Convert MRI Philips images into 'Brucker style' images, to make them InTag

processable.
-> First stage : deal with the filestore

diff --git a/Example/PhilipsToBrucker.cxx b/Example/PhilipsToBrucker.cxx
new file mode 100755 (executable)
index 0000000..9b20f74
--- /dev/null
+++ b/Example/PhilipsToBrucker.cxx
@@ -0,0 +1,249 @@
+/*=========================================================================
+                                                                                
+  Program:   gdcm
+  Module:    $RCSfile: PhilipsToBrucker.cxx,v $
+  Language:  C++
+  Date:      $Date: 2005/12/21 15:01:04 $
+  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.
+                                                                                
+=========================================================================*/
+#include "gdcmDocEntry.h"
+#include "gdcmDicomDir.h"
+#include "gdcmDicomDirPatient.h"
+#include "gdcmFile.h"
+#include "gdcmDirList.h"
+#include "gdcmDebug.h"
+#include "gdcmArgMgr.h"
+#include "gdcmUtil.h"
+#include "gdcmSerieHelper.h"
+
+#include <iostream>
+
+/**
+  * \brief   
+  *          - explores recursively the given directory
+  *          - keeps the requested series
+  *          - orders the gdcm-readable found Files
+  *            according 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<std::string, gdcm::File*> SortedFiles;
+
+int main(int argc, char *argv[]) 
+{
+/*
+   START_USAGE(usage)
+   " \n PhilipsToBrucker :\n                                                  ",
+   " Explores recursively the given directory,                                ",
+   "                                                                          ", 
+   " usage: PhilipsToBrucker dirin=rootDirectoryName                          ",
+   "                         dirout=outputDirectoryName                       ",
+   "        [noshadowseq][noshadow][noseq] [debug]                            ",
+   "                                                                          ",
+   "        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                    ",
+   "        debug    : user wants to run the program in 'debug mode'          ",
+   FINISH_USAGE
+*/
+const char **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;
+   }
+
+   char *dirNamein;   
+   dirNamein  = am->ArgMgrGetString("dirin",(char *)"."); 
+
+   char *dirNameout;   
+   dirNameout  = am->ArgMgrGetString("dirout",(char *)".");  
+   
+   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();
+ 
+   // 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 -----
+
+   std::string strDirNamein(dirNamein);
+   gdcm::DirList dirList(strDirNamein, true); 
+   
+ /*  
+   std::cout << "---------------File list found ------------" << std::endl;
+   dirList.Print();
+ */   
+
+   gdcm::DirListType fileNames;
+   fileNames = dirList.GetFilenames();
+   gdcm::SerieHelper *s;  
+   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;
+
+/*    
+   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();
+   }
+*/
+   
+   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)
+   {
+      //std::cout << "File Name : " << *it << std::endl;
+      f = gdcm::File::New();
+      f->SetLoadMode(gdcm::LD_ALL);
+      f->SetFileName( *it );
+      f->Load();
+
+      userFileIdentifier=s->CreateUserDefinedFileIdentifier(f);        
+      //std::cout << "                           [" <<
+      //        userFileIdentifier  << "]" << std::endl;
+      // storing in a map ensures automatic sorting !      
+      sf[userFileIdentifier] = f;
+   }
+      
+   std::vector<std::string> tokens;
+   std::string fullFilename;
+   std::string previousPatientName, currentPatientName;
+   std::string previousSerieInstanceUID, currentSerieInstanceUID;
+   std::string previousImagePosition, currentImagePosition;
+   std::string previousPhaseEncodingDirection, currentPhaseEncodingDirection;
+   
+   SortedFiles::iterator it2 = sf.begin();
+      
+   gdcm::Util::Tokenize (it2->first, tokens, "_");
+   
+   previousPatientName            = tokens[0];
+   previousSerieInstanceUID       = tokens[1];
+   previousImagePosition          = tokens[2];
+   previousPhaseEncodingDirection = tokens[3];
+   std::cout << "==== new Patient "                            << currentPatientName      << std::endl;   
+   std::cout << "==== === new Serie "                          << currentSerieInstanceUID << std::endl;
+   std::cout << "==== === === new Position "                   << currentImagePosition    << std::endl; 
+   std::cout << "==== === === === new PhaseEncodingDirection " << currentImagePosition    << std::endl;
+   std::cout << "==== === === ===    "                         << it2->first              << std::endl; 
+    
+   it2++;
+   
+   for ( ; it2 != sf.end(); ++it2)
+   {
+      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;
+         std::cout << "==== new Patient " << currentPatientName << std::endl;
+         previousPatientName            = currentPatientName;
+         previousSerieInstanceUID       = currentSerieInstanceUID;
+         previousImagePosition          = currentImagePosition;
+         previousPhaseEncodingDirection = currentPhaseEncodingDirection;
+      }
+
+      if (previousSerieInstanceUID != currentSerieInstanceUID)
+      {        
+         std::cout << "==== === new Serie " << currentSerieInstanceUID << std::endl;
+         previousSerieInstanceUID       = currentSerieInstanceUID;
+         previousImagePosition          = currentImagePosition;
+         previousPhaseEncodingDirection = currentPhaseEncodingDirection;
+      }
+
+      if (previousImagePosition != currentImagePosition)
+      {        
+         std::cout << "==== === === new Position " << currentImagePosition << std::endl;
+         previousImagePosition          = currentImagePosition;
+         previousPhaseEncodingDirection = currentPhaseEncodingDirection;
+      }      
+
+      if (previousPhaseEncodingDirection != currentPhaseEncodingDirection)
+      {        
+         std::cout << "==== === === === new PhaseEncodingDirection " << currentImagePosition << std::endl;
+         previousPhaseEncodingDirection = currentPhaseEncodingDirection;
+      } 
+      fullFilename =  (it2->second)->GetFileName();          
+      std::cout << "==== === === ===    " << it2->first << "  " << (it2->second)->GetFileName() << " " 
+                << gdcm::Util::GetName( fullFilename ) <<std::endl;
+      
+   }
+ }
+