diff --git a/imaging/Thermal/GateMaterials.db b/imaging/Thermal/Hyperthermia/GateMaterials.db similarity index 100% rename from imaging/Thermal/GateMaterials.db rename to imaging/Thermal/Hyperthermia/GateMaterials.db diff --git a/imaging/Thermal/MOBY1cmTumor.h33 b/imaging/Thermal/Hyperthermia/MOBY1cmTumor.h33 similarity index 100% rename from imaging/Thermal/MOBY1cmTumor.h33 rename to imaging/Thermal/Hyperthermia/MOBY1cmTumor.h33 diff --git a/imaging/Thermal/MOBY1cmTumor.i33 b/imaging/Thermal/Hyperthermia/MOBY1cmTumor.i33 similarity index 100% rename from imaging/Thermal/MOBY1cmTumor.i33 rename to imaging/Thermal/Hyperthermia/MOBY1cmTumor.i33 diff --git a/imaging/Thermal/Materials.xml b/imaging/Thermal/Hyperthermia/Materials.xml similarity index 100% rename from imaging/Thermal/Materials.xml rename to imaging/Thermal/Hyperthermia/Materials.xml diff --git a/imaging/Thermal/ThermalTherapy.mac b/imaging/Thermal/Hyperthermia/ThermalTherapy.mac similarity index 100% rename from imaging/Thermal/ThermalTherapy.mac rename to imaging/Thermal/Hyperthermia/ThermalTherapy.mac diff --git a/imaging/Thermal/attenuation.dat b/imaging/Thermal/Hyperthermia/attenuation.dat similarity index 100% rename from imaging/Thermal/attenuation.dat rename to imaging/Thermal/Hyperthermia/attenuation.dat diff --git a/imaging/Thermal/OpticalStimulation/Materials.xml b/imaging/Thermal/OpticalStimulation/Materials.xml new file mode 100644 index 00000000..46788676 --- /dev/null +++ b/imaging/Thermal/OpticalStimulation/Materials.xml @@ -0,0 +1,145 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/imaging/Thermal/OpticalStimulation/data/GateMaterials.db b/imaging/Thermal/OpticalStimulation/data/GateMaterials.db new file mode 100644 index 00000000..d7691baf --- /dev/null +++ b/imaging/Thermal/OpticalStimulation/data/GateMaterials.db @@ -0,0 +1,520 @@ +[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 +Silver: S= Ag ; Z= 47. ; A= 107.868 g/mole +Cadmium: S= Cd ; Z= 48. ; A= 112.41 g/mole +Tin: S= Sn ; Z= 50. ; A= 118.71 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 +Gold: S= Au ; Z= 79. ; A= 196.967 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 + +AluminiumEGS: d=2.702 g/cm3 ; n=1 ; state=solid + +el: name=Aluminium ; 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 + +Biomimic: d=1.05 g/cm3 ; n=3; state=solid + +el: name=Carbon ; n=5 + +el: name=Hydrogen ; n=8 + +el: name=Oxygen ; n=2 + +FITC: d=1.0 g/cm3 ; n=1 + +el: name=Carbon ; n=1 + +RhB: d=1.0 g/cm3 ; n=1 + +el: name=Carbon ; n=1 + +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 + +Epidermis: 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 + +Hypodermis: 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 + +G4_WATER: d=1.00 g/cm3; n=2 ; state=liquid + +el: name=Hydrogen ; n=2 + +el: name=Oxygen; n=1 + +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=Oxygen; f=0.319613 + +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 + +Carbide: d=15.8 g/cm3; n=2 ; state=Solid + +el: name=Tungsten ; n=1 + +el: name=Carbon ; n=1 + +WhiteMatter: 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 + +GreyMatter: 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 + +CSF: d=1.00 g/cm3; n=2 ; state=liquid + +el: name=Hydrogen ; n=2 + +el: name=Oxygen; n=1 diff --git a/imaging/Thermal/OpticalStimulation/data/HU2Mat.txt b/imaging/Thermal/OpticalStimulation/data/HU2Mat.txt new file mode 100644 index 00000000..6e336658 --- /dev/null +++ b/imaging/Thermal/OpticalStimulation/data/HU2Mat.txt @@ -0,0 +1,4 @@ +0 0 Air +1 1 CSF +2 2 WhiteMatter +3 3 GreyMatter \ No newline at end of file diff --git a/imaging/Thermal/OpticalStimulation/data/MonkeyMR_71_88_57.mhd b/imaging/Thermal/OpticalStimulation/data/MonkeyMR_71_88_57.mhd new file mode 100644 index 00000000..5bfc7bb7 --- /dev/null +++ b/imaging/Thermal/OpticalStimulation/data/MonkeyMR_71_88_57.mhd @@ -0,0 +1,13 @@ +ObjectType = Image +NDims = 3 +BinaryData = True +BinaryDataByteOrderMSB = False +CompressedData = False +TransformMatrix = 1 0 0 0 1 0 0 0 1 +Offset = 0 0 0 +CenterOfRotation = 0 0 0 +AnatomicalOrientation = RAI +ElementSpacing = 0.75 0.75 0.75 +DimSize = 71 88 57 +ElementType = MET_FLOAT +ElementDataFile = MonkeyMR_71_88_57.raw diff --git a/imaging/Thermal/OpticalStimulation/data/MonkeyMR_71_88_57.raw b/imaging/Thermal/OpticalStimulation/data/MonkeyMR_71_88_57.raw new file mode 100644 index 00000000..8ed0c034 --- /dev/null +++ b/imaging/Thermal/OpticalStimulation/data/MonkeyMR_71_88_57.raw @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:d29f81061c3850ac97df9fb7f71bfa342c3e79595e75cb21166a8d05177aece9 +size 1424544 diff --git a/imaging/Thermal/OpticalStimulation/data/measurementFile.txt b/imaging/Thermal/OpticalStimulation/data/measurementFile.txt new file mode 100644 index 00000000..42199c68 --- /dev/null +++ b/imaging/Thermal/OpticalStimulation/data/measurementFile.txt @@ -0,0 +1,9 @@ +###### List of measurement ROI according to time +###### Column 1 is point label +###### Column 2 is TimeStep in s (second) +###### Column 6,4 are deltaX in pixel +###### Column 5,6 are deltaY in pixel +###### Column 7,8 are deltaZ in pixel +Time s +1 0.5 37 39 42 44 0 0 +2 0.5 37 39 42 44 7 7 diff --git a/imaging/Thermal/OpticalStimulation/data/perfusionRateMap.mhd b/imaging/Thermal/OpticalStimulation/data/perfusionRateMap.mhd new file mode 100644 index 00000000..356344b4 --- /dev/null +++ b/imaging/Thermal/OpticalStimulation/data/perfusionRateMap.mhd @@ -0,0 +1,13 @@ +ObjectType = Image +NDims = 3 +BinaryData = True +BinaryDataByteOrderMSB = False +CompressedData = False +TransformMatrix = 1 0 0 0 1 0 0 0 1 +Offset = -26.25 -32.625 -21 +CenterOfRotation = 0 0 0 +AnatomicalOrientation = RAI +ElementSpacing = 0.75 0.75 0.75 +DimSize = 71 88 57 +ElementType = MET_DOUBLE +ElementDataFile = perfusionRateMap.raw diff --git a/imaging/Thermal/OpticalStimulation/data/perfusionRateMap.raw b/imaging/Thermal/OpticalStimulation/data/perfusionRateMap.raw new file mode 100644 index 00000000..e1bc1ba1 --- /dev/null +++ b/imaging/Thermal/OpticalStimulation/data/perfusionRateMap.raw @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:3741a7f878a0c7242089dc32e70fe1b56c05ccfa5e6fb261d1d8e8f18dc6baea +size 2849088 diff --git a/imaging/Thermal/OpticalStimulation/mac/main.mac b/imaging/Thermal/OpticalStimulation/mac/main.mac new file mode 100644 index 00000000..df6ebaa7 --- /dev/null +++ b/imaging/Thermal/OpticalStimulation/mac/main.mac @@ -0,0 +1,113 @@ +#===================================================== +# VISUALISATION and VERBOSE +#===================================================== + +#/control/execute mac/visu.mac +/control/execute mac/verbose.mac + +#===================================================== +# GEOMETRY +#===================================================== + +/gate/geometry/setMaterialDatabase data/GateMaterials.db + +#===================================================== +# W O R L D +#===================================================== + +/gate/world/geometry/setXLength 200. cm +/gate/world/geometry/setYLength 200. cm +/gate/world/geometry/setZLength 200. cm +/gate/world/setMaterial Air + +#======================================================= +# G E O M E T R Y +#======================================================= + +/gate/world/daughters/name monkey +/gate/world/daughters/insert ImageNestedParametrisedVolume +/gate/monkey/geometry/setHUToMaterialFile data/HU2Mat.txt +/gate/monkey/geometry/setImage data/MonkeyMR_71_88_57.mhd +/gate/monkey/placement/setTranslation 0. 0. 0. mm + +/gate/world/daughters/name sourceBox +/gate/world/daughters/insert box +/gate/sourceBox/geometry/setXLength 5.0 mm +/gate/sourceBox/geometry/setYLength 5.0 mm +/gate/sourceBox/geometry/setZLength 1.0 nm +/gate/sourceBox/setMaterial Air +/gate/sourceBox/placement/setTranslation 2.625 0. -21.4 mm + +#===================================================== +# P H Y S I C S +#===================================================== + +/gate/physics/addProcess OpticalAbsorption +/gate/physics/addProcess OpticalRayleigh +/gate/physics/addProcess OpticalBoundary +/gate/physics/addProcess OpticalMie +/gate/physics/addProcess OpticalWLS + +/gate/physics/processList Enabled +/gate/physics/processList Initialized + +#===================================================== +# A C T O R +#===================================================== + +/gate/actor/addActor MultiMaterialThermalActor heat +/gate/actor/heat/attachTo monkey +/gate/actor/heat/stepHitType random +/gate/actor/heat/setPosition 0. 0. 0. cm +/gate/actor/heat/setVoxelSize 0.75 0.75 0.75 mm +/gate/actor/heat/setRelaxationTime 10 s +/gate/actor/heat/enableStepDiffusion true +# heat capacity in [J.kg-1.K-1] and perfusionRate in [s-1] +/gate/actor/heat/setBloodPerfusionRateByConstant 50.0e-6 +#/gate/actor/heat/setBloodPerfusionRateByMaterial true +#/gate/actor/heat/setBloodPerfusionRateByImage data/perfusionRateMap.mhd +/gate/actor/heat/setBloodDensity 1.06 g/cm3 +/gate/actor/heat/setBloodHeatCapacity 3600.0 +#/gate/actor/heat/setTissueHeatCapacity 3650.0 +/gate/actor/heat/setMeasurementFilename data/measurementFile.txt +/gate/actor/heat/save output/heat.mhd + +# This actor will record information on your simulation: +/gate/actor/addActor SimulationStatisticActor stat +/gate/actor/stat/save output/stat.txt +/gate/actor/stat/saveEveryNSeconds 60 + + +#===================================================== +# INITIALISATION +#===================================================== + +/gate/run/initialize + +#===================================================== +# S O U R C E +#===================================================== + +/control/execute mac/source.mac + +#===================================================== +# R A N D O M +#===================================================== + +/gate/random/setEngineName MersenneTwister +/gate/random/setEngineSeed auto +#/gate/random/verbose 1 + +#===================================================== +# START +#===================================================== + +# A C Q U I S I T I O N +# If using DAQ: setActivity is needed in the source +/gate/application/setTimeSlice 10 s +/gate/application/setTimeStart 0 s +/gate/application/setTimeStop 10 s +/gate/application/startDAQ + + + diff --git a/imaging/Thermal/OpticalStimulation/mac/source.mac b/imaging/Thermal/OpticalStimulation/mac/source.mac new file mode 100644 index 00000000..b2c19393 --- /dev/null +++ b/imaging/Thermal/OpticalStimulation/mac/source.mac @@ -0,0 +1,67 @@ +/gate/source/addSource Mysource1 gps +/gate/source/Mysource1/attachTo sourceBox +/gate/source/Mysource1/gps/particle opticalphoton +/gate/source/Mysource1/gps/energytype Mono +/gate/source/Mysource1/setActivity 1e4 becquerel +/gate/source/Mysource1/gps/polarization 1 0 0 +/gate/source/Mysource1/gps/monoenergy 1.8395 eV +/gate/source/Mysource1/gps/type Plane +/gate/source/Mysource1/gps/pos/shape Circle +/gate/source/Mysource1/gps/pos/radius 0.5 mm +/gate/source/Mysource1/gps/angtype iso +/gate/source/Mysource1/gps/mintheta 144.5495 deg +/gate/source/Mysource1/gps/maxtheta 180. deg +/gate/source/Mysource1/gps/minphi 0. deg +/gate/source/Mysource1/gps/maxphi 360. deg +/gate/source/Mysource1/gps/centre 2. 2. 0. mm + +/gate/source/addSource Mysource2 gps +/gate/source/Mysource2/attachTo sourceBox +/gate/source/Mysource2/gps/particle opticalphoton +/gate/source/Mysource2/gps/energytype Mono +/gate/source/Mysource2/setActivity 1e4 becquerel +/gate/source/Mysource2/gps/polarization 1 0 0 +/gate/source/Mysource2/gps/monoenergy 1.8395 eV +/gate/source/Mysource2/gps/type Plane +/gate/source/Mysource2/gps/pos/shape Circle +/gate/source/Mysource2/gps/pos/radius 0.5 mm +/gate/source/Mysource2/gps/angtype iso +/gate/source/Mysource2/gps/mintheta 144.5495 deg +/gate/source/Mysource2/gps/maxtheta 180. deg +/gate/source/Mysource2/gps/minphi 0. deg +/gate/source/Mysource2/gps/maxphi 360. deg +/gate/source/Mysource2/gps/centre 2. -2. 0. mm + +/gate/source/addSource Mysource3 gps +/gate/source/Mysource3/attachTo sourceBox +/gate/source/Mysource3/gps/particle opticalphoton +/gate/source/Mysource3/gps/energytype Mono +/gate/source/Mysource3/setActivity 1e4 becquerel +/gate/source/Mysource3/gps/polarization 1 0 0 +/gate/source/Mysource3/gps/monoenergy 1.8395 eV +/gate/source/Mysource3/gps/type Plane +/gate/source/Mysource3/gps/pos/shape Circle +/gate/source/Mysource3/gps/pos/radius 0.5 mm +/gate/source/Mysource3/gps/angtype iso +/gate/source/Mysource3/gps/mintheta 144.5495 deg +/gate/source/Mysource3/gps/maxtheta 180. deg +/gate/source/Mysource3/gps/minphi 0. deg +/gate/source/Mysource3/gps/maxphi 360. deg +/gate/source/Mysource3/gps/centre -2. 2. 0. mm + +/gate/source/addSource Mysource4 gps +/gate/source/Mysource4/attachTo sourceBox +/gate/source/Mysource4/gps/particle opticalphoton +/gate/source/Mysource4/gps/energytype Mono +/gate/source/Mysource4/setActivity 1e4 becquerel +/gate/source/Mysource4/gps/polarization 1 0 0 +/gate/source/Mysource4/gps/monoenergy 1.8395 eV +/gate/source/Mysource4/gps/type Plane +/gate/source/Mysource4/gps/pos/shape Circle +/gate/source/Mysource4/gps/pos/radius 0.5 mm +/gate/source/Mysource4/gps/angtype iso +/gate/source/Mysource4/gps/mintheta 144.5495 deg +/gate/source/Mysource4/gps/maxtheta 180. deg +/gate/source/Mysource4/gps/minphi 0. deg +/gate/source/Mysource4/gps/maxphi 360. deg +/gate/source/Mysource4/gps/centre -2. -2. 0. mm diff --git a/imaging/Thermal/OpticalStimulation/mac/verbose.mac b/imaging/Thermal/OpticalStimulation/mac/verbose.mac new file mode 100644 index 00000000..6e28b61f --- /dev/null +++ b/imaging/Thermal/OpticalStimulation/mac/verbose.mac @@ -0,0 +1,34 @@ +# ********************************************************************* +# * DISCLAIMER * +# * * +# * Neither the authors of this software system, nor their employing * +# * institutes, nor the agencies providing financial support for this * +# * work make any representation or warranty, express or implied, * +# * regarding this software system or assume any liability for its * +# * use. * +# * * +# * This code implementation is the intellectual property of the * +# * OpenGATE collaboration. * +# * By copying, distributing or modifying the Program (or any work * +# * based on the Program) you indicate your acceptance of this * +# * statement, and all its terms. * +# ********************************************************************* + +/gate/verbose Physic 2 +/gate/verbose Cuts 0 +/gate/verbose SD 0 +/gate/verbose Actions 0 +/gate/verbose Actor 0 +/gate/verbose Step 0 +/gate/verbose Error 0 +/gate/verbose Warning 0 +/gate/verbose Output 0 +/gate/verbose Beam 0 +/gate/verbose Volume 1 +/gate/verbose Image 0 +/gate/verbose Geometry 1 +/gate/verbose Core 0 + +/run/verbose 0 +/event/verbose 0 +/tracking/verbose 0 diff --git a/imaging/Thermal/OpticalStimulation/mac/visu.mac b/imaging/Thermal/OpticalStimulation/mac/visu.mac new file mode 100644 index 00000000..822ec33a --- /dev/null +++ b/imaging/Thermal/OpticalStimulation/mac/visu.mac @@ -0,0 +1,26 @@ +# ********************************************************************* +# * DISCLAIMER * +# * * +# * Neither the authors of this software system, nor their employing * +# * institutes, nor the agencies providing financial support for this * +# * work make any representation or warranty, express or implied, * +# * regarding this software system or assume any liability for its * +# * use. * +# * * +# * This code implementation is the intellectual property of the * +# * OpenGATE collaboration. * +# * By copying, distributing or modifying the Program (or any work * +# * based on the Program) you indicate your acceptance of this * +# * statement, and all its terms. * +# ********************************************************************* + +/vis/open OGLI +/vis/drawVolume +/vis/scene/add/trajectories +/vis/viewer/zoom 20 +/vis/scene/add/axes 0 0 0 5 cm +/vis/viewer/set/hiddenMarker 1 +/vis/scene/endOfEventAction accumulate +/vis/viewer/set/viewpointThetaPhi 90 0 + +/vis/scene/add/hits diff --git a/imaging/Thermal/OpticalStimulation/output/readme.txt b/imaging/Thermal/OpticalStimulation/output/readme.txt new file mode 100644 index 00000000..335e97c0 --- /dev/null +++ b/imaging/Thermal/OpticalStimulation/output/readme.txt @@ -0,0 +1,2 @@ + +Put your results files in this folder \ No newline at end of file