matRad_scanDicomImportFolder

 matRad function to scan a folder for dicom data
 
 call
   [ fileList, patientList ] = matRad_scanDicomImportFolder( patDir )

 input
   patDir:         folder to be scanned

 output
   fileList:       matlab struct with a list of dicom files including meta
                   infomation (type, series number etc.)
   patientList:    list of patients with dicom data in the folder

 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 [ fileList, patientList ] = matRad_scanDicomImportFolder( patDir )
0002 % matRad function to scan a folder for dicom data
0003 %
0004 % call
0005 %   [ fileList, patientList ] = matRad_scanDicomImportFolder( patDir )
0006 %
0007 % input
0008 %   patDir:         folder to be scanned
0009 %
0010 % output
0011 %   fileList:       matlab struct with a list of dicom files including meta
0012 %                   infomation (type, series number etc.)
0013 %   patientList:    list of patients with dicom data in the folder
0014 %
0015 % References
0016 %   -
0017 %
0018 % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
0019 %
0020 % Copyright 2015 the matRad development team.
0021 %
0022 % This file is part of the matRad project. It is subject to the license
0023 % terms in the LICENSE file found in the top-level directory of this
0024 % distribution and at https://github.com/e0404/matRad/LICENSES.txt. No part
0025 % of the matRad project, including this file, may be copied, modified,
0026 % propagated, or distributed except according to the terms contained in the
0027 % LICENSE file.
0028 %
0029 % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
0030 
0031 matRad_cfg = MatRad_Config.instance();
0032 
0033 %% print current status of the import script
0034 matRad_cfg.dispInfo('Dose series matched to the different plans are displayed and could be selected.\n');
0035 matRad_cfg.dispInfo('Rechecking of correct matching procedure is recommended.\n');
0036 
0037 global warnDlgDICOMtagShown;
0038 warnDlgDICOMtagShown = false;
0039 
0040 %% get all files in search directory
0041 
0042 % dicom import needs image processing toolbox -> check if available
0043 if ~license('checkout','image_toolbox')
0044     matRad_cfg.dispError('image processing toolbox and/or corresponding licence not available');
0045 end
0046 
0047 fileList = matRad_listAllFiles(patDir);
0048 
0049 if ~isempty(fileList)
0050     %% check for dicom files and differentiate patients, types, and series
0051     numOfFiles = numel(fileList(:,1));
0052     h = waitbar(0,'Please wait...');
0053     %h.WindowStyle = 'Modal';
0054     steps = numOfFiles;
0055     for i = numOfFiles:-1:1
0056         waitbar((numOfFiles+1-i) / steps)
0057         try % try to get DicomInfo
0058             if verLessThan('matlab','9')
0059                 info = dicominfo(fileList{i});
0060             else
0061                 info = dicominfo(fileList{i},'UseDictionaryVR',true);
0062             end
0063         catch
0064             fileList(i,:) = [];
0065             matRad_progress(numOfFiles+1-i, numOfFiles);
0066             continue;
0067         end
0068         try
0069             fileList{i,2} = info.Modality;
0070         catch
0071             fileList{i,2} = NaN;
0072         end
0073         
0074         fileList = parseDicomTag(fileList,info,'PatientID',i,3);
0075         
0076         switch fileList{i,2}
0077             case 'CT'
0078                
0079                fileList = parseDicomTag(fileList,info,'SeriesInstanceUID',i,4);
0080                 
0081             case {'RTPLAN','RTDOSE','RTSTRUCT'}
0082                
0083                fileList = parseDicomTag(fileList,info,'SOPInstanceUID',i,4);
0084 
0085            otherwise
0086                
0087               fileList = parseDicomTag(fileList,info,'SeriesInstanceUID',i,4);
0088 
0089         end
0090         
0091         fileList = parseDicomTag(fileList,info,'SeriesNumber',i,5,@seriesnum2str); %We want to make sure the series number is stored as string
0092         fileList = parseDicomTag(fileList,info,'FamilyName',i,6);
0093         fileList = parseDicomTag(fileList,info,'GivenName',i,7);
0094         fileList = parseDicomTag(fileList,info,'PatientBirthDate',i,8);
0095 
0096         try
0097             if strcmp(info.Modality,'CT')
0098                 fileList{i,9} = num2str(info.PixelSpacing(1));
0099             else
0100                 fileList{i,9} = NaN;
0101             end
0102         catch
0103             fileList{i,9} = NaN;
0104         end
0105         try
0106             if strcmp(info.Modality,'CT')
0107                 fileList{i,10} = num2str(info.PixelSpacing(2));
0108             else
0109                 fileList{i,10} = NaN;
0110             end
0111         catch
0112             fileList{i,10} = NaN;
0113         end
0114         try
0115             if strcmp(info.Modality,'CT')
0116                 %usually the Attribute should be SliceThickness, but it
0117                 %seems like some data uses "SpacingBetweenSlices" instead.
0118                 if isfield(info,'SliceThickness') && ~isempty(info.SliceThickness)
0119                     fileList{i,11} = num2str(info.SliceThickness);
0120                 elseif isfield(info,'SpacingBetweenSlices')
0121                     fileList{i,11} = num2str(info.SpacingBetweenSlices);
0122                 else
0123                     matRad_cfg.dispError('Could not identify spacing between slices since neither ''SliceThickness'' nor ''SpacingBetweenSlices'' are specified');
0124                 end
0125             else
0126                 fileList{i,11} = NaN;
0127             end
0128         catch
0129             fileList{i,11} = NaN;
0130         end
0131         try
0132             if strcmp(info.Modality,'RTDOSE')
0133                 dosetext_helper = strcat('Instance','_', num2str(info.InstanceNumber),'_', ...
0134                     info.DoseSummationType, '_', info.DoseType);
0135                 fileList{i,12} = dosetext_helper;
0136             else
0137                 fileList{i,12} = NaN;
0138             end
0139         catch
0140             fileList{i,12} = NaN;
0141         end
0142         % writing corresponding dose dist.
0143         try
0144             if strcmp(fileList{i,2},'RTPLAN')
0145                 corrDose = [];
0146                 numDose = length(fieldnames(info.ReferencedDoseSequence));
0147                 for j = 1:numDose
0148                     fieldName = strcat('Item_',num2str(j));
0149                     corrDose{j} = info.ReferencedDoseSequence.(fieldName).ReferencedSOPInstanceUID;
0150                 end
0151                 fileList{i,13} = corrDose;
0152             else
0153                 fileList{i,13} = {'NaN'};
0154             end
0155 
0156         catch
0157             fileList{i,13} = {'NaN'};
0158         end
0159         matRad_progress(numOfFiles+1-i, numOfFiles);
0160         
0161     end
0162     close(h)
0163     
0164     if ~isempty(fileList)
0165         patientList = unique(fileList(:,3));
0166         
0167         if isempty(patientList)
0168             msgbox('No patient found with DICOM CT _and_ RT structure set in patient directory!', 'Error','error');
0169         end
0170     else
0171         msgbox('No DICOM files found in patient directory!', 'Error','error');
0172         %h.WindowStyle = 'Modal';
0173         %error('No DICOM files found in patient directory');
0174     end
0175 else
0176     msgbox('Search folder empty!', 'Error','error');
0177     
0178 end
0179 
0180 clear warnDlgDICOMtagShown;
0181 
0182 end
0183 
0184 function fileList = parseDicomTag(fileList,info,tag,row,column,parsefcn)
0185 
0186 global warnDlgDICOMtagShown;
0187 
0188 defaultPlaceHolder = '001';
0189 
0190 if nargin < 6
0191     parsefcn = @(x) x;
0192 end
0193 
0194 try
0195    if isfield(info,tag)
0196       if ~isempty(info.(tag))
0197          fileList{row,column} = parsefcn(info.(tag));
0198       else
0199          fileList{row,column} = defaultPlaceHolder;
0200       end
0201    else
0202       fileList{row,column} = defaultPlaceHolder;
0203    end
0204 catch
0205    fileList{row,column} = NaN;
0206 end
0207 
0208 if ~warnDlgDICOMtagShown && strcmp(fileList{row,column},defaultPlaceHolder) && (column == 3 || column == 4)
0209  
0210    dlgTitle    = 'Dicom Tag import';
0211    dlgQuestion = ['matRad_scanDicomImportFolder: Could not parse dicom tag: ' tag '. Using placeholder ' defaultPlaceHolder ' instead. Please check imported data carefully! Do you want to continue?'];
0212    answer      = questdlg(dlgQuestion,dlgTitle,'Yes','No', 'Yes');
0213    
0214    warnDlgDICOMtagShown = true;
0215    
0216    switch answer
0217       case 'No'
0218          matRad_cfg.dispError('Inconsistency in DICOM tags')  
0219    end
0220 end
0221 
0222 end
0223 
0224 function value = seriesnum2str(value)
0225     if isnumeric(value)
0226         value = num2str(value);
0227     end
0228 end
0229 
0230 
0231 
0232