├── .gitignore ├── 3rdparty ├── catch.hpp ├── compact_mem_mgr.hpp ├── compact_mem_mgr.txx ├── cuda_helper_math.h ├── interp_poly_kernel.cu ├── libmorton │ ├── .gitattributes │ ├── .gitignore │ ├── LICENSE │ ├── README.md │ ├── libmorton │ │ └── include │ │ │ ├── morton.h │ │ │ ├── morton2D.h │ │ │ ├── morton2D_LUTs.h │ │ │ ├── morton3D.h │ │ │ ├── morton3D_LUTs.h │ │ │ ├── morton_BMI.h │ │ │ ├── morton_LUT_generators.h │ │ │ └── morton_common.h │ └── test │ │ ├── build_linux.sh │ │ ├── libmorton_test.cpp │ │ ├── libmorton_test.h │ │ ├── libmorton_test_3D.h │ │ ├── msvc2015 │ │ ├── libmorton_test.sln │ │ ├── libmorton_test.vcxproj │ │ └── libmorton_test.vcxproj.filters │ │ ├── msvc2017 │ │ ├── libmorton_test.sln │ │ ├── libmorton_test.vcxproj │ │ └── libmorton_test.vcxproj.filters │ │ ├── timer.h │ │ ├── todo.txt │ │ └── util.h ├── math_func.cu ├── pvfmm │ └── include │ │ ├── common.hpp │ │ ├── mem_mgr.hpp │ │ ├── mem_mgr.txx │ │ └── pvfmm.hpp ├── timings │ ├── EventTimings.cpp │ └── EventTimings.hpp └── version.cu ├── LICENSE.md ├── README.md ├── SConscript ├── SConstruct ├── TODO.md ├── app ├── test.cpp └── tusolver.cpp ├── clean.sh ├── compile.sh ├── config ├── test_forward_config.txt ├── test_forward_sin_config.txt ├── test_sparsetil_config.txt └── test_sparsetil_sin_config.txt ├── doc ├── README-OUT-INV-ENSEMBLE.md ├── README-OUT-TIL.md ├── README-TEMPORAL-STATS.md ├── README-TU-INV-STAT.md ├── configs │ ├── cpu_opt_single.py │ └── cuda_opt_single_sm70.py ├── figs │ └── GLIA.png ├── install.md └── memory-usage.txt ├── include ├── Parameters.h ├── Solver.h ├── SolverInterface.h ├── grad │ ├── DerivativeOperators.h │ └── SpectralOperators.h ├── mat │ ├── DiffCoef.h │ ├── MatProp.h │ ├── Obs.h │ ├── Phi.h │ ├── ReacCoef.h │ └── Tumor.h ├── opt │ ├── MEOptimizer.h │ ├── Optimizer.h │ ├── RDOptimizer.h │ ├── SparseTILOptimizer.h │ ├── TILOptimizer.h │ └── TaoInterface.h ├── pde │ ├── AdvectionSolver.h │ ├── DiffusionSolver.h │ ├── ElasticitySolver.h │ └── PdeOperators.h ├── test │ └── helper.h └── utils │ ├── IO.h │ ├── Interp.h │ ├── TypeDefs.h │ ├── Utils.h │ └── UtilsCuda.h ├── nvcc.py ├── paraview_states ├── movie.pvsm ├── synthetic_multiview.pvsm └── synthetic_testcase.pvsm ├── scripts ├── README.md ├── __init__.py ├── forward.py ├── gridcont │ ├── __init__.py │ ├── batch_sparsetil.py │ ├── extract_stats.py │ ├── run_sparsetil_multilevel.py │ └── run_sparsetil_multilevel_multigpu.py ├── helpers │ ├── convert_to_netcdf.py │ ├── convert_to_nifti.py │ ├── copy_til.py │ ├── forward_select.py │ ├── majority_vote.py │ ├── resize_image.py │ ├── run_several_forward.py │ ├── video.py │ └── video_mf.py ├── inverse.py ├── inverse_alzh.py ├── inverse_ensemble.py ├── inverse_gridcont.py ├── inverse_masseffect.py ├── inverse_til.py ├── masseffect │ ├── analysis.py │ ├── analysis.sh │ ├── extract_forward_stats.py │ ├── extract_stats.py │ ├── gridcont.py │ ├── old.py │ ├── register.py │ ├── run_masseffect.py │ ├── run_multiple_patients.py │ ├── run_nomasseffect.py │ ├── submit.sh │ ├── submit_extract_stats.sh │ └── update_tu_config.py ├── params.py ├── postproc │ ├── __init__.py │ ├── compute_hessian_cond.py │ ├── create_mask.py │ ├── hp_stats.py │ ├── postop_pat.py │ ├── resample.py │ ├── tmi20 │ │ ├── atlas.py │ │ ├── concomp.py │ │ ├── funcatlas_analysis.py │ │ ├── postproc-brats-grid-cont-results-CMP-GRAD-GRADOBJ.py │ │ ├── postproc-brats-grid-cont-results-CMP-SIGMA-SPARSITY.py │ │ ├── postproc-brats-grid-cont-results-newlog.py │ │ ├── postproc-brats-grid-cont-results.py │ │ ├── postproc_utils.py │ │ ├── postprocess.py │ │ ├── read_it-grad-newlog.py │ │ ├── read_it-grad.py │ │ ├── survival.py │ │ ├── survival_2.py │ │ └── svm-pp.py │ └── vis.py ├── run │ ├── cbica │ │ └── irun-grid-cont.sh │ ├── frontera │ │ └── irun-grid-cont.sh │ ├── hazelhen │ │ ├── irun-cm-data-comparison.sh │ │ ├── irun-grid-cont-batch.sh │ │ ├── irun-grid-cont.sh │ │ ├── irun-obs-mask.sh │ │ ├── irun-postproc-concomp.sh │ │ └── irun-postproc.sh │ └── stampede2 │ │ ├── irun-grid-cont-batch.sh │ │ ├── irun-grid-cont.sh │ │ ├── irun-obs-mask.sh │ │ └── irun-postproc.sh ├── utils │ ├── __init__.py │ ├── create_brain_stats.py │ ├── file_io.py │ ├── image_tools.py │ └── utils_gridcont.py └── vis │ ├── vis_all_brats_images.py │ ├── vis_localize.py │ ├── vis_masseffect_stats.py │ ├── vis_quick.py │ ├── vis_til_recons.py │ └── vis_til_single.py ├── src ├── Solver.cpp ├── SolverInterface.cpp ├── cuda │ ├── AdvectionSolver.cu │ ├── DerivativeOperators.cu │ ├── DiffCoef.cu │ ├── ElasticitySolver.cu │ ├── Interpolation.cu │ ├── InterpolationTexture.cu │ ├── PdeOperators.cu │ ├── Phi.cu │ ├── SpectralOperators.cu │ ├── Tumor.cu │ └── UtilsCuda.cu ├── grad │ ├── DerivativeOperators.cpp │ ├── DerivativeOperatorsKL.cpp │ ├── DerivativeOperatorsMassEffect.cpp │ ├── DerivativeOperatorsRD.cpp │ ├── DerivativeOperatorsRDObj.cpp │ ├── DerivativeOperatorsRDOnlyFD.cpp │ └── SpectralOperators.cpp ├── mat │ ├── DiffCoef.cpp │ ├── MatProp.cpp │ ├── Obs.cpp │ ├── Phi.cpp │ ├── ReacCoef.cpp │ └── Tumor.cpp ├── opt │ ├── MEOptimizer.cpp │ ├── Optimizer.cpp │ ├── RDOptimizer.cpp │ ├── SparseTILOptimizer.cpp │ ├── TILOptimizer.cpp │ └── TaoInterface.cpp ├── pde │ ├── AdvectionSolver.cpp │ ├── DiffusionSolver.cpp │ ├── ElasticitySolver.cpp │ ├── PdeOperators.cpp │ ├── PdeOperatorsMassEffect.cpp │ └── PdeOperatorsMultiSpecies.cpp ├── test │ ├── discussion.txt │ ├── grad.cpp │ ├── helper.cpp │ ├── pdesolver.cpp │ └── simulator.cpp └── utils │ ├── IO.cpp │ ├── Interp.cpp │ └── Utils.cpp ├── temp ├── InvSolver.cpp ├── InvSolver.h ├── README.md ├── TaoInterfaceLandfill.cpp ├── TumorSolverInterface.cpp ├── TumorSolverInterface.h ├── blmvm.c ├── forward.cpp ├── inverse.cpp ├── inversedata.cpp ├── opt.InvSolver.cpp └── opt.InvSolver.h └── testdata ├── README.md ├── atlas.nc ├── atlas_t1.nc ├── patient.nc ├── patient_tumor.nc ├── patient_tumor_IC.nc ├── patient_vt.nc └── sinusoid.nc /.gitignore: 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