X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=Example%2FBrukerToMhd.cxx;fp=Example%2FBrukerToMhd.cxx;h=a4be43e3a15bf370cd39a53c36590b932de63c94;hb=0928b363175e554f311cec5a173374d8ede1a7df;hp=0000000000000000000000000000000000000000;hpb=424aa9cf676116e2ab43f97334c159dccff15ed4;p=gdcm.git diff --git a/Example/BrukerToMhd.cxx b/Example/BrukerToMhd.cxx new file mode 100644 index 00000000..a4be43e3 --- /dev/null +++ b/Example/BrukerToMhd.cxx @@ -0,0 +1,519 @@ +/*========================================================================= + + Program: gdcm + Module: $RCSfile: BrukerToMhd.cxx,v $ + Language: C++ + Date: $Date: 2010/09/01 14:40:00 $ + Version: $Revision: 1.1 $ + + Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de + l'Image). All rights reserved. See Doc/License.txt or + http://www.creatis.insa-lyon.fr/Public/Gdcm/License.html for details. + + This software is distributed WITHOUT ANY WARRANTY; without even + the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR + PURPOSE. See the above copyright notices for more information. + +=========================================================================*/ + +/** + * Writes an old style Bruker Dicom file, InTag compliant, from a Raw File + * User has to supply parameters. + * + */ +#include "gdcmFile.h" +#include "gdcmFileHelper.h" +#include "gdcmDebug.h" +#include "gdcmUtil.h" +#include "gdcmDirList.h" + +#include "gdcmArgMgr.h" + +#include +#include + +void DealWithNiveau1(std::string level1Directory); +void DealWithNiveau2(std::string level2Directory); +void DealWithNiveau3(std::string level3Directory); +/** + * \brief + * - explores the given root directory e.g. : + * B67d1.Bp1 + * subject + * AdjStatePerStudy + * 1 + * acqp + * fid + * imnd + * pulseprogram + * spnam0 + * spnam1 + * pdata + * 1 + * 2dseq + * d3proc + * isa + * meta + * procs + * roi + * 2 + * ... + * + * 2 + * acqp + * fid + * ... + * pdata + * 3 + * ... + * - fills a single level Directory with *all* the files, + * converted into a Brucker-like Dicom, Intags compliant + */ + + + + +int main(int argc, char *argv[]) +{ + START_USAGE(usage) + " \n BrukerToMhd : \n ", + " - explores the given directory, at the 3 levels, ", + " - fills an equivalent Directory with the MHD files, ", + " converted into a Brucker-like Dicom, InTags compliant ", + " usage: BrukerToMhd dirin=rootDirectoryName ", + " dirout=outputDirectoryName ", + " [{b|l}] b:BigEndian,l:LittleEndian default : l ", + " [debug] [verbose] [listonly] ", + " ", + " debug : developper wants to run the program in 'debug mode' ", + FINISH_USAGE + + + // ------------ Initialize Arguments Manager ---------------- + GDCM_NAME_SPACE::ArgMgr *am= new GDCM_NAME_SPACE::ArgMgr(argc, argv); + + if (argc == 1 || am->ArgMgrDefined("usage") ) + { + am->ArgMgrUsage(usage); // Display 'usage' + delete am; + return 1; + } + + const char *dirNamein; + dirNamein = am->ArgMgrGetString("dirin","."); + + const char *dirNameout; + dirNameout = am->ArgMgrGetString("dirout","."); + + int b = am->ArgMgrDefined("b"); + int l = am->ArgMgrDefined("l"); + + if (am->ArgMgrDefined("debug")) + GDCM_NAME_SPACE::Debug::DebugOn(); + + int verbose = am->ArgMgrDefined("verbose"); + int listonly = am->ArgMgrDefined("listonly"); + + /* if unused Param we give up */ + if ( am->ArgMgrPrintUnusedLabels() ) + { + am->ArgMgrUsage(usage); + delete am; + return 1; + } + + delete am; // we don't need Argument Manager any longer + + // ----------- End Arguments Manager --------- + + + // ----- Begin Processing ----- + + + bool bigEndian = GDCM_NAME_SPACE::Util::IsCurrentProcessorBigEndian(); + + + if ( ! GDCM_NAME_SPACE::DirList::IsDirectory(dirNamein) ) + { + std::cout << "KO : [" << dirNamein << "] is not a Directory." << std::endl; + return 0; + + } + else + { + std::cout << "OK : [" << dirNamein << "] is a Directory." << std::endl; + } + + std::string systemCommand; + + std::cout << "Check for output directory :[" << dirNameout << "]." + <read((char*)pixels, (size_t)dataSizeIn); + + if ( pixelSize !=1 && ( (l && bigEndian) || (b && ! bigEndian) ) ) + { + ConvertSwapZone(pixelSize, pixels, dataSizeIn); + } + +if (verbose) + std::cout << "After ConvertSwapZone" << std::endl; + +// Copy (and convert) pixels of a single plane + + switch ( pixelTypeCode ) + { + case 8 : CFR(PU8); break; + case -8 : CFR(PS8); break; + case -16 : CFR(PU16); break; + case 16 : CFR(PS16); break; + case -32 : CFR(PS32); break; + case 32 : CFR(PU32); break; + case 33 : CFR(PF32); break; + case 64 : CFR(PD64); break; + } + +if (verbose) + std::cout << "After CFR" << std::endl; + +// Create an empty FileHelper + + GDCM_NAME_SPACE::FileHelper *fileH = GDCM_NAME_SPACE::FileHelper::New(); + + // Get the (empty) image header. + GDCM_NAME_SPACE::File *fileToBuild = fileH->GetFile(); + + // 'Study Instance UID' + // The user is allowed to create his own Study, + // keeping the same 'Study Instance UID' for various images + // The user may add images to a 'Manufacturer Study', + // adding new Series to an already existing Study + + fileToBuild->InsertEntryString(strStudyUID,0x0020,0x000d,"UI"); // Study UID + + // 'Serie Instance UID' + // The user is allowed to create his own Series, + // keeping the same 'Serie Instance UID' for various images + // The user shouldn't add any image to a 'Manufacturer Serie' + // but there is no way no to prevent him for doing that + + fileToBuild->InsertEntryString(strSerieUID,0x0020,0x000e,"UI"); // Serie UID + + std::ostringstream str; + + // Set the image size + str.str(""); + str << nX; + fileToBuild->InsertEntryString(str.str(),0x0028,0x0011, "US"); // Columns + str.str(""); + str << nY; + fileToBuild->InsertEntryString(str.str(),0x0028,0x0010, "US"); // Rows + + if (verbose) + std::cout << "before debut des choses serieuses2"<< std::endl; + +// str.str(""); +// str << nZ; +// fileToBuild->InsertEntryString(str.str(),0x0028,0x0008, "IS"); // Number of Frames + + // Set the pixel type + + str.str(""); + str << pixelSizeOut*8; + fileToBuild->InsertEntryString(str.str(),0x0028,0x0100, "US"); // Bits Allocated + + str.str(""); + str << pixelSizeOut*8; + fileToBuild->InsertEntryString(str.str(),0x0028,0x0101, "US"); // Bits Stored + + str.str(""); + str << ( pixelSizeOut*8 - 1 ); + fileToBuild->InsertEntryString(str.str(),0x0028,0x0102, "US"); // High Bit + + str.str(""); + str << pixelSign; + fileToBuild->InsertEntryString(str.str(),0x0028,0x0103, "US"); // Pixel Representation + +// If you deal with a Serie of images, as slices of a volume, +// it's up to you to tell gdcm, for each image, what are the values of : +// +// 0020 0032 DS 3 Image Position (Patient) +// 0020 0037 DS 6 Image Orientation (Patient) + + str.str(""); + str << "0.0\\0.0\\0.0"; + +// take Frame Index as position (we don't know anything else) NO! + + fileToBuild->InsertEntryString(str.str(),0x0020,0x0032, "DS"); + + fileToBuild->InsertEntryString("1.0\\0.0\\0.0\\0.0\\1.0\\0.0",0x0020,0x0037, "DS"); //[1\0\0\0\1\0] : Axial + + + + + str.str(""); + str << samplesPerPixel; + fileToBuild->InsertEntryString(str.str(),0x0028,0x0002, "US"); // Samples per Pixel + + if (strlen(patientName) != 0) + fileToBuild->InsertEntryString(patientName,0x0010,0x0010, "PN"); // Patient's Name + + // 0=white + if(monochrome1) + fileH->SetPhotometricInterpretationToMonochrome1(); + +// Special InTag, now. + + fileH->InsertEntryString(chSessionIndex, 0x0020, 0x0012, "IS"); + + // Deal with 0x0021, 0x1020 : 'SLICE INDEX' + // will stay to 0, since the stuff deals with single slice directories + char chSliceIndex[5]; + sprintf(chSliceIndex, "%04d", sliceIndex); + std::string strChSliceIndex(chSliceIndex); + + // Deal with 0x0021, 0x1040 : 'FRAME INDEX' + + str.str(""); + str << frameIndex; + frameIndex++; // be ready for next one + + fileH->InsertEntryString(strChSliceIndex, 0x0021, 0x1020, "IS"); + fileH->InsertEntryString(str.str(), 0x0021, 0x1040, "IS"); + + // Pixel Size + /// \TODO Ask user to supply 'Pixel Size' value + float pxSzX = 1.0; + float pxSzY = 1.0; + + // Field of view + char fov[64]; + sprintf(fov, "%f\\%f",nX*pxSzX, nY*pxSzY); + fileH->InsertEntryString(fov, 0x0019, 0x1000, "DS"); + + +// Set the image Pixel Data + fileH->SetImageData(planePixelsOut,singlePlaneDataSize); + +// Set the writting mode and write the image + fileH->SetWriteModeToRaw(); + + + + // Write a DICOM Explicit VR file + fileH->SetWriteTypeToDcmExplVR(); + + + outputFileName = strDirNameout + GDCM_NAME_SPACE::GDCM_FILESEPARATOR + *it + "_ForInTag.dcm"; + if( !fileH->Write(outputFileName ) ) + { + std::cout << "Failed for [" << outputFileName << "]\n" + << " File is unwrittable\n"; + } + +// End of : for (GDCM_NAME_SPACE::DirListType::iterator it = fileNames.begin() ... + + + + fileH->Delete(); + + delete[] pixels; + delete[] planePixelsOut; + } +*/ + // return 1; + } // end of : for (GDCM_NAME_SPACE::DirListType::iterator it + + + +void DealWithNiveau1(std::string level1Directory){ + + GDCM_NAME_SPACE::DirList dirList(level1Directory, false, true); // DON'T get recursively the list of files + + GDCM_NAME_SPACE::DirListType fileNames; + fileNames = dirList.GetFilenames(); + // ----------------------------------------------------- + // Iterate to ALL the objets(files/directories) found in the input directory + // ----------------------------------------------------- + GDCM_NAME_SPACE::DirListType::iterator it; + + for (it = fileNames.begin(); + it != fileNames.end(); + ++it) + { + if ( ! GDCM_NAME_SPACE::DirList::IsDirectory(*it) ) + { + std::cout << "--- [" << *it << "] is a file" << std::endl; + } + + } + + for (it = fileNames.begin(); + it != fileNames.end(); + ++it) + { + if ( GDCM_NAME_SPACE::DirList::IsDirectory(*it) ) + { + std::cout << "--- [" << *it << "] is a directory" << std::endl; + DealWithNiveau2(*it); + } + } +} + + +void DealWithNiveau2(std::string level2Directory){ + + GDCM_NAME_SPACE::DirList dirList(level2Directory, false, true); // DON'T get recursively the list of files + + GDCM_NAME_SPACE::DirListType fileNames; + fileNames = dirList.GetFilenames(); + + // ----------------------------------------------------- + // Iterate to ALL the objets(files/directories) found in the input directory + // ----------------------------------------------------- + GDCM_NAME_SPACE::DirListType::iterator it; + + for (it = fileNames.begin(); + it != fileNames.end(); + ++it) + { + if ( ! GDCM_NAME_SPACE::DirList::IsDirectory(*it) ) + { + std::cout << "--- --- [" << *it << "] is a file" << std::endl; + } + + } + + for (it = fileNames.begin(); + it != fileNames.end(); + ++it) + { + if ( GDCM_NAME_SPACE::DirList::IsDirectory(*it) ) + { + std::cout << "--- --- [" << *it << "] is a directory" << std::endl; + DealWithNiveau3(*it); + } + } +} + + +void DealWithNiveau3(std::string level3Directory){ + + GDCM_NAME_SPACE::DirList dirList(level3Directory, false, true); // DON'T get recursively the list of files + + GDCM_NAME_SPACE::DirListType fileNames; + fileNames = dirList.GetFilenames(); + + // ----------------------------------------------------- + // Iterate fo ALL the directories found in the input directory + // ----------------------------------------------------- + + for (GDCM_NAME_SPACE::DirListType::iterator it = fileNames.begin(); + it != fileNames.end(); + ++it) + { + + if ( ! GDCM_NAME_SPACE::DirList::IsDirectory(*it) ) + { + std::cout << "--- --- --- [" << *it << "] is a file" << std::endl; + } + else + { + std::cout << "--- --- --- [" << *it << "] is a directory" << std::endl; + + } + } +}