├── .github └── workflows │ ├── draft-paper.yml │ └── python-test.yml ├── .gitignore ├── .readthedocs.yml ├── .zenodo.json ├── LICENSE ├── README.md ├── docs ├── Makefile ├── conf.py ├── index.rst ├── make.bat ├── modules.rst ├── pyssam.rst ├── requirements-docs.txt ├── requirements.txt └── tutorial │ ├── fit_parameters_example.ipynb │ ├── mesh_morphing_example.ipynb │ ├── sam_example.ipynb │ ├── ssam_example.ipynb │ └── ssm_example.ipynb ├── example_data ├── lung_landmarks │ ├── edgesCartesian0LLL-case8684.csv │ ├── edgesIndex0LLL-case8684.csv │ ├── landmarks0LLL-case8684.csv │ ├── landmarksLLL-case0576.csv │ ├── landmarksLLL-case0596.csv │ ├── landmarksLLL-case0645.csv │ ├── landmarksLLL-case0723.csv │ ├── landmarksLLL-case0739.csv │ ├── landmarksLLL-case1276.csv │ ├── landmarksLLL-case1437.csv │ ├── landmarksLLL-case1442.csv │ ├── landmarksLLL-case1616.csv │ ├── landmarksLLL-case1943.csv │ ├── landmarksLLL-case2456.csv │ ├── landmarksLLL-case2523.csv │ ├── landmarksLLL-case2827.csv │ ├── landmarksLLL-case3948.csv │ ├── landmarksLLL-case4002.csv │ ├── landmarksLLL-case4301.csv │ ├── landmarksLLL-case4444.csv │ ├── landmarksLLL-case4702.csv │ ├── landmarksLLL-case5216.csv │ ├── landmarksLLL-case5268.csv │ ├── landmarksLLL-case5359.csv │ ├── landmarksLLL-case5513.csv │ ├── landmarksLLL-case5800.csv │ ├── landmarksLLL-case5837.csv │ ├── landmarksLLL-case6262.csv │ ├── landmarksLLL-case6359.csv │ ├── landmarksLLL-case6493.csv │ ├── landmarksLLL-case6708.csv │ ├── landmarksLLL-case6730.csv │ ├── landmarksLLL-case6796.csv │ ├── landmarksLLL-case6972.csv │ ├── landmarksLLL-case7179.csv │ ├── landmarksLLL-case7422.csv │ ├── landmarksLLL-case7538.csv │ ├── landmarksLLL-case7713.csv │ ├── landmarksLLL-case7734.csv │ ├── landmarksLLL-case7742.csv │ ├── landmarksLLL-case7830.csv │ ├── landmarksLLL-case8059.csv │ ├── landmarksLLL-case8748.csv │ ├── landmarksLLL-case8865.csv │ ├── landmarksLLL-case8990.csv │ ├── landmarksLLL-case9210.csv │ ├── landmarksLLL-case9228.csv │ ├── landmarksLLL-case9377.csv │ ├── landmarksLLL-case9484.csv │ └── landmarksLLL-case9768.csv └── reconstructed_xrays │ ├── 1276 │ ├── drr-1276.md │ └── drr-1276.png │ ├── 1437 │ ├── drr-1437.md │ └── drr-1437.png │ ├── 1442 │ ├── drr-1442.md │ └── drr-1442.png │ ├── 1616 │ ├── drr-1616.md │ └── drr-1616.png │ ├── 1943 │ ├── drr-1943.md │ └── drr-1943.png │ ├── 2456 │ ├── drr-2456.md │ └── drr-2456.png │ ├── 2523 │ ├── drr-2523.md │ └── drr-2523.png │ ├── 2827 │ ├── drr-2827.md │ └── drr-2827.png │ ├── 3948 │ ├── drr-3948.md │ └── drr-3948.png │ ├── 4002 │ ├── drr-4002.md │ └── drr-4002.png │ ├── 4301 │ ├── drr-4301.md │ └── drr-4301.png │ ├── 4444 │ ├── drr-4444.md │ └── drr-4444.png │ ├── 4702 │ ├── drr-4702.md │ └── drr-4702.png │ ├── 5216 │ ├── drr-5216.md │ └── drr-5216.png │ ├── 5268 │ ├── drr-5268.md │ └── drr-5268.png │ ├── 5359 │ ├── drr-5359.md │ └── drr-5359.png │ ├── 5513 │ ├── drr-5513.md │ └── drr-5513.png │ ├── 5800 │ ├── drr-5800.md │ └── drr-5800.png │ ├── 5837 │ ├── drr-5837.md │ └── drr-5837.png │ ├── 6262 │ ├── drr-6262.md │ └── drr-6262.png │ ├── 6359 │ ├── drr-6359.md │ └── drr-6359.png │ ├── 6493 │ ├── drr-6493.md │ └── drr-6493.png │ ├── 6708 │ ├── drr-6708.md │ └── drr-6708.png │ ├── 6730 │ ├── drr-6730.md │ └── drr-6730.png │ ├── 6796 │ ├── drr-6796.md │ └── drr-6796.png │ ├── 6972 │ ├── drr-6972.md │ └── drr-6972.png │ ├── 7179 │ ├── drr-7179.md │ └── drr-7179.png │ ├── 7422 │ ├── drr-7422.md │ └── drr-7422.png │ ├── 7538 │ ├── drr-7538.md │ └── drr-7538.png │ ├── 7713 │ ├── drr-7713.md │ └── drr-7713.png │ ├── 7734 │ ├── drr-7734.md │ └── drr-7734.png │ ├── 7742 │ ├── drr-7742.md │ └── drr-7742.png │ ├── 7830 │ ├── drr-7830.md │ └── drr-7830.png │ ├── 8059 │ ├── drr-8059.md │ └── drr-8059.png │ ├── 8684 │ ├── drr-8684.md │ └── drr-8684.png │ ├── 8748 │ ├── drr-8748.md │ └── drr-8748.png │ ├── 8865 │ ├── drr-8865.md │ └── drr-8865.png │ ├── 8990 │ ├── drr-8990.md │ └── drr-8990.png │ ├── 9210 │ ├── drr-9210.md │ └── drr-9210.png │ ├── 9228 │ ├── drr-9228.md │ └── drr-9228.png │ ├── 9377 │ ├── drr-9377.md │ └── drr-9377.png │ ├── 9484 │ ├── drr-9484.md │ └── drr-9484.png │ ├── 9768 │ ├── drr-9768.md │ └── drr-9768.png │ ├── 0576 │ ├── drr-0576.md │ └── drr-0576.png │ ├── 0596 │ ├── drr-0596.md │ └── drr-0596.png │ ├── 0645 │ ├── drr-0645.md │ └── drr-0645.png │ ├── 0723 │ ├── drr-0723.md │ └── drr-0723.png │ ├── 0739 │ ├── drr-0739.md │ └── drr-0739.png │ ├── origins │ └── origins │ │ ├── drr-origin-0576.md │ │ ├── drr-origin-0596.md │ │ ├── drr-origin-0645.md │ │ ├── drr-origin-0723.md │ │ ├── drr-origin-0739.md │ │ ├── drr-origin-1276.md │ │ ├── drr-origin-1437.md │ │ ├── drr-origin-1442.md │ │ ├── drr-origin-1616.md │ │ ├── drr-origin-1943.md │ │ ├── drr-origin-2456.md │ │ ├── drr-origin-2523.md │ │ ├── drr-origin-2827.md │ │ ├── drr-origin-3948.md │ │ ├── drr-origin-4002.md │ │ ├── drr-origin-4301.md │ │ ├── drr-origin-4444.md │ │ ├── drr-origin-4702.md │ │ ├── drr-origin-5216.md │ │ ├── drr-origin-5268.md │ │ ├── drr-origin-5359.md │ │ ├── drr-origin-5513.md │ │ ├── drr-origin-5800.md │ │ ├── drr-origin-5837.md │ │ ├── drr-origin-6262.md │ │ ├── drr-origin-6359.md │ │ ├── drr-origin-6493.md │ │ ├── drr-origin-6708.md │ │ ├── drr-origin-6730.md │ │ ├── drr-origin-6796.md │ │ ├── drr-origin-6972.md │ │ ├── drr-origin-7179.md │ │ ├── drr-origin-7422.md │ │ ├── drr-origin-7538.md │ │ ├── drr-origin-7713.md │ │ ├── drr-origin-7734.md │ │ ├── drr-origin-7742.md │ │ ├── drr-origin-7830.md │ │ ├── drr-origin-8059.md │ │ ├── drr-origin-8684.md │ │ ├── drr-origin-8748.md │ │ ├── drr-origin-8865.md │ │ ├── drr-origin-8990.md │ │ ├── drr-origin-9210.md │ │ ├── drr-origin-9228.md │ │ ├── drr-origin-9377.md │ │ ├── drr-origin-9484.md │ │ └── drr-origin-9768.md │ └── transforms │ ├── transformParams_case0576_m_LLL.dat │ ├── transformParams_case0596_m_LLL.dat │ ├── transformParams_case0645_m_LLL.dat │ ├── transformParams_case0723_m_LLL.dat │ ├── transformParams_case0739_m_LLL.dat │ ├── transformParams_case1276_m_LLL.dat │ ├── transformParams_case1437_m_LLL.dat │ ├── transformParams_case1442_m_LLL.dat │ ├── transformParams_case1616_m_LLL.dat │ ├── transformParams_case1943_m_LLL.dat │ ├── transformParams_case2456_m_LLL.dat │ ├── transformParams_case2523_m_LLL.dat │ ├── transformParams_case2827_m_LLL.dat │ ├── transformParams_case3948_m_LLL.dat │ ├── transformParams_case4002_m_LLL.dat │ ├── transformParams_case4301_m_LLL.dat │ ├── transformParams_case4444_m_LLL.dat │ ├── transformParams_case4702_m_LLL.dat │ ├── transformParams_case5216_m_LLL.dat │ ├── transformParams_case5268_m_LLL.dat │ ├── transformParams_case5359_m_LLL.dat │ ├── transformParams_case5513_m_LLL.dat │ ├── transformParams_case5800_m_LLL.dat │ ├── transformParams_case5837_m_LLL.dat │ ├── transformParams_case6262_m_LLL.dat │ ├── transformParams_case6359_m_LLL.dat │ ├── transformParams_case6493_m_LLL.dat │ ├── transformParams_case6708_m_LLL.dat │ ├── transformParams_case6730_m_LLL.dat │ ├── transformParams_case6796_m_LLL.dat │ ├── transformParams_case6972_m_LLL.dat │ ├── transformParams_case7179_m_LLL.dat │ ├── transformParams_case7422_m_LLL.dat │ ├── transformParams_case7538_m_LLL.dat │ ├── transformParams_case7713_m_LLL.dat │ ├── transformParams_case7734_m_LLL.dat │ ├── transformParams_case7742_m_LLL.dat │ ├── transformParams_case7830_m_LLL.dat │ ├── transformParams_case8059_m_LLL.dat │ ├── transformParams_case8684_m_LLL.dat │ ├── transformParams_case8748_m_LLL.dat │ ├── transformParams_case8865_m_LLL.dat │ ├── transformParams_case8990_m_LLL.dat │ ├── transformParams_case9210_m_LLL.dat │ ├── transformParams_case9228_m_LLL.dat │ ├── transformParams_case9377_m_LLL.dat │ ├── transformParams_case9484_m_LLL.dat │ └── transformParams_case9768_m_LLL.dat ├── paper ├── figures │ ├── code-schematic.pdf │ ├── figure2-tree-example.pdf │ └── figure3-300.png ├── paper.bib └── paper.md ├── pyproject.toml ├── pyssam ├── __init__.py ├── datasets.py ├── morph_mesh.py ├── sam.py ├── 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