StreamImageReaderTest.cxx

/*=========================================================================
 
  Program: GDCM (Grassroots DICOM). A DICOM library
 
  Copyright (c) 2006-2011 Mathieu Malaterre
  All rights reserved.
  See Copyright.txt or http://gdcm.sourceforge.net/Copyright.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 notice for more information.
 
=========================================================================*/
// This work was realised during the GSOC 2011 by Manoj Alwani
 
#include "gdcmStreamImageReader.h"
#include "gdcmFileMetaInformation.h"
#include "gdcmSystem.h"
#include "gdcmFilename.h"
#include "gdcmByteSwap.h"
#include "gdcmTrace.h"
#include "gdcmTesting.h"
#include "gdcmImageHelper.h"
#include "gdcmImageReader.h"
#include "gdcmImage.h"
#include "gdcmMediaStorage.h"
#include "gdcmRAWCodec.h"
#include "gdcmJPEGLSCodec.h"
#include "gdcmUIDGenerator.h"
#include "gdcmStreamImageWriter.h"
#include "gdcmAttribute.h"
#include "gdcmFile.h"
#include "gdcmTag.h"
 
bool StreamImageRead(gdcm::StreamImageWriter & theStreamWriter,
  const char* filename, const char* outfilename, int resolution)
{
  gdcm::StreamImageReader reader;
 
  reader.SetFileName( filename );
 
  if (!reader.ReadImageInformation())
    {
    std::cerr << "unable to read image information" << std::endl;
    return 1; //unable to read tags as expected.
    }
  //let's be tricky; each image will be read in portions, first the top half, then the bottom
  //that way, we can test how the stream handles fragmentation of the data
  //we could also loop this to get various different size combinations, but I'm not sure
  //that's useful, yet.
  std::vector<unsigned int> extent =
    gdcm::ImageHelper::GetDimensionsValue(reader.GetFile());
  // std::cout << extent[0];
  //at this point, these values aren't used, but may be in the future
  //unsigned short xmin = 0;
  //unsigned short xmax = extent[0];
  //unsigned short ymin = 0;
  //unsigned short ymax = extent[1];
  //unsigned short zmin = 0;
  //unsigned short zmax = extent[2];
 
  std::cout<< "\n Row: "<<extent[0] <<"\n Col :"<< extent[1]<< "\n Resolution :"<< extent[2] << std::endl;
 
  int a =1;
  for (int i=1; i<=(extent[2]-resolution);++i)
    a = a*2;
 
  reader.DefinePixelExtent(0, extent[0]/a, 0, extent[1]/a, resolution-1, resolution);
 
  unsigned long len = reader.DefineProperBufferLength();
  char* finalBuffer = new char[len];
  memset(finalBuffer, 0, sizeof(char)*len);
 
  if (reader.CanReadImage())
    {
    bool result = reader.Read(finalBuffer, len);
    if( !result )
      {
      std::cout << "res2 failure:" << filename << std::endl;
      delete [] finalBuffer;
      return 1;
      }
    else
      {
      std::cout<< "Able to read";
      }
    }
  else
    {
    std::cerr<< "Not able to put in buffer"<< std::endl;
    }
/*
    //now, read in smaller buffer extents
    reader.DefinePixelExtent(xmin, xmax, ymin, ymax);
    len = reader.DefineProperBufferLength();
 
    char* buffer = new char[len];
    bool res2 = reader.Read(buffer, len);
    if( !res2 ){
      std::cerr << "res2 failure:" << filename << std::endl;
      return 1;
    }
    //copy the result into finalBuffer
    memcpy(finalBuffer, buffer, len);
 
    //now read the next half of the image
    ymin = ymax;
    ymax = extent[1];
 
    reader.DefinePixelExtent(xmin, xmax, ymin, ymax);
 
    //std::cerr << "Success to read image from file: " << filename << std::endl;
    unsigned long len2 = reader.DefineProperBufferLength();
 
    char* buffer2 = new char[len2];
    bool res3 = reader.Read(buffer2, len2);
    if( !res3 ){
      std::cerr << "res3 failure:" << filename << std::endl;
      return 1;
    }
    //copy the result into finalBuffer
    memcpy(&(finalBuffer[len]), buffer2, len2);
 
    delete [] buffer;
    delete [] buffer2;
*/
 
  gdcm::Writer w;
  gdcm::File &file = w.GetFile();
  gdcm::DataSet &ds = file.GetDataSet();
 
  file.GetHeader().SetDataSetTransferSyntax( gdcm::TransferSyntax::ExplicitVRLittleEndian );
 
  gdcm::UIDGenerator uid;
  gdcm::DataElement de( gdcm::Tag(0x8,0x18) ); // SOP Instance UID
  de.SetVR( gdcm::VR::UI );
  const char *u = uid.Generate();
  de.SetByteValue( u, strlen(u) );
  ds.Insert( de );
 
  gdcm::DataElement de1( gdcm::Tag(0x8,0x16) );
  de1.SetVR( gdcm::VR::UI );
  gdcm::MediaStorage ms( gdcm::MediaStorage::VLWholeSlideMicroscopyImageStorage );
  de1.SetByteValue( ms.GetString(), strlen(ms.GetString()));
  ds.Insert( de1 );
 
  const char mystr[] = "MONOCHROME2 ";
  gdcm::DataElement de2( gdcm::Tag(0x28,0x04) );
  //de.SetTag(gdcm::Tag(0x28,0x04));
  de2.SetVR( gdcm::VR::CS );
  de2.SetByteValue(mystr, strlen(mystr));
  ds.Insert( de2 );
 
   gdcm::Attribute<0x0028,0x0008> Number_Of_Frames = {1};
   ds.Insert( Number_Of_Frames.GetAsDataElement() );
 
   gdcm::Attribute<0x0028,0x0010> row = {extent[0]/a};//
   ds.Insert( row.GetAsDataElement() );
 
   gdcm::Attribute<0x0028,0x0011> col = {extent[1]/a};//
   ds.Insert( col.GetAsDataElement() );
 
   gdcm::Attribute<0x0028,0x0100> at = {8};
   ds.Insert( at.GetAsDataElement() );
 
   gdcm::Attribute<0x0028,0x0002> at1 = {1};//
   ds.Insert( at1.GetAsDataElement() );
 
   gdcm::Attribute<0x0028,0x0101> at2 = {8};
   ds.Insert( at2.GetAsDataElement() );
 
   gdcm::Attribute<0x0028,0x0102> at3 = {7};
   ds.Insert( at3.GetAsDataElement() );
    /*
   ds1.Remove( gdcm::Tag(0x0028,0x0008) );
 
   gdcm::Attribute<0x0028,0x0008> Number_Of_Frames = {1};
   ds1.Insert( Number_Of_Frames.GetAsDataElement() );
*/
   theStreamWriter.SetFile(file);
 
   if (!theStreamWriter.WriteImageInformation())
     {
     std::cerr << "unable to write image information" << std::endl;
     return 1; //the CanWrite function should prevent getting here, else,
     //that's a test failure
     }
    std::vector<unsigned int> extent1 = gdcm::ImageHelper::GetDimensionsValue(file);
 
    unsigned short xmax = extent1[0];
    unsigned short ymax = extent1[1];
    unsigned short theChunkSize = 1;
    unsigned short ychunk = extent1[1]/theChunkSize; //go in chunk sizes of theChunkSize
    unsigned short zmax = 1;
 
    std::cout<< "\n Row: "<<extent1[0] <<"\n Col :"<< extent1[1]<< "\n Resolution :"<< extent1[2] << std::endl;
 
    if (xmax == 0 || ymax == 0)
      {
      std::cerr << "Image has no size, unable to write zero-sized image." << std::endl;
      return 0;
      }
 
    int z, y, nexty;
    unsigned long prevLen = 0; //when going through the char buffer, make sure to grab
    //the bytes sequentially.  So, store how far you got in the buffer with each iteration.
 
    for (z = 0; z < zmax; ++z){
      for (y = 0; y < ymax; y += ychunk){
        nexty = y + ychunk;
        if (nexty > ymax) nexty = ymax;
        theStreamWriter.DefinePixelExtent(0, xmax, y, nexty, z, z+1);
        unsigned long len = theStreamWriter.DefineProperBufferLength();
        std::cout << "\n" <<len;
        char* finalBuffer1 = new char[len];
        memcpy(finalBuffer1, &(finalBuffer[prevLen]), len);
        std::cout << "\nable to write";
 
        if (!theStreamWriter.Write(finalBuffer1, len)){
          std::cerr << "writing failure:" << "output.dcm" << " at y = " << y << " and z= " << z << std::endl;
          delete [] finalBuffer1;
          delete [] finalBuffer;
          return 1;
        }
        delete [] finalBuffer1;
        prevLen += len;
      }
    }
   delete [] finalBuffer;
   std::cout << "all is set";
 
  return true;
}
 
 
int main(int argc, char *argv[])
{
  if( argc < 3 )
    {
    std::cerr << argv[0] << " input.dcm output.dcm Resolution" << std::endl;
    return 1;
    }
 
  const char *filename = argv[1];
  const char *outfilename = argv[2];
  char *res = argv[3];
 
  int resolution = atoi(res);
 
  gdcm::StreamImageWriter theStreamWriter;
 
  std::ofstream of;
  of.open( outfilename, std::ios::out | std::ios::binary );
  theStreamWriter.SetStream(of);
 
  // else
  // First of get rid of warning/debug message
  gdcm::Trace::DebugOn();
  gdcm::Trace::WarningOn();
 
  if(!StreamImageRead( theStreamWriter, filename, outfilename, resolution))
    return 1;
 
  uint16_t firstTag1 =  0xfffe;
  uint16_t secondTag1 = 0xe0dd;
  uint32_t thirdTag1 =  0x00000000;
  //uint16_t fourthTag1 = 0xffff;
  const int theBufferSize1 = 2*sizeof(uint16_t)+sizeof(uint32_t);
  char* tmpBuffer2 = new char[theBufferSize1];
  memcpy(&(tmpBuffer2[0]), &firstTag1, sizeof(uint16_t));
  memcpy(&(tmpBuffer2[sizeof(uint16_t)]), &secondTag1, sizeof(uint16_t));
  memcpy(&(tmpBuffer2[2*sizeof(uint16_t)]), &thirdTag1, sizeof(uint32_t));
  //memcpy(&(tmpBuffer2[3*sizeof(uint16_t)]), &fourthTag1, sizeof(uint16_t));
  assert( of && !of.eof() && of.good() );
  of.write(tmpBuffer2, theBufferSize1);
  of.flush();
  assert( of );
 
  return 0;
}