├── .gitignore ├── LICENSE ├── README.md ├── README_cmdline_options.md └── cpab ├── __init__.py ├── clean_pyc.py ├── cpa1d ├── CpaSpace.py ├── Multiscale.py ├── Tessellation.py ├── TransformWrapper.py ├── TransformWrapper_example.py ├── Visualize.py ├── __init__.py ├── calcs │ ├── ClosedFormInt.py │ ├── ClosedFormInt_usage_example.py │ ├── _CpaCalcs.py │ ├── __init__.py │ └── _default_params_flow_int.py ├── inference │ ├── __init__.py │ └── transformation │ │ ├── MonotonicRegression.py │ │ ├── MonotonicRegression_example.py │ │ └── __init__.py ├── model │ ├── __init__.py │ └── transformations │ │ ├── __init__.py │ │ └── landmarks │ │ ├── _ScaleDependentLogLikelihoodGaussian.py │ │ ├── _ScaleDependentLogLikelihoodGeneral.py │ │ ├── __init__.py │ │ └── gpu │ │ ├── __init__.py │ │ └── gaussian.py ├── needful_things.py └── utils │ ├── __init__.py │ ├── _create_cells.py │ ├── _create_verts_and_H.py │ └── constraints │ ├── __init__.py │ ├── _create_constraint_mat_bdry.py │ ├── _create_constraint_mat_warp_around.py │ └── _create_cont_constraint_mat.py ├── cpa2d ├── ConfigPlt.py ├── CpaSpace.py ├── Multiscale.py ├── Tessellation.py ├── TransformWrapper.py ├── TransformWrapper_example.py ├── TransformWrapper_example_cmdline.py ├── __init__.py ├── apps │ ├── __init__.py │ ├── landmarks │ │ ├── InferenceParamsDefault.py │ │ ├── InferenceParamsLFW.py │ │ ├── disp.py │ │ ├── example_data │ │ │ └── LFW │ │ │ │ └── landmarks_5_and_6.npz │ │ ├── get_data_LFW.py │ │ ├── inference_example_LFW.py │ │ └── visualize_results_LFW.py │ └── register │ │ ├── get_data.py │ │ └── register_images_MNIST.py ├── calcs │ ├── _CpaCalcs.py │ ├── __init__.py │ ├── _default_params_flow_int.py │ └── expm_hacked.py ├── inference │ ├── __init__.py │ └── transformation │ │ ├── Register.py │ │ ├── TransformationFitter.py │ │ └── __init__.py ├── model │ ├── __init__.py │ └── transformations │ │ ├── __init__.py │ │ ├── landmarks │ │ ├── _ScaleDependentLogLikelihoodGaussian.py │ │ ├── _ScaleDependentLogLikelihoodGeneral.py │ │ ├── __init__.py │ │ └── gpu │ │ │ ├── __init__.py │ │ │ └── gaussian.py │ │ └── register │ │ ├── _ScaleDependentLogLikelihoodGaussian.py │ │ ├── _ScaleDependentLogLikelihoodGeneral.py │ │ ├── __init__.py │ │ └── gpu │ │ ├── __init__.py │ │ └── gaussian.py ├── needful_things.py └── utils │ ├── HOLD_IT_get_stuff_for_the_local_version.py │ ├── __init__.py │ ├── _create_cells.py │ ├── _create_grid_lines.py │ ├── _invert_y_axis_if_needed.py │ ├── colored_squares.py │ └── constraints │ ├── __init__.py │ ├── _create_constraint_mat_bdry.py │ ├── _create_cont_constraint_mat.py │ └── _create_cont_constraint_mat_separable.py ├── cpa3d ├── CpaSpace.py ├── Multiscale.py ├── Tessellation.py ├── TransformWrapper.py ├── TransformWrapper_example.py ├── __init__.py ├── calcs │ ├── _CpaCalcs.py │ ├── __init__.py │ └── _default_params_flow_int.py ├── needful_things.py └── utils │ ├── __init__.py │ ├── _create_cells.py │ ├── _create_verts_and_H_type_I.py │ ├── _create_verts_and_H_type_II.py │ └── constraints │ ├── __init__.py │ ├── _create_constraint_mat_bdry.py │ ├── _create_cont_constraint_mat.py │ └── _create_cont_constraint_mat_separable.py ├── cpaHd ├── CpaSpace.py ├── Tessellation.py ├── __init__.py ├── calcs │ ├── _CpaCalcs.py │ ├── __init__.py │ └── _default_params_flow_int.py └── utils │ ├── __init__.py │ ├── _create_cells.py │ ├── _create_verts_and_H.py │ └── constraints │ ├── __init__.py │ ├── _create_constraint_mat_bdry.py │ └── _create_cont_constraint_mat.py ├── cpaNd ├── ExpmEff.py ├── _AffineFlow.py ├── _CpaCalcs.py ├── _CpaSpace.py ├── _Multiscale.py ├── _PAT.py ├── _Tessellation.py ├── _TransformWrapper.py ├── __init__.py ├── cy │ ├── Makefile │ ├── __init__.py │ ├── expm.pyx │ ├── expm.so │ ├── libc │ │ ├── Makefile │ │ ├── c8lib.h │ │ ├── c8lib.sh │ │ ├── include │ │ │ ├── c8lib.h │ │ │ ├── matrix_exponential.h │ │ │ ├── r8lib.h │ │ │ └── test_matrix_exponential.h │ │ ├── matrix_exponential.h │ │ ├── matrix_exponential.sh │ │ ├── my_test │ │ ├── my_test.sh │ │ ├── my_test_output.txt │ │ ├── r8lib.h │ │ ├── r8lib.sh │ │ ├── setup.py │ │ ├── test_call_from_cy.py │ │ ├── test_call_from_cy.pyx │ │ ├── test_call_from_cy.so │ │ ├── test_matrix_exponential.h │ │ ├── test_matrix_exponential.sh │ │ ├── test_matrix_exponential_prb.sh │ │ └── test_matrix_exponential_prb_output.txt │ └── setup.py ├── decide_sharedmemory.py ├── expm_affine_2D.py ├── expm_affine_3D.py ├── inference │ ├── InferenceAlgorithm.py │ ├── MCMC_InferenceAlgorithm.py │ ├── Metropolis.py │ ├── Proposal.py │ ├── ProposalSphericalGaussian.py │ └── __init__.py ├── model │ ├── _LogLikelihood.py │ ├── _LogPrior.py │ ├── _ScaleDependentLogPrior.py │ ├── _ScaleDependentLogPriorGeneral.py │ └── __init__.py └── utils │ ├── __init__.py │ ├── _create_constraint_mat_preserve_vol.py │ ├── _create_constraint_mat_zerovals.py │ ├── _get_stuff_for_the_local_version.py │ └── _null.py ├── dirnames.py ├── distributions ├── CpaCovs.py ├── MultiscaleCoarse2FinePrior.py ├── __init__.py ├── cpa_simple_mean.py ├── create_cov_velTess.py ├── create_joint_algebra_cov.py ├── draw_from_normal_in_cpa_space.py └── standard_cdfs.py └── gpu ├── Calcs.py ├── __init__.py ├── calc.cu ├── calc_1Dto1D.cu ├── calc_2Dto2D.cu ├── calc_2Dto2D_no_shared.cu ├── calc_2Dto2D_only_As_are_shared.cu ├── calc_3Dto3D.cu ├── calc_3Dto3D_no_shared.cu ├── calc_3Dto3D_only_As_are_shared.cu ├── calc_HDtoHD.cu ├── calc_HDtoHD_no_shared.cu ├── demo.py ├── demo_3d.py ├── expm ├── __init__.py ├── cy │ ├── Makefile │ ├── __init__.py │ ├── expm.pyx │ ├── expm.so │ ├── libc │ │ ├── Makefile │ │ ├── c8lib.h │ │ ├── c8lib.sh │ │ ├── include │ │ │ ├── c8lib.h │ │ │ ├── matrix_exponential.h │ │ │ ├── r8lib.h │ │ │ └── test_matrix_exponential.h │ │ ├── matrix_exponential.h │ │ ├── matrix_exponential.sh │ │ ├── my_test │ │ ├── my_test.sh │ │ ├── my_test_output.txt │ │ ├── r8lib.h │ │ ├── r8lib.sh │ │ ├── setup.py │ │ ├── test_call_from_cy.py │ │ ├── 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