X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=Example%2FWriteDicomAsJPEG2000.cxx;h=f66c7c30835d4d61fdcf2b6ef88571d3f3eca028;hb=3b1f653b219f72d841e3b52ef2ae20d2c7c91220;hp=ab27c4729493ecb999567b311cbae520de3ec790;hpb=a47eebc871810a0d4ce25ddfd5c9c21b9bcce811;p=gdcm.git

diff --git a/Example/WriteDicomAsJPEG2000.cxx b/Example/WriteDicomAsJPEG2000.cxx
index ab27c472..f66c7c30 100644
--- a/Example/WriteDicomAsJPEG2000.cxx
+++ b/Example/WriteDicomAsJPEG2000.cxx
@@ -3,8 +3,8 @@
   Program:   gdcm
   Module:    $RCSfile: WriteDicomAsJPEG2000.cxx,v $
   Language:  C++
-  Date:      $Date: 2006/07/12 09:35:38 $
-  Version:   $Revision: 1.2 $
+  Date:      $Date: 2007/08/29 08:13:40 $
+  Version:   $Revision: 1.10 $
                                                                                 
   Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
   l'Image). All rights reserved. See Doc/License.txt or
@@ -19,13 +19,15 @@
 #include "gdcmFile.h"
 #include "gdcmFileHelper.h"
 #include "gdcmUtil.h"
+#include "gdcmDebug.h"
 
-// Open a dicom file and compress it as JPEG 2000 stream
+// Open a dicom file and compress it as JPEG2000 stream
 int main(int argc, char *argv[])
 {
   if( argc < 2)
     {
-    std::cerr << argv[0] << " inputfilename.dcm\n";
+    std::cerr << argv[0] << " inputfilename.dcm [ outputfilename.dcm"
+              << " quality debug]\n";
     return 1;
     }
 
@@ -37,18 +39,17 @@ int main(int argc, char *argv[])
    if( argc >= 4 )
      quality = atoi(argv[3]);
    std::cerr << "Using quality: " << quality << std::endl;
-
-// Step 1 : Create the header of the image
-   //gdcm::File *f = new gdcm::File();
-   // gdcm1.3 syntax. Sorry
-   gdcm::File *f = gdcm::File::New();
-   f->SetLoadMode ( gdcm::LD_ALL ); // Load everything
+   
+   if (argc > 4)
+      GDCM_NAME_SPACE::Debug::DebugOn();
+      
+// Step 1 : Read the image
+   GDCM_NAME_SPACE::File *f = GDCM_NAME_SPACE::File::New();
+   f->SetLoadMode ( GDCM_NAME_SPACE::LD_ALL ); // Load everything
    f->SetFileName( filename );
    f->Load();
 
-   //gdcm::FileHelper *tested = new gdcm::FileHelper( f );
-   // gdcm1.3 syntax. Sorry   
-   gdcm::FileHelper *tested = gdcm::FileHelper::New( f );
+   GDCM_NAME_SPACE::FileHelper *tested = GDCM_NAME_SPACE::FileHelper::New( f );
    std::string PixelType = tested->GetFile()->GetPixelType();
    int xsize = f->GetXSize();
    int ysize = f->GetYSize();
@@ -56,96 +57,115 @@ int main(int argc, char *argv[])
    //tested->Print( std::cout );
 
    int samplesPerPixel = f->GetSamplesPerPixel();
-   size_t testedDataSize    = tested->GetImageDataSize();
-   uint8_t *testedImageData = tested->GetImageData();
-
-// Step 1 : Create the header of the image
-
-//   gdcm::File *fileToBuild = new gdcm::File();
-   // gdcm1.3 syntax. Sorry !
-   gdcm::File *fileToBuild = gdcm::File::New();
+   size_t testedDataSize    = tested->GetImageDataRawSize(); // Raw : Don't convert gray pixels+LUT to RBG pixels
+   uint8_t *testedImageData = tested->GetImageDataRaw();
    
+   if( GDCM_NAME_SPACE::Debug::GetDebugFlag() ) { 
+      tested->Print( std::cout );
+      std::cout << "-------------------------------------------------------------------------------" << std::endl;
+   }
+// Step 1 : Create the header of the new file
+   GDCM_NAME_SPACE::File *fileToBuild = GDCM_NAME_SPACE::File::New();
    std::ostringstream str;
 
    // Set the image size
    str.str("");
    str << xsize;
-   //fileToBuild->InsertValEntry(str.str(),0x0028,0x0011); // Columns
-   // gdcm1.3 syntax. Sorry !
-   fileToBuild->InsertEntryString(str.str(),0x0028,0x0011, "UI"); // Columns
+   fileToBuild->InsertEntryString(str.str(),0x0028,0x0011,"US"); // Columns
    str.str("");
    str << ysize;
-   //fileToBuild->InsertValEntry(str.str(),0x0028,0x0010); // Rows
-   // gdcm1.3 syntax. Sorry !
-   fileToBuild->InsertEntryString(str.str(),0x0028,0x0010, "UI"); // Rows
+   fileToBuild->InsertEntryString(str.str(),0x0028,0x0010,"US"); // Rows
 
    if(zsize>1)
    {
       str.str("");
       str << zsize;
-      //fileToBuild->InsertValEntry(str.str(),0x0028,0x0008); // Number of Frames
-   // gdcm1.3 syntax. Sorry !
-      fileToBuild->InsertEntryString(str.str(),0x0028,0x0008, "UI"); // Number of Frames
+      fileToBuild->InsertEntryString(str.str(),0x0028,0x0008,"IS"); // Number of Frames
    }
+
    int bitsallocated = f->GetBitsAllocated();
-   int bitsstored = f->GetBitsStored();
-   int highbit = f->GetHighBitPosition();
+   int bitsstored    = f->GetBitsStored();
+   int highbit       = f->GetHighBitPosition();
    //std::string pixtype = f->GetPixelType();
    int sign = f->IsSignedPixelData();
 
    // Set the pixel type
    str.str("");
    str << bitsallocated;
-   //fileToBuild->InsertValEntry(str.str(),0x0028,0x0100); // Bits Allocated
-   // gdcm1.3 syntax. Sorry !
-   fileToBuild->InsertEntryString(str.str(),0x0028,0x0100,"US"); // Bits Allocated
-   
+   fileToBuild->InsertEntryString(str.str(),0x0028,0x0100,"US");// Bits Allocated
    str.str("");
-   str << bitsstored;  
-   //fileToBuild->InsertValEntry(str.str(),0x0028,0x0101); // Bits Stored   
-   // gdcm1.3 syntax. Sorry !
-   fileToBuild->InsertEntryString(str.str(),0x0028,0x0101, "UI"); // Bits Stored
+   str << bitsstored;
+   fileToBuild->InsertEntryString(str.str(),0x0028,0x0101,"US");  // Bits Stored
+
    str.str("");
    str << highbit;
-   //fileToBuild->InsertValEntry(str.str(),0x0028,0x0102); // High Bit
-   // gdcm1.3 syntax. Sorry !
-   fileToBuild->InsertEntryString(str.str(),0x0028,0x0102, "UI"); // High Bit
+   fileToBuild->InsertEntryString(str.str(),0x0028,0x0102,"US"); // High Bit
 
    // Set the pixel representation
    str.str("");
    str << sign;
-   //fileToBuild->InsertValEntry(str.str(),0x0028,0x0103); // Pixel Representation
-   // gdcm1.3 syntax. Sorry !
-   fileToBuild->InsertEntryString(str.str(),0x0028,0x0103, "UI"); // Pixel Representation
-
+   fileToBuild->InsertEntryString(str.str(),0x0028,0x0103,"US"); // Pixel Representation
 
    // Set the samples per pixel
    str.str("");
    str << samplesPerPixel; //img.components;
-   //fileToBuild->InsertValEntry(str.str(),0x0028,0x0002); // Samples per Pixel
-   // gdcm1.3 syntax. Sorry !
-   fileToBuild->InsertEntryString(str.str(),0x0028,0x0002, "UI"); // Samples per Pixel
-
+   fileToBuild->InsertEntryString(str.str(),0x0028,0x0002,"US"); // Samples per Pixel
+
+// The image may be displayed uncorectly if these fields are missing
+
+   // Set the Pixel Aspect Ratio, if any
+   std::string par = f->GetEntryString(0x0028,0x0034);
+   std::cerr <<"Pixel Aspect Ratio [" << par << "]" << std::endl;
+   if ( par != GDCM_NAME_SPACE::GDCM_UNFOUND )
+      fileToBuild->InsertEntryString(par,0x0028,0x0034,"IS"); // Pixel Aspect Ratio
+
+   // Set the Modality, if any
+   std::string modality = f->GetEntryString(0x0008,0x0060);
+   std::cerr <<"Modality [" << modality << "]" << std::endl;
+   if ( modality != GDCM_NAME_SPACE::GDCM_UNFOUND )
+      fileToBuild->InsertEntryString(modality,0x0008,0x0060,"CS"); // Modality
+
+   // Set the Media Storage SOP Class UID, if any
+   std::string mssop = f->GetEntryString(0x0002,0x0002);
+   std::cerr <<"Media Storage SOP Class UID [" << mssop << "]" << std::endl;
+   if ( mssop != GDCM_NAME_SPACE::GDCM_UNFOUND )
+      fileToBuild->InsertEntryString(mssop,0x0002,0x0002,"UI"); // Media Storage SOP Class UID
+
+   // This one is mandatory to deal with Pixel Aspect Ratio, in ultrasound images !
+   // Set the SOP Class UID, if any
+   std::string sop = f->GetEntryString(0x0008,0x0016);
+   std::cerr <<"SOP Class UID [" << sop << "]" << std::endl;
+   if ( sop != GDCM_NAME_SPACE::GDCM_UNFOUND )
+      fileToBuild->InsertEntryString(sop,0x0008,0x0016,"UI"); // SOP Class UID
+     
 // Step 2 : Create the output image
-   //gdcm::FileHelper *fileH = new gdcm::FileHelper(fileToBuild);
-   // gdcm1.3 syntax. Sorry !
-   gdcm::FileHelper *fileH = gdcm::FileHelper::New(fileToBuild);
+   size_t size = xsize * ysize * zsize
+               * samplesPerPixel  * bitsallocated / 8;
+
+   GDCM_NAME_SPACE::FileHelper *fileH = GDCM_NAME_SPACE::FileHelper::New(fileToBuild);
+
+   // Consider that pixels are unmodified
+   fileH->SetContentType(GDCM_NAME_SPACE::UNMODIFIED_PIXELS_IMAGE);
+   std::cerr << "xsize " << xsize << " ysize " << ysize << " zsize " << zsize << " samplesPerPixel " << samplesPerPixel
+             << " bitsallocated " << bitsallocated << std::endl;
+   std::cerr << "size " << size << " testedDataSize " << testedDataSize <<
+                 std::endl;
+   assert(abs (size-testedDataSize) <= 1 );
    fileH->SetWriteTypeToJPEG2000(  );
-   fileH->SetImageData(testedImageData, testedDataSize);
+   //fileH->SetImageData(testedImageData, testedDataSize);
+
+   // SetUserData will ensure the compression
+   fileH->SetUserData(testedImageData, testedDataSize);
    if( !fileH->Write(outfilename) )
      {
      std::cerr << "write fails" << std::endl;
      }
-
-   //delete f;
-   // gdcm1.3 syntax. Sorry !   
+   
    f->Delete();
-   //delete tested;
    tested->Delete();
-   //delete fileToBuild;
    fileToBuild->Delete();
-   //delete fileH;
    fileH->Delete();
 
    return 0;
 }
+