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.
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Section (3a) - Baseline
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Source:
part_base_sdumont_specific.cpp
part_base_sdumont_specific.srm
Analysis and graphics:
plot_baseline.py
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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.
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Section (3b) - Aspect ratio
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Source:
part_ar_sdumont.cpp
part_ar_sdumont.srm
Analysis and graphics:
plot_ar.py
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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.
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Section (3c) - Multiple Input
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Source: rsMultipleInput.cpp
Analysis and graphics:
comparison.py
bestBalance.py
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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.
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Section (3d) - Prototypal cerebral cortex
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Step 1 - Generation of base tree
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Source:
100k_base.cpp
100k_base.srm
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Input:
pial_11_03_2021_hull.vtk
Output:
100k_base_pXX.cco
100k_base_pXX.vtp
Obs:
XX is 15, 25 or 36.
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Step 2 - Generation of parallel trees 
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Source:
100k_net_full_direct.srm
100k_parts.cpp
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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.
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Step 3 - Generation of sequential tree
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Source:
100k_sequential.cpp
100k_sequential.srm
100k_sequential_step.sh
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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.
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Step 4 - Generation of merged tree
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Source:
100k_merge.cpp
Analysis and graphics:
plot_100k.py
plot_time.py
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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.
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Section (3e) - Renal vasculature
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Step 1 - Generation of initial tree
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Source:
renal_artery_to_core_2021.cpp
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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
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Step 2 - Generation of base tree
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Source:
kidney_base_power.cpp
kidney_base_power.srm
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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
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Step 3 - Generation of parallel trees
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Source:
kidney_parts_power_specific.cpp
kidney_100k_parts.srm
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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.
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Step 4 - Generation of final merged tree
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Source:
kidney_merge_power.cpp
Analysis and graphics:
kidney_rs.py
plot_kidney.py
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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
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