This file describes the relationship between files (including source code of the corresponding git repository - https://github.com/lfmc/pdccoRSOS) and how they were used in our article. -------------------------------------------------------------------------------- Section (3a) - Baseline -------------------------------------------------------------------------------- Source: part_base_sdumont_specific.cpp part_base_sdumont_specific.srm Analysis and graphics: plot_baseline.py -------------------------------------------------------------------------------- Input: part_base_(2*XX-1).param part_ar_d100.vtk part_ar_d100_p01.vtk part_ar_d100_p02.vtk part_ar_d100_p03.vtk part_ar_d100_p04.vtk Output: part_baseline_seedXX_termYYYY_base.vtp part_baseline_seedXX_termYYYY_p01.vtp part_baseline_seedXX_termYYYY_p02.vtp part_baseline_seedXX_termYYYY_p03.vtp part_baseline_seedXX_termYYYY_p04.vtp part_baseline_seedXX_termYYYY_merged.vtp part_baseline_seedXX_termYYYY_full.vtp part_baseline_seedXX_termYYYY_merged.csv part_baseline_seedXX_termYYYY_full.csv Obs: XX goes from 01 to 10. YYYY goes from 0500 to 4500 in steps of 500. -------------------------------------------------------------------------------- Section (3b) - Aspect ratio -------------------------------------------------------------------------------- Source: part_ar_sdumont.cpp part_ar_sdumont.srm Analysis and graphics: plot_ar.py -------------------------------------------------------------------------------- Input: part_ar_XX.param part_ar_dZZZ.vtk part_ar_dZZZ_p01.vtk part_ar_dZZZ_p02.vtk part_ar_dZZZ_p03.vtk part_ar_dZZZ_p04.vtk Output: part_ar_seedXX_dZZZ_base.vtp part_ar_seedXX_dZZZ_p_01_.vtp part_ar_seedXX_dZZZ_p_02_.vtp part_ar_seedXX_dZZZ_p_03_.vtp part_ar_seedXX_dZZZ_p_04_.vtp part_ar_seedXX_dZZZ_merged.vtp part_ar_seedXX_dZZZ_full_.vtp part_ar_seedXX_dZZZ_merged.csv part_ar_seedXX_dZZZ_full_.csv OBS: XX goes from 01 to 10. ZZZ is 025, 050, 075, 100, 150 or 200. -------------------------------------------------------------------------------- Section (3c) - Multiple Input -------------------------------------------------------------------------------- Source: rsMultipleInput.cpp Analysis and graphics: comparison.py bestBalance.py -------------------------------------------------------------------------------- Input: rsMultipleInputhull.vtk rsMultipleInput_new.cco rsMultipleInputpWW.vtk Output: rsMultipleInput_func_XXXXX_YYYYY_ZZZZZ_base.vtp rsMultipleInput_func_XXXXX_YYYYY_ZZZZZ_base.csv rsMultipleInput_func_01000_08000_01000_merged.vtp rsMultipleInput_func_06000_00000_04000_merged.vtp rsMultipleInput_func_01000_08000_01000_merged.csv rsMultipleInput_func_06000_00000_04000_merged.csv Obs: WW goes from 01 to 08. -------------------------------------------------------------------------------- Section (3d) - Prototypal cerebral cortex -------------------------------------------------------------------------------- Step 1 - Generation of base tree -------------------------------------------------------------------------------- Source: 100k_base.cpp 100k_base.srm -------------------------------------------------------------------------------- Input: pial_11_03_2021_hull.vtk Output: 100k_base_pXX.cco 100k_base_pXX.vtp Obs: XX is 15, 25 or 36. -------------------------------------------------------------------------------- Step 2 - Generation of parallel trees -------------------------------------------------------------------------------- Source: 100k_net_full_direct.srm 100k_parts.cpp -------------------------------------------------------------------------------- Input: 100k_base_pXX.cco network_pXX_YYY.vtk Output: 100k_pXX_YYY.vtp Obs: XX is 15, 25 or 36. YYY goes from 01 to 0XX. -------------------------------------------------------------------------------- Step 3 - Generation of sequential tree -------------------------------------------------------------------------------- Source: 100k_sequential.cpp 100k_sequential.srm 100k_sequential_step.sh -------------------------------------------------------------------------------- Input: 100k_base_p25.cco pial_11_03_2021_hull.vtk Output: 100k_XXXXX_XXXXX.vtp times.ods time_processed.csv Obs: XXXXX is 1000, 2000, 3000, 4000, 5000, 6000, 7000, 8000, 9000, 10000, 15000, 20000, 25000, 30000 or 35000. -------------------------------------------------------------------------------- Step 4 - Generation of merged tree -------------------------------------------------------------------------------- Source: 100k_merge.cpp Analysis and graphics: plot_100k.py plot_time.py -------------------------------------------------------------------------------- Input: 100k_base_pXX.cco Output: 100k_merged_pXX.vtp 100k_merged_pXX.csv comparison_times.ods pXX_times.ods Obs: XX is 15, 25 or 36. -------------------------------------------------------------------------------- Section (3e) - Renal vasculature -------------------------------------------------------------------------------- Step 1 - Generation of initial tree -------------------------------------------------------------------------------- Source: renal_artery_to_core_2021.cpp -------------------------------------------------------------------------------- Input: renal_arteries_tri_simplified_04_02_2021.cco left_core_06_07_2020_LFC_decimated.vtk left_pelvis_06_07_2020_LFC_decimated.vtk left_pyramids_06_07_2020_LFC_decimated.vtk Output: left_kidney_13_pyramids_renal_artery_tri_radius_func_09990_00005_00005_09_02_2021_19_20_21.cco left_kidney_13_pyramids_renal_artery_tri_radius_func_09990_00005_00005_09_02_2021_19_20_21.vtp -------------------------------------------------------------------------------- Step 2 - Generation of base tree -------------------------------------------------------------------------------- Source: kidney_base_power.cpp kidney_base_power.srm -------------------------------------------------------------------------------- Input: k_base_power_03.param left_kidney_13_pyramids_renal_artery_tri_radius_func_09990_00005_00005_09_02_2021_19_20_21.cco left_core_06_07_2020_LFC_decimated.vtk left_pelvis_06_07_2020_LFC_decimated.vtk left_pyramids_06_07_2020_LFC_decimated.vtk left_surface_06_07_2020_LFC_decimated.vtk left_cortex_06_07_2020_LFC_decimated.vtk Output: kidney_base_gam30.cco kidney_base_gam30.vtp -------------------------------------------------------------------------------- Step 3 - Generation of parallel trees -------------------------------------------------------------------------------- Source: kidney_parts_power_specific.cpp kidney_100k_parts.srm -------------------------------------------------------------------------------- Input: kidney_base_power_03_part.param left_core_06_07_2020_LFC_decimated.vtk left_pelvis_06_07_2020_LFC_decimated.vtk left_pyramids_06_07_2020_LFC_decimated.vtk left_surface_06_07_2020_LFC_decimated.vtk left_cortex_region_XX_20_09_2020_cube.vtk kidney_base_gam30.cco Output: kidney_region_XX_gam30.vtp Obs: XX goes from 01 to 08. -------------------------------------------------------------------------------- Step 4 - Generation of final merged tree -------------------------------------------------------------------------------- Source: kidney_merge_power.cpp Analysis and graphics: kidney_rs.py plot_kidney.py -------------------------------------------------------------------------------- Input: kidney_base_gam30.cco Output: kidney_merged_gam30.vtp kidney_merged_gam30_strahler.vtp kidney_100k_connectivity_strahler.csv kidney_100k_summary_strahler.csv kidney_merged_gam30.csv kidney_merged_gam30_strahler.csv --------------------------------------------------------------------------------