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buildPatientPlan.py
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#!/usr/bin/env python
# coding=utf-8
import logging
import os
import sys
import time
import imView
import numpy as np
from box import BoxList
from pinn2Json import pinn2Json
from parsePatientPlan import parsePatientPlan
import pydicom
from pydicom import Dataset, Sequence, FileDataset
from dicompylercore import dicomparser, dvhcalc
from dicompylercore.dvh import DVH
class buildPatientPlan(object):
def __init__(self):
pass
def createStructDS(self, planData, ImageInfoUIDs, setupPosition, roiShiftVector):
print("Creating Data structure")
# create RS SOPInstanceUID
structSOPInstanceUID = pydicom.uid.generate_uid()
structSeriesInstanceUID = pydicom.uid.generate_uid()
# get image header info from ImageSet_0.ImageInfo
structFrameUID = ''
structStudyInstanceUID = ''
structSeriesUID = ''
structClassUID = '1.2.840.10008.5.1.4.1.1.481.3'
if "ImageInfoList" in ImageInfoUIDs:
structFrameUID = ImageInfoUIDs.ImageInfoList[0].FrameUID
structStudyInstanceUID = ImageInfoUIDs.ImageInfoList[0].StudyInstanceUID
structSeriesUID = ImageInfoUIDs.ImageInfoList[0].SeriesUID
# structClassUID = ImageInfoUIDs.ImageInfoList[0].ClassUID
# Populate required values for file meta information
file_meta = Dataset()
# RT Structure Set Storage
file_meta.MediaStorageSOPClassUID = structClassUID
file_meta.MediaStorageSOPInstanceUID = structSOPInstanceUID
structfilename = "RS." + structSOPInstanceUID + ".dcm"
# this value remains static since implementation for creating file is the same
file_meta.ImplementationClassUID = '1.2.826.0.1.3680043.8.498.75006884747854523615841001'
# Create the FileDataset instance (initially no data elements, but file_meta supplied)
ds = FileDataset(structfilename, {}, file_meta=file_meta,
preamble=b'\x00' * 128)
# print(file_meta.preamble)
# add info_data,basic patientinfo
# [0008,0005] - [0008,0018]
ds.SpecificCharacterSet = 'ISO_IR 100'
ds.InstanceCreationDate = time.strftime("%Y%m%d")
ds.InstanceCreationTime = time.strftime("%H%M%S")
ds.SOPClassUID = structClassUID
ds.SOPInstanceUID = structSOPInstanceUID
ds.Modality = 'RTSTRUCT'
ds.AccessionNumber = ""
ds.Manufacturer = 'Pinnalce3' # from sample dicom file, maybe should change?
# not sure where to get information for this element can find this and read in from
ds.StationName = "adacp3u7"
# ds.ManufacturersModelName = 'Pinnacle3'
ds = self.modifyPatientInfo(ds, planData)
# [0008,1110]
ds.ReferencedStudySequence = Sequence()
ReferencedStudy1 = Dataset()
ds.ReferencedStudySequence.append(ReferencedStudy1)
# Study Component Management SOP Class (chosen from template)
ds.ReferencedStudySequence[0].ReferencedSOPClassUID = '1.2.840.10008.3.1.2.3.2'
ds.ReferencedStudySequence[0].ReferencedSOPInstanceUID = structStudyInstanceUID
# ds.StudyInstanceUID = StudyInstanceUID
print("Setting structure file study instance: " +
str(structStudyInstanceUID))
# [0020,000d]
ds.StudyInstanceUID = structStudyInstanceUID
# [0020,000e]
ds.SeriesInstanceUID = structSeriesInstanceUID
# [3006,0010]
ds.ReferencedFrameOfReferenceSequence = Sequence()
ReferencedFrameofReference1 = Dataset()
ds.ReferencedFrameOfReferenceSequence.append(
ReferencedFrameofReference1)
ds.ReferencedFrameOfReferenceSequence[0].FrameofReferenceUID = structFrameUID
# [3006,0012]
ds.ReferencedFrameOfReferenceSequence[0].RTReferencedStudySequence = Sequence(
)
RTReferencedStudy1 = Dataset()
ds.ReferencedFrameOfReferenceSequence[0].RTReferencedStudySequence.append(
RTReferencedStudy1)
ds.ReferencedFrameOfReferenceSequence[0].RTReferencedStudySequence[
0].ReferencedSOPClassUID = '1.2.840.10008.3.1.2.3.2'
ds.ReferencedFrameOfReferenceSequence[0].RTReferencedStudySequence[
0].ReferencedSOPInstanceUID = structStudyInstanceUID
# ds.StudyInstanceUID = StudyInstanceUID
# [3006,0014]
ds.ReferencedFrameOfReferenceSequence[0].RTReferencedStudySequence[0].RTReferencedSeriesSequence = Sequence(
)
RTReferencedSeries1 = Dataset()
ds.ReferencedFrameOfReferenceSequence[0].RTReferencedStudySequence[0].RTReferencedSeriesSequence.append(
RTReferencedSeries1)
ds.ReferencedFrameOfReferenceSequence[0].RTReferencedStudySequence[
0].RTReferencedSeriesSequence[0].SeriesInstanceUID = structSeriesUID
# [3006,0016]
ds.ReferencedFrameOfReferenceSequence[0].RTReferencedStudySequence[
0].RTReferencedSeriesSequence[0].ContourImageSequence = Sequence()
# [fffe,e000]
for i, value in enumerate(ImageInfoUIDs.ImageInfoList, 1):
exec("ContourImage%d = Dataset()" % i)
exec(
"ds.ReferencedFrameOfReferenceSequence[0].RTReferencedStudySequence[0].RTReferencedSeriesSequence[0].ContourImageSequence.append(ContourImage%d)" % i)
ds.ReferencedFrameOfReferenceSequence[0].RTReferencedStudySequence[0].RTReferencedSeriesSequence[
0].ContourImageSequence[i - 1].ReferencedSOPClassUID = value.ClassUID
ds.ReferencedFrameOfReferenceSequence[0].RTReferencedStudySequence[0].RTReferencedSeriesSequence[
0].ContourImageSequence[i - 1].ReferencedSOPInstanceUID = value.InstanceUID
# exec("del ContourImage%d" % i)
# [3006,0020]
roiListData = planData.planROIsRawData.roiList
ds.StructureSetROISequence = Sequence()
for i, value in enumerate(roiListData, 1):
exec("ROISet%d = Dataset()" % i)
exec("ds.StructureSetROISequence.append(ROISet%d)" % i)
ds.StructureSetROISequence[i - 1].ROIName = value.name
ds.StructureSetROISequence[i - 1].ROINumber = i
ds.StructureSetROISequence[i -
1].ReferencedFrameOfReferenceUID = structFrameUID
if 'volume' in value:
ds.StructureSetROISequence[i - 1].ROIVolume = value.volume
ds.StructureSetROISequence[i -
1].ROIGenerationAlgorithm = value.roiinterpretedtype
# [3006,0039]get each ROI
ds.ROIContourSequence = Sequence()
for i, value in enumerate(roiListData, 1):
exec("ContourSequence%d = Dataset()" % i)
exec("ds.ROIContourSequence.append(ContourSequence%d)" % i)
ds.ROIContourSequence[i - 1].ROIDisplayColor = [0, 255, 0]
ds.ROIContourSequence[i - 1].ReferencedROINumber = i
# get all curves in current ROI
ds.ROIContourSequence[i - 1].ContourSequence = Sequence()
planROIsCurvesList = value.num_curve
# get each ROI_Curvers
for j, data in enumerate(planROIsCurvesList, 1):
exec("CurvesPoint%d = Dataset()" % j)
exec(
"ds.ROIContourSequence[i - 1].ContourSequence.append(CurvesPoint%d)" % j)
# [3006,0040]
ds.ROIContourSequence[i - 1].ContourSequence[j -
1].ContourImageSequence = Sequence()
coutourImage1 = Dataset()
ds.ROIContourSequence[i - 1].ContourSequence[j -
1].ContourImageSequence.append(coutourImage1)
ds.ROIContourSequence[i - 1].ContourSequence[j -
1].ContourImageSequence[0].ReferencedSOPClassUID = structClassUID
ds.ROIContourSequence[i - 1].ContourSequence[j - 1].ContourImageSequence[0].ReferencedSOPInstanceUID = self.getCTInstanceUID(
data.Points[0], setupPosition, ImageInfoUIDs)
# [3006,0042]
ds.ROIContourSequence[i - 1].ContourSequence[j -
1].ContourGeometricType = "CLOSED_PLANAR"
ds.ROIContourSequence[i - 1].ContourSequence[j -
1].NumberOfContourPoints = data.num_points
# get each ROI_Curves_Points, using data.Points
ds.ROIContourSequence[i - 1].ContourSequence[j - 1].ContourData = self.getContourCurvePoints(
data.Points, setupPosition, roiShiftVector)
# [3006,0080]
ds.RTROIObservationsSequence = Sequence()
for i, current_roi in enumerate(ds.StructureSetROISequence, 1):
exec("Observation%d = Dataset()" % i)
exec("ds.RTROIObservationsSequence.append(Observation%d)" % i)
ds.RTROIObservationsSequence[i -
1].ObservationNumber = current_roi.ROINumber
ds.RTROIObservationsSequence[i -
1].ReferencedROINumber = current_roi.ROINumber
ds.RTROIObservationsSequence[i - 1].RTROIInterpretedType = 'ORGAN'
ds.RTROIObservationsSequence[i - 1].ROIInterpreter = ""
# find out where to get if its been approved or not
ds.ApprovalStatus = 'UNAPPROVED'
# Set the transfer syntax
ds.is_little_endian = True
ds.is_implicit_VR = True
# # Create the FileDataset instance (initially no data elements, but file_meta supplied)
# structds = FileDataset(structfilename, {},
# file_meta=ds, preamble=b'\x00' * 128)
# structfilepath=outputfolder + patientfolder + "/" + structfilename
# structds.save_as("structfilepath")
# print("Structure file being saved\n")
ds.save_as(os.getenv('HOME') + '/PinnWork/' + structfilename)
#
# dcmds = pydicom.dcmread(ds)
# print(dcmds)
return ds
def modifyPatientInfo(self, ds, rawData):
ds.StructureSetName = 'POIandROI'
ds.SeriesNumber = '1'
ds.PatientsName = rawData.FirstName + rawData.LastName + rawData.MiddleName
ds.PatientID = rawData.MedicalRecordNumber
ds.ReferringPhysiciansName = rawData.Physician
ds.PhysiciansOfRecord = rawData.Physician
ds.PatientsSex = rawData.Gender
# ds.SoftwareVersions = rawData.PinnacleVersionDescription
ds.ManufacturersModelName = 'Pinnacle3'
# birthday
dobstr = rawData.DateOfBirth
if dobstr:
if '-' in dobstr[0]:
dob_list = dobstr[0].split('-')
elif '/' in dobstr[0]:
dob_list = dobstr[0].split('/')
else:
dob_list = dobstr[0].split(' ')
dob = ""
for num in dob_list:
if len(num) == 1:
num = '0' + num
if num == dob_list[-1] and len(num) == 2:
num = "19" + num
dob = dob + num
ds.PatientsBirthDate = dob
# date and time
dateAndTime = rawData.TimeStamp
arr = dateAndTime.split()
ds.StructureSetDate = arr[1] + arr[2] + arr[-1]
ds.StructureSetTime = arr[-2].replace(':', '')
ds.StudyDate = ds.StructureSetDate
ds.StudyTime = ds.StructureSetTime
return ds
def createImagesDS(self, ds, ImageInfoUIDs):
# imageUIDs = pinn2Json().read(imageInfoFile)
if "ImageInfoList" in ImageInfoUIDs:
ds.FrameUID = ImageInfoUIDs.ImageInfoList[0].FrameUID
ds.StudyInstanceUID = ImageInfoUIDs.ImageInfoList[0].StudyInstanceUID
ds.SeriesUID = ImageInfoUIDs.ImageInfoList[0].SeriesUID
ds.ClassUIDD = ImageInfoUIDs.ImageInfoList[0].ClassUID
def buildPlan(self, planRawDataDict):
planRawData = planRawDataDict.patientBaseDict
if 'planListRawData' in planRawData:
for plan in planRawData.planListRawData:
logging.info('planName:%s', plan.PlanName)
refImageID = plan.PrimaryCTImageSetID
refImageHder = None
refImageInfo = None
refImageData = None
for image in planRawData.imageSetListRawData:
if image.ImageSetID == refImageID:
refImageHder = image.CTHeader
refImageInfo = image.CTInfo
refImageData = image.CTData
break
setupPosition = None
roiShiftVector = None
if refImageHder:
setupPosition = refImageHder.patient_position
roiShiftVector = self.getStructShift(refImageHder)
# if 'planPointsRawData' in plan.planData:
# pointsDict = self.getPoints(
# plan.planData.planPointsRawData, setupPosition, roiShiftVector)
if 'planROIsRawData' in plan.planData:
# contourDict = self.getContours(
# plan.planData.planROIsRawData, setupPosition, roiShiftVector)
# createStructDS(patientInfoDict, ImageInfoUIDs, planROIsRawData,setupPosition, roiShiftVector)
RS_ds = self.createStructDS(plan.planData,
refImageInfo,
setupPosition,
roiShiftVector)
rsObject = dicomparser.DicomParser(RS_ds)
structs = rsObject.GetStructures()
for (key, Roi) in structs.items():
# print('============================')
planes = rsObject.GetStructureCoordinates(key)
thickness = rsObject.CalculatePlaneThickness(planes)
volume = rsObject.CalculateStructureVolume(planes,thickness)
logging.info('key=%d,name=%s,volume=%s', key, Roi['name'],str(volume))
print('end')
# if 'planTrialsRawData' in plan.planData:
# trialData = self.getTrialData(
# plan.planData.planTrialsRawData)
def getTrialData(self, planTrialData):
if 'trialListRawData' in planTrialData:
currentTrailList = planTrialData['TrialList']
logging.info("PlanHave %d Trials", len(currentTrailList))
for currentTrail in currentTrailList:
logging.info("Trial:%s", currentTrail.Name)
data = self.readTrialMaxtrixData(
planDirAbsPath, currentTrail, planDict)
else:
logging.info('======================')
logging.info("Trial:%s", planTrialData.Trial.Name)
data = self.readTrialMaxtrixData(
planDirAbsPath, planTrialData['Trial'], planDict)
def getContours(self, planControurData, patient_position, shiftVector):
# roiListData =
if 'roiList' in planControurData:
for curROI in planControurData['roiList']:
logging.info("ROIName:%s", curROI.name)
logging.info("ROICTName:%s", curROI.volume_name)
logging.info('num_curve:%d', len(curROI.num_curve))
for i, curve in enumerate(curROI.num_curve, 0):
curvePoints = []
for curr_points in curve.Points:
if patient_position == 'HFS':
# curr_points = [str(float(curr_points[0])*10), str(float(curr_points[1])*10), str(float(curr_points[2])*10)]
curr_points = [str(float(curr_points[0]) * 10 - shiftVector[0]), str(-float(
curr_points[1]) * 10 - shiftVector[1]), str(-float(curr_points[2]) * 10)]
elif patient_position == 'HFP':
curr_points = [str(-float(curr_points[0]) * 10 - shiftVector[0]), str(
float(curr_points[1]) * 10 - shiftVector[1]), str(-float(curr_points[2]) * 10)]
elif patient_position == 'FFP':
curr_points = [str(float(curr_points[0]) * 10 - shiftVector[0]), str(
float(curr_points[1]) * 10 - shiftVector[1]), str(float(curr_points[2]) * 10)]
elif patient_position == 'FFS':
curr_points = [str(-float(curr_points[0]) * 10 - shiftVector[0]), str(-float(
curr_points[1]) * 10 - shiftVector[1]), str(float(curr_points[2]) * 10)]
curvePoints = curvePoints + curr_points
def getContourCurvePoints(self, planPointsData, patient_position, shiftVector):
Points = []
for point in planPointsData:
x_coord = 0.0
y_coord = 0.0
z_coord = 0.0
if patient_position == 'HFS':
x_coord = str(float(point[0]) * 10)
y_coord = str(-float(point[1]) * 10)
z_coord = str(-float(point[2]) * 10)
elif patient_position == 'HFP':
x_coord = str(-float(point[0]) * 10)
y_coord = str(float(point[1]) * 10)
z_coord = str(-float(point[2]) * 10)
elif patient_position == 'FFS':
x_coord = str(-float(point[0]) * 10)
y_coord = str(-float(point[1]) * 10)
z_coord = str(float(point[2]) * 10)
elif patient_position == 'FFP':
x_coord = str(float(point[0]) * 10)
y_coord = str(-float(point[1]) * 10)
z_coord = str(float(point[2]) * 10)
Points.append(x_coord)
Points.append(y_coord)
Points.append(z_coord)
# logging.info(x_coord, y_coord, z_coord)
return Points
def getCTInstanceUID(self, point_data, patient_position, ImageInfoUIDs):
# CT location th<0.02cm
Z_throth = 0.02
# units are CM, not mm
point_ZCoord = point_data[-1]
for ct in ImageInfoUIDs.ImageInfoList:
if patient_position == 'HFS' or patient_position == 'HFP':
CT_Zcoord = -float(ct.CouchPos)
elif patient_position == 'FFS' or patient_position == 'FFP':
CT_Zcoord = float(ct.CouchPos)
if abs(point_ZCoord - CT_Zcoord) < Z_throth:
return ct.InstanceUID
####################################################################################################################################################
# Function: getstructshift()
# Purpose: reads in values from ImageSet_0.header to get x and y shift
####################################################################################################################################################
def getStructShift(self, imgHdr):
xshift = 0
yshift = 0
zshift = 0
# imgHdr = pinn2Json().read(imageHeadFile)
x_dim = float(imgHdr.x_dim)
y_dim = float(imgHdr.y_dim)
z_dim = float(imgHdr.z_dim)
xpixdim = float(imgHdr.x_pixdim)
ypixdim = float(imgHdr.y_pixdim)
zpixdim = float(imgHdr.z_pixdim)
# pinnacle version differences
# xstart = float(imgHdr.x_start_dicom)
# ystart = float(imgHdr.y_start_dicom)
xstart = float(imgHdr.x_start)
ystart = float(imgHdr.y_start)
zstart = float(imgHdr.z_start)
patient_position = imgHdr.patient_position
if patient_position == 'HFS':
xshift = ((x_dim * xpixdim / 2) + xstart) * 10
yshift = -((y_dim * ypixdim / 2) + ystart) * 10
zshift = -((z_dim * zpixdim / 2) + zstart) * 10
elif patient_position == 'HFP':
xshift = -((x_dim * xpixdim / 2) + xstart) * 10
yshift = ((y_dim * ypixdim / 2) + ystart) * 10
zshift = -((z_dim * zpixdim / 2) + zstart) * 10
elif patient_position == 'FFP':
xshift = ((x_dim * xpixdim / 2) + xstart) * 10
yshift = ((y_dim * ypixdim / 2) + ystart) * 10
zshift = ((z_dim * zpixdim / 2) + zstart) * 10
elif patient_position == 'FFS':
xshift = -((x_dim * xpixdim / 2) + xstart) * 10
yshift = -((y_dim * ypixdim / 2) + ystart) * 10
zshift = ((z_dim * zpixdim / 2) + zstart) * 10
logging.info("X shift = %s", xshift)
logging.info("Y shift = %s", yshift)
logging.info("Z shift = %s", zshift)
return [xshift, yshift, zshift]
def readTrialMaxtrixData(self, trialBasePath, curTrial, planDict):
planPoints = planDict['Points']
doseHdr = curTrial.DoseGrid
dose = np.zeros((doseHdr.Dimension.Z,
doseHdr.Dimension.Y,
doseHdr.Dimension.X))
for pInd, ps in enumerate(curTrial.PrescriptionList):
logging.info('%s:%d:%d', ps.Name, ps.PrescriptionDose,
ps.NumberOfFractions)
for bInd, bm in enumerate(curTrial.BeamList):
try:
# Get the name of the file where the beam dose is saved -
# PREVIOUSLY USED DoseVarVolume ?
doseFile = os.path.join(trialBasePath,
"plan.Trial.binary.%03d" %
int(bm.DoseVolume.split('-')[1]))
# Read the dose from the file
bmDose = np.fromfile(doseFile, dtype='float32')
if bmDose.nbytes == 0:
raise DoseInvalidException('')
except IOError or SystemError:
raise DoseInvalidException('')
# Reshape to a 3D array
bmDose = bmDose.reshape((doseHdr.Dimension.Z,
doseHdr.Dimension.Y,
doseHdr.Dimension.X))
# Solaris uses big endian schema.
# Almost everything else is little endian
if sys.byteorder == 'little':
bmDose = bmDose.byteswap(True)
bmFactor = bm.MonitorUnitInfo.NormalizedDose * \
bm.MonitorUnitInfo.CollimatorOutputFactor * \
bm.MonitorUnitInfo.TotalTransmissionFraction
dosePerMU = 0.665
# getting dose/Mu from the plan.Pinnacle.Machines file
# dosePerMU = self.getDosePerMU()
MUs = bm.MonitorUnitInfo.PrescriptionDose / \
(bmFactor * dosePerMU)
logging.info('%s:%d', bm.Name, MUs)
# Weight the dose cube by the beam weight
dose += (bmDose * bm.Weight)
# rescale dose to prescriptionDose
totalPrescriptionDose = ps.PrescriptionDose * ps.NumberOfFractions
doseAtPoint = totalPrescriptionDose * 1
if ps.Name == bm.PrescriptionName:
if ps.WeightsProportionalTo == 'Point Dose':
for pt in planPoints['PoiList']:
if pt.Name == ps.PrescriptionPoint:
doseAtPoint = self.doseAtCoord(
dose, doseHdr, pt.XCoord, pt.YCoord, pt.ZCoord)
logging.info(doseAtPoint)
dose = dose * (doseAtPoint / totalPrescriptionDose)
return dose, doseHdr
def readDoses(self, planTrialData, planBasePath):
"""
input: Read a dose cube for a trial in a given plan and
return: a numpy array
Currently tested for:
(1) Dose is prescribed to a norm point;
beam weights are proportional to point dose
and control point dose is not stored.
(2) Dose is prescribed to mean dose of target;
"""
# trialFile = os.path.join(self.sourceDir, 'plan.Trial')
# if not os.path.isfile(trialFile):
# self.logging.info("not such file %s", trialFile)
# return None
# trialData = pinn2Json().read(trialFile)
# pts = pinn2Json().read(os.path.join(self.sourceDir, 'plan.Points'))
if not planTrialData:
raise IOError
pts = pinn2Json().read(
os.path.join(planBasePath, 'plan.Points'))
# pts = pointsList['']
trialList = []
doseDataDict = {}
dose = None
if 'TrialList' in planTrialData:
logging.info(
('plan has %d Trials', len(planTrialData.TrialList)))
for curTrial in planTrialData.TrialList:
trialList.append(curTrial)
else:
logging.info(('plan has %d Trials', len(planTrialData.Trial)))
trialList.append(planTrialData.Trial)
for curTrial in trialList:
doseHdr = curTrial.DoseGrid
doseData = np.zeros((doseHdr.Dimension.Z,
doseHdr.Dimension.Y,
doseHdr.Dimension.X))
for bInd, bm in enumerate(curTrial.BeamList):
try:
# Get the name of the file where the beam dose is saved -
# PREVIOUSLY USED DoseVarVolume ?
doseFile = os.path.join(planBasePath,
"plan.Trial.binary.%03d" %
int(bm.DoseVolume.split('-')[1]))
# Read the dose from the file
bmDose = np.fromfile(doseFile, dtype='float32')
if bmDose.nbytes == 0:
raise DoseInvalidException('')
except IOError or SystemError:
raise DoseInvalidException('')
# Reshape to a 3D array
bmDose = bmDose.reshape((doseHdr.Dimension.Z,
doseHdr.Dimension.Y,
doseHdr.Dimension.X))
# Solaris uses big endian schema.
# Almost everything else is little endian
if sys.byteorder == 'little':
bmDose = bmDose.byteswap(True)
doseFactor = 1.0
# Weight the dose cube by the beam weight
# Assume dose is prescribed to a norm point and beam weights are proportional to point dose
doseAtPoint = 0.0
prescriptionPoint = []
prescriptionDose = []
prescriptionPointDose = []
prescriptionPointDoseFactor = []
for pp in curTrial.PrescriptionList:
if pp.Name == bm.PrescriptionName:
prescriptionDose.append(
pp.PrescriptionDose * pp.NumberOfFractions)
if pp.WeightsProportionalTo == 'Point Dose':
for pt in pts.PoiList:
if pt.Name == pp.PrescriptionPoint:
doseAtPoint = self.doseAtCoord(
bmDose, doseHdr, pt.XCoord, pt.YCoord, pt.ZCoord)
doseFactor = pp.PrescriptionDose * \
pp.NumberOfFractions * \
(bm.Weight * 0.01 / doseAtPoint)
prescriptionPoint.append(
[pt.XCoord, pt.YCoord, pt.ZCoord])
prescriptionPointDose.append(doseAtPoint)
prescriptionPointDoseFactor.append(
doseFactor)
elif pp.WeightsProportionalTo == 'ROI Mean':
logging.info('get ROI mean dose')
dose += (bmDose * doseFactor)
for bm, pD, pp in zip(range(len(prescriptionPointDose)), prescriptionPointDose, prescriptionPoint):
indPP = coordToIndex(doseHdr, pp[0], pp[1], pp[2])
return dose, doseHdr
# doseData += bmDose
# doseDataDict[(curTrial.Name + 'DoseArray')] = doseData
# return doseDataDict
def coordToIndex(self, imHdr, xCoord, yCoord, zCoord):
"""
Convert corrdinate positions to coordinate indices
"""
# coord in cm from primary image centre
xCoord -= imHdr.Origin.X
yCoord = imHdr.Origin.Y + imHdr.Dimension.Y * imHdr.VoxelSize.Y - yCoord
zCoord -= imHdr.Origin.Z
# coord now in cm from start of dose cube
xCoord /= imHdr.VoxelSize.X
yCoord /= imHdr.VoxelSize.Y
zCoord /= imHdr.VoxelSize.Z
# coord now in pixels from start of dose cube
return xCoord, yCoord, zCoord
# ----------------------------------------- #
def doseAtCoord(self, doseData, doseHdr, xCoord, yCoord, zCoord):
"""
Linearly interpolate the dose at a set of coordinates
"""
xCoord, yCoord, zCoord = self.coordToIndex(
doseHdr, xCoord, yCoord, zCoord)
xP = np.floor(xCoord)
yP = np.floor(yCoord)
zP = np.floor(zCoord)
xF = xCoord - xP
yF = yCoord - yP
zF = zCoord - zP
dose = self.doseAtIndex(doseData, zP, yP, xP) * (1.0 - zF) * (1.0 - yF) * (1.0 - xF) + \
self.doseAtIndex(doseData, zP, yP, xP + 1) * (1.0 - zF) * (1.0 - yF) * xF + \
self.doseAtIndex(doseData, zP, yP + 1, xP) * (1.0 - zF) * yF * (1.0 - xF) + \
self.doseAtIndex(doseData, zP, yP + 1, xP + 1) * (1.0 - zF) * yF * xF + \
self.doseAtIndex(doseData, zP + 1, yP, xP) * zF * (1.0 - yF) * (1.0 - xF) + \
self.doseAtIndex(doseData, zP + 1, yP, xP + 1) * zF * (1.0 - yF) * xF + \
self.doseAtIndex(doseData, zP + 1, yP + 1, xP) * zF * yF * (1.0 - xF) + \
self.doseAtIndex(doseData, zP + 1, yP + 1, xP + 1) * zF * yF * xF
return dose
# ----------------------------------------- #
def doseAtIndex(self, dose, indZ, indY, indX):
"""
Return dose at indices.
Beyond end of dose array return zero
"""
try:
dd = dose[indZ, indY, indX]
if indZ > 0 and indY > 0 and indX > 0:
return dd
else:
return 0.0
except IndexError:
return 0.0
# ----------------------------------------- #
class DoseInvalidException(Exception):
pass
if __name__ == '__main__':
workingPath = os.path.join(os.getenv('HOME'), 'PinnWork')
# inputfolder = os.path.join(workingPath, 'DCM_Pinn')
#
# planData = parsePatientPlan(os.path.join(inputfolder, 'Patient_35995'))
planData = parsePatientPlan(os.path.join(workingPath, 'Patient_36089'))
planData.getPatientDict()
planData.printPatientDict()
newPlanObject = buildPatientPlan()
newPlanObject.buildPlan(planData)