Source code for utils.dicom2xml

import dicom, SetBeam20, scaleConverter
from xml.etree import ElementTree as ET
import numpy as np
#from utils import SetBeam20
from . import SetBeam20

# Author: Pankaj Mishra, Jul 7, 2014
# Update: 7/29/2014 Removed hardcoded path -CLW
# Fixed mm to cm conversion error - CLW 10/24/2014, see #3

class Dicom2Xml:

    def __init__(self, filename, outxml):
        self.filename = filename
        self.outxml = outxml

    def dicomToDataset(self):
        dataset = dicom.read_file(self.filename, force=True)
        self.ds = dataset

    def getLeafJaws(self, leafJawsSequence, cp):
        ''' Extract Mlc, X or Y jaws (if present)
         and then add it to the existinXML string
        '''
        selectionStr = {"MLCX": "Mlc", "ASYMX": "X", "ASYMY": "Y", "X": "X", "Y": "Y"}

        for lj in leafJawsSequence:
            if(selectionStr[lj.RTBeamLimitingDeviceType] == "Y"):
                # Fixed mm to cm conversion error - CLW 10/24/2014
                ET.SubElement(cp, 'Y1').text = str(lj.LeafJawPositions[0]/10.0)
                ET.SubElement(cp, 'Y2').text = str(lj.LeafJawPositions[1]/10.0)
            elif(selectionStr[lj.RTBeamLimitingDeviceType] == "X"):
                # Fixed mm to cm conversion error - CLW 10/24/2014
                ET.SubElement(cp, 'X1').text = str(lj.LeafJawPositions[0]/10.0)
                ET.SubElement(cp, 'X2').text = str(lj.LeafJawPositions[1]/10.0)
            elif(selectionStr[lj.RTBeamLimitingDeviceType] == "Mlc"):
                mlcTag = ET.SubElement(cp,'Mlc')
                ET.SubElement(mlcTag,'ID').text = '1'
                # Fixed mm to cm conversion error - CLW 10/24/2014
                Barr=map(lambda x:float(x)/10.0,lj.LeafJawPositions[:60])
                Aarr=map(lambda x:float(x)/10.0,lj.LeafJawPositions[60:])
                ET.SubElement(mlcTag, 'B').text = " ".join(map(str,Barr))
                ET.SubElement(mlcTag, 'A').text = " ".join(map(str,Aarr))

    def findMlcModel(self, inMlc):
        '''
        Determine the MLCModel type. Currently NDS120, NDS120HD, NDS80 are supported.
        :param inMlc: MLC array from the DICOM file
        '''

        # MLC model pattern NDS120 (in mm)
        firstLast10 = np.array(10*np.ones(10, dtype='float', order = 'C'))
        middle40 =  np.array(5*np.ones(40, dtype='float', order = 'C'))
        nds120 = np.concatenate((firstLast10, middle40, firstLast10))

        # MLC model pattern ND120HD (in mm)
        firstLast14 = np.array(5*np.ones(14, dtype=np.float32, order = 'C'))
        middle32 =  np.array(2.5*np.ones(32, dtype=np.float32, order = 'C'))
        nds120HD = np.concatenate((firstLast14, middle32, firstLast14))

        # Now some constants
        mlcLength = len(inMlc)
        if mlcLength == 61:
            if np.all(np.diff(inMlc) == nds120):
                return 'NDS120'
            elif np.all(np.diff(inMlc) == nds120HD):
                return 'NDS120HD'
        elif mlcLength == 41:
            return 'NDS80'

    def extractControlPoints(self):

        lookupTable = {'NominalBeamEnergy' : 'Energy', \
                       'DoseRateSet' : 'DRate', \
                       'GantryAngle' : 'GantryRtn', \
                       'BeamLimitingDeviceAngle' : 'CollRtn',\
                       'TableTopVerticalPosition' : 'CouchVrt',\
                       'TableTopLongitudinalPosition' : 'CouchLng', \
                       'TableTopLateralPosition' : 'CouchLat',\
                       'PatientSupportAngle' : 'CouchRtn',\
                       'CumulativeMetersetWeight' : 'Mu',\
                       'BeamLimitingDevicePositionSequence' : 'MlcJaws'
                       }

        energyType = {"PHOTON": "x", "ELECTRON": "e"}

        dose = 0;

        root = ET.Element('VarianResearchBeam')
        sb = ET.SubElement(root,'SetBeam')
        ET.SubElement(sb, 'Id').text = '1'

        # Determine the MLCModel type: NDS80, NDS120, NDS120HD
        inMlc = [float(s) for s in self.ds.BeamSequence[0].BeamLimitingDeviceSequence[2].LeafPositionBoundaries]
        ET.SubElement(sb, 'MLCModel').text = self.findMlcModel(inMlc)

        ET.SubElement(sb, 'Accs').text = ''

        controlpoint = ET.SubElement(sb, 'ControlPoints')
        dosePrev = 0.0  # For cumulative dose

        for (beam, frac) in zip(self.ds.BeamSequence, self.ds.FractionGroupSequence[0].ReferencedBeamSequence):

            # Control point
            for cnt in range(0, beam.NumberofControlPoints):
                cp = ET.SubElement(controlpoint, 'Cp')

                for elem in beam.ControlPointSequence[cnt]:
                    keyTag = elem.name.replace(" ", "")
                    if(keyTag in lookupTable.keys()):
                        if (lookupTable[keyTag] == 'Energy'):
                            ET.SubElement(cp, lookupTable[keyTag]).text = str(elem.value) + energyType[beam.RadiationType]
                        elif (lookupTable[keyTag] == "MlcJaws"):
                            self.getLeafJaws(elem, cp)
                        elif(lookupTable[keyTag] == "Mu"):
                            dose = dosePrev + frac.BeamMeterset*elem.value
                            ET.SubElement(cp, lookupTable[keyTag]).text = str(dose)
                        else:
                            ET.SubElement(cp, lookupTable[keyTag]).text = str(elem.value)

            dosePrev = dosePrev + frac.BeamMeterset # Cumulative dose

        #------------------------------------ Validate and write output XML file
        # Convert IEC (from DICOM) to Varian Scale
        # NOTE: Please fix the schema check part SOOOOON!!!!!
        tree = ET.ElementTree(root)
        tree.write(self.outxml)
        fp = scaleConverter.ScaleConverter(self.outxml)
        fp.convertScale('VarianScale')
        fp.tree.write(self.outxml)