--- a
+++ b/fileRelationship.txt
@@ -0,0 +1,221 @@
+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
+--------------------------------------------------------------------------------