###################################################################

# This code is part of PYCOM, The Python DICOM Processing Toolkit.

# PYCOM is distributed open source under GPL v3 license.

###################################################################

#

# Python DICOM RD generator

#

# This script generates DOCOM Dose file from the 3ddose file of DOSXYZnrc

#

# usage: python pycom_dose.py [-h] -p DCMPLAN -d DCMDOSE -m MCDOSE -c PPICDOSE

# [-B BEAMDIR] [-D DOSXYZDIR] [-O OUTPUTDIR]

# [-T DCMDOSETEMPLATEDIR]

#

# optional arguments:

# -h, --help show this help message and exit

# -p DCMPLAN, --dcmplan DCMPLAN

# DICOM Plan input. If --dcmdosetemplatedir is not

# presented, path is required.

# -d DCMDOSE, --dcmdose DCMDOSE

# DICOM Dose input. if --dcmdosetemplatedir is not

# presented, path is required

# -m MCDOSE, --mcdose MCDOSE

# Monte Carlo 3ddose input, default to dosxyznrc folder,

# if no path specified.

# -c PPICDOSE, --ppicdose PPICDOSE

# Parallel Plate Ion Chamber Dose, from MC simulation.

# -B BEAMDIR, --beamdir BEAMDIR

# Directory for BEAM model

# -D DOSXYZDIR, --dosxyzdir DOSXYZDIR

# Directory for dosxyznrc

# -O OUTPUTDIR, --outputdir OUTPUTDIR

# Output directory for the converted DICOM RD file.

# -T DCMDOSETEMPLATEDIR, -I DCMDOSETEMPLATEDIR, --dcmdosetemplatedir DCMDOSETEMPLATEDIR

# Directory that DICOM dose template exist. Once this is

# provided, only filename is required for both dcmplan

# and dcmdose; otherwise, paths for both dcmplan and

# dcmdose need to be specified.

#

# Example:

#

# python pycom_dose.py -p /path/to/dcm/plan/rp.dcm -d /path/to/dcm/dose/rd.dcm

# -m /path/to/dosxyznrc/mc.3ddose -c 3.459e-15

# -O /path/for/dcm/dose/output/

#

# Before using this script, you need to perform an absolute dose calibration

# first. The absolute dose calibration method is following

# Popescu et al Phys. Med. Biol. 50:3375-3392, 2005.

#

# Suppose your calibration is using water phantom and results in

# 1cGy/MU at depth d=5cm with calibration geometry SSD=100cm and FS=10x10cm2.

# Your MC simulation using the exact same calibration setup obtains

# scored dose in the parallel plate chamber of the Linac head is 3.459e-15,

# and dose in water phantom at d=5cm is 1.43915e-16. You can then find

# variables d_cal_ch, d_depcal, and D_cal_abs and change to their corresponding

# values as below:

#

# d_cal_ch = 3.459e-15 # chamber dose from MC calib.

# d_depcal = 1.43915e-16 # dose @ d=5cm from MC calib.

# D_cal_abs = 0.01 # 1 cGy/MU = 0.01 Gy/MU

#

# Once you have finished absolute dose calibration, you can then convert

# your DOSXYZnrc generated 3ddose file to DICOM RD format using this tool.

#

#########################################################

# Developed by Lixin Zhan (lixinzhan AT gmail DOT com). #

#########################################################

import os

import argparse

import struct

import StringIO as sio

import numpy as np

import dicom

from pycomuid import get_dicomuid

parser = argparse.ArgumentParser(description='Create DICOM RD from MC 3ddose file')

parser.add_argument('-p', '--dcmplan', help='DICOM Plan input. If --dcmdosetemplatedir is not presented, path is required.', required=True)

parser.add_argument('-d', '--dcmdose', help='DICOM Dose input. if --dcmdosetemplatedir is not presented, path is required', required=True)

parser.add_argument('-m', '--mcdose', help='Monte Carlo 3ddose input, default to dosxyznrc folder, if no path specified.', required=True)

parser.add_argument('-c', '--ppicdose', type=float, help='Parallel Plate Ion Chamber Dose, from MC simulation.', required=True)

parser.add_argument('-B', '--beamdir', help='Directory for BEAM model')

parser.add_argument('-D', '--dosxyzdir', help='Directory for dosxyznrc')

parser.add_argument('-O', '--outputdir', help='Output directory for the converted DICOM RD file.')

parser.add_argument('-T', '-I', '--dcmdosetemplatedir', help='Directory that DICOM dose template exist. Once this is provided, only filename is required for both dcmplan and dcmdose; otherwise, paths for both dcmplan and dcmdose need to be specified.')

args = parser.parse_args()

if args.beamdir:

beamdir = args.beamdir

else:

beamdir = os.getenv('EGS_HOME') + '/BEAM_ARC'

if args.dosxyzdir:

dosxyzdir = args.dosxyzdir

else:

dosxyzdir = os.getenv('EGS_HOME') + '/dosxyznrc'

d_ch = args.ppicdose

if os.path.normpath(args.mcdose)==os.path.basename(args.mcdose):

mcdosefile = dosxyzdir+'/'+args.mcdose

else:

mcdosefile = os.path.normpath(args.mcdose)

if args.dcmdosetemplatedir:

dcmplanfile = args.dcmdosetemplatedir+'/'+args.dcmplan

dcmdosefile = args.dcmdosetemplatedir+'/'+args.dcmdose

else:

dcmplanfile = args.dcmplan

dcmdosefile = args.dcmdose

if args.outputdir:

outfile = args.outputdir + '/mc_' + os.path.basename(dcmdosefile)

else:

outfile = os.path.dirname(os.path.abspath(dcmdosefile)) + \

'/mc_'+os.path.basename(dcmdosefile)

print

print '#################################'

print 'BEAMnrc Dir: ' + os.path.normpath(beamdir)

print 'DOSXYZnrc Dir: ' + os.path.normpath(dosxyzdir)

print 'DCM RP Input: ' + os.path.normpath(dcmplanfile)

print 'DCM RD Template: ' + os.path.normpath(dcmdosefile)

print 'MC 3ddose file: ' + os.path.normpath(mcdosefile)

print 'New DCM RD output: ' + os.path.normpath(outfile)

print

print '#################################'

print

################################################################################

# This part is to be change by user for corresponding absolute dose calibration.

d_depcal = 1.43915e-16 # calibration @ d=5cm

d_cal_ch = 3.459e-15 # chamber dose

D_cal_abs = 0.01 # 1 cGy/MU = 0.01 Gy/MU

################################################################################

# Ion chamber absolute dose (in Gy) per MU. D_ch_MU are obtained from numbers above.

D_ch_MU = D_cal_abs * d_cal_ch/d_depcal

print 'MC Chamber Dose: ', d_ch

print 'Calibration Factor: ', D_ch_MU

print

###### Info from DICOM RP file

dcmplan = dicom.read_file(dcmplanfile)

RefBeam = {}

MUtot = 0

#DoseTot = 0

for rbeam in dcmplan.FractionGroups[0].ReferencedBeams:

if hasattr(rbeam,'BeamMeterset'):

RefBeam[rbeam.ReferencedBeamNumber] = rbeam.BeamMeterset

MUtot = MUtot + rbeam.BeamMeterset

#DoseTot = DoseTot + rbeam.BeamDose

print 'MU for each beam: ', RefBeam

print 'Total MU: ', MUtot

#print 'Total Dose', DoseTot

nFrac = dcmplan.FractionGroups[0].NumberofFractionsPlanned

print 'nFrac = ', nFrac

print

# Info from the model DICOM RT Dose file

dcmdose = dicom.read_file(dcmdosefile)

xsizeold = dcmdose.Columns

ysizeold = dcmdose.Rows

zsizeold = dcmdose.NumberofFrames

DoseSumType = dcmdose.DoseSummationType

if DoseSumType=='FRACTION':

MU = MUtot/nFrac

elif DoseSumType=='PLAN':

MU = MUtot

elif DoseSumType=='BEAM':

MU = MUtot

print 'BEAM ONLY !!!'

else:

print 'DoseSumType ',DoseSumType, ' not supported.'

print

print 'DoseSumType: ', DoseSumType, ' MUtot: ', MUtot, ' Fracions: ',nFrac, 'MU used for Generating DICOM RD: ', MU

print

dosescaling = dcmdose.DoseGridScaling

length = xsizeold*ysizeold*zsizeold

BitsAllocated = dcmdose.BitsAllocated

if BitsAllocated==32:

format = 'I'*length

elif BitsAllocated==16:

format = 'H'*length

else:

print 'BitsAllocated: ', BitsAllocated, ' is not supported yet.'

pdata = struct.unpack(format, dcmdose.PixelData)

pdmax = max(pdata)

print '#################################'

print 'ImagePos:', dcmdose.ImagePositionPatient

print 'xsizeold:',xsizeold, 'ysizeold:',ysizeold, 'zsizeold:',zsizeold

print 'DoseGridScaling', dosescaling

print 'MaxDose(INT):',pdmax, 'MaxDose(Gy):',pdmax*dosescaling, '<--'

print 'TotLength:',length, 'Bits:',length*dcmdose.BitsAllocated/8

print 'OffsetVector Length:', np.size(dcmdose.GridFrameOffsetVector)

print '-----------------------------'

# Info from the DOSXYZnrc 3ddose file

dose3d = open(mcdosefile)

xsize, ysize, zsize = np.array(dose3d.readline().split(),np.int)

x = np.array(dose3d.readline().split(),np.float)

y = np.array(dose3d.readline().split(),np.float)

z = np.array(dose3d.readline().split(),np.float)

d = np.array(dose3d.readline().split(),np.float) # dose

e = np.array(dose3d.readline().split(),np.float) # dose error

dx = x[1]-x[0]

dy = y[1]-y[0]

dz = z[1]-z[0]

dcmdose.SeriesDescription = 'DOSXYZnrc Doses'

dcmdose.ManufacturersModelName = 'DOSXYZnrc'

dcmdose.DeviceSerialNumber = '000000000'

dcmdose.Rows = ysize

dcmdose.Columns = xsize

dcmdose.NumberofFrames = zsize

dcmdose.ImagePositionPatient = [(x[0]+dx/2.0)*10.0, (y[0]+dy/2.0)*10.0,

(z[0]+dz/2.0)*10.0]

z0 = float(dcmdose.ImagePositionPatient[2])

dcmdose.PixelSpacing = [(x[-1]-x[0])*10.0/xsize,(y[-1]-y[0])*10.0/ysize]

dcmdose.GridFrameOffsetVector = ((z[1:]-dz/2.0)*10.0-z0).tolist()

length = xsize * ysize * zsize

#format = 'I'*length

if BitsAllocated==32:

format = 'I'*length

elif BitsAllocated==16:

format = 'H'*length

else:

print 'BitsAllocated: ', BitsAllocated, ' is not supported yet.'

# di = np.array(d*pdmax/d.max(),np.int)

# di = np.array(0.01*(d/d_cal5cm)*MU*nFrac/dosescaling,np.int)

di = np.array((d/d_ch)*nFrac*MU*D_ch_MU/dosescaling,np.int)

dcmdose.PixelData = struct.pack(format,*(di.tolist()))

print 'check dose volume sizes'

print 'Pixel Range:', x[0],x[-1],y[0],y[-1],z[0],z[-1]

print 'dx, dy, dz:', dx, dy, dz

print 'ImageOrigien:',dcmdose.ImagePositionPatient

print 'sizes:',xsize, ysize, zsize, np.size(x),np.size(y),np.size(z)

print 'Max D/Ne:',d.max(), 'Abs Dmax:',d.max()*MU*nFrac*D_ch_MU/d_ch, '<--'

print 'PixelSpacing:',dcmdose.PixelSpacing, 'MaxDose:',di.max()

print length, np.size(d), np.size(e)

print 'New Image Position:', dcmdose.ImagePositionPatient

print 'OffsetVector Length:', np.size(dcmdose.GridFrameOffsetVector)

print

dcmdose.SOPInstanceUID = get_dicomuid()

dcmdose.StudyUID = get_dicomuid()

dcmdose.SeriesUID = get_dicomuid()

dcmdose.FrameUID = get_dicomuid()

dcmdose.SyncUID = get_dicomuid()

dcmdose.SrUID = get_dicomuid()

dcmdose.StudyInstanceUID = get_dicomuid()

dcmdose.SeriesInstanceUID = get_dicomuid()

dicom.write_file(outfile, dcmdose)

print 'New DCM RD file created: ',outfile

#print xsize, ysize, zsize, length, length*dcmdose.BitsAllocated/8, max(di)