/*=========================================================================
-
+
Program: gdcm
Module: $RCSfile: gdcmPixelReadConvert.cxx,v $
Language: C++
- Date: $Date: 2004/12/10 13:49:07 $
- Version: $Revision: 1.5 $
+ Date: $Date: 2005/01/06 20:03:28 $
+ Version: $Revision: 1.14 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
// For JPEG 2000, body in file gdcmJpeg2000.cxx
bool gdcm_read_JPEG2000_file (std::ifstream* fp, void* image_buffer);
+#define JOCTET uint8_t
// For JPEG 8 Bits, body in file gdcmJpeg8.cxx
-bool gdcm_read_JPEG_file8 (std::ifstream* fp, void* image_buffer);
-
+bool gdcm_read_JPEG_file8 (std::ifstream *fp, void *image_buffer);
+bool gdcm_read_JPEG_memory8 (const JOCTET *buffer, const size_t buflen,
+ void *image_buffer,
+ size_t *howManyRead, size_t *howManyWritten);
+//
// For JPEG 12 Bits, body in file gdcmJpeg12.cxx
-bool gdcm_read_JPEG_file12 (std::ifstream* fp, void* image_buffer);
+bool gdcm_read_JPEG_file12 (std::ifstream *fp, void *image_buffer);
+bool gdcm_read_JPEG_memory12 (const JOCTET *buffer, const size_t buflen,
+ void *image_buffer,
+ size_t *howManyRead, size_t *howManyWritten);
// For JPEG 16 Bits, body in file gdcmJpeg16.cxx
// Beware this is misleading there is no 16bits DCT algorithm, only
// jpeg lossless compression exist in 16bits.
-bool gdcm_read_JPEG_file16 (std::ifstream* fp, void* image_buffer);
+bool gdcm_read_JPEG_file16 (std::ifstream *fp, void *image_buffer);
+bool gdcm_read_JPEG_memory16 (const JOCTET *buffer, const size_t buflen,
+ void* image_buffer,
+ size_t *howManyRead, size_t *howManyWritten);
//-----------------------------------------------------------------------------
* \brief Read from file a 12 bits per pixel image and decompress it
* into a 16 bits per pixel image.
*/
-void PixelReadConvert::ReadAndDecompress12BitsTo16Bits( std::ifstream* fp )
+void PixelReadConvert::ReadAndDecompress12BitsTo16Bits( std::ifstream *fp )
throw ( FormatError )
{
int nbPixels = XSize * YSize;
*/
bool PixelReadConvert::DecompressRLE16BitsFromRLE8Bits( int NumberOfFrames )
{
- size_t PixelNumber = XSize * YSize;
- size_t RawSize = XSize * YSize * NumberOfFrames;
+ size_t pixelNumber = XSize * YSize;
+ size_t rawSize = XSize * YSize * NumberOfFrames;
// We assumed Raw contains the decoded RLE pixels but as
// 8 bits per pixel. In order to convert those pixels to 16 bits
// per pixel we cannot work in place within Raw and hence
// we copy it in a safe place, say copyRaw.
- uint8_t* copyRaw = new uint8_t[ RawSize * 2 ];
- memmove( copyRaw, Raw, RawSize * 2 );
+ uint8_t* copyRaw = new uint8_t[ rawSize * 2 ];
+ memmove( copyRaw, Raw, rawSize * 2 );
uint8_t* x = Raw;
uint8_t* a = copyRaw;
- uint8_t* b = a + PixelNumber;
+ uint8_t* b = a + pixelNumber;
for ( int i = 0; i < NumberOfFrames; i++ )
{
- for ( unsigned int j = 0; j < PixelNumber; j++ )
+ for ( unsigned int j = 0; j < pixelNumber; j++ )
{
*(x++) = *(b++);
*(x++) = *(a++);
* @param fp File Pointer: on entry the position should be the one of
* the fragment to be decoded.
*/
-bool PixelReadConvert::ReadAndDecompressRLEFragment( uint8_t* subRaw,
+bool PixelReadConvert::ReadAndDecompressRLEFragment( uint8_t *subRaw,
long fragmentSize,
long RawSegmentSize,
- std::ifstream* fp )
+ std::ifstream *fp )
{
int8_t count;
long numberOfOutputBytes = 0;
* at which the pixel data should be copied
* @return Boolean
*/
-bool PixelReadConvert::ReadAndDecompressRLEFile( std::ifstream* fp )
+bool PixelReadConvert::ReadAndDecompressRLEFile( std::ifstream *fp )
{
- uint8_t* subRaw = Raw;
+ uint8_t *subRaw = Raw;
long RawSegmentSize = XSize * YSize;
// Loop on the frame[s]
if( BitsAllocated == 16 )
{
- uint16_t* im16 = (uint16_t*)Raw;
+ uint16_t *im16 = (uint16_t*)Raw;
switch( SwapCode )
{
case 0:
}
}
+
/**
* \brief Reads from disk the Pixel Data of JPEG Dicom encapsulated
- & file and decompress it.
+ * file and decompress it. This funciton assumes that each
+ * jpeg fragment contains a whole frame (jpeg file).
* @param fp File Pointer
* @return Boolean
*/
-bool PixelReadConvert::ReadAndDecompressJPEGFile( std::ifstream* fp )
+bool PixelReadConvert::ReadAndDecompressJPEGFramesFromFile( std::ifstream *fp )
{
- uint8_t* localRaw = Raw;
+ uint8_t *localRaw = Raw;
// Loop on the fragment[s]
for( JPEGFragmentsInfo::JPEGFragmentsList::iterator
it = JPEGInfo->Fragments.begin();
{
fp->seekg( (*it)->Offset, std::ios::beg);
- if ( IsJPEG2000 )
- {
- if ( ! gdcm_read_JPEG2000_file( fp,localRaw ) )
- {
- return false;
- }
- }
- else if ( BitsStored == 8)
+ if ( BitsStored == 8)
{
// JPEG Lossy : call to IJG 6b
if ( ! gdcm_read_JPEG_file8( fp, localRaw ) )
return true;
}
+/**
+ * \brief Reads from disk the Pixel Data of JPEG Dicom encapsulated
+ * file and decompress it. This function assumes that the dicom
+ * image is a single frame split into several JPEG fragments.
+ * Those fragments will be glued together into a memory buffer
+ * before being read.
+ * @param fp File Pointer
+ * @return Boolean
+ */
+bool PixelReadConvert::
+ReadAndDecompressJPEGSingleFrameFragmentsFromFile( std::ifstream *fp )
+{
+ // Loop on the fragment[s] to get total length
+ size_t totalLength = 0;
+ JPEGFragmentsInfo::JPEGFragmentsList::iterator it;
+ for( it = JPEGInfo->Fragments.begin();
+ it != JPEGInfo->Fragments.end();
+ ++it )
+ {
+ totalLength += (*it)->Length;
+ }
+
+ // Concatenate the jpeg fragments into a local buffer
+ JOCTET *buffer = new JOCTET [totalLength];
+ JOCTET *p = buffer;
+
+ // Loop on the fragment[s]
+ for( it = JPEGInfo->Fragments.begin();
+ it != JPEGInfo->Fragments.end();
+ ++it )
+ {
+ fp->seekg( (*it)->Offset, std::ios::beg);
+ size_t len = (*it)->Length;
+ fp->read((char *)p,len);
+ p += len;
+ }
+
+ size_t howManyRead = 0;
+ size_t howManyWritten = 0;
+
+ if ( BitsStored == 8)
+ {
+ if ( ! gdcm_read_JPEG_memory8( buffer, totalLength, Raw,
+ &howManyRead, &howManyWritten ) )
+ {
+ dbg.Error(
+ "PixelConvert::ReadAndDecompressJPEGFile: failed to read jpeg8 "
+ );
+ delete [] buffer;
+ return false;
+ }
+ }
+ else if ( BitsStored <= 12)
+ {
+ if ( ! gdcm_read_JPEG_memory12( buffer, totalLength, Raw,
+ &howManyRead, &howManyWritten ) )
+ {
+ dbg.Error(
+ "PixelConvert::ReadAndDecompressJPEGFile: failed to read jpeg12 "
+ );
+ delete [] buffer;
+ return false;
+ }
+ }
+ else if ( BitsStored <= 16)
+ {
+
+ if ( ! gdcm_read_JPEG_memory16( buffer, totalLength, Raw,
+ &howManyRead, &howManyWritten ) )
+ {
+ dbg.Error(
+ "PixelConvert::ReadAndDecompressJPEGFile: failed to read jpeg16 "
+ );
+ delete [] buffer;
+ return false;
+ }
+ }
+ else
+ {
+ // other JPEG lossy not supported
+ dbg.Error("PixelConvert::ReadAndDecompressJPEGFile: unknown "
+ "jpeg lossy compression ");
+ delete [] buffer;
+ return false;
+ }
+
+ // free local buffer
+ delete [] buffer;
+
+ return true;
+}
+
+/**
+ * \brief Reads from disk the Pixel Data of JPEG Dicom encapsulated
+ * file and decompress it. This function handles the generic
+ * and complex case where the DICOM contains several frames,
+ * and some of the frames are possibly split into several JPEG
+ * fragments.
+ * @param fp File Pointer
+ * @return Boolean
+ */
+bool PixelReadConvert::
+ReadAndDecompressJPEGFragmentedFramesFromFile( std::ifstream *fp )
+{
+ // Loop on the fragment[s] to get total length
+ size_t totalLength = 0;
+ JPEGFragmentsInfo::JPEGFragmentsList::iterator it;
+ for( it = JPEGInfo->Fragments.begin();
+ it != JPEGInfo->Fragments.end();
+ ++it )
+ {
+ totalLength += (*it)->Length;
+ }
+
+ // Concatenate the jpeg fragments into a local buffer
+ JOCTET *buffer = new JOCTET [totalLength];
+ JOCTET *p = buffer;
+
+ // Loop on the fragment[s]
+ for( it = JPEGInfo->Fragments.begin();
+ it != JPEGInfo->Fragments.end();
+ ++it )
+ {
+ fp->seekg( (*it)->Offset, std::ios::beg);
+ size_t len = (*it)->Length;
+ fp->read((char *)p,len);
+ p+=len;
+ }
+
+ size_t howManyRead = 0;
+ size_t howManyWritten = 0;
+ size_t fragmentLength = 0;
+
+ for( it = JPEGInfo->Fragments.begin() ;
+ (it != JPEGInfo->Fragments.end()) && (howManyRead < totalLength);
+ ++it )
+ {
+ fragmentLength += (*it)->Length;
+
+ if (howManyRead > fragmentLength) continue;
+
+ if ( BitsStored == 8)
+ {
+ if ( ! gdcm_read_JPEG_memory8( buffer+howManyRead, totalLength-howManyRead,
+ Raw+howManyWritten,
+ &howManyRead, &howManyWritten ) )
+ {
+ dbg.Error("PixelConvert::ReadAndDecompressJPEGFile: failed to read jpeg8 ");
+ delete [] buffer;
+ return false;
+ }
+ }
+ else if ( BitsStored <= 12)
+ {
+
+ if ( ! gdcm_read_JPEG_memory12( buffer+howManyRead, totalLength-howManyRead,
+ Raw+howManyWritten,
+ &howManyRead, &howManyWritten ) )
+ {
+ dbg.Error("PixelConvert::ReadAndDecompressJPEGFile: failed to read jpeg12 ");
+ delete [] buffer;
+ return false;
+ }
+ }
+ else if ( BitsStored <= 16)
+ {
+
+ if ( ! gdcm_read_JPEG_memory16( buffer+howManyRead, totalLength-howManyRead,
+ Raw+howManyWritten,
+ &howManyRead, &howManyWritten ) )
+ {
+ dbg.Error("PixelConvert::ReadAndDecompressJPEGFile: failed to read jpeg16 ");
+ delete [] buffer;
+ return false;
+ }
+ }
+ else
+ {
+ // other JPEG lossy not supported
+ dbg.Error("PixelConvert::ReadAndDecompressJPEGFile: unknown "
+ "jpeg lossy compression ");
+ delete [] buffer;
+ return false;
+ }
+
+ if (howManyRead < fragmentLength)
+ howManyRead = fragmentLength;
+ }
+
+ // free local buffer
+ delete [] buffer;
+
+ return true;
+}
+
+/**
+ * \brief Reads from disk the Pixel Data of JPEG Dicom encapsulated
+ * file and decompress it.
+ * @param fp File Pointer
+ * @return Boolean
+ */
+bool PixelReadConvert::ReadAndDecompressJPEGFile( std::ifstream *fp )
+{
+ if ( IsJPEG2000 )
+ {
+ fp->seekg( (*JPEGInfo->Fragments.begin())->Offset, std::ios::beg);
+ if ( ! gdcm_read_JPEG2000_file( fp,Raw ) )
+ return false;
+ }
+
+ if ( ( ZSize == 1 ) && ( JPEGInfo->Fragments.size() > 1 ) )
+ {
+ // we have one frame split into several fragments
+ // we will pack those fragments into a single buffer and
+ // read from it
+ return ReadAndDecompressJPEGSingleFrameFragmentsFromFile( fp );
+ }
+ else if (JPEGInfo->Fragments.size() == (size_t)ZSize)
+ {
+ // suppose each fragment is a frame
+ return ReadAndDecompressJPEGFramesFromFile( fp );
+ }
+ else
+ {
+ // The dicom image contains frames containing fragments of images
+ // a more complex algorithm :-)
+ return ReadAndDecompressJPEGFragmentedFramesFromFile( fp );
+ }
+}
+
/**
* \brief Re-arrange the bits within the bytes.
* @return Boolean
*/
void PixelReadConvert::ConvertYcBcRPlanesToRGBPixels()
{
- uint8_t* localRaw = Raw;
- uint8_t* copyRaw = new uint8_t[ RawSize ];
+ uint8_t *localRaw = Raw;
+ uint8_t *copyRaw = new uint8_t[ RawSize ];
memmove( copyRaw, localRaw, RawSize );
// to see the tricks about YBR_FULL, YBR_FULL_422,
int l = XSize * YSize;
int nbFrames = ZSize;
- uint8_t* a = copyRaw;
- uint8_t* b = copyRaw + l;
- uint8_t* c = copyRaw + l + l;
+ uint8_t *a = copyRaw;
+ uint8_t *b = copyRaw + l;
+ uint8_t *c = copyRaw + l + l;
double R, G, B;
/// \todo : Replace by the 'well known' integer computation
*/
void PixelReadConvert::ConvertRGBPlanesToRGBPixels()
{
- uint8_t* localRaw = Raw;
- uint8_t* copyRaw = new uint8_t[ RawSize ];
+ uint8_t *localRaw = Raw;
+ uint8_t *copyRaw = new uint8_t[ RawSize ];
memmove( copyRaw, localRaw, RawSize );
int l = XSize * YSize * ZSize;
delete[] copyRaw;
}
-bool PixelReadConvert::ReadAndDecompressPixelData( std::ifstream* fp )
+bool PixelReadConvert::ReadAndDecompressPixelData( std::ifstream *fp )
{
// ComputeRawAndRGBSizes is already made by
// ::GrabInformationsFromHeader. So, the structure sizes are
}
}
-void PixelReadConvert::GrabInformationsFromHeader( Header* header )
+void PixelReadConvert::GrabInformationsFromHeader( Header *header )
{
// Number of Bits Allocated for storing a Pixel is defaulted to 16
// when absent from the header.
if ( HasLUT )
{
// Just in case some access to a Header element requires disk access.
- // Note: gdcmDocument::Fp is leaved open after OpenFile.
LutRedDescriptor = header->GetEntryByNumber( 0x0028, 0x1101 );
LutGreenDescriptor = header->GetEntryByNumber( 0x0028, 0x1102 );
LutBlueDescriptor = header->GetEntryByNumber( 0x0028, 0x1103 );
return true;
}
+/**
+ * \brief Print self.
+ * @param os Stream to print to.
+ */
+void PixelReadConvert::Print( std::ostream &os )
+{
+ Print("",os);
+}
+
/**
* \brief Print self.
* @param indent Indentation string to be prepended during printing.
<< std::endl;
os << indent
<< "Pixel Data: offset " << PixelOffset
- << " x" << std::hex << PixelOffset << std::dec
- << " length " << PixelDataLength
- << " x" << std::hex << PixelDataLength << std::dec
- << std::endl;
+ << " x(" << std::hex << PixelOffset << std::dec
+ << ") length " << PixelDataLength
+ << " x(" << std::hex << PixelDataLength << std::dec
+ << ")" << std::endl;
if ( IsRLELossless )
{
// User
// ---> GetImageDataRaw
// ---> GetImageDataIntoVectorRaw
+
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff