ .. autofunction:: real_sph_harm sfactorial ~~~~~~~~~~ .. autofunction:: sfactorial sph_harm_ind_list ~~~~~~~~~~~~~~~~~ .. autofunction:: sph_harm_ind_list warn ~~~~ .. autofunction:: warn .. currentmodule:: dipy.reconst.mcsd :class:`MSDeconvFit` ~~~~~~~~~~~~~~~~~~~~ .. autoclass:: MSDeconvFit :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`MultiShellDeconvModel` ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autoclass:: MultiShellDeconvModel :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`MultiShellResponse` ~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autoclass:: MultiShellResponse :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`QpFitter` ~~~~~~~~~~~~~~~~~ .. autoclass:: QpFitter :members: :undoc-members: :show-inheritance: .. automethod:: __init__ multi_tissue_basis ~~~~~~~~~~~~~~~~~~ .. autofunction:: multi_tissue_basis multi_voxel_fit ~~~~~~~~~~~~~~~ .. autofunction:: multi_voxel_fit optional_package ~~~~~~~~~~~~~~~~ .. autofunction:: optional_package solve_qp ~~~~~~~~ .. autofunction:: solve_qp .. currentmodule:: dipy.reconst.msdki :class:`MeanDiffusionKurtosisFit` ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autoclass:: MeanDiffusionKurtosisFit :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`MeanDiffusionKurtosisModel` ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autoclass:: MeanDiffusionKurtosisModel :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`ReconstModel` ~~~~~~~~~~~~~~~~~~~~~ .. autoclass:: ReconstModel :members: :undoc-members: :show-inheritance: .. automethod:: __init__ auto_attr ~~~~~~~~~ .. autofunction:: auto_attr check_multi_b ~~~~~~~~~~~~~ .. autofunction:: check_multi_b design_matrix ~~~~~~~~~~~~~ .. autofunction:: design_matrix mean_signal_bvalue ~~~~~~~~~~~~~~~~~~ .. autofunction:: mean_signal_bvalue msdki_prediction ~~~~~~~~~~~~~~~~ .. autofunction:: msdki_prediction ndindex ~~~~~~~ .. autofunction:: ndindex round_bvals ~~~~~~~~~~~ .. autofunction:: round_bvals unique_bvals ~~~~~~~~~~~~ .. autofunction:: unique_bvals wls_fit_msdki ~~~~~~~~~~~~~ .. autofunction:: wls_fit_msdki .. currentmodule:: dipy.reconst.multi_voxel :class:`CallableArray` ~~~~~~~~~~~~~~~~~~~~~~ .. autoclass:: CallableArray :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`MultiVoxelFit` ~~~~~~~~~~~~~~~~~~~~~~ .. autoclass:: MultiVoxelFit :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`ReconstFit` ~~~~~~~~~~~~~~~~~~~ .. autoclass:: ReconstFit :members: :undoc-members: :show-inheritance: .. automethod:: __init__ as_strided ~~~~~~~~~~ .. autofunction:: as_strided multi_voxel_fit ~~~~~~~~~~~~~~~ .. autofunction:: multi_voxel_fit ndindex ~~~~~~~ .. autofunction:: ndindex .. currentmodule:: dipy.reconst.odf :class:`OdfFit` ~~~~~~~~~~~~~~~ .. autoclass:: OdfFit :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`OdfModel` ~~~~~~~~~~~~~~~~~ .. autoclass:: OdfModel :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`ReconstFit` ~~~~~~~~~~~~~~~~~~~ .. autoclass:: ReconstFit :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`ReconstModel` ~~~~~~~~~~~~~~~~~~~~~ .. autoclass:: ReconstModel :members: :undoc-members: :show-inheritance: .. automethod:: __init__ gfa ~~~ .. autofunction:: gfa minmax_normalize ~~~~~~~~~~~~~~~~ .. autofunction:: minmax_normalize .. currentmodule:: dipy.reconst.qtdmri :class:`Cache` ~~~~~~~~~~~~~~ .. autoclass:: Cache :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`QtdmriFit` ~~~~~~~~~~~~~~~~~~ .. autoclass:: QtdmriFit :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`QtdmriModel` ~~~~~~~~~~~~~~~~~~~~ .. autoclass:: QtdmriModel :members: :undoc-members: :show-inheritance: .. automethod:: __init__ GCV_cost_function ~~~~~~~~~~~~~~~~~ .. autofunction:: GCV_cost_function H ~ .. autofunction:: H angular_basis_EAP_opt ~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: angular_basis_EAP_opt angular_basis_opt ~~~~~~~~~~~~~~~~~ .. autofunction:: angular_basis_opt cart2sphere ~~~~~~~~~~~ .. autofunction:: cart2sphere create_rt_space_grid ~~~~~~~~~~~~~~~~~~~~ .. autofunction:: create_rt_space_grid design_matrix_spatial ~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: design_matrix_spatial elastic_crossvalidation ~~~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: elastic_crossvalidation factorial ~~~~~~~~~ .. autofunction:: factorial factorial2 ~~~~~~~~~~ .. autofunction:: factorial2 fmin_l_bfgs_b ~~~~~~~~~~~~~ .. autofunction:: fmin_l_bfgs_b generalized_crossvalidation ~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: generalized_crossvalidation genlaguerre ~~~~~~~~~~~ .. autofunction:: genlaguerre gradient_table_from_gradient_strength_bvecs ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: gradient_table_from_gradient_strength_bvecs l1_crossvalidation ~~~~~~~~~~~~~~~~~~ .. autofunction:: l1_crossvalidation multi_voxel_fit ~~~~~~~~~~~~~~~ .. autofunction:: multi_voxel_fit optional_package ~~~~~~~~~~~~~~~~ .. autofunction:: optional_package part1_reg_matrix_tau ~~~~~~~~~~~~~~~~~~~~ .. autofunction:: part1_reg_matrix_tau part23_iso_reg_matrix_q ~~~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: part23_iso_reg_matrix_q part23_reg_matrix_q ~~~~~~~~~~~~~~~~~~~ .. autofunction:: part23_reg_matrix_q part23_reg_matrix_tau ~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: part23_reg_matrix_tau part4_iso_reg_matrix_q ~~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: part4_iso_reg_matrix_q part4_reg_matrix_q ~~~~~~~~~~~~~~~~~~ .. autofunction:: part4_reg_matrix_q part4_reg_matrix_tau ~~~~~~~~~~~~~~~~~~~~ .. autofunction:: part4_reg_matrix_tau qtdmri_anisotropic_scaling ~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: qtdmri_anisotropic_scaling qtdmri_eap_matrix ~~~~~~~~~~~~~~~~~ .. autofunction:: qtdmri_eap_matrix qtdmri_eap_matrix_ ~~~~~~~~~~~~~~~~~~ .. autofunction:: qtdmri_eap_matrix_ qtdmri_index_matrix ~~~~~~~~~~~~~~~~~~~ .. autofunction:: qtdmri_index_matrix qtdmri_isotropic_eap_matrix ~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: qtdmri_isotropic_eap_matrix qtdmri_isotropic_eap_matrix_ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: qtdmri_isotropic_eap_matrix_ qtdmri_isotropic_index_matrix ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: qtdmri_isotropic_index_matrix qtdmri_isotropic_laplacian_reg_matrix ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: qtdmri_isotropic_laplacian_reg_matrix qtdmri_isotropic_scaling ~~~~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: qtdmri_isotropic_scaling qtdmri_isotropic_signal_matrix ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: qtdmri_isotropic_signal_matrix qtdmri_isotropic_signal_matrix_ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: qtdmri_isotropic_signal_matrix_ qtdmri_isotropic_to_mapmri_matrix ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: qtdmri_isotropic_to_mapmri_matrix qtdmri_laplacian_reg_matrix ~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: qtdmri_laplacian_reg_matrix qtdmri_mapmri_isotropic_normalization ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: qtdmri_mapmri_isotropic_normalization qtdmri_mapmri_normalization ~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: qtdmri_mapmri_normalization qtdmri_number_of_coefficients ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: qtdmri_number_of_coefficients qtdmri_signal_matrix ~~~~~~~~~~~~~~~~~~~~ .. autofunction:: qtdmri_signal_matrix qtdmri_signal_matrix_ ~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: qtdmri_signal_matrix_ qtdmri_temporal_normalization ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: qtdmri_temporal_normalization qtdmri_to_mapmri_matrix ~~~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: qtdmri_to_mapmri_matrix radial_basis_EAP_opt ~~~~~~~~~~~~~~~~~~~~ .. autofunction:: radial_basis_EAP_opt radial_basis_opt ~~~~~~~~~~~~~~~~ .. autofunction:: radial_basis_opt real_sph_harm ~~~~~~~~~~~~~ .. autofunction:: real_sph_harm temporal_basis ~~~~~~~~~~~~~~ .. autofunction:: temporal_basis visualise_gradient_table_G_Delta_rainbow ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: visualise_gradient_table_G_Delta_rainbow warn ~~~~ .. autofunction:: warn .. currentmodule:: dipy.reconst.sfm :class:`Cache` ~~~~~~~~~~~~~~ .. autoclass:: Cache :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`ExponentialIsotropicFit` ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autoclass:: ExponentialIsotropicFit :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`ExponentialIsotropicModel` ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autoclass:: ExponentialIsotropicModel :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`IsotropicFit` ~~~~~~~~~~~~~~~~~~~~~ .. autoclass:: IsotropicFit :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`IsotropicModel` ~~~~~~~~~~~~~~~~~~~~~~~ .. autoclass:: IsotropicModel :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`ReconstFit` ~~~~~~~~~~~~~~~~~~~ .. autoclass:: ReconstFit :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`ReconstModel` ~~~~~~~~~~~~~~~~~~~~~ .. autoclass:: ReconstModel :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`SparseFascicleFit` ~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autoclass:: SparseFascicleFit :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`SparseFascicleModel` ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autoclass:: SparseFascicleModel :members: :undoc-members: :show-inheritance: .. automethod:: __init__ auto_attr ~~~~~~~~~ .. autofunction:: auto_attr nanmean ~~~~~~~ .. autofunction:: nanmean optional_package ~~~~~~~~~~~~~~~~ .. autofunction:: optional_package sfm_design_matrix ~~~~~~~~~~~~~~~~~ .. autofunction:: sfm_design_matrix .. currentmodule:: dipy.reconst.shm :class:`Cache` ~~~~~~~~~~~~~~ .. autoclass:: Cache :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`CsaOdfModel` ~~~~~~~~~~~~~~~~~~~~ .. autoclass:: CsaOdfModel :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`LooseVersion` ~~~~~~~~~~~~~~~~~~~~~ .. autoclass:: LooseVersion :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`OdfFit` ~~~~~~~~~~~~~~~ .. autoclass:: OdfFit :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`OdfModel` ~~~~~~~~~~~~~~~~~ .. autoclass:: OdfModel :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`OpdtModel` ~~~~~~~~~~~~~~~~~~ .. autoclass:: OpdtModel :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`QballBaseModel` ~~~~~~~~~~~~~~~~~~~~~~~ .. autoclass:: QballBaseModel :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`QballModel` ~~~~~~~~~~~~~~~~~~~ .. autoclass:: QballModel :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`ResidualBootstrapWrapper` ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autoclass:: ResidualBootstrapWrapper :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`SphHarmFit` ~~~~~~~~~~~~~~~~~~~ .. autoclass:: SphHarmFit :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`SphHarmModel` ~~~~~~~~~~~~~~~~~~~~~ .. autoclass:: SphHarmModel :members: :undoc-members: :show-inheritance: .. automethod:: __init__ anisotropic_power ~~~~~~~~~~~~~~~~~ .. autofunction:: anisotropic_power auto_attr ~~~~~~~~~ .. autofunction:: auto_attr bootstrap_data_array ~~~~~~~~~~~~~~~~~~~~ .. autofunction:: bootstrap_data_array bootstrap_data_voxel ~~~~~~~~~~~~~~~~~~~~ .. autofunction:: bootstrap_data_voxel calculate_max_order ~~~~~~~~~~~~~~~~~~~ .. autofunction:: calculate_max_order cart2sphere ~~~~~~~~~~~ .. autofunction:: cart2sphere concatenate ~~~~~~~~~~~ .. autofunction:: concatenate diag ~~~~ .. autofunction:: diag diff ~~~~ .. autofunction:: diff dot ~~~ .. autofunction:: dot empty ~~~~~ .. autofunction:: empty eye ~~~ .. autofunction:: eye forward_sdeconv_mat ~~~~~~~~~~~~~~~~~~~ .. autofunction:: forward_sdeconv_mat gen_dirac ~~~~~~~~~ .. autofunction:: gen_dirac hat ~~~ .. autofunction:: hat lazy_index ~~~~~~~~~~ .. autofunction:: lazy_index lcr_matrix ~~~~~~~~~~ .. autofunction:: lcr_matrix lpn ~~~ .. autofunction:: lpn normalize_data ~~~~~~~~~~~~~~ .. autofunction:: normalize_data order_from_ncoef ~~~~~~~~~~~~~~~~ .. autofunction:: order_from_ncoef pinv ~~~~ .. autofunction:: pinv randint ~~~~~~~ .. autofunction:: randint real_sph_harm ~~~~~~~~~~~~~ .. autofunction:: real_sph_harm real_sym_sh_basis ~~~~~~~~~~~~~~~~~ .. autofunction:: real_sym_sh_basis real_sym_sh_mrtrix ~~~~~~~~~~~~~~~~~~ .. autofunction:: real_sym_sh_mrtrix sf_to_sh ~~~~~~~~ .. autofunction:: sf_to_sh sh_to_rh ~~~~~~~~ .. autofunction:: sh_to_rh sh_to_sf ~~~~~~~~ .. autofunction:: sh_to_sf sh_to_sf_matrix ~~~~~~~~~~~~~~~ .. autofunction:: sh_to_sf_matrix smooth_pinv ~~~~~~~~~~~ .. autofunction:: smooth_pinv sph_harm_ind_list ~~~~~~~~~~~~~~~~~ .. autofunction:: sph_harm_ind_list spherical_harmonics ~~~~~~~~~~~~~~~~~~~ .. autofunction:: spherical_harmonics svd ~~~ .. autofunction:: svd unique ~~~~~~ .. autofunction:: unique .. currentmodule:: dipy.reconst.shore :class:`Cache` ~~~~~~~~~~~~~~ .. autoclass:: Cache :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`ShoreFit` ~~~~~~~~~~~~~~~~~ .. autoclass:: ShoreFit :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`ShoreModel` ~~~~~~~~~~~~~~~~~~~ .. autoclass:: ShoreModel :members: :undoc-members: :show-inheritance: .. automethod:: __init__ cart2sphere ~~~~~~~~~~~ .. autofunction:: cart2sphere create_rspace ~~~~~~~~~~~~~ .. autofunction:: create_rspace factorial ~~~~~~~~~ .. autofunction:: factorial genlaguerre ~~~~~~~~~~~ .. autofunction:: genlaguerre l_shore ~~~~~~~ .. autofunction:: l_shore multi_voxel_fit ~~~~~~~~~~~~~~~ .. autofunction:: multi_voxel_fit n_shore ~~~~~~~ .. autofunction:: n_shore optional_package ~~~~~~~~~~~~~~~~ .. autofunction:: optional_package real_sph_harm ~~~~~~~~~~~~~ .. autofunction:: real_sph_harm shore_indices ~~~~~~~~~~~~~ .. autofunction:: shore_indices shore_matrix ~~~~~~~~~~~~ .. autofunction:: shore_matrix shore_matrix_odf ~~~~~~~~~~~~~~~~ .. autofunction:: shore_matrix_odf shore_matrix_pdf ~~~~~~~~~~~~~~~~ .. autofunction:: shore_matrix_pdf shore_order ~~~~~~~~~~~ .. autofunction:: shore_order warn ~~~~ .. autofunction:: warn .. currentmodule:: dipy.reconst.utils dki_design_matrix ~~~~~~~~~~~~~~~~~ .. autofunction:: dki_design_matrix