Upload Process library

b51cd04 verified over 2 years ago

18.1 kB

import pydicom
import numpy as np
import math
import time
import pickle, scipy



class RTplan:

  def __init__(self):
    self.SeriesInstanceUID = ""
    self.SOPInstanceUID = ""
    self.PatientInfo = {}
    self.StudyInfo = {}
    self.DcmFile = ""
    self.Modality = ""
    self.RadiationType = ""
    self.ScanMode = ""
    self.TreatmentMachineName = ""
    self.NumberOfFractionsPlanned = 1
    self.NumberOfSpots = 0
    self.Beams = []
    self.TotalMeterset = 0.0
    self.PlanName = ""
    self.isLoaded = 0
    self.beamlets = []
    self.OriginalDicomDataset = []
    
    
    
  def print_plan_info(self, prefix=""):
    print(prefix + "Plan: " + self.SeriesInstanceUID)
    print(prefix + "   " + self.DcmFile)
    
    
  
  def import_Dicom_plan(self):
    if(self.isLoaded == 1):
      print("Warning: RTplan " + self.SeriesInstanceUID + " is already loaded")
      return
      
    dcm = pydicom.dcmread(self.DcmFile)
    
    self.OriginalDicomDataset = dcm
    
    # Photon plan
    if dcm.SOPClassUID == "1.2.840.10008.5.1.4.1.1.481.5": 
      print("ERROR: Conventional radiotherapy (photon) plans are not supported")
      self.Modality = "Radiotherapy"
      return
  
    # Ion plan  
    elif dcm.SOPClassUID == "1.2.840.10008.5.1.4.1.1.481.8":
      self.Modality = "Ion therapy"
    
      if dcm.IonBeamSequence[0].RadiationType == "PROTON":
        self.RadiationType = "Proton"
      else:
        print("ERROR: Radiation type " + dcm.IonBeamSequence[0].RadiationType + " not supported")
        self.RadiationType = dcm.IonBeamSequence[0].RadiationType
        return
       
      if dcm.IonBeamSequence[0].ScanMode == "MODULATED":
        self.ScanMode = "MODULATED" # PBS
      else:
        print("ERROR: Scan mode " + dcm.IonBeamSequence[0].ScanMode + " not supported")
        self.ScanMode = dcm.IonBeamSequence[0].ScanMode
        return 
    
    # Other  
    else:
      print("ERROR: Unknown SOPClassUID " + dcm.SOPClassUID + " for file " + self.DcmFile)
      self.Modality = "Unknown"
      return
      
    # Start parsing PBS plan
    self.SOPInstanceUID = dcm.SOPInstanceUID
    self.NumberOfFractionsPlanned = int(dcm.FractionGroupSequence[0].NumberOfFractionsPlanned)
    self.NumberOfSpots = 0
    self.TotalMeterset = 0  
    
    if(hasattr(dcm.IonBeamSequence[0], 'TreatmentMachineName')):
      self.TreatmentMachineName = dcm.IonBeamSequence[0].TreatmentMachineName
    else:
      self.TreatmentMachineName = ""
  
    for dcm_beam in dcm.IonBeamSequence:
      if dcm_beam.TreatmentDeliveryType != "TREATMENT":
        continue
      
      first_layer = dcm_beam.IonControlPointSequence[0]
      
      beam = Plan_IonBeam()
      beam.SeriesInstanceUID = self.SeriesInstanceUID
      beam.BeamName = dcm_beam.BeamName
      beam.IsocenterPosition = [float(first_layer.IsocenterPosition[0]), float(first_layer.IsocenterPosition[1]), float(first_layer.IsocenterPosition[2])]
      beam.GantryAngle = float(first_layer.GantryAngle)
      beam.PatientSupportAngle = float(first_layer.PatientSupportAngle)
      beam.FinalCumulativeMetersetWeight = float(dcm_beam.FinalCumulativeMetersetWeight)
    
      # find corresponding beam in FractionGroupSequence (beam order may be different from IonBeamSequence)
      ReferencedBeam_id = next((x for x, val in enumerate(dcm.FractionGroupSequence[0].ReferencedBeamSequence) if val.ReferencedBeamNumber == dcm_beam.BeamNumber), -1)
      if ReferencedBeam_id == -1:
        print("ERROR: Beam number " + dcm_beam.BeamNumber + " not found in FractionGroupSequence.")
        print("This beam is therefore discarded.")
        continue
      else: beam.BeamMeterset = float(dcm.FractionGroupSequence[0].ReferencedBeamSequence[ReferencedBeam_id].BeamMeterset)
    
      self.TotalMeterset += beam.BeamMeterset
    
      if dcm_beam.NumberOfRangeShifters == 0:
        beam.RangeShifterID = ""
        beam.RangeShifterType = "none"
      elif dcm_beam.NumberOfRangeShifters == 1:
        beam.RangeShifterID = dcm_beam.RangeShifterSequence[0].RangeShifterID
        if dcm_beam.RangeShifterSequence[0].RangeShifterType == "BINARY":
          beam.RangeShifterType = "binary"
        elif dcm_beam.RangeShifterSequence[0].RangeShifterType == "ANALOG":
          beam.RangeShifterType = "analog"
        else:
          print("ERROR: Unknown range shifter type for beam " + dcm_beam.BeamName)
          beam.RangeShifterType = "none"
      else: 
        print("ERROR: More than one range shifter defined for beam " + dcm_beam.BeamName)
        beam.RangeShifterID = ""
        beam.RangeShifterType = "none"
      
      
      SnoutPosition = 0
      if hasattr(first_layer, 'SnoutPosition'):
        SnoutPosition = float(first_layer.SnoutPosition)
    
      IsocenterToRangeShifterDistance = SnoutPosition
      RangeShifterWaterEquivalentThickness = ""
      RangeShifterSetting = "OUT"
      ReferencedRangeShifterNumber = 0
    
      if hasattr(first_layer, 'RangeShifterSettingsSequence'):
        if hasattr(first_layer.RangeShifterSettingsSequence[0], 'IsocenterToRangeShifterDistance'):
          IsocenterToRangeShifterDistance = float(first_layer.RangeShifterSettingsSequence[0].IsocenterToRangeShifterDistance)
        if hasattr(first_layer.RangeShifterSettingsSequence[0], 'RangeShifterWaterEquivalentThickness'):
          RangeShifterWaterEquivalentThickness = float(first_layer.RangeShifterSettingsSequence[0].RangeShifterWaterEquivalentThickness)
        if hasattr(first_layer.RangeShifterSettingsSequence[0], 'RangeShifterSetting'):
          RangeShifterSetting = first_layer.RangeShifterSettingsSequence[0].RangeShifterSetting
        if hasattr(first_layer.RangeShifterSettingsSequence[0], 'ReferencedRangeShifterNumber'):
          ReferencedRangeShifterNumber = int(first_layer.RangeShifterSettingsSequence[0].ReferencedRangeShifterNumber)
       
      CumulativeMeterset = 0
    
      for dcm_layer in dcm_beam.IonControlPointSequence:
        if dcm_layer.NumberOfScanSpotPositions == 1: sum_weights = dcm_layer.ScanSpotMetersetWeights
        else: sum_weights = sum(dcm_layer.ScanSpotMetersetWeights)
      
        if sum_weights == 0.0:
          continue
        
        layer = Plan_IonLayer()
        layer.SeriesInstanceUID = self.SeriesInstanceUID
            
        if hasattr(dcm_layer, 'SnoutPosition'):
          SnoutPosition = float(dcm_layer.SnoutPosition)
        
        if hasattr(dcm_layer, 'NumberOfPaintings'): layer.NumberOfPaintings = int(dcm_layer.NumberOfPaintings)
        else: layer.NumberOfPaintings = 1
       
        layer.NominalBeamEnergy = float(dcm_layer.NominalBeamEnergy)
        layer.ScanSpotPositionMap_x = dcm_layer.ScanSpotPositionMap[0::2]
        layer.ScanSpotPositionMap_y = dcm_layer.ScanSpotPositionMap[1::2]
        layer.ScanSpotMetersetWeights = dcm_layer.ScanSpotMetersetWeights
        layer.SpotMU = np.array(dcm_layer.ScanSpotMetersetWeights) * beam.BeamMeterset / beam.FinalCumulativeMetersetWeight # spot weights are converted to MU
        if layer.SpotMU.size == 1: layer.SpotMU = [layer.SpotMU]
        else: layer.SpotMU = layer.SpotMU.tolist()
      
        self.NumberOfSpots += len(layer.SpotMU)
        CumulativeMeterset += sum(layer.SpotMU)
        layer.CumulativeMeterset = CumulativeMeterset
            
        if beam.RangeShifterType != "none":        
          if hasattr(dcm_layer, 'RangeShifterSettingsSequence'):
            RangeShifterSetting = dcm_layer.RangeShifterSettingsSequence[0].RangeShifterSetting
            ReferencedRangeShifterNumber = dcm_layer.RangeShifterSettingsSequence[0].ReferencedRangeShifterNumber
            if hasattr(dcm_layer.RangeShifterSettingsSequence[0], 'IsocenterToRangeShifterDistance'):
              IsocenterToRangeShifterDistance = dcm_layer.RangeShifterSettingsSequence[0].IsocenterToRangeShifterDistance
            if hasattr(dcm_layer.RangeShifterSettingsSequence[0], 'RangeShifterWaterEquivalentThickness'):
              RangeShifterWaterEquivalentThickness = dcm_layer.RangeShifterSettingsSequence[0].RangeShifterWaterEquivalentThickness
        
          layer.RangeShifterSetting = RangeShifterSetting
          layer.IsocenterToRangeShifterDistance = IsocenterToRangeShifterDistance
          layer.RangeShifterWaterEquivalentThickness = RangeShifterWaterEquivalentThickness
          layer.ReferencedRangeShifterNumber = ReferencedRangeShifterNumber
        
        
        beam.Layers.append(layer)
      
      self.Beams.append(beam)
      
    self.isLoaded = 1

  def export_Dicom_with_new_UID(self, OutputFile):
    # generate new uid
    initial_uid = self.OriginalDicomDataset.SOPInstanceUID
    new_uid = pydicom.uid.generate_uid()
    self.OriginalDicomDataset.SOPInstanceUID = new_uid

    # save dicom file
    print("Export dicom RTPLAN: " + OutputFile)
    self.OriginalDicomDataset.save_as(OutputFile)

    # restore initial uid
    self.OriginalDicomDataset.SOPInstanceUID = initial_uid

    return new_uid



  def save(self, file_path):
    beamlets = self.beamlets
    self.beamlets = []

    with open(file_path, 'wb') as fid:
      pickle.dump(self.__dict__, fid)

    self.beamlets = beamlets



  def load(self, file_path):
    with open(file_path, 'rb') as fid:
      tmp = pickle.load(fid)

    self.__dict__.update(tmp)

  def compute_cartesian_coordinates(self, CT, Scanner, beams, RangeShifters=[]):
    time_start = time.time()
    
    SPR = SPRimage()
    SPR.convert_CT_to_SPR(CT, Scanner)
    
    CTborders_x = [SPR.ImagePositionPatient[0], SPR.ImagePositionPatient[0] + SPR.GridSize[0] * SPR.PixelSpacing[0]]
    CTborders_y = [SPR.ImagePositionPatient[1], SPR.ImagePositionPatient[1] + SPR.GridSize[1] * SPR.PixelSpacing[1]]
    CTborders_z = [SPR.ImagePositionPatient[2], SPR.ImagePositionPatient[2] + SPR.GridSize[2] * SPR.PixelSpacing[2]]
    
    spot_positions = []
    spot_directions = []
    spot_ranges = []

    # initialize spot info for raytracing
    for beam in self.Beams:
      #beam = self.Beams[b]

      RangeShifter = -1
      if beam.RangeShifterType == "binary":
        RangeShifter = next((RS for RS in RangeShifters if RS.ID == beam.RangeShifterID), -1)

      for layer in beam.Layers:

        range_in_water = SPR.energyToRange(layer.NominalBeamEnergy)*10
        if(layer.RangeShifterSetting == 'IN'):
          if(layer.RangeShifterWaterEquivalentThickness != ""): RangeShifter_WET = layer.RangeShifterWaterEquivalentThickness
          elif(RangeShifter != -1): RangeShifter_WET = RangeShifter.WET
          else: RangeShifter_WET = 0.0

          if(RangeShifter_WET > 0.0): range_in_water -= RangeShifter_WET

        for s in range(len(layer.ScanSpotPositionMap_x)):
          
          # BEV coordinates to 3D coordinates: position (x,y,z) and direction (u,v,w)
          x,y,z = layer.ScanSpotPositionMap_x[s], 0, layer.ScanSpotPositionMap_y[s]
          u,v,w = 1e-10, 1.0, 1e-10
          
          # rotation for gantry angle (around Z axis)
          angle = math.radians(beam.GantryAngle)
          [x,y,z] = self.Rotate_vector([x,y,z], angle, 'z')
          [u,v,w] = self.Rotate_vector([u,v,w], angle, 'z')
          
          # rotation for couch angle (around Y axis)
          angle = math.radians(beam.PatientSupportAngle)
          [x,y,z] = self.Rotate_vector([x,y,z], angle, 'y')
          [u,v,w] = self.Rotate_vector([u,v,w], angle, 'y')
          
          # Dicom CT coordinates
          x = x + beam.IsocenterPosition[0]
          y = y + beam.IsocenterPosition[1]
          z = z + beam.IsocenterPosition[2]
          
          # translate initial position at the CT image border
          Translation = np.array([1.0, 1.0, 1.0])
          Translation[0] = (x - CTborders_x[int(u<0)]) / u
          Translation[1] = (y - CTborders_y[int(v<0)]) / v
          Translation[2] = (z - CTborders_z[int(w<0)]) / w
          Translation = Translation[np.argmin(np.absolute(Translation))]
          x = x - Translation * u
          y = y - Translation * v
          z = z - Translation * w

          # append data to the list of spots to process
          spot_positions.append([x,y,z])
          spot_directions.append([u,v,w])
          spot_ranges.append(range_in_water)


    CartesianSpotPositions = compute_position_from_range(SPR, spot_positions, spot_directions, spot_ranges)
          
    print("Spot RayTracing: " + str(time.time()-time_start) + " sec")
    return CartesianSpotPositions 

  #TO ADAPT
  def compute_spot_maps(self, CT, plan, Struct, RangeShifters):
    
    # Find BODY
    for ROI in Struct.Contours:
        if ROI.ROIName == 'BODY':
            BODY = ROI 
            break

    # Initialize Spot Maps
    SpotMapBinary = np.full((CT.GridSize[0], CT.GridSize[1], CT.GridSize[2], len(plan.Beams)), False)
    SpotMapWeights = np.zeros((CT.GridSize[0], CT.GridSize[1], CT.GridSize[2], len(plan.Beams)))

    
    #Compute cartesian coordinates
    CartesianCoordinates = plan.compute_cartesian_coordinates(CT, 'UCL_Toshiba', plan.Beams, RangeShifters)

    # Initialize SpotID
    SpotsID = np.zeros((plan.NumberOfSpots, 4),dtype=int)
    SpotNumber = 0
    SpotsOutsideBody = 0
    # Repeat = [] 
    # SpotsID_repeat = [] 

    print('ImagePositionPatient',CT.ImagePositionPatient)
    # Compute SpotsID
    print('\n')
    counter = 0
    for beamNumber, beam in enumerate(plan.Beams):
        print('nb of layers',len(beam.Layers))
        for layer in beam.Layers: 
            for weight in layer.SpotMU:
                #print('SpotNumber',SpotNumber)
                #print('CartesianCoordinates',CartesianCoordinates[SpotNumber])
                #print('ImagePositionPatient',CT.ImagePositionPatient)
                #print('PixelSpacing',CT.PixelSpacing)
                # x = int((CartesianCoordinates[SpotNumber][0] - CT.ImagePositionPatient[0])/CT.PixelSpacing[0])-1
                # y = int((CartesianCoordinates[SpotNumber][1] - CT.ImagePositionPatient[1])/CT.PixelSpacing[1])-1
                # z = int((CartesianCoordinates[SpotNumber][2] - CT.ImagePositionPatient[2])/CT.PixelSpacing[2])-1

                x = int(CartesianCoordinates[SpotNumber][0]/CT.PixelSpacing[0])
                y = int(CartesianCoordinates[SpotNumber][1]/CT.PixelSpacing[1])
                z = int(CartesianCoordinates[SpotNumber][2]/CT.PixelSpacing[2])
                
                SpotsID[SpotNumber,:] = [x,y,z,beamNumber]
                #print('coordinates',[x,y,z,beamNumber])
                #print('Spots ID',SpotsID[SpotNumber,:])
                
                SpotNumber += 1

                if BODY.Mask[x,y,z]==False:  # avoid spots outside BODY 
                    SpotsOutsideBody += 1
                    print('This spot is outside the body',[x,y,z])
                    continue
                
                # if (x,y,z,beamNumber) in SpotsID_repeat:
                #     Repeat.append((x,y,z,beamNumber))     
                
                # SpotsID_repeat.append((x,y,z,beamNumber))
                SpotMapBinary[x,y,z,beamNumber] = True
                SpotMapWeights[x,y,z,beamNumber] = weight 
                counter+=1
    # We can get SpotMapBinary as boolean SpotMapWeights 
    # plan.SpotMapBinary = SpotMapBinary
    plan.SpotMapWeights = SpotMapWeights     
    
    #     print('SpotsID beam_' + str(beamNumber) + ' computed...')    
    # print('nb of iteration',counter)
    # save_file_binary = os.path.join(dst_dir, 'SpotMapBinary_beams.npz') 
    # np.savez_compressed(save_file_binary,SpotMapBinary)   
    # print('\nSpot Map Binary saved = ' + save_file_binary)
    
    # save_file_weights = os.path.join(dst_dir, 'SpotMapWeights_beams.npz')
    # np.savez_compressed(save_file_weights, SpotMapWeights.astype(np.float16))
    # print('Spot Map Weights saved = ' + save_file_weights)
    
    # save_file_ID = os.path.join(dst_dir, 'spotsID.npz')    
    # np.savez_compressed(save_file_ID, SpotsID)
    # print('SpotsID saved = ' + save_file_ID)
    
    # print('\nNumber of Spots in plan = ' + str(plan.NumberOfSpots))
    # print('Number of Spots in binary mask = ' + str(np.ndarray.flatten(SpotMapBinary).tolist().count(True)))
    # print('Spots placed outside the body = ' + (str(SpotsOutsideBody)))  
    
    # if len(Repeat)!=0:  
    #     spots_repeated_by_patient.append(['Patient_' + str(PatientNumber) + ' (' + Patient.PatientInfo.PatientName + ')', len(Repeat)])
        
    # print('\nAt this point, there are ' + str(len(spots_repeated_by_patient)) + ' patients with spots repeated')
    # for repeat in spots_repeated_by_patient:
    #     print(repeat[0] + ' has ' + str(repeat[1]) + ' spots repeated')
    # print('\n')

  def Rotate_vector(self, vec, angle, axis):
      if axis == 'x':
        x = vec[0]
        y = vec[1] * math.cos(angle) - vec[2] * math.sin(angle)
        z = vec[1] * math.sin(angle) + vec[2] * math.cos(angle)
      elif axis ==  'y':
        x = vec[0] * math.cos(angle) + vec[2] * math.sin(angle)
        y = vec[1]
        z = -vec[0] * math.sin(angle) + vec[2] * math.cos(angle)
      elif axis == 'z':
        x = vec[0] * math.cos(angle) - vec[1] * math.sin(angle)
        y = vec[0] * math.sin(angle) + vec[1] * math.cos(angle)
        z = vec[2]
        
      return [x,y,z]
  
      
class Plan_IonBeam:

  def __init__(self):
    self.SeriesInstanceUID = ""
    self.BeamName = ""
    self.IsocenterPosition = [0,0,0]
    self.GantryAngle = 0.0
    self.PatientSupportAngle = 0.0
    self.FinalCumulativeMetersetWeight = 0.0
    self.BeamMeterset = 0.0
    self.RangeShifter = "none"
    self.Layers = []
  
  
  
class Plan_IonLayer:

  def __init__(self):
    self.SeriesInstanceUID = ""
    self.NumberOfPaintings = 1
    self.NominalBeamEnergy = 0.0
    self.ScanSpotPositionMap_x = []
    self.ScanSpotPositionMap_y = []
    self.ScanSpotMetersetWeights = []
    self.SpotMU = []
    self.CumulativeMeterset = 0.0
    self.RangeShifterSetting = 'OUT'
    self.IsocenterToRangeShifterDistance = 0.0
    self.RangeShifterWaterEquivalentThickness = 0.0
    self.ReferencedRangeShifterNumber = 0
    
    
    

	import pydicom
	import numpy as np
	import math
	import time
	import pickle, scipy



	class RTplan:

	def __init__(self):
	self.SeriesInstanceUID = ""
	self.SOPInstanceUID = ""
	self.PatientInfo = {}
	self.StudyInfo = {}
	self.DcmFile = ""
	self.Modality = ""
	self.RadiationType = ""
	self.ScanMode = ""
	self.TreatmentMachineName = ""
	self.NumberOfFractionsPlanned = 1
	self.NumberOfSpots = 0
	self.Beams = []
	self.TotalMeterset = 0.0
	self.PlanName = ""
	self.isLoaded = 0
	self.beamlets = []
	self.OriginalDicomDataset = []



	def print_plan_info(self, prefix=""):
	print(prefix + "Plan: " + self.SeriesInstanceUID)
	print(prefix + " " + self.DcmFile)



	def import_Dicom_plan(self):
	if(self.isLoaded == 1):
	print("Warning: RTplan " + self.SeriesInstanceUID + " is already loaded")
	return

	dcm = pydicom.dcmread(self.DcmFile)

	self.OriginalDicomDataset = dcm

	# Photon plan
	if dcm.SOPClassUID == "1.2.840.10008.5.1.4.1.1.481.5":
	print("ERROR: Conventional radiotherapy (photon) plans are not supported")
	self.Modality = "Radiotherapy"
	return

	# Ion plan
	elif dcm.SOPClassUID == "1.2.840.10008.5.1.4.1.1.481.8":
	self.Modality = "Ion therapy"

	if dcm.IonBeamSequence[0].RadiationType == "PROTON":
	self.RadiationType = "Proton"
	else:
	print("ERROR: Radiation type " + dcm.IonBeamSequence[0].RadiationType + " not supported")
	self.RadiationType = dcm.IonBeamSequence[0].RadiationType
	return

	if dcm.IonBeamSequence[0].ScanMode == "MODULATED":
	self.ScanMode = "MODULATED" # PBS
	else:
	print("ERROR: Scan mode " + dcm.IonBeamSequence[0].ScanMode + " not supported")
	self.ScanMode = dcm.IonBeamSequence[0].ScanMode
	return

	# Other
	else:
	print("ERROR: Unknown SOPClassUID " + dcm.SOPClassUID + " for file " + self.DcmFile)
	self.Modality = "Unknown"
	return

	# Start parsing PBS plan
	self.SOPInstanceUID = dcm.SOPInstanceUID
	self.NumberOfFractionsPlanned = int(dcm.FractionGroupSequence[0].NumberOfFractionsPlanned)
	self.NumberOfSpots = 0
	self.TotalMeterset = 0

	if(hasattr(dcm.IonBeamSequence[0], 'TreatmentMachineName')):
	self.TreatmentMachineName = dcm.IonBeamSequence[0].TreatmentMachineName
	else:
	self.TreatmentMachineName = ""

	for dcm_beam in dcm.IonBeamSequence:
	if dcm_beam.TreatmentDeliveryType != "TREATMENT":
	continue

	first_layer = dcm_beam.IonControlPointSequence[0]

	beam = Plan_IonBeam()
	beam.SeriesInstanceUID = self.SeriesInstanceUID
	beam.BeamName = dcm_beam.BeamName
	beam.IsocenterPosition = [float(first_layer.IsocenterPosition[0]), float(first_layer.IsocenterPosition[1]), float(first_layer.IsocenterPosition[2])]
	beam.GantryAngle = float(first_layer.GantryAngle)
	beam.PatientSupportAngle = float(first_layer.PatientSupportAngle)
	beam.FinalCumulativeMetersetWeight = float(dcm_beam.FinalCumulativeMetersetWeight)

	# find corresponding beam in FractionGroupSequence (beam order may be different from IonBeamSequence)
	ReferencedBeam_id = next((x for x, val in enumerate(dcm.FractionGroupSequence[0].ReferencedBeamSequence) if val.ReferencedBeamNumber == dcm_beam.BeamNumber), -1)
	if ReferencedBeam_id == -1:
	print("ERROR: Beam number " + dcm_beam.BeamNumber + " not found in FractionGroupSequence.")
	print("This beam is therefore discarded.")
	continue
	else: beam.BeamMeterset = float(dcm.FractionGroupSequence[0].ReferencedBeamSequence[ReferencedBeam_id].BeamMeterset)

	self.TotalMeterset += beam.BeamMeterset

	if dcm_beam.NumberOfRangeShifters == 0:
	beam.RangeShifterID = ""
	beam.RangeShifterType = "none"
	elif dcm_beam.NumberOfRangeShifters == 1:
	beam.RangeShifterID = dcm_beam.RangeShifterSequence[0].RangeShifterID
	if dcm_beam.RangeShifterSequence[0].RangeShifterType == "BINARY":
	beam.RangeShifterType = "binary"
	elif dcm_beam.RangeShifterSequence[0].RangeShifterType == "ANALOG":
	beam.RangeShifterType = "analog"
	else:
	print("ERROR: Unknown range shifter type for beam " + dcm_beam.BeamName)
	beam.RangeShifterType = "none"
	else:
	print("ERROR: More than one range shifter defined for beam " + dcm_beam.BeamName)
	beam.RangeShifterID = ""
	beam.RangeShifterType = "none"


	SnoutPosition = 0
	if hasattr(first_layer, 'SnoutPosition'):
	SnoutPosition = float(first_layer.SnoutPosition)

	IsocenterToRangeShifterDistance = SnoutPosition
	RangeShifterWaterEquivalentThickness = ""
	RangeShifterSetting = "OUT"
	ReferencedRangeShifterNumber = 0

	if hasattr(first_layer, 'RangeShifterSettingsSequence'):
	if hasattr(first_layer.RangeShifterSettingsSequence[0], 'IsocenterToRangeShifterDistance'):
	IsocenterToRangeShifterDistance = float(first_layer.RangeShifterSettingsSequence[0].IsocenterToRangeShifterDistance)
	if hasattr(first_layer.RangeShifterSettingsSequence[0], 'RangeShifterWaterEquivalentThickness'):
	RangeShifterWaterEquivalentThickness = float(first_layer.RangeShifterSettingsSequence[0].RangeShifterWaterEquivalentThickness)
	if hasattr(first_layer.RangeShifterSettingsSequence[0], 'RangeShifterSetting'):
	RangeShifterSetting = first_layer.RangeShifterSettingsSequence[0].RangeShifterSetting
	if hasattr(first_layer.RangeShifterSettingsSequence[0], 'ReferencedRangeShifterNumber'):
	ReferencedRangeShifterNumber = int(first_layer.RangeShifterSettingsSequence[0].ReferencedRangeShifterNumber)

	CumulativeMeterset = 0

	for dcm_layer in dcm_beam.IonControlPointSequence:
	if dcm_layer.NumberOfScanSpotPositions == 1: sum_weights = dcm_layer.ScanSpotMetersetWeights
	else: sum_weights = sum(dcm_layer.ScanSpotMetersetWeights)

	if sum_weights == 0.0:
	continue

	layer = Plan_IonLayer()
	layer.SeriesInstanceUID = self.SeriesInstanceUID

	if hasattr(dcm_layer, 'SnoutPosition'):
	SnoutPosition = float(dcm_layer.SnoutPosition)

	if hasattr(dcm_layer, 'NumberOfPaintings'): layer.NumberOfPaintings = int(dcm_layer.NumberOfPaintings)
	else: layer.NumberOfPaintings = 1

	layer.NominalBeamEnergy = float(dcm_layer.NominalBeamEnergy)
	layer.ScanSpotPositionMap_x = dcm_layer.ScanSpotPositionMap[0::2]
	layer.ScanSpotPositionMap_y = dcm_layer.ScanSpotPositionMap[1::2]
	layer.ScanSpotMetersetWeights = dcm_layer.ScanSpotMetersetWeights
	layer.SpotMU = np.array(dcm_layer.ScanSpotMetersetWeights) * beam.BeamMeterset / beam.FinalCumulativeMetersetWeight # spot weights are converted to MU
	if layer.SpotMU.size == 1: layer.SpotMU = [layer.SpotMU]
	else: layer.SpotMU = layer.SpotMU.tolist()

	self.NumberOfSpots += len(layer.SpotMU)
	CumulativeMeterset += sum(layer.SpotMU)
	layer.CumulativeMeterset = CumulativeMeterset

	if beam.RangeShifterType != "none":
	if hasattr(dcm_layer, 'RangeShifterSettingsSequence'):
	RangeShifterSetting = dcm_layer.RangeShifterSettingsSequence[0].RangeShifterSetting
	ReferencedRangeShifterNumber = dcm_layer.RangeShifterSettingsSequence[0].ReferencedRangeShifterNumber
	if hasattr(dcm_layer.RangeShifterSettingsSequence[0], 'IsocenterToRangeShifterDistance'):
	IsocenterToRangeShifterDistance = dcm_layer.RangeShifterSettingsSequence[0].IsocenterToRangeShifterDistance
	if hasattr(dcm_layer.RangeShifterSettingsSequence[0], 'RangeShifterWaterEquivalentThickness'):
	RangeShifterWaterEquivalentThickness = dcm_layer.RangeShifterSettingsSequence[0].RangeShifterWaterEquivalentThickness

	layer.RangeShifterSetting = RangeShifterSetting
	layer.IsocenterToRangeShifterDistance = IsocenterToRangeShifterDistance
	layer.RangeShifterWaterEquivalentThickness = RangeShifterWaterEquivalentThickness
	layer.ReferencedRangeShifterNumber = ReferencedRangeShifterNumber


	beam.Layers.append(layer)

	self.Beams.append(beam)

	self.isLoaded = 1

	def export_Dicom_with_new_UID(self, OutputFile):
	# generate new uid
	initial_uid = self.OriginalDicomDataset.SOPInstanceUID
	new_uid = pydicom.uid.generate_uid()
	self.OriginalDicomDataset.SOPInstanceUID = new_uid

	# save dicom file
	print("Export dicom RTPLAN: " + OutputFile)
	self.OriginalDicomDataset.save_as(OutputFile)

	# restore initial uid
	self.OriginalDicomDataset.SOPInstanceUID = initial_uid

	return new_uid



	def save(self, file_path):
	beamlets = self.beamlets
	self.beamlets = []

	with open(file_path, 'wb') as fid:
	pickle.dump(self.__dict__, fid)

	self.beamlets = beamlets



	def load(self, file_path):
	with open(file_path, 'rb') as fid:
	tmp = pickle.load(fid)

	self.__dict__.update(tmp)

	def compute_cartesian_coordinates(self, CT, Scanner, beams, RangeShifters=[]):
	time_start = time.time()

	SPR = SPRimage()
	SPR.convert_CT_to_SPR(CT, Scanner)

	CTborders_x = [SPR.ImagePositionPatient[0], SPR.ImagePositionPatient[0] + SPR.GridSize[0] * SPR.PixelSpacing[0]]
	CTborders_y = [SPR.ImagePositionPatient[1], SPR.ImagePositionPatient[1] + SPR.GridSize[1] * SPR.PixelSpacing[1]]
	CTborders_z = [SPR.ImagePositionPatient[2], SPR.ImagePositionPatient[2] + SPR.GridSize[2] * SPR.PixelSpacing[2]]

	spot_positions = []
	spot_directions = []
	spot_ranges = []

	# initialize spot info for raytracing
	for beam in self.Beams:
	#beam = self.Beams[b]

	RangeShifter = -1
	if beam.RangeShifterType == "binary":
	RangeShifter = next((RS for RS in RangeShifters if RS.ID == beam.RangeShifterID), -1)

	for layer in beam.Layers:

	range_in_water = SPR.energyToRange(layer.NominalBeamEnergy)*10
	if(layer.RangeShifterSetting == 'IN'):
	if(layer.RangeShifterWaterEquivalentThickness != ""): RangeShifter_WET = layer.RangeShifterWaterEquivalentThickness
	elif(RangeShifter != -1): RangeShifter_WET = RangeShifter.WET
	else: RangeShifter_WET = 0.0

	if(RangeShifter_WET > 0.0): range_in_water -= RangeShifter_WET

	for s in range(len(layer.ScanSpotPositionMap_x)):

	# BEV coordinates to 3D coordinates: position (x,y,z) and direction (u,v,w)
	x,y,z = layer.ScanSpotPositionMap_x[s], 0, layer.ScanSpotPositionMap_y[s]
	u,v,w = 1e-10, 1.0, 1e-10

	# rotation for gantry angle (around Z axis)
	angle = math.radians(beam.GantryAngle)
	[x,y,z] = self.Rotate_vector([x,y,z], angle, 'z')
	[u,v,w] = self.Rotate_vector([u,v,w], angle, 'z')

	# rotation for couch angle (around Y axis)
	angle = math.radians(beam.PatientSupportAngle)
	[x,y,z] = self.Rotate_vector([x,y,z], angle, 'y')
	[u,v,w] = self.Rotate_vector([u,v,w], angle, 'y')

	# Dicom CT coordinates
	x = x + beam.IsocenterPosition[0]
	y = y + beam.IsocenterPosition[1]
	z = z + beam.IsocenterPosition[2]

	# translate initial position at the CT image border
	Translation = np.array([1.0, 1.0, 1.0])
	Translation[0] = (x - CTborders_x[int(u<0)]) / u
	Translation[1] = (y - CTborders_y[int(v<0)]) / v
	Translation[2] = (z - CTborders_z[int(w<0)]) / w
	Translation = Translation[np.argmin(np.absolute(Translation))]
	x = x - Translation * u
	y = y - Translation * v
	z = z - Translation * w

	# append data to the list of spots to process
	spot_positions.append([x,y,z])
	spot_directions.append([u,v,w])
	spot_ranges.append(range_in_water)


	CartesianSpotPositions = compute_position_from_range(SPR, spot_positions, spot_directions, spot_ranges)

	print("Spot RayTracing: " + str(time.time()-time_start) + " sec")
	return CartesianSpotPositions

	#TO ADAPT
	def compute_spot_maps(self, CT, plan, Struct, RangeShifters):

	# Find BODY
	for ROI in Struct.Contours:
	if ROI.ROIName == 'BODY':
	BODY = ROI
	break

	# Initialize Spot Maps
	SpotMapBinary = np.full((CT.GridSize[0], CT.GridSize[1], CT.GridSize[2], len(plan.Beams)), False)
	SpotMapWeights = np.zeros((CT.GridSize[0], CT.GridSize[1], CT.GridSize[2], len(plan.Beams)))


	#Compute cartesian coordinates
	CartesianCoordinates = plan.compute_cartesian_coordinates(CT, 'UCL_Toshiba', plan.Beams, RangeShifters)

	# Initialize SpotID
	SpotsID = np.zeros((plan.NumberOfSpots, 4),dtype=int)
	SpotNumber = 0
	SpotsOutsideBody = 0
	# Repeat = []
	# SpotsID_repeat = []

	print('ImagePositionPatient',CT.ImagePositionPatient)
	# Compute SpotsID
	print('\n')
	counter = 0
	for beamNumber, beam in enumerate(plan.Beams):
	print('nb of layers',len(beam.Layers))
	for layer in beam.Layers:
	for weight in layer.SpotMU:
	#print('SpotNumber',SpotNumber)
	#print('CartesianCoordinates',CartesianCoordinates[SpotNumber])
	#print('ImagePositionPatient',CT.ImagePositionPatient)
	#print('PixelSpacing',CT.PixelSpacing)
	# x = int((CartesianCoordinates[SpotNumber][0] - CT.ImagePositionPatient[0])/CT.PixelSpacing[0])-1
	# y = int((CartesianCoordinates[SpotNumber][1] - CT.ImagePositionPatient[1])/CT.PixelSpacing[1])-1
	# z = int((CartesianCoordinates[SpotNumber][2] - CT.ImagePositionPatient[2])/CT.PixelSpacing[2])-1

	x = int(CartesianCoordinates[SpotNumber][0]/CT.PixelSpacing[0])
	y = int(CartesianCoordinates[SpotNumber][1]/CT.PixelSpacing[1])
	z = int(CartesianCoordinates[SpotNumber][2]/CT.PixelSpacing[2])

	SpotsID[SpotNumber,:] = [x,y,z,beamNumber]
	#print('coordinates',[x,y,z,beamNumber])
	#print('Spots ID',SpotsID[SpotNumber,:])

	SpotNumber += 1

	if BODY.Mask[x,y,z]==False: # avoid spots outside BODY
	SpotsOutsideBody += 1
	print('This spot is outside the body',[x,y,z])
	continue

	# if (x,y,z,beamNumber) in SpotsID_repeat:
	# Repeat.append((x,y,z,beamNumber))

	# SpotsID_repeat.append((x,y,z,beamNumber))
	SpotMapBinary[x,y,z,beamNumber] = True
	SpotMapWeights[x,y,z,beamNumber] = weight
	counter+=1
	# We can get SpotMapBinary as boolean SpotMapWeights
	# plan.SpotMapBinary = SpotMapBinary
	plan.SpotMapWeights = SpotMapWeights

	# print('SpotsID beam_' + str(beamNumber) + ' computed...')
	# print('nb of iteration',counter)
	# save_file_binary = os.path.join(dst_dir, 'SpotMapBinary_beams.npz')
	# np.savez_compressed(save_file_binary,SpotMapBinary)
	# print('\nSpot Map Binary saved = ' + save_file_binary)

	# save_file_weights = os.path.join(dst_dir, 'SpotMapWeights_beams.npz')
	# np.savez_compressed(save_file_weights, SpotMapWeights.astype(np.float16))
	# print('Spot Map Weights saved = ' + save_file_weights)

	# save_file_ID = os.path.join(dst_dir, 'spotsID.npz')
	# np.savez_compressed(save_file_ID, SpotsID)
	# print('SpotsID saved = ' + save_file_ID)

	# print('\nNumber of Spots in plan = ' + str(plan.NumberOfSpots))
	# print('Number of Spots in binary mask = ' + str(np.ndarray.flatten(SpotMapBinary).tolist().count(True)))
	# print('Spots placed outside the body = ' + (str(SpotsOutsideBody)))

	# if len(Repeat)!=0:
	# spots_repeated_by_patient.append(['Patient_' + str(PatientNumber) + ' (' + Patient.PatientInfo.PatientName + ')', len(Repeat)])

	# print('\nAt this point, there are ' + str(len(spots_repeated_by_patient)) + ' patients with spots repeated')
	# for repeat in spots_repeated_by_patient:
	# print(repeat[0] + ' has ' + str(repeat[1]) + ' spots repeated')
	# print('\n')

	def Rotate_vector(self, vec, angle, axis):
	if axis == 'x':
	x = vec[0]
	y = vec[1] * math.cos(angle) - vec[2] * math.sin(angle)
	z = vec[1] * math.sin(angle) + vec[2] * math.cos(angle)
	elif axis == 'y':
	x = vec[0] * math.cos(angle) + vec[2] * math.sin(angle)
	y = vec[1]
	z = -vec[0] * math.sin(angle) + vec[2] * math.cos(angle)
	elif axis == 'z':
	x = vec[0] * math.cos(angle) - vec[1] * math.sin(angle)
	y = vec[0] * math.sin(angle) + vec[1] * math.cos(angle)
	z = vec[2]

	return [x,y,z]


	class Plan_IonBeam:

	def __init__(self):
	self.SeriesInstanceUID = ""
	self.BeamName = ""
	self.IsocenterPosition = [0,0,0]
	self.GantryAngle = 0.0
	self.PatientSupportAngle = 0.0
	self.FinalCumulativeMetersetWeight = 0.0
	self.BeamMeterset = 0.0
	self.RangeShifter = "none"
	self.Layers = []



	class Plan_IonLayer:

	def __init__(self):
	self.SeriesInstanceUID = ""
	self.NumberOfPaintings = 1
	self.NominalBeamEnergy = 0.0
	self.ScanSpotPositionMap_x = []
	self.ScanSpotPositionMap_y = []
	self.ScanSpotMetersetWeights = []
	self.SpotMU = []
	self.CumulativeMeterset = 0.0
	self.RangeShifterSetting = 'OUT'
	self.IsocenterToRangeShifterDistance = 0.0
	self.RangeShifterWaterEquivalentThickness = 0.0
	self.ReferencedRangeShifterNumber = 0