X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=Example%2FPhilipsToBrucker.cxx;fp=Example%2FPhilipsToBrucker.cxx;h=0000000000000000000000000000000000000000;hb=317592bf538baef94dbc465c9bb1aea77e217d10;hp=a1cbe760c4ca4ff6492046818e8c62d46d797d71;hpb=ba4495175f2189e1cfba96f568d8c33053da8260;p=gdcm.git diff --git a/Example/PhilipsToBrucker.cxx b/Example/PhilipsToBrucker.cxx deleted file mode 100755 index a1cbe760..00000000 --- a/Example/PhilipsToBrucker.cxx +++ /dev/null @@ -1,437 +0,0 @@ -/*========================================================================= - - Program: gdcm - Module: $RCSfile: PhilipsToBrucker.cxx,v $ - Language: C++ - Date: $Date: 2006/01/26 15:52:42 $ - Version: $Revision: 1.6 $ - - 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 PhilipsToBrucker :\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, 0x1312) In-plane Phase Encoding Direction ", - " (0x0018, 0x1060) Trigger Time ", - " - 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 ! -", - " ", - " usage: ", - " PhilipsToBrucker dirin=rootDirectoryName ", - " dirout=outputDirectoryName ", - " { [keep= list of seriesNumber to process] ", - " | [drop= list of seriesNumber to ignore] } ", - " [extent=image suffix (.IMA, .NEMA, .DCM, ...)] ", - " [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 ", - " extent : DO NOT forget the leading '.' ! ", - " 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 - - // ----- 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(); - - bool verbose = am->ArgMgrDefined("verbose"); - - 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; - } - - 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; - exit(0); - } - else - { - std::cout << "OK : [" << dirNamein << "]" << " is a Directory" << std::endl; - } - - - std::string systemCommand; - if ( ! gdcm::DirList::IsDirectory(dirNameout) ) // dirout not found - { - std::string strDirNameout(dirNameout); // to please gcc 4 - systemCommand = "mkdir " +strDirNameout; // create it! - if (verbose) - std::cout << systemCommand << std::endl; - system (systemCommand.c_str()); - if ( ! gdcm::DirList::IsDirectory(dirNameout) ) // be sure it worked - { - std::cout << "KO : not a dir : [" << dirNameout << "] (creation failure ?)" << std::endl; - exit(0); - } - else - { - std::cout << "Directory [" << dirNameout << "]" << " created" << std::endl; - } - } - else - { - std::cout << "Output Directory [" << dirNameout << "]" << " already exists; Used as is." << std::endl; - } - std::string strDirNamein(dirNamein); - gdcm::DirList dirList(strDirNamein, true); // get recursively the list of files - -/* - std::cout << "---------------List of found files ------------" << std::endl; - dirList.Print(); - */ - - gdcm::DirListType fileNames; - fileNames = dirList.GetFilenames(); - gdcm::SerieHelper *s; // Needed only to may use SerieHelper::AddSeriesDetail() - s = gdcm::SerieHelper::New(); - -/* - std::cout << "---------------Print Serie--------------" << std::endl; - s->SetDirectory(dirNamein, true); // true : recursive exploration - s->SetUseSeriesDetails(true); - s->AddSeriesDetail(0x0018, 0x1312); - s->Print(); -*/ - - gdcm::File *f; - gdcm::FileHelper *fh; -/* - 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, 0x1312, false); // In-plane Phase Encoding Direction - s->AddSeriesDetail(0x0018, 0x1060, true); // Trigger Time - - for (gdcm::DirListType::iterator it = fileNames.begin(); - it != fileNames.end(); - ++it) - { - f = gdcm::File::New(); - f->SetLoadMode(loadMode); - f->SetFileName( *it ); - f->Load(); - - // keep only requested Series - std::string strSeriesNumber; - int seriesNumber; - int j; - - 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); - //std::cout << " [" << - // userFileIdentifier << "]" << std::endl; - - // storing in a map ensures automatic sorting ! - sf[userFileIdentifier] = f; - } - - std::vector tokens; - std::string fullFilename, lastFilename; - std::string previousPatientName, currentPatientName; - std::string previousSerieInstanceUID, currentSerieInstanceUID; - std::string previousImagePosition, currentImagePosition; - std::string previousPhaseEncodingDirection, currentPhaseEncodingDirection; - - std::string writeDir, currentWriteDir; - - writeDir = gdcm::Util::NormalizePath(dirNameout); - SortedFiles::iterator it2; - - previousPatientName = ""; - previousSerieInstanceUID = ""; - previousImagePosition = ""; - previousPhaseEncodingDirection = ""; - - int sliceIndex = 0; - int frameIndex = 0; - - gdcm::File *currentFile; - - for (it2 = sf.begin() ; it2 != sf.end(); ++it2) - { - currentFile = it2->second; - - fullFilename = currentFile->GetFileName(); - lastFilename = gdcm::Util::GetName( fullFilename ); - - - tokens.clear(); - gdcm::Util::Tokenize (it2->first, tokens, "_"); - - currentPatientName = tokens[0]; - currentSerieInstanceUID = tokens[1]; - currentImagePosition = tokens[2]; - currentPhaseEncodingDirection = tokens[3]; - - if (previousPatientName != currentPatientName) - { - previousPatientName = currentPatientName; - if (verbose) - std::cout << "==== new Patient " << currentPatientName << std::endl; - previousPatientName = currentPatientName; - previousSerieInstanceUID = ""; //currentSerieInstanceUID; - previousImagePosition = ""; //currentImagePosition; - previousPhaseEncodingDirection = ""; //currentPhaseEncodingDirection; - - currentWriteDir = writeDir + currentPatientName; - if ( ! gdcm::DirList::IsDirectory(currentWriteDir) ) - { - systemCommand = "mkdir " + currentWriteDir; - if (verbose) - std::cout << systemCommand << std::endl; - system ( systemCommand.c_str() ); - } - } - - if (previousSerieInstanceUID != currentSerieInstanceUID) - { - if (verbose) - std::cout << "==== === new Serie " << currentSerieInstanceUID - << std::endl; - previousSerieInstanceUID = currentSerieInstanceUID; - previousImagePosition = ""; //currentImagePosition; - previousPhaseEncodingDirection = ""; //currentPhaseEncodingDirection; - } - - if (previousImagePosition != currentImagePosition) - { - if (verbose) - std::cout << "=== === === new Position " << currentImagePosition - << std::endl; - previousImagePosition = currentImagePosition; - previousPhaseEncodingDirection = ""; //currentPhaseEncodingDirection; - sliceIndex += 1; - } - - if (previousPhaseEncodingDirection != currentPhaseEncodingDirection) - { - if (verbose) - std::cout << "==== === === === new PhaseEncodingDirection " - << currentPhaseEncodingDirection << std::endl; - previousPhaseEncodingDirection = currentPhaseEncodingDirection; - } - frameIndex++; - 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); - currentFile->InsertEntryString(fov, 0x0019, 0x1000, "DS"); - - // Deal with 0x0020, 0x0012 : 'SESSION INDEX' - std::string chSessionIndex; - if (currentPhaseEncodingDirection == "ROW") - chSessionIndex = "1"; - else - chSessionIndex = "2"; // suppose it's "COLUMN" ! - currentFile->InsertEntryString(chSessionIndex, 0x0020, 0x0012, "IS"); - - // Deal with 0x0021, 01020 : 'SLICE INDEX' - char chSliceIndex[5]; - sprintf(chSliceIndex, "%04d", sliceIndex); - std::string strChSliceIndex(chSliceIndex); - currentFile->InsertEntryString(strChSliceIndex, 0x0021, 0x1020, "IS"); - - // Deal with 0x0021, 01040 : 'FRAME INDEX' - char chFrameIndex[5]; - sprintf(chFrameIndex, "%04d", frameIndex); - currentFile->InsertEntryString(chFrameIndex, 0x0021, 0x1040, "IS"); - - std::string strExtent(extent); - std::string fullWriteFilename = currentWriteDir + 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); - fh->GetImageDataRaw(); // Don't convert (Gray Pixels + LUT) into (RGB pixels) ?!? - fh->SetWriteTypeToDcmExplVR(); - fh->Write(fullWriteFilename); - fh->Delete(); - } - }