Program: gdcm
Module: $RCSfile: gdcmPixelConvert.cxx,v $
Language: C++
- Date: $Date: 2004/10/08 16:27:20 $
- Version: $Revision: 1.3 $
+ Date: $Date: 2004/11/25 10:24:34 $
+ Version: $Revision: 1.33 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
=========================================================================*/
-////////////////// TEMPORARY NOT
+////////////////// TEMPORARY NOTE
// look for "fixMem" and convert that to a member of this class
// Removing the prefix fixMem and dealing with allocations should do the trick
-#define str2num(str, typeNum) *((typeNum *)(str))
+//
+// grep PIXELCONVERT everywhere and clean up !
#include "gdcmDebug.h"
#include "gdcmPixelConvert.h"
+#include <fstream>
+#include <stdio.h>
+
+namespace gdcm
+{
+#define str2num(str, typeNum) *((typeNum *)(str))
+
+// For JPEG 2000, body in file gdcmJpeg2000.cxx
+bool gdcm_read_JPEG2000_file (std::ifstream* fp, void* image_buffer);
+
+// For JPEG 8 Bits, body in file gdcmJpeg8.cxx
+bool gdcm_read_JPEG_file8 (std::ifstream* fp, void* image_buffer);
+
+// For JPEG 12 Bits, body in file gdcmJpeg12.cxx
+bool gdcm_read_JPEG_file12 (std::ifstream* fp, void* image_buffer);
+
+// 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);
//-----------------------------------------------------------------------------
// Constructor / Destructor
-gdcmPixelConvert::gdcmPixelConvert()
+PixelConvert::PixelConvert()
{
RGB = 0;
RGBSize = 0;
- Uncompressed = 0;
- UncompressedSize = 0;
+ Decompressed = 0;
+ DecompressedSize = 0;
+ LutRGBA = 0;
+ LutRedData = 0;
+ LutGreenData = 0;
+ LutBlueData =0;
}
-void gdcmPixelConvert::Squeeze()
+void PixelConvert::Squeeze()
{
- if ( RGB ) {
+ if ( RGB )
+ {
delete [] RGB;
}
- if ( Uncompressed ) {
- delete [] Uncompressed;
+ RGB = 0;
+
+ if ( Decompressed )
+ {
+ delete [] Decompressed;
}
+ Decompressed = 0;
+
+ if ( LutRGBA )
+ {
+ delete [] LutRGBA;
+ }
+ LutRGBA = 0;
}
-gdcmPixelConvert::~gdcmPixelConvert()
+PixelConvert::~PixelConvert()
{
Squeeze();
}
-void gdcmPixelConvert::AllocateRGB()
+void PixelConvert::AllocateRGB()
{
if ( RGB ) {
delete [] RGB;
}
- RGB = new uint8_t[RGBSize];
+ RGB = new uint8_t[ RGBSize ];
}
-void gdcmPixelConvert::AllocateUncompressed()
+void PixelConvert::AllocateDecompressed()
{
- if ( Uncompressed ) {
- delete [] Uncompressed;
+ if ( Decompressed ) {
+ delete [] Decompressed;
}
- Uncompressed = new uint8_t[ UncompressedSize ];
+ Decompressed = new uint8_t[ DecompressedSize ];
}
/**
- * \brief Read from file a 12 bits per pixel image and uncompress it
+ * \brief Read from file a 12 bits per pixel image and decompress it
* into a 16 bits per pixel image.
*/
-bool gdcmPixelConvert::ReadAndUncompress12Bits( FILE* filePointer,
- size_t uncompressedSize,
- size_t PixelNumber )
+void PixelConvert::ReadAndDecompress12BitsTo16Bits( std::ifstream* fp )
+ throw ( FormatError )
{
- SetUncompressedSize( uncompressedSize );
- AllocateUncompressed();
+ int nbPixels = XSize * YSize;
+ uint16_t* localDecompres = (uint16_t*)Decompressed;
- uint16_t* pdestination = (uint16_t*)Uncompressed;
-
- for(int p = 0; p < PixelNumber; p += 2 )
+ for( int p = 0; p < nbPixels; p += 2 )
{
- // 2 pixels 12bit = [0xABCDEF]
- // 2 pixels 16bit = [0x0ABD] + [0x0FCE]
uint8_t b0, b1, b2;
- size_t ItemRead;
- ItemRead = fread( &b0, 1, 1, filePointer);
- if ( ItemRead != 1 )
+
+ fp->read( (char*)&b0, 1);
+ if ( fp->fail() || fp->eof() )//Fp->gcount() == 1
{
- return false;
+ throw FormatError( "PixelConvert::ReadAndDecompress12BitsTo16Bits()",
+ "Unfound first block" );
}
- ItemRead = fread( &b1, 1, 1, filePointer);
- if ( ItemRead != 1 )
+
+ fp->read( (char*)&b1, 1 );
+ if ( fp->fail() || fp->eof())//Fp->gcount() == 1
{
- return false;
+ throw FormatError( "PixelConvert::ReadAndDecompress12BitsTo16Bits()",
+ "Unfound second block" );
}
- ItemRead = fread( &b2, 1, 1, filePointer);
- if ( ItemRead != 1 )
+
+ fp->read( (char*)&b2, 1 );
+ if ( fp->fail() || fp->eof())//Fp->gcount() == 1
{
- return false;
+ throw FormatError( "PixelConvert::ReadAndDecompress12BitsTo16Bits()",
+ "Unfound second block" );
}
-
- //Two steps are necessary to please VC++
- *pdestination++ = ((b0 >> 4) << 8) + ((b0 & 0x0f) << 4) + (b1 & 0x0f);
- // A B D
- *pdestination++ = ((b2 & 0x0f) << 8) + ((b1 >> 4) << 4) + (b2 >> 4);
- // F C E
-
- /// \todo JPR Troubles expected on Big-Endian processors ?
- }
- return true;
-}
-/**
- * \brief Read from file an uncompressed image.
- */
-bool gdcmPixelConvert::ReadUncompressed( FILE* filePointer,
- size_t uncompressedSize,
- size_t expectedSize )
-{
- if ( expectedSize > uncompressedSize )
- {
- dbg.Verbose(0, "gdcmPixelConvert::ReadUncompressed: expectedSize"
- "is bigger than it should");
- return false;
- }
- SetUncompressedSize( uncompressedSize );
- AllocateUncompressed();
- size_t ItemRead = fread( (void*)Uncompressed, expectedSize, 1, filePointer);
- if ( ItemRead != 1 )
- {
- return false;
- }
- return true;
-}
-
-/**
- * \brief Convert a Gray plane and ( Lut R, Lut G, Lut B ) into an
- * RGB plane.
- * @return True on success.
- */
-bool gdcmPixelConvert::ConvertGrayAndLutToRGB( uint8_t *lutRGBA )
-
-{
- /// We assume Uncompressed contains the decompressed gray plane
- /// and build the RGB image.
- SetRGBSize( UncompressedSize );
- AllocateRGB();
+ // Two steps are necessary to please VC++
+ //
+ // 2 pixels 12bit = [0xABCDEF]
+ // 2 pixels 16bit = [0x0ABD] + [0x0FCE]
+ // A B D
+ *localDecompres++ = ((b0 >> 4) << 8) + ((b0 & 0x0f) << 4) + (b1 & 0x0f);
+ // F C E
+ *localDecompres++ = ((b2 & 0x0f) << 8) + ((b1 >> 4) << 4) + (b2 >> 4);
-//aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa
-//AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
-//COPY HERE THE CODE OF GetImageDataIntoVector
-
- /// \todo check that operator new []didn't fail, and sometimes return false
- return true;
+ /// \todo JPR Troubles expected on Big-Endian processors ?
+ }
}
/**
* \brief Try to deal with RLE 16 Bits.
* We assume the RLE has allready been parsed and loaded in
- * Uncompressed (through \ref ReadAndUncompressRLE8Bits ).
+ * Decompressed (through \ref ReadAndDecompressJPEGFile ).
* We here need to make 16 Bits Pixels from Low Byte and
* High Byte 'Planes'...(for what it may mean)
* @return Boolean
*/
-bool gdcmPixelConvert::UncompressRLE16BitsFromRLE8Bits(
- int XSize,
- int YSize,
- int NumberOfFrames,
- uint8_t* fixMemUncompressed )
+bool PixelConvert::DecompressRLE16BitsFromRLE8Bits( int NumberOfFrames )
{
size_t PixelNumber = XSize * YSize;
- size_t fixMemUncompressedSize = XSize * YSize * NumberOfFrames;
+ size_t decompressedSize = XSize * YSize * NumberOfFrames;
- // We assumed Uncompressed contains the decoded RLE pixels but as
+ // We assumed Decompressed 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 Uncompressed and hence
- // we copy Uncompressed in a safe place, say OldUncompressed.
+ // per pixel we cannot work in place within Decompressed and hence
+ // we copy it in a safe place, say copyDecompressed.
- uint8_t* OldUncompressed = new uint8_t[ fixMemUncompressedSize * 2 ];
- memmove( OldUncompressed, fixMemUncompressed, fixMemUncompressedSize * 2);
+ uint8_t* copyDecompressed = new uint8_t[ decompressedSize * 2 ];
+ memmove( copyDecompressed, Decompressed, decompressedSize * 2 );
- uint8_t* x = fixMemUncompressed;
- uint8_t* a = OldUncompressed;
+ uint8_t* x = Decompressed;
+ uint8_t* a = copyDecompressed;
uint8_t* b = a + PixelNumber;
for ( int i = 0; i < NumberOfFrames; i++ )
{
- for ( int j = 0; j < PixelNumber; j++ )
+ for ( unsigned int j = 0; j < PixelNumber; j++ )
{
- *(x++) = *(a++);
*(x++) = *(b++);
+ *(x++) = *(a++);
}
}
- delete[] OldUncompressed;
+ delete[] copyDecompressed;
/// \todo check that operator new []didn't fail, and sometimes return false
return true;
}
/**
- * \brief Implementation of the RLE decoding algorithm for uncompressing
+ * \brief Implementation of the RLE decoding algorithm for decompressing
* a RLE fragment. [refer to PS 3.5-2003, section G.3.2 p 86]
+ * @param subDecompressed Sub region of \ref Decompressed where the de
+ * decoded fragment should be placed.
+ * @param fragmentSize The length of the binary fragment as found on the disk.
+ * @param decompressedSegmentSize The expected length of the fragment ONCE
+ * decompressed.
+ * @param fp File Pointer: on entry the position should be the one of
+ * the fragment to be decoded.
*/
-bool gdcmPixelConvert::ReadAndUncompressRLEFragment( uint8_t* decodedZone,
- long fragmentSize,
- long uncompressedSegmentSize,
- FILE* fp )
+bool PixelConvert::ReadAndDecompressRLEFragment( uint8_t* subDecompressed,
+ long fragmentSize,
+ long decompressedSegmentSize,
+ std::ifstream* fp )
{
int8_t count;
long numberOfOutputBytes = 0;
long numberOfReadBytes = 0;
-
- while( numberOfOutputBytes < uncompressedSegmentSize )
+
+ while( numberOfOutputBytes < decompressedSegmentSize )
{
- fread( &count, 1, 1, fp );
+ fp->read( (char*)&count, 1 );
numberOfReadBytes += 1;
if ( count >= 0 )
// Note: count <= 127 comparison is always true due to limited range
// signed integer of width N is 2^(N-1) - 1, which for int8_t
// is 127].
{
- fread( decodedZone, count + 1, 1, fp);
- numberOfReadBytes += count + 1;
- decodedZone += count + 1;
+ fp->read( (char*)subDecompressed, count + 1);
+ numberOfReadBytes += count + 1;
+ subDecompressed += count + 1;
numberOfOutputBytes += count + 1;
}
else
if ( ( count <= -1 ) && ( count >= -127 ) )
{
int8_t newByte;
- fread( &newByte, 1, 1, fp);
+ fp->read( (char*)&newByte, 1);
numberOfReadBytes += 1;
for( int i = 0; i < -count + 1; i++ )
{
- decodedZone[i] = newByte;
+ subDecompressed[i] = newByte;
}
- decodedZone += -count + 1;
+ subDecompressed += -count + 1;
numberOfOutputBytes += -count + 1;
}
}
if ( numberOfReadBytes > fragmentSize )
{
- dbg.Verbose(0, "gdcmFile::gdcm_read_RLE_fragment: we read more "
- "bytes than the segment size.");
+ dbg.Verbose(0, "PixelConvert::ReadAndDecompressRLEFragment: we "
+ "read more bytes than the segment size.");
return false;
}
}
/**
* \brief Reads from disk the Pixel Data of 'Run Length Encoded'
- * Dicom encapsulated file and uncompress it.
+ * Dicom encapsulated file and decompress it.
* @param fp already open File Pointer
- * @param image_buffer destination Address (in caller's memory space)
* at which the pixel data should be copied
* @return Boolean
*/
-bool gdcmPixelConvert::gdcm_read_RLE_file( void* image_buffer,
- int XSize,
- int YSize,
- int ZSize,
- int BitsAllocated,
- gdcmRLEFramesInfo* RLEInfo,
- FILE* fp )
+bool PixelConvert::ReadAndDecompressRLEFile( std::ifstream* fp )
{
- uint8_t* im = (uint8_t*)image_buffer;
- long uncompressedSegmentSize = XSize * YSize;
-
-
+ uint8_t* subDecompressed = Decompressed;
+ long decompressedSegmentSize = XSize * YSize;
+
// Loop on the frame[s]
- for( gdcmRLEFramesInfo::RLEFrameList::iterator
+ for( RLEFramesInfo::RLEFrameList::iterator
it = RLEInfo->Frames.begin();
it != RLEInfo->Frames.end();
++it )
// Loop on the fragments
for( unsigned int k = 1; k <= (*it)->NumberFragments; k++ )
{
- fseek( fp, (*it)->Offset[k] ,SEEK_SET);
- (void)gdcmPixelConvert::ReadAndUncompressRLEFragment(
- (uint8_t*) im, (*it)->Length[k],
- uncompressedSegmentSize, fp );
- im += uncompressedSegmentSize;
+ fp->seekg( (*it)->Offset[k] , std::ios_base::beg );
+ (void)ReadAndDecompressRLEFragment( subDecompressed,
+ (*it)->Length[k],
+ decompressedSegmentSize,
+ fp );
+ subDecompressed += decompressedSegmentSize;
}
}
-
+
if ( BitsAllocated == 16 )
{
// Try to deal with RLE 16 Bits
- (void)gdcmPixelConvert::UncompressRLE16BitsFromRLE8Bits(
- XSize,
- YSize,
- ZSize,
- (uint8_t*) image_buffer);
+ (void)DecompressRLE16BitsFromRLE8Bits( ZSize );
+ }
+
+ return true;
+}
+
+/**
+ * \brief Swap the bytes, according to \ref SwapCode.
+ */
+void PixelConvert::ConvertSwapZone()
+{
+ unsigned int i;
+
+ if( BitsAllocated == 16 )
+ {
+ uint16_t* im16 = (uint16_t*)Decompressed;
+ switch( SwapCode )
+ {
+ case 0:
+ case 12:
+ case 1234:
+ break;
+ case 21:
+ case 3412:
+ case 2143:
+ case 4321:
+ for( i = 0; i < DecompressedSize / 2; i++ )
+ {
+ im16[i]= (im16[i] >> 8) | (im16[i] << 8 );
+ }
+ break;
+ default:
+ dbg.Verbose( 0, "PixelConvert::ConvertSwapZone: SwapCode value "
+ "(16 bits) not allowed." );
+ }
+ }
+ else if( BitsAllocated == 32 )
+ {
+ uint32_t s32;
+ uint16_t high;
+ uint16_t low;
+ uint32_t* im32 = (uint32_t*)Decompressed;
+ switch ( SwapCode )
+ {
+ case 0:
+ case 1234:
+ break;
+ case 4321:
+ for( i = 0; i < DecompressedSize / 4; i++ )
+ {
+ low = im32[i] & 0x0000ffff; // 4321
+ high = im32[i] >> 16;
+ high = ( high >> 8 ) | ( high << 8 );
+ low = ( low >> 8 ) | ( low << 8 );
+ s32 = low;
+ im32[i] = ( s32 << 16 ) | high;
+ }
+ break;
+ case 2143:
+ for( i = 0; i < DecompressedSize / 4; i++ )
+ {
+ low = im32[i] & 0x0000ffff; // 2143
+ high = im32[i] >> 16;
+ high = ( high >> 8 ) | ( high << 8 );
+ low = ( low >> 8 ) | ( low << 8 );
+ s32 = high;
+ im32[i] = ( s32 << 16 ) | low;
+ }
+ break;
+ case 3412:
+ for( i = 0; i < DecompressedSize / 4; i++ )
+ {
+ low = im32[i] & 0x0000ffff; // 3412
+ high = im32[i] >> 16;
+ s32 = low;
+ im32[i] = ( s32 << 16 ) | high;
+ }
+ break;
+ default:
+ dbg.Verbose( 0, "PixelConvert::ConvertSwapZone: SwapCode value "
+ "(32 bits) not allowed." );
+ }
+ }
+}
+
+/**
+ * \brief Deal with endianity i.e. re-arange bytes inside the integer
+ */
+void PixelConvert::ConvertReorderEndianity()
+{
+ if ( BitsAllocated != 8 )
+ {
+ ConvertSwapZone();
+ }
+
+ // Special kludge in order to deal with xmedcon broken images:
+ if ( ( BitsAllocated == 16 )
+ && ( BitsStored < BitsAllocated )
+ && ( ! PixelSign ) )
+ {
+ int l = (int)( DecompressedSize / ( BitsAllocated / 8 ) );
+ uint16_t *deb = (uint16_t *)Decompressed;
+ for(int i = 0; i<l; i++)
+ {
+ if( *deb == 0xffff )
+ {
+ *deb = 0;
+ }
+ deb++;
+ }
+ }
+}
+
+/**
+ * \brief Reads from disk the Pixel Data of JPEG Dicom encapsulated
+ & file and decompress it.
+ * @param fp File Pointer
+ * @return Boolean
+ */
+bool PixelConvert::ReadAndDecompressJPEGFile( std::ifstream* fp )
+{
+ uint8_t* localDecompressed = Decompressed;
+ // Loop on the fragment[s]
+ for( JPEGFragmentsInfo::JPEGFragmentsList::iterator
+ it = JPEGInfo->Fragments.begin();
+ it != JPEGInfo->Fragments.end();
+ ++it )
+ {
+ fp->seekg( (*it)->Offset, std::ios_base::beg);
+
+ if ( IsJPEG2000 )
+ {
+ if ( ! gdcm_read_JPEG2000_file( fp,localDecompressed ) )
+ {
+ return false;
+ }
+ }
+ else if ( BitsStored == 8)
+ {
+ // JPEG Lossy : call to IJG 6b
+ if ( ! gdcm_read_JPEG_file8( fp, localDecompressed ) )
+ {
+ return false;
+ }
+ }
+ else if ( BitsStored <= 12)
+ {
+ // Reading Fragment pixels
+ if ( ! gdcm_read_JPEG_file12 ( fp, localDecompressed ) )
+ {
+ return false;
+ }
+ }
+ else if ( BitsStored <= 16)
+ {
+ // Reading Fragment pixels
+ if ( ! gdcm_read_JPEG_file16 ( fp, localDecompressed ) )
+ {
+ return false;
+ }
+ //assert( IsJPEGLossless );
+ }
+ else
+ {
+ // other JPEG lossy not supported
+ dbg.Error("PixelConvert::ReadAndDecompressJPEGFile: unknown "
+ "jpeg lossy compression ");
+ return false;
+ }
+
+ // Advance to next free location in Decompressed
+ // for next fragment decompression (if any)
+ int length = XSize * YSize * SamplesPerPixel;
+ int numberBytes = BitsAllocated / 8;
+
+ localDecompressed += length * numberBytes;
+ }
+ return true;
+}
+
+/**
+ * \brief Re-arrange the bits within the bytes.
+ * @return Boolean
+ */
+bool PixelConvert::ConvertReArrangeBits() throw ( FormatError )
+{
+ if ( BitsStored != BitsAllocated )
+ {
+ int l = (int)( DecompressedSize / ( BitsAllocated / 8 ) );
+ if ( BitsAllocated == 16 )
+ {
+ uint16_t mask = 0xffff;
+ mask = mask >> ( BitsAllocated - BitsStored );
+ uint16_t* deb = (uint16_t*)Decompressed;
+ for(int i = 0; i<l; i++)
+ {
+ *deb = (*deb >> (BitsStored - HighBitPosition - 1)) & mask;
+ deb++;
+ }
+ }
+ else if ( BitsAllocated == 32 )
+ {
+ uint32_t mask = 0xffffffff;
+ mask = mask >> ( BitsAllocated - BitsStored );
+ uint32_t* deb = (uint32_t*)Decompressed;
+ for(int i = 0; i<l; i++)
+ {
+ *deb = (*deb >> (BitsStored - HighBitPosition - 1)) & mask;
+ deb++;
+ }
+ }
+ else
+ {
+ dbg.Verbose(0, "PixelConvert::ConvertReArrangeBits: weird image");
+ throw FormatError( "PixelConvert::ConvertReArrangeBits()",
+ "weird image !?" );
+ }
+ }
+ return true;
+}
+
+/**
+ * \brief Convert (Y plane, cB plane, cR plane) to RGB pixels
+ * \warning Works on all the frames at a time
+ */
+void PixelConvert::ConvertYcBcRPlanesToRGBPixels()
+{
+ uint8_t* localDecompressed = Decompressed;
+ uint8_t* copyDecompressed = new uint8_t[ DecompressedSize ];
+ memmove( copyDecompressed, localDecompressed, DecompressedSize );
+
+ // to see the tricks about YBR_FULL, YBR_FULL_422,
+ // YBR_PARTIAL_422, YBR_ICT, YBR_RCT have a look at :
+ // ftp://medical.nema.org/medical/dicom/final/sup61_ft.pdf
+ // and be *very* affraid
+ //
+ int l = XSize * YSize;
+ int nbFrames = ZSize;
+
+ uint8_t* a = copyDecompressed;
+ uint8_t* b = copyDecompressed + l;
+ uint8_t* c = copyDecompressed + l + l;
+ double R, G, B;
+
+ /// \todo : Replace by the 'well known' integer computation
+ /// counterpart. Refer to
+ /// http://lestourtereaux.free.fr/papers/data/yuvrgb.pdf
+ /// for code optimisation.
+
+ for ( int i = 0; i < nbFrames; i++ )
+ {
+ for ( int j = 0; j < l; j++ )
+ {
+ R = 1.164 *(*a-16) + 1.596 *(*c -128) + 0.5;
+ G = 1.164 *(*a-16) - 0.813 *(*c -128) - 0.392 *(*b -128) + 0.5;
+ B = 1.164 *(*a-16) + 2.017 *(*b -128) + 0.5;
+
+ if (R < 0.0) R = 0.0;
+ if (G < 0.0) G = 0.0;
+ if (B < 0.0) B = 0.0;
+ if (R > 255.0) R = 255.0;
+ if (G > 255.0) G = 255.0;
+ if (B > 255.0) B = 255.0;
+
+ *(localDecompressed++) = (uint8_t)R;
+ *(localDecompressed++) = (uint8_t)G;
+ *(localDecompressed++) = (uint8_t)B;
+ a++;
+ b++;
+ c++;
+ }
+ }
+ delete[] copyDecompressed;
+}
+
+/**
+ * \brief Convert (Red plane, Green plane, Blue plane) to RGB pixels
+ * \warning Works on all the frames at a time
+ */
+void PixelConvert::ConvertRGBPlanesToRGBPixels()
+{
+ uint8_t* localDecompressed = Decompressed;
+ uint8_t* copyDecompressed = new uint8_t[ DecompressedSize ];
+ memmove( copyDecompressed, localDecompressed, DecompressedSize );
+
+ int l = XSize * YSize * ZSize;
+
+ uint8_t* a = copyDecompressed;
+ uint8_t* b = copyDecompressed + l;
+ uint8_t* c = copyDecompressed + l + l;
+
+ for (int j = 0; j < l; j++)
+ {
+ *(localDecompressed++) = *(a++);
+ *(localDecompressed++) = *(b++);
+ *(localDecompressed++) = *(c++);
+ }
+ delete[] copyDecompressed;
+}
+
+bool PixelConvert::ReadAndDecompressPixelData( std::ifstream* fp )
+{
+ // ComputeDecompressedAndRGBSizes is already made by
+ // ::GrabInformationsFromHeader. So, the structure sizes are
+ // correct
+ Squeeze();
+
+ //////////////////////////////////////////////////
+ //// First stage: get our hands on the Pixel Data.
+ if ( !fp )
+ {
+ dbg.Verbose( 0, "PixelConvert::ReadAndDecompressPixelData: "
+ "unavailable file pointer." );
+ return false;
+ }
+
+ fp->seekg( PixelOffset, std::ios_base::beg );
+ if( fp->fail() || fp->eof()) //Fp->gcount() == 1
+ {
+ dbg.Verbose( 0, "PixelConvert::ReadAndDecompressPixelData: "
+ "unable to find PixelOffset in file." );
+ return false;
+ }
+
+ AllocateDecompressed();
+
+ //////////////////////////////////////////////////
+ //// Second stage: read from disk dans decompress.
+ if ( BitsAllocated == 12 )
+ {
+ ReadAndDecompress12BitsTo16Bits( fp);
+ }
+ else if ( IsDecompressed )
+ {
+ // This problem can be found when some obvious informations are found
+ // after the field containing the image datas. In this case, these
+ // bad datas are added to the size of the image (in the PixelDataLength
+ // variable). But DecompressedSize is the right size of the image !
+ if( PixelDataLength != DecompressedSize)
+ {
+ dbg.Verbose( 0, "PixelConvert::ReadAndDecompressPixelData: "
+ "Mismatch between PixelConvert and DecompressedSize." );
+ }
+ if( PixelDataLength > DecompressedSize)
+ {
+ fp->read( (char*)Decompressed, DecompressedSize);
+ }
+ else
+ {
+ fp->read( (char*)Decompressed, PixelDataLength);
+ }
+
+ if ( fp->fail() || fp->eof())//Fp->gcount() == 1
+ {
+ dbg.Verbose( 0, "PixelConvert::ReadAndDecompressPixelData: "
+ "reading of decompressed pixel data failed." );
+ return false;
+ }
+ }
+ else if ( IsRLELossless )
+ {
+ if ( ! ReadAndDecompressRLEFile( fp ) )
+ {
+ dbg.Verbose( 0, "PixelConvert::ReadAndDecompressPixelData: "
+ "RLE decompressor failed." );
+ return false;
+ }
+ }
+ else
+ {
+ // Default case concerns JPEG family
+ if ( ! ReadAndDecompressJPEGFile( fp ) )
+ {
+ dbg.Verbose( 0, "PixelConvert::ReadAndDecompressPixelData: "
+ "JPEG decompressor failed." );
+ return false;
+ }
+ }
+
+ ////////////////////////////////////////////
+ //// Third stage: twigle the bytes and bits.
+ ConvertReorderEndianity();
+ ConvertReArrangeBits();
+ ConvertHandleColor();
+
+ return true;
+}
+
+void PixelConvert::ConvertHandleColor()
+{
+ //////////////////////////////////
+ // Deal with the color decoding i.e. handle:
+ // - R, G, B planes (as opposed to RGB pixels)
+ // - YBR (various) encodings.
+ // - LUT[s] (or "PALETTE COLOR").
+ //
+ // The classification in the color decoding schema is based on the blending
+ // of two Dicom tags values:
+ // * "Photometric Interpretation" for which we have the cases:
+ // - [Photo A] MONOCHROME[1|2] pictures,
+ // - [Photo B] RGB or YBR_FULL_422 (which acts as RGB),
+ // - [Photo C] YBR_* (with the above exception of YBR_FULL_422)
+ // - [Photo D] "PALETTE COLOR" which indicates the presence of LUT[s].
+ // * "Planar Configuration" for which we have the cases:
+ // - [Planar 0] 0 then Pixels are already RGB
+ // - [Planar 1] 1 then we have 3 planes : R, G, B,
+ // - [Planar 2] 2 then we have 1 gray Plane and 3 LUTs
+ //
+ // Now in theory, one could expect some coherence when blending the above
+ // cases. For example we should not encounter files belonging at the
+ // time to case [Planar 0] and case [Photo D].
+ // Alas, this was only theory ! Because in practice some odd (read ill
+ // formated Dicom) files (e.g. gdcmData/US-PAL-8-10x-echo.dcm) we encounter:
+ // - "Planar Configuration" = 0,
+ // - "Photometric Interpretation" = "PALETTE COLOR".
+ // Hence gdcm shall use the folowing "heuristic" in order to be tolerant
+ // towards Dicom-non-conformance files:
+ // << whatever the "Planar Configuration" value might be, a
+ // "Photometric Interpretation" set to "PALETTE COLOR" forces
+ // a LUT intervention >>
+ //
+ // Now we are left with the following handling of the cases:
+ // - [Planar 0] OR [Photo A] no color decoding (since respectively
+ // Pixels are already RGB and monochrome pictures have no color :),
+ // - [Planar 1] AND [Photo B] handled with ConvertRGBPlanesToRGBPixels()
+ // - [Planar 1] AND [Photo C] handled with ConvertYcBcRPlanesToRGBPixels()
+ // - [Planar 2] OR [Photo D] requires LUT intervention.
+
+ if ( ! IsDecompressedRGB() )
+ {
+ // [Planar 2] OR [Photo D]: LUT intervention done outside
+ return;
+ }
+
+ if ( PlanarConfiguration == 1 )
+ {
+ if ( IsYBRFull )
+ {
+ // [Planar 1] AND [Photo C] (remember YBR_FULL_422 acts as RGB)
+ ConvertYcBcRPlanesToRGBPixels();
+ }
+ else
+ {
+ // [Planar 1] AND [Photo C]
+ ConvertRGBPlanesToRGBPixels();
+ }
+ return;
}
+ // When planarConf is 0, and RLELossless (forbidden by Dicom norm)
+ // pixels need to be RGB-fied anyway
+ if (IsRLELossless)
+ {
+ ConvertRGBPlanesToRGBPixels();
+ }
+ // In *normal *case, when planarConf is 0, pixels are already in RGB
+}
+
+/**
+ * \brief Predicate to know wether the image[s] (once decompressed) is RGB.
+ * \note See comments of \ref ConvertHandleColor
+ */
+bool PixelConvert::IsDecompressedRGB()
+{
+ if ( IsMonochrome
+ || PlanarConfiguration == 2
+ || IsPaletteColor )
+ {
+ return false;
+ }
return true;
}
+void PixelConvert::ComputeDecompressedAndRGBSizes()
+{
+ int bitsAllocated = BitsAllocated;
+ // Number of "Bits Allocated" is fixed to 16 when it's 12, since
+ // in this case we will expand the image to 16 bits (see
+ // \ref ReadAndDecompress12BitsTo16Bits() )
+ if ( BitsAllocated == 12 )
+ {
+ bitsAllocated = 16;
+ }
+
+ DecompressedSize = XSize * YSize * ZSize
+ * ( bitsAllocated / 8 )
+ * SamplesPerPixel;
+ if ( HasLUT )
+ {
+ RGBSize = 3 * DecompressedSize;
+ }
+ else
+ {
+ RGBSize = DecompressedSize;
+ }
+}
+
+void PixelConvert::GrabInformationsFromHeader( Header* header )
+{
+ // Just in case some access to a Header element requires disk access.
+ // Note: gdcmDocument::Fp is leaved open after OpenFile.
+ std::ifstream* fp = header->OpenFile();
+ // Number of Bits Allocated for storing a Pixel is defaulted to 16
+ // when absent from the header.
+ BitsAllocated = header->GetBitsAllocated();
+ if ( BitsAllocated == 0 )
+ {
+ BitsAllocated = 16;
+ }
+
+ // Number of "Bits Stored" defaulted to number of "Bits Allocated"
+ // when absent from the header.
+ BitsStored = header->GetBitsStored();
+ if ( BitsStored == 0 )
+ {
+ BitsStored = BitsAllocated;
+ }
+
+ // High Bit Position
+ HighBitPosition = header->GetHighBitPosition();
+ if ( HighBitPosition == 0 )
+ {
+ HighBitPosition = BitsAllocated - 1;
+ }
+
+ XSize = header->GetXSize();
+ YSize = header->GetYSize();
+ ZSize = header->GetZSize();
+ SamplesPerPixel = header->GetSamplesPerPixel();
+ PixelSize = header->GetPixelSize();
+ PixelSign = header->IsSignedPixelData();
+ SwapCode = header->GetSwapCode();
+ TransferSyntaxType ts = header->GetTransferSyntax();
+ IsDecompressed =
+ ( ! header->IsDicomV3() )
+ || ts == ImplicitVRLittleEndian
+ || ts == ImplicitVRLittleEndianDLXGE
+ || ts == ExplicitVRLittleEndian
+ || ts == ExplicitVRBigEndian
+ || ts == DeflatedExplicitVRLittleEndian;
+ IsJPEG2000 = header->IsJPEG2000();
+ IsJPEGLossless = header->IsJPEGLossless();
+ IsRLELossless = ( ts == RLELossless );
+ PixelOffset = header->GetPixelOffset();
+ PixelDataLength = header->GetPixelAreaLength();
+ RLEInfo = header->GetRLEInfo();
+ JPEGInfo = header->GetJPEGInfo();
+
+ PlanarConfiguration = header->GetPlanarConfiguration();
+ IsMonochrome = header->IsMonochrome();
+ IsPaletteColor = header->IsPaletteColor();
+ IsYBRFull = header->IsYBRFull();
+
+ /////////////////////////////////////////////////////////////////
+ // LUT section:
+ HasLUT = header->HasLUT();
+ if ( HasLUT )
+ {
+ LutRedDescriptor = header->GetEntryByNumber( 0x0028, 0x1101 );
+ LutGreenDescriptor = header->GetEntryByNumber( 0x0028, 0x1102 );
+ LutBlueDescriptor = header->GetEntryByNumber( 0x0028, 0x1103 );
+
+ // Depending on the value of Document::MAX_SIZE_LOAD_ELEMENT_VALUE
+ // [ refer to invocation of Document::SetMaxSizeLoadEntry() in
+ // Document::Document() ], the loading of the value (content) of a
+ // [Bin|Val]Entry occurence migth have been hindered (read simply NOT
+ // loaded). Hence, we first try to obtain the LUTs data from the header
+ // and when this fails we read the LUTs data directely from disk.
+ /// \todo Reading a [Bin|Val]Entry directly from disk is a kludge.
+ /// We should NOT bypass the [Bin|Val]Entry class. Instead
+ /// an access to an UNLOADED content of a [Bin|Val]Entry occurence
+ /// (e.g. BinEntry::GetBinArea()) should force disk access from
+ /// within the [Bin|Val]Entry class itself. The only problem
+ /// is that the [Bin|Val]Entry is unaware of the FILE* is was
+ /// parsed from. Fix that. FIXME.
+
+ ////// Red round:
+ LutRedData = (uint8_t*)header->GetEntryBinAreaByNumber( 0x0028, 0x1201 );
+ if ( ! LutRedData )
+ {
+ // Read the Lut Data from disk
+ DocEntry* lutRedDataEntry = header->GetDocEntryByNumber( 0x0028,
+ 0x1201 );
+ LutRedData = new uint8_t[ lutRedDataEntry->GetLength() ];
+ fp->seekg( lutRedDataEntry->GetOffset() ,std::ios_base::beg );
+ fp->read( (char*)LutRedData, (size_t)lutRedDataEntry->GetLength());
+ if ( fp->fail() || fp->eof())//Fp->gcount() == 1
+ {
+ dbg.Verbose(0, "PixelConvert::GrabInformationsFromHeader: "
+ "unable to read red LUT data" );
+ }
+ }
+
+ ////// Green round:
+ LutGreenData = (uint8_t*)header->GetEntryBinAreaByNumber(0x0028, 0x1202 );
+ if ( ! LutGreenData)
+ {
+ // Read the Lut Data from disk
+ DocEntry* lutGreenDataEntry = header->GetDocEntryByNumber( 0x0028,
+ 0x1202 );
+ LutGreenData = new uint8_t[ lutGreenDataEntry->GetLength() ];
+ fp->seekg( lutGreenDataEntry->GetOffset() , std::ios_base::beg );
+ fp->read( (char*)LutGreenData, (size_t)lutGreenDataEntry->GetLength() );
+ if ( fp->fail() || fp->eof())//Fp->gcount() == 1
+ {
+ dbg.Verbose(0, "PixelConvert::GrabInformationsFromHeader: "
+ "unable to read green LUT data" );
+ }
+ }
+
+ ////// Blue round:
+ LutBlueData = (uint8_t*)header->GetEntryBinAreaByNumber( 0x0028, 0x1203 );
+ if ( ! LutBlueData )
+ {
+ // Read the Lut Data from disk
+ DocEntry* lutBlueDataEntry = header->GetDocEntryByNumber( 0x0028,
+ 0x1203 );
+ LutBlueData = new uint8_t[ lutBlueDataEntry->GetLength() ];
+ fp->seekg( lutBlueDataEntry->GetOffset() , std::ios_base::beg );
+ fp->read( (char*)LutBlueData, (size_t)lutBlueDataEntry->GetLength() );
+ if ( fp->fail() || fp->eof())//Fp->gcount() == 1
+ {
+ dbg.Verbose(0, "PixelConvert::GrabInformationsFromHeader: "
+ "unable to read blue LUT data" );
+ }
+ }
+ }
+
+ ComputeDecompressedAndRGBSizes();
+
+ if(fp)
+ {
+ header->CloseFile();
+ }
+}
+
+/**
+ * \brief Build Red/Green/Blue/Alpha LUT from Header
+ * when (0028,0004),Photometric Interpretation = [PALETTE COLOR ]
+ * and (0028,1101),(0028,1102),(0028,1102)
+ * - xxx Palette Color Lookup Table Descriptor - are found
+ * and (0028,1201),(0028,1202),(0028,1202)
+ * - xxx Palette Color Lookup Table Data - are found
+ * \warning does NOT deal with :
+ * 0028 1100 Gray Lookup Table Descriptor (Retired)
+ * 0028 1221 Segmented Red Palette Color Lookup Table Data
+ * 0028 1222 Segmented Green Palette Color Lookup Table Data
+ * 0028 1223 Segmented Blue Palette Color Lookup Table Data
+ * no known Dicom reader deals with them :-(
+ * @return a RGBA Lookup Table
+ */
+void PixelConvert::BuildLUTRGBA()
+{
+ if ( LutRGBA )
+ {
+ return;
+ }
+ // Not so easy : see
+ // http://www.barre.nom.fr/medical/dicom2/limitations.html#Color%20Lookup%20Tables
+
+ if ( ! IsPaletteColor )
+ {
+ return;
+ }
+
+ if ( LutRedDescriptor == GDCM_UNFOUND
+ || LutGreenDescriptor == GDCM_UNFOUND
+ || LutBlueDescriptor == GDCM_UNFOUND )
+ {
+ return;
+ }
+
+ ////////////////////////////////////////////
+ // Extract the info from the LUT descriptors
+ int lengthR; // Red LUT length in Bytes
+ int debR; // Subscript of the first Lut Value
+ int nbitsR; // Lut item size (in Bits)
+ int nbRead = sscanf( LutRedDescriptor.c_str(),
+ "%d\\%d\\%d",
+ &lengthR, &debR, &nbitsR );
+ if( nbRead != 3 )
+ {
+ dbg.Verbose(0, "PixelConvert::BuildLUTRGBA: wrong red LUT descriptor");
+ }
+
+ int lengthG; // Green LUT length in Bytes
+ int debG; // Subscript of the first Lut Value
+ int nbitsG; // Lut item size (in Bits)
+ nbRead = sscanf( LutGreenDescriptor.c_str(),
+ "%d\\%d\\%d",
+ &lengthG, &debG, &nbitsG );
+ if( nbRead != 3 )
+ {
+ dbg.Verbose(0, "PixelConvert::BuildLUTRGBA: wrong green LUT descriptor");
+ }
+
+ int lengthB; // Blue LUT length in Bytes
+ int debB; // Subscript of the first Lut Value
+ int nbitsB; // Lut item size (in Bits)
+ nbRead = sscanf( LutRedDescriptor.c_str(),
+ "%d\\%d\\%d",
+ &lengthB, &debB, &nbitsB );
+ if( nbRead != 3 )
+ {
+ dbg.Verbose(0, "PixelConvert::BuildLUTRGBA: wrong blue LUT descriptor");
+ }
+
+ ////////////////////////////////////////////////////////
+ if ( ( ! LutRedData ) || ( ! LutGreenData ) || ( ! LutBlueData ) )
+ {
+ return;
+ }
+
+ ////////////////////////////////////////////////
+ // forge the 4 * 8 Bits Red/Green/Blue/Alpha LUT
+ LutRGBA = new uint8_t[ 1024 ]; // 256 * 4 (R, G, B, Alpha)
+ if ( !LutRGBA )
+ {
+ return;
+ }
+ memset( LutRGBA, 0, 1024 );
+
+ int mult;
+ if ( ( nbitsR == 16 ) && ( BitsAllocated == 8 ) )
+ {
+ // when LUT item size is different than pixel size
+ mult = 2; // high byte must be = low byte
+ }
+ else
+ {
+ // See PS 3.3-2003 C.11.1.1.2 p 619
+ mult = 1;
+ }
+
+ // if we get a black image, let's just remove the '+1'
+ // from 'i*mult+1' and check again
+ // if it works, we shall have to check the 3 Palettes
+ // to see which byte is ==0 (first one, or second one)
+ // and fix the code
+ // We give up the checking to avoid some (useless ?)overhead
+ // (optimistic asumption)
+ int i;
+ uint8_t* a = LutRGBA + 0;
+ for( i=0; i < lengthR; ++i )
+ {
+ *a = LutRedData[i*mult+1];
+ a += 4;
+ }
+
+ a = LutRGBA + 1;
+ for( i=0; i < lengthG; ++i)
+ {
+ *a = LutGreenData[i*mult+1];
+ a += 4;
+ }
+
+ a = LutRGBA + 2;
+ for(i=0; i < lengthB; ++i)
+ {
+ *a = LutBlueData[i*mult+1];
+ a += 4;
+ }
+
+ a = LutRGBA + 3;
+ for(i=0; i < 256; ++i)
+ {
+ *a = 1; // Alpha component
+ a += 4;
+ }
+}
+
+/**
+ * \brief Build the RGB image from the Decompressed imagage and the LUTs.
+ */
+bool PixelConvert::BuildRGBImage()
+{
+ if ( RGB )
+ {
+ // The job is already done.
+ return true;
+ }
+
+ if ( ! Decompressed )
+ {
+ // The job can't be done
+ return false;
+ }
+
+ BuildLUTRGBA();
+ if ( ! LutRGBA )
+ {
+ // The job can't be done
+ return false;
+ }
+
+ // Build RGB Pixels
+ AllocateRGB();
+ uint8_t* localRGB = RGB;
+ for (size_t i = 0; i < DecompressedSize; ++i )
+ {
+ int j = Decompressed[i] * 4;
+ *localRGB++ = LutRGBA[j];
+ *localRGB++ = LutRGBA[j+1];
+ *localRGB++ = LutRGBA[j+2];
+ }
+ return true;
+}
+
+/**
+ * \brief Print self.
+ * @param indent Indentation string to be prepended during printing.
+ * @param os Stream to print to.
+ */
+void PixelConvert::Print( std::string indent, std::ostream &os )
+{
+ os << indent
+ << "--- Pixel information -------------------------"
+ << std::endl;
+ os << indent
+ << "Pixel Data: offset " << PixelOffset
+ << " x" << std::hex << PixelOffset << std::dec
+ << " length " << PixelDataLength
+ << " x" << std::hex << PixelDataLength << std::dec
+ << std::endl;
+
+ if ( IsRLELossless )
+ {
+ if ( RLEInfo )
+ {
+ RLEInfo->Print( indent, os );
+ }
+ else
+ {
+ dbg.Verbose(0, "PixelConvert::Print: set as RLE file "
+ "but NO RLEinfo present.");
+ }
+ }
+
+ if ( IsJPEG2000 || IsJPEGLossless )
+ {
+ if ( JPEGInfo )
+ {
+ JPEGInfo->Print( indent, os );
+ }
+ else
+ {
+ dbg.Verbose(0, "PixelConvert::Print: set as JPEG file "
+ "but NO JPEGinfo present.");
+ }
+ }
+}
+
+} // end namespace gdcm
+
+// NOTES on File internal calls
+// User
+// ---> GetImageData
+// ---> GetImageDataIntoVector
+// |---> GetImageDataIntoVectorRaw
+// | lut intervention
+// User
+// ---> GetImageDataRaw
+// ---> GetImageDataIntoVectorRaw
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff