libraries/Process/PatientData.py

import os
import pydicom

from libraries.Process.CTimage import *
from libraries.Process.MRimage import *
from libraries.Process.RTdose import *
from libraries.Process.RTstruct import *
from libraries.Process.RTplan import *

class PatientList:

  def __init__(self):
    self.list = []
    
    
  
  def find_CT_image(self, display_id):
    count = -1
    for patient_id in range(len(self.list)):
      for ct_id in range(len(self.list[patient_id].CTimages)):
        if(self.list[patient_id].CTimages[ct_id].isLoaded == 1): count += 1
        if(count == display_id): break
      if(count == display_id): break
      
    return patient_id, ct_id
    
    
  
  def find_dose_image(self, display_id):
    count = -1
    for patient_id in range(len(self.list)):
      for dose_id in range(len(self.list[patient_id].RTdoses)):
        if(self.list[patient_id].RTdoses[dose_id].isLoaded == 1): count += 1
        if(count == display_id): break
      if(count == display_id): break
      
    return patient_id, dose_id
      
    
  
  def find_contour(self, ROIName):
    for patient_id in range(len(self.list)):
      for struct_id in range(len(self.list[patient_id].RTstructs)):
        if(self.list[patient_id].RTstructs[struct_id].isLoaded == 1):
          for contour_id in range(len(self.list[patient_id].RTstructs[struct_id].Contours)):
            if(self.list[patient_id].RTstructs[struct_id].Contours[contour_id].ROIName == ROIName):
              return patient_id, struct_id, contour_id
    
    
    
  def list_dicom_files(self, folder_path, recursive):
    file_list = os.listdir(folder_path)
    #print("len file_list", len(file_list), "folderpath",folder_path)
    for file_name in file_list:
      file_path = os.path.join(folder_path, file_name)
      
      # folders
      if os.path.isdir(file_path):
        if recursive == True:
          subfolder_list = self.list_dicom_files(file_path, True)
          #join_patient_lists(Patients, subfolder_list)
          
      # files
      elif os.path.isfile(file_path):
      
        try:
          dcm = pydicom.dcmread(file_path)
        except:
          print("Invalid Dicom file: " + file_path)
          continue
        
        patient_id = next((x for x, val in enumerate(self.list) if val.PatientInfo.PatientID == dcm.PatientID), -1)

        
        if patient_id == -1:
          Patient = PatientData()
          Patient.PatientInfo.PatientID = dcm.PatientID
          Patient.PatientInfo.PatientName = str(dcm.PatientName)
          Patient.PatientInfo.PatientBirthDate = dcm.PatientBirthDate
          Patient.PatientInfo.PatientSex = dcm.PatientSex
          self.list.append(Patient)
          patient_id = len(self.list) - 1

        # Dicom CT
        if dcm.SOPClassUID == "1.2.840.10008.5.1.4.1.1.2":
          ct_id = next((x for x, val in enumerate(self.list[patient_id].CTimages) if val.SeriesInstanceUID == dcm.SeriesInstanceUID), -1)
          if ct_id == -1:
            CT = CTimage()
            CT.SeriesInstanceUID = dcm.SeriesInstanceUID
            CT.SOPClassUID == "1.2.840.10008.5.1.4.1.1.2"
            CT.PatientInfo = self.list[patient_id].PatientInfo
            CT.StudyInfo = StudyInfo()
            CT.StudyInfo.StudyInstanceUID = dcm.StudyInstanceUID
            CT.StudyInfo.StudyID = dcm.StudyID
            CT.StudyInfo.StudyDate = dcm.StudyDate
            CT.StudyInfo.StudyTime = dcm.StudyTime
            if(hasattr(dcm, 'SeriesDescription') and dcm.SeriesDescription != ""): CT.ImgName = dcm.SeriesDescription
            else: CT.ImgName = dcm.SeriesInstanceUID
            self.list[patient_id].CTimages.append(CT)
            ct_id = len(self.list[patient_id].CTimages) - 1

          self.list[patient_id].CTimages[ct_id].DcmFiles.append(file_path)
        
        # Dicom MR
        elif dcm.SOPClassUID == "1.2.840.10008.5.1.4.1.1.4":
          mr_id = next((x for x, val in enumerate(self.list[patient_id].MRimages) if val.SeriesInstanceUID == dcm.SeriesInstanceUID), -1)
          if mr_id == -1:
            MR = MRimage()
            MR.SeriesInstanceUID = dcm.SeriesInstanceUID
            MR.SOPClassUID == "1.2.840.10008.5.1.4.1.1.4"
            MR.PatientInfo = self.list[patient_id].PatientInfo
            MR.StudyInfo = StudyInfo()
            MR.StudyInfo.StudyInstanceUID = dcm.StudyInstanceUID
            MR.StudyInfo.StudyID = dcm.StudyID
            MR.StudyInfo.StudyDate = dcm.StudyDate
            MR.StudyInfo.StudyTime = dcm.StudyTime
            if(hasattr(dcm, 'SeriesDescription') and dcm.SeriesDescription != ""): MR.ImgName = dcm.SeriesDescription
            else: MR.ImgName = dcm.SeriesInstanceUID
            self.list[patient_id].MRimages.append(MR)
            mr_id = len(self.list[patient_id].MRimages) - 1

          self.list[patient_id].MRimages[mr_id].DcmFiles.append(file_path)

        # Dicom dose
        elif dcm.SOPClassUID == "1.2.840.10008.5.1.4.1.1.481.2":
          dose_id = next((x for x, val in enumerate(self.list[patient_id].RTdoses) if val.SOPInstanceUID == dcm.SOPInstanceUID), -1)
          if dose_id == -1:
            dose = RTdose()
            dose.SOPInstanceUID = dcm.SOPInstanceUID
            dose.SeriesInstanceUID = dcm.SeriesInstanceUID
            dose.PatientInfo = self.list[patient_id].PatientInfo
            dose.StudyInfo = StudyInfo()
            dose.StudyInfo.StudyInstanceUID = dcm.StudyInstanceUID
            dose.StudyInfo.StudyID = dcm.StudyID
            dose.StudyInfo.StudyDate = dcm.StudyDate
            dose.StudyInfo.StudyTime = dcm.StudyTime
            if dcm.DoseSummationType == "BEAM":
              dose.beam_number = str(dcm.ReferencedRTPlanSequence[0].ReferencedFractionGroupSequence[0].ReferencedBeamSequence[0].ReferencedBeamNumber)
            elif dcm.DoseSummationType == "PRIOR_TARGET":
              dose.beam_number = "PRIOR_TARGET"
            elif "PRIOR_TARGET_OAR" in dcm.DoseSummationType :
              dose.beam_number = "PRIOR_TARGET_OAR"
            else:
              dose.beam_number = "PLAN"
            if(hasattr(dcm, 'SeriesDescription') and dcm.SeriesDescription != ""): dose.ImgName = dcm.SeriesDescription
            else: dose.ImgName = dcm.SeriesInstanceUID
            dose.DcmFile = file_path
            self.list[patient_id].RTdoses.append(dose)

        # Dicom struct
        elif dcm.SOPClassUID == "1.2.840.10008.5.1.4.1.1.481.3":
          #struct_id = next((x for x, val in enumerate(self.list[patient_id].RTstructs_CT) if val.SeriesInstanceUID == dcm.SeriesInstanceUID), -1)
          #if struct_id == -1:
          struct = RTstruct()
          struct.SeriesInstanceUID = dcm.SeriesInstanceUID
          struct.PatientInfo = self.list[patient_id].PatientInfo
          struct.StudyInfo = StudyInfo()
          struct.StudyInfo.StudyInstanceUID = dcm.StudyInstanceUID
          struct.StudyInfo.StudyID = dcm.StudyID
          struct.StudyInfo.StudyDate = dcm.StudyDate
          struct.StudyInfo.StudyTime = dcm.StudyTime
          struct.DcmFile = file_path
          
          # Avoid ContourSequence of the first contour is not present! 
          stop = 0
          for s in range(len(dcm.ROIContourSequence)):
              if hasattr(dcm.ROIContourSequence[s], 'ContourSequence') and stop == 0:
                  stop = 1
                  if dcm.ROIContourSequence[s].ContourSequence[0].ContourImageSequence[0].ReferencedSOPClassUID=="1.2.840.10008.5.1.4.1.1.2":
                    self.list[patient_id].RTstructs_CT.append(struct)
                  elif dcm.ROIContourSequence[s].ContourSequence[0].ContourImageSequence[0].ReferencedSOPClassUID=="1.2.840.10008.5.1.4.1.1.4":
                    self.list[patient_id].RTstructs_MR.append(struct)
              else:
                  continue


        # Dicom plans
        elif dcm.SOPClassUID == "1.2.840.10008.5.1.4.1.1.481.5" or dcm.SOPClassUID == "1.2.840.10008.5.1.4.1.1.481.8":
          plan_id = next((x for x, val in enumerate(self.list[patient_id].RTplans) if val.SeriesInstanceUID == dcm.SeriesInstanceUID), -1)
          if plan_id == -1:
            plan = RTplan()
            plan.SeriesInstanceUID = dcm.SeriesInstanceUID
            plan.PatientInfo = self.list[patient_id].PatientInfo
            plan.StudyInfo = StudyInfo()
            plan.StudyInfo.StudyInstanceUID = dcm.StudyInstanceUID
            plan.StudyInfo.StudyID = dcm.StudyID
            plan.StudyInfo.StudyDate = dcm.StudyDate
            plan.StudyInfo.StudyTime = dcm.StudyTime
            if(hasattr(dcm, 'SeriesDescription') and dcm.SeriesDescription != ""): plan.PlanName = dcm.SeriesDescription
            else: plan.PlanName = dcm.SeriesInstanceUID
            plan.DcmFile = file_path
            self.list[patient_id].RTplans.append(plan)
        
        else:
          print("Unknown SOPClassUID " + dcm.SOPClassUID + " for file " + file_path)

      # other
      else:
        print("Unknown file type " + file_path)


  def print_patient_list(self):
    print("")
    for patient in self.list:
      patient.print_patient_info()

    print("")



class PatientData:

  def __init__(self):
    self.PatientInfo = PatientInfo()
    self.CTimages = []
    self.MRimages = []
    self.RTdoses = []
    self.RTplans = []
    self.RTstructs_CT = []
    self.RTstructs_MR = []
    
  def print_patient_info(self, prefix=""):
    print("")
    print(prefix + "PatientName: " + self.PatientInfo.PatientName)
    print(prefix+ "PatientID: " + self.PatientInfo.PatientID)
    
    for ct in self.CTimages:
      print("")
      ct.print_CT_info(prefix + "   ")
    print("")

    for mr in self.MRimages:
      print("")
      mr.print_MR_info(prefix + "   ")

    print("")
    for dose in self.RTdoses:
      print("")
      dose.print_dose_info(prefix + "   ")

    print("")
    for struct in self.RTstructs_CT:
      print("")
      struct.print_struct_info(prefix + "   ")
    
    print("")
    for struct in self.RTstructs_MR:
      print("")
      struct.print_struct_info(prefix + "   ")
    

  def import_patient_data(self,newvoxelsize=None):
    # import CT images
    for i,ct in enumerate(self.CTimages):
      if(ct.isLoaded == 1): continue
      ct.import_Dicom_CT()
    # import MR images
    for i,mr in enumerate(self.MRimages):
      if(mr.isLoaded == 1): continue
      mr.import_Dicom_MR()
    # import RTstructs linked to CT
    for i, struct in enumerate(self.RTstructs_CT):
      struct.import_Dicom_struct(self.CTimages[i]) # to be improved: user select CT image
    # import RTstructs linked to MR
    for i, struct in enumerate(self.RTstructs_MR):
      struct.import_Dicom_struct(self.MRimages[i]) # to be improved: user select CT image
    # import RTPlan
    for i,plan in enumerate(self.RTplans):
      if(plan.isLoaded == 1): continue
      plan.import_Dicom_plan() 
    #RESAMPLE ONLY IF NEWVOXELSIZE IS NOT NONE
    if newvoxelsize is not None:
        # Resample CT images
        for i,ct in enumerate(self.CTimages):
          ct.resample_CT(newvoxelsize)
        # Resample MR images
        for i,mr in enumerate(self.MRimages):
          mr.resample_MR(newvoxelsize)
        # Resample RTstructs linked to CT images
        for i, struct in enumerate(self.RTstructs_CT):
          struct.resample_struct(newvoxelsize) # to be improved: user select CT image
    # import dose distributions
    for i, dose in enumerate(self.RTdoses):
      if(dose.isLoaded == 1): continue
      dose.import_Dicom_dose(self.CTimages[0]) # to be improved: user select CT image
    



class PatientInfo:

  def __init__(self):
    self.PatientID = ''
    self.PatientName = ''
    self.PatientBirthDate = ''
    self.PatientSex = ''




class StudyInfo:

  def __init__(self):
    self.StudyInstanceUID = ''
    self.StudyID = ''
    self.StudyDate = ''
    self.StudyTime = ''