From 1a4ae4ff20a77859a8a1dc609d5d8efa4c617f2d Mon Sep 17 00:00:00 2001 From: Alexis Pereda Date: Mon, 18 Mar 2024 15:50:18 +0100 Subject: [PATCH 1/2] Add t34 test for biodose actor --- .gitignore | 1 + t34_biodose_actor/data/GateMaterials.db | 476 +++++++++++++++++++++++ t34_biodose_actor/data/HSG_NanOx.db | 416 ++++++++++++++++++++ t34_biodose_actor/mac/carbon.mac | 3 + t34_biodose_actor/mac/main.mac | 115 ++++++ t34_biodose_actor/mac/physics_carbon.mac | 1 + t34_biodose_actor/mac/physics_proton.mac | 1 + t34_biodose_actor/mac/proton.mac | 3 + t34_biodose_actor/mac/source_carbon.mac | 15 + t34_biodose_actor/mac/source_proton.mac | 14 + t34_biodose_actor/output/.gitkeep | 0 t34_biodose_actor/runAnalysis.py | 74 ++++ t34_biodose_actor/runTest.sh | 2 + 13 files changed, 1121 insertions(+) create mode 100644 t34_biodose_actor/data/GateMaterials.db create mode 100644 t34_biodose_actor/data/HSG_NanOx.db create mode 100644 t34_biodose_actor/mac/carbon.mac create mode 100644 t34_biodose_actor/mac/main.mac create mode 100644 t34_biodose_actor/mac/physics_carbon.mac create mode 100644 t34_biodose_actor/mac/physics_proton.mac create mode 100644 t34_biodose_actor/mac/proton.mac create mode 100644 t34_biodose_actor/mac/source_carbon.mac create mode 100644 t34_biodose_actor/mac/source_proton.mac create mode 100644 t34_biodose_actor/output/.gitkeep create mode 100755 t34_biodose_actor/runAnalysis.py create mode 100755 t34_biodose_actor/runTest.sh diff --git a/.gitignore b/.gitignore index 1e9680d..ec7a2f5 100644 --- a/.gitignore +++ b/.gitignore @@ -21,6 +21,7 @@ t*_*/output/*raw t*_*/output/*root t*_*/output/*mhd t*_*/output/*txt +t*_*/output/*.pdf t*_*/output/mac t*_*/output/data t*_*/output/run.log diff --git a/t34_biodose_actor/data/GateMaterials.db b/t34_biodose_actor/data/GateMaterials.db new file mode 100644 index 0000000..aedc6fa --- /dev/null +++ b/t34_biodose_actor/data/GateMaterials.db @@ -0,0 +1,476 @@ +[Elements] +Hydrogen: S= H ; Z= 1. ; A= 1.01 g/mole +Helium: S= He ; Z= 2. ; A= 4.003 g/mole +Lithium: S= Li ; Z= 3. ; A= 6.941 g/mole +Beryllium: S= Be ; Z= 4. ; A= 9.012 g/mole +Boron: S= B ; Z= 5. ; A= 10.811 g/mole +Carbon: S= C ; Z= 6. ; A= 12.01 g/mole +Nitrogen: S= N ; Z= 7. ; A= 14.01 g/mole +Oxygen: S= O ; Z= 8. ; A= 16.00 g/mole +Fluorine: S= F ; Z= 9. ; A= 18.998 g/mole +Neon: S= Ne ; Z= 10. ; A= 20.180 g/mole +Sodium: S= Na ; Z= 11. ; A= 22.99 g/mole +Magnesium: S= Mg ; Z= 12. ; A= 24.305 g/mole +Aluminium: S= Al ; Z= 13. ; A= 26.98 g/mole +Silicon: S= Si ; Z= 14. ; A= 28.09 g/mole +Phosphor: S= P ; Z= 15. ; A= 30.97 g/mole +Sulfur: S= S ; Z= 16. ; A= 32.066 g/mole +Chlorine: S= Cl ; Z= 17. ; A= 35.45 g/mole +Argon: S= Ar ; Z= 18. ; A= 39.95 g/mole +Potassium: S= K ; Z= 19. ; A= 39.098 g/mole +Calcium: S= Ca ; Z= 20. ; A= 40.08 g/mole +Scandium: S= Sc ; Z= 21. ; A= 44.956 g/mole +Titanium: S= Ti ; Z= 22. ; A= 47.867 g/mole +Vandium: S= V ; Z= 23. ; A= 50.942 g/mole +Chromium: S= Cr ; Z= 24. ; A= 51.996 g/mole +Manganese: S= Mn ; Z= 25. ; A= 54.938 g/mole +Iron: S= Fe ; Z= 26. ; A= 55.845 g/mole +Cobalt: S= Co ; Z= 27. ; A= 58.933 g/mole +Nickel: S= Ni ; Z= 28. ; A= 58.693 g/mole +Copper: S= Cu ; Z= 29. ; A= 63.39 g/mole +Zinc: S= Zn ; Z= 30. ; A= 65.39 g/mole +Gallium: S= Ga ; Z= 31. ; A= 69.723 g/mole +Germanium: S= Ge ; Z= 32. ; A= 72.61 g/mole +Yttrium: S= Y ; Z= 39. ; A= 88.91 g/mole +Cadmium: S= Cd ; Z= 48. ; A= 112.41 g/mole +Tellurium: S= Te ; Z= 52. ; A= 127.6 g/mole +Iodine: S= I ; Z= 53. ; A= 126.90 g/mole +Cesium: S= Cs ; Z= 55. ; A= 132.905 g/mole +Gadolinium: S= Gd ; Z= 64. ; A= 157.25 g/mole +Lutetium: S= Lu ; Z= 71. ; A= 174.97 g/mole +Tungsten: S= W ; Z= 74. ; A= 183.84 g/mole +Thallium: S= Tl ; Z= 81. ; A= 204.37 g/mole +Lead: S= Pb ; Z= 82. ; A= 207.20 g/mole +Bismuth: S= Bi ; Z= 83. ; A= 208.98 g/mole +Uranium: S= U ; Z= 92. ; A= 238.03 g/mole + +[Materials] +Vacuum: d=0.000001 mg/cm3 ; n=1 + +el: name=Hydrogen ; n=1 + +Aluminium: d=2.7 g/cm3 ; n=1 ; state=solid + +el: name=auto ; n=1 + +Uranium: d=18.90 g/cm3 ; n=1 ; state=solid + +el: name=auto ; n=1 + +Silicon: d=2.33 g/cm3 ; n=1 ; state=solid + +el: name=auto ; n=1 + +Germanium: d=5.32 g/cm3 ; n=1 ; state=solid + +el: name=auto ; n=1 + +Yttrium: d=4.47 g/cm3 ; n=1 + +el: name=auto ; n=1 + +Gadolinium: d=7.9 g/cm3 ; n=1 + +el: name=auto ; n=1 + +Lutetium: d=9.84 g/cm3 ; n=1 + +el: name=auto ; n=1 + +Tungsten: d=19.3 g/cm3 ; n=1 ; state=solid + +el: name=auto ; n=1 + +Lead: d=11.4 g/cm3 ; n=1 ; state=solid + +el: name=auto ; n=1 + +Bismuth: d=9.75 g/cm3 ; n=1 ; state=solid + +el: name=auto ; n=1 + +NaI: d=3.67 g/cm3; n=2; state=solid + +el: name=Sodium ; n=1 + +el: name=Iodine ; n=1 + +PWO: d=8.28 g/cm3; n=3 ; state=Solid + +el: name=Lead; n=1 + +el: name=Tungsten; n=1 + +el: name=Oxygen; n=4 + +BGO: d=7.13 g/cm3; n= 3 ; state=solid + +el: name=Bismuth; n=4 + +el: name=Germanium; n=3 + +el: name=Oxygen; n=12 + +LSO: d=7.4 g/cm3; n=3 ; state=Solid + +el: name=Lutetium ; n=2 + +el: name=Silicon; n=1 + +el: name=Oxygen; n=5 + +Plexiglass: d=1.19 g/cm3; n=3; state=solid + +el: name=Hydrogen; f=0.080538 + +el: name=Carbon; f=0.599848 + +el: name=Oxygen; f=0.319614 + + +GSO: d=6.7 g/cm3; n=3 ; state=Solid + +el: name=Gadolinium ; n=2 + +el: name=Silicon; n=1 + +el: name=Oxygen; n=5 + +LuAP: d=8.34 g/cm3; n=3 ; state=Solid + +el: name=Lutetium ; n=1 + +el: name=Aluminium; n=1 + +el: name=Oxygen; n=3 + +YAP: d=5.55 g/cm3; n=3 ; state=Solid + +el: name=Yttrium ; n=1 + +el: name=Aluminium; n=1 + +el: name=Oxygen; n=3 + +Water: d=1.00 g/cm3; n=2 ; state=liquid + +el: name=Hydrogen ; n=2 + +el: name=Oxygen; n=1 + +Quartz: d=2.2 g/cm3; n=2 ; state=Solid + +el: name=Silicon ; n=1 + +el: name=Oxygen ; n=2 + +Breast: d=1.020 g/cm3 ; n = 8 + +el: name=Oxygen; f=0.5270 + +el: name=Carbon; f=0.3320 + +el: name=Hydrogen ; f=0.1060 + +el: name=Nitrogen; f=0.0300 + +el: name=Sulfur ; f=0.0020 + +el: name=Sodium ; f=0.0010 + +el: name=Phosphor; f=0.0010 + +el: name=Chlorine ; f=0.0010 + +Air: d= 1.29 mg/cm3 ; n=4 ; state=gas + +el: name=Nitrogen; f=0.755268 + +el: name=Oxygen; f=0.231781 + +el: name=Argon; f=0.012827 + +el: name=Carbon; f=0.000124 + +Glass: d=2.5 g/cm3; n=4; state=solid + +el: name=Sodium ; f=0.1020 + +el: name=Calcium; f=0.0510 + +el: name=Silicon; f=0.2480 + +el: name=Oxygen; f=0.5990 + +Scinti-C9H10: d=1.032 g/cm3 ; n=2 + +el: name=Carbon; n=9 + +el: name=Hydrogen; n=10 + +LuYAP-70: d=7.1 g/cm3 ; n=4 + +el: name=Lutetium ; n= 7 + +el: name=Yttrium ; n= 3 + +el: name=Aluminium; n=10 + +el: name=Oxygen; n=30 + +LuYAP-80: d=7.5 g/cm3 ; n=4 + +el: name=Lutetium ; n= 8 + +el: name=Yttrium ; n= 2 + +el: name=Aluminium; n=10 + +el: name=Oxygen; n=30 + +Plastic: d=1.18 g/cm3 ; n=3; state=solid + +el: name=Carbon ; n=5 + +el: name=Hydrogen ; n=8 + +el: name=Oxygen ; n=2 + +CZT: d=5.68 g/cm3 ; n=3; state=solid + +el: name=Cadmium ; n=9 + +el: name=Zinc ; n=1 + +el: name=Tellurium ; n=10 + +Lung: d=0.26 g/cm3 ; n=9 + +el: name=Hydrogen ; f=0.103 + +el: name=Carbon ; f=0.105 + +el: name=Nitrogen ; f=0.031 + +el: name=Oxygen ; f=0.749 + +el: name=Sodium ; f=0.002 + +el: name=Phosphor ; f=0.002 + +el: name=Sulfur ; f=0.003 + +el: name=Chlorine ; f=0.003 + +el: name=Potassium ; f=0.002 + +Polyethylene: d=0.96 g/cm3 ; n=2 + +el: name=Hydrogen ; n=2 + +el: name=Carbon ; n=1 + +PVC: d=1.65 g/cm3 ; n=3 ; state=solid + +el: name=Hydrogen ; n=3 + +el: name=Carbon ; n=2 + +el: name=Chlorine ; n=1 + +SS304: d=7.92 g/cm3 ; n=4 ; state=solid + +el: name=Iron ; f=0.695 + +el: name=Chromium ; f=0.190 + +el: name=Nickel ; f=0.095 + +el: name=Manganese ; f=0.020 + +PTFE: d= 2.18 g/cm3 ; n=2 ; state=solid + +el: name=Carbon ; n=1 + +el: name=Fluorine ; n=2 + + +LYSO: d=5.37 g/cm3; n=4 ; state=Solid + +el: name=Lutetium ; f=0.31101534 + +el: name=Yttrium ; f=0.368765605 + +el: name=Silicon; f=0.083209699 + +el: name=Oxygen; f=0.237009356 + +Body: d=1.00 g/cm3 ; n=2 + +el: name=Hydrogen ; f=0.112 + +el: name=Oxygen ; f=0.888 + +Muscle: d=1.05 g/cm3 ; n=11 + +el: name=Hydrogen ; f=0.102 + +el: name=Carbon ; f=0.143 + +el: name=Nitrogen ; f=0.034 + +el: name=Oxygen ; f=0.71 + +el: name=Sodium ; f=0.001 + +el: name=Phosphor ; f=0.002 + +el: name=Sulfur ; f=0.003 + +el: name=Chlorine ; f=0.001 + +el: name=Potassium ; f=0.004 + +el: name=Calcium ; f=0.0 + +el: name=Scandium ; f=0.0 + +LungMoby: d=0.30 g/cm3 ; n=6 + +el: name=Hydrogen ; f=0.099 + +el: name=Carbon ; f=0.100 + +el: name=Nitrogen ; f=0.028 + +el: name=Oxygen ; f=0.740 + +el: name=Phosphor ; f=0.001 + +el: name=Calcium ; f=0.032 + +SpineBone: d=1.42 g/cm3 ; n=11 + +el: name=Hydrogen ; f=0.063 + +el: name=Carbon ; f=0.261 + +el: name=Nitrogen ; f=0.039 + +el: name=Oxygen ; f=0.436 + +el: name=Sodium ; f=0.001 + +el: name=Magnesium ; f=0.001 + +el: name=Phosphor ; f=0.061 + +el: name=Sulfur ; f=0.003 + +el: name=Chlorine ; f=0.001 + +el: name=Potassium ; f=0.001 + +el: name=Calcium ; f=0.133 + +RibBone: d=1.92 g/cm3 ; n=11 + +el: name=Hydrogen ; f=0.034 + +el: name=Carbon ; f=0.155 + +el: name=Nitrogen ; f=0.042 + +el: name=Oxygen ; f=0.435 + +el: name=Sodium ; f=0.001 + +el: name=Magnesium ; f=0.002 + +el: name=Phosphor ; f=0.103 + +el: name=Sulfur ; f=0.003 + +el: name=Calcium ; f=0.225 + +el: name=Scandium ; f=0.0 + +el: name=Titanium ; f=0.0 + +Adipose: d=0.92 g/cm3 ; n=11 + +el: name=Hydrogen ; f=0.120 + +el: name=Carbon ; f=0.640 + +el: name=Nitrogen ; f=0.008 + +el: name=Oxygen ; f=0.229 + +el: name=Phosphor ; f=0.002 + +el: name=Calcium ; f=0.001 + +el: name=Scandium ; f=0.0 + +el: name=Titanium ; f=0.0 + +el: name=Vandium . f=0.0 + +el: name=Chromium ; f=0.0 + +el: name=Manganese ; f=0.0 + +Blood: d=1.06 g/cm3 ; n=11 + +el: name=Hydrogen ; f=0.102 + +el: name=Carbon ; f=0.11 + +el: name=Nitrogen ; f=0.033 + +el: name=Oxygen ; f=0.745 + +el: name=Sodium ; f=0.001 + +el: name=Phosphor ; f=0.001 + +el: name=Sulfur ; f=0.002 + +el: name=Chlorine ; f=0.003 + +el: name=Potassium ; f=0.002 + +el: name=Iron ; f=0.001 + +el: name=Cobalt ; f=0.0 + +Heart: d=1.05 g/cm3 ; n=11 + +el: name=Hydrogen ; f=0.104 + +el: name=Carbon ; f=0.139 + +el: name=Nitrogen ; f=0.029 + +el: name=Oxygen ; f=0.718 + +el: name=Sodium ; f=0.001 + +el: name=Phosphor ; f=0.002 + +el: name=Sulfur ; f=0.002 + +el: name=Chlorine ; f=0.002 + +el: name=Potassium ; f=0.003 + +el: name=Calcium ; f=0.0 + +el: name=Scandium ; f=0.0 + +Kidney: d=1.05 g/cm3 ; n=11 + +el: name=Hydrogen ; f=0.103 + +el: name=Carbon ; f=0.132 + +el: name=Nitrogen ; f=0.03 + +el: name=Oxygen ; f=0.724 + +el: name=Sodium ; f=0.002 + +el: name=Phosphor ; f=0.002 + +el: name=Sulfur ; f=0.002 + +el: name=Chlorine ; f=0.002 + +el: name=Potassium ; f=0.002 + +el: name=Calcium ; f=0.001 + +el: name=Scandium ; f=0.0 + +Liver: d=1.06 g/cm3 ; n=11 + +el: name=Hydrogen ; f=0.102 + +el: name=Carbon ; f=0.139 + +el: name=Nitrogen ; f=0.03 + +el: name=Oxygen ; f=0.716 + +el: name=Sodium ; f=0.002 + +el: name=Phosphor ; f=0.003 + +el: name=Sulfur ; f=0.003 + +el: name=Chlorine ; f=0.002 + +el: name=Potassium ; f=0.003 + +el: name=Calcium ; f=0.0 + +el: name=Scandium ; f=0.0 + +Lymph: d=1.03 g/cm3 ; n=11 + +el: name=Hydrogen ; f=0.108 + +el: name=Carbon ; f=0.041 + +el: name=Nitrogen ; f=0.011 + +el: name=Oxygen ; f=0.832 + +el: name=Sodium ; f=0.003 + +el: name=Sulfur ; f=0.001 + +el: name=Chlorine ; f=0.004 + +el: name=Argon ; f=0.0 + +el: name=Potassium ; f=0.0 + +el: name=Calcium ; f=0.0 + +el: name=Scandium ; f=0.0 + +Pancreas: d=1.04 g/cm3 ; n=11 + +el: name=Hydrogen ; f=0.106 + +el: name=Carbon ; f=0.169 + +el: name=Nitrogen ; f=0.022 + +el: name=Oxygen ; f=0.694 + +el: name=Sodium ; f=0.002 + +el: name=Phosphor ; f=0.002 + +el: name=Sulfur ; f=0.001 + +el: name=Chlorine ; f=0.002 + +el: name=Potassium ; f=0.002 + +el: name=Calcium ; f=0.0 + +el: name=Scandium ; f=0.0 + +Intestine: d=1.03 g/cm3 ; n=11 + +el: name=Hydrogen ; f=0.106 + +el: name=Carbon ; f=0.115 + +el: name=Nitrogen ; f=0.022 + +el: name=Oxygen ; f=0.751 + +el: name=Sodium ; f=0.001 + +el: name=Phosphor ; f=0.001 + +el: name=Sulfur ; f=0.001 + +el: name=Chlorine ; f=0.002 + +el: name=Potassium ; f=0.001 + +el: name=Calcium ; f=0.0 + +el: name=Scandium ; f=0.0 + +Skull: d=1.61 g/cm3 ; n=11 + +el: name=Hydrogen ; f=0.05 + +el: name=Carbon ; f=0.212 + +el: name=Nitrogen ; f=0.04 + +el: name=Oxygen ; f=0.435 + +el: name=Sodium ; f=0.001 + +el: name=Magnesium ; f=0.002 + +el: name=Phosphor ; f=0.081 + +el: name=Sulfur ; f=0.003 + +el: name=Calcium ; f=0.176 + +el: name=Scandium ; f=0.0 + +el: name=Titanium ; f=0.0 + +Cartilage: d=1.10 g/cm3 ; n=11 + +el: name=Hydrogen ; f=0.096 + +el: name=Carbon ; f=0.099 + +el: name=Nitrogen ; f=0.022 + +el: name=Oxygen ; f=0.744 + +el: name=Sodium ; f=0.005 + +el: name=Phosphor ; f=0.022 + +el: name=Sulfur ; f=0.009 + +el: name=Chlorine ; f=0.003 + +el: name=Argon ; f=0.0 + +el: name=Potassium ; f=0.0 + +el: name=Calcium ; f=0.0 + +Brain: d=1.04 g/cm3 ; n=11 + +el: name=Hydrogen ; f=0.107 + +el: name=Carbon ; f=0.145 + +el: name=Nitrogen ; f=0.022 + +el: name=Oxygen ; f=0.712 + +el: name=Sodium ; f=0.002 + +el: name=Phosphor ; f=0.004 + +el: name=Sulfur ; f=0.002 + +el: name=Chlorine ; f=0.003 + +el: name=Potassium ; f=0.003 + +el: name=Calcium ; f=0.0 + +el: name=Scandium ; f=0.0 + +Spleen: d=1.06 g/cm3 ; n=11 + +el: name=Hydrogen ; f=0.103 + +el: name=Carbon ; f=0.113 + +el: name=Nitrogen ; f=0.032 + +el: name=Oxygen ; f=0.741 + +el: name=Sodium ; f=0.001 + +el: name=Phosphor ; f=0.003 + +el: name=Sulfur ; f=0.002 + +el: name=Chlorine ; f=0.002 + +el: name=Potassium ; f=0.003 + +el: name=Calcium ; f=0.0 + +el: name=Scandium ; f=0.0 + +Testis: d=1.04 g/cm3 ; n=9 + +el: name=Hydrogen ; f=0.106000 + +el: name=Carbon ; f=0.099000 + +el: name=Nitrogen ; f=0.020000 + +el: name=Oxygen ; f=0.766000 + +el: name=Sodium ; f=0.002000 + +el: name=Phosphor ; f=0.001000 + +el: name=Sulfur ; f=0.002000 + +el: name=Chlorine ; f=0.002000 + +el: name=Potassium ; f=0.002000 + +PMMA: d=1.195 g/cm3; n=3 ; state=Solid + +el: name=Hydrogen ; f=0.080541 + +el: name=Carbon ; f=0.599846 + +el: name=Sulfur; f=0.319613 + +MRGEL: d=1.04 g/cm3; n=5 ; state=Solid + +el: name=Hydrogen ; f=0.104161105 + +el: name=Carbon ; f=0.095211486 + +el: name=Nitrogen ; f=0.016995 + +el: name=Oxygen ; f=0.783004584 + +el: name=Sulfur ; f=0.000627825 + +Epoxy: d=1.0 g/cm3; n=3; state=Solid + +el: name=Carbon; n=1 + +el: name=Hydrogen; n=1 + +el: name=Oxygen; n=1 + +Mylar: d=1.4 g/cm3; n=3; state=Solid + +el: name=Hydrogen; f=0.041959 + +el: name=Carbon; f=0.625017 + +el: name=Oxygen; f=0.333025 + +Kapton: d=1.42 g/cm3; n=4; state=Solid + +el: name=Hydrogen; f=0.026362 + +el: name=Carbon; f=0.691133 + +el: name=Nitrogen; f=0.073270 + +el: name=Oxygen; f=0.209235 + +Nomex: d=0.95 g/cm3; n=4; state=Solid + +el: name=Hydrogen; n=10 + +el: name=Carbon; n=14 + +el: name=Nitrogen; n=2 + +el: name=Oxygen; n=2 + +TiO: d=4.24 g/cm3; n=2; state=Solid + +el: name=Titanium; n=1 + +el: name=Oxygen; n=1 + +NitrogenGas: d=1.29 mg/cm3 ; n=1 ; state=gas + +el: name=Nitrogen; f=1 + +Hostapan: d=1.4 g/cm3; n=3; state=Solid + +el: name=Hydrogen; f=0.041959 + +el: name=Carbon; f=0.625017 + +el: name=Oxygen; f=0.333025 diff --git a/t34_biodose_actor/data/HSG_NanOx.db b/t34_biodose_actor/data/HSG_NanOx.db new file mode 100644 index 0000000..c701270 --- /dev/null +++ b/t34_biodose_actor/data/HSG_NanOx.db @@ -0,0 +1,416 @@ +Fragment 1; +0.1 3.52785 0.0586794 +0.125 3.58379 0.0219491 +0.15 3.64192 0.0977552 +0.175 3.64134 0.045627 +0.2 3.59205 0.0522845 +0.225 3.48742 0.0763334 +0.25 3.38711 0.0486352 +0.275 3.23556 0.0140717 +0.3 3.10038 0.0564686 +0.325 2.92819 0.0736448 +0.35 2.74536 0.0440922 +0.375 2.64766 0.068873 +0.4 2.50822 0.0519665 +0.425 2.35826 0.0598118 +0.45 2.24049 0.0523686 +0.475 2.11282 0.0327819 +0.5 2.00902 0.0619912 +0.525 1.90411 0.048899 +0.55 1.81201 0.03943 +0.6 1.64405 0.0482093 +0.625 1.5553 0.0315918 +0.65 1.50294 0.0514883 +0.675 1.42643 0.0530718 +0.7 1.37338 0.0520192 +0.725 1.30831 0.0516787 +0.75 1.27779 0.0520332 +0.775 1.22202 0.0610424 +0.8 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0.0580988 +150 0.621408 0.0605031 +160 0.602909 0.0606604 +180 0.576667 0.0703917 +200 0.556955 0.0680523 +250 0.517284 0.0828523 +300 0.493476 0.0861731 +350 0.47441 0.0914356 diff --git a/t34_biodose_actor/mac/carbon.mac b/t34_biodose_actor/mac/carbon.mac new file mode 100644 index 0000000..a1098c7 --- /dev/null +++ b/t34_biodose_actor/mac/carbon.mac @@ -0,0 +1,3 @@ +/control/alias particleName "carbon" +/gate/application/setTotalNumberOfPrimaries 2000 +/control/execute mac/main.mac diff --git a/t34_biodose_actor/mac/main.mac b/t34_biodose_actor/mac/main.mac new file mode 100644 index 0000000..6198ef3 --- /dev/null +++ b/t34_biodose_actor/mac/main.mac @@ -0,0 +1,115 @@ +#===================================================== +# GEOMETRY +#===================================================== + +/gate/geometry/setMaterialDatabase data/GateMaterials.db + +# World +/gate/world/geometry/setXLength 5 m +/gate/world/geometry/setYLength 5 m +/gate/world/geometry/setZLength 5 m +/gate/world/setMaterial Air + +# Global Box +/gate/world/daughters/name mainbox1 +/gate/world/daughters/insert box +/gate/mainbox1/geometry/setXLength 20 cm +/gate/mainbox1/geometry/setYLength 20 cm +/gate/mainbox1/geometry/setZLength 20 cm +/gate/mainbox1/placement/setTranslation 0.0 0.0 10 cm +/gate/mainbox1/setMaterial G4_WATER +/gate/mainbox1/vis/setVisible 1 +/gate/mainbox1/vis/setColor blue + +#===================================================== +# PHYSICS +#===================================================== + +/control/execute mac/physics_{particleName}.mac + +/gate/physics/Gamma/SetCutInRegion world 100 m +/gate/physics/Electron/SetCutInRegion world 100 m +/gate/physics/Positron/SetCutInRegion world 100 m + +/gate/physics/Gamma/SetCutInRegion mainbox1 100 m +/gate/physics/Electron/SetCutInRegion mainbox1 100 m +/gate/physics/Positron/SetCutInRegion mainbox1 100 m + +/gate/physics/SetMaxStepSizeInRegion mainbox1 10 um +/gate/physics/ActivateStepLimiter proton +/gate/physics/ActivateStepLimiter deuteron +/gate/physics/ActivateStepLimiter triton +/gate/physics/ActivateStepLimiter alpha +/gate/physics/ActivateStepLimiter GenericIon + +/gate/physics/displayCuts + +#===================================================== +# MATRIX FOR DOSE MAP OUTPUT +#===================================================== + +/gate/actor/addActor DoseActor doseDistribution +/gate/actor/doseDistribution/save output/dose_{particleName}.mhd +/gate/actor/doseDistribution/attachTo mainbox1 +/gate/actor/doseDistribution/stepHitType random +/gate/actor/doseDistribution/setPosition 0 0 0 cm +/gate/actor/doseDistribution/setResolution 1 1 200 +/gate/actor/doseDistribution/saveEveryNSeconds 60 +/gate/actor/doseDistribution/enableEdep false +/gate/actor/doseDistribution/enableUncertaintyEdep false +/gate/actor/doseDistribution/enableDose true +/gate/actor/doseDistribution/enableUncertaintyDose false +/gate/actor/doseDistribution/enableNumberOfHits false + +/gate/actor/addActor BioDoseActor bio +/gate/actor/bio/attachTo mainbox1 +/gate/actor/bio/setVoxelSize 200 200 1 mm +/gate/actor/bio/setPosition 0 0 0 +/gate/actor/bio/setCellLine HSG +/gate/actor/bio/setBioPhysicalModel NanOx +/gate/actor/bio/setAlphaRef 0.313 +/gate/actor/bio/setBetaRef 0.0615 +/gate/actor/bio/enableDose true +/gate/actor/bio/enableAlphaMix false +/gate/actor/bio/enableSqrtBetaMix false +/gate/actor/bio/enableRBE false +/gate/actor/bio/enableUncertainty false +/gate/actor/bio/enableUncertaintyDetails false +/gate/actor/bio/enableHitEventCount false +/gate/actor/bio/save output/biodose_{particleName}.mhd + +/gate/actor/addActor SimulationStatisticActor stat +/gate/actor/stat/save output/stat_{particleName}.txt + +#===================================================== +# INITIALISATION +#===================================================== + +/gate/run/initialize + +#===================================================== +# BEAMS +#===================================================== + +/control/execute mac/source_{particleName}.mac + +#===================================================== +# VISUALISATION & VERBOSE +#===================================================== + +#/vis/disable +#/control/execute mac/visu.mac +#/control/execute mac/verbose.mac +# /gate/random/verbose 1 +# /gate/source/verbose 0 + +#===================================================== +# START BEAMS +#===================================================== + +/gate/random/setEngineName MersenneTwister +/gate/random/setEngineSeed 12345678910 + +/gate/application/noGlobalOutput + +/gate/application/start diff --git a/t34_biodose_actor/mac/physics_carbon.mac b/t34_biodose_actor/mac/physics_carbon.mac new file mode 100644 index 0000000..c3a1eaf --- /dev/null +++ b/t34_biodose_actor/mac/physics_carbon.mac @@ -0,0 +1 @@ +/gate/physics/addPhysicsList Shielding_EMZ diff --git a/t34_biodose_actor/mac/physics_proton.mac b/t34_biodose_actor/mac/physics_proton.mac new file mode 100644 index 0000000..ab9415e --- /dev/null +++ b/t34_biodose_actor/mac/physics_proton.mac @@ -0,0 +1 @@ +/gate/physics/addPhysicsList QGSP_BIC_HP_EMZ diff --git a/t34_biodose_actor/mac/proton.mac b/t34_biodose_actor/mac/proton.mac new file mode 100644 index 0000000..f0f5a47 --- /dev/null +++ b/t34_biodose_actor/mac/proton.mac @@ -0,0 +1,3 @@ +/control/alias particleName "proton" +/gate/application/setTotalNumberOfPrimaries 4000 +/control/execute mac/main.mac diff --git a/t34_biodose_actor/mac/source_carbon.mac b/t34_biodose_actor/mac/source_carbon.mac new file mode 100644 index 0000000..0ca1fc2 --- /dev/null +++ b/t34_biodose_actor/mac/source_carbon.mac @@ -0,0 +1,15 @@ +/gate/source/addSource mybeam gps + +/gate/source/mybeam/gps/particle ion +/gate/source/mybeam/gps/ion 6 12 +/gate/source/mybeam/gps/pos/type Beam +/gate/source/mybeam/gps/pos/rot1 0 1 0 +/gate/source/mybeam/gps/pos/rot2 1 0 0 +/gate/source/mybeam/gps/pos/shape Circle +/gate/source/mybeam/gps/pos/centre 0 0 0 mm +/gate/source/mybeam/gps/pos/sigma_x 3 mm +/gate/source/mybeam/gps/pos/sigma_y 3 mm +/gate/source/mybeam/gps/ene/mono 2500 MeV +/gate/source/mybeam/gps/ene/type Gauss +/gate/source/mybeam/gps/ene/sigma 25.0 MeV +/gate/source/mybeam/gps/direction 0 0 1 diff --git a/t34_biodose_actor/mac/source_proton.mac b/t34_biodose_actor/mac/source_proton.mac new file mode 100644 index 0000000..7cfd28f --- /dev/null +++ b/t34_biodose_actor/mac/source_proton.mac @@ -0,0 +1,14 @@ +/gate/source/addSource mybeam gps + +/gate/source/mybeam/gps/particle proton +/gate/source/mybeam/gps/pos/type Beam +/gate/source/mybeam/gps/pos/rot1 0 1 0 +/gate/source/mybeam/gps/pos/rot2 1 0 0 +/gate/source/mybeam/gps/pos/shape Circle +/gate/source/mybeam/gps/pos/centre 0 0 0 mm +/gate/source/mybeam/gps/pos/sigma_x 3 mm +/gate/source/mybeam/gps/pos/sigma_y 3 mm +/gate/source/mybeam/gps/ene/mono 150 MeV +/gate/source/mybeam/gps/ene/type Gauss +/gate/source/mybeam/gps/ene/sigma 2.0 MeV +/gate/source/mybeam/gps/direction 0 0 1 diff --git a/t34_biodose_actor/output/.gitkeep b/t34_biodose_actor/output/.gitkeep new file mode 100644 index 0000000..e69de29 diff --git a/t34_biodose_actor/runAnalysis.py b/t34_biodose_actor/runAnalysis.py new file mode 100755 index 0000000..4d1bcca --- /dev/null +++ b/t34_biodose_actor/runAnalysis.py @@ -0,0 +1,74 @@ +#!/usr/bin/env python3 + +import click +import numpy as np +import SimpleITK as sitk +import matplotlib as mpl +import matplotlib.pyplot as plt + + +def load(mhd: str): + img = sitk.ReadImage(mhd) + data = np.array(sitk.GetArrayFromImage(img)) + return data[:, 0, 0] + + +@click.command() +@click.argument('output_folders', nargs=-1, required=True, type=click.Path(exists=True, dir_okay=True)) +@click.option('--figures', is_flag=True) +@click.option('--show', is_flag=True) +def analyse_click(output_folders, figures: bool, show: bool): + if figures: + mpl.use('tkagg') + + r = True + for output_folder in output_folders: + for particle_name in ["carbon", "proton"]: + cur_r = analyse_particle(output_folder, particle_name, figures, show) + if not cur_r: + print(f"Test failed for: {output_folder}, {particle_name}") + + r = r and cur_r + + print(f'Test result: {r}') + + +def analyse_particle(output_folder, particle_name, figures, show): + dose = load(f"{output_folder}/dose_{particle_name}-Dose.mhd") + dose_from_bio = load(f"{output_folder}/biodose_{particle_name}_dose.mhd") + biodose = load(f"{output_folder}/biodose_{particle_name}_biodose.mhd") + + dose_err = np.divide(np.abs(dose - dose_from_bio), dose, out=np.zeros_like(dose), where=dose == 0) + dose_mean_err = np.mean(dose_err) + dose_ok = dose_mean_err < .05 + # print(f"dose relative difference: (mean) {dose_mean_err*100:.2f}%, (max) {np.max(dose_err)*100:.2f}%") + + rbe = np.divide(biodose, dose_from_bio, out=np.ones_like(biodose), where=dose_from_bio != 0) + min_rbe = np.min(rbe) + rbe_ok = min_rbe >= 1 + # print(f"RBE always > 1: {rbe_ok}") + + if figures: + fig, ax = plt.subplots(figsize=(6.5, 5), dpi=300) + ax.set_xlabel('depth (mm)') + ax.set_ylabel('dose (Gy)') + + ax.plot(dose, color='blue', label='dose', linestyle='dashed') + ax.plot(dose_from_bio, color='blue', label='dose (from biodose actor)') + ax.plot(biodose, color='orange', label='biodose') + + plt.legend() + + plt.title(f"Data for {output_folder}, {particle_name}") + + plt.tight_layout() + plt.savefig(f"{output_folder}/fig_{particle_name}.pdf") + if show: + plt.show() + plt.close(fig) + + return dose_ok and rbe_ok + + +if __name__ == '__main__': + analyse_click() diff --git a/t34_biodose_actor/runTest.sh b/t34_biodose_actor/runTest.sh new file mode 100755 index 0000000..3ad1e09 --- /dev/null +++ b/t34_biodose_actor/runTest.sh @@ -0,0 +1,2 @@ +Gate mac/proton.mac +Gate mac/carbon.mac From cca60852739381e5548d8e064582e0e0c2231d64 Mon Sep 17 00:00:00 2001 From: Alexis Pereda Date: Tue, 19 Mar 2024 15:40:23 +0100 Subject: [PATCH 2/2] add t34_biodose_actor to CI --- .github/workflows/main.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index f3e419c..4c5f53b 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -43,7 +43,8 @@ jobs: t30_dna, t31_vpgTLE-tt, t32_isotopes, - t33_invert_filter] + t33_invert_filter, + t34_biodose_actor] steps: - name: Checkout github repo