X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=lib%2Fsrc1%2Fbruker2dicom.cxx;h=32cb9b29bb75041a6674d21063d7d330abfc6e6f;hb=fe149fbb0bb17796095186132dc484884e7e8be2;hp=0c8dbe526c1a7107e77be1f9026dabbb3d92e58b;hpb=7b7bbcd11996dd24d3b670c2befb7cdad14310b5;p=creaBruker.git diff --git a/lib/src1/bruker2dicom.cxx b/lib/src1/bruker2dicom.cxx index 0c8dbe5..32cb9b2 100644 --- a/lib/src1/bruker2dicom.cxx +++ b/lib/src1/bruker2dicom.cxx @@ -1,3 +1,29 @@ +/* + # --------------------------------------------------------------------- + # + # Copyright (c) CREATIS (Centre de Recherche en Acquisition et Traitement de l'Image + # pour la Santé) + # Authors : Eduardo Davila, Frederic Cervenansky, Claire Mouton + # Previous Authors : Laurent Guigues, Jean-Pierre Roux + # CreaTools website : www.creatis.insa-lyon.fr/site/fr/creatools_accueil + # + # This software is governed by the CeCILL-B license under French law and + # abiding by the rules of distribution of free software. You can use, + # modify and/ or redistribute the software under the terms of the CeCILL-B + # license as circulated by CEA, CNRS and INRIA at the following URL + # http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html + # or in the file LICENSE.txt. + # + # As a counterpart to the access to the source code and rights to copy, + # modify and redistribute granted by the license, users are provided only + # with a limited warranty and the software's author, the holder of the + # economic rights, and the successive licensors have only limited + # liability. + # + # The fact that you are presently reading this means that you have had + # knowledge of the CeCILL-B license and that you accept its terms. + # ------------------------------------------------------------------------ +*/ #include "bruker2dicom.h" #include #include @@ -9,6 +35,7 @@ bool Bruker2Dicom::Execute() { + int dimension = 1; // ----- Check input directory name ----- bool bigEndian = GDCM_NAME_SPACE::Util::IsCurrentProcessorBigEndian(); @@ -83,7 +110,7 @@ bool Bruker2Dicom::Execute() switch (type) { - case 1: { + case 1: { bool canOpen = br_subject.LoadFile(subject); if (!canOpen) { @@ -99,7 +126,7 @@ bool Bruker2Dicom::Execute() subject_name = b_name.GetStringValue()[0]; strPatientName = subject_name; cleanString(subject_name); - DealWithSingleStudyDirectory (fileNames); + DealWithSingleStudyDirectory (fileNames, dimension); } break; } @@ -107,13 +134,13 @@ bool Bruker2Dicom::Execute() case 2: { subject_name = "defaultPatName"; strPatientName = subject_name; - DealWithSingleStudyDirectory (fileNames); + DealWithSingleStudyDirectory (fileNames, dimension); break; } case 3: { std::cout << " User passed a 'non study' directory; Hope it's a *non recursive* 'set of studies' directory! (recursive not yet dealt with)" << std::endl; - DealWithMultiStudyDirectory (fileNames); + DealWithMultiStudyDirectory (fileNames, dimension); break; } } @@ -121,7 +148,7 @@ bool Bruker2Dicom::Execute() // ---------------------------------------------------------------------------------------------------------- -void Bruker2Dicom::DealWithMultiStudyDirectory (GDCM_NAME_SPACE::DirListType &dirNames) +void Bruker2Dicom::DealWithMultiStudyDirectory (GDCM_NAME_SPACE::DirListType &dirNames, int dimension) { GDCM_NAME_SPACE::DirListType::iterator it; @@ -164,7 +191,7 @@ void Bruker2Dicom::DealWithMultiStudyDirectory (GDCM_NAME_SPACE::DirListType &di subject_name = b_name.GetStringValue()[0]; strPatientName = subject_name; cleanString(subject_name); - DealWithSingleStudyDirectory(fileNames); + DealWithSingleStudyDirectory(fileNames,dimension); } } else @@ -177,12 +204,14 @@ void Bruker2Dicom::DealWithMultiStudyDirectory (GDCM_NAME_SPACE::DirListType &di // ---------------------------------------------------------------------------------------------------------- -void Bruker2Dicom::DealWithSingleStudyDirectory (GDCM_NAME_SPACE::DirListType &fileNames) +void Bruker2Dicom::DealWithSingleStudyDirectory (GDCM_NAME_SPACE::DirListType &fileNames, int dimension) { bool res; // creation directory : 'nom du patient' std::string tempStringPatDir(OutputDirName); - tempStringPatDir = tempStringPatDir + GDCM_NAME_SPACE::GDCM_FILESEPARATOR + subject_name; + + tempStringPatDir = tempStringPatDir + "/"+ subject_name; + //GDCM_NAME_SPACE::GDCM_FILESEPARATOR + subject_name; //FCY TO MODIFY res=CreateDirectory(tempStringPatDir); if (!res) { @@ -221,7 +250,10 @@ void Bruker2Dicom::DealWithSingleStudyDirectory (GDCM_NAME_SPACE::DirListType &f subject_study_name = "defStudyName"; // Why not? } // subject_name is already in 'Patient Name' - strStudyDescr = /*subject_name + "." + */ subject_study_name + "." + subject_entry + "." + subject_position + "." + subject_date; + if (0) // We don't realy need so much information for 'Study' + strStudyDescr = /*subject_name + "." + */ subject_study_name + "." + subject_entry + "." + subject_position + "." + subject_date; + else + strStudyDescr = /*subject_name + "." + */ subject_study_name /*+ "." + subject_entry + "." + subject_position + "." + subject_date*/; // creation directory : 'nom de la Study' @@ -316,7 +348,7 @@ void Bruker2Dicom::DealWithSingleStudyDirectory (GDCM_NAME_SPACE::DirListType &f if (verbose) printf ("outputDirName [%s]\n", outputDirName); try { - DealWithNiveau1(*it, strOutputDirName); + DealWithNiveau1(*it, strOutputDirName, dimension); } catch (BrukerHopelessException &e) { @@ -329,7 +361,7 @@ void Bruker2Dicom::DealWithSingleStudyDirectory (GDCM_NAME_SPACE::DirListType &f // ===================================================================== -void Bruker2Dicom::DealWithNiveau1(std::string &level1Directory, std::string ¤tOutputDirName) { +void Bruker2Dicom::DealWithNiveau1(std::string &level1Directory, std::string ¤tOutputDirName, int dimension) { // // e.g. : at level 1, in B67d1.Bp1/6 // @@ -431,7 +463,7 @@ void Bruker2Dicom::DealWithNiveau1(std::string &level1Directory, std::string &cu 7 1 */ try { - DealWithNiveau2(*it, strOutputDirName); + DealWithNiveau2(*it, strOutputDirName, dimension); } catch (BrukerHopelessException &e) { @@ -444,7 +476,7 @@ void Bruker2Dicom::DealWithNiveau1(std::string &level1Directory, std::string &cu // ===================================================================== -void Bruker2Dicom::DealWithNiveau2(std::string &level2Directory, std::string ¤tOutputDirName) { +void Bruker2Dicom::DealWithNiveau2(std::string &level2Directory, std::string ¤tOutputDirName, int dimension) { // e.g. : at level 2 in B67d1.Bp1/6/pdata // @@ -488,32 +520,32 @@ void Bruker2Dicom::DealWithNiveau2(std::string &level2Directory, std::string &cu ++it) { if ( boost::filesystem::is_directory(*it) ) - { - + { + if (verbose) std::cout << "--- --- [" << *it << "] is a directory" << std::endl; - // sprintf(outputDirName, "%s%c%s", currentOutputDirName.c_str(), + // sprintf(outputDirName, "%s%c%s", currentOutputDirName.c_str(), // GDCM_NAME_SPACE::GDCM_FILESEPARATOR, // GDCM_NAME_SPACE::Util::GetName(*it).c_str() ); // MUST be 'pdata'! // // (interest of previous method : -// If unaware user changed the pdata name, it goes on working +// If unaware user changed the pdata name, it goes on working // std::string str_isa; str_isa = (*it) + GDCM_NAME_SPACE::GDCM_FILESEPARATOR + "isa"; - std::string str_isa_func_name; + std::string str_isa_func_name; canOpen = br_isa.LoadFile(str_isa); if (!canOpen) { sprintf(outputDirName, "%s%c%s", currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR, - GDCM_NAME_SPACE::Util::GetName(*it).c_str() ); + GDCM_NAME_SPACE::Util::GetName(*it).c_str() ); } else { @@ -530,7 +562,7 @@ void Bruker2Dicom::DealWithNiveau2(std::string &level2Directory, std::string &cu } std::string strOutputDirName(outputDirName); try { - DealWithNiveau3(*it, strOutputDirName); + DealWithNiveau3(*it, strOutputDirName, dimension); } catch (BrukerHopelessException &e) { @@ -543,7 +575,7 @@ void Bruker2Dicom::DealWithNiveau2(std::string &level2Directory, std::string &cu std::cout << "And Init Exception was thrown in DealWithNiveau3 (" << e.what() << "); " << " We skip [" << level2Directory << "]" << std::endl; continue; - } + } } } } @@ -552,7 +584,7 @@ void Bruker2Dicom::DealWithNiveau2(std::string &level2Directory, std::string &cu // ===================================================================== // -void Bruker2Dicom::DealWithNiveau3(std::string &level3Directory, std::string ¤tOutputDirName){ +void Bruker2Dicom::DealWithNiveau3(std::string &level3Directory, std::string ¤tOutputDirName, int dimension){ // // e.g. at level 3, in @@ -594,7 +626,7 @@ void Bruker2Dicom::DealWithNiveau3(std::string &level3Directory, std::string &cu if (verbose) std::cout << "d3proc: --- => [" << char_d3proc << "]" << std::endl; - std::string str_d3proc(char_d3proc); + std::string str_d3proc(char_d3proc); canOpen = br_d3proc.LoadFile(str_d3proc); if (!canOpen) @@ -609,7 +641,7 @@ void Bruker2Dicom::DealWithNiveau3(std::string &level3Directory, std::string &cu { std::cout << "Hopeless! FillMap failed on 'd3proc'" << std::endl; throw ( BrukerHopelessException ("Hopeless! FillMap failed on 'd3proc'")); - //exit(0); /// \TODO throw an exception ! + //exit(0); /// \TODO throw an exception ! } //-------------- end try d3proc; @@ -658,7 +690,7 @@ void Bruker2Dicom::DealWithNiveau3(std::string &level3Directory, std::string &cu } else { if (verbose) std::cout << "[" << str_reco << "] successfully Mapped" << std::endl; - } + } //std::cout << "------------------------------------------------------------------------------------------------" << std::cout; // br_reco.PrintSelf(); @@ -717,20 +749,31 @@ void Bruker2Dicom::DealWithNiveau3(std::string &level3Directory, std::string &cu // Better we use 'get' accessors from BrukerImage class, as Denis wrote them BrukerFieldData fov = br_reco.GetFieldData("RECO_fov"); - double fovX = fov.GetDoubleValue()[0]; - double fovY = fov.GetDoubleValue()[1]; + + double fovX; + double fovY; + fovX= fov.GetDoubleValue()[0]; + if(fov.GetDoubleValue().size() > 1) + fovY = fov.GetDoubleValue()[1]; if (verbose) std::cout << "FOV (ds reco) " << fovX << " " << fovY << std::endl; BrukerFieldData size = br_reco.GetFieldData("RECO_size"); - double sizeX = size.GetDoubleValue()[0]; - double sizeY = size.GetDoubleValue()[1]; + double sizeX; + double sizeY; + sizeX = size.GetDoubleValue()[0]; + + if(fov.GetDoubleValue().size() > 1) + sizeY = size.GetDoubleValue()[1]; if (verbose) std::cout << "SIZE (ds reco) " << sizeX << " " << sizeY << std::endl; - double spatResolX = fovX / sizeX; - double spatResolY = fovY / sizeY; + double spatResolX; + double spatResolY; + spatResolX = fovX / sizeX; + if(fov.GetDoubleValue().size() > 1) + spatResolY = fovY / sizeY; if (verbose) std::cout << "spatResol (ds reco : fov/size) " << spatResolX << " " << spatResolY << std::endl; @@ -739,10 +782,12 @@ void Bruker2Dicom::DealWithNiveau3(std::string &level3Directory, std::string &cu /// \TODO probabely a more sophisticated accessor will be necessary : /// (cf : non contiguous slices, overlapping, slice thickness, space between slices, etc) - + double sliceDistance; + if(dimension > 1) + { BrukerFieldData bsliceDistance = br_method.GetFieldData("PVM_SPackArrSliceDistance"); - double sliceDistance = bsliceDistance.GetDoubleValue()[0]; - + sliceDistance = bsliceDistance.GetDoubleValue()[0]; + } if (verbose) std::cout << "SPackArrSliceDistance (ds method) " << sliceDistance << std::endl; @@ -770,6 +815,8 @@ void Bruker2Dicom::DealWithNiveau3(std::string &level3Directory, std::string &cu if (verbose) std::cout << "nbSlices " << nbSlices << std::endl; int k; + if(dimension ==1) + nbSlices = 1; int nbInstants = nbFrames/nbSlices; if (verbose) std::cout << "nbInstants (deduced)" << nbInstants << std::endl; @@ -807,7 +854,7 @@ void Bruker2Dicom::DealWithNiveau3(std::string &level3Directory, std::string &cu // This one will be important! // --------------------------- try { - imageSet = CreateImageSet ( ); + imageSet = CreateImageSet ( dimension); } catch (BrukerInitException& e) { @@ -1196,7 +1243,7 @@ void Bruker2Dicom::dealWithCarto(GDCM_NAME_SPACE::DirListType &fileNames, int NX int Bruker2Dicom::CheckUserDirectory(std::string &userDirName) { GDCM_NAME_SPACE::DirList dirList(userDirName, false, true); // DON'T get recursively the list of files - + GDCM_NAME_SPACE::DirListType fileNames; fileNames = dirList.GetFilenames(); @@ -1219,7 +1266,7 @@ int Bruker2Dicom::CheckUserDirectory(std::string &userDirName) acqpFound= true; // user passes a 'serie', not a 'study' else acqpFound = false; // user passed a 'non study' directory; Hope it's a 'set of studies' directory! - + int type; if (subjectFound ) type = 1; // user passed a 'study else if (acqpFound) type = 2; // user passed a 'serie' @@ -1281,10 +1328,10 @@ void Bruker2Dicom::cleanString(std::string &s) l--; s = s.substr(0, l); } - + if (s[0] == '<') s= s.substr(1,l-2); - std::string repChar("_"); + std::string repChar("_"); GDCM_NAME_SPACE::Util::ReplaceSpecChar(s, repChar); } @@ -1358,18 +1405,18 @@ void Bruker2Dicom::getImhDataType(BrukerFieldData &bDPT, std::string &mhdDataPix // =========================================================================================== -std::vector Bruker2Dicom::CreateImageSet ( ) +std::vector Bruker2Dicom::CreateImageSet ( int dimension) { std::vector imageSet; - br_acqp.SetLoopStructure(); + br_acqp.SetLoopStructure(dimension); std::vector tempVect = br_acqp.GetLoopStructure() ; std::map map = br_acqp.GetBrukerHeaderMap(); - + bool result = br_acqp.ObjectVaryingProperties.init(map,tempVect); if (result == false) { - throw ( BrukerInitException ("ObjectVaryingProperties.init() failure in Bruker2Dicom::CreateImageSet()") ); + throw ( BrukerInitException ("ObjectVaryingProperties.init() failure in Bruker2Dicom::CreateImageSet()") ); } br_acqp.SetImageLoopStructure(); @@ -1437,8 +1484,8 @@ void Bruker2Dicom::MakeDicomImage(unsigned char *tabPixels, std::ostringstream str; GDCM_NAME_SPACE::File *file; - file = GDCM_NAME_SPACE::File::New(); - + file = GDCM_NAME_SPACE::File::New(); + // Set the image size str.str(""); str << X; @@ -1457,7 +1504,9 @@ void Bruker2Dicom::MakeDicomImage(unsigned char *tabPixels, // Set the pixel type // //8, 16, 32, 64 (for double ?) str.str(""); - str << pixelSize*8; + str << pixelSize*8; + + // Bits Allocated file->InsertEntryString(str.str(),0x0028,0x0100,"US"); // Bits Allocated file->InsertEntryString(str.str(),0x0028,0x0101,"US"); // Bits Stored @@ -1468,7 +1517,7 @@ void Bruker2Dicom::MakeDicomImage(unsigned char *tabPixels, // Set the pixel representation // 0/1 , 0=unsigned file->InsertEntryString("1",0x0028,0x0103, "US"); // Pixel Representation - + // Set the samples per pixel // 1:Grey level, 3:RGB file->InsertEntryString("1",0x0028,0x0002, "US"); // Samples per Pixel @@ -1476,25 +1525,25 @@ void Bruker2Dicom::MakeDicomImage(unsigned char *tabPixels, str.str(""); str << spacingX << "\\" << spacingY; file->InsertEntryString(str.str(),0x0028,0x0030, "DS"); // Pixel Spacing - + // 0018 0050 DS 1 Slice Thickness str.str(""); str << sliceDistance; file->InsertEntryString(str.str(),0x0018,0x0050, "DS"); - + // 0020 0011 IS 1 Series Number str.str(""); str << serieNumber; file->InsertEntryString(str.str(),0x0020,0x0011, "IS"); - + // 0020|0013 [IS] [Instance Number] instanceNumber++; str.str(""); str << instanceNumber; file->InsertEntryString(str.str(),0x0020,0x0013, "IS"); - + // 1.2.840.10008.5.1.4.1.1.4.1 : Enhanced MR Image Storage - // file->InsertEntryString("1.2.840.10008.5.1.4.1.1.4.1" , 0x0002, 0x0002, "UI"); // [Media Storage SOP Class UID] + // file->InsertEntryString("1.2.840.10008.5.1.4.1.1.4.1" , 0x0002, 0x0002, "UI"); // [Media Storage SOP Class UID] // file->InsertEntryString("1.2.840.10008.5.1.4.1.1.4.1" , 0x0008, 0x0016, "UI"); // [SOP Class UID] // OK : MR is NOT multiframe, but I want just a quick an dirty solution @@ -1509,7 +1558,7 @@ void Bruker2Dicom::MakeDicomImage(unsigned char *tabPixels, file->InsertEntryString(studyUID, 0x0020, 0x000d, "UI"); file->InsertEntryString(serieUID, 0x0020, 0x000e, "UI"); - + // 0008 0020 DA 1 Study Date // 0008 0030 TM 1 Study Time @@ -1542,7 +1591,7 @@ std::cout << "charImageOrientation " << imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][0], imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][1], imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][2] ) ; - + file->InsertEntryString(charImageOrientation,0x0020,0x0037, "DS"); // 0020 0032 DS 3 Image Position (Patient) @@ -1552,13 +1601,12 @@ std::cout << "charImageOrientation " << imageSet[imgNum].getTranslationVectorRPS2XYZ()[0], imageSet[imgNum].getTranslationVectorRPS2XYZ()[1], imageSet[imgNum].getTranslationVectorRPS2XYZ()[2]); - + file->InsertEntryString(charImagePosition,0x0020,0x0032, "DS"); //0020 0032 DS 3 Image Position (Patient) - - + // Private creator /* - + 0029|0010 [LO] [Private Creator] [CREATIS HEADER ] 0029|0011 [LO] [Private Creator] [CREATIS for BRUKER to DICOM] 0029|1031 [LO] [] [4.0.7571167 ] @@ -1592,46 +1640,46 @@ std::cout << "charImageOrientation " << > 138 1600 > */ - + file->InsertEntryString("CREATIS HEADER", 0x0029,0x0010, "LO"); file->InsertEntryString("CREATIS FOR BRUKER-TO-DICOM", 0x0029,0x0011, "LO"); - - BrukerFieldData brf_method = br_method.GetFieldData("Method"); + + BrukerFieldData brf_method = br_method.GetFieldData("Method"); const std::vector method = brf_method.GetStringValue(); // std::string method = br_method.GetFieldData("Method").GetStringValue(); file->InsertEntryString(method[0], 0x0029,0x0100, "LO"); - + std::cout << " method[" << method[0] << "]" << std::endl; if (method[0] == "DtiEpi" || method[0] == "DtiStandard") { // const std::vector NDiffDir = br_method.GetFieldData("PVM_DwNDiffDir").GetIntValue(); - BrukerFieldData brf_NDiffDir = br_method.GetFieldData("PVM_DwNDiffDir"); + BrukerFieldData brf_NDiffDir = br_method.GetFieldData("PVM_DwNDiffDir"); const std::vector NDiffDir = brf_NDiffDir.GetIntValue(); - + //const std::vector NDiffExpEach = br_method.GetFieldData("PVM_DwNDiffExpEach").GetIntValue(); - BrukerFieldData brf_NDiffExpEach = br_method.GetFieldData("PVM_DwNDiffExpEach"); + BrukerFieldData brf_NDiffExpEach = br_method.GetFieldData("PVM_DwNDiffExpEach"); const std::vector NDiffExpEach =brf_NDiffExpEach.GetIntValue(); - + // const std::vector AoImages = br_method.GetFieldData("PVM_DwAoImages").GetIntValue(); - BrukerFieldData brf_AoImages = br_method.GetFieldData("PVM_DwAoImages"); + BrukerFieldData brf_AoImages = br_method.GetFieldData("PVM_DwAoImages"); const std::vector AoImages = brf_AoImages.GetIntValue(); - - BrukerFieldData brf_DwBvalEach = br_method.GetFieldData("PVM_DwBvalEach"); + + BrukerFieldData brf_DwBvalEach = br_method.GetFieldData("PVM_DwBvalEach"); const std::vector DwBvalEach = brf_DwBvalEach.GetDoubleValue(); - + std::cout << "nb directions : " << NDiffDir[0] << " nb valeurs de b par direction : " << NDiffExpEach[0] << " nb images for b=0 : " << AoImages[0] << std::endl; - + str.str(""); str << NDiffDir[0]; - file->InsertEntryString(str.str(),0x0029,0x0101,"US"); // directions + file->InsertEntryString(str.str(),0x0029,0x0101,"US"); // nb de directions str.str(""); str << NDiffExpEach[0]; - file->InsertEntryString(str.str(),0x0029,0x0102,"US"); // valeurs de b par direction + file->InsertEntryString(str.str(),0x0029,0x0102,"US"); // nb valeurs de b par direction str.str(""); str << AoImages[0]; - file->InsertEntryString(str.str(),0x0029,0x0103,"US"); // image pour b=0 + file->InsertEntryString(str.str(),0x0029,0x0103,"US"); // nb images pour b=0 str.str(""); for (unsigned int i=0; iInsertEntryString(str.str(),0x0029,0x0104,"DS"); // Valeurs de b + file->InsertEntryString(str.str(),0x0029,0x0104,"DS"); // Valeurs de b } // 0020 0x1041 DS 1 Slice Location @@ -1659,8 +1707,8 @@ std::cout << "charImageOrientation " << GDCM_NAME_SPACE::FileHelper *fileH; fileH = GDCM_NAME_SPACE::FileHelper::New(file); - fileH->SetContentType(contentType); - + fileH->SetContentType(contentType); + // cast is just to avoid warnings (*no* conversion is performed) //fileH->SetImageData((uint8_t *)img,int(maxX*maxY)*sizeof(uint16_t)); // troubles when maxX, mayY are *actually* float!