Add a small utility to extract (and create DICOM images) the overlays from all the

images within a directory

diff --git a/Example/ExtractOverlays.cxx b/Example/ExtractOverlays.cxx
new file mode 100755 (executable)
index 0000000..14d89d9
--- /dev/null
+++ b/Example/ExtractOverlays.cxx
@@ -0,0 +1,222 @@
+/*=========================================================================
+                                                                                
+  Program:   gdcm
+  Module:    $RCSfile: ExtractOverlays.cxx,v $
+  Language:  C++
+  Date:      $Date: 2007/03/16 15:14:37 $
+  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 "gdcmFile.h"
+#include "gdcmFileHelper.h"
+#include "gdcmCommon.h"
+#include "gdcmDebug.h"
+#include "gdcmDataEntry.h"
+#include "gdcmDirList.h"
+
+#include "gdcmArgMgr.h"
+#include <iostream>
+
+// Each BIT of Overlay Data (0x6000,0x3000) corresponds 
+// to a BYTE of overlay image.
+void explodeByte(unsigned char byte, unsigned char* result) 
+{
+   unsigned char mask = 1;
+   for (int i=0;i<8;i++) 
+   {
+      if ((byte & mask)==0) 
+         result[i]=0;
+      else 
+         result[i]=1;
+      mask<<=1;
+   }
+   return;
+}
+
+
+int main(int argc, char *argv[])
+{
+   START_USAGE(usage)
+   " \n ExtractOverlays :\n                                                   ",
+   " Extract overlay images from all DICOM image within a directory           ",
+   "          Warning : probably segfaults if no overlay                      ",
+   " usage: ExtractOverlays dirin=inputDirectoryName  [debug]                 ",
+   "        debug    : developper 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 *dirIn  = am->ArgMgrWantString("dirin", usage);
+
+   if (am->ArgMgrDefined("debug"))
+      gdcm::Debug::DebugOn();
+      
+   if (am->ArgMgrDefined("warning"))
+      gdcm::Debug::WarningOn();
+      
+   // 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
+
+
+   // ========================== Now, we can do the job! ================ 
+
+
+   // ======================== more checking on the params ==============
+
+   if ( ! gdcm::DirList::IsDirectory(dirIn) )
+   {
+      std::cout << "KO : [" << dirIn << "] is not a Directory." << std::endl;
+      return 0;
+
+   }
+ 
+   char outputFileName[1024]; // Hope it's enough for a file name!
+   
+   gdcm::File *f;
+        
+   gdcm::DirList dirList(dirIn,true); // gets (recursively) the file list
+   gdcm::DirListType fileList = dirList.GetFilenames();
+   for( gdcm::DirListType::iterator it  = fileList.begin();
+                                 it != fileList.end();
+                                 ++it )
+   {
+   //   Just to see *all* the file names:
+   //   std::cout << "file [" << it->c_str() << "]" << std::endl;     
+   
+   //   Read the input file.
+
+   f = gdcm::File::New(  );
+   f->SetLoadMode( gdcm::LD_ALL );
+   f->SetFileName( it->c_str() );
+   
+   f->AddForceLoadElement(0x6000,0x3000);  // Overlay Data
+   f->AddForceLoadElement(0x6002,0x3000); 
+   f->AddForceLoadElement(0x6004,0x3000); 
+   f->AddForceLoadElement(0x6006,0x3000);    
+   f->AddForceLoadElement(0x6008,0x3000);    
+   f->AddForceLoadElement(0x600a,0x3000); 
+   f->AddForceLoadElement(0x600c,0x3000); 
+   f->AddForceLoadElement(0x600e,0x3000);
+             
+   int res = f->Load();
+
+   if ( !res )
+   {
+       std::cerr << "Sorry, " << it->c_str() <<"  not a gdcm-readable "
+                 << "DICOM / ACR File" <<std::endl;
+       f->Delete();
+       continue;
+   }
+   std::cout << " ... is readable " << std::endl;
+
+   // ============================================================
+   //   Load the Overlays in memory (the first one)
+   // ============================================================
+
+/// \todo : deal with *each* overlay Data Element (not only the first one!)
+
+   unit16_t ovlyGroup = 0x6000;
+
+   gdcm::DataEntry *e = f->GetDataEntry(ovlyGroup, 0x3000);  
+   if (e == 0)
+   {
+      std::cout << " Image doesn't contain any Overlay " << std::endl;
+      f->Delete();
+      continue;
+   }   
+   std::cout << " File is read! " << std::endl;
+
+   uint8_t *overlay = (uint8_t *)(e->GetBinArea());
+   if ( overlay == 0 )
+   {
+       std::cerr << "Sorry, Overlays of" << it->c_str() <<"  are not "
+                 << " gdcm-readable."    << std::endl;
+       f->Delete();
+       continue;
+   }
+
+   // ============================================================
+   //  Image data generation.
+   // ============================================================   
+
+   unsigned int dimX= f->GetXSize();
+   unsigned int dimY= f->GetYSize();
+
+   unsigned int dimXY=dimX*dimY;
+   std::cout << "DimX : "<< dimX <<" DimY : " << dimY 
+             << " DimXY : " <<dimXY << std::endl;
+   unsigned char *outputData = new unsigned char[dimXY];
+
+   unsigned char *result=outputData;
+   for (unsigned int i=0;i<(dimXY/8);i++) 
+   {
+      explodeByte(overlay[i], result);
+      result+=8;
+   }
+   
+   // ============================================================
+   //   Write a new file
+   // ============================================================
+   gdcm::File *f2;
+   f2 = gdcm::File::New(  );
+   
+   char temp[256];
+   
+   sprintf(temp,"%d ",dimX);
+   f2->InsertEntryString(temp,0x0028,0x0011, "US"); // Columns
+   sprintf(temp,"%d ",dimY);
+   f2->InsertEntryString(temp,0x0028,0x0010, "US"); // Rows
+
+   f2->InsertEntryString("8",0x0028,0x0100, "US"); // Bits Allocated
+   f2->InsertEntryString("8",0x0028,0x0101, "US"); // Bits Stored
+   f2->InsertEntryString("7",0x0028,0x0102, "US"); // High Bit
+   f2->InsertEntryString("0",0x0028,0x0103, "US"); // Pixel Representation
+   f2->InsertEntryString("1",0x0028,0x0002, "US"); // Samples per Pixel
+   f2->InsertEntryString("MONOCHROME2 ",0x0028,0x0004, "LO");  
+   
+   sprintf(outputFileName, "%s.ovly.dcm",it->c_str() );
+
+   // feel free to add any field (Dicom Data Entry) you like, here.
+   // ...
+   gdcm::FileHelper *fh = gdcm::FileHelper::New(f2);
+       
+   fh->SetImageData(outputData,dimXY);
+   fh->WriteDcmExplVR(outputFileName);
+   std::cout <<"End WriteOverlayImage" << std::endl;
+
+   delete outputData;
+   f->Delete();
+   f2->Delete();  
+   fh->Delete();
+   
+}  // end of loop on files
+ 
+   return 0;
+}
+