mitkDicomDiffusionImageHeaderReader.cpp
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00001 /*========================================================================= 00002 00003 Program: Medical Imaging & Interaction Toolkit 00004 Language: C++ 00005 Date: $Date: 2007-12-11 14:46:19 +0100 (Di, 11 Dez 2007) $ 00006 Version: $Revision: 13129 $ 00007 00008 Copyright (c) German Cancer Research Center, Division of Medical and 00009 Biological Informatics. All rights reserved. 00010 See MITKCopyright.txt or https://www.mitk.org/copyright.html for details. 00011 00012 This software is distributed WITHOUT ANY WARRANTY; without even 00013 the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 00014 PURPOSE. See the above copyright notices for more information. 00015 00016 =========================================================================*/ 00017 00018 00019 #include "mitkDicomDiffusionImageHeaderReader.h" 00020 00021 #include "mitkGEDicomDiffusionImageHeaderReader.h" 00022 #include "mitkPhilipsDicomDiffusionImageHeaderReader.h" 00023 #include "mitkSiemensDicomDiffusionImageHeaderReader.h" 00024 #include "mitkSiemensMosaicDicomDiffusionImageHeaderReader.h" 00025 00026 void InsertUnique( std::vector<float> & vec, float value ) 00027 { 00028 int n = vec.size(); 00029 if (n == 0) 00030 { 00031 vec.push_back( value ); 00032 return; 00033 } 00034 00035 for (int k = 0; k < n ; k++) 00036 { 00037 if (vec[k] == value) 00038 { 00039 return; 00040 } 00041 } 00042 00043 // if we get here, it means value is not in vec. 00044 vec.push_back( value ); 00045 return; 00046 00047 } 00048 00049 mitk::DicomDiffusionImageHeaderReader::DicomDiffusionImageHeaderReader() 00050 { 00051 m_SliceOrderIS = true; 00052 m_SingleSeries = true; 00053 } 00054 00055 mitk::DicomDiffusionImageHeaderReader::~DicomDiffusionImageHeaderReader() 00056 { 00057 } 00058 00059 mitk::DicomDiffusionImageHeaderReader::SupportedVendors 00060 mitk::DicomDiffusionImageHeaderReader::GetVendorID() 00061 { 00062 // adapted from namic-sandbox 00063 // DicomToNrrdConverter.cxx 00064 00065 m_GdcmIO = ImageIOType::New(); 00066 m_GdcmIO->LoadPrivateTagsOn(); 00067 m_GdcmIO->SetMaxSizeLoadEntry( 65536 ); 00068 00069 m_VolumeReader = VolumeReaderType::New(); 00070 m_VolumeReader->SetImageIO( m_GdcmIO ); 00071 m_VolumeReader->SetFileNames( m_DicomFilenames ); 00072 00073 try 00074 { 00075 m_VolumeReader->Update(); 00076 } 00077 catch (itk::ExceptionObject &excp) 00078 { 00079 std::cerr << "Exception thrown while reading slice" << std::endl; 00080 std::cerr << excp << std::endl; 00081 return SV_UNKNOWN_VENDOR; 00082 } 00083 00084 VolumeReaderType::DictionaryArrayRawPointer inputDict 00085 = m_VolumeReader->GetMetaDataDictionaryArray(); 00086 00087 std::string vendor; 00088 itk::ExposeMetaData<std::string> ( *(*inputDict)[0], "0008|0070", vendor ); 00089 // std::cout << vendor << std::endl; 00090 00091 std::string ImageType; 00092 itk::ExposeMetaData<std::string> ( *(*inputDict)[0], "0008|0008", ImageType ); 00093 //std::cout << ImageType << std::endl; 00094 00095 if ( vendor.find("GE") != std::string::npos ) 00096 { 00097 // for GE data 00098 return SV_GE; 00099 } 00100 else if( vendor.find("SIEMENS") != std::string::npos ) 00101 { 00102 if ( ImageType.find("MOSAIC") != std::string::npos ) 00103 { 00104 // for Siemens MOSAIC 00105 return SV_SIEMENS_MOSAIC; 00106 } 00107 else 00108 { 00109 // for Siemens SPLIT 00110 return SV_SIEMENS; 00111 } 00112 } 00113 else if( vendor.find("PHILIPS") != std::string::npos ) 00114 { 00115 // for philips data 00116 return SV_PHILIPS; 00117 } 00118 else 00119 { 00120 // for unrecognized vendors 00121 return SV_UNKNOWN_VENDOR; 00122 } 00123 } 00124 00125 // do the work 00126 void mitk::DicomDiffusionImageHeaderReader::Update() 00127 { 00128 00129 // check if there are filenames 00130 if(m_DicomFilenames.size()) 00131 { 00132 00133 m_Output = mitk::DiffusionImageHeaderInformation::New(); 00134 m_Output->m_DicomFilenames = m_DicomFilenames; 00135 00136 // create correct reader 00137 switch(GetVendorID()) 00138 { 00139 case(SV_GE): 00140 { 00141 GEDicomDiffusionImageHeaderReader::Pointer reader 00142 = GEDicomDiffusionImageHeaderReader::New(); 00143 reader->SetSeriesDicomFilenames(this->m_DicomFilenames); 00144 reader->SetGdcmIO(this->m_GdcmIO); 00145 reader->SetVolumeReader(this->m_VolumeReader); 00146 reader->SetOutputPointer(this->m_Output); 00147 reader->Update(); 00148 this->m_Output = reader->GetOutput(); 00149 break; 00150 } 00151 case(SV_SIEMENS): 00152 { 00153 SiemensDicomDiffusionImageHeaderReader::Pointer reader 00154 = SiemensDicomDiffusionImageHeaderReader::New(); 00155 reader->SetSeriesDicomFilenames(this->m_DicomFilenames); 00156 reader->SetGdcmIO(this->m_GdcmIO); 00157 reader->SetVolumeReader(this->m_VolumeReader); 00158 reader->SetOutputPointer(this->m_Output); 00159 reader->Update(); 00160 this->m_Output = reader->GetOutput(); 00161 break; 00162 } 00163 case(SV_SIEMENS_MOSAIC): 00164 { 00165 00166 SiemensMosaicDicomDiffusionImageHeaderReader::Pointer reader 00167 = SiemensMosaicDicomDiffusionImageHeaderReader::New(); 00168 reader->SetSeriesDicomFilenames(this->m_DicomFilenames); 00169 reader->SetGdcmIO(this->m_GdcmIO); 00170 reader->SetVolumeReader(this->m_VolumeReader); 00171 reader->SetOutputPointer(this->m_Output); 00172 reader->Update(); 00173 this->m_Output = reader->GetOutput(); 00174 break; 00175 } 00176 case(SV_PHILIPS): 00177 { 00178 00179 PhilipsDicomDiffusionImageHeaderReader::Pointer reader 00180 = PhilipsDicomDiffusionImageHeaderReader::New(); 00181 reader->SetSeriesDicomFilenames(this->m_DicomFilenames); 00182 reader->SetGdcmIO(this->m_GdcmIO); 00183 reader->SetVolumeReader(this->m_VolumeReader); 00184 reader->SetOutputPointer(this->m_Output); 00185 reader->Update(); 00186 this->m_Output = reader->GetOutput(); 00187 break; 00188 } 00189 case(SV_UNKNOWN_VENDOR): 00190 { 00191 std::cerr << "diffusion header reader: unknown vendor" << std::endl; 00192 break; 00193 } 00194 } 00195 } 00196 } 00197 00198 // return output 00199 mitk::DiffusionImageHeaderInformation::Pointer 00200 mitk::DicomDiffusionImageHeaderReader::GetOutput() 00201 { 00202 return m_Output; 00203 } 00204 00205 void mitk::DicomDiffusionImageHeaderReader::ReadPublicTags() 00206 { 00207 VolumeReaderType::DictionaryArrayRawPointer inputDict 00208 = m_VolumeReader->GetMetaDataDictionaryArray(); 00209 00210 // load in all public tags 00211 m_nSlice = inputDict->size(); 00212 std::string tag; 00213 00214 tag.clear(); 00215 itk::ExposeMetaData<std::string> ( *(*inputDict)[0], "0008|103e", tag ); 00216 this->m_Output->seriesDescription = tag.c_str(); 00217 00218 tag.clear(); 00219 itk::ExposeMetaData<std::string> ( *(*inputDict)[0], "0020|0011", tag ); 00220 this->m_Output->seriesNumber = atoi(tag.c_str()); 00221 00222 tag.clear(); 00223 itk::ExposeMetaData<std::string> ( *(*inputDict)[0], "0010|0010", tag ); 00224 this->m_Output->patientName = tag.c_str(); 00225 00226 tag.clear(); 00227 itk::ExposeMetaData<std::string> ( *(*inputDict)[0], "0028|0010", tag ); 00228 this->m_Output->nRows = atoi( tag.c_str() ); 00229 00230 tag.clear(); 00231 itk::ExposeMetaData<std::string> ( *(*inputDict)[0], "0028|0011", tag ); 00232 this->m_Output->nCols = atoi( tag.c_str() ); 00233 00234 tag.clear(); 00235 itk::ExposeMetaData<std::string> ( *(*inputDict)[0], "0028|0030", tag ); 00236 sscanf( tag.c_str(), "%f\\%f", &this->m_Output->xRes, &this->m_Output->yRes ); 00237 00238 tag.clear(); 00239 itk::ExposeMetaData<std::string> ( *(*inputDict)[0], "0020|0032", tag ); 00240 sscanf( tag.c_str(), "%f\\%f\\%f", &this->m_Output->xOrigin, &this->m_Output->yOrigin, &this->m_Output->zOrigin ); 00241 00242 tag.clear(); 00243 itk::ExposeMetaData<std::string> ( *(*inputDict)[0], "0018|0050", tag ); 00244 this->m_Output->sliceThickness = atof( tag.c_str() ); 00245 00246 tag.clear(); 00247 itk::ExposeMetaData<std::string> ( *(*inputDict)[0], "0018|0088", tag ); 00248 this->m_Output->sliceSpacing = atof( tag.c_str() ); 00249 00250 // figure out how many slices are there in a volume, each unique 00251 // SliceLocation represent one slice 00252 for (int k = 0; k < m_nSlice; k++) 00253 { 00254 tag.clear(); 00255 itk::ExposeMetaData<std::string> ( *(*inputDict)[k], "0020|1041", tag); 00256 float sliceLocation = atof( tag.c_str() ); 00257 InsertUnique( m_sliceLocations, sliceLocation ); 00258 } 00259 00260 // check ImageOrientationPatient and figure out slice direction in 00261 // L-P-I (right-handed) system. 00262 // In Dicom, the coordinate frame is L-P by default. Look at 00263 // http://medical.nema.org/dicom/2007/07_03pu.pdf , page 301 00264 tag.clear(); 00265 itk::ExposeMetaData<std::string> ( *(*inputDict)[0], "0020|0037", tag ); 00266 float xRow, yRow, zRow, xCol, yCol, zCol, xSlice, ySlice, zSlice /*, orthoSliceSpacing*/; 00267 sscanf( tag.c_str(), "%f\\%f\\%f\\%f\\%f\\%f", &xRow, &yRow, &zRow, &xCol, &yCol, &zCol ); 00268 //std::cout << "ImageOrientationPatient (0020:0037): "; 00269 //std::cout << xRow << ", " << yRow << ", " << zRow << "; "; 00270 //std::cout << xCol << ", " << yCol << ", " << zCol << "\n"; 00271 00272 // In Dicom, the measurement frame is L-P by default. Look at 00273 // http://medical.nema.org/dicom/2007/07_03pu.pdf , page 301, in 00274 // order to make this compatible with Slicer's RAS frame, we 00275 // multiply the direction cosines by the negatives of the resolution 00276 // (resolution is required by nrrd format). Direction cosine is not 00277 // affacted since the resulting frame is still a right-handed frame. 00278 xRow = -xRow; 00279 yRow = -yRow; 00280 00281 xCol = -xCol; 00282 yCol = -yCol; 00283 00284 // Cross product, this gives I-axis direction 00285 xSlice = (yRow*zCol-zRow*yCol)*this->m_Output->sliceSpacing; 00286 ySlice = (zRow*xCol-xRow*zCol)*this->m_Output->sliceSpacing; 00287 zSlice = (xRow*yCol-yRow*xCol)*this->m_Output->sliceSpacing; 00288 00289 xRow *= this->m_Output->xRes; 00290 yRow *= this->m_Output->xRes; 00291 zRow *= this->m_Output->xRes; 00292 00293 xCol *= this->m_Output->yRes; 00294 yCol *= this->m_Output->yRes; 00295 zCol *= this->m_Output->yRes; 00296 00297 this->m_Output->xRow = xRow; 00298 this->m_Output->yRow = yRow; 00299 this->m_Output->zRow = zRow; 00300 this->m_Output->xCol = xCol; 00301 this->m_Output->yCol = yCol; 00302 this->m_Output->zCol = zCol; 00303 this->m_Output->xSlice = xSlice; 00304 this->m_Output->ySlice = ySlice; 00305 this->m_Output->zSlice = zSlice; 00306 00307 } 00308 00309 // nRows, nCols, xRes, yRes, xOrigin,yOrigin, 00310 // zOrigin, sliceThickness, sliceSpacing,nSliceInVolume, xRow, yRow, 00311 // zRow, xCol,yCol, zCol, xSlice, ySlice, zSlice,bValues[0], DiffusionVectors[0], 00312 // vendor,SliceMosaic 00313 00314 void mitk::DicomDiffusionImageHeaderReader::ReadPublicTags2() 00315 { 00316 00317 if (!m_SliceOrderIS) 00318 { 00319 this->m_Output->xSlice = -this->m_Output->xSlice; 00320 this->m_Output->ySlice = -this->m_Output->ySlice; 00321 this->m_Output->zSlice = -this->m_Output->zSlice; 00322 } 00323 00324 //std::cout << "Row: " << this->m_Output->xRow << ", " << this->m_Output->yRow << ", " << this->m_Output->zRow << std::endl; 00325 //std::cout << "Col: " << this->m_Output->xCol << ", " << this->m_Output->yCol << ", " << this->m_Output->zCol << std::endl; 00326 //std::cout << "Sli: " << this->m_Output->xSlice << ", " << this->m_Output->ySlice << ", " << this->m_Output->zSlice << std::endl; 00327 00328 //orthoSliceSpacing = fabs(zSlice); 00329 00330 //int nVolume; 00331 00332 //float maxBvalue = 0; 00333 //int nBaseline = 0; 00334 00335 } 00336 00337 void mitk::DicomDiffusionImageHeaderReader::TransformGradients() 00338 { 00339 // transform gradient directions into RAS frame 00340 if ( !m_SliceOrderIS ) 00341 { 00342 this->m_Output->DiffusionVector[2] = -this->m_Output->DiffusionVector[2]; // I -> S 00343 } 00344 } 00345
