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samcUtil.py
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# this is a file containing utility scripts for the Skane Automatic Monte Carlo
# Rickard Cronholm, 2013
import re
import math
import os
import random
import dicom
import numpy as np
# config file path goes here
confFile = 'samc.conf'
class struct:
def __init__(self):
pass
def rreplace(s, old, new, occurence):
li = s.rsplit(old, occurence)
return new.join(li)
def typeCast(cv, variables, types):
for i in range(0, len(variables)):
try:
setattr(cv, variables[i], map(types[i], getattr(cv, variables[i])))
except TypeError:
if types[i] == int:
setattr(cv, variables[i], int(getattr(cv, variables[i])))
except ValueError:
pass
return cv
def getPartOfstringFromList(lst, lookFor, delimiter, splitIndx=False, returnType=False):
value = lst[[i for i, s in enumerate(lst) if lookFor in s][0]]
if splitIndx:
value = value.split(delimiter)[splitIndx].strip()
else:
value = value.strip()
if not returnType:
return value
else:
return np.asarray(value).astype(returnType).tolist()
def validateRP(RTP):
(beams, corrBeams) = getBeams(RTP)
# get treatmentMachine hereby assuming that all beams are planned on
# the same linac
treatmentMachine = RTP.BeamSequence[corrBeams[0]].TreatmentMachineName
# get nominal energy and fluence mode
nomEnfluMod = getEnFlu(RTP, corrBeams)
print ' '.join([treatmentMachine, nomEnfluMod[0]])
valid = True
# make sure that there exists a config file for the treatmentMachine
try:
with open(treatmentMachine, 'r') as f:
content = f.readlines()
except IOError:
return False # no config file for treatmentMachine
# only consider unique nomEnfluMods
nomEnfluMod = list(set(nomEnfluMod))
for i in range(0, len(nomEnfluMod)):
# synthesize string
lookFor = ' '.join(['absCalib', nomEnfluMod[i]])
# make sure that absCalib exists for the current nomEnfluMod
if len([i for i, s in enumerate(content) if lookFor in s]) == 0:
return False
return valid
def getConfVars(cv, wtg, content):
for item in wtg: # loop over what to get
for elem in content: # loop over content
if elem.startswith(item): # if found
name = elem.split()[0].split('.')[-1]
val = elem.split()[1]
try:
val = float(val)
except ValueError:
pass
setattr(cv, name, val) # add to confvariables
return cv
def flatten(seq, container=None):
if container is None:
container = []
for s in seq:
if hasattr(s, '__iter__'):
flatten(s, container)
else:
container.append(s)
return container
def writeTimeToFile(fileName, newTime):
f = open(fileName, 'w')
f.write('{0}\n'.format(newTime))
f.close()
def getVariable(confFile, varName):
with open(confFile, 'r') as f:
content = f.readlines()
try:
return content[[i for i, s in enumerate(content)
if s.startswith(varName)][0]].split(' ')[1].rstrip()
except IndexError:
print varName, ' not found in configuration file\n'
return ''
def getID(RTP,timeStamp):
try:
ID = RTP.PatientID
except AttributeError:
ID = int(timeStamp)
return ID
def getName(RTP):
try:
name = RTP.PatientName
except AttributeError:
name = 'N^N'
return " ".join(name.split('^'))
def getBeams(RTP):
numBeams = len(RTP.BeamSequence)
beams = []
corrBeams = []
for i in range(0, numBeams):
if RTP.BeamSequence[i].TreatmentDeliveryType == 'TREATMENT':
beams.append(int(RTP.BeamSequence[i].BeamNumber))
corrBeams.append(i)
return (beams, corrBeams)
def getBeamNames(RTP, corrBeams):
beamNames = []
for i in range(0, len(corrBeams)):
beamNames.append(RTP.BeamSequence[corrBeams[i]].BeamName)
return beamNames
def getMU(RTP, beams):
MUs = []
for i in range(0, len(beams)):
count = 0
while int(RTP.FractionGroupSequence[0].ReferencedBeamSequence[count].ReferencedBeamNumber) != beams[i]:
count += 1
MUs.append(float(RTP.FractionGroupSequence[0].ReferencedBeamSequence[count].BeamMeterset))
return MUs
def getEnFlu(RTP, beams):
nomEnfluMod = []
for i in range(0, len(beams)):
nomE = ''.join([(RTP.BeamSequence[beams[i]].ControlPointSequence[0].NominalBeamEnergy).original_string, 'X'])
fluMod = (RTP.BeamSequence[beams[i]].PrimaryFluenceModeSequence[0].FluenceMode)
nomEnfluMod.append('_'.join([nomE, fluMod]).rstrip())
return nomEnfluMod
def getAngles(RTP,beams):
gantry = []
couch = []
coll = []
for i in range(0,len(beams)):
thisGantry = []
thisCouch = []
thisColl = []
numCtrlPts = int(RTP.BeamSequence[beams[i]].NumberOfControlPoints)
for j in range(0, numCtrlPts):
if j == 0: # then this information is certain to exist
thisGantry.append(float(RTP.BeamSequence[beams[i]].ControlPointSequence[j].GantryAngle))
thisCouch.append(float(RTP.BeamSequence[beams[i]].ControlPointSequence[j].PatientSupportAngle))
thisColl.append(float(RTP.BeamSequence[beams[i]].ControlPointSequence[j].BeamLimitingDeviceAngle))
lastGantry = float(RTP.BeamSequence[beams[i]].ControlPointSequence[j].GantryAngle)
lastCouch = float(RTP.BeamSequence[beams[i]].ControlPointSequence[j].PatientSupportAngle)
lastColl = float(RTP.BeamSequence[beams[i]].ControlPointSequence[j].BeamLimitingDeviceAngle)
else:
try:
thisGantry.append(float(RTP.BeamSequence[beams[i]].ControlPointSequence[j].GantryAngle))
lastGantry = float(RTP.BeamSequence[beams[i]].ControlPointSequence[j].GantryAngle)
except AttributeError:
thisGantry.append(lastGantry)
try:
thisCouch.append(float(RTP.BeamSequence[beams[i]].ControlPointSequence[j].PatientSupportAngle))
lastCouch = float(RTP.BeamSequence[beams[i]].ControlPointSequence[j].PatientSupportAngle)
except AttributeError:
thisCouch.append(lastCouch)
try:
thisColl.append(float(RTP.BeamSequence[beams[i]].ControlPointSequence[j].BeamLimitingDeviceAngle))
lastColl = float(RTP.BeamSequence[beams[i]].ControlPointSequence[j].BeamLimitingDeviceAngle)
except AttributeError:
thisColl.append(lastColl)
gantry.append(thisGantry)
couch.append(thisCouch)
coll.append(thisColl)
return (gantry, couch, coll)
def getMUindx(RTP,beams,MUs):
MUindx = []
for i in range(0, len(beams)):
thisMUindx = []
numCtrlPts = int(RTP.BeamSequence[beams[i]].NumberOfControlPoints)
for j in range(0, numCtrlPts):
if j == 0: # then this information is certain to exist
thisMUindx.append(float(RTP.BeamSequence[beams[i]].ControlPointSequence[j].CumulativeMetersetWeight))
lastMUindx = float(RTP.BeamSequence[beams[i]].ControlPointSequence[j].CumulativeMetersetWeight)
else:
try:
thisMUindx.append(float(RTP.BeamSequence[beams[i]].ControlPointSequence[j].CumulativeMetersetWeight))
lastMUindx = float(RTP.BeamSequence[beams[i]].ControlPointSequence[j].CumulativeMetersetWeight)
except AttributeError:
thisMUindx.append(lastMUindx)
MUindx.append(thisMUindx)
return MUindx
def getMUindxScaled(RTP, beams, MUs):
MUindx = []
for i in range(0, len(beams)):
scale = MUs[i] / math.fsum(MUs)
addThis = 0
if i != 0:
for j in range(0, i):
addThis += MUs[j]
addThis = addThis / math.fsum(MUs)
thisMUindx = []
numCtrlPts = int(RTP.BeamSequence[beams[i]].NumberOfControlPoints)
for j in range(0, numCtrlPts):
if j == 0: # then this information is certain to exist
thisMUindx.append(float(RTP.BeamSequence[beams[i]].ControlPointSequence[j].CumulativeMetersetWeight)*scale + addThis)
lastMUindx = float(RTP.BeamSequence[beams[i]].ControlPointSequence[j].CumulativeMetersetWeight)*scale + addThis
else:
try:
thisMUindx.append(float(RTP.BeamSequence[beams[i]].ControlPointSequence[j].CumulativeMetersetWeight)*scale + addThis)
lastMUindx = float(RTP.BeamSequence[beams[i]].ControlPointSequence[j].CumulativeMetersetWeight)*scale + addThis
except AttributeError:
thisMUindx.append(lastMUindx)
MUindx.append(thisMUindx)
return MUindx
def getISO(RTP, beams):
ISO = []
for i in range(0, len(beams)):
thisISO = []
thisISO = RTP.BeamSequence[beams[i]].ControlPointSequence[0].IsocenterPosition
thisISO = [float(thisISO) / 10 for thisISO in thisISO] # mm to cm
beamISO = []
numCtrlPts = int(RTP.BeamSequence[beams[i]].NumberOfControlPoints)
for j in range(0,numCtrlPts):
beamISO.append(thisISO)
ISO.append(beamISO)
return ISO
def isEDW(RTP, beams):
EDW = []
for i in range(0, len(beams)):
try:
len(RTP.BeamSequence[beams[i]].WedgeSequence)
EDW.append(1)
except AttributeError:
EDW.append(0)
return EDW
def getBLDPos(RTP, beams, limiter):
nLeafPair = 60 # hard coded the number of leaf pairs
parkPos = 20 # hard coded the half field opening for parked MLC
limiterPos = []
for i in range(0, len(beams)):
thisLimPos = []
numCtrlPts = int(RTP.BeamSequence[beams[i]].NumberOfControlPoints)
lastLimPos = []
for j in range(0, numCtrlPts):
try:
len(RTP.BeamSequence[beams[i]].ControlPointSequence[j].BeamLimitingDevicePositionSequence)
doGo = True
except AttributeError:
lastLimPos = leafPos
doGo = False
if doGo:
leafPos = []
# look for the current limiter
iamLimiter = -1
for k in range(0, len(RTP.BeamSequence[beams[i]].ControlPointSequence[j].BeamLimitingDevicePositionSequence)):
for l in range(0, len(limiter)):
if limiter[l] == RTP.BeamSequence[beams[i]].ControlPointSequence[j].BeamLimitingDevicePositionSequence[k].RTBeamLimitingDeviceType:
iamLimiter = k
if iamLimiter < 0 and j == 0:
for n in range(0, nLeafPair):
lastLimPos.append(-parkPos)
for n in range(0, nLeafPair):
lastLimPos.append(parkPos)
if iamLimiter >= 0:
leafPos = RTP.BeamSequence[beams[i]].ControlPointSequence[j].BeamLimitingDevicePositionSequence[iamLimiter][0x300a,0x11c].value
leafPos = [float(leafPos) / 10 for leafPos in leafPos] # mm to cm
lastLimPos = leafPos
else:
leafPos = lastLimPos
thisLimPos.append(leafPos)
limiterPos.append(thisLimPos)
return limiterPos
def machineTypeLookUp(fileName, machineName):
f = open(fileName, "r")
# add a trailing white character
machineName = ' '.join([machineName, ''])
for line in f:
if re.search(machineName, line):
thisLine = line
break
return thisLine[thisLine.find(":",
thisLine.find("TreatmentMachineType")) + 1:len(thisLine) - 1].rstrip()
def keeptrack(timeStamp, patID, patName, planLabel):
fileName = ''.join([timeStamp, '.keepTrack'])
f = open(fileName, 'w')
ktstr = '{tS}\t{pID}\t{pN}\t{plL}\n'.format(tS=timeStamp,
pID=patID, pN=patName, plL=planLabel)
f.write(ktstr)
f.close()
return
def numBeams(timeStamp, numBeams):
fileName = ''.join([timeStamp, '.numBeams'])
f = open(fileName, 'w')
f.write(str(numBeams))
f.close()
return
def beamDir(timeStamp, beamDir, suffix):
fileName = '.'.join([timeStamp, suffix])
f = open(fileName, 'w')
f.write(str(beamDir))
f.close()
return
def absCalib(timeStamp, machineName, eflu, MUs, nFrac, corr):
fileName = ''.join([timeStamp, '.absCalib'])
fout = open(fileName, 'w')
with open(machineName, 'r') as fmachine:
cont = fmachine.readlines()
lookFor = ' '.join(['absCalib', eflu])
try:
absCalib = float(cont[[i for i, s in enumerate(cont)
if s.startswith(lookFor)][0]].split(' ')[-1].rstrip())
except IndexError:
absCalib = 1.0 # set to unity if no matched found
fout.write(str(absCalib * math.fsum(MUs) * nFrac * corr))
fout.close()
return
def BEAMegsinp(timeStamp, templateType, machineType, nomEnfluMod, phspDir, EGS_HOME, ncase):
confFile = 'samc.conf'
# get templateDir
templateDir = getVariable(confFile, 'common.templateDir')
phspInType = getVariable(confFile, 'daemonA.phspInType')
fileNameIn = ''.join([templateDir, templateType,
'_BEAMnrc_template.egsinp'])
fIn = open(fileNameIn, 'r')
if nomEnfluMod == '_BEAMnrc':
fileName = ''.join([timeStamp, '_MLCnrc.egsinp'])
else:
fileName = ''.join([timeStamp, '_BEAMnrc.egsinp'])
fOut = open(fileName, 'w')
# the first line in the template file is the BEAMnrc directory
beamDir = (fIn.readline()).rstrip()
# write title
fOut.write('{0}\n'.format(timeStamp))
# Change the stuff below to simple search replace
while True:
thisLine = fIn.readline()
if not thisLine:
break
if thisLine.find('{phsp}') >= 0:
thisLine = thisLine.format(phsp=''.join([phspDir,
machineType, '_', nomEnfluMod, phspInType]))
if thisLine.find('phspType=') > 0:
phspType = int(thisLine[thisLine.rindex('phspType=') + len('phspType=')])
thisLine = thisLine.format(phspType=phspType)
if thisLine.rstrip() == 'syncjawSequence':
thisLine = ''.join([EGS_HOME, beamDir, os.path.sep,
timeStamp, '_BEAMnrc.jaw\n'])
if thisLine.rstrip() == 'syncmlcSequence':
if nomEnfluMod == '_BEAMnrc':
thisLine = ''.join([EGS_HOME, beamDir, os.path.sep,
timeStamp, '_MLCnrc.mlc\n'])
else:
thisLine = ''.join([EGS_HOME, beamDir, os.path.sep,
timeStamp, '_BEAMnrc.mlc\n'])
if thisLine.startswith('{NCASE}'):
thisLine = thisLine.format(NCASE=ncase,
IXXIN=str(random.randint(1, 31328)),
JXXIN=str(random.randint(1, 30081)))
if thisLine.find('{myPhsp}') >= 0:
thisLine = thisLine.format(myPhsp=''.join([EGS_HOME, machineType,
timeStamp, nomEnfluMod, phspDir]))
fOut.write(thisLine)
fOut.close()
fIn.close()
return (beamDir, phspType)
def DOSXYZegsinp(timeStamp, EGS_HOME, egsPhant, mlcLib, beamDir, phspEnd, VCUinp, ISO, gantry, couch, coll, MUindx, dSource, ncase, PatientPosition):
numCtrlPts = len(flatten(MUindx))
ISO = flatten(ISO)
gantry = flatten(gantry)
couch = flatten(couch)
coll = flatten(coll)
MUindx = flatten(MUindx)
# convert angels in DICOM format to EGSnrc format (in a nasty for loop)
theta = []
phi = []
phiCol = []
for i in range(0, numCtrlPts):
(thisTheta, thisPhi, thisPhiCol) = dcm2dosxyz(gantry[i], couch[i], coll[i], PatientPosition)
theta.append(thisTheta)
phi.append(thisPhi)
phiCol.append(thisPhiCol)
confFile = 'samc.conf'
# get templateDir
templateDir = getVariable(confFile, 'common.templateDir')
if numCtrlPts > 0:
fileNameIn = ''.join([templateDir, 'DOSXYZnrc_template.egsinp'])
fileName = ''.join([timeStamp, '_DOSXYZnrc.egsinp'])
else:
fileNameIn = ''.join([templateDir, mlcLib, '_template.egsinp'])
fileName = ''.join([timeStamp, '_MLC.egsinp'])
fIn = open(fileNameIn, 'r')
fOut = open(fileName, 'w')
# the first line in the template file is the DOSXYZnrc directory
dosDir = (fIn.readline()).rstrip()
# write title
fOut.write('{0}\n'.format(timeStamp))
# Change the stuff below to simple search replace
while True:
loopNow = False
thisLine = fIn.readline()
if not thisLine:
break
if thisLine.find('{myEgsphant}') >= 0:
thisLine = thisLine.format(myEgsphant=''.join([EGS_HOME, dosDir,
os.path.sep, egsPhant]))
if thisLine.find('{myMlcLib}') >= 0:
if VCUinp == '0':
thisLine = thisLine.format(myMlcLib=VCUinp,
myPhsp=''.join([EGS_HOME, beamDir, os.path.sep, timeStamp,
'_BEAMnrc', phspEnd]), myVcuTxt=VCUinp)
elif VCUinp == mlcLib:
thisLine = thisLine.format(myMlcLib=mlcLib,
myPhsp=''.join([EGS_HOME, beamDir, os.path.sep, timeStamp,
'_BEAMnrc', phspEnd]),
myVcuTxt=''.join([timeStamp, '_MLCnrc']))
else:
thisLine = thisLine.format(myMlcLib=mlcLib,
myPhsp=''.join([EGS_HOME, beamDir, os.path.sep, timeStamp,
'_BEAMnrc', phspEnd]),
myVcuTxt=''.join([VCUinp, timeStamp, '_vcu.txt']))
if thisLine.find('{NCASE}') >= 0:
thisLine = thisLine.format(NCASE=ncase,
IXXIN=str(random.randint(1, 31328)),
JXXIN=str(random.randint(1, 30081)))
if thisLine.find('{myNumCtrlPts}') > 0:
thisLine = thisLine.format(myNumCtrlPts=numCtrlPts)
loopNow = True
if thisLine.startswith('{myPhsp}'):
thisLine = thisLine.format(myPhsp=''.join([EGS_HOME, beamDir,
os.path.sep, timeStamp, '_BEAMnrc', phspEnd]))
if thisLine.startswith('{MLCseq}'):
thisLine = thisLine.format(MLCseq=VCUinp)
fOut.write(thisLine)
if loopNow:
# loop over numCtrlPts and write:
# ISO(x), ISO(y), ISO(z), theta, phi, phiCol, dSource, MUindx
for i in range(0, numCtrlPts):
fOut.write('{isox:.4f}, {isoy:.4f}, {isoz:.4f}, {th:.4f}, {ph:.4f}, {phC:.4f}, {dS:.4f}, {MUi:.4f}\n'.format(isox=ISO[3*i], isoy=ISO[3*i+1], isoz=ISO[3*i+2], th=theta[i], ph=phi[i], phC=phiCol[i], dS=dSource, MUi=MUindx[i]))
fOut.close()
fIn.close()
return
def syncjawSeq(timeStamp, xJawPos, yJawPos, MUindx):
# syncjawSeq for Varian TrueBeam and Clinac iX, valid for the BEAMnrc CM SYNCJAWS
numCtrlPts = len(flatten(MUindx))
fileName = ''.join([timeStamp, '_BEAMnrc.jaw'])
f = open(fileName, 'w')
# write title
f.write('{0}\n'.format(timeStamp))
# write numCtrlPts
f.write('{0}\n'.format(str(numCtrlPts)))
for i in range(0, len(MUindx)):
for j in range(0, len(MUindx[i])):
# write MUindx[i][j]
f.write('{0:.4f}\n'.format(MUindx[i][j]))
# calculate BEAMnrc SYNCJAW parameters
thisJawPos = calcSyncjawPos(xJawPos[i][j], yJawPos[i][j])
# write SYNCJAW parameters
f.write('{0:.4f}, {1:.4f}, {2:.4f}, {3:.4f}, {4:.4f}, {5:.4f}, \n{6:.4f}, {7:.4f}, {8:.4f}, {9:.4f}, {10:.4f}, {11:.4f}, \n'.format(thisJawPos[0][0], thisJawPos[0][1], thisJawPos[0][2], thisJawPos[0][3], thisJawPos[0][4], thisJawPos[0][5], thisJawPos[1][0], thisJawPos[1][1], thisJawPos[1][2], thisJawPos[1][3], thisJawPos[1][4], thisJawPos[1][5]))
f.close()
return
def syncmlcSeq(timeStamp, leafPos, MUindx, SCD, SAD, leafRadius, is_static, physicalLeafOffset):
# syncmlcSeq for Varian TrueBeam and Clinac iX, valid for the BEAMnrc CMs SYNCVMLC andde SYNCHDMLC
numCtrlPts = len(flatten(MUindx))
bankA, bankB = calcMLCphysPos(leafPos, SAD, SCD, leafRadius, is_static,
physicalLeafOffset, numCtrlPts)
# reshape MUindx according to numCtrlPts
MUindx = np.asarray(flatten(MUindx)).reshape((1, numCtrlPts)).tolist()
fileName = ''.join([timeStamp, '_MLCnrc.mlc'])
f = open(fileName, 'w')
# write title
f.write('{0}\n'.format(timeStamp))
# write numCtrlPts
f.write('{0}\n'.format(str(numCtrlPts)))
for i in range(0, len(MUindx)):
for j in range(0, len(MUindx[i])):
# write MUindx[i][j]
f.write('{0:.4f}\n'.format(MUindx[i][j]))
for k in range(0, len(bankA[i][j])):
f.write('{0:.4f}, {1:.4f}, 1\n'.format(bankA[i][j][-(k + 1)],
bankB[i][j][-(k + 1)])) # invert leaf order
f.close()
return
def vcuMLC(timeStamp, leafPos, MUindx):
numCtrlPts = len(flatten(MUindx))
numLeafs = len(leafPos[0][0])
fileName = ''.join([timeStamp, '_vcu.mlc'])
f = open(fileName, 'w')
# write title and base information
f.write('File Rev = G\nTreatment = Dynamic Dose\nLast Name = {tS}\nFirst Name = {tS}\nPatient ID = {tS}\nNumber of Fields = {nF}\nNumber of Leaves = {nL}\nTolerance = 0.2000\n\n'.format(tS=timeStamp, nF=str(numCtrlPts), nL=str(numLeafs)))
counter = 0
for i in range(0, len(MUindx)):
for j in range(0, len(MUindx[i])):
# write controlpoint header
f.write('Field = 0-{cnt}\nIndex = {indx:.4f}\nCarriage Group = 1\nOperator = \nCollimator = 0.00\n'.format(cnt=str(counter),indx=MUindx[i][j]))
# write leaf positions, bank A
for k in range(0, numLeafs / 2):
if k < 9:
f.write('Leaf ')
else:
f.write('Leaf ')
f.write('{n}A = {i:6.2f}\n'.format(n=str(k + 1),
i=leafPos[i][j][k + numLeafs / 2]))
# write leaf positions, bank B
for k in range(0, numLeafs / 2):
if k < 9:
f.write('Leaf ')
else:
f.write('Leaf ')
f.write('{n}B = {i:6.2f}\n'.format(n=str(k + 1),
i=-leafPos[i][j][k])) # note sign shift for bank B
# write control point footer
f.write('Note = 0\nShape = 0\nMagnification = 1.0\n\n')
counter += 1
# write checksum
f.write('CRC = 8415') # just use a static checksum
f.close()
return
def calcMLCphysPos(leafPos, SAD, SCD, R, is_static, physicalLeafOffset, numCtrlPts):
SAD = float(SAD)
SCD = float(SCD)
R = float(R)
# get nLeafs per bank
nLeafs = len(leafPos[0][0]) / 2
# convert to np.array
leafPos = flatten(leafPos)
leafPos = np.asarray(leafPos).reshape((1, numCtrlPts, nLeafs * 2))
bankA = leafPos[:, :, 0:nLeafs]
bankB = leafPos[:, :, nLeafs:2 * nLeafs]
# adjust for physical Leaf Offset in non-nice loop fashion
#for n in range(0, bankA.shape[0]):
# for i in range(0, bankA.shape[-2]):
# for j in range(0, bankA.shape[-1]):
# if not is_static[n][i][j] and bankB[n][i][j] - bankA[n][i][j] < physicalLeafOffset:
# midpoint = np.mean([bankB[n][i][j], bankA[n][i][j]])
# bankA[n][i][j] = midpoint - physicalLeafOffset/2.
# bankB[n][i][j] = midpoint + physicalLeafOffset/2.
bankA = computeMLCphysPos(-bankA, SAD, SCD, R) * -1
bankB = computeMLCphysPos(bankB, SAD, SCD, R)
return bankA.tolist(), bankB.tolist()
def computeMLCphysPos(bank, SAD, SCD, R):
# compute theta
theta = np.arctan(bank / SAD)
# comnpute light field/MLC cross point
bank = bank / SAD * (SCD + R * np.sin(theta))
# compute physical position
bank = bank - R + R * np.cos(theta)
return bank
def syncMLC(timeStamp, leafPos, MUindx, MLCtype, MLCeffZ, templateDir, SAD):
numCtrlPts = len(flatten(MUindx))
# numLeafs = len(leafPos[0][0])
fileName = ''.join([timeStamp, '_MLCnrc.mlc'])
f = open(fileName, 'w')
# write title
f.write('{0}\n'.format(timeStamp))
# write numCtrlPts
f.write('{0}\n'.format(str(numCtrlPts)))
for i in range(0, len(MUindx)):
for j in range(0, len(MUindx[i])):
# write MUindx[i][j]
f.write('{0:.4f}\n'.format(MUindx[i][j]))
# calculate BEAMnrc SYNCJAW parameters
bankA, bankB = computePhysMLCpos(leafPos[i][j], MLCtype, MLCeffZ,
templateDir, SAD)
for k in range(0, len(bankA)):
# write leafPosition
f.write('{0:.6f}, {1:.6f}, \n'.format(bankB[k], bankA[k]))
f.close()
return
def vcuTXT(timeStamp, machineType, EGS_HOME, beamDir, VCUinp, phspEnd):
confFile = 'samc.conf'
# get templateDir
templateDir = getVariable(confFile, 'common.templateDir')
fileNameIn = ''.join([templateDir, machineType, '_vcuMLC_template.txt'])
fIn = open(fileNameIn, 'r')
fileName = ''.join([timeStamp, '_vcu.txt'])
fOut = open(fileName, 'w')
# Possibly change below to simple search replace.
# Not sure if I can be bothered though, since vcu mlc is kinda outdated
while True:
thisLine = fIn.readline()
if not thisLine:
break
if thisLine.find('{title}') >= 0:
thisLine = thisLine.format(title=timeStamp)
if thisLine.find('{mlcPosFile}') >= 0:
thisLine = thisLine.format(mlcPosFile=''.join([VCUinp,
timeStamp, '_vcu.mlc']))
if thisLine.find('{phspFile}') >= 0:
thisLine = thisLine.format(phspFile=''.join([EGS_HOME, beamDir,
os.path.sep, timeStamp, phspEnd]))
if thisLine.find('{bin}') >= 0:
thisLine = thisLine.format(bin=''.join([EGS_HOME, 'bin']))
fOut.write(thisLine)
fOut.close()
fIn.close()
return
def calcSyncjawPos(xJawPos, yJawPos):
# define static defaults.
# borrowed (with permission) from T.Popescu and C.Shaw
# Applies to both Varian iX and TB
SAD = 100.0
fieldfocus = 0.0
wjaws = 7.873769
zrady = 27.9389
x1 = xJawPos[0]
x2 = xJawPos[1]
y1 = yJawPos[0]
y2 = yJawPos[1]
htY2 = zrady * SAD / math.sqrt(pow(y2, 2) + pow(SAD, 2))
htY1 = zrady * SAD / math.sqrt(pow(y1, 2) + pow(SAD, 2))
htY = (htY2 + htY1) / 2
hbY2 = htY2 + wjaws * SAD / math.sqrt(pow(y2, 2) + pow(SAD, 2))
hbY1 = htY1 + wjaws * SAD / math.sqrt(pow(y1, 2) + pow(SAD, 2))
hbY = (hbY2 + hbY1) / 2
tfY2 = (-1) * (htY - fieldfocus) * y2 / SAD
tbY2 = (-1) * (hbY - fieldfocus) * y2 / SAD
tfY1 = (htY - fieldfocus) * y1 / SAD
tbY1 = (hbY - fieldfocus) * y1 / SAD
htX2 = 36.82855 - wjaws * 20 / math.sqrt(pow(20.0, 2) + pow(SAD, 2))
htX1 = 36.82855
htX = (htX2 + htX1) / 2
hbX2 = htX + wjaws * SAD / math.sqrt(pow(x2, 2) + pow(SAD, 2))
hbX1 = htX + wjaws * SAD / math.sqrt(pow(x1, 2) + pow(SAD, 2))
hbX = (hbX2 + hbX1) / 2
tfX2 = (htX - fieldfocus) * x2 / SAD
tbX2 = (hbX - fieldfocus) * x2 / SAD
tfX1 = (-1) * (htX - fieldfocus) * x1 / SAD
tbX1 = (-1) * (hbX - fieldfocus) * x1 / SAD
jawParams = []
jawParams.append([htY, hbY, -tfY1, -tbY1, tfY2, tbY2])
jawParams.append([htX, hbX, tfX2, tbX2, -tfX1, -tbX1])
return jawParams
def returnAngle(angle, lowBound, upBound):
while angle < lowBound:
angle += upBound
while angle >= upBound:
angle -= upBound
return angle
def rewriteRP(RP, prefix):
# Need to change
# SOPInstanceUID, RTPlanLabel, RTPlanDescription
# SOPInstanceUID
RP.SOPInstanceUID = dicom.UID.generate_uid()
# RTPlanLabel - just add _suffix
s = '_'.join([prefix, RP.RTPlanLabel])
s = s.split(':')
if len(s[0]) > 13: # Eclipse has a limit of 13 chars
s[0] = s[0][0:13]
s = ':'.join(s)
RP.RTPlanLabel = s
# RTPlanDescription
if prefix == 'gamma':
RP.RTPlanDescription = '3D gamma distribution'
else:
RP.RTPlanDescription = 'Monte Carlo simulation; Not for clinical use'
RP.ApprovalStatus = 'REJECTED'
return RP
def rotateByOrientation(matrix, orientation):
# rotate matrix, depending on PatientOrientation
if orientation == 'FFS':
# flip about x and z
matrix = matrix[::-1, ::, ::-1]
elif orientation == 'HFP':
# flip about y and z
matrix = matrix[::, ::-1, ::-1]
elif orientation == 'FFP':
# flip about x and z
matrix = matrix[::-1, ::, ::-1]
# flip about y and z
matrix = matrix[::, ::-1, ::-1]
elif orientation == 'HFDL':
# transpose
matrix = np.transpose(matrix, (0, 2, 1))
# flip about z
matrix = matrix[::, ::, ::-1]
elif orientation == 'FFDL':
# transpose
matrix = np.transpose(matrix, (0, 2, 1))
# flip about z
matrix = matrix[::, ::, ::-1]
# flip about x and z
matrix = matrix[::-1, ::, ::-1]
elif orientation == 'HFDR':
# transpose
matrix = np.transpose(matrix, (0, 2, 1))
# flip about z
matrix = matrix[::, ::, ::-1]
# flip about y and z
matrix = matrix[::, ::-1, ::-1]
elif orientation == 'FFDR':
# transpose
matrix = np.transpose(matrix, (0, 2, 1))
# flip about z
matrix = matrix[::, ::, ::-1]
# flip about y and z
matrix = matrix[::, ::-1, ::-1]
# flip about x and z
matrix = matrix[::-1, ::, ::-1]
return matrix
def rewriteRD(RD, RefSOPuid, doseDist, timeStamp, PatientPosition):
# Need to change
# SOPInstanceUID, ReferencedSOPInstanceUD, DoseGridScaling, PixelData
# SOPInstanceUID
RD.SOPInstanceUID = dicom.UID.generate_uid()
# ReferencedSOPInstanceUID
RD.ReferencedRTPlanSequence[0].ReferencedSOPInstanceUID = RefSOPuid
# rotate matrix, depending on PatientPosition
doseDist = rotateByOrientation(doseDist, PatientPosition)
'''
if PatientPosition == 'FFS':
# flip about x and z
doseDist = doseDist[::-1,::,::-1]
if PatientPosition == 'HFP':
# flip about y and z
doseDist = doseDist[::,::-1,::-1]
if PatientPosition == 'FFP':
# flip about x and z
doseDist = doseDist[::-1,::,::-1]
# flip about y and z
doseDist = doseDist[::,::-1,::-1]
if PatientPosition == 'HFDL':
# transpose
doseDist = np.transpose(doseDist, (0, 2, 1))
# flip about z
doseDist = doseDist[::,::,::-1]
if PatientPosition == 'FFDL':
# transpose
doseDist = np.transpose(doseDist, (0, 2, 1))
# flip about z
doseDist = doseDist[::,::,::-1]
# flip about x and z
doseDist = doseDist[::-1,::,::-1]
if PatientPosition == 'HFDR':
# transpose
doseDist = np.transpose(doseDist, (0, 2, 1))
# flip about z
doseDist = doseDist[::,::,::-1]
# flip about y and z
doseDist = doseDist[::,::-1,::-1]
if PatientPosition == 'FFDR':
# transpose
doseDist = np.transpose(doseDist, (0, 2, 1))
# flip about z
doseDist = doseDist[::,::,::-1]
# flip about y and z
doseDist = doseDist[::,::-1,::-1]
# flip about x and z
doseDist = doseDist[::-1,::,::-1]
'''
if int(RD.Rows) != int(doseDist.shape[1]) or int(RD.Columns) != int(doseDist.shape[2]) or int(RD.NumberOfFrames) != int(doseDist.shape[0]):
ImagePositionPatient = []
GridFrameOffsetVector = []
Rows = doseDist.shape[1]
Columns = doseDist.shape[2]
nof = doseDist.shape[0]
with open(os.path.join(timeStamp, timeStamp + '.doseGrid')) as f:
lines = f.read().splitlines()
for i in range(0, len(lines)):
data = lines[i].split()
val = str(float(data[0]) * 10) # cm to mm
ImagePositionPatient.append(val)
dist = float(RD.GridFrameOffsetVector[1]) - float(RD.GridFrameOffsetVector[0])
GridFrameOffsetVector.append('0.0')
for i in range(1, int(data[2])):
GridFrameOffsetVector.append(str(float(GridFrameOffsetVector[i - 1]) + dist))
RD.Rows = Rows
RD.Columns = Columns
RD.NumberOfFrames = nof
RD.ImagePositionPatient = ImagePositionPatient
RD.GridFrameOffsetVector = GridFrameOffsetVector
# set DoseGridScaling to 1e-6
RD.DoseGridScaling = str(1e-6)
# convert to uint32 using RD.DoseGridScaling
doseDist[doseDist < 0] = 0 # get rid of negative doses.
doseDist = (doseDist / float(RD.DoseGridScaling)).astype('uint32')
# PixelData
RD.PixelData = doseDist.tostring()
return RD
def addRDs(fileA, fileB):
# read fileA
A = dicom.read_file(fileA)
# read fileB
B = dicom.read_file(fileB)
# add doses, assuming that they have the same grid
totDose = A.pixel_array * float(A.DoseGridScaling) + B.pixel_array * float(B.DoseGridScaling)
# convert to uint32 using RD.DoseGridScaling
totDose = (totDose / float(A.DoseGridScaling)).astype('uint32')
# PixelData
A.PixelData = totDose.tostring()
# save as fileA
A.save_as(fileA)
return
def addTPSRDs(fileA, fileB):
# read files
A, Adose, Ax, Ay, Az = readRD(fileA)
B, Bdose, Bx, By, Bz = readRD(fileB)
# check which of the A and B that is most extreme
if (min(Ax) < min(Bx)):
minX = min(Bx)
else:
minX = min(Ax)
if (max(Ax) > max(Bx)):
maxX = max(Bx)
else:
maxX = max(Ax)
if (min(Ay) < min(By)):
minY = min(By)
else:
minY = min(Ay)
if (max(Ay) > max(By)):
maxY = max(By)
else:
maxY = max(Ay)
if (min(Az) < min(Bz)):
minZ = min(Bz)
else:
minZ = min(Az)
if (max(Az) > max(Bz)):
maxZ = max(Bz)
else:
maxZ = max(Az)
# find start and stop indices
iA = []
iA.append(find_nearest_indx(Ax, minX))
iA.append(find_nearest_indx(Ax, maxX))
jA = []
jA.append(find_nearest_indx(Ay, minY))
jA.append(find_nearest_indx(Ay, maxY))
kA = []
kA.append(find_nearest_indx(Az, minZ))
kA.append(find_nearest_indx(Az, maxZ))
iB = []
iB.append(find_nearest_indx(Bx, minX))
iB.append(find_nearest_indx(Bx, maxX))
jB = []
jB.append(find_nearest_indx(By, minY))
jB.append(find_nearest_indx(By, maxY))
kB = []
kB.append(find_nearest_indx(Bz, minZ))
kB.append(find_nearest_indx(Bz, maxZ))
change = False
if len(Adose) * len(Adose[0]) * len(Adose[0][0]) > len(Bdose) * len(Bdose[0]) * len(Bdose[0][0]):
change = True
# crop dose ndarrays
Adose = Adose[kA[0]:kA[1] + 1, jA[0]:jA[1] + 1, iA[0]:iA[1] + 1]
Bdose = Bdose[kA[0]:kA[1] + 1, jA[0]:jA[1] + 1, iA[0]:iA[1] + 1]
# add doses
totDose = Adose + Bdose
#check which is smaller A or B
if change:
# convert to uint32 using RD.DoseGridScaling
totDose = (totDose / float(B.DoseGridScaling)).astype('uint32')
A = B
else:
# convert to uint32 using RD.DoseGridScaling
totDose = (totDose / float(A.DoseGridScaling)).astype('uint32')
# PixelData
A.PixelData = totDose.tostring()
# save as fileA
A.save_as(fileA)
return
def readRD(fileName):
rd = dicom.read_file(fileName)
dose = rd.pixel_array * rd.DoseGridScaling
rows = rd.Rows
columns = rd.Columns
pixel_spacing = rd.PixelSpacing
image_position = rd.ImagePositionPatient
x = np.arange(columns) * pixel_spacing[0] + image_position[0]
y = np.arange(rows) * pixel_spacing[1] + image_position[1]
z = np.array(rd.GridFrameOffsetVector) + image_position[2]
return rd, dose, x, y, z
def find_nearest_indx(array, value):
array = np.asarray(array)
idx = (np.abs(array - value)).argmin()
return idx
def readNlist(fileID, n, a):
thisList = []
thatList = []
while len(thisList) < n: