Program: gdcm
Module: $RCSfile: gdcmPixelReadConvert.cxx,v $
Language: C++
- Date: $Date: 2005/01/28 15:42:22 $
- Version: $Revision: 1.37 $
+ Date: $Date: 2005/02/02 16:34:55 $
+ Version: $Revision: 1.45 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
namespace gdcm
{
+//-----------------------------------------------------------------------------
#define str2num(str, typeNum) *((typeNum *)(str))
-
//-----------------------------------------------------------------------------
// Constructor / Destructor
PixelReadConvert::PixelReadConvert()
{
- RGB = 0;
- RGBSize = 0;
- Raw = 0;
- RawSize = 0;
- LutRGBA = 0;
- LutRedData = 0;
+ RGB = 0;
+ RGBSize = 0;
+ Raw = 0;
+ RawSize = 0;
+ LutRGBA = 0;
+ LutRedData = 0;
LutGreenData = 0;
- LutBlueData =0;
-}
-
-void PixelReadConvert::Squeeze()
-{
- if ( RGB )
- delete [] RGB;
- RGB = 0;
-
- if ( Raw )
- delete [] Raw;
- Raw = 0;
-
- if ( LutRGBA )
- delete [] LutRGBA;
- LutRGBA = 0;
+ LutBlueData = 0;
}
PixelReadConvert::~PixelReadConvert()
Squeeze();
}
-void PixelReadConvert::AllocateRGB()
+//-----------------------------------------------------------------------------
+// Public
+/**
+ * \brief Predicate to know wether the image[s] (once Raw) is RGB.
+ * \note See comments of \ref ConvertHandleColor
+ */
+bool PixelReadConvert::IsRawRGB()
{
- if ( RGB )
- delete [] RGB;
- RGB = new uint8_t[RGBSize];
+ if ( IsMonochrome
+ || PlanarConfiguration == 2
+ || IsPaletteColor )
+ {
+ return false;
+ }
+ return true;
}
-void PixelReadConvert::AllocateRaw()
+void PixelReadConvert::GrabInformationsFromFile( File *file )
{
- if ( Raw )
- delete [] Raw;
- Raw = new uint8_t[RawSize];
-}
+ // Number of Bits Allocated for storing a Pixel is defaulted to 16
+ // when absent from the file.
+ BitsAllocated = file->GetBitsAllocated();
+ if ( BitsAllocated == 0 )
+ {
+ BitsAllocated = 16;
+ }
-/**
- * \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 )
- throw ( FormatError )
-{
- int nbPixels = XSize * YSize;
- uint16_t* localDecompres = (uint16_t*)Raw;
+ // Number of "Bits Stored", defaulted to number of "Bits Allocated"
+ // when absent from the file.
+ BitsStored = file->GetBitsStored();
+ if ( BitsStored == 0 )
+ {
+ BitsStored = BitsAllocated;
+ }
- for( int p = 0; p < nbPixels; p += 2 )
+ // High Bit Position, defaulted to "Bits Allocated" - 1
+ HighBitPosition = file->GetHighBitPosition();
+ if ( HighBitPosition == 0 )
{
- uint8_t b0, b1, b2;
+ HighBitPosition = BitsAllocated - 1;
+ }
- fp->read( (char*)&b0, 1);
- if ( fp->fail() || fp->eof() )//Fp->gcount() == 1
+ XSize = file->GetXSize();
+ YSize = file->GetYSize();
+ ZSize = file->GetZSize();
+ SamplesPerPixel = file->GetSamplesPerPixel();
+ PixelSize = file->GetPixelSize();
+ PixelSign = file->IsSignedPixelData();
+ SwapCode = file->GetSwapCode();
+ std::string ts = file->GetTransferSyntax();
+ IsRaw =
+ ( ! file->IsDicomV3() )
+ || Global::GetTS()->GetSpecialTransferSyntax(ts) == TS::ImplicitVRLittleEndian
+ || Global::GetTS()->GetSpecialTransferSyntax(ts) == TS::ImplicitVRLittleEndianDLXGE
+ || Global::GetTS()->GetSpecialTransferSyntax(ts) == TS::ExplicitVRLittleEndian
+ || Global::GetTS()->GetSpecialTransferSyntax(ts) == TS::ExplicitVRBigEndian
+ || Global::GetTS()->GetSpecialTransferSyntax(ts) == TS::DeflatedExplicitVRLittleEndian;
+
+ IsJPEG2000 = Global::GetTS()->IsJPEG2000(ts);
+ IsJPEGLS = Global::GetTS()->IsJPEGLS(ts);
+ IsJPEGLossy = Global::GetTS()->IsJPEGLossy(ts);
+ IsJPEGLossless = Global::GetTS()->IsJPEGLossless(ts);
+ IsRLELossless = Global::GetTS()->IsRLELossless(ts);
+
+ PixelOffset = file->GetPixelOffset();
+ PixelDataLength = file->GetPixelAreaLength();
+ RLEInfo = file->GetRLEInfo();
+ JPEGInfo = file->GetJPEGInfo();
+
+ PlanarConfiguration = file->GetPlanarConfiguration();
+ IsMonochrome = file->IsMonochrome();
+ IsPaletteColor = file->IsPaletteColor();
+ IsYBRFull = file->IsYBRFull();
+
+ /////////////////////////////////////////////////////////////////
+ // LUT section:
+ HasLUT = file->HasLUT();
+ if ( HasLUT )
+ {
+ // Just in case some access to a File element requires disk access.
+ LutRedDescriptor = file->GetEntryValue( 0x0028, 0x1101 );
+ LutGreenDescriptor = file->GetEntryValue( 0x0028, 0x1102 );
+ LutBlueDescriptor = file->GetEntryValue( 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 file
+ // and when this fails we read the LUTs data directly 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
+ file->LoadEntryBinArea(0x0028, 0x1201);
+ LutRedData = (uint8_t*)file->GetEntryBinArea( 0x0028, 0x1201 );
+ if ( ! LutRedData )
{
- throw FormatError( "PixelReadConvert::ReadAndDecompress12BitsTo16Bits()",
- "Unfound first block" );
+ gdcmVerboseMacro( "Unable to read Red LUT data" );
}
- fp->read( (char*)&b1, 1 );
- if ( fp->fail() || fp->eof())//Fp->gcount() == 1
+ ////// Green round:
+ file->LoadEntryBinArea(0x0028, 0x1202);
+ LutGreenData = (uint8_t*)file->GetEntryBinArea(0x0028, 0x1202 );
+ if ( ! LutGreenData)
{
- throw FormatError( "PixelReadConvert::ReadAndDecompress12BitsTo16Bits()",
- "Unfound second block" );
+ gdcmVerboseMacro( "Unable to read Green LUT data" );
}
- fp->read( (char*)&b2, 1 );
- if ( fp->fail() || fp->eof())//Fp->gcount() == 1
+ ////// Blue round:
+ file->LoadEntryBinArea(0x0028, 0x1203);
+ LutBlueData = (uint8_t*)file->GetEntryBinArea( 0x0028, 0x1203 );
+ if ( ! LutBlueData )
{
- throw FormatError( "PixelReadConvert::ReadAndDecompress12BitsTo16Bits()",
- "Unfound second block" );
+ gdcmVerboseMacro( "Unable to read Blue LUT data" );
}
-
- // 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);
-
- /// \todo JPR Troubles expected on Big-Endian processors ?
}
+
+ ComputeRawAndRGBSizes();
}
-/**
- * \brief Try to deal with RLE 16 Bits.
- * We assume the RLE has already been parsed and loaded in
- * Raw (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 PixelReadConvert::DecompressRLE16BitsFromRLE8Bits( int NumberOfFrames )
+bool PixelReadConvert::ReadAndDecompressPixelData( std::ifstream *fp )
{
- 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* x = Raw;
- uint8_t* a = copyRaw;
- uint8_t* b = a + pixelNumber;
+ // ComputeRawAndRGBSizes is already made by
+ // ::GrabInformationsFromfile. So, the structure sizes are
+ // correct
+ Squeeze();
- for ( int i = 0; i < NumberOfFrames; i++ )
+ //////////////////////////////////////////////////
+ //// First stage: get our hands on the Pixel Data.
+ if ( !fp )
{
- for ( unsigned int j = 0; j < pixelNumber; j++ )
- {
- *(x++) = *(b++);
- *(x++) = *(a++);
- }
+ gdcmVerboseMacro( "Unavailable file pointer." );
+ return false;
}
- delete[] copyRaw;
-
- /// \todo check that operator new []didn't fail, and sometimes return false
- return true;
-}
+ fp->seekg( PixelOffset, std::ios::beg );
+ if( fp->fail() || fp->eof())
+ {
+ gdcmVerboseMacro( "Unable to find PixelOffset in file." );
+ return false;
+ }
-/**
- * \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 subRaw Sub region of \ref Raw where the decoded fragment
- * should be placed.
- * @param fragmentSize The length of the binary fragment as found on the disk.
- * @param RawSegmentSize The expected length of the fragment ONCE
- * Raw.
- * @param fp File Pointer: on entry the position should be the one of
- * the fragment to be decoded.
- */
-bool PixelReadConvert::ReadAndDecompressRLEFragment( uint8_t *subRaw,
- long fragmentSize,
- long RawSegmentSize,
- std::ifstream *fp )
-{
- int8_t count;
- long numberOfOutputBytes = 0;
- long numberOfReadBytes = 0;
+ AllocateRaw();
- while( numberOfOutputBytes < RawSegmentSize )
+ //////////////////////////////////////////////////
+ //// Second stage: read from disk dans decompress.
+ if ( BitsAllocated == 12 )
+ {
+ ReadAndDecompress12BitsTo16Bits( fp);
+ }
+ else if ( IsRaw )
{
- fp->read( (char*)&count, 1 );
- 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].
+ // This problem can be found when some obvious informations are found
+ // after the field containing the image data. In this case, these
+ // bad data are added to the size of the image (in the PixelDataLength
+ // variable). But RawSize is the right size of the image !
+ if( PixelDataLength != RawSize)
{
- fp->read( (char*)subRaw, count + 1);
- numberOfReadBytes += count + 1;
- subRaw += count + 1;
- numberOfOutputBytes += count + 1;
+ gdcmVerboseMacro( "Mismatch between PixelReadConvert and RawSize." );
+ }
+ if( PixelDataLength > RawSize)
+ {
+ fp->read( (char*)Raw, RawSize);
}
else
{
- if ( ( count <= -1 ) && ( count >= -127 ) )
- {
- int8_t newByte;
- fp->read( (char*)&newByte, 1);
- numberOfReadBytes += 1;
- for( int i = 0; i < -count + 1; i++ )
- {
- subRaw[i] = newByte;
- }
- subRaw += -count + 1;
- numberOfOutputBytes += -count + 1;
- }
+ fp->read( (char*)Raw, PixelDataLength);
}
- // if count = 128 output nothing
-
- if ( numberOfReadBytes > fragmentSize )
+
+ if ( fp->fail() || fp->eof())
{
- gdcmVerboseMacro( "Read more bytes than the segment size.");
+ gdcmVerboseMacro( "Reading of Raw pixel data failed." );
return false;
}
- }
- return true;
-}
-
-/**
- * \brief Reads from disk the Pixel Data of 'Run Length Encoded'
- * Dicom encapsulated file and decompress it.
- * @param fp already open File Pointer
- * at which the pixel data should be copied
- * @return Boolean
- */
-bool PixelReadConvert::ReadAndDecompressRLEFile( std::ifstream *fp )
-{
- uint8_t *subRaw = Raw;
- long RawSegmentSize = XSize * YSize;
-
- // Loop on the frame[s]
- RLEFrame *frame = RLEInfo->GetFirstFrame();
- while( frame )
+ }
+ else if ( IsRLELossless )
{
- // Loop on the fragments
- for( unsigned int k = 1; k <= frame->GetNumberOfFragments(); k++ )
+ if ( ! RLEInfo->DecompressRLEFile( fp, Raw, XSize, YSize, ZSize, BitsAllocated ) )
{
- fp->seekg(frame->GetOffset(k),std::ios::beg);
- ReadAndDecompressRLEFragment(subRaw,
- frame->GetLength(k),
- RawSegmentSize,
- fp);
- subRaw += RawSegmentSize;
+ gdcmVerboseMacro( "RLE decompressor failed." );
+ return false;
}
- frame = RLEInfo->GetNexttFrame();
}
-
- if ( BitsAllocated == 16 )
+ else
{
- // Try to deal with RLE 16 Bits
- (void)DecompressRLE16BitsFromRLE8Bits( ZSize );
+ // Default case concerns JPEG family
+ if ( ! ReadAndDecompressJPEGFile( fp ) )
+ {
+ gdcmVerboseMacro( "JPEG decompressor failed." );
+ return false;
+ }
}
+ ////////////////////////////////////////////
+ //// Third stage: twigle the bytes and bits.
+ ConvertReorderEndianity();
+ ConvertReArrangeBits();
+ ConvertHandleColor();
+
return true;
}
-/**
- * \brief Swap the bytes, according to \ref SwapCode.
- */
-void PixelReadConvert::ConvertSwapZone()
+void PixelReadConvert::Squeeze()
{
- unsigned int i;
-
- if( BitsAllocated == 16 )
- {
- uint16_t *im16 = (uint16_t*)Raw;
- switch( SwapCode )
- {
- case 1234:
- break;
- case 3412:
- case 2143:
- case 4321:
- for( i = 0; i < RawSize / 2; i++ )
- {
- im16[i]= (im16[i] >> 8) | (im16[i] << 8 );
- }
- break;
- default:
- gdcmVerboseMacro("SwapCode value (16 bits) not allowed.");
- }
- }
- else if( BitsAllocated == 32 )
- {
- uint32_t s32;
- uint16_t high;
- uint16_t low;
- uint32_t* im32 = (uint32_t*)Raw;
- switch ( SwapCode )
- {
- case 1234:
- break;
- case 4321:
- for( i = 0; i < RawSize / 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 < RawSize / 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 < RawSize / 4; i++ )
- {
- low = im32[i] & 0x0000ffff; // 3412
- high = im32[i] >> 16;
- s32 = low;
- im32[i] = ( s32 << 16 ) | high;
- }
- break;
- default:
- gdcmVerboseMacro("SwapCode value (32 bits) not allowed." );
- }
- }
+ if ( RGB )
+ delete [] RGB;
+ RGB = 0;
+
+ if ( Raw )
+ delete [] Raw;
+ Raw = 0;
+
+ if ( LutRGBA )
+ delete [] LutRGBA;
+ LutRGBA = 0;
}
/**
- * \brief Deal with endianness i.e. re-arange bytes inside the integer
+ * \brief Build the RGB image from the Raw imagage and the LUTs.
*/
-void PixelReadConvert::ConvertReorderEndianity()
+bool PixelReadConvert::BuildRGBImage()
{
- if ( BitsAllocated != 8 )
+ if ( RGB )
{
- ConvertSwapZone();
+ // The job is already done.
+ return true;
}
- // Special kludge in order to deal with xmedcon broken images:
- if ( BitsAllocated == 16
- && BitsStored < BitsAllocated
- && !PixelSign )
+ if ( ! Raw )
{
- int l = (int)( RawSize / ( BitsAllocated / 8 ) );
- uint16_t *deb = (uint16_t *)Raw;
- for(int i = 0; i<l; i++)
- {
- if( *deb == 0xffff )
- {
- *deb = 0;
- }
- deb++;
- }
+ // The job can't be done
+ return false;
}
-}
-
-
-/**
- * \brief Reads from disk the Pixel Data of JPEG Dicom encapsulated
- * file and decompress it. This function assumes that each
- * jpeg fragment contains a whole frame (jpeg file).
- * @param fp File Pointer
- * @return Boolean
- */
-bool PixelReadConvert::ReadAndDecompressJPEGFramesFromFile( std::ifstream *fp )
-{
- // Pointer to the Raw image
- //uint8_t *localRaw = Raw;
-
- // Precompute the offset localRaw will be shifted with
- int length = XSize * YSize * SamplesPerPixel;
- int numberBytes = BitsAllocated / 8;
-// // Loop on the fragment[s]
-// for( JPEGFragmentsInfo::JPEGFragmentsList::iterator
-// it = JPEGInfo->Fragments.begin();
-// it != JPEGInfo->Fragments.end();
-// ++it )
-// {
-// (*it)->DecompressJPEGFramesFromFile(fp, localRaw, BitsStored );
-//
-// // Advance to next free location in Raw
-// // for next fragment decompression (if any)
-//
-// localRaw += length * numberBytes;
-// }
- JPEGInfo->DecompressJPEGFramesFromFile(fp, Raw, BitsStored, numberBytes, length );
+ 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 < RawSize; ++i )
+ {
+ int j = Raw[i] * 4;
+ *localRGB++ = LutRGBA[j];
+ *localRGB++ = LutRGBA[j+1];
+ *localRGB++ = LutRGBA[j+2];
+ }
return true;
}
+//-----------------------------------------------------------------------------
+// Protected
+
+//-----------------------------------------------------------------------------
+// Private
/**
- * \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
+ * \brief Read from file a 12 bits per pixel image and decompress it
+ * into a 16 bits per pixel image.
*/
-bool PixelReadConvert::
-ReadAndDecompressJPEGSingleFrameFragmentsFromFile( std::ifstream *fp )
+void PixelReadConvert::ReadAndDecompress12BitsTo16Bits( std::ifstream *fp )
+ throw ( FormatError )
{
- // Loop on the fragment[s] to get total length
- size_t totalLength = JPEGInfo->GetFragmentsLength();
+ int nbPixels = XSize * YSize;
+ uint16_t *localDecompres = (uint16_t*)Raw;
- // Concatenate the jpeg fragments into a local buffer
- JOCTET *buffer = new JOCTET [totalLength];
- // Fill in the buffer:
- JPEGInfo->ReadAllFragments(fp, buffer);
+ for( int p = 0; p < nbPixels; p += 2 )
+ {
+ uint8_t b0, b1, b2;
- // kludge: // FIXME
- JPEGFragment *fragment = JPEGInfo->GetFirstFragment();
- fragment->DecompressJPEGSingleFrameFragmentsFromFile(buffer, totalLength, Raw, BitsStored);
+ fp->read( (char*)&b0, 1);
+ if ( fp->fail() || fp->eof() )
+ {
+ throw FormatError( "PixelReadConvert::ReadAndDecompress12BitsTo16Bits()",
+ "Unfound first block" );
+ }
- // free local buffer
- delete [] buffer;
-
- return true;
-}
+ fp->read( (char*)&b1, 1 );
+ if ( fp->fail() || fp->eof())
+ {
+ throw FormatError( "PixelReadConvert::ReadAndDecompress12BitsTo16Bits()",
+ "Unfound second block" );
+ }
-/**
- * \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 = JPEGInfo->GetFragmentsLength();
+ fp->read( (char*)&b2, 1 );
+ if ( fp->fail() || fp->eof())
+ {
+ throw FormatError( "PixelReadConvert::ReadAndDecompress12BitsTo16Bits()",
+ "Unfound second block" );
+ }
- // Concatenate the jpeg fragments into a local buffer
- JOCTET *buffer = new JOCTET [totalLength];
- // Fill in the buffer:
- JPEGInfo->ReadAllFragments(fp, buffer);
+ // 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);
- size_t howManyRead = 0;
- size_t howManyWritten = 0;
- size_t fragmentLength = 0;
-
- JPEGFragment *fragment = JPEGInfo->GetFirstFragment();
- while( fragment )
- {
- fragmentLength += fragment->GetLength();
-
- if (howManyRead > fragmentLength) continue;
-
- fragment->DecompressJPEGFragmentedFramesFromFile(buffer, Raw, BitsStored,
- howManyRead, howManyWritten,
- totalLength);
-
- if (howManyRead < fragmentLength)
- howManyRead = fragmentLength;
-
- fragment = JPEGInfo->GetNextFragment();
+ /// \todo JPR Troubles expected on Big-Endian processors ?
}
-
- // free local buffer
- delete [] buffer;
-
- return true;
}
/**
return false;
}
- if ( ( ZSize == 1 ) && ( JPEGInfo->GetFragmentCount() > 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->GetFragmentCount() == (size_t)ZSize)
- {
- }
-// 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 );
-// }
+ // else ??
+ // Precompute the offset localRaw will be shifted with
+ int length = XSize * YSize * SamplesPerPixel;
+ int numberBytes = BitsAllocated / 8;
+
+ JPEGInfo->DecompressFromFile(fp, Raw, BitsStored, numberBytes, length );
+ return true;
}
/**
- * \brief Re-arrange the bits within the bytes.
- * @return Boolean
+ * \brief Build Red/Green/Blue/Alpha LUT from File
+ * 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
*/
-bool PixelReadConvert::ConvertReArrangeBits() throw ( FormatError )
+void PixelReadConvert::BuildLUTRGBA()
{
- if ( BitsStored != BitsAllocated )
+ if ( LutRGBA )
{
- int l = (int)( RawSize / ( BitsAllocated / 8 ) );
- if ( BitsAllocated == 16 )
- {
- uint16_t mask = 0xffff;
- mask = mask >> ( BitsAllocated - BitsStored );
- uint16_t* deb = (uint16_t*)Raw;
- 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*)Raw;
- for(int i = 0; i<l; i++)
- {
- *deb = (*deb >> (BitsStored - HighBitPosition - 1)) & mask;
- deb++;
- }
- }
- else
- {
- gdcmVerboseMacro("Weird image");
- throw FormatError( "Weird image !?" );
- }
+ 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;
}
- return true;
-}
-/**
- * \brief Convert (cY plane, cB plane, cR plane) to RGB pixels
- * \warning Works on all the frames at a time
- */
-void PixelReadConvert::ConvertYcBcRPlanesToRGBPixels()
-{
- 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,
- // 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 = copyRaw;
- uint8_t *b = copyRaw + l;
- uint8_t *c = copyRaw + 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++ )
+ ////////////////////////////////////////////
+ // 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 )
{
- 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;
-
- *(localRaw++) = (uint8_t)R;
- *(localRaw++) = (uint8_t)G;
- *(localRaw++) = (uint8_t)B;
- a++;
- b++;
- c++;
- }
+ gdcmVerboseMacro( "Wrong Red LUT descriptor" );
}
- delete[] copyRaw;
-}
-
-/**
- * \brief Convert (Red plane, Green plane, Blue plane) to RGB pixels
- * \warning Works on all the frames at a time
- */
-void PixelReadConvert::ConvertRGBPlanesToRGBPixels()
-{
- uint8_t *localRaw = Raw;
- uint8_t *copyRaw = new uint8_t[ RawSize ];
- memmove( copyRaw, localRaw, RawSize );
-
- int l = XSize * YSize * ZSize;
-
- uint8_t* a = copyRaw;
- uint8_t* b = copyRaw + l;
- uint8_t* c = copyRaw + l + l;
-
- for (int j = 0; j < l; j++)
+
+ 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 )
{
- *(localRaw++) = *(a++);
- *(localRaw++) = *(b++);
- *(localRaw++) = *(c++);
+ gdcmVerboseMacro( "Wrong Green LUT descriptor" );
}
- delete[] copyRaw;
-}
-
-bool PixelReadConvert::ReadAndDecompressPixelData( std::ifstream *fp )
-{
- // ComputeRawAndRGBSizes is already made by
- // ::GrabInformationsFromfile. So, the structure sizes are
- // correct
- Squeeze();
-
- //////////////////////////////////////////////////
- //// First stage: get our hands on the Pixel Data.
- if ( !fp )
+
+ 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 )
{
- gdcmVerboseMacro( "Unavailable file pointer." );
- return false;
+ gdcmVerboseMacro( "Wrong Blue LUT descriptor" );
}
-
- fp->seekg( PixelOffset, std::ios::beg );
- if( fp->fail() || fp->eof())
+
+ ////////////////////////////////////////////////////////
+ if ( ( ! LutRedData ) || ( ! LutGreenData ) || ( ! LutBlueData ) )
{
- gdcmVerboseMacro( "Unable to find PixelOffset in file." );
- return false;
+ return;
}
- AllocateRaw();
+ ////////////////////////////////////////////////
+ // forge the 4 * 8 Bits Red/Green/Blue/Alpha LUT
+ LutRGBA = new uint8_t[ 1024 ]; // 256 * 4 (R, G, B, Alpha)
+ if ( !LutRGBA )
+ return;
- //////////////////////////////////////////////////
- //// Second stage: read from disk dans decompress.
- if ( BitsAllocated == 12 )
+ memset( LutRGBA, 0, 1024 );
+
+ int mult;
+ if ( ( nbitsR == 16 ) && ( BitsAllocated == 8 ) )
{
- ReadAndDecompress12BitsTo16Bits( fp);
+ // when LUT item size is different than pixel size
+ mult = 2; // high byte must be = low byte
}
- else if ( IsRaw )
+ else
{
- // This problem can be found when some obvious informations are found
- // after the field containing the image data. In this case, these
- // bad data are added to the size of the image (in the PixelDataLength
- // variable). But RawSize is the right size of the image !
- if( PixelDataLength != RawSize)
- {
- gdcmVerboseMacro( "Mismatch between PixelReadConvert and RawSize." );
- }
- if( PixelDataLength > RawSize)
- {
- fp->read( (char*)Raw, RawSize);
- }
- else
- {
- fp->read( (char*)Raw, PixelDataLength);
- }
-
- if ( fp->fail() || fp->eof())
- {
- gdcmVerboseMacro( "Reading of Raw pixel data failed." );
- return false;
- }
- }
- else if ( IsRLELossless )
+ // 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 )
{
- if ( ! ReadAndDecompressRLEFile( fp ) )
- {
- gdcmVerboseMacro( "RLE decompressor failed." );
- return false;
- }
+ *a = LutRedData[i*mult+1];
+ a += 4;
}
- else
+
+ a = LutRGBA + 1;
+ for( i=0; i < lengthG; ++i)
{
- // Default case concerns JPEG family
- if ( ! ReadAndDecompressJPEGFile( fp ) )
- {
- gdcmVerboseMacro( "JPEG decompressor failed." );
- return false;
- }
+ *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;
}
-
- ////////////////////////////////////////////
- //// Third stage: twigle the bytes and bits.
- ConvertReorderEndianity();
- ConvertReArrangeBits();
- ConvertHandleColor();
-
- return true;
}
-void PixelReadConvert::ConvertHandleColor()
+/**
+ * \brief Swap the bytes, according to \ref SwapCode.
+ */
+void PixelReadConvert::ConvertSwapZone()
{
- //////////////////////////////////
- // 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 will 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.
+ unsigned int i;
+
+ if( BitsAllocated == 16 )
+ {
+ uint16_t *im16 = (uint16_t*)Raw;
+ switch( SwapCode )
+ {
+ case 1234:
+ break;
+ case 3412:
+ case 2143:
+ case 4321:
+ for( i = 0; i < RawSize / 2; i++ )
+ {
+ im16[i]= (im16[i] >> 8) | (im16[i] << 8 );
+ }
+ break;
+ default:
+ gdcmVerboseMacro("SwapCode value (16 bits) not allowed.");
+ }
+ }
+ else if( BitsAllocated == 32 )
+ {
+ uint32_t s32;
+ uint16_t high;
+ uint16_t low;
+ uint32_t *im32 = (uint32_t*)Raw;
+ switch ( SwapCode )
+ {
+ case 1234:
+ break;
+ case 4321:
+ for( i = 0; i < RawSize / 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 < RawSize / 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 < RawSize / 4; i++ )
+ {
+ low = im32[i] & 0x0000ffff; // 3412
+ high = im32[i] >> 16;
+ s32 = low;
+ im32[i] = ( s32 << 16 ) | high;
+ }
+ break;
+ default:
+ gdcmVerboseMacro("SwapCode value (32 bits) not allowed." );
+ }
+ }
+}
- if ( ! IsRawRGB() )
+/**
+ * \brief Deal with endianness i.e. re-arange bytes inside the integer
+ */
+void PixelReadConvert::ConvertReorderEndianity()
+{
+ if ( BitsAllocated != 8 )
{
- // [Planar 2] OR [Photo D]: LUT intervention done outside
- return;
+ ConvertSwapZone();
}
-
- if ( PlanarConfiguration == 1 )
+
+ // Special kludge in order to deal with xmedcon broken images:
+ if ( BitsAllocated == 16
+ && BitsStored < BitsAllocated
+ && !PixelSign )
{
- if ( IsYBRFull )
- {
- // [Planar 1] AND [Photo C] (remember YBR_FULL_422 acts as RGB)
- ConvertYcBcRPlanesToRGBPixels();
- }
- else
+ int l = (int)( RawSize / ( BitsAllocated / 8 ) );
+ uint16_t *deb = (uint16_t *)Raw;
+ for(int i = 0; i<l; i++)
{
- // [Planar 1] AND [Photo C]
- ConvertRGBPlanesToRGBPixels();
+ if( *deb == 0xffff )
+ {
+ *deb = 0;
+ }
+ deb++;
}
- 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 Raw) is RGB.
- * \note See comments of \ref ConvertHandleColor
+ * \brief Re-arrange the bits within the bytes.
+ * @return Boolean
*/
-bool PixelReadConvert::IsRawRGB()
+bool PixelReadConvert::ConvertReArrangeBits() throw ( FormatError )
{
- if ( IsMonochrome
- || PlanarConfiguration == 2
- || IsPaletteColor )
+ if ( BitsStored != BitsAllocated )
{
- return false;
+ int l = (int)( RawSize / ( BitsAllocated / 8 ) );
+ if ( BitsAllocated == 16 )
+ {
+ uint16_t mask = 0xffff;
+ mask = mask >> ( BitsAllocated - BitsStored );
+ uint16_t *deb = (uint16_t*)Raw;
+ 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*)Raw;
+ for(int i = 0; i<l; i++)
+ {
+ *deb = (*deb >> (BitsStored - HighBitPosition - 1)) & mask;
+ deb++;
+ }
+ }
+ else
+ {
+ gdcmVerboseMacro("Weird image");
+ throw FormatError( "Weird image !?" );
+ }
}
return true;
}
-void PixelReadConvert::ComputeRawAndRGBSizes()
+/**
+ * \brief Convert (Red plane, Green plane, Blue plane) to RGB pixels
+ * \warning Works on all the frames at a time
+ */
+void PixelReadConvert::ConvertRGBPlanesToRGBPixels()
{
- 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;
- }
-
- RawSize = XSize * YSize * ZSize
- * ( bitsAllocated / 8 )
- * SamplesPerPixel;
- if ( HasLUT )
- {
- RGBSize = 3 * RawSize;
- }
- else
- {
- RGBSize = RawSize;
- }
-}
+ uint8_t *localRaw = Raw;
+ uint8_t *copyRaw = new uint8_t[ RawSize ];
+ memmove( copyRaw, localRaw, RawSize );
-void PixelReadConvert::GrabInformationsFromFile( File *file )
-{
- // Number of Bits Allocated for storing a Pixel is defaulted to 16
- // when absent from the file.
- BitsAllocated = file->GetBitsAllocated();
- if ( BitsAllocated == 0 )
- {
- BitsAllocated = 16;
- }
+ int l = XSize * YSize * ZSize;
- // Number of "Bits Stored", defaulted to number of "Bits Allocated"
- // when absent from the file.
- BitsStored = file->GetBitsStored();
- if ( BitsStored == 0 )
- {
- BitsStored = BitsAllocated;
- }
+ uint8_t *a = copyRaw;
+ uint8_t *b = copyRaw + l;
+ uint8_t *c = copyRaw + l + l;
- // High Bit Position, defaulted to "Bits Allocated" - 1
- HighBitPosition = file->GetHighBitPosition();
- if ( HighBitPosition == 0 )
+ for (int j = 0; j < l; j++)
{
- HighBitPosition = BitsAllocated - 1;
+ *(localRaw++) = *(a++);
+ *(localRaw++) = *(b++);
+ *(localRaw++) = *(c++);
}
+ delete[] copyRaw;
+}
- XSize = file->GetXSize();
- YSize = file->GetYSize();
- ZSize = file->GetZSize();
- SamplesPerPixel = file->GetSamplesPerPixel();
- PixelSize = file->GetPixelSize();
- PixelSign = file->IsSignedPixelData();
- SwapCode = file->GetSwapCode();
- std::string ts = file->GetTransferSyntax();
- IsRaw =
- ( ! file->IsDicomV3() )
- || Global::GetTS()->GetSpecialTransferSyntax(ts) == TS::ImplicitVRLittleEndian
- || Global::GetTS()->GetSpecialTransferSyntax(ts) == TS::ImplicitVRLittleEndianDLXGE
- || Global::GetTS()->GetSpecialTransferSyntax(ts) == TS::ExplicitVRLittleEndian
- || Global::GetTS()->GetSpecialTransferSyntax(ts) == TS::ExplicitVRBigEndian
- || Global::GetTS()->GetSpecialTransferSyntax(ts) == TS::DeflatedExplicitVRLittleEndian;
-
- IsJPEG2000 = Global::GetTS()->IsJPEG2000(ts);
- IsJPEGLS = Global::GetTS()->IsJPEGLS(ts);
- IsJPEGLossy = Global::GetTS()->IsJPEGLossy(ts);
- IsJPEGLossless = Global::GetTS()->IsJPEGLossless(ts);
- IsRLELossless = Global::GetTS()->IsRLELossless(ts);
-
- PixelOffset = file->GetPixelOffset();
- PixelDataLength = file->GetPixelAreaLength();
- RLEInfo = file->GetRLEInfo();
- JPEGInfo = file->GetJPEGInfo();
+/**
+ * \brief Convert (cY plane, cB plane, cR plane) to RGB pixels
+ * \warning Works on all the frames at a time
+ */
+void PixelReadConvert::ConvertYcBcRPlanesToRGBPixels()
+{
+ uint8_t *localRaw = Raw;
+ uint8_t *copyRaw = new uint8_t[ RawSize ];
+ memmove( copyRaw, localRaw, RawSize );
- PlanarConfiguration = file->GetPlanarConfiguration();
- IsMonochrome = file->IsMonochrome();
- IsPaletteColor = file->IsPaletteColor();
- IsYBRFull = file->IsYBRFull();
+ // 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;
- /////////////////////////////////////////////////////////////////
- // LUT section:
- HasLUT = file->HasLUT();
- if ( HasLUT )
- {
- // Just in case some access to a File element requires disk access.
- LutRedDescriptor = file->GetEntryValue( 0x0028, 0x1101 );
- LutGreenDescriptor = file->GetEntryValue( 0x0028, 0x1102 );
- LutBlueDescriptor = file->GetEntryValue( 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 file
- // and when this fails we read the LUTs data directly 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
- file->LoadEntryBinArea(0x0028, 0x1201);
- LutRedData = (uint8_t*)file->GetEntryBinArea( 0x0028, 0x1201 );
- if ( ! LutRedData )
- {
- gdcmVerboseMacro( "Unable to read Red LUT data" );
- }
+ uint8_t *a = copyRaw;
+ uint8_t *b = copyRaw + l;
+ uint8_t *c = copyRaw + l + l;
+ double R, G, B;
- ////// Green round:
- file->LoadEntryBinArea(0x0028, 0x1202);
- LutGreenData = (uint8_t*)file->GetEntryBinArea(0x0028, 0x1202 );
- if ( ! LutGreenData)
- {
- gdcmVerboseMacro( "Unable to read Green LUT data" );
- }
+ /// \todo : Replace by the 'well known' integer computation
+ /// counterpart. Refer to
+ /// http://lestourtereaux.free.fr/papers/data/yuvrgb.pdf
+ /// for code optimisation.
- ////// Blue round:
- file->LoadEntryBinArea(0x0028, 0x1203);
- LutBlueData = (uint8_t*)file->GetEntryBinArea( 0x0028, 0x1203 );
- if ( ! LutBlueData )
+ for ( int i = 0; i < nbFrames; i++ )
+ {
+ for ( int j = 0; j < l; j++ )
{
- gdcmVerboseMacro( "Unable to read Blue LUT data" );
+ 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;
+
+ *(localRaw++) = (uint8_t)R;
+ *(localRaw++) = (uint8_t)G;
+ *(localRaw++) = (uint8_t)B;
+ a++;
+ b++;
+ c++;
}
}
-
- ComputeRawAndRGBSizes();
+ delete[] copyRaw;
}
-/**
- * \brief Build Red/Green/Blue/Alpha LUT from File
- * 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 PixelReadConvert::BuildLUTRGBA()
+void PixelReadConvert::ConvertHandleColor()
{
- if ( LutRGBA )
+ //////////////////////////////////
+ // 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 will 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 ( ! IsRawRGB() )
{
+ // [Planar 2] OR [Photo D]: LUT intervention done outside
return;
}
- // Not so easy : see
- // http://www.barre.nom.fr/medical/dicom2/limitations.html#Color%20Lookup%20Tables
- if ( ! IsPaletteColor )
+ 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;
}
- if ( LutRedDescriptor == GDCM_UNFOUND
- || LutGreenDescriptor == GDCM_UNFOUND
- || LutBlueDescriptor == GDCM_UNFOUND )
+ // When planarConf is 0, and RLELossless (forbidden by Dicom norm)
+ // pixels need to be RGB-fied anyway
+ if (IsRLELossless)
{
- return;
+ ConvertRGBPlanesToRGBPixels();
}
+ // In *normal *case, when planarConf is 0, pixels are already in RGB
+}
- ////////////////////////////////////////////
- // 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 )
- {
- gdcmVerboseMacro( "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 )
- {
- gdcmVerboseMacro( "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 )
- {
- gdcmVerboseMacro( "Wrong Blue LUT descriptor" );
- }
-
- ////////////////////////////////////////////////////////
- if ( ( ! LutRedData ) || ( ! LutGreenData ) || ( ! LutBlueData ) )
+void PixelReadConvert::ComputeRawAndRGBSizes()
+{
+ 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 )
{
- return;
+ bitsAllocated = 16;
}
-
- ////////////////////////////////////////////////
- // 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 ) )
+ RawSize = XSize * YSize * ZSize
+ * ( bitsAllocated / 8 )
+ * SamplesPerPixel;
+ if ( HasLUT )
{
- // when LUT item size is different than pixel size
- mult = 2; // high byte must be = low byte
+ RGBSize = 3 * RawSize;
}
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;
+ RGBSize = RawSize;
}
}
-/**
- * \brief Build the RGB image from the Raw imagage and the LUTs.
- */
-bool PixelReadConvert::BuildRGBImage()
+void PixelReadConvert::AllocateRGB()
{
- if ( RGB )
- {
- // The job is already done.
- return true;
- }
-
- if ( ! Raw )
- {
- // The job can't be done
- return false;
- }
+ if ( RGB )
+ delete [] RGB;
+ RGB = new uint8_t[RGBSize];
+}
- 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 < RawSize; ++i )
- {
- int j = Raw[i] * 4;
- *localRGB++ = LutRGBA[j];
- *localRGB++ = LutRGBA[j+1];
- *localRGB++ = LutRGBA[j+2];
- }
- return true;
+void PixelReadConvert::AllocateRaw()
+{
+ if ( Raw )
+ delete [] Raw;
+ Raw = new uint8_t[RawSize];
}
+//-----------------------------------------------------------------------------
+// Print
/**
* \brief Print self.
* @param indent Indentation string to be prepended during printing.
* @param os Stream to print to.
*/
-void PixelReadConvert::Print( std::ostream &os, std::string const & indent )
+void PixelReadConvert::Print( std::ostream &os, std::string const &indent )
{
os << indent
<< "--- Pixel information -------------------------"
}
}
+//-----------------------------------------------------------------------------
} // end namespace gdcm
// NOTES on File internal calls
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff