Program: gdcm
Module: $RCSfile: gdcmPixelConvert.cxx,v $
Language: C++
- Date: $Date: 2004/10/08 08:56:48 $
- Version: $Revision: 1.2 $
+ Date: $Date: 2004/10/13 04:05:04 $
+ 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
=========================================================================*/
-////////////////// 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"
+// External JPEG decompression
+
+// for JPEGLosslessDecodeImage
+#include "jpeg/ljpg/jpegless.h"
+
+namespace gdcm
+{
+
+#define str2num(str, typeNum) *((typeNum *)(str))
+
+// For JPEG 2000, body in file gdcmJpeg2000.cxx
+bool gdcm_read_JPEG2000_file (FILE* fp, void* image_buffer);
+
+// For JPEG 8 Bits, body in file gdcmJpeg8.cxx
+bool gdcm_read_JPEG_file (FILE* fp, void* image_buffer);
+
+// For JPEG 12 Bits, body in file gdcmJpeg12.cxx
+bool gdcm_read_JPEG_file12 (FILE* fp, void* image_buffer);
+
+
//-----------------------------------------------------------------------------
// Constructor / Destructor
-gdcmPixelConvert::gdcmPixelConvert()
+PixelConvert::PixelConvert()
{
RGB = 0;
RGBSize = 0;
- Uncompressed = 0;
- UncompressedSize = 0;
+ Decompressed = 0;
+ DecompressedSize = 0;
}
-void gdcmPixelConvert::Squeeze()
+void PixelConvert::Squeeze()
{
if ( RGB ) {
delete [] RGB;
}
- if ( Uncompressed ) {
- delete [] Uncompressed;
+ if ( Decompressed ) {
+ delete [] Decompressed;
}
}
-gdcmPixelConvert::~gdcmPixelConvert()
+PixelConvert::~PixelConvert()
{
Squeeze();
}
-void gdcmPixelConvert::AllocateRGB()
+void PixelConvert::AllocateRGB()
{
if ( RGB ) {
delete [] RGB;
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
* into a 16 bits per pixel image.
*/
-bool gdcmPixelConvert::ReadAndUncompress12Bits( FILE* filePointer,
- size_t uncompressedSize,
- size_t PixelNumber )
+void PixelConvert::Decompress12BitsTo16Bits(
+ uint8_t* pixelZone,
+ FILE* filePtr)
+ throw ( FormatError )
{
- SetUncompressedSize( uncompressedSize );
- AllocateUncompressed();
-
- uint16_t* pdestination = (uint16_t*)Uncompressed;
+ int nbPixels = XSize * YSize;
+ uint16_t* destination = (uint16_t*)pixelZone;
- 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);
+
+ ItemRead = fread( &b0, 1, 1, filePtr);
if ( ItemRead != 1 )
{
- return false;
+ throw FormatError( "File::Decompress12BitsTo16Bits()",
+ "Unfound first block" );
}
- ItemRead = fread( &b1, 1, 1, filePointer);
+
+ ItemRead = fread( &b1, 1, 1, filePtr);
if ( ItemRead != 1 )
{
- return false;
+ throw FormatError( "File::Decompress12BitsTo16Bits()",
+ "Unfound second block" );
}
- ItemRead = fread( &b2, 1, 1, filePointer);
+
+ ItemRead = fread( &b2, 1, 1, filePtr);
if ( ItemRead != 1 )
{
- return false;
+ throw FormatError( "File::Decompress12BitsTo16Bits()",
+ "Unfound second block" );
}
- //Two steps are necessary to please VC++
- *pdestination++ = ((b0 >> 4) << 8) + ((b0 & 0x0f) << 4) + (b1 & 0x0f);
+ // Two steps are necessary to please VC++
+ //
+ // 2 pixels 12bit = [0xABCDEF]
+ // 2 pixels 16bit = [0x0ABD] + [0x0FCE]
// A B D
- *pdestination++ = ((b2 & 0x0f) << 8) + ((b1 >> 4) << 4) + (b2 >> 4);
+ *destination++ = ((b0 >> 4) << 8) + ((b0 & 0x0f) << 4) + (b1 & 0x0f);
// F C E
+ *destination++ = ((b2 & 0x0f) << 8) + ((b1 >> 4) << 4) + (b2 >> 4);
/// \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();
-
-//aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa
-//AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
-//COPY HERE THE CODE OF GetImageDataIntoVector
-
- /// \todo check that operator new []didn't fail, and sometimes return false
- return true;
}
/**
* \brief Try to deal with RLE 16 Bits.
* We assume the RLE has allready been parsed and loaded in
- * Uncompressed (through \ref ReadAndUncompressRLE8Bits ).
+ * Uncompressed (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
*/
-uint8_t* gdcmPixelConvert::UncompressRLE16BitsFromRLE8Bits(
- int XSize,
- int YSize,
+bool PixelConvert::UncompressRLE16BitsFromRLE8Bits(
int NumberOfFrames,
uint8_t* fixMemUncompressed )
{
// We assumed Uncompressed 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.
- // Here is how we handle things:
- // - First stage: copy Uncompressed in a safe place, say OldUncompressed
- // - Second stage: reallocate Uncompressed with the needed space
- // - Third stage: expand from OldUncompressed to Uncompressed
- // - Fourth stage: clean up OldUncompressed
-
- /// First stage:
+ // per pixel we cannot work in place within Uncompressed and hence
+ // we copy Uncompressed in a safe place, say OldUncompressed.
+
uint8_t* OldUncompressed = new uint8_t[ fixMemUncompressedSize * 2 ];
memmove( OldUncompressed, fixMemUncompressed, fixMemUncompressedSize * 2);
- /// Second stage:
- //fixMem SetUncompressedSize( 2 * UncompressedSize );
- //fixMem AllocateUncompressed();
- uint8_t* fixMemNewUncompressed = new uint8_t[fixMemUncompressedSize * 2];
-
- /// Third stage:
- uint8_t* x = fixMemNewUncompressed;
+ uint8_t* x = fixMemUncompressed;
uint8_t* a = OldUncompressed;
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++);
}
}
- // Fourth stage:
delete[] OldUncompressed;
/// \todo check that operator new []didn't fail, and sometimes return false
- return fixMemNewUncompressed;
+ return true;
+}
+
+/**
+ * \brief Implementation of the RLE decoding algorithm for uncompressing
+ * a RLE fragment. [refer to PS 3.5-2003, section G.3.2 p 86]
+ */
+bool PixelConvert::ReadAndUncompressRLEFragment( uint8_t* decodedZone,
+ long fragmentSize,
+ long uncompressedSegmentSize,
+ FILE* fp )
+{
+ int8_t count;
+ long numberOfOutputBytes = 0;
+ long numberOfReadBytes = 0;
+
+ while( numberOfOutputBytes < uncompressedSegmentSize )
+ {
+ fread( &count, 1, 1, fp );
+ numberOfReadBytes += 1;
+ if ( count >= 0 )
+ // Note: count <= 127 comparison is always true due to limited range
+ // of data type int8_t [since the maximum of an exact width
+ // 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;
+ numberOfOutputBytes += count + 1;
+ }
+ else
+ {
+ if ( ( count <= -1 ) && ( count >= -127 ) )
+ {
+ int8_t newByte;
+ fread( &newByte, 1, 1, fp);
+ numberOfReadBytes += 1;
+ for( int i = 0; i < -count + 1; i++ )
+ {
+ decodedZone[i] = newByte;
+ }
+ decodedZone += -count + 1;
+ numberOfOutputBytes += -count + 1;
+ }
+ }
+ // if count = 128 output nothing
+
+ if ( numberOfReadBytes > fragmentSize )
+ {
+ dbg.Verbose(0, "File::gdcm_read_RLE_fragment: we read more "
+ "bytes than the segment size.");
+ return false;
+ }
+ }
+ return true;
}
+
+/**
+ * \brief Reads from disk the Pixel Data of 'Run Length Encoded'
+ * Dicom encapsulated file and uncompress 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 PixelConvert::ReadAndDecompressRLEFile(
+ void* image_buffer,
+ FILE* fp )
+{
+ uint8_t* im = (uint8_t*)image_buffer;
+ long uncompressedSegmentSize = XSize * YSize;
+
+
+ // Loop on the frame[s]
+ for( RLEFramesInfo::RLEFrameList::iterator
+ it = RLEInfo->Frames.begin();
+ it != RLEInfo->Frames.end();
+ ++it )
+ {
+ // Loop on the fragments
+ for( int k = 1; k <= (*it)->NumberFragments; k++ )
+ {
+ fseek( fp, (*it)->Offset[k] ,SEEK_SET );
+ (void)PixelConvert::ReadAndUncompressRLEFragment(
+ (uint8_t*) im, (*it)->Length[k],
+ uncompressedSegmentSize, fp );
+ im += uncompressedSegmentSize;
+ }
+ }
+
+ if ( BitsAllocated == 16 )
+ {
+ // Try to deal with RLE 16 Bits
+ (void)UncompressRLE16BitsFromRLE8Bits( ZSize,
+ (uint8_t*) image_buffer);
+ }
+
+ return true;
+}
+
+/**
+ * \brief Swap the bytes, according to swap code.
+ * \warning not end user intended
+ * @param im area to deal with
+ */
+void PixelConvert::SwapZone( uint8_t* im )
+{
+ unsigned int i;
+
+ if( BitsAllocated == 16 )
+ {
+ uint16_t* im16 = (uint16_t*)im;
+ 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::SwapZone: SwapCode value "
+ "(16 bits) not allowed." );
+ }
+ }
+ else if( BitsAllocated == 32 )
+ {
+ uint32_t s32;
+ uint16_t fort, faible;
+ uint32_t* im32 = (uint32_t*)im;
+ switch ( SwapCode )
+ {
+ case 0:
+ case 1234:
+ break;
+ case 4321:
+ for( i = 0; i < DecompressedSize / 4; i++ )
+ {
+ faible = im32[i] & 0x0000ffff; // 4321
+ fort = im32[i] >> 16;
+ fort = ( fort >> 8 ) | ( fort << 8 );
+ faible = ( faible >> 8 ) | ( faible << 8);
+ s32 = faible;
+ im32[i] = ( s32 << 16 ) | fort;
+ }
+ break;
+ case 2143:
+ for( i = 0; i < DecompressedSize / 4; i++ )
+ {
+ faible = im32[i] & 0x0000ffff; // 2143
+ fort = im32[i] >> 16;
+ fort = ( fort >> 8 ) | ( fort << 8 );
+ faible = ( faible >> 8) | ( faible << 8);
+ s32 = fort;
+ im32[i] = ( s32 << 16 ) | faible;
+ }
+ break;
+ case 3412:
+ for( i = 0; i < DecompressedSize / 4; i++ )
+ {
+ faible = im32[i] & 0x0000ffff; // 3412
+ fort = im32[i] >> 16;
+ s32 = faible;
+ im32[i] = ( s32 << 16 ) | fort;
+ }
+ break;
+ default:
+ dbg.Verbose( 0, "PixelConvert::SwapZone: SwapCode value "
+ "(32 bits) not allowed." );
+ }
+ }
+}
+
+/**
+ * \brief Deal with endianity i.e. re-arange bytes inside the integer
+ */
+void PixelConvert::ReorderEndianity( uint8_t* pixelZone )
+{
+ if ( BitsAllocated != 8 )
+ {
+ SwapZone( pixelZone );
+ }
+
+ // 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 *)pixelZone;
+ 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 uncompress it.
+ * @param fp already open File Pointer
+ * @param destination Where decompressed fragments should end up
+ * @return Boolean
+ */
+bool PixelConvert::ReadAndDecompressJPEGFile(
+ uint8_t* destination,
+ FILE* fp )
+{
+ // Loop on the fragment[s]
+ for( JPEGFragmentsInfo::JPEGFragmentsList::iterator
+ it = JPEGInfo->Fragments.begin();
+ it != JPEGInfo->Fragments.end();
+ ++it )
+ {
+ fseek( fp, (*it)->Offset, SEEK_SET );
+
+ if ( IsJPEG2000 )
+ {
+ if ( ! gdcm_read_JPEG2000_file( fp, destination ) )
+ {
+ return false;
+ }
+ }
+ else if ( IsJPEGLossless )
+ {
+ // JPEG LossLess : call to xmedcom Lossless JPEG
+ JPEGLosslessDecodeImage( fp,
+ (uint16_t*)destination,
+ PixelSize * 8 * SamplesPerPixel,
+ (*it)->Length );
+ }
+ else if ( BitsStored == 8)
+ {
+ // JPEG Lossy : call to IJG 6b
+ if ( ! gdcm_read_JPEG_file ( fp, destination ) )
+ {
+ return false;
+ }
+ }
+ else if ( BitsStored == 12)
+ {
+ // Reading Fragment pixels
+ if ( ! gdcm_read_JPEG_file12 ( fp, destination ) )
+ {
+ return false;
+ }
+ }
+ else
+ {
+ // other JPEG lossy not supported
+ dbg.Error(" File::ReadAndDecompressJPEGFile: unknown jpeg lossy "
+ " compression ");
+ return false;
+ }
+
+ // Advance to next free location in destination
+ // for next fragment decompression (if any)
+ int length = XSize * YSize * SamplesPerPixel;
+ int numberBytes = BitsAllocated / 8;
+
+ destination = (uint8_t*)destination + length * numberBytes;
+
+ }
+ return true;
+}
+
+/**
+ * \brief Re-arrange the bits within the bytes.
+ * @param fp already open File Pointer
+ * @param destination Where decompressed fragments should end up
+ * @return Boolean
+ */
+bool PixelConvert::ReArrangeBits( uint8_t* pixelZone )
+ 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*)pixelZone;
+ 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*)pixelZone;
+ for(int i = 0; i<l; i++)
+ {
+ *deb = (*deb >> (BitsStored - HighBitPosition - 1)) & mask;
+ deb++;
+ }
+ }
+ else
+ {
+ dbg.Verbose(0, "PixelConvert::ReArrangeBits: weird image");
+ throw FormatError( "File::ReArrangeBits()",
+ "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* destination,
+ size_t imageDataSize )
+{
+ uint8_t* oldPixelZone = new uint8_t[ imageDataSize ];
+ memmove( oldPixelZone, destination, imageDataSize );
+
+ // 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 = oldPixelZone;
+ uint8_t* b = oldPixelZone + l;
+ uint8_t* c = oldPixelZone + 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;
+
+ *(destination++) = (uint8_t)R;
+ *(destination++) = (uint8_t)G;
+ *(destination++) = (uint8_t)B;
+ a++;
+ b++;
+ c++;
+ }
+ }
+ delete[] oldPixelZone;
+}
+
+/**
+ * \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* destination,
+ size_t imageDataSize )
+{
+ uint8_t* oldPixelZone = new uint8_t[ imageDataSize ];
+ memmove( oldPixelZone, destination, imageDataSize );
+
+ int l = XSize * YSize * ZSize;
+
+ uint8_t* a = oldPixelZone;
+ uint8_t* b = oldPixelZone + l;
+ uint8_t* c = oldPixelZone + l + l;
+
+ for (int j = 0; j < l; j++)
+ {
+ *(destination++) = *(a++);
+ *(destination++) = *(b++);
+ *(destination++) = *(c++);
+ }
+ delete[] oldPixelZone;
+}
+
+bool PixelConvert::ReadAndDecompressPixelData( void* destination, FILE* fp )
+{
+ if ( !fp )
+ {
+ return false;
+ }
+
+ if ( fseek(fp, PixelOffset, SEEK_SET) == -1 )
+ {
+ return false;
+ }
+
+ if ( BitsAllocated == 12 )
+ {
+ Decompress12BitsTo16Bits( (uint8_t*)destination, fp);
+ return true;
+ }
+
+ //////////// Decompressed File
+ if ( IsUncompressed )
+ {
+ size_t ItemRead = fread( destination, PixelDataLength, 1, fp);
+ if ( ItemRead != 1 )
+ {
+ return false;
+ }
+ else
+ {
+ return true;
+ }
+ }
+
+ ///////////// Run Length Encoding
+ if ( IsRLELossless )
+ {
+ return ReadAndDecompressRLEFile( destination, fp );
+ }
+
+ ///////////// SingleFrame/Multiframe JPEG Lossless/Lossy/2000
+ return ReadAndDecompressJPEGFile( (uint8_t*)destination, fp );
+}
+
+void PixelConvert::ComputeDecompressedImageDataSize()
+{
+ int 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 Decompress12BitsTo16Bits() )
+ if ( BitsAllocated == 12 )
+ {
+ bitsAllocated = 16;
+ }
+
+ DecompressedSize = XSize * YSize * ZSize
+ * ( bitsAllocated / 8 )
+ * SamplesPerPixel;
+}
+
+} // end namespace gdcm
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff