From: jpr <jpr>
Date: Mon, 17 Jul 2006 13:21:05 +0000 (+0000)
Subject: Some old versions of VTK? ITK ? SeriesWriter weren't too much strict
X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=commitdiff_plain;h=7802cf7e80609b42a3d9ab4d175b69226dca584a;p=gdcm.git

Some old versions of VTK? ITK ? SeriesWriter weren't too much strict
 when they did the job.
 A lot of people has a lot of 'supposed to be Serie' directories
 that, actually, aren't at all.
 The following program converts them (hope so!)
---

diff --git a/Example/exMoveImagesToSingleSerieUID.cxx b/Example/exMoveImagesToSingleSerieUID.cxx
new file mode 100755
index 00000000..0e383413
--- /dev/null
+++ b/Example/exMoveImagesToSingleSerieUID.cxx
@@ -0,0 +1,312 @@
+/*=========================================================================
+                                                                                
+  Program:   gdcm
+  Module:    $RCSfile: exMoveImagesToSingleSerieUID.cxx,v $
+  Language:  C++
+  Date:      $Date: 2006/07/17 13:21:05 $
+  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.
+                                                                                
+=========================================================================*/
+/*
+Some old versions of VTK? ITK ? SeriesWriter weren't too much strict
+ when they did the job.
+ A lot of people has a lot of 'supposed to be Serie' directories
+ that, actually, aren't at all.
+ The following program converts them (hope so!)
+ 
+ Le programme 'de convertion' s'utilise comme les 'filtres LibIDO'
+(mots-clés et valeurs par defaut).
+
+exMoveImagesToSingleSerieUID
+                                     ",
+Converts the a Dicom file inside a single-level Directory
+ into a 'Single Study UID - Single SerieUID      
+  usage:
+exMoveImagesToSingleSerieUID
+      dirin=inputDirectoryName                                   
+      dirout=outputDirectoryName                                  
+       [studyUID = ] [patName = ] [Zspacing = ]
+       [ { [noshadowseq] | [noshadow][noseq] } ]  [debug]
+       [verbose]",
+
+
+  dirin : single-level Directory containing the images 
+           (no recursive parsing)
+  dirout : will be created if doesn't exist                
+  studyUID   : *aware* user wants to add the serie  
+                    to an already existing study 
+
+
+dirin : directory (un seul niveau) contenant les images
+dirout : directory de sortie (cree s'il n'existe pas); le nom des images
+est conservé.
+studyUID : si on veut *ajouter* la serie qui va etre creee a une study
+qui existe deja (il faut connaitre son Study UID)
+patName : nom du patient (ca peut servir pour y voir plus clair sur les
+logiciels cliniques)
+Zspacing : si c'est important pour la visu 3D. Ca servira a calculer le
+Slice Location (s'il n'existe pas deja) et la composante Z de
+ImagePositionPatient (s'il n'existe pas)
+
+// if Image Orientation (Patient) is not present
+//    I create one, (as Axial)
+//    if Image Position (Patient) is not present
+//       I create one, incrementing  zPositionComponent up by user
+supplied zSpacing
+//    if Slice Location is not present
+//       I create one, as zPositionComponent
+//
+*/
+#include "gdcmFile.h"
+#include "gdcmFileHelper.h"
+#include "gdcmCommon.h"
+#include "gdcmDebug.h"
+#include "gdcmDirList.h"
+#include "gdcmUtil.h"
+
+#include "gdcmArgMgr.h"
+
+#include <iostream>
+
+int main(int argc, char *argv[])
+{   
+   START_USAGE(usage)
+   "\n exMoveImagesToSingleSerieUID :\n                                       ",
+   " Converts the Dicom files inside a single-level Directory                 ",
+   " into a 'Single Study UID - Single SerieUID                               ",
+   " usage: exMoveImagesToSingleSerieUID                                      ",
+   "              dirin=inputDirectoryName                                    ",
+   "              dirout=outputDirectoryName                                  ",
+   "              [studyUID = ] [patName = ] [Zspacing = ]                    ",
+   "              [ { [noshadowseq] | [noshadow][noseq] } ]  [debug] [verbose]",
+   "                                                                          ",
+   "       dirin : single-level Directory containing the images               ",
+   "                                        (no recursive parsing)            ",   
+   "       dirout : will be created if doesn't exist                          ",
+   "                                                                          ",
+   "       studyUID   : *aware* user wants to add the serie                   ",
+   "                                             to an already existing study ",
+   "       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      : developper wants to run the program in 'debug mode'   ",
+   FINISH_USAGE
+   
+   
+     // ----- Initialize Arguments Manager ------
+  
+   gdcm::ArgMgr *am = new gdcm::ArgMgr(argc, argv);
+  
+   if (am->ArgMgrDefined("usage") || argc == 1) 
+   {
+      am->ArgMgrUsage(usage); // Display 'usage'
+      delete am;
+      return 0;
+   }
+
+   if (am->ArgMgrDefined("debug"))
+      gdcm::Debug::DebugOn(); 
+   int verbose  = am->ArgMgrDefined("verbose");
+   
+   std::string patName = am->ArgMgrGetString("patname", "g^PatientName");
+   float zSpacing = am->ArgMgrGetFloat("zSpacing", 1.0);
+      
+   const char *dirIn  = am->ArgMgrGetString("dirin");
+   const char *dirOut  = am->ArgMgrGetString("dirout");
+   
+   bool userDefinedStudy = am->ArgMgrDefined("studyUID");
+   const char *studyUID  = am->ArgMgrGetString("studyUID");
+
+// not described *on purpose* in the Usage ! 
+   bool userDefinedSerie = am->ArgMgrDefined("serieUID");   
+   const char *serieUID  = am->ArgMgrGetString("serieUID");      
+ 
+   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 unused Param we give up */
+   if ( am->ArgMgrPrintUnusedLabels() )
+   {
+      am->ArgMgrUsage(usage);
+      delete am;
+      return 0;
+   }
+
+   delete am;  // ------ we don't need Arguments Manager any longer ------
+   
+ // ====== Deal with a (single level, single Patient) Directory ======
+ 
+ 
+   //std::cout << "dirIn [" << dirIn << "]" << std::endl;
+   if ( ! gdcm::DirList::IsDirectory(dirIn) )
+   {
+      std::cout << "KO : [" << dirIn << "] is not a Directory." << std::endl;
+      return 0;
+
+   }
+   else
+   {
+      if (verbose)
+         std::cout << "OK : [" << dirIn << "] is a Directory." << std::endl;
+   }   
+  
+   std::string systemCommand;
+   std::string strDirNameout(dirOut);          // to please gcc 4   
+   std::cout << "Check for output directory :[" << dirOut << "]."
+             <<std::endl;
+   if ( ! gdcm::DirList::IsDirectory(dirOut) )    // dirout not found
+   {
+      systemCommand = "mkdir " +strDirNameout;        // create it!
+      if (verbose)
+         std::cout << systemCommand << std::endl;
+      system (systemCommand.c_str());
+      if ( ! gdcm::DirList::IsDirectory(dirOut) ) // be sure it worked
+      {
+          std::cout << "KO : not a dir : [" << dirOut << "] (creation failure ?)" << std::endl;
+      return 0;
+
+      }
+      else
+      {
+        if (verbose)
+           std::cout << "Directory [" << dirOut << "] created." << std::endl;
+      }
+   }
+   else
+   {
+      std::cout << "Output Directory [" << dirOut << "] already exists; Used as is." << std::endl;
+   }  
+
+   gdcm::DirList dirList(dirIn,false); // gets (at single level) the file list
+   gdcm::DirListType fileList = dirList.GetFilenames();
+
+   // '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
+   std::string strStudyUID;
+   if ( !userDefinedStudy)
+      strStudyUID =  gdcm::Util::CreateUniqueUID();
+   else
+      strStudyUID = studyUID;
+
+
+   // '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
+   
+   std::string strSerieUID; 
+   if ( !userDefinedSerie)   
+      strSerieUID =  gdcm::Util::CreateUniqueUID();
+   else      
+      strSerieUID = serieUID;
+        
+   gdcm::File *f;
+   gdcm::FileHelper *fh;
+   std::string fullFilename, lastFilename;
+   float zPositionComponent = 0.0;
+   
+   for( gdcm::DirListType::iterator it  = fileList.begin();
+                                 it != fileList.end();
+                                 ++it )
+   {
+      fullFilename = *it;
+      f = gdcm::File::New( );
+      f->SetLoadMode(loadMode);
+      f->SetFileName( it->c_str() );
+
+      if (verbose)
+         std::cout << "file [" << it->c_str() << "]" << std::endl;
+      if ( !f->Load() )
+      {
+         if (verbose)
+            std::cout << "fail to load [" << it->c_str() << "]" << std::endl;      
+         f->Delete();
+         continue;
+      }
+
+      // Load the pixels in RAM.    
+      
+      fh = gdcm::FileHelper::New(f);     
+      uint8_t *imageData = fh->GetImageDataRaw(); // Don't convert (Gray Pixels + LUT) into (RGB pixels) ?!?
+      if (!imageData)
+         std::cout << "fail to read [" << it->c_str() << std::endl;
+      fh->SetWriteTypeToDcmExplVR();
+
+      fh->InsertEntryString(strStudyUID,0x0020,0x000d,"UI");      
+      fh->InsertEntryString(strSerieUID,0x0020,0x000e,"UI");
+      fh->InsertEntryString(patName,0x0010,0x0010, "PN");   // Patient's Name
+
+// ==================================================================================================
+
+// This is a dirty heuristics, but no other way :-(
+
+// if Image Orientation (Patient) is not present
+//    I create one, (as Axial) 
+//    if Image Position (Patient) is not present
+//       I create one, incrementing  zPositionComponent up by user supplied zSpacing
+//    if Slice Location is not present 
+//       I create one, as zPositionComponent
+//
+// Aware use is free to supply his own one !    
+    
+      if (! f->CheckIfEntryExist(0x0020,0x0037) ) // 0020 0037 DS 6 Image Orientation (Patient)
+      {
+         fh->InsertEntryString("1.0\\0.0\\0.0\\0.0\\1.0\\0.0",0x0020,0x0037, "DS"); //[1\0\0\0\1\0] : Axial
+
+         char charImagePosition[256];
+     
+         sprintf(charImagePosition,"%f\\0.0\\0.0",zPositionComponent);
+         zPositionComponent += zSpacing;
+ 
+         if (! f->CheckIfEntryExist(0x0020,0x0032) ) //0020 0032 DS 3 Image Position (Patient)
+            fh->InsertEntryString(charImagePosition,0x0020,0x0032, "DS"); 
+    
+         if (! f->CheckIfEntryExist(0x0020,0x1041) ) // 0020 0x1041 DS 1 Slice Location
+         {
+            sprintf(charImagePosition,"%f",zPositionComponent);
+            fh->InsertEntryString(charImagePosition,0x0020,0x1041, "DS");
+          }    
+      } 
+
+// ==================================================================================================
+
+              
+      fh->SetContentType(gdcm::UNMODIFIED_PIXELS_IMAGE);
+      
+      lastFilename =  gdcm::Util::GetName( fullFilename );
+      std::string fullWriteFilename = strDirNameout + gdcm::GDCM_FILESEPARATOR 
+                                        + lastFilename;
+      if (verbose)
+         std::cout << "Write : [" << fullWriteFilename << "]" << std::endl;
+
+      if (!fh->Write(fullWriteFilename))
+      {
+         std::cout << "Fail to write :[" << fullWriteFilename << "]"
+                   << std::endl;
+      } 
+ 
+      fh->Delete();
+      f->Delete();
+   }
+}