Program: gdcm
Module: $RCSfile: gdcmPixelConvert.cxx,v $
Language: C++
- Date: $Date: 2004/10/08 08:56:48 $
- Version: $Revision: 1.2 $
+ Date: $Date: 2004/10/08 17:02:53 $
+ Version: $Revision: 1.4 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
* \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 gdcmPixelConvert::ConvertDecompress12BitsTo16Bits(
+ uint8_t* pixelZone,
+ int sizeX,
+ int sizeY,
+ FILE* filePtr)
+ throw ( gdcmFormatError )
{
- SetUncompressedSize( uncompressedSize );
- AllocateUncompressed();
-
- uint16_t* pdestination = (uint16_t*)Uncompressed;
+ int nbPixels = sizeX * sizeY;
+ 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 gdcmFormatError( "gdcmFile::ConvertDecompress12BitsTo16Bits()",
+ "Unfound first block" );
}
- ItemRead = fread( &b1, 1, 1, filePointer);
+
+ ItemRead = fread( &b1, 1, 1, filePtr);
if ( ItemRead != 1 )
{
- return false;
+ throw gdcmFormatError( "gdcmFile::ConvertDecompress12BitsTo16Bits()",
+ "Unfound second block" );
}
- ItemRead = fread( &b2, 1, 1, filePointer);
+
+ ItemRead = fread( &b2, 1, 1, filePtr);
if ( ItemRead != 1 )
{
- return false;
+ throw gdcmFormatError( "gdcmFile::ConvertDecompress12BitsTo16Bits()",
+ "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;
}
/**
* High Byte 'Planes'...(for what it may mean)
* @return Boolean
*/
-uint8_t* gdcmPixelConvert::UncompressRLE16BitsFromRLE8Bits(
+bool gdcmPixelConvert::UncompressRLE16BitsFromRLE8Bits(
int XSize,
int YSize,
int NumberOfFrames,
// 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;
}
}
- // 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 gdcmPixelConvert::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, "gdcmFile::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 gdcmPixelConvert::gdcm_read_RLE_file( void* image_buffer,
+ int XSize,
+ int YSize,
+ int ZSize,
+ int BitsAllocated,
+ gdcmRLEFramesInfo* RLEInfo,
+ FILE* fp )
+{
+ uint8_t* im = (uint8_t*)image_buffer;
+ long uncompressedSegmentSize = XSize * YSize;
+
+
+ // Loop on the frame[s]
+ for( gdcmRLEFramesInfo::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;
+ }
+ }
+
+ if ( BitsAllocated == 16 )
+ {
+ // Try to deal with RLE 16 Bits
+ (void)gdcmPixelConvert::UncompressRLE16BitsFromRLE8Bits(
+ XSize,
+ YSize,
+ 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
+ * @param swap swap code
+ * @param lgr Area Length
+ * @param nb Pixels Bit number
+ */
+void gdcmPixelConvert::SwapZone(void* im, int swap, int lgr, int nb)
+{
+ int i;
+
+ if( nb == 16 )
+ {
+ uint16_t* im16 = (uint16_t*)im;
+ switch( swap )
+ {
+ case 0:
+ case 12:
+ case 1234:
+ break;
+ case 21:
+ case 3412:
+ case 2143:
+ case 4321:
+ for(i=0; i < lgr/2; i++)
+ {
+ im16[i]= (im16[i] >> 8) | (im16[i] << 8 );
+ }
+ break;
+ default:
+ std::cout << "SWAP value (16 bits) not allowed :i" << swap <<
+ std::endl;
+ }
+ }
+ else if( nb == 32 )
+ {
+ uint32_t s32;
+ uint16_t fort, faible;
+ uint32_t* im32 = (uint32_t*)im;
+ switch ( swap )
+ {
+ case 0:
+ case 1234:
+ break;
+ case 4321:
+ for(i = 0; i < lgr/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 < lgr/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 < lgr/4; i++)
+ {
+ faible = im32[i] & 0x0000ffff; // 3412
+ fort = im32[i] >> 16;
+ s32 = faible;
+ im32[i] = ( s32 << 16 ) | fort;
+ }
+ break;
+ default:
+ std::cout << "SWAP value (32 bits) not allowed : " << swap <<
+ std::endl;
+ }
+ }
+}
+
+
+
+/**
+ * \brief Deal with endianity i.e. re-arange bytes inside the integer
+ */
+void gdcmPixelConvert::ConvertReorderEndianity( uint8_t* pixelZone,
+ size_t imageDataSize,
+ int numberBitsStored,
+ int numberBitsAllocated,
+ int swapCode,
+ bool signedPixel)
+{
+ if ( numberBitsAllocated != 8 )
+ {
+ SwapZone( pixelZone, swapCode, imageDataSize, numberBitsAllocated );
+ }
+
+ // Special kludge in order to deal with xmedcon broken images:
+ if ( ( numberBitsAllocated == 16 )
+ && ( numberBitsStored < numberBitsAllocated )
+ && ( ! signedPixel ) )
+ {
+ int l = (int)(imageDataSize / (numberBitsAllocated/8));
+ uint16_t *deb = (uint16_t *)pixelZone;
+ for(int i = 0; i<l; i++)
+ {
+ if( *deb == 0xffff )
+ {
+ *deb = 0;
+ }
+ deb++;
+ }
+ }
}
+
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