├── .gitignore ├── LICENSE.txt ├── README.rst ├── VERSION ├── demo ├── readme.txt ├── recon_3d │ └── shepp-logan-3D │ │ ├── README.txt │ │ ├── gen_data_shepplogan.m │ │ ├── proj_angles.bin │ │ ├── proj_times.bin │ │ ├── projections.bin │ │ ├── recon_times.bin │ │ ├── run_cluster.sh │ │ ├── run_unix.sh │ │ └── weights.bin └── recon_4d │ └── cahn-hilliard-4D │ ├── README.txt │ ├── proj_angles.bin │ ├── proj_times.bin │ ├── projections.bin │ ├── recon_times.bin │ ├── run_cluster.sh │ ├── run_unix.sh │ └── weights.bin ├── doc ├── Makefile ├── collection │ ├── APS_32ID │ │ ├── interlaced │ │ │ ├── APS1510_AlCu.py │ │ │ ├── APS1510_AlCu_TIMBIR.py │ │ │ ├── TIMBIR_angles.py │ │ │ ├── combine_bin.py │ │ │ ├── kwarg.py │ │ │ ├── reader.py │ │ │ └── recon.py │ │ └── non-interlaced │ │ │ ├── APS1504_AlCu_D_Coarsening-test.py │ │ │ ├── APS1510_AlCu.py │ │ │ ├── combine_bin.py │ │ │ ├── kwarg.py │ │ │ ├── reader.py │ │ │ └── recon.py │ └── readme.txt ├── conf.py ├── index.rst └── source │ ├── about.rst │ ├── bibtex │ └── cite.bib │ ├── collection.rst │ ├── credits.rst │ ├── demo.rst │ ├── devguide.rst │ ├── faq.rst │ ├── img │ ├── clone-in-desktop.png │ ├── commit-screen.png │ ├── create-pr.png │ ├── create-revision.png │ ├── fork-repo.png │ └── tomopy-logo.png │ └── install.rst ├── requirements-doc.txt └── src ├── MBIR_4D ├── Makefile ├── README.txt ├── TiffUtilities.h ├── TiffWrite.h ├── XT_AMatrix.c ├── XT_AMatrix.h ├── XT_Constants.h ├── XT_Debug.h ├── XT_Engine.c ├── XT_ForwardProject.c ├── XT_ForwardProject.h ├── XT_ICD_update.c ├── XT_ICD_update.h ├── XT_IOMisc.c ├── XT_IOMisc.h ├── XT_Init.c ├── XT_Init.h ├── XT_MPI.c ├── XT_MPI.h ├── XT_MPIIO.c ├── XT_MPIIO.h ├── XT_NHICD.c ├── XT_NHICD.h ├── XT_OffsetError.c ├── XT_OffsetError.h ├── XT_Profile.c ├── XT_Profile.h ├── XT_Structures.h ├── XT_VoxUpdate.c ├── XT_VoxUpdate.h ├── XT_genSinogram.c ├── XT_genSinogram.h ├── allocate.c ├── allocate.h ├── invert.c ├── invert.h ├── nrutil.c ├── nrutil.h ├── randlib.c ├── 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