/*========================================================================= Program: gdcm Module: $RCSfile: ToInTag.cxx,v $ Language: C++ Date: $Date: 2006/06/08 13:41:28 $ Version: $Revision: 1.5 $ 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. =========================================================================*/ #include "gdcmDocEntry.h" #include "gdcmDicomDir.h" #include "gdcmDicomDirPatient.h" #include "gdcmFile.h" #include "gdcmFileHelper.h" #include "gdcmDirList.h" #include "gdcmDebug.h" #include "gdcmArgMgr.h" #include "gdcmUtil.h" #include "gdcmSerieHelper.h" #include /** * \brief * - explores recursively the given directory * - keeps the requested series * - orders the gdcm-readable found Files * according to their Patient/Study/Serie/Image characteristics * - fills a single level Directory with *all* the files, * converted into a Brucker-like Dicom, Intags compliant */ typedef std::map SortedFiles; int main(int argc, char *argv[]) { START_USAGE(usage) " \n ToInTag :\n ", " - explores recursively the given directory, ", " - keeps the requested series/ drops the unrequested series ", " - orders the gdcm-readable found Files according to their ", " (0x0010, 0x0010) Patient's Name ", " (0x0020, 0x000e) Series Instance UID ", " (0x0020, 0x0032) Image Position (Patient) ", " (0x0018, 0x1060) Trigger Time ", " (0x0018, 0x1312) In-plane Phase Encoding Direction ", " - fills a single level (*) Directory with *all* the files, ", " converted into a Brucker-like Dicom, InTags compliant ", " (*) actually : creates as many directories as Patients ", " -that shouldn't appear, but being carefull is better ! -", " or ", " - fills a tree-like structure of directories as : ", " - Patient ", " -- Serie ", " --- Position ", " Images are (sorted by Trigger Time / ", " Encoding Direction (Row, Column) ", " use : ", " 0x0021, 0x1020 : 'SLICE INDEX' ", " 0x0021, 0x1040 : 'FRAME INDEX' ", " 0x0020, 0x0012 : 'SESSION INDEX' (Acquisition Number) ", " usage: ", " PhilipsToBrucker dirin=rootDirectoryName ", " dirout=outputDirectoryName ", " { [keep= list of seriesNumber to process] ", " | [drop= list of seriesNumber to ignore] } ", " [taggrid] [skel] ", " [input = {ACR|DCM}] ", " [extent=image suffix (.IMA, .NEMA, .DCM, ...)] ", " [listonly] [split] ", " [noshadowseq][noshadow][noseq] [verbose] [debug] ", " ", " dirout : will be created if doesn't exist ", " keep : if user wants to process a limited number of series ", " he gives the list of 'SeriesNumber' (tag 0020|0011) ", " drop : if user wants to ignore a limited number of series ", " he gives the list of 'SeriesNumber' (tag 0020|0011) ", " SeriesNumber are short enough to be human readable ", " e.g : 1030,1035,1043 ", " taggrid : user knows all the images are 'grid' -ie : not 'col', not 'raw'", " extent : DO NOT forget the leading '.' ! ", " skel: name skeleton eg : patName_1.nema -> skel=patName_ ", " split: creates a tree-like structure of directories as : ", " - Patient ", " -- Serie ", " --- Position ", " Images are (sorted by Trigger Time / ", " Encoding Direction (Row, Column) ", " noshadowseq: user doesn't want to load Private Sequences ", " noshadow : user doesn't want to load Private groups (odd number) ", " noseq : user doesn't want to load Sequences ", " verbose : user wants to run the program in 'verbose mode' ", " debug : *developer* wants to run the program in 'debug mode' ", FINISH_USAGE std::cout << "inside ToInTag" << std::endl; // ----- Initialize Arguments Manager ------ gdcm::ArgMgr *am = new gdcm::ArgMgr(argc, argv); if (argc == 1 || am->ArgMgrDefined("usage")) { am->ArgMgrUsage(usage); // Display 'usage' delete am; return 0; } const char *dirNamein; dirNamein = am->ArgMgrGetString("dirin","."); const char *dirNameout; dirNameout = am->ArgMgrGetString("dirout","."); int loadMode = gdcm::LD_ALL; if ( am->ArgMgrDefined("noshadowseq") ) loadMode |= gdcm::LD_NOSHADOWSEQ; else { if ( am->ArgMgrDefined("noshadow") ) loadMode |= gdcm::LD_NOSHADOW; if ( am->ArgMgrDefined("noseq") ) loadMode |= gdcm::LD_NOSEQ; } if (am->ArgMgrDefined("debug")) gdcm::Debug::DebugOn(); int verbose = am->ArgMgrDefined("verbose"); int split = am->ArgMgrDefined("split"); int listonly = am->ArgMgrDefined("listonly"); int nbSeriesToKeep; int *seriesToKeep = am->ArgMgrGetListOfInt("keep", &nbSeriesToKeep); int nbSeriesToDrop; int *seriesToDrop = am->ArgMgrGetListOfInt("drop", &nbSeriesToDrop); if ( nbSeriesToKeep!=0 && nbSeriesToDrop!=0) { std::cout << "KEEP and DROP are mutually exclusive !" << std::endl; delete am; return 0; } int taggrid = am->ArgMgrDefined("taggrid"); int hasSkel = am->ArgMgrDefined("skel"); const char *skel; if (hasSkel) skel = am->ArgMgrGetString("skel"); const char *extent = am->ArgMgrGetString("extent",".DCM"); // if unused Param we give up if ( am->ArgMgrPrintUnusedLabels() ) { am->ArgMgrUsage(usage); delete am; return 0; } delete am; // we don't need Argument Manager any longer // ----- Begin Processing ----- if ( ! gdcm::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 << "]." <SetDirectory(dirNamein, true); // true : recursive exploration s->SetUseSeriesDetails(true); s->AddSeriesDetail(0x0018, 0x1312); s->Print(); */ gdcm::File *f; gdcm::FileHelper *fh; std::vector tokens; std::vector tokensForFileName; /* std::cout << "---------------Print Unique Series identifiers---------" << std::endl; std::string uniqueSeriesIdentifier; for (gdcm::DirListType::iterator it) = fileNames.begin(); it != fileNames.end(); ++it) { std::cout << "File Name : " << *it << std::endl; f = gdcm::File::New(); f->SetLoadMode(gdcm::LD_ALL); f->SetFileName( *it ); f->Load(); uniqueSeriesIdentifier=s->CreateUniqueSeriesIdentifier(f); std::cout << " [" << uniqueSeriesIdentifier << "]" << std::endl; f->Delete(); } */ if (verbose) std::cout << "------------------Print Break levels-----------------" << std::endl; std::string userFileIdentifier; SortedFiles sf; s->AddSeriesDetail(0x0010, 0x0010, false); // Patient's Name s->AddSeriesDetail(0x0020, 0x000e, false); // Series Instance UID s->AddSeriesDetail(0x0020, 0x0032, false); // Image Position (Patient) s->AddSeriesDetail(0x0018, 0x1060, true); // Trigger Time (true: convert to keep numerical order) s->AddSeriesDetail(0x0018, 0x1312, false); // In-plane Phase Encoding Direction //uint8_t *imageData; // Useless : pixels will not be loaded // (images are overwritten) for (gdcm::DirListType::iterator it = fileNames.begin(); it != fileNames.end(); ++it) { f = gdcm::File::New(); f->SetLoadMode(loadMode); f->SetFileName( *it ); f->Load(); std::string strSeriesNumber; int seriesNumber; int j; // keep only requested Series bool keep = false; if (nbSeriesToKeep != 0) { strSeriesNumber = f->GetEntryString(0x0020, 0x0011 ); seriesNumber = atoi( strSeriesNumber.c_str() ); for (j=0;jDelete(); continue; } } // drop all unrequested Series bool drop = false; if (nbSeriesToDrop != 0) { strSeriesNumber = f->GetEntryString(0x0020, 0x0011 ); seriesNumber = atoi( strSeriesNumber.c_str() ); for (j=0;jDelete(); continue; } } userFileIdentifier=s->CreateUserDefinedFileIdentifier(f); tokens.clear(); gdcm::Util::Tokenize (userFileIdentifier, tokens, token); int imageNum; // Within FileName char newName[1024]; if ( tokens[3] == "gdcmUnfound") // sometimes Trigger Time is not found. CreateUserDefinedFileIdentifier is not aware of the pb. { ///this is a trick to build up a lexicographical compliant name : /// eg : fich001.ima vs fich100.ima as opposed to fich1.ima vs fich100.ima std::string name = gdcm::Util::GetName( *it ); if (hasSkel) { gdcm::Util::Tokenize (name, tokensForFileName, skel); imageNum = atoi ( tokensForFileName[0].c_str() ); // probabely we could write something much more complicated using C++ ! sprintf (newName, "%s%06d%s", skel, imageNum, extent); tokens[3] = newName; tokensForFileName.clear(); } else tokens[3] = name; userFileIdentifier = tokens[0] + token + tokens[1] + token + tokens[2] + token + tokens[3] + token + tokens[4] + token; } if (verbose) std::cout << "[" << userFileIdentifier << "]" << std::endl; // storing in a map ensures automatic sorting ! sf[userFileIdentifier] = f; } std::string fullFilename, lastFilename; std::string previousPatientName, currentPatientName; std::string previousSerieInstanceUID, currentSerieInstanceUID; std::string previousImagePosition, currentImagePosition; std::string previousPhaseEncodingDirection, currentPhaseEncodingDirection; std::string previousTriggerTime, currentTriggerTime; std::string currentStudyUID; std::string writeDir, currentWriteDir; std::string currentPatientWriteDir, currentSerieWriteDir, currentPositionWriteDir, currentPhaseEncodingDirectionWriteDir; std::string fullWriteFilename; std::string strExtent(extent); writeDir = gdcm::Util::NormalizePath(dirNameout); SortedFiles::iterator it2; previousPatientName = ""; previousSerieInstanceUID = ""; previousImagePosition = ""; previousPhaseEncodingDirection = ""; previousTriggerTime = ""; int sliceIndex = 0; // Is incremented *at the beginning* of processing int frameIndex = 1; int flag = 0; gdcm::File *currentFile; std::string defaultStudyUID = gdcm::Util::CreateUniqueUID(); std::string defaultSerieUID; for (it2 = sf.begin() ; it2 != sf.end(); ++it2) { currentFile = it2->second; fullFilename = currentFile->GetFileName(); lastFilename = gdcm::Util::GetName( fullFilename ); std::cout << "Rewrite [" <first, tokens, token); currentPatientName = tokens[0]; currentSerieInstanceUID = tokens[1]; currentImagePosition = tokens[2]; currentTriggerTime = tokens[3]; currentPhaseEncodingDirection = tokens[4]; if ( currentImagePosition[0] == '-') currentImagePosition[0] = 'M'; if ( currentImagePosition[0] == '+') currentImagePosition[0] = 'P'; if (previousPatientName != currentPatientName) { if ( currentFile->GetEntryString(0x0020,0x000d) == gdcm::GDCM_UNFOUND) { if (verbose) std::cout << "--- new Study UID created" << std::endl; defaultStudyUID = gdcm::Util::CreateUniqueUID(); currentFile->InsertEntryString(defaultStudyUID, 0x0020, 0x000d, "UI" ); } previousPatientName = currentPatientName; if (verbose) std::cout << "==== new Patient [" << currentPatientName << "]" << std::endl; previousPatientName = currentPatientName; previousSerieInstanceUID = ""; //currentSerieInstanceUID; previousImagePosition = ""; //currentImagePosition; previousTriggerTime = ""; previousPhaseEncodingDirection = ""; //currentPhaseEncodingDirection; currentPatientWriteDir = writeDir + currentPatientName; //if ( ! gdcm::DirList::IsDirectory(currentPatientWriteDir) ) { systemCommand = "mkdir " + currentPatientWriteDir; if (verbose) std::cout << systemCommand << std::endl; system ( systemCommand.c_str() ); } } if (previousSerieInstanceUID != currentSerieInstanceUID) { if (verbose) std::cout << "==== === new Serie [" << currentSerieInstanceUID << "]" << std::endl; if ( currentFile->GetEntryString(0x0020,0x000e) == gdcm::GDCM_UNFOUND) { if (verbose) std::cout << "--- --- new Serie UID created" << std::endl; defaultSerieUID = gdcm::Util::CreateUniqueUID(); currentFile->InsertEntryString(defaultSerieUID, 0x0020, 0x000e, "UI" ); } if (split) { currentSerieWriteDir = currentPatientWriteDir + gdcm::GDCM_FILESEPARATOR + currentSerieInstanceUID; systemCommand = "mkdir " + currentSerieWriteDir; system (systemCommand.c_str()); } previousSerieInstanceUID = currentSerieInstanceUID; previousImagePosition = ""; //currentImagePosition; previousPhaseEncodingDirection = ""; //currentPhaseEncodingDirection; } if (previousImagePosition != currentImagePosition) { frameIndex = 1; flag = 0; if (verbose) std::cout << "=== === === new Position [" << currentImagePosition << "]" << std::endl; if (split) { currentPositionWriteDir = currentSerieWriteDir + gdcm::GDCM_FILESEPARATOR + currentImagePosition; systemCommand = "mkdir " + currentPositionWriteDir; system (systemCommand.c_str()); } previousImagePosition = currentImagePosition; previousPhaseEncodingDirection = ""; //currentPhaseEncodingDirection; if (split) sliceIndex = 1; // only *one* slice in a given directory else sliceIndex += 1; } // We don't split on Row/Column! /* if (previousPhaseEncodingDirection != currentPhaseEncodingDirection) { if (verbose) std::cout << "==== === === === new PhaseEncodingDirection [" << currentPhaseEncodingDirection << "]" << std::endl; if (split) { currentPhaseEncodingDirectionWriteDir = currentPositionWriteDir + gdcm::GDCM_FILESEPARATOR + currentPhaseEncodingDirection; systemCommand = "mkdir " + currentPhaseEncodingDirectionWriteDir; system (systemCommand.c_str()); } previousPhaseEncodingDirection = currentPhaseEncodingDirection; } */ if (verbose) std::cout << "--- --- --- --- --- " << (it2->second)->GetFileName() << std::endl; if ( gdcm::Debug::GetDebugFlag()) std::cout << "--- --- --- --- --- " << it2->first << " " << (it2->second)->GetFileName() << " " << gdcm::Util::GetName( fullFilename ) << std::endl; // Transform the image to be 'Brucker-Like' // ---------------------------------------- // Deal with 0x0019, 0x1000 : 'FOV' int nX = currentFile->GetXSize(); int nY = currentFile->GetYSize(); float pxSzX = currentFile->GetXSpacing(); float pxSzY = currentFile->GetYSpacing(); char fov[64]; sprintf(fov, "%f\\%f",nX*pxSzX, nY*pxSzY); if (currentFile->IsVRCoherent(0x0019) == 1 ) currentFile->InsertEntryString(fov, 0x0019, 0x1000, " "); else currentFile->InsertEntryString(fov, 0x0019, 0x1000, "DS"); // Deal with 0x0020, 0x0012 : 'SESSION INDEX' (Acquisition Number) std::string chSessionIndex; // CLEANME if (taggrid) chSessionIndex = "1"; else { if (currentPhaseEncodingDirection == "COL" || currentPhaseEncodingDirection == "COL " || currentPhaseEncodingDirection == " COL") chSessionIndex = "1"; else if (currentPhaseEncodingDirection == "ROW" || currentPhaseEncodingDirection == "ROW "|| currentPhaseEncodingDirection == " ROW") chSessionIndex = "2"; else { std::cout << "====================== PhaseEncodingDirection " << " neither COL nor ROW (?!?) : [ " << currentPhaseEncodingDirection << "]" << std::endl; chSessionIndex = "1"; } } if (currentFile->IsVRCoherent(0x0020) == 1 ) currentFile->InsertEntryString(chSessionIndex, 0x0020, 0x0012, " "); else currentFile->InsertEntryString(chSessionIndex, 0x0020, 0x0012, "IS"); // Deal with 0x0021, 0x1020 : 'SLICE INDEX' char chSliceIndex[5]; sprintf(chSliceIndex, "%04d", sliceIndex); std::string strChSliceIndex(chSliceIndex); // Deal with 0x0021, 0x1040 : 'FRAME INDEX' char chFrameIndex[5]; sprintf(chFrameIndex, "%04d", frameIndex); std::string stringVR; if (currentFile->IsVRCoherent(0x0021) == 1 ) stringVR = " "; else stringVR = "IS"; currentFile->InsertEntryString(strChSliceIndex, 0x0021, 0x1020, stringVR); currentFile->InsertEntryString(chFrameIndex, 0x0021, 0x1040, stringVR); std::string strImagePositionPatient = currentFile->GetEntryString(0x0020, 0x0032 ); if (strImagePositionPatient == gdcm::GDCM_UNFOUND) currentFile->InsertEntryString(currentFile->GetEntryString(0x0020, 0x0030), 0x0020, 0x0032, "DS" ); std::string strImageOrientationPatient = f->GetEntryString(0x0020, 0x0037 ); if (strImageOrientationPatient == gdcm::GDCM_UNFOUND) currentFile->InsertEntryString(currentFile->GetEntryString(0x0020, 0x0035), 0x0020, 0x0037, "DS" ); if (taggrid) frameIndex++; else { if (flag == 0) { flag = 1; } else { frameIndex++; flag = 0; } } if (split) //fullWriteFilename = currentPhaseEncodingDirectionWriteDir + gdcm::GDCM_FILESEPARATOR // + lastFilename + strExtent; fullWriteFilename = currentPositionWriteDir + gdcm::GDCM_FILESEPARATOR + lastFilename + strExtent; else fullWriteFilename = currentPatientWriteDir + gdcm::GDCM_FILESEPARATOR + lastFilename + strExtent; /* systemCommand = "cp " + fullFilename + " " + fullWriteFilename; std::cout << systemCommand << std::endl; system ( systemCommand.c_str() ); */ // Load the pixels in RAM. fh = gdcm::FileHelper::New(currentFile); uint8_t *imageData = fh->GetImageDataRaw(); // Don't convert (Gray Pixels + LUT) into (RGB pixels) ?!? fh->SetWriteTypeToDcmExplVR(); // We didn't modify pixels -> keep unchanged the following : // 'Media Storage SOP Class UID' (0x0002,0x0002) // 'SOP Class UID' (0x0008,0x0016) // 'Image Type' (0x0008,0x0008) // 'Conversion Type' (0x0008,0x0064) // Put to Black the burnt-in number. nX = currentFile->GetXSize(); nY = currentFile->GetYSize(); for(int y=nY-15; ySetContentType(gdcm::UNMODIFIED_PIXELS_IMAGE); if (!fh->Write(fullWriteFilename)) { std::cout << "Fail to write :[" << fullWriteFilename << "]" << std::endl; } fh->Delete(); } return 0; }