From: jpr <jpr>
Date: Fri, 9 Dec 2005 10:17:52 +0000 (+0000)
Subject: First check to extract overlays.
X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=commitdiff_plain;h=4c0fe0142482ede7dd8f5408f9303d78c213435b;p=gdcm.git

First check to extract overlays.
(Necessary, to visualize Scout views and/or results of medical processings
performed on clinical consoles)
---

diff --git a/Example/CMakeLists.txt b/Example/CMakeLists.txt
index 932776c8..0a9ede3b 100644
--- a/Example/CMakeLists.txt
+++ b/Example/CMakeLists.txt
@@ -12,7 +12,8 @@ SET(EXAMPLE_SOURCES
   exGrey2RGB
   exGC
   exImageLighten
-  exOverlaysACR
+  #exOverlaysACR
+  exOverlaysDCM
   exCurveData
   exExtractTag
   exSerieHelper
diff --git a/Example/exOverlaysDCM.cxx b/Example/exOverlaysDCM.cxx
new file mode 100755
index 00000000..5e5cdfaa
--- /dev/null
+++ b/Example/exOverlaysDCM.cxx
@@ -0,0 +1,219 @@
+/*=========================================================================
+                                                                                
+  Program:   gdcm
+  Module:    $RCSfile: exOverlaysDCM.cxx,v $
+  Language:  C++
+  Date:      $Date: 2005/12/09 10:17:52 $
+  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 "gdcmDocEntry.h"
+#include "gdcmDataEntry.h"
+
+#include <iostream>
+#include <stdio.h> // for fseek... FIXME
+#include <stdlib.h> // for atoi
+ 
+ // WARNING :
+ // unfinished : DO NOT to be used as is !
+ 
+
+int main(int argc, char *argv[])
+{  
+   gdcm::File *f;
+ 
+   //gdcm::Debug::DebugOn();
+
+   std::cout << "------------------------------------------------" << std::endl;
+   std::cout << "Gets the 'Overlays' from a full gdcm-readable DCM image "
+             << "uncompressed image" << std::endl;
+   std::cout << "Writes them in a DicomV3 file named 'gdcmOverlay.dcm'"
+             << std::endl;
+   std::cout << "------------------------------------------------" << std::endl;
+
+   std::string fileName;
+   if( argc > 1 )
+      fileName = argv[1];
+   else
+      fileName = "SIEMENS_GBS_III-16-ACR_NEMA_1.acr";  
+
+   std::cout << fileName << std::endl;
+// ============================================================
+//   Read the input image.
+// ============================================================
+
+   //std::cout << argv[1] << std::endl;
+
+   f = gdcm::File::New( );
+
+   f->SetLoadMode(gdcm::LD_ALL);
+   f->SetFileName( fileName );
+   f->AddForceLoadElement(0x6000,0x3000);  // Overlay Data
+   bool res = f->Load();  
+
+   if( gdcm::Debug::GetDebugFlag() )
+   {
+      std::cout << "---------------------------------------------" << std::endl;
+      f->Print();
+      std::cout << "---------------------------------------------" << std::endl;
+   }
+   if (!res) {
+       std::cout << "Sorry, " << fileName <<"  not a gdcm-readable "
+           << "DICOM / ACR File"
+           <<std::endl;
+      f->Delete();
+      return 0;
+   }
+   std::cout << " ... is readable " << std::endl;
+
+// ============================================================
+//   Check whether image contains Overlays ACR-NEMA style.
+// ============================================================
+
+   int bitsAllocated = f->GetBitsAllocated();
+   
+   gdcm::DataEntry *e = f->GetDataEntry(0x6000, 0x3000);
+   
+   if (e == 0)
+   {
+      std::cout << " Image doesn't contain any Overlay " << std::endl;
+      f->Delete();
+      return 0;
+   }
+   
+   std::cout << " File is read! " << std::endl;
+   
+// ============================================================
+//   Get usefull info from FileHelper.
+// ============================================================ 
+
+   
+   uint32_t overlayPixelLength = e->GetLength();
+   
+/*
+   if ( overlayPixelLength != (size_t)nx*ny*sizeof( uint16_t) )
+   {
+       std::cout << "Sorry, Pixels of" << fileName << "  are not "
+                 << "readable. expected length :" << nx*ny*sizeof( uint16_t) 
+                 << "  " << "read length : " << overlayPixelLength
+                 << std::endl;
+       f->Delete();
+       delete pixels;  
+       return 0;
+   }
+   else
+   {
+      std::cout << "Pixels read as expected : length = " << lgt << std::endl;
+   } 
+*/
+   uint32_t nx = f->GetXSize();
+   uint32_t ny = f->GetYSize();
+
+   uint8_t *overlayPixelArea = (uint8_t *)(e->GetBinArea());
+   
+   // should check overlayPixelLength == nx*ny/8 !)
+   
+   uint8_t *overlayPixelImage = new uint8_t[nx*ny];// uint8 is enough to hold 1 bit !
+   
+   uint16_t m;
+   for (unsigned int j=0; j<overlayPixelLength; j++)
+   {
+      if (overlayPixelArea[j] != 0)
+      { 
+         std::cout << "j : " << std::dec << j << " Ox(" << std::hex <<(int)overlayPixelArea[j]
+           << ")" << std::endl; 
+         for (unsigned int k=0; k<8; k++)
+         {
+            m = overlayPixelArea[j]<<k;
+            //printf("m : %04x ", m);
+            m = m & 0x00ff;
+            //printf(" : %04x \n", m);
+            overlayPixelImage[j*8 +k] =  ( m > 127)?255:0;
+    
+            printf("%04x ", overlayPixelImage[j*8 +k]);
+         }
+         std::cout << std::endl;
+      }
+   }
+
+
+   if( gdcm::Debug::GetDebugFlag() )
+         std::cout << "About to built empty file"  << std::endl;
+
+   gdcm::File *fileToBuild = gdcm::File::New();
+
+   if( gdcm::Debug::GetDebugFlag() )
+         std::cout << "Finish to built empty file"  << std::endl;
+
+   std::ostringstream str;
+   str.str("");
+   str << nx;
+   fileToBuild->InsertEntryString(str.str(),0x0028,0x0011); // Columns
+   str.str("");
+   str << ny;
+   fileToBuild->InsertEntryString(str.str(),0x0028,0x0010); // Rows
+
+   fileToBuild->InsertEntryString("8",0x0028,0x0100); // Bits Allocated
+   fileToBuild->InsertEntryString("8",0x0028,0x0101); // Bits Stored
+   fileToBuild->InsertEntryString("7",0x0028,0x0102); // High Bit
+   fileToBuild->InsertEntryString("0",0x0028,0x0103); // Pixel Representation
+   fileToBuild->InsertEntryString("1",0x0028,0x0002); // Samples per Pixel
+
+   fileToBuild->InsertEntryString("MONOCHROME2 ",0x0028,0x0004);
+      // Other mandatory fields will be set automatically,
+      // just before Write(), by FileHelper::CheckMandatoryElements()
+
+   if( gdcm::Debug::GetDebugFlag() )
+         std::cout << "-------------About to built FileHelper"  << std::endl;
+
+   gdcm::FileHelper *fh = gdcm::FileHelper::New(fileToBuild);
+
+   if( gdcm::Debug::GetDebugFlag() )
+         std::cout << "-------------Finish to built FileHelper"  << std::endl;
+
+      fh->SetImageData(overlayPixelImage,nx*ny);
+      fh->SetWriteTypeToDcmExplVR();
+
+      str.str("");
+      str<<"gdcmOverlay" << ".dcm";
+      //   Write the current 'overlay' file
+
+      if( !fh->Write(str.str()) )
+      {
+         std::cout << "Failed\n"
+                   << "File in unwrittable\n";
+         fh->Delete();
+         if (fileToBuild)
+            fileToBuild->Delete();
+         delete overlayPixelImage;
+         
+         return 0;
+      }
+      else
+      {
+         std::cout << "File written successfully" << std::endl;
+      }
+  
+   if (f)
+      fh->Delete();
+   if (fileToBuild)
+      fileToBuild->Delete();
+   f->Delete();
+   delete overlayPixelImage;
+   
+
+   return 0;
+}
+