def readCT(planTrialFile):
"""
Read a CT cube for a plan
"""
fp1 = open(os.path.join(os.path.dirname(planTrialFile), 'plan.defaults'))
imFile = fp1.readline().split(':')[1].strip()
fp1.close()
imFile = os.path.join(os.path.dirname(planTrialFile), imFile)
imHdr = pinn.read(imFile + '.header')
# Read the data from the file
imData = np.fromfile(imFile + '.img', dtype='int16')
# Reshape to a 3D array
imData = imData.reshape((imHdr.z_dim, imHdr.y_dim, imHdr.x_dim))
# Solaris uses big endian schema. Almost everything else is little endian
if sys.byteorder == 'little':
if imHdr.byte_order == 1:
imData = imData.byteswap(True)
else:
if imHdr.byte_order == 0:
imData = imData.byteswap(True)
return imData, imHdr
def readPlanTrial(patientPlanDir):
"""
Read all the information out of a plan.Trial file for a given patient plan directory.
"""
planTrialFile = os.path.join(patientPlanDir, 'plan.Trial')
planTrial = pinn.read(planTrialFile)
return planTrial
def readDose(planTrialFile, trNum, chooseBmInd=-1):
"""
Read a dose cube for a trial in a given plan and return as a numpy array
Need to test reading dose for a variety of different prescriptions
Currently tested for:
Dose is prescribed to a norm point,
beam weights are proportional to point dose
and control point dose is not stored.
"""
pln1 = pinn.read(os.path.join(
os.path.dirname(planTrialFile), 'plan.Trial'))
pts = pinn.read(os.path.join(
os.path.dirname(planTrialFile), 'plan.Points'))
nTrials = 1
if pln1.has_key('TrialList'):
nTrials = len(pln1.TrialList)
assert(trNum >= 0)
assert(trNum < nTrials)
if pln1.has_key('TrialList'):
curTr = pln1.TrialList[trNum]
else:
curTr = pln1.Trial
doseHdr = curTr.DoseGrid
dose = np.zeros(
(doseHdr.Dimension.Z, doseHdr.Dimension.Y, doseHdr.Dimension.X))
prescriptionPoint = []
prescriptionDose = []
prescriptionPointDose = []
prescriptionPointDoseFactor = []
for bInd, bm in enumerate(curTr.BeamList):
if chooseBmInd >= 0 and bInd != chooseBmInd:
continue
try:
# Get the name of the file where the beam dose is saved - PREVIOUSLY USED DoseVarVolume ?
doseFile = os.path.join(os.path.dirname(planTrialFile),
"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:
raise DoseInvalidException('Beam %d in trial %d has no stored dose. Try other trial [0-%d]'
% (bInd, trNum, nTrials - 1))
# 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
for pp in curTr.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 = 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)
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