Program: gdcm
Module: $RCSfile: WriteDicomAsJPEG2000.cxx,v $
Language: C++
- Date: $Date: 2007/06/21 15:01:00 $
- Version: $Revision: 1.4 $
+ 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
#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;
}
if( argc >= 4 )
quality = atoi(argv[3]);
std::cerr << "Using quality: " << quality << std::endl;
-
-// Step 1 : Create the header of the image
- //GDCM_NAME_SPACE::File *f = new GDCM_NAME_SPACE::File();
- // gdcm1.3 syntax. Sorry
+
+ 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_NAME_SPACE::FileHelper *tested = new GDCM_NAME_SPACE::FileHelper( f );
- // gdcm1.3 syntax. Sorry
GDCM_NAME_SPACE::FileHelper *tested = GDCM_NAME_SPACE::FileHelper::New( f );
std::string PixelType = tested->GetFile()->GetPixelType();
int xsize = f->GetXSize();
//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_NAME_SPACE::File *fileToBuild = new GDCM_NAME_SPACE::File();
- // gdcm1.3 syntax. Sorry !
- GDCM_NAME_SPACE::File *fileToBuild = GDCM_NAME_SPACE::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, "US"); // 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, "US"); // 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, "IS"); // 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, "US"); // 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, "US"); // 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, "US"); // 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, "US"); // 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_NAME_SPACE::FileHelper *fileH = new GDCM_NAME_SPACE::FileHelper(fileToBuild);
- // gdcm1.3 syntax. Sorry !
+ 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;
}
+
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff