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README.txt
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 | -------------------------------------------------------------------------------- This file summarises the repository data and informs the repositories for the source code used associated with the results presented in the manuscript "Parallel generation of extensive vascular networks with application to an archetypal human kidney model" by L.F.M. Cury, G.D. Maso Talou, M. Younes-Ibrahim and P.J. Blanco. For further details contact: g.masotalou@auckland.ac.nz or pjblanco@lncc.br -------------------------------------------------------------------------------- Directory structure for this repository: Root directory: where our explanatory files are located. \->CCO: Location for ".cco" files. \->CSV: Location for ".csv" files. \->ODS: Location for ".ods" files. \->Param: Location for ".param" files. \->VTK: Location for ".vtk" files. \->VTP: Location for ".vtp" files. -------------------------------------------------------------------------------- We explain our files types in their corresponding README files: README_CCO_TYPE01.txt and README_CCO_TYPE02.txt for .cco files. These are plain text files used by the VItA library. README_CSV_TYPE01.txt README_CSV_TYPE02.txt. These are plain text files for tabular data. README_ODS.txt. These are open-standard spreadsheet data. README_PARAM.txt. These are plain text files used as parameters for our source code. README_VTK.txt. These are plain text or binary files used by Paraview. README_VTP.txt. These are a binary XML file used by Paraview. -------------------------------------------------------------------------------- In fileRelationship.txt we explain the relationship between the files in this repository describing how they were used in out article. -------------------------------------------------------------------------------- In listCCO.txt we describe each file in the "CCO/" directory. In listCSV.txt we describe each file in the "CSV/" directory. In listODS.txt we describe each file in the "ODS/" directory. In listParam.txt we describe each file in the "Param/" directory. In listVTK.txt we describe each file in the "VTK/" directory. In listVTP.txt we describe each file in the "VTP/" directory. -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Software used for generation and analysis of this dataset. -------------------------------------------------------------------------------- CMake -------------------------------------------------------------------------------- A working version of CMake is required to compile and install VTK and VItA. It is available at <https://cmake.org/download/>. -------------------------------------------------------------------------------- VTK -------------------------------------------------------------------------------- A working install of VTK 8.1.2 is required. The main repository is available at <https://gitlab.kitware.com/vtk/vtk> and the specific version at <https://gitlab.kitware.com/vtk/vtk/-/tree/v8.1.2>. The authors are keeping a fork of the repo at <https://github.com/lfmc/VTK> and the specific version at <https://github.com/lfmc/VTK/tree/Cury2021_et_al_PDCCO>. -------------------------------------------------------------------------------- VItA -------------------------------------------------------------------------------- Next, install the VItA library branch containing our implementations of DCCO and PDDCO. The master branch is kept at <https://github.com/GonzaloMaso/VItA> and the tag used in this work is at <https://github.com/lfmc/VItA/tree/Cury2021_et_al_PDCCO>. -------------------------------------------------------------------------------- ParaView -------------------------------------------------------------------------------- We used ParaView v5.8 to visualize vascular trees saved as .vtp files. -------------------------------------------------------------------------------- Plotting -------------------------------------------------------------------------------- Our plots were generated with: 1. Python 3.8.5 2. Pandas 1.1.3 3. Numpy 1.19.2 4. Matplotlib 3.3.2 -------------------------------------------------------------------------------- |