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write_PCF.py
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import pathlib
############################################################################################################################################
############################################################################################################################################
############################################################################################################################################
############################################################################################################################################
############################################################################################################################################
def GetTsTimeFunctionParameters(parmName, times, values, unit):
n = len(times)
stimes = ' '.join('{:1.2f}'.format(t) for t in times)
svalues = ' '.join('{:1.4f}'.format(v) for v in values)
par1 = ('s:Tf/%s/Function = "Step"' % parmName)
par2 = ('dv:Tf/%s/Times = %d %s s' % (parmName, n, stimes))
if unit != '':
par3 = ('dv:Tf/%s/Values = %d %s %s' % (parmName, n, svalues, unit))
else:
par3 = ('uv:Tf/%s/Values = %d %s' % (parmName, n, svalues))
return [par1, par2, par3]
############################################################################################################################################
############################################################################################################################################
############################################################################################################################################
############################################################################################################################################
############################################################################################################################################
def SaveTsTimeFunctionParameters(parmName, times, values, unit, directory):
n = len(times)
stimes = ' '.join('{:1.2f}'.format(t) for t in times)
svalues = ' '.join('{:1.3f}'.format(v) for v in values)
if unit == 'u':
if 'MUper' in parmName:
svalues = ' '.join('{:1.4f}'.format(v) for v in values)
else:
svalues = ' '.join('{:1.5e}'.format(v) for v in values)
if unit == 'i':
svalues = ' '.join('{:d}'.format(v) for v in values)
oFile = open('./%s/%s_TimeFeatures.txt' %(directory, parmName),'w')
oFile.write('s:Tf/%s/Function = "Step"\n' % parmName)
oFile.write('dv:Tf/%s/Times = %d %s s\n' % (parmName, n, stimes))
if unit != 'u' and unit != 'i':
oFile.write('dv:Tf/%s/Values = %d %s %s\n' % (parmName, n, svalues, unit))
else:
oFile.write('%sv:Tf/%s/Values = %d %s\n' % (unit,parmName, n, svalues))
oFile.close()
############################################################################################################################################
############################################################################################################################################
############################################################################################################################################
############################################################################################################################################
############################################################################################################################################
def WriteTimeFeaturesPCF(DATA,PLAN_DATA):
directory = DATA["project_name"]
# Saving data into OpenTOPAS PCF
SaveTsTimeFunctionParameters('CollimatorAngles',\
PLAN_DATA["TsStepTimes"],\
PLAN_DATA["TsCollimatorAngles"], 'deg', directory)
SaveTsTimeFunctionParameters('TableAngles',\
PLAN_DATA["TsStepTimes"],\
PLAN_DATA["TsTableAngles"], 'deg', directory)
SaveTsTimeFunctionParameters('GantryAngles',\
PLAN_DATA["TsStepTimes"],\
PLAN_DATA["TsGantryAngles"], 'deg', directory)
SaveTsTimeFunctionParameters('JawX1',\
PLAN_DATA["TsStepTimes"],\
PLAN_DATA["TsJawX1"], 'cm', directory)
SaveTsTimeFunctionParameters('JawX2',\
PLAN_DATA["TsStepTimes"],\
PLAN_DATA["TsJawX2"], 'cm', directory)
SaveTsTimeFunctionParameters('JawY1',\
PLAN_DATA["TsStepTimes"],\
PLAN_DATA["TsJawY1"], 'cm', directory)
SaveTsTimeFunctionParameters('JawY2',\
PLAN_DATA["TsStepTimes"],\
PLAN_DATA["TsJawY2"], 'cm', directory)
SaveTsTimeFunctionParameters('MUperSegment',\
PLAN_DATA["TsStepTimes"],\
PLAN_DATA["TsWeights"], 'u', directory)
SaveTsTimeFunctionParameters('CalibrationFactor',\
PLAN_DATA["TsStepTimes"],\
PLAN_DATA["TsCalFactor"], 'u', directory)
SaveTsTimeFunctionParameters('PrimariesPerSegment',\
PLAN_DATA["TsStepTimes"],\
PLAN_DATA["TsPrimaries"], 'i', directory)
# Save MLC positions for each control point
mlcAsingle = []
mlcBsingle = []
oFile = open('./%s/MLC_TimeFeatures.txt' %directory,'w')
for key in PLAN_DATA["TsMLCX1"]:
aName = 'MLCX1_' + str(key)
aPars = GetTsTimeFunctionParameters(aName, PLAN_DATA["TsStepTimes"], PLAN_DATA["TsMLCX1"][key], 'cm')
for apar in aPars:
oFile.write(apar + '\n')
oFile.write('\n')
for key in PLAN_DATA["TsMLCX2"]:
aName = 'MLCX2_' + str(key)
aPars = GetTsTimeFunctionParameters(aName, PLAN_DATA["TsStepTimes"], PLAN_DATA["TsMLCX2"][key], 'cm')
for apar in aPars:
oFile.write(apar + '\n')
oFile.write('\n')
oFile.close()
# Save isocenter positions for each beam
oFile = open('./%s/Isocenter_TimeFeatures.txt' %directory,'w')
for key in PLAN_DATA["TsIsocenter"]:
aName = 'Iso' + str(key)
aPars = GetTsTimeFunctionParameters(aName, PLAN_DATA["TsBeamTimes"], PLAN_DATA["TsIsocenter"][key], 'cm')
for apar in aPars:
oFile.write(apar + '\n')
oFile.write('\n')
oFile.close()
############################################################################################################################################
############################################################################################################################################
############################################################################################################################################
############################################################################################################################################
############################################################################################################################################
def WritePlanParameterFile(DATA,CT_DATA,PLAN_DATA):
directory = DATA["project_name"]
# Setup and Time feature parameters
parFile = open('./%s/planParameters.txt'%(directory),'w')
parFile.write('includeFile = CollimatorAngles_TimeFeatures.txt TableAngles_TimeFeatures.txt\n')
parFile.write('includeFile = JawY1_TimeFeatures.txt JawY2_TimeFeatures.txt JawX1_TimeFeatures.txt JawX2_TimeFeatures.txt\n')
parFile.write('includeFile = MLC_TimeFeatures.txt GantryAngles_TimeFeatures.txt\n')
parFile.write('includeFile = MUperSegment_TimeFeatures.txt \n')
parFile.write('includeFile = Isocenter_TimeFeatures.txt\n')
parFile.write('includeFile = CalibrationFactor_TimeFeatures.txt\n')
parFile.write('\n')
parFile.write('s:RS/DicomDirectory = \"%s\"\n' % DATA["dicom_dirname"])
parFile.write('s:RS/DicomDoseFileName = \"%s\"\n' % DATA["RD_filename"])
parFile.write('d:Tf/VirtualSimulationTimeEnd = %1.2f s\n' % (PLAN_DATA["finalTime"]-1))
parFile.write('i:Tf/VirtualSimulationNumberOfSequentialTimes = %d\n' % int(PLAN_DATA["finalTime"]-1))
parFile.write('\n')
parFile.write('# Dicom center\n')
parFile.write('d:Ge/cx = %1.4f cm\n' % CT_DATA["cx"])
parFile.write('d:Ge/cy = %1.4f cm\n' % CT_DATA["cy"])
parFile.write('d:Ge/cz = %1.4f cm\n' % CT_DATA["cz"])
parFile.write('\n')
parFile.write('# Isocenter\n')
parFile.write('d:Ge/isox = Tf/IsoX/Value cm\n')
parFile.write('d:Ge/isoy = Tf/IsoY/Value cm\n')
parFile.write('d:Ge/isoz = Tf/IsoZ/Value cm\n')
parFile.write('\n')
parFile.write('d:Ge/Gantry_Angle = Tf/GantryAngles/Value deg\n')
parFile.write('d:Ge/Couch_Angle = Tf/TableAngles/Value deg\n')
parFile.write('d:Ge/Collimator_Angle = Tf/CollimatorAngles/Value deg\n')
parFile.write('u:So/calibrationFactorPerHistory = Tf/CalibrationFactor/Value * %1.5e \n' %(1/PLAN_DATA["phspChunk"]) )
parFile.write('u:So/ScalingFactor = So/calibrationFactorPerHistory * Tf/MUperSegment/Value\n')
parFile.write('\n')
parFile.write('d:Ge/JawX1 = Tf/JawX1/Value cm\n')
parFile.write('d:Ge/JawX2 = Tf/JawX2/Value cm\n')
parFile.write('d:Ge/JawY1 = Tf/JawY1/Value cm\n')
parFile.write('d:Ge/JawY2 = Tf/JawY2/Value cm\n')
parFile.write('d:Ge/PhSpX1 = 0.75 * Tf/JawX1/Value cm\n')
parFile.write('d:Ge/PhSpX2 = 0.75 * Tf/JawX2/Value cm\n')
parFile.write('d:Ge/PhSpY1 = 0.75 * Tf/JawY1/Value cm\n')
parFile.write('d:Ge/PhSpY2 = 0.75 * Tf/JawY2/Value cm\n')
parFile.write('\n')
parFile.write('\n')
if DATA["MLC_model"] == "generic" or DATA["MLC_model"] == "generichd":
parFile.write('dv:Ge/MLC/NegativeFieldSetting = 60 ')
for i in range(1,60+1,1):
parFile.write('Tf/MLCX1_%d/Value ' % i)
parFile.write('cm\n')
parFile.write('dv:Ge/MLC/PositiveFieldSetting = 60 ')
for i in range(1,60+1,1):
parFile.write('Tf/MLCX2_%d/Value ' % i)
parFile.write('cm\n')
if DATA["MLC_model"] == "VarianMillenium" or DATA["MLC_model"] == "VarianMilleniumHD":
parFile.write('dv:Ge/MLC/NegativeFieldSetting = 60 ')
for i in range(1,60+1,1):
parFile.write('Tf/MLCX1_%d/Value ' % i)
parFile.write('cm\n')
parFile.write('dv:Ge/MLC/PositiveFieldSetting = 60 ')
for i in range(1,60+1,1):
parFile.write('Tf/MLCX2_%d/Value ' % i)
parFile.write('cm\n')
parFile.close()
############################################################################################################################################
############################################################################################################################################
############################################################################################################################################
############################################################################################################################################
############################################################################################################################################
def WriteGeometryFile(DATA,ROI_DATA):
directory = DATA["project_name"]
# Geometry
parFile = open('./%s/Geometry.txt'%(directory),'w')
parFile.write('#\n')
parFile.write('includeFile = planParameters.txt HUtoMaterialSchneider.txt\n')
parFile.write('\n')
parFile.write('###################################################\n')
parFile.write('# Materials\n')
parFile.write('####################################################\n')
for name, material in ROI_DATA["materials"].items():
if ' ' in name:
name = name.replace(' ','_')
if '.' in name:
name = name.replace('.','_')
n = len(material[0])
parFile.write('sv:Ma/%s/Components = %d ' % (name, n))
for i in range(n):
parFile.write('"%s" ' % ROI_DATA["elements"][material[0][i]])
parFile.write('\n')
parFile.write('uv:Ma/%s/Fractions = %d ' % (name, n))
for i in range(n):
parFile.write('%f ' % material[1][i])
parFile.write('\n')
parFile.write('d:Ma/%s/Density = %f g/cm3\n' % (name, material[2]))
parFile.write('d:Ma/%s/MeanExcitationEnergy = %f eV\n' % (name, material[3]))
parFile.write('\n')
parFile.write('###################################################\n')
parFile.write('# Patient in DICOM\n')
parFile.write('####################################################\n')
parFile.write('s:Ge/Patient/Parent = "DICOM_to_IEC"\n')
parFile.write('s:Ge/Patient/Type = "TsDicomPatient"\n')
parFile.write('s:Ge/Patient/Material = "G4_WATER"\n')
parFile.write('d:Ge/Patient/RotX = 0.0 deg\n')
parFile.write('d:Ge/Patient/RotY = 0.0 deg\n')
parFile.write('d:Ge/Patient/RotZ = 0.0 deg\n')
parFile.write('d:Ge/Patient/TransX = 0 cm \n')
parFile.write('d:Ge/Patient/TransY = 0 cm \n')
parFile.write('d:Ge/Patient/TransZ = 0 cm \n')
parFile.write('s:Ge/Patient/HUtoMaterialConversionMethod = "Schneider"\n')
parFile.write('s:Ge/Patient/DicomDirectory = RS/DicomDirectory \n')
parFile.write('b:Ge/Patient/IgnoreInconsistentFrameOfReferenceUID = "True"\n')
parFile.write('sv:Ge/Patient/DicomModalityTags = 1 "CT"\n')
parFile.write('iv:Ge/Patient/ShowSpecificSlicesZ = 1 33 \n')
parFile.write('s:Ge/Patient/CloneRTDoseGridFrom = RS/DicomDoseFileName \n')
if len(ROI_DATA["roiWithMaterials"]) > 0:
parFile.write('sv:Ge/Patient/MaterialByRTStructNames = %d ' % len(ROI_DATA["roiWithMaterials"]))
for roi, name in ROI_DATA["roiWithMaterials"].items():
parFile.write('"'+roi+'" ')
parFile.write('\n')
parFile.write('sv:Ge/Patient/MaterialByRTStructMaterials = %d ' % len(ROI_DATA["roiWithMaterials"]))
for roi, name in ROI_DATA["roiWithMaterials"].items():
if ' ' in name:
name = name.replace(' ','_')
if '.' in name:
name = name.replace('.','_')
parFile.write('"'+name+'" ')
parFile.write('\n')
# Global control parameter files
parFile.write('\n')
parFile.write('###################################################\n')
parFile.write('# Jaws \n')
parFile.write('####################################################\n')
parFile.write('s:Ge/JawPos/Parent = "IEC_B"\n')
parFile.write('s:Ge/JawPos/Type = "Group"\n')
parFile.write('#d:Ge/JawPos/RotZ = -1 * Ge/Collimator_Angle deg\n')
parFile.write('\n')
parFile.write('dc:Ge/JawX/PositiveFieldSetting = Ge/JawX2 cm \n')
parFile.write('dc:Ge/JawX/NegativeFieldSetting = +1 * Ge/JawX1 cm \n')
parFile.write('s:Ge/JawX/Parent = "JawPos" #IEC_B"\n')
parFile.write('s:Ge/JawX/Type = "TsJaws"\n')
parFile.write('s:Ge/JawX/Material = "G4_W"\n')
parFile.write('s:Ge/JawX/Color = "red"\n')
parFile.write('s:Ge/JawX/DrawingStyle = "Solid"\n')
parFile.write('d:Ge/JawX/LX = 13.462 cm \n')
parFile.write('d:Ge/JawX/LY = 21.844 cm \n')
parFile.write('d:Ge/JawX/LZ = 7.77 cm \n')
parFile.write('dc:Ge/JawX/SourceToUpstreamSurfaceDistance = 27.89 cm \n')
parFile.write('d:Ge/JawX/SAD = 100 cm \n')
parFile.write('d:Ge/JawX/DistSourceToSAD = Ge/JawX/SAD - Ge/JawX/SourceToUpstreamSurfaceDistance cm\n')
parFile.write('d:Ge/JawX/HalfThickness = 0.5 * Ge/JawX/LZ cm\n')
parFile.write('d:Ge/JawX/TransZ = Ge/JawX/DistSourceToSAD - Ge/JawX/HalfThickness cm\n')
parFile.write('d:Ge/JawX/TravelAxisX = 0. deg \n')
parFile.write('d:Ge/JawX/TravelAxisY = 90. deg \n')
parFile.write('d:Ge/JawX/RotZ = Ge/JawX/TravelAxisX deg \n')
parFile.write('s:Ge/JawX/AssignToRegionNamed = "jaws"\n')
parFile.write('\n')
parFile.write('dc:Ge/JawY/PositiveFieldSetting = Ge/JawY2 cm \n')
parFile.write('dc:Ge/JawY/NegativeFieldSetting = +1 * Ge/JawY1 cm \n')
parFile.write('s:Ge/JawY/Parent = "JawPos" #IEC_B"\n')
parFile.write('s:Ge/JawY/Type = "TsJaws"\n')
parFile.write('s:Ge/JawY/Material = "G4_W"\n')
parFile.write('s:Ge/JawY/Color = "blue"\n')
parFile.write('s:Ge/JawY/DrawingStyle = "Solid"\n')
parFile.write('d:Ge/JawY/LX = 11.937 cm \n')
parFile.write('d:Ge/JawY/LY = 18.796 cm \n')
parFile.write('d:Ge/JawY/LZ = 7.77 cm \n')
parFile.write('dc:Ge/JawY/SourceToUpstreamSurfaceDistance = 36.61 cm \n')
parFile.write('d:Ge/JawY/SAD = 100 cm \n')
parFile.write('d:Ge/JawY/DistSourceToSAD = Ge/JawY/SAD - Ge/JawY/SourceToUpstreamSurfaceDistance cm\n')
parFile.write('d:Ge/JawY/HalfThickness = 0.5 * Ge/JawY/LZ cm\n')
parFile.write('d:Ge/JawY/TransZ = Ge/JawY/DistSourceToSAD - Ge/JawY/HalfThickness cm\n')
parFile.write('d:Ge/JawY/TravelAxisX = 0. deg \n')
parFile.write('d:Ge/JawY/TravelAxisY = -90. deg ### CHANGED FROM +90deg\n')
parFile.write('d:Ge/JawY/RotZ = Ge/JawY/TravelAxisY deg \n')
parFile.write('s:Ge/JawY/AssignToRegionNamed = "jaws"\n')
parFile.write('\n')
parFile.write('###################################################\n')
parFile.write('# Base plate below the jaws \n')
parFile.write('####################################################\n')
parFile.write('s:Ge/BasePlate/Parent = "IEC_B"\n')
parFile.write('s:Ge/BasePlate/Type = "TsCylinder"\n')
parFile.write('s:Ge/BasePlate/Material = "Steel"\n')
parFile.write('s:Ge/BasePlate/Color = "yellow" \n')
parFile.write('d:Ge/BasePlate/RMax = 30.226 cm \n')
parFile.write('d:Ge/BasePlate/RMin = 11.557 cm \n')
parFile.write('d:Ge/BasePlate/HL = 0.762 cm\n')
parFile.write('d:Ge/BasePlate/TransZ = 54.062 cm\n')
parFile.write('s:Ge/BasePlate/DrawingStyle = "Solid"\n')
parFile.write('\n')
parFile.write('###################################################\n')
parFile.write('# MLCs \n')
parFile.write('####################################################\n')
parFile.write('s:Ge/MLCPos/Parent = "IEC_B"\n')
parFile.write('s:Ge/MLCPos/Type = "Group"\n')
if DATA["MLC_model"] == "VarianMillenium" or DATA["MLC_model"] == "VarianMilleniumHD":
parFile.write('d:Ge/MLCPos/TransZ = 49.02 cm\n')
parFile.write('\n')
if DATA["MLC_model"] == "generic" or DATA["MLC_model"] == "generichd":
parFile.write(' # --- %s selected\n' %(DATA["MLC_model"]))
parFile.write('### IMPORTANT NOTE\n')
parFile.write('# generic and genericHD specifications from literature (see write_PCF.py for references)\n')
parFile.write('# user: change values if more accurate data is available\n')
parFile.write('\n')
generic_thickness = 6.7 # cm
genericHD_thickness = 6.9 # cm
generic_distToIso = 49.0 # cm
generic_SAD = 100.0 # cm
generic_SUSD = generic_SAD - generic_distToIso - generic_thickness*0.5
parFile.write('s:Ge/MLC/Type = "TsDivergingMLC"\n')
parFile.write('s:Ge/MLC/Parent = "MLCPos"\n')
parFile.write('s:Ge/MLC/Material = "G4_W"\n')
parFile.write('s:Ge/MLC/Color = "gray"\n')
parFile.write('s:Ge/MLC/DrawingStyle = "Solid"\n')
parFile.write('d:Ge/MLC/SAD = %s cm\n' %generic_SAD)
parFile.write('d:Ge/MLC/SourceToUpstreamSurfaceDistance = %s cm\n' %generic_SUSD)
parFile.write('d:Ge/MLC/DistSourceToSAD = Ge/MLC/SAD - Ge/MLC/SourceToUpstreamSurfaceDistance cm\n')
parFile.write('d:Ge/MLC/MaxLeafOpen = 20 cm\n')
parFile.write('d:Ge/MLC/Length = 19 cm\n')
parFile.write('s:Ge/MLC/LeafTravelAxis = "Xb"\n')
parFile.write('dv:Ge/MLC/LeafWidths = 60 ')
if DATA["MLC_model"] == "generic":
for leaf_pair in range(60):
leaf_pair += 1
if leaf_pair > 10 and leaf_pair < 51:
parFile.write('5.0 ')
else:
parFile.write('10.0 ')
parFile.write('mm\n')
parFile.write('d:Ge/MLC/Thickness = %s cm\n' %generic_thickness)
else:
for leaf_pair in range(60):
leaf_pair += 1
if leaf_pair > 14 and leaf_pair < 47:
parFile.write('2.5 ')
else:
parFile.write('5.0 ')
parFile.write('mm\n')
parFile.write('d:Ge/MLC/Thickness = %s cm\n' %genericHD_thickness)
parFile.write('d:Ge/MLC/HalfThickness = 0.5 * Ge/MLC/Thickness cm\n')
parFile.write('d:Ge/MLC/TransZ = Ge/MLC/DistSourceToSAD - Ge/MLC/HalfThickness cm\n')
parFile.write('#d:Ge/MLCPos/RotZ = -1 * Ge/Collimator_Angle deg\n')
parFile.write('\n')
if DATA["MLC_model"] == "VarianMillenium" or DATA["MLC_model"] == "VarianMilleniumHD":
parFile.write('s:Ge/MLC/Type = "TsTrueBeamMLC"\n')
if DATA["MLC_model"] == "VarianMillenium":
parFile.write('s:Ge/MLC/MLCModel = "NDS120"\n')
if DATA["MLC_model"] == "VarianMilleniumHD":
parFile.write('s:Ge/MLC/MLCModel = "NDS120HD"\n')
parFile.write('s:Ge/MLC/Parent = "MLCPos"\n')
parFile.write('s:Ge/MLC/Material = "G4_W"\n')
parFile.write('s:Ge/MLC/Color = "gray"\n')
parFile.write('s:Ge/MLC/DrawingStyle = "Solid"\n')
parFile.write('d:Ge/MLC/MinLeafAperture = 0.05 cm\n')
parFile.write('d:Ge/MLC/MaxLeafAperture = 20 cm\n')
parFile.write('b:Ge/MLC/CheckForOverlapsBetweenLeafs = "false"\n')
parFile.write('#d:Ge/MLC/RotZ = -1 * Ge/Collimator_Angle deg\n')
parFile.write('\n')
parFile.write('###################################################\n')
parFile.write('# Mylar window at treatment head exit\n')
parFile.write('####################################################\n')
parFile.write('s:Ge/Tray/Parent = "IEC_B"\n')
parFile.write('s:Ge/Tray/Type = "TsBox"\n')
parFile.write('s:Ge/Tray/Material = "Mylar"\n')
parFile.write('s:Ge/Tray/Color = "green"\n')
parFile.write('d:Ge/Tray/HLX = 15 cm\n')
parFile.write('d:Ge/Tray/HLY = 15 cm\n')
parFile.write('d:Ge/Tray/HLZ = 0.00508 cm\n')
parFile.write('d:Ge/Tray/TransZ = 44.3 cm\n')
parFile.write('\n')
parFile.write('\n')
# parallel volumes to prevent overlapping
parFile.write('b:Ge/Tray/IsParallel = "True"\n')
parFile.write('b:Ge/MLC/IsParallel = "True"\n')
parFile.write('\n')
parFile.close()
def WriteMainWithVisualizationFile(DATA):
directory = DATA["project_name"]
# Visualization
parFile = open('./%s/Main_with_Visualization.txt'%(directory),'w')
parFile.write('###################################################\n')
parFile.write('# Get the main file\n')
parFile.write('####################################################\n')
parFile.write('includeFile = Main.txt\n')
parFile.write('\n')
parFile.write('###################################################\n')
parFile.write('# Visualization\n')
parFile.write('####################################################\n')
parFile.write('b:Ts/UseQt = "True"\n')
parFile.write('s:Gr/ViewA/Type = "OpenGL"\n')
parFile.write('i:Gr/ViewA/WindowSizeX = 900\n')
parFile.write('i:Gr/ViewA/WindowSizeY = 900\n')
parFile.write('d:Gr/ViewA/Theta = 89.9 deg\n')
parFile.write('d:Gr/ViewA/Phi = -90 deg\n')
parFile.write('b:Gr/ViewA/IncludeAxes = "true"\n')
parFile.write('d:Gr/ViewA/AxesSize = 100 cm \n')
parFile.write('u:Gr/ViewA/Zoom = 1.\n')
parFile.write('i:Gr/ShowOnlyOutlineIfVoxelCountExceeds = 100000000\n')
parFile.write('\n')
parFile.write('# Select a specific dicom slice to show\n')
parFile.write('#iv:Ge/Patient/ShowSpecificSlicesX = 1 -1\n')
parFile.write('#iv:Ge/Patient/ShowSpecificSlicesY = 1 -1\n')
parFile.write('iv:Ge/Patient/ShowSpecificSlicesZ = 1 -1\n')
parFile.write('\n')
parFile.write('# comment the follow line in Geometry.txt to avoid displaying the RT Dose Grid\n')
parFile.write('#s:Ge/Patient/CloneRTDoseGridFrom = RS/DicomDoseFileName \n')
parFile.close()
def WriteMainFile(DATA,PLAN_DATA):
directory = DATA["project_name"]
# Main PCF
parFile = open('./%s/Main.txt'%(directory),'w')
parFile.write('##################################################\n')
parFile.write('includeFile = planParameters.txt Geometry.txt PrimariesPerSegment_TimeFeatures.txt\n')
parFile.write('sv:Ph/Default/Modules = 1 "g4em-standard_opt4"\n')
parFile.write('d:Ph/Default/LowestElectronEnergy = 189 keV\n')
parFile.write('d:Ph/Default/ForRegion/jaws/CutForGamma = 1 mm\n')
parFile.write('d:Ph/Default/ForRegion/jaws/CutForElectron = 0.3 mm\n')
parFile.write('\n')
parFile.write('sv:Ph/Default/LayeredMassGeometryWorlds = 2 "MLC" "Tray"\n')
parFile.write('\n')
parFile.write('s:Ge/World/Material = "Air"\n')
parFile.write('d:Ge/World/HLX = 1.5 m\n')
parFile.write('d:Ge/World/HLY = 1.5 m\n')
parFile.write('d:Ge/World/HLZ = 1.5 m\n')
parFile.write('b:Ge/World/Invisible = "True"\n')
parFile.write('\n')
parFile.write('# Fixed system IEC_F, parent Geant4 world - e.g. Xf; (Xf,Yf,Zf) is world (X,Y,Z)^M\n')
parFile.write('s:Ge/IEC_F/Parent = "World"\n')
parFile.write('s:Ge/IEC_F/Type = "Group"\n')
parFile.write('d:Ge/IEC_F/RotZ = +1 * Ge/Collimator_Angle deg\n')
parFile.write('\n')
parFile.write('s:Ge/IEC_W/Parent = "World"\n')
parFile.write('s:Ge/IEC_W/Type = "Group"\n')
parFile.write('\n')
parFile.write('# Gantry system IEC_G, parent IEC_F - e.g. Xg; Gantry rotates about Yg by IEC_G/RotY^M\n')
parFile.write('# Gantry rotation, if any, is applied in the includeFile (see above)^M\n')
parFile.write('s:Ge/IEC_G/Parent = "IEC_F"\n')
parFile.write('s:Ge/IEC_G/Type = "Group"\n')
parFile.write('dc:Ge/IEC_G/RotY_S = Ge/Gantry_Angle deg \n')
parFile.write('#d:Ge/IEC_G/RotY = -1 * Ge/IEC_G/RotY_S deg\n')
parFile.write('d:Ge/IEC_G/RotY = +1 * Ge/IEC_G/RotY_S deg # to rotate the patient instead\n')
parFile.write('\n')
parFile.write('# Beam limiting system IEC_B, parent IEC_G - e.g. Xb; Collimator rotates about Zb by IEC_B/RotZ^M\n')
parFile.write('# Collimator rotation, if any, is applied in the includeFile (see above)^M\n')
parFile.write('s:Ge/IEC_B/Parent = "IEC_W" # "IEC_G" to rotate the patient\n')
parFile.write('s:Ge/IEC_B/Type = "Group"\n')
parFile.write('\n')
parFile.write('# Patient support system (couch) IEC_S, parent IEC_F - couch rotates by RotZs^M\n')
parFile.write('# Couch rotation, if any, is applied in the includeFile (see above)^M\n')
parFile.write('s:Ge/IEC_S/Parent = "IEC_G" # "IEC_F" to rotate patient instead\n')
parFile.write('s:Ge/IEC_S/Type = "Group"\n')
parFile.write('d:Ge/IEC_S/TransX = -1 * Ge/Isox cm \n')
parFile.write('d:Ge/IEC_S/TransY = -1 * Ge/Isoz cm \n')
parFile.write('d:Ge/IEC_S/TransZ = +1 * Ge/Isoy cm \n')
parFile.write('dc:Ge/IEC_S/RotZ_S = Ge/Couch_Angle deg \n')
parFile.write('d:Ge/IEC_S/RotZ = -1 * Ge/IEC_S/RotZ_S deg\n')
parFile.write('\n')
parFile.write('s:Ge/DICOM_to_IEC/Type = "Group"\n')
parFile.write('s:Ge/DICOM_to_IEC/Parent = "IEC_S"\n')
parFile.write('d:Ge/DICOM_to_IEC/TransX = Ge/cx cm \n')
parFile.write('d:Ge/DICOM_to_IEC/TransY = Ge/cz cm \n')
parFile.write('d:Ge/DICOM_to_IEC/TransZ = -1 * Ge/cy cm # Swap Y <-> Z and invert the sigh\n')
parFile.write('d:Ge/DICOM_to_IEC/RotX = 90.0 deg # This rotation brings back Z <-> Y\n')
parFile.write('\n')
if DATA["multipleUse"] > 1:
parFile.write('#########################\n')
parFile.write('# Geometry for vrt\n')
parFile.write('#########################\n')
parFile.write('s:Ge/VrtParallelWorld/Type = "TsBox"\n')
parFile.write('s:Ge/VrtParallelWorld/Parent = "World"\n')
parFile.write('d:Ge/VrtParallelWorld/HLX = 35 cm\n')
parFile.write('d:Ge/VrtParallelWorld/HLY = 35 cm\n')
parFile.write('d:Ge/VrtParallelWorld/HLZ = 80 cm\n')
parFile.write('s:Ge/VrtParallelWorld/Color = "grass"\n')
parFile.write('b:Ge/VrtParallelWorld/IsParallel = "true"\n')
parFile.write('\n')
parFile.write('s:Ge/subComponent1/Parent = "VrtParallelWorld"\n')
parFile.write('s:Ge/subComponent1/Type = "TsBox"\n')
parFile.write('s:Ge/subComponent1/Color = "blue"\n')
parFile.write('b:Ge/subComponent1/IsParallel = "True"\n')
parFile.write('d:Ge/subComponent1/HLX = 35 cm\n')
parFile.write('d:Ge/subComponent1/HLY = 35 cm\n')
parFile.write('d:Ge/subComponent1/HLZ = 45 cm\n')
parFile.write('\n')
parFile.write('##########################\n')
parFile.write('# Variance reduction\n')
parFile.write('##########################\n')
parFile.write('b:Vr/UseVarianceReduction = "true"\n')
parFile.write('b:Vr/ParticleSplit/Active = "true"\n')
parFile.write('sv:Vr/ParticleSplit/ParticleName = 3 "gamma" "e-" "e+"\n')
parFile.write('s:Vr/ParticleSplit/Component = "VrtParallelWorld"\n')
parFile.write('sv:Vr/ParticleSplit/SubComponents = 1 "subComponent1"\n')
parFile.write('s:Vr/ParticleSplit/Type = "GeometricalParticleSplit"\n')
parFile.write('iv:Vr/ParticleSplit/SplitNumber = 1 %d\n' % DATA["multipleUse"])
parFile.write('bv:Vr/ParticleSplit/Symmetric = 1 "false"\n')
parFile.write('d:Vr/ParticleSplit/RussianRoulette/ROIRadius = 60 cm\n')
parFile.write('d:Vr/ParticleSplit/RussianRoulette/ROITrans = 2 cm\n')
parFile.write('bv:Vr/ParticleSplit/RussianRoulette = 1 "false"\n')
parFile.write('s:Vr/ParticleSplit/SplitAxis = "zaxis"\n')
parFile.write('\n')
parFile.write('####################################################\n')
parFile.write('# Beam is at Gantry coordination\n')
parFile.write('####################################################\n')
parFile.write('s:Ge/BeamPosition/Parent = "IEC_F" # "IEC_G" to rotate the patient instead\n')
parFile.write('d:Ge/BeamPosition/RotX = 180 deg\n')
parFile.write('d:Ge/BeamPosition/TransZ = 100 cm \n')
parFile.write('\n')
parFile.write('s:Ge/source/Type = "Group" \n')
parFile.write('s:Ge/source/Parent = "BeamPosition"\n')
parFile.write('d:Ge/source/TransZ = 26.7 cm #for TrueBeam phaseSpaceFile\n')
parFile.write('\n')
parFile.write('s:So/phsp/Type = "PhaseSpace"\n')
parFile.write('s:So/phsp/Component = "source"\n')
parFile.write('s:So/phsp/PhaseSpaceFileName = "%s"\n' % DATA["phsp_filename"])
parFile.write('b:So/phsp/PhaseSpacePrecheck = "F"\n')
parFile.write('i:So/phsp/PhaseSpaceMultipleUse = 0\n')
parFile.write('i:So/phsp/NumberOfHistoriesInRun = Tf/PrimariesPerSegment/Value #10 * Ts/ShowHistoryCountAtInterval\n')
parFile.write('b:So/phsp/LimitedAssumeFirstParticleIsNewHistory = "True" #if IAEA phsp\n')
parFile.write('b:So/phsp/LimitedAssumePhotonIsNewHistory = "True" #if IAEA phsp\n')
parFile.write('\n')
parFile.write('s:Sc/Dose/Quantity = "%s" \n' % (DATA["scoring_quantity"]))
parFile.write('u:Sc/Dose/OutputWeightingFactor = So/ScalingFactor\n')
parFile.write('b:Sc/Dose/PreCalculateStoppingPowerRatios = "True"\n')
parFile.write('s:Sc/Dose/Component = "Patient/RTDoseGrid" \n')
parFile.write('s:Sc/Dose/IfOutputfileAlreadyExists = "Overwrite"\n')
parFile.write('s:Sc/Dose/OutputType = "%s" \n' % DATA["output_format"])
parFile.write('s:Sc/Dose/OutputFile = "./output/%s" \n' % (DATA["output_file"]))
parFile.write('\n')
parFile.write('d:Tf/TimeLineEnd = Tf/VirtualSimulationTimeEnd s\n')
parFile.write('i:Tf/NumberOfSequentialTimes = Tf/VirtualSimulationNumberOfSequentialTimes\n')
parFile.write('i:Ts/Seed = 1\n')
parFile.write('i:Ts/NumberOfThreads = 0\n')
parFile.write('b:Ts/ShowCPUTime = "True"\n')
countAtInterval = int(PLAN_DATA["phspChunk"]/10)
parFile.write('i:Ts/ShowHistoryCountAtInterval = %d \n' % countAtInterval)
parFile.write('i:Ts/ParameterizationErrorMaxCount = 1000000000\n')
parFile.write('i:Ts/ParameterizationErrorMaxReports = 10\n')
parFile.write('\n')
# References
# 10.1016/j.rpor.2018.09.001
# 10.1186/1748-717X-4-22
# 10.1002/acm2.12197
# 10.1120/jacmp.v12i3.3475
# https://www.oncologysystems.com/resources/linear-accelerator-guides/varian-high-energy-linear-accelerators-comparison-chart/