X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=lib%2Fsrc1%2Fbruker2dicom.cxx;h=daf97a8fdcdc2159b34b43a395013f93f289a7af;hb=360e0f8bbbb16a0d7604e65e1059541a0e9d83c8;hp=bf947e7bee044ac51b33d73586e2d226edfe51bb;hpb=5a38892e9f13150c99d0af186aa8c0741146f9e4;p=creaBruker.git diff --git a/lib/src1/bruker2dicom.cxx b/lib/src1/bruker2dicom.cxx index bf947e7..daf97a8 100644 --- a/lib/src1/bruker2dicom.cxx +++ b/lib/src1/bruker2dicom.cxx @@ -83,7 +83,7 @@ bool Bruker2Dicom::Execute() switch (type) { - case 1: { + case 1: { bool canOpen = br_subject.LoadFile(subject); if (!canOpen) { @@ -221,7 +221,10 @@ 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' @@ -488,32 +491,32 @@ 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 { @@ -543,7 +546,7 @@ 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; - } + } } } } @@ -594,7 +597,7 @@ 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 +612,7 @@ 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 +661,7 @@ 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(); @@ -1196,7 +1199,7 @@ 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 +1222,7 @@ 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 +1284,10 @@ 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); } @@ -1364,7 +1367,7 @@ std::vector Bruker2Dicom::CreateImageSet ( ) br_acqp.SetLoopStructure(); std::vector tempVect = br_acqp.GetLoopStructure() ; std::map map = br_acqp.GetBrukerHeaderMap(); - + bool result = br_acqp.ObjectVaryingProperties.init(map,tempVect); if (result == false) @@ -1437,8 +1440,8 @@ 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 +1460,9 @@ 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 +1473,7 @@ 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 +1481,25 @@ 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 +1514,7 @@ 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 +1547,7 @@ 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 +1557,12 @@ 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 +1596,46 @@ 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"); 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"); 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"); 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"); const std::vector AoImages = brf_AoImages.GetIntValue(); - + 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 +1663,8 @@ 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!