Trying to normalize JPEG Writing (not yet finished)

diff --git a/src/gdcmDataEntry.cxx b/src/gdcmDataEntry.cxx
index 5678ac8f5290a8464aaacc03302674ac6bf25f82..9e35cc59477afef874e9f71c6d5b90cb2cb9c061 100644 (file)
--- a/src/gdcmDataEntry.cxx
+++ b/src/gdcmDataEntry.cxx
@@ -3,8 +3,8 @@
   Program:   gdcm
   Module:    $RCSfile: gdcmDataEntry.cxx,v $
   Language:  C++
-  Date:      $Date: 2007/08/22 16:14:03 $
-  Version:   $Revision: 1.45 $
+  Date:      $Date: 2007/08/27 16:14:47 $
+  Version:   $Revision: 1.46 $
                                                                                 
   Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
   l'Image). All rights reserved. See Doc/License.txt or
@@ -90,7 +90,10 @@ DataEntry::~DataEntry ()
 /**
  * \brief Sets the value (non string) of the current DataEntry
  * @param area area
- * @param self self
+ * @param self self=true : The area : *belongs" to the DataEntry 
+ *                                  : will be delete with the DataEntry
+ *             self=false  The area *is not* deleted with the DataEntry
+ *              
  */
 void DataEntry::SetBinArea( uint8_t *area, bool self )  
 { 
@@ -118,7 +121,7 @@ void DataEntry::CopyBinArea( uint8_t *area, uint32_t length )
       NewBinArea();
       memcpy(BinArea,area,length);
       if( length!=lgh )
-         BinArea[length]=0;
+         BinArea[length]=0; // padd with zero
 
       State = STATE_LOADED;
    }

diff --git a/src/gdcmFile.cxx b/src/gdcmFile.cxx
index 0d1072a0db2b98ae629aec819a1303f5b4a327bb..2fe57fcc54bb20c9d5c34c4aac29f1ec156f5194 100644 (file)
--- a/src/gdcmFile.cxx
+++ b/src/gdcmFile.cxx
@@ -3,8 +3,8 @@
   Program:   gdcm
   Module:    $RCSfile: gdcmFile.cxx,v $
   Language:  C++
-  Date:      $Date: 2007/08/24 10:45:18 $
-  Version:   $Revision: 1.335 $
+  Date:      $Date: 2007/08/27 16:14:47 $
+  Version:   $Revision: 1.336 $
                                                                                 
   Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
   l'Image). All rights reserved. See Doc/License.txt or
@@ -1997,10 +1997,10 @@ bool File::Write(std::string fileName, FileType writetype)
    }
 
    /// \todo FIXME : Derma?.dcm does not have it...let's remove it ?!? JPRx
-   if( writetype != JPEG )
+   if( writetype != JPEG && writetype != JPEG2000)
    {
       int i_lgPix = GetEntryLength(GrPixel, NumPixel);
-      if (i_lgPix != -2)
+      if (i_lgPix != -2)  /// \todo wtf "-2" ?!?
       {
          // no (GrPixel, NumPixel) element
          std::string s_lgPix = Util::Format("%d", i_lgPix+12);

diff --git a/src/gdcmFileHelper.cxx b/src/gdcmFileHelper.cxx
index 997c37a24772dc16733a61a46240930eb1092e2b..6c2c3f86e42db278afb929c52b2f3cb165f5912f 100644 (file)
--- a/src/gdcmFileHelper.cxx
+++ b/src/gdcmFileHelper.cxx
@@ -4,8 +4,8 @@
   Module:    $RCSfile: gdcmFileHelper.cxx,v $
   Language:  C++
 
-  Date:      $Date: 2007/08/24 10:45:18 $
-  Version:   $Revision: 1.121 $
+  Date:      $Date: 2007/08/27 16:14:47 $
+  Version:   $Revision: 1.122 $
                                                                                 
   Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
   l'Image). All rights reserved. See Doc/License.txt or
@@ -97,7 +97,6 @@ fh->Write(newFileName);      // overwrites the file, if any
 
 
 
-// ----------------------------- WARNING -------------------------
 
 These lines will be moved to the document-to-be 'Developer's Guide'
 
@@ -105,7 +104,12 @@ WriteMode : WMODE_RAW / WMODE_RGB
 WriteType : ImplicitVR, ExplicitVR, ACR, ACR_LIBIDO
 PhotometricInterpretation : MONOCHROME2 (0=black), MONOCHROME2 (0=white)
 
-
+fh->SetImageData( userPixels, userPixelsLength);
+or
+fh->SetUserData( userPixels, userPixelsLength);
+   PixelWriteConverter->SetUserData(inData, expectedSize);
+   
+   
 fh->SetWriteMode(WMODE_RAW / WMODE_RGB)
 
 fh->SetWriteType( ImplicitVR/ExplicitVR/ACR/ACR_LIBIDO/JPEG/JPEG2000)
@@ -509,6 +513,8 @@ size_t FileHelper::GetImageDataIntoVector (void *destination, size_t maxSize)
 void FileHelper::SetImageData(uint8_t *inData, size_t expectedSize)
 {
    PixelWriteConverter->SetUserData(inData, expectedSize);
+   /// \todo : shouldn't we call SetCompressJPEGUserData/SetCompressJPEG2000UserData
+   ///         here, too?
 }
 
 /**
@@ -521,6 +527,8 @@ void FileHelper::SetImageData(uint8_t *inData, size_t expectedSize)
  */
 void FileHelper::SetUserData(uint8_t *inData, size_t expectedSize)
 {
+  // Shouldn't we move theese lines to FileHelper::Write()?
+/*  
    if( WriteType == JPEG2000 )
    {
       PixelWriteConverter->SetCompressJPEG2000UserData(inData, expectedSize, FileInternal);
@@ -533,6 +541,9 @@ void FileHelper::SetUserData(uint8_t *inData, size_t expectedSize)
    {
       PixelWriteConverter->SetUserData(inData, expectedSize);
    }
+   */
+   // Just try!
+   PixelWriteConverter->SetUserData(inData, expectedSize);
 }
 
 /**
@@ -727,38 +738,8 @@ bool FileHelper::Write(std::string const &fileName)
  
       case Unknown:  // should never happen; ExplicitVR is the default value
       case ExplicitVR:
-
-   // User should ask gdcm to write an image in Explicit VR mode
-   // only when he is sure *all* the VR of *all* the DataElements is known.
-   // i.e : when there are *only* Public Groups
-   // or *all* the Shadow Groups are fully described in the relevant Shadow
-   // Dictionnary
-   // Let's just *dream* about it; *never* trust a user !
-   // We turn to Implicit VR if at least the VR of one element is unknown.
    
-   // Better we let DocEntry::WriteContent to put vr=UN for undocumented Shadow Groups !
-
-/*
-         e = FileInternal->GetFirstEntry();
-         while (e != 0)
-         {
-            if (e->GetVR() == "  ")  
-            {
-               SetWriteTypeToDcmImplVR();
-               SetWriteFileTypeToImplicitVR();
-               flag = true;
-               break;         
-            } 
-            e = FileInternal->GetNextEntry();
-         }        
-
-         if (!flag)
-         {
-            SetWriteFileTypeToExplicitVR();
-         }
-         break;
-*/
-
+   // We let DocEntry::WriteContent to put vr=UN for undocumented Shadow Groups !
          SetWriteFileTypeToExplicitVR();
 
   break;
@@ -777,13 +758,27 @@ bool FileHelper::Write(std::string const &fileName)
         // SetWriteFileTypeToImplicitVR(); // ACR IS implicit VR !
          break;
  
-      /// \todo FIXME : JPEG may be either ExplicitVR or ImplicitVR
+      /// \todo FIXME : JPEG/JPEG2000 may be either ExplicitVR or ImplicitVR      
       case JPEG:
          SetWriteFileTypeToJPEG();
+         // was :
+         //PixelWriteConverter->SetCompressJPEGUserData(
+         //   inData, expectedSize, FileInternal);
+ PixelWriteConverter->SetCompressJPEGUserData(
+    PixelWriteConverter->GetUserData(),
+    PixelWriteConverter->GetUserDataSize(),FileInternal);
          break;
 
       case JPEG2000:
+         /// \TODO Maybe we should consider doing the compression here !
+         // PixelWriteConverter->SetCompressJPEG2000UserData(inData, expectedSize, FileInternal);
+
          SetWriteFileTypeToJPEG2000();
+         PixelWriteConverter->SetCompressJPEG2000UserData(
+            PixelWriteConverter->GetUserData(),
+            PixelWriteConverter->GetUserDataSize(),
+            FileInternal);
+ 
          break;
    }
 
@@ -901,7 +896,7 @@ bool FileHelper::CheckWriteIntegrity()
  *       (modifies, when necessary, photochromatic interpretation, 
  *       bits allocated, Pixels element VR)
  *       WARNING : if SetPhotometricInterpretationToMonochrome1() was called
- *                 before Pixel Elements if modified :-( 
+ *                 before Pixel Elements is modified :-( 
  */ 
 void FileHelper::SetWriteToRaw()
 {
@@ -934,7 +929,7 @@ void FileHelper::SetWriteToRaw()
          vr = "OW";
       if ( FileInternal->GetBitsAllocated()==24 ) // For RGB ACR files 
          vr = "OB";
-       // For non RAW data. Mainly JPEG
+       // For non RAW data. Mainly JPEG/JPEG2000
       if( WriteType == JPEG || WriteType == JPEG2000)
       {
          vr = "OW";
@@ -974,13 +969,13 @@ void FileHelper::SetWriteToRGB()
       PixelReadConverter->BuildRGBImage();
       
       DataEntry *spp = CopyDataEntry(0x0028,0x0002,"US");
-      spp->SetString("3 ");
+      spp->SetString("3 ");  // Don't drop trailing space
 
       DataEntry *planConfig = CopyDataEntry(0x0028,0x0006,"US");
-      planConfig->SetString("0 ");
+      planConfig->SetString("0 "); // Don't drop trailing space
 
       DataEntry *photInt = CopyDataEntry(0x0028,0x0004,"CS");
-      photInt->SetString("RGB ");
+      photInt->SetString("RGB "); // Don't drop trailing space
 
       if ( PixelReadConverter->GetRGB() )
       {
@@ -2272,3 +2267,8 @@ void RescaleFunction(ImageIOBase::IOComponentType bufferType,
     }
 }
 */
+
+      ::itk::ExceptionObject e(__FILE__, __LINE__, message.str().c_str(),ITK_LOCATION);
+      throw e;
+    }
+}

diff --git a/src/gdcmPixelWriteConvert.cxx b/src/gdcmPixelWriteConvert.cxx
index 00a3fbf25c6b9df7abdcb6f850cf9144a6ffe01f..2b5e41690ab1ddebb64e22be417d2dead27fcb67 100644 (file)
--- a/src/gdcmPixelWriteConvert.cxx
+++ b/src/gdcmPixelWriteConvert.cxx
@@ -3,8 +3,8 @@
   Program:   gdcm
   Module:    $RCSfile: gdcmPixelWriteConvert.cxx,v $
   Language:  C++
-  Date:      $Date: 2007/08/24 10:45:18 $
-  Version:   $Revision: 1.17 $
+  Date:      $Date: 2007/08/27 16:14:47 $
+  Version:   $Revision: 1.18 $
                                                                                 
   Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
   l'Image). All rights reserved. See Doc/License.txt or
@@ -240,8 +240,8 @@ void PixelWriteConvert::SetCompressJPEG2000UserData(uint8_t *data, size_t size,
 
    std::ostringstream *of = new std::ostringstream();
     int xsize = image->GetXSize();
-   int ysize = image->GetYSize();
-  int zsize =  image->GetZSize();
+    int ysize = image->GetYSize();
+    int zsize = image->GetZSize();
     int samplesPerPixel = image->GetSamplesPerPixel();
    //std::cout << "X: " << xsize << std::endl;
    //std::cout << "Y: " << ysize << std::endl;
@@ -367,7 +367,7 @@ void PixelWriteConvert::SetCompressJPEGUserData(uint8_t *data, size_t size, File
     size_t end = of->tellp();
     //static int i = 0;
     JpegPair &jp = JpegFragmentSize[i];
-      jp.second = (uint32_t)(end-beg);
+    jp.second = (uint32_t)(end-beg);
     if( ((end-beg) % 2) )
       {
       of->put( '\0' );