matRad_exportDicomRTDoses

 matRad function to exportt resultGUI to dicom RT dose. 
 Function of matRad_DicomExporter
 
 call
   matRad_DicomExporter.matRad_exportDicomRTDoses()

 References
   -

 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

 Copyright 2015 the matRad development team. 
 
 This file is part of the matRad project. It is subject to the license 
 terms in the LICENSE file found in the top-level directory of this 
 distribution and at https://github.com/e0404/matRad/LICENSES.txt. No part 
 of the matRad project, including this file, may be copied, modified, 
 propagated, or distributed except according to the terms contained in the 
 LICENSE file.

 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

0001 function obj = matRad_exportDicomRTDoses(obj)
0002 % matRad function to exportt resultGUI to dicom RT dose.
0003 % Function of matRad_DicomExporter
0004 %
0005 % call
0006 %   matRad_DicomExporter.matRad_exportDicomRTDoses()
0007 %
0008 % References
0009 %   -
0010 %
0011 % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
0012 %
0013 % Copyright 2015 the matRad development team.
0014 %
0015 % This file is part of the matRad project. It is subject to the license
0016 % terms in the LICENSE file found in the top-level directory of this
0017 % distribution and at https://github.com/e0404/matRad/LICENSES.txt. No part
0018 % of the matRad project, including this file, may be copied, modified,
0019 % propagated, or distributed except according to the terms contained in the
0020 % LICENSE file.
0021 %
0022 % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
0023 
0024  matRad_cfg = MatRad_Config.instance();
0025 matRad_cfg.dispInfo('Exporting DICOM RTDose...\n');
0026 
0027 env = matRad_getEnvironment();
0028 isOctave = strcmp(env,'OCTAVE');
0029 
0030 if isOctave
0031     matRad_cfg.dispWarning('RTDose export currently not supported by matRad running in Octave using the dicom package! Skipping...');
0032     return;
0033 end
0034 
0035 %% CT check
0036 ct = obj.ct;
0037 if ~any(isfield(ct,{'x','y','z'}))
0038     %positionOffset = transpose(ct.cubeDim ./ 2);
0039     positionOffset = ct.cubeDim ./ 2;
0040     ct.x = ct.resolution.x*[0:ct.cubeDim(2)-1] - positionOffset(2);
0041     ct.y = ct.resolution.y*[0:ct.cubeDim(1)-1] - positionOffset(1);
0042     ct.z = ct.resolution.z*[0:ct.cubeDim(3)-1] - positionOffset(3);
0043 end
0044 
0045 %% Meta data
0046 storageClass = '1.2.840.10008.5.1.4.1.1.481.2';
0047 meta.MediaStorageSOPClassUID = storageClass;
0048 meta.SOPClassUID = storageClass;
0049 
0050 %TransferSyntaxUID = '1.2.840.10008.1.2.1'; %Explicit VR little endian?
0051 %meta.TransferSyntaxUID = TransferSyntaxUID;
0052 
0053 meta.Modality = 'RTDOSE';
0054 meta.Manufacturer = '';
0055 meta.DoseUnits = 'GY';
0056 
0057 %Reference
0058 %ID of the CT
0059 meta.StudyInstanceUID = obj.StudyInstanceUID;
0060 meta.StudyID = obj.StudyID; 
0061 
0062 
0063 
0064 %Dates & Times
0065 currDate = now;
0066 currDateStr = datestr(currDate,'yyyymmdd');
0067 currTimeStr = datestr(currDate,'HHMMSS');
0068 meta.InstanceCreationDate = currDateStr;
0069 meta.InstanceCreationTime = currTimeStr;
0070 meta.StudyDate = obj.StudyDate;
0071 meta.StudyTime = obj.StudyTime;
0072 
0073 meta.FrameOfReferenceUID = obj.FrameOfReferenceUID;
0074 meta.PositionReferenceIndicator = '';
0075 
0076 
0077 %Remaining stuff
0078 meta.AccessionNumber = '';
0079 meta.StationName = '';
0080 meta.OperatorsName = obj.OperatorsName;
0081 meta.ReferringPhysicianName = obj.dicomName();
0082 
0083 meta.PatientName = obj.PatientName;
0084 meta.PatientID = obj.PatientID;
0085 meta.PatientBirthDate = obj.PatientBirthDate;
0086 meta.PatientSex = obj.PatientSex;
0087 
0088 %This RTDose series
0089 meta.SeriesInstanceUID = dicomuid;
0090 
0091 %Now image meta
0092 resolution = ct.resolution;
0093 meta.PixelSpacing = [resolution.y; resolution.x];
0094 meta.SliceThickness = resolution.z;
0095 
0096 meta.ImagePositionPatient = [ct.x(1); ct.y(1); ct.z(1)];
0097 meta.ImageOrientationPatient = [1;0;0;0;1;0];
0098 
0099 
0100 %No (Re)scaling
0101 meta.RescaleSlope = 1;
0102 meta.RescaleIntercept = 0;
0103 meta.RescaleType = 'US';
0104 
0105 %RTDose is stored as multiframe image
0106 meta.ImagesInAcquisition = ct.cubeDim(3);
0107 meta.NumberOfFrames = ct.cubeDim(3);
0108 meta.GridFrameOffsetVector = transpose(ct.z - ct.z(1));
0109 
0110 %Referenced Plan
0111 try
0112     rtPlanUID = obj.rtPlanMeta.SOPInstanceUID;
0113     rtPlanClassID = obj.rtPlanMeta.SOPClassUID;
0114     meta.ReferencedRTPlanSequence.Item_1.ReferencedSOPClassUID = rtPlanClassID;
0115     meta.ReferencedRTPlanSequence.Item_1.ReferencedSOPInstanceUID = rtPlanUID;
0116 catch
0117     rtPlanUID = '';
0118     rtPlanClassID = '';
0119 end
0120     
0121 
0122 
0123 if nargin < 4 || isempty(doseFieldNames)
0124     doseFieldNames = cell(0);
0125     fn = fieldnames(obj.resultGUI);
0126     for i = 1:numel(fn)
0127         if numel(size(obj.resultGUI.(fn{i}))) == 3
0128             doseFieldNames{end+1} = fn{i};
0129         end
0130     end
0131 end
0132 
0133 
0134 
0135 
0136 
0137 obj.rtDoseMetas = struct([]);
0138 obj.rtDoseExportStatus = struct([]);
0139 
0140 for i = 1:numel(doseFieldNames)
0141     doseName = doseFieldNames{i};
0142     
0143     %Now check if we export physical or RBE weighted dose, they are known
0144     %to dicom
0145     if strncmp(doseName,'physicalDose',12)
0146         doseType = 'PHYSICAL';
0147     elseif strncmp(doseName,'RBExDose',8)
0148         doseType = 'EFFECTIVE';
0149     else
0150         fprintf('Dose Cube ''%s'' of unknown type for DICOM. Not exported!\n',doseName);
0151         continue;
0152     end
0153     
0154     %Now check if we export a single beam
0155     if ~isempty(regexp(doseName,'_beam(\d+)','once'))
0156         %We export a single beam fraction
0157         deliveryType = 'BEAM_SESSION';
0158     else
0159         deliveryType = 'FRACTION';
0160     end
0161     
0162     
0163     doseCube = zeros(ct.cubeDim(1),ct.cubeDim(2),1,ct.cubeDim(3));
0164     doseCube(:,:,1,:) = obj.resultGUI.(doseFieldNames{i});
0165     
0166     minDose = min(doseCube(:));
0167     maxDose = max(doseCube(:));
0168     
0169     if minDose < 0
0170         fprintf('Dose Cube ''%s'' has negative values. Not exported!\n',doseName);
0171         continue;
0172     end
0173     
0174     doseCubeFac = maxDose / double(uint16(Inf));   
0175     doseCube = uint16(doseCube ./ doseCubeFac);
0176          
0177     metaCube = meta;
0178     metaCube.DoseType = doseType;
0179     metaCube.DoseSummationType = deliveryType;
0180        
0181     %ID of the RTDose
0182     meta.SeriesInstanceUID = dicomuid;    
0183     metaCube.SeriesNumber = i;
0184     metaCube.InstanceNumber = 1;
0185     metaCube.DoseGridScaling = doseCubeFac;
0186     
0187     meta.SOPInstanceUID = dicomuid;
0188     meta.MediaStorageSOPInstanceUID = meta.SOPInstanceUID;
0189     
0190     fileName = [obj.rtDoseFilePrefix num2str(i) '_' doseName '.dcm'];
0191     
0192     env = matRad_getEnvironment();
0193     if strcmp(env,'OCTAVE')
0194         dicomwrite(doseCube,fullfile(obj.dicomDir,fileName),metaCube);
0195     else
0196         status = dicomwrite(doseCube,fullfile(obj.dicomDir,fileName),metaCube,'CreateMode','copy');%,'TransferSyntax',TransferSyntaxUID);
0197         if ~isempty(status)
0198             obj.rtDoseExportStatus = obj.addStruct2StructArray(obj.rtDoseExportStatus,status,i);
0199         end
0200     end
0201     
0202     
0203     obj.rtDoseMetas = obj.addStruct2StructArray(obj.rtDoseMetas,metaCube);
0204     
0205     obj.rtDoseNames{i} = doseFieldNames{i};
0206     
0207     matRad_progress(i,numel(doseFieldNames));
0208 end
0209                
0210 
0211 end