def readImageSetHeader(pfpath, imgsetid=0):
fname = '%s/ImageSet_%s.header' % (pfpath, imgsetid)
pdict = readPFile(fname, 'ImageSet.header', 'dict')
pfObj = PFImgSetHeader(**pdict)
return pfObj
if __name__ == '__main__':
prjpath = os.path.dirname(os.path.abspath(__file__)) + '/../'
FORMAT = "[%(asctime)s %(levelname)s - %(funcName)s] %(message)s"
logging.basicConfig(format=FORMAT,
filename=prjpath + 'logs/test.log',
level=logging.INFO)
logging.info('Project foler is %s' % os.path.abspath(prjpath))
# Patient
Pdict = readPFile(prjpath + 'examples/Patient_6204/ImageSet_0.header',
'ImageSet.header', 'dict')
pfImgSetHeader = PFImgSetHeader(**Pdict)
#print(Pdict)
print(pfImgSetHeader.z_dim)
print(pfImgSetHeader.z_pixdim)
print(pfImgSetHeader.patient_id)
print(pfImgSetHeader.modality)
def readPlanTrial(pfpath, planid=0):
fname = '%s/Plan_%s/plan.Trial' % (pfpath, planid)
pdict = readPFile(fname, 'plan.Trial', 'dict')
pfObj = PFPlanTrial(**pdict)
return pfObj
from logging import lastResort
import os
import pytest
from pftools.readPFile import readPFile
import logging
prjpath = os.path.dirname(os.path.abspath(__file__)) + '/../'
FORMAT = "[%(asctime)s %(levelname)s - %(funcName)s] %(message)s"
logging.basicConfig(format=FORMAT,
filename=prjpath + 'logs/pytest.log',
level=logging.WARNING)
Patient = readPFile(prjpath + 'examples/Patient_6204/Patient', 'Patient')
Header = readPFile(prjpath + 'examples/Patient_6204/ImageSet_0.header',
'ImageSet.header')
ImgSetInfo = readPFile(prjpath + 'examples/Patient_6204/ImageSet_0.ImageInfo',
'ImageSet.ImageInfo')
ImageSet = readPFile(prjpath + 'examples/Patient_6204/ImageSet_0.ImageSet',
'ImageSet.ImageSet')
PlanLaser = readPFile(prjpath + 'examples/Patient_6204/Plan_0/plan.Laser',
'plan.Laser')
PatientSetup = readPFile(
prjpath + 'examples/Patient_6204/Plan_0/plan.PatientSetup',
'plan.PatientSetup')
PlanInfo = readPFile(prjpath + 'examples/Patient_6204/Plan_0/plan.PlanInfo',
'plan.PlanInfo')
PlanPoints = readPFile(prjpath + 'examples/Patient_6204/Plan_0/plan.Points',
'plan.Points')
ROIList = readPFile(prjpath + 'examples/Patient_6204/Plan_0/plan.roi',
'plan.roi')
PlanTrial0 = readPFile(prjpath + 'examples/Patient_6204/Plan_0/plan.Trial',
def readPlanInfo(pfpath, planid=0):
fname = '%s/Plan_%s/plan.PlanInfo' % (pfpath, planid)
pdict = readPFile(fname, 'plan.PlanInfo', 'dict')
pfObj = PFPlanInfo(**pdict)
return pfObj
pfObj = PFPlanTrial(**pdict)
return pfObj
if __name__ == '__main__':
prjpath = os.path.dirname(os.path.abspath(__file__)) + '/../'
FORMAT = "[%(asctime)s %(levelname)s - %(funcName)s] %(message)s"
logging.basicConfig(format=FORMAT,
filename=prjpath + 'logs/test.log',
level=logging.INFO)
logging.info('Project foler is %s' % os.path.abspath(prjpath))
# Patient
Pdict = readPFile(prjpath + 'examples/Patient_6204/Plan_0/plan.Trial',
'plan.Trial', 'dict')
#print(Pdict)
#print(len(Pdict))
pfPlanTrial = PFPlanTrial(**Pdict)
ntrial = len(pfPlanTrial.Trial)
print('Number of Trials: %s' % ntrial)
for i in range(ntrial):
print(pfPlanTrial.Trial[i].Name)
print(pfPlanTrial.Trial[i].PrescriptionList.Prescription[0].
PrescriptionDose)
print(pfPlanTrial.Trial[i].BeamList.Beam[0].Name)
cpmgr0 = pfPlanTrial.Trial[i].BeamList.Beam[
0].CPManager.CPManagerObject[0]
print(cpmgr0.NumberOfControlPoints)
def readPatient(pfpath):
fname = '%s/Patient' % pfpath
pdict = readPFile(fname, 'Patient', 'dict')
pfObj = PFPatient(**pdict)
return pfObj
def readImageInfo(pfpath, imgsetid=0):
fname = '%s/ImageSet_%s.ImageInfo' % (pfpath, imgsetid)
pdict = readPFile(fname, 'ImageSet.ImageInfo', 'dict')
pfObj = PFImgInfo(**pdict)
return pfObj
def readPlanPatientSetup(pfpath, planid=0):
fname = '%s/Plan_%s/plan.PatientSetup' % (pfpath, planid)
pdict = readPFile(fname, 'plan.PatientSetup', 'dict')
pfObj = PFPlanPatientSetup(**pdict)
return pfObj
def readImageSetInfo(pfpath, imgsetid):
fname = '%s/ImageSet_%s.ImageSet' % (pfpath, imgsetid)
pdict = readPFile(fname, 'plan.ImageSet', 'dict')
pfObj = PFImageSetInfo(**pdict)
return pfObj
def readMachine(pfpath, planid=0):
fname = '%s/Plan_%s/plan.Pinnacle.Machines' % (pfpath, planid)
pdict = readPFile(fname, 'plan.Machine', 'dict')
pfObj = PFMachine(**pdict)
return pfObj
TableMotion = ''
ProductionLevel: Optional[int]
ObjectVersion: Optional[_ObjectVersion] = None
def readPlanPatientSetup(pfpath, planid=0):
fname = '%s/Plan_%s/plan.PatientSetup' % (pfpath, planid)
pdict = readPFile(fname, 'plan.PatientSetup', 'dict')
pfObj = PFPlanPatientSetup(**pdict)
return pfObj
if __name__ == '__main__':
prjpath = os.path.dirname(os.path.abspath(__file__)) + '/../'
FORMAT = "[%(asctime)s %(levelname)s - %(funcName)s] %(message)s"
logging.basicConfig(format=FORMAT,
filename=prjpath + 'logs/test.log',
level=logging.INFO)
logging.info('Project foler is %s' % os.path.abspath(prjpath))
# Patient
Pdict = readPFile(
prjpath + 'examples/Patient_6204/Plan_0/plan.PatientSetup',
'plan.PatientSetup', 'dict')
#print(Pdict)
#print(len(Pdict))
pfPlanPtSetup = PFPlanPatientSetup(**Pdict)
print(pfPlanPtSetup.Orientation)
pfObj = PFMachine(**pdict)
return pfObj
if __name__ == '__main__':
prjpath = os.path.dirname(os.path.abspath(__file__)) + '/../'
FORMAT = "[%(asctime)s %(levelname)s - %(funcName)s] %(message)s"
logging.basicConfig(format=FORMAT,
filename=prjpath + 'logs/test.log',
level=logging.INFO)
logging.info('Project foler is %s' % os.path.abspath(prjpath))
# Patient
Pdict = readPFile(
prjpath + 'examples/Patient_6204/Plan_0/plan.Pinnacle.Machines',
'plan.Machine', 'dict')
# print(Pdict['Machine'][0]['PhotonEnergyList'] ) #['MachineEnergy'])
pfMachine = PFMachine(**Pdict)
print(pfMachine.Machine[0].MachineType)
xenergy = pfMachine.Machine[0].PhotonEnergyList.MachineEnergy
for xe in xenergy:
print('Photon Energy: ', xe.Name)
xenergy = pfMachine.Machine[0].ElectronEnergyList.MachineEnergy
for xe in xenergy:
print('Electron Energy: ', xe.Name)
def readPlanPoints(pfpath, planid=0):
fname = '%s/Plan_%s/plan.Points' % (pfpath, planid)
pdict = readPFile(fname, 'plan.Points', 'dict')
pfObj = PFPlanPoints(**pdict)
return pfObj
def readPlanROI(pfpath, planid=0):
fname = '%s/Plan_%s/plan.roi' % (pfpath, planid)
pdict = readPFile(fname, 'plan.roi', 'dict')
if pdict is None: return None
pfObj = PFPlanROI(**pdict)
return pfObj
def readImageSetHeader(pfpath, imgsetid=0):
fname = '%s/ImageSet_%s.header' % (pfpath, imgsetid)
pdict = readPFile(fname, 'ImageSet.header', 'dict')
pfObj = PFImgSetHeader(**pdict)
return pfObj
class PFImgInfo(BaseModel):
ImageInfo: List[_ImageInfo] = None
def readImageInfo(pfpath, imgsetid=0):
fname = '%s/ImageSet_%s.ImageInfo' % (pfpath, imgsetid)
pdict = readPFile(fname, 'ImageSet.ImageInfo', 'dict')
pfObj = PFImgInfo(**pdict)
return pfObj
if __name__ == '__main__':
prjpath = os.path.dirname(os.path.abspath(__file__)) + '/../'
FORMAT = "[%(asctime)s %(levelname)s - %(funcName)s] %(message)s"
logging.basicConfig(format=FORMAT,
filename=prjpath + 'logs/test.log',
level=logging.INFO)
logging.info('Project foler is %s' % os.path.abspath(prjpath))
# Patient
Pdict = readPFile(prjpath + 'examples/Patient_6204/ImageSet_0.ImageInfo',
'ImageSet.ImageInfo', 'dict')
#print(Pdict)
pfImgInfo = PFImgInfo(**Pdict)
print(pfImgInfo.ImageInfo[0].TablePosition)
print(pfImgInfo.ImageInfo[1].SliceNumber)
print(pfImgInfo.ImageInfo[97].InstanceUID)
def __init__(self, ptpath) -> None:
fname = '%s/Patient' % ptpath
logging.info('Reading file: %s' % fname)
pfdict = readPFile(fname, 'Patient', 'dict')
self.Patient = PFPatient(**pfdict)
self.NumberOfImageSets = len(self.Patient.ImageSetList.ImageSet)
self.NumberOfPlans = len(self.Patient.PlanList.Plan)
imgsetID = []
for iset in self.Patient.ImageSetList.ImageSet:
imgsetID.append(iset.ImageSetID)
planID = []
for plan in self.Patient.PlanList.Plan:
planID.append(plan.PlanID)
self.ImageSet: List[_ImageSet] = []
for id in imgsetID:
imgset = _ImageSet()
imgset.ImageSetID = id
# obtain header
fname = '%s/ImageSet_%s.header' % (ptpath, id)
logging.info('Reading file: %s' % fname)
pfdict = readPFile(fname, 'ImageSet.header', 'dict')
imgset.Header = PFImgSetHeader(**pfdict)
# obtain info for all slices
fname = '%s/ImageSet_%s.ImageInfo' % (ptpath, id)
logging.info('Reading file: %s' % fname)
pfdict = readPFile(fname, 'ImageSet.ImageInfo', 'dict')
imgset.ImageInfoList = PFImgInfo(**pfdict)
self.ImageSet.append(imgset)
print('Reading ImageSet_%s done.' % id)
self.Plan: List[_PPlan] = []
for id in planID:
pplan = _PPlan()
pplan.PlanID = id
# PlanPatientSetup
fname = '%s/Plan_%s/plan.PatientSetup' % (ptpath, id)
logging.info('Reading file: %s' % fname)
pfdict = readPFile(fname, 'plan.PatientSetup', 'dict')
pplan.PlanPatientSetup = PFPlanPatientSetup(**pfdict)
# PlanInfo
fname = '%s/Plan_%s/plan.PlanInfo' % (ptpath, id)
logging.info('Reading file: %s' % fname)
pfdict = readPFile(fname, 'plan.PlanInfo', 'dict')
pplan.PlanInfo = PFPlanInfo(**pfdict)
# PlanPoints
fname = '%s/Plan_%s/plan.Points' % (ptpath, id)
logging.info('Reading file: %s' % fname)
pfdict = readPFile(fname, 'plan.Points', 'dict')
pplan.PlanPoints = PFPlanPoints(**pfdict)
# PlanROI
fname = '%s/Plan_%s/plan.roi' % (ptpath, id)
logging.info('Reading file: %s' % fname)
pfdict = readPFile(fname, 'plan.roi', 'dict')
pplan.PlanROI = PFPlanROI(**pfdict)
# PlanTrial
fname = '%s/Plan_%s/plan.Trial' % (ptpath, id)
logging.info('Reading file: %s' % fname)
pfdict = readPFile(fname, 'plan.Trial', 'dict')
pplan.PlanTrial = PFPlanTrial(**pfdict)
self.Plan.append(pplan)
print('Reading Plan_%s done.' % id)
PlanList: Optional[_PlanList] = None
ObjectVersion: Optional[_ObjectVersion] = None
def readPatient(pfpath):
fname = '%s/Patient' % pfpath
pdict = readPFile(fname, 'Patient', 'dict')
pfObj = PFPatient(**pdict)
return pfObj
if __name__ == '__main__':
prjpath = os.path.dirname(os.path.abspath(__file__))+'/../'
FORMAT = "[%(asctime)s %(levelname)s - %(funcName)s] %(message)s"
logging.basicConfig(format=FORMAT, filename=prjpath+'logs/test.log', level=logging.INFO)
logging.info('Project foler is %s' % os.path.abspath(prjpath))
# Patient
Pdict = readPFile(prjpath+'examples/Patient_6204/Patient', 'Patient', 'dict')
#print(Pdict)
#print(len(Pdict))
pfPatient = PFPatient(**Pdict)
print(pfPatient.MedicalRecordNumber)
print(pfPatient.ImageSetList.ImageSet[0].NumberOfImages)
print(pfPatient.ImageSetList.ImageSet[0].ScanTimeFromScanner)
print(pfPatient.PlanList.Plan[1].PlanName)
print(pfPatient.PlanList.Plan[0].ObjectVersion.WriteTimeStamp)
print(pfPatient.ObjectVersion.CreateTimeStamp)