/*=========================================================================
-
+
Program: gdcm
Module: $RCSfile: gdcmPixelReadConvert.cxx,v $
Language: C++
- Date: $Date: 2005/01/24 14:52:50 $
- Version: $Revision: 1.33 $
+ Date: $Date: 2008/05/20 09:22:03 $
+ Version: $Revision: 1.128 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
=========================================================================*/
+#include "gdcmPixelReadConvert.h"
#include "gdcmDebug.h"
#include "gdcmFile.h"
#include "gdcmGlobal.h"
#include "gdcmTS.h"
-#include "gdcmPixelReadConvert.h"
#include "gdcmDocEntry.h"
#include "gdcmRLEFramesInfo.h"
#include "gdcmJPEGFragmentsInfo.h"
+#include "gdcmSegmentedPalette.h"
#include <fstream>
#include <stdio.h> //for sscanf
-namespace gdcm
+#if defined(__BORLANDC__)
+ #include <mem.h> // for memset
+#endif
+
+namespace GDCM_NAME_SPACE
{
-#define str2num(str, typeNum) *((typeNum *)(str))
+//bool ReadMPEGFile (std::ifstream *fp, char *inputdata, size_t lenght);
+bool gdcm_read_JPEG2000_file (void* raw,
+ char *inputdata, size_t inputlength);
+//-----------------------------------------------------------------------------
+#define str2num(str, typeNum) *((typeNum *)(str))
//-----------------------------------------------------------------------------
// Constructor / Destructor
-PixelReadConvert::PixelReadConvert()
+/// Constructor
+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;
+ LutBlueData = 0;
+ RLEInfo = 0;
+ JPEGInfo = 0;
+ UserFunction = 0;
+ FileInternal = 0;
}
-void PixelReadConvert::Squeeze()
+/// Canonical Destructor
+PixelReadConvert::~PixelReadConvert()
{
- if ( RGB )
+ Squeeze();
+}
+
+//-----------------------------------------------------------------------------
+// Public
+/**
+ * \brief Predicate to know whether the image[s] (once Raw) is RGB.
+ * \note See comments of ConvertHandleColor
+ */
+bool PixelReadConvert::IsRawRGB()
+{
+ if ( IsMonochrome
+ || PlanarConfiguration == 2
+ || IsPaletteColor )
{
- delete [] RGB;
- }
- RGB = 0;
+ return false;
+ }
+ return true;
+}
+/**
+ * \brief Gets various usefull informations from the file header
+ * @param file gdcm::File pointer
+ * @param fileHelper gdcm::FileHelper pointer
+ */
+void PixelReadConvert::GrabInformationsFromFile( File *file,
+ FileHelper *fileHelper )
+{
+ // 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;
+ }
+ else if ( BitsAllocated > 8 && BitsAllocated < 16 && BitsAllocated != 12 )
+ {
+ BitsAllocated = 16;
+ }
- if ( Raw )
+ // Number of "Bits Stored", defaulted to number of "Bits Allocated"
+ // when absent from the file.
+ BitsStored = file->GetBitsStored();
+ if ( BitsStored == 0 )
{
- delete [] Raw;
+ BitsStored = BitsAllocated;
}
- Raw = 0;
- if ( LutRGBA )
+ // High Bit Position, defaulted to "Bits Allocated" - 1
+ HighBitPosition = file->GetHighBitPosition();
+ if ( HighBitPosition == 0 )
+ {
+ HighBitPosition = BitsAllocated - 1;
+ }
+
+ XSize = file->GetXSize();
+ YSize = file->GetYSize();
+ ZSize = file->GetZSize();
+ TSize = file->GetTSize();
+ SamplesPerPixel = file->GetSamplesPerPixel();
+ //PixelSize = file->GetPixelSize(); Useless
+ PixelSign = file->IsSignedPixelData();
+ SwapCode = file->GetSwapCode();
+
+ IsPrivateGETransferSyntax = IsMPEG
+ = IsJPEG2000 = IsJPEGLS = IsJPEGLossy
+ = IsJPEGLossless = IsRLELossless
+ = false;
+
+ if (! file->IsDicomV3() ) // Should be ACR-NEMA file
+ {
+ IsRaw = true;
+ }
+ else
+ {
+ std::string ts = file->GetTransferSyntax();
+
+ IsRaw = false;
+ while (true) // shorter to write than 'if elseif elseif elseif' ...
+ {
+ // mind the order : check the most usual first.
+ if( IsRaw = (Global::GetTS()->GetSpecialTransferSyntax(ts) == TS::ExplicitVRLittleEndian)) break;
+ if( IsRaw = (Global::GetTS()->GetSpecialTransferSyntax(ts) == TS::ImplicitVRLittleEndian)) break;
+ if( IsRaw = (Global::GetTS()->GetSpecialTransferSyntax(ts) == TS::ExplicitVRBigEndian)) break;
+ if( IsRaw = (Global::GetTS()->GetSpecialTransferSyntax(ts) == TS::ImplicitVRBigEndianPrivateGE)) break;
+ // DeflatedExplicitVRLittleEndian syntax means the whole Dataset (Header + Pixels) is compressed !
+ // Not dealt with ! (Parser hangs)
+ //if( IsRaw = Global::GetTS()->GetSpecialTransferSyntax(ts) == TS::DeflatedExplicitVRLittleEndian) break;
+ break;
+ }
+ // cache whether this is a strange GE transfer syntax (which uses
+ // a little endian transfer syntax for the header and a big endian
+ // transfer syntax for the pixel data).
+ IsPrivateGETransferSyntax =
+ ( Global::GetTS()->GetSpecialTransferSyntax(ts) == TS::ImplicitVRBigEndianPrivateGE );
+
+ IsMPEG = IsJPEG2000 = IsJPEGLS = IsJPEGLossy = IsJPEGLossless = IsRLELossless = false;
+ if (!IsRaw)
+ {
+ while(true)
+ {
+ // mind the order : check the most usual first.
+ if( IsJPEGLossy = (Global::GetTS()->IsJPEGLossy(ts))) break;
+ if( IsJPEGLossless = (Global::GetTS()->IsJPEGLossless(ts))) break;
+ if( IsRLELossless = (Global::GetTS()->IsRLELossless(ts))) break;
+ if( IsJPEG2000 = (Global::GetTS()->IsJPEG2000(ts))) break;
+ if( IsMPEG = (Global::GetTS()->IsMPEG(ts))) break;
+ if( IsJPEGLS = (Global::GetTS()->IsJPEGLS(ts))) break;
+ // DeflatedExplicitVRLittleEndian is considered as 'Unexpected'
+ // (we don't know yet how to process !)
+ gdcmWarningMacro("Unexpected Transfer Syntax :[" << ts << "]");
+ break;
+ }
+ }
+ }
+
+ PixelOffset = file->GetPixelOffset();
+ PixelDataLength = file->GetPixelAreaLength();
+ RLEInfo = file->GetRLEInfo();
+ JPEGInfo = file->GetJPEGInfo();
+
+ IsMonochrome = file->IsMonochrome();
+ IsMonochrome1 = file->IsMonochrome1();
+ IsPaletteColor = file->IsPaletteColor();
+ IsYBRFull = file->IsYBRFull();
+
+ PlanarConfiguration = file->GetPlanarConfiguration();
+
+ /////////////////////////////////////////////////////////////////
+ // LUT section:
+ HasLUT = file->HasLUT();
+ if ( HasLUT )
{
- delete [] LutRGBA;
+/*
+ C.7.6.3.1.5
+ The three values of Palette Color Lookup Table Descriptor (0028,1101-1103)
+ describe the format of the Lookup Table Data in the corresponding
+ Data Element (0028,1201-1203) or (0028,1221-1223).
+
+ The first value is the number of entries in the lookup table.
+ When the number of table entries is equal to 2**16 then this value shall be 0.
+
+ The second value is the first stored pixel value mapped.
+ This pixel value is mapped to the first entry in the Lookup Table Data.
+ All image pixel values less than the first entry value mapped are also
+ mapped to the first entry in the Lookup Table Data.
+ An image pixel value one greater than the first entry value mapped is
+ mapped to the second entry in the Lookup Table Data.
+ Subsequent image pixel values are mapped to the subsequent entries in
+ the Lookup Table Data up to an image pixel value equal to number of
+ entries + first entry value mapped - 1 which is mapped to the last entry
+ in the Lookup Table Data.
+ Image pixel values greater than or equal to number of entries + first entry
+ value mapped are also mapped to the last entry in the Lookup Table Data.
+
+ The third value specifies the number of bits for each entry in the Lookup
+ Table Data. It shall take the value of 8 or 16.
+ The LUT Data shall be stored in a format equivalent to 8 or 16 bits
+ allocated where the high bit is equal to bits allocated-1.
+
+ When the Palette Color Lookup Table Descriptor (0028,1101-1103) are used as
+ part of the Palette Color Lookup Table Module, the third value shall be
+ equal to 16.
+
+ Note: A value of 16 indicates the Lookup Table Data will range from (0,0,0)
+ minimum intensity to (65535,65535,65535) maximum intensity.
+
+*/
+
+ // Just in case some access to a File element requires disk access.
+ LutRedDescriptor = file->GetEntryString( 0x0028, 0x1101 );
+ LutGreenDescriptor = file->GetEntryString( 0x0028, 0x1102 );
+ LutBlueDescriptor = file->GetEntryString( 0x0028, 0x1103 );
+ // Is it a Segmented Palette ? Check if we find the red one:
+ if( file->GetDocEntry(0x0028,0x1221) ) // no need to check for blue & green
+ {
+ GDCM_NAME_SPACE::TagKey DCM_RedPaletteColorLookupTableDescriptor (0x0028, 0x1101);
+ GDCM_NAME_SPACE::TagKey DCM_GreenPaletteColorLookupTableDescriptor (0x0028, 0x1102);
+ GDCM_NAME_SPACE::TagKey DCM_BluePaletteColorLookupTableDescriptor (0x0028, 0x1103);
+
+ GDCM_NAME_SPACE::TagKey DCM_SegmentedRedPaletteColorLookupTableData (0x0028, 0x1221);
+ GDCM_NAME_SPACE::TagKey DCM_SegmentedGreenPaletteColorLookupTableData (0x0028, 0x1222);
+ GDCM_NAME_SPACE::TagKey DCM_SegmentedBluePaletteColorLookupTableData (0x0028, 0x1223);
+
+
+ LutRedData = new uint8_t[65535*2]; // FIXME: leak
+ LutGreenData = new uint8_t[65535*2];
+ LutBlueData = new uint8_t[65535*2];
+ // TODO need to check file is indeed PALETTE COLOR:
+ ReadPaletteInto(file, DCM_RedPaletteColorLookupTableDescriptor,
+ DCM_SegmentedRedPaletteColorLookupTableData,LutRedData);
+ ReadPaletteInto(file, DCM_GreenPaletteColorLookupTableDescriptor,
+ DCM_SegmentedGreenPaletteColorLookupTableData,LutGreenData);
+ ReadPaletteInto(file, DCM_BluePaletteColorLookupTableDescriptor,
+ DCM_SegmentedBluePaletteColorLookupTableData,LutBlueData);
+
+ }
+ else
+ {
+
+ // FIXME : The following comment is probabely meaningless, since LUT are *always*
+ // loaded at parsing time, whatever their length is.
+
+ // 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. DataEntry::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 )
+ {
+ gdcmWarningMacro("Unable to read Red Palette Color Lookup Table data");
+ }
+
+ // //// Green round:
+ file->LoadEntryBinArea(0x0028, 0x1202);
+ LutGreenData = (uint8_t*)file->GetEntryBinArea(0x0028, 0x1202 );
+ if ( ! LutGreenData)
+ {
+ gdcmWarningMacro("Unable to read Green Palette Color Lookup Table data");
+ }
+
+ // //// Blue round:
+ file->LoadEntryBinArea(0x0028, 0x1203);
+ LutBlueData = (uint8_t*)file->GetEntryBinArea( 0x0028, 0x1203 );
+ if ( ! LutBlueData )
+ {
+ gdcmWarningMacro("Unable to read Blue Palette Color Lookup Table data");
+ }
+ }
}
- LutRGBA = 0;
+ FileInternal = file;
+ FH = fileHelper;
+ ComputeRawAndRGBSizes();
}
-PixelReadConvert::~PixelReadConvert()
+/// \brief Reads from disk and decompresses Pixels
+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 )
+ {
+ gdcmWarningMacro( "Unavailable file pointer." );
+ return false;
+ }
+
+ fp->seekg( PixelOffset, std::ios::beg );
+ if ( fp->fail() || fp->eof() )
+ {
+ gdcmWarningMacro( "Unable to find PixelOffset in file." );
+ return false;
+ }
+
+ AllocateRaw();
+
+ //////////////////////////////////////////////////
+
+ CallStartMethod(); // for progress bar
+ unsigned int count = 0;
+ unsigned int frameSize;
+ unsigned int bitsAllocated = BitsAllocated;
+ //if(bitsAllocated == 12)
+ if(bitsAllocated > 8 && bitsAllocated < 16)
+ bitsAllocated = 16;
+ frameSize = XSize*YSize*SamplesPerPixel*bitsAllocated/8;
+
+ //// Second stage: read from disk and decompress.
+
+ if ( BitsAllocated == 12 ) // We suppose 'BitsAllocated' = 12 only exist for uncompressed files
+ {
+ ReadAndDecompress12BitsTo16Bits( fp);
+ }
+ else if ( IsRaw )
+ {
+ // 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 )
+ {
+ gdcmWarningMacro( "Mismatch between PixelReadConvert : "
+ << PixelDataLength << " and RawSize : " << RawSize );
+ }
+
+ //todo : is it the right patch?
+ char *raw = (char*)Raw;
+ uint32_t remainingLength;
+ unsigned int i;
+ unsigned int lengthToRead;
+
+ if ( PixelDataLength > RawSize )
+ lengthToRead = RawSize;
+ else
+ lengthToRead = PixelDataLength;
+
+ // perform a frame by frame reading
+ remainingLength = lengthToRead;
+ unsigned int nbFrames = lengthToRead / frameSize;
+ for (i=0;i<nbFrames; i++)
+ {
+ Progress = (float)(count+1)/(float)nbFrames;
+ fp->read( raw, frameSize);
+ raw += frameSize;
+ remainingLength -= frameSize;
+ count++;
+ }
+ if (remainingLength !=0 )
+ fp->read( raw, remainingLength);
+
+ if ( fp->fail() || fp->eof())
+ {
+ gdcmWarningMacro( "Reading of Raw pixel data failed." );
+ return false;
+ }
+ }
+ else if ( IsRLELossless )
+ {
+ if ( ! RLEInfo->DecompressRLEFile
+ ( fp, Raw, XSize, YSize, ZSize, TSize, BitsAllocated ) )
+ {
+ gdcmWarningMacro( "RLE decompressor failed." );
+ return false;
+ }
+ }
+ else if ( IsMPEG )
+ {
+ //gdcmWarningMacro( "Sorry, MPEG not yet taken into account" );
+ //return false;
+ // fp has already been seek to start of mpeg
+ //ReadMPEGFile(fp, (char*)Raw, PixelDataLength);
+ return true;
+ }
+ else
+ {
+ // Default case concerns JPEG family
+ if ( ! ReadAndDecompressJPEGFile( fp ) )
+ {
+ gdcmWarningMacro( "JPEG decompressor ( ReadAndDecompressJPEGFile()"
+ << " method ) failed." );
+ return false;
+ }
+ }
+
+ ////////////////////////////////////////////
+ //// Third stage: twigle the bytes and bits.
+ ConvertReorderEndianity();
+ ConvertReArrangeBits();
+ ConvertFixGreyLevels();
+ if (UserFunction) // user is allowed to Mirror, TopDown, Rotate,...the image
+ UserFunction( Raw, FileInternal);
+ ConvertHandleColor();
+
+ return true;
}
-void PixelReadConvert::AllocateRGB()
+/// Deletes Pixels Area
+void PixelReadConvert::Squeeze()
{
- if ( RGB ) {
- delete [] RGB;
- }
- RGB = new uint8_t[ RGBSize ];
+ if ( RGB )
+ delete [] RGB;
+ RGB = 0;
+
+ if ( Raw )
+ delete [] Raw;
+ Raw = 0;
+
+ //if ( LutRGBA )
+ // delete [] LutRGBA;
+ //LutRGBA = 0;
}
-void PixelReadConvert::AllocateRaw()
+/**
+ * \brief Build the RGB image from the Raw image and the LUTs.
+ */
+bool PixelReadConvert::BuildRGBImage()
{
- if ( Raw ) {
- delete [] Raw;
- }
- Raw = new uint8_t[ RawSize ];
+ if ( RGB )
+ {
+ // The job is already done.
+ return true;
+ }
+
+ if ( ! Raw )
+ {
+ // The job can't be done
+ return false;
+ }
+
+ BuildLUTRGBA();
+ if ( ! LutRGBA )
+ {
+ // The job can't be done
+ return false;
+ }
+
+ gdcmDebugMacro( "--> BuildRGBImage" );
+
+ // Build RGB Pixels
+ AllocateRGB();
+
+ int j;
+ if ( BitsAllocated <= 8 )
+ {
+ uint8_t *localRGB = RGB;
+ for (size_t i = 0; i < RawSize; ++i )
+ {
+ j = Raw[i] * 4;
+ *localRGB++ = LutRGBA[j];
+ *localRGB++ = LutRGBA[j+1];
+ *localRGB++ = LutRGBA[j+2];
+ }
+ }
+
+ else // deal with 16 bits pixels and 16 bits Palette color
+ {
+ uint16_t *localRGB = (uint16_t *)RGB;
+ for (size_t i = 0; i < RawSize/2; ++i )
+ {
+ j = ((uint16_t *)Raw)[i] * 4;
+ *localRGB++ = ((uint16_t *)LutRGBA)[j];
+ *localRGB++ = ((uint16_t *)LutRGBA)[j+1];
+ *localRGB++ = ((uint16_t *)LutRGBA)[j+2];
+ }
+ }
+
+ return true;
}
+//-----------------------------------------------------------------------------
+// Protected
+
+//-----------------------------------------------------------------------------
+// Private
/**
* \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;
+ /// \todo Fix the 3D, 4D pb
+ int nbPixels = XSize * YSize * TSize;
+ uint16_t *localDecompres = (uint16_t*)Raw;
for( int p = 0; p < nbPixels; p += 2 )
{
uint8_t b0, b1, b2;
fp->read( (char*)&b0, 1);
- if ( fp->fail() || fp->eof() )//Fp->gcount() == 1
+ if ( fp->fail() || fp->eof() )
{
throw FormatError( "PixelReadConvert::ReadAndDecompress12BitsTo16Bits()",
"Unfound first block" );
}
fp->read( (char*)&b1, 1 );
- if ( fp->fail() || fp->eof())//Fp->gcount() == 1
+ if ( fp->fail() || fp->eof())
{
throw FormatError( "PixelReadConvert::ReadAndDecompress12BitsTo16Bits()",
"Unfound second block" );
}
fp->read( (char*)&b2, 1 );
- if ( fp->fail() || fp->eof())//Fp->gcount() == 1
+ if ( fp->fail() || fp->eof())
{
throw FormatError( "PixelReadConvert::ReadAndDecompress12BitsTo16Bits()",
"Unfound second block" );
}
/**
- * \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)
+ * \brief Reads from disk the Pixel Data of JPEG Dicom encapsulated
+ * file and decompress it.
+ * @param fp File Pointer
* @return Boolean
*/
-bool PixelReadConvert::DecompressRLE16BitsFromRLE8Bits( int NumberOfFrames )
+bool PixelReadConvert::ReadAndDecompressJPEGFile( 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;
-
- for ( int i = 0; i < NumberOfFrames; i++ )
+ if ( IsJPEG2000 )
{
- for ( unsigned int j = 0; j < pixelNumber; j++ )
+ // make sure this is the right JPEG compression
+ assert( !IsJPEGLossless || !IsJPEGLossy || !IsJPEGLS );
+ // FIXME this is really ugly but it seems I have to load the complete
+ // jpeg2000 stream to use jasper:
+ // I don't think we'll ever be able to deal with multiple fragments properly
+
+ if( ZSize == 1 )
+ {
+ unsigned long inputlength = 0;
+ JPEGFragment *jpegfrag = JPEGInfo->GetFirstFragment();
+ while( jpegfrag )
+ {
+ inputlength += jpegfrag->GetLength();
+ jpegfrag = JPEGInfo->GetNextFragment();
+ }
+ gdcmAssertMacro( inputlength != 0);
+ uint8_t *inputdata = new uint8_t[inputlength];
+ char *pinputdata = (char*)inputdata;
+ jpegfrag = JPEGInfo->GetFirstFragment();
+ while( jpegfrag )
+ {
+ fp->seekg( jpegfrag->GetOffset(), std::ios::beg);
+ fp->read(pinputdata, jpegfrag->GetLength());
+ pinputdata += jpegfrag->GetLength();
+ jpegfrag = JPEGInfo->GetNextFragment();
+ }
+ // Warning the inputdata buffer is deleted in the function
+ if ( gdcm_read_JPEG2000_file( Raw,
+ (char*)inputdata, inputlength ) )
+ {
+ return true;
+ }
+ // wow what happen, must be an error
+ gdcmWarningMacro( "gdcm_read_JPEG2000_file() failed ");
+ return false;
+ }
+ else
+ {
+ if( (unsigned int)ZSize != JPEGInfo->GetFragmentCount() )
+ {
+ gdcmErrorMacro( "Sorry GDCM does not handle this type of fragments" );
+ return false;
+ }
+ // Hopefully every dicom fragment is *exactly* the j2k stream
+ JPEGFragment *jpegfrag = JPEGInfo->GetFirstFragment();
+ char *praw = (char*)Raw;
+ while( jpegfrag )
+ {
+ unsigned long inputlength = jpegfrag->GetLength();
+ char *inputdata = new char[inputlength];
+ fp->seekg( jpegfrag->GetOffset(), std::ios::beg);
+ fp->read(inputdata, jpegfrag->GetLength());
+ // Warning the inputdata buffer is deleted in the function
+ gdcm_read_JPEG2000_file( praw,
+ inputdata, inputlength) ;
+ praw += XSize*YSize*SamplesPerPixel*(BitsAllocated/8);
+ jpegfrag = JPEGInfo->GetNextFragment();
+ }
+ return true;
+ }
+ }
+ else if ( IsJPEGLS )
+ {
+ // make sure this is the right JPEG compression
+ assert( !IsJPEGLossless || !IsJPEGLossy || !IsJPEG2000 );
+ // WARNING : JPEG-LS is NOT the 'classical' Jpeg Lossless :
+ // [JPEG-LS is the basis for new lossless/near-lossless compression
+ // standard for continuous-tone images intended for JPEG2000. The standard
+ // is based on the LOCO-I algorithm (LOw COmplexity LOssless COmpression
+ // for Images) developed at Hewlett-Packard Laboratories]
+ //
+ // see http://datacompression.info/JPEGLS.shtml
+ //
+#if 0
+ std::cerr << "count:" << JPEGInfo->GetFragmentCount() << std::endl;
+ unsigned long inputlength = 0;
+ JPEGFragment *jpegfrag = JPEGInfo->GetFirstFragment();
+ while( jpegfrag )
{
- *(x++) = *(b++);
- *(x++) = *(a++);
+ inputlength += jpegfrag->GetLength();
+ jpegfrag = JPEGInfo->GetNextFragment();
}
- }
-
- delete[] copyRaw;
+ gdcmAssertMacro( inputlength != 0);
+ uint8_t *inputdata = new uint8_t[inputlength];
+ char *pinputdata = (char*)inputdata;
+ jpegfrag = JPEGInfo->GetFirstFragment();
+ while( jpegfrag )
+ {
+ fp->seekg( jpegfrag->GetOffset(), std::ios::beg);
+ fp->read(pinputdata, jpegfrag->GetLength());
+ pinputdata += jpegfrag->GetLength();
+ jpegfrag = JPEGInfo->GetNextFragment();
+ }
- /// \todo check that operator new []didn't fail, and sometimes return false
- return true;
+ //fp->read((char*)Raw, PixelDataLength);
+
+ std::ofstream out("/tmp/jpegls.jpg");
+ out.write((char*)inputdata, inputlength);
+ out.close();
+ delete[] inputdata;
+#endif
+
+ gdcmWarningMacro( "Sorry, JPEG-LS not yet taken into account" );
+ fp->seekg( JPEGInfo->GetFirstFragment()->GetOffset(), std::ios::beg);
+// if ( ! gdcm_read_JPEGLS_file( fp,Raw ) )
+ return false;
+ }
+ else if( JPEGInfo )
+ {
+ // make sure this is the right JPEG compression
+ assert( !IsJPEGLS || !IsJPEG2000 );
+ // Precompute the offset localRaw will be shifted with
+ int length = XSize * YSize * ZSize * SamplesPerPixel;
+ int numberBytes = BitsAllocated / 8;
+
+ // to avoid major troubles when BitsStored == 8 && BitsAllocated==16 !
+ int dummy;
+ if (BitsStored == 8 && BitsAllocated==16)
+ dummy = 16;
+ else
+ dummy = BitsStored;
+ JPEGInfo->DecompressFromFile(fp, Raw, dummy, numberBytes, length );
+ return true;
+ }
+ //else (not sure how get there...), must be one of those crazy DICOM 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.
+ * \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::ReadAndDecompressRLEFragment( uint8_t *subRaw,
- long fragmentSize,
- long RawSegmentSize,
- std::ifstream *fp )
+void PixelReadConvert::BuildLUTRGBA()
{
- int8_t count;
- long numberOfOutputBytes = 0;
- long numberOfReadBytes = 0;
- while( numberOfOutputBytes < RawSegmentSize )
+ // Note to code reviewers :
+ // The problem is *much more* complicated, since a lot of manufacturers
+ // Don't follow the norm :
+ // have a look at David Clunie's remark at the end of this .cxx file.
+ 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 )
+ {
+ gdcmWarningMacro( "(At least) a LUT Descriptor is missing" );
+ 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; // nb of items in LUT descriptor (must be = 3)
+
+ nbRead = sscanf( LutRedDescriptor.c_str(),
+ "%d\\%d\\%d",
+ &lengthR, &debR, &nbitsR );
+ if ( nbRead != 3 )
+ {
+ gdcmWarningMacro( "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 )
+ {
+ gdcmWarningMacro( "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 )
+ {
+ gdcmWarningMacro( "Wrong Blue LUT descriptor" );
+ }
+
+ gdcmDebugMacro(" lengthR " << lengthR << " debR "
+ << debR << " nbitsR " << nbitsR);
+ gdcmDebugMacro(" lengthG " << lengthG << " debG "
+ << debG << " nbitsG " << nbitsG);
+ gdcmDebugMacro(" lengthB " << lengthB << " debB "
+ << debB << " nbitsB " << nbitsB);
+
+ if ( !lengthR ) // if = 2^16, this shall be 0 see : CP-143
+ lengthR=65536;
+ if ( !lengthG ) // if = 2^16, this shall be 0
+ lengthG=65536;
+ if ( !lengthB ) // if = 2^16, this shall be 0
+ lengthB=65536;
+
+ ////////////////////////////////////////////////////////
+
+ if ( ( ! LutRedData ) || ( ! LutGreenData ) || ( ! LutBlueData ) )
+ {
+ gdcmWarningMacro( "(At least) a LUT is missing" );
+ return;
+ }
+
+ // -------------------------------------------------------------
+
+ if ( BitsAllocated <= 8 )
{
- 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].
+ // forge the 4 * 8 Bits Red/Green/Blue/Alpha LUT
+ LutRGBA = new uint8_t[ 1024 ]; // 256 * 4 (R, G, B, Alpha)
+ if ( !LutRGBA )
+ return;
+ LutItemNumber = 256;
+ LutItemSize = 8;
+ memset( LutRGBA, 0, 1024 );
+
+ int mult;
+ if ( ( nbitsR == 16 ) && ( BitsAllocated == 8 ) )
{
- fp->read( (char*)subRaw, count + 1);
- numberOfReadBytes += count + 1;
- subRaw += count + 1;
- numberOfOutputBytes += count + 1;
+ // when LUT item size is different than pixel size
+ mult = 2; // high byte must be = low byte
}
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;
- }
+ // See PS 3.3-2003 C.11.1.1.2 p 619
+ mult = 1;
}
- // if count = 128 output nothing
- if ( numberOfReadBytes > fragmentSize )
+ // 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;
+
+ //take "Subscript of the first Lut Value" (debR,debG,debB) into account!
+
+ //FIXME : +1 : to get 'low value' byte
+ // Trouble expected on Big Endian Processors ?
+ // 16 BIts Per Pixel Palette Color to be swapped?
+
+ a = LutRGBA + 0 + debR;
+ for( i=0; i < lengthR; ++i )
{
- gdcmVerboseMacro( "Read more bytes than the segment size.");
- return false;
+ *a = LutRedData[i*mult+1];
+ a += 4;
+ }
+
+ a = LutRGBA + 1 + debG;
+ for( i=0; i < lengthG; ++i)
+ {
+ *a = LutGreenData[i*mult+1];
+ a += 4;
+ }
+
+ a = LutRGBA + 2 + debB;
+ 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;
}
}
- 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]
- for( RLEFramesInfo::RLEFrameList::iterator
- it = RLEInfo->Frames.begin();
- it != RLEInfo->Frames.end();
- ++it )
+ else
{
- // Loop on the fragments
- for( unsigned int k = 1; k <= (*it)->NumberFragments; k++ )
+ // Probabely the same stuff is to be done for 16 Bits Pixels
+ // with 65536 entries LUT ?!?
+ // Still looking for accurate info on the web :-(
+
+ gdcmWarningMacro( "Sorry Palette Color Lookup Tables not yet dealt with"
+ << " for 16 Bits Per Pixel images" );
+
+ // forge the 4 * 16 Bits Red/Green/Blue/Alpha LUT
+
+ LutRGBA = (uint8_t *)new uint16_t[ 65536*4 ]; // 2^16 * 4 (R, G, B, Alpha)
+ if ( !LutRGBA )
+ return;
+ memset( LutRGBA, 0, 65536*4*2 ); // 16 bits = 2 bytes ;-)
+
+ LutItemNumber = 65536;
+ LutItemSize = 16;
+
+ int i;
+ uint16_t *a16;
+
+ //take "Subscript of the first Lut Value" (debR,debG,debB) into account!
+
+ a16 = (uint16_t*)LutRGBA + 0 + debR;
+ for( i=0; i < lengthR; ++i )
{
- fp->seekg( (*it)->Offset[k] , std::ios::beg );
- (void)ReadAndDecompressRLEFragment( subRaw,
- (*it)->Length[k],
- RawSegmentSize,
- fp );
- subRaw += RawSegmentSize;
+ *a16 = ((uint16_t*)LutRedData)[i];
+ a16 += 4;
}
- }
+
+ a16 = (uint16_t*)LutRGBA + 1 + debG;
+ for( i=0; i < lengthG; ++i)
+ {
+ *a16 = ((uint16_t*)LutGreenData)[i];
+ a16 += 4;
+ }
+
+ a16 = (uint16_t*)LutRGBA + 2 + debB;
+ for(i=0; i < lengthB; ++i)
+ {
+ *a16 = ((uint16_t*)LutBlueData)[i];
+ a16 += 4;
+ }
+
+ a16 = (uint16_t*)LutRGBA + 3 ;
+ for(i=0; i < 65536; ++i)
+ {
+ *a16 = 1; // Alpha component
+ a16 += 4;
+ }
+// Just to 'see' the LUT, at debug time
+// Don't remove this commented out code.
- if ( BitsAllocated == 16 )
- {
- // Try to deal with RLE 16 Bits
- (void)DecompressRLE16BitsFromRLE8Bits( ZSize );
- }
+ a16=(uint16_t*)LutRGBA;
+ for (int j=0;j<65536;j++)
+ {
+ std::cout << *a16 << " " << *(a16+1) << " "
+ << *(a16+2) << " " << *(a16+3) << std::endl;
+ a16+=4;
+ }
- return true;
+ }
}
/**
- * \brief Swap the bytes, according to \ref SwapCode.
+ * \brief Swap the bytes, according to SwapCode.
*/
void PixelReadConvert::ConvertSwapZone()
{
unsigned int i;
- if( BitsAllocated == 16 )
+ // If this file is 'ImplicitVR BigEndian PrivateGE Transfer Syntax',
+ // then the header is in little endian format and the pixel data is in
+ // big endian format. When reading the header, GDCM has already established
+ // a byte swapping code suitable for this machine to read the
+ // header. In TS::ImplicitVRBigEndianPrivateGE, this code will need
+ // to be switched in order to read the pixel data. This must be
+ // done REGARDLESS of the processor endianess!
+ //
+ // Example: Assume we are on a little endian machine. When
+ // GDCM reads the header, the header will match the machine
+ // endianess and the swap code will be established as a no-op.
+ // When GDCM reaches the pixel data, it will need to switch the
+ // swap code to do big endian to little endian conversion.
+ //
+ // Now, assume we are on a big endian machine. When GDCM reads the
+ // header, the header will be recognized as a different endianess
+ // than the machine endianess, and a swap code will be established
+ // to convert from little endian to big endian. When GDCM readers
+ // the pixel data, the pixel data endianess will now match the
+ // machine endianess. But we currently have a swap code that
+ // converts from little endian to big endian. In this case, we
+ // need to switch the swap code to a no-op.
+ //
+ // Therefore, in either case, if the file is in
+ // 'ImplicitVR BigEndian PrivateGE Transfer Syntax', then GDCM needs to switch
+ // the byte swapping code when entering the pixel data.
+
+ int tempSwapCode = SwapCode;
+ if ( IsPrivateGETransferSyntax )
+ {
+ gdcmWarningMacro(" IsPrivateGETransferSyntax found; turn the SwapCode");
+ // PrivateGETransferSyntax only exists for 'true' Dicom images
+ // we assume there is no 'exotic' 32 bits endianess!
+ if (SwapCode == 1234)
+ {
+ tempSwapCode = 4321;
+ }
+ else if (SwapCode == 4321)
+ {
+ tempSwapCode = 1234;
+ }
+ }
+
+ if ( BitsAllocated == 16 )
{
uint16_t *im16 = (uint16_t*)Raw;
- switch( SwapCode )
+ switch( tempSwapCode )
{
case 1234:
break;
}
break;
default:
- gdcmVerboseMacro("SwapCode value (16 bits) not allowed.");
+ gdcmWarningMacro("SwapCode value (16 bits) not allowed."
+ << tempSwapCode);
}
}
- else if( BitsAllocated == 32 )
+ else if ( BitsAllocated == 32 )
{
uint32_t s32;
uint16_t high;
uint16_t low;
- uint32_t* im32 = (uint32_t*)Raw;
- switch ( SwapCode )
+ uint32_t *im32 = (uint32_t*)Raw;
+ switch ( tempSwapCode )
{
case 1234:
break;
}
break;
default:
- gdcmVerboseMacro("SwapCode value (32 bits) not allowed." );
+ gdcmWarningMacro("SwapCode value (32 bits) not allowed." << tempSwapCode );
}
}
}
uint16_t *deb = (uint16_t *)Raw;
for(int i = 0; i<l; i++)
{
- if( *deb == 0xffff )
+ if ( *deb == 0xffff )
{
*deb = 0;
}
}
}
-
/**
- * \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
+ * \brief Deal with Grey levels i.e. re-arange them
+ * to have low values = dark, high values = bright
*/
-bool PixelReadConvert::ReadAndDecompressJPEGFramesFromFile( std::ifstream *fp )
+void PixelReadConvert::ConvertFixGreyLevels()
{
- // 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 );
- return true;
-}
-
-/**
- * \brief Reads from disk the Pixel Data of JPEG Dicom encapsulated
- * file and decompress it. This function assumes that the dicom
- * image is a single frame split into several JPEG fragments.
- * Those fragments will be glued together into a memory buffer
- * before being read.
- * @param fp File Pointer
- * @return Boolean
- */
-bool PixelReadConvert::
-ReadAndDecompressJPEGSingleFrameFragmentsFromFile( std::ifstream *fp )
-{
- // Loop on the fragment[s] to get total length
- size_t totalLength = JPEGInfo->GetFragmentsLength();
-
- // Concatenate the jpeg fragments into a local buffer
- JOCTET *buffer = new JOCTET [totalLength];
- // Fill in the buffer:
- JPEGInfo->ReadAllFragments(fp, buffer);
-
- // kludge: // FIXME
- JPEGFragmentsInfo::JPEGFragmentsList::const_iterator it = JPEGInfo->Fragments.begin();
- (*it)->DecompressJPEGSingleFrameFragmentsFromFile(buffer, totalLength, Raw, BitsStored);
-
- // free local buffer
- delete [] buffer;
-
- return true;
-}
-
-/**
- * \brief Reads from disk the Pixel Data of JPEG Dicom encapsulated
- * file and decompress it. This function handles the generic
- * and complex case where the DICOM contains several frames,
- * and some of the frames are possibly split into several JPEG
- * fragments.
- * @param fp File Pointer
- * @return Boolean
- */
-bool PixelReadConvert::
-ReadAndDecompressJPEGFragmentedFramesFromFile( std::ifstream *fp )
-{
- // Loop on the fragment[s] to get total length
- size_t totalLength = JPEGInfo->GetFragmentsLength();
+ if (!IsMonochrome1)
+ return;
- // Concatenate the jpeg fragments into a local buffer
- JOCTET *buffer = new JOCTET [totalLength];
- // Fill in the buffer:
- JPEGInfo->ReadAllFragments(fp, buffer);
+ uint32_t i; // to please M$VC6
+ int16_t j;
- size_t howManyRead = 0;
- size_t howManyWritten = 0;
- size_t fragmentLength = 0;
-
- JPEGFragmentsInfo::JPEGFragmentsList::const_iterator it;
- for( it = JPEGInfo->Fragments.begin() ;
- (it != JPEGInfo->Fragments.end()) && (howManyRead < totalLength);
- ++it )
+ if (!PixelSign)
{
- fragmentLength += (*it)->Length;
-
- if (howManyRead > fragmentLength) continue;
-
- (*it)->DecompressJPEGFragmentedFramesFromFile(buffer, Raw, BitsStored, howManyRead, howManyWritten, totalLength);
-
- if (howManyRead < fragmentLength)
- howManyRead = fragmentLength;
- }
+ if ( BitsAllocated == 8 )
+ {
+ uint8_t *deb = (uint8_t *)Raw;
+ for (i=0; i<RawSize; i++)
+ {
+ *deb = 255 - *deb;
+ deb++;
+ }
+ return;
+ }
- // free local buffer
- delete [] buffer;
-
- return true;
-}
+ if ( BitsAllocated == 16 )
+ {
+ uint16_t mask =1;
+ for (j=0; j<BitsStored-1; j++)
+ {
+ mask = (mask << 1) +1; // will be fff when BitsStored=12
+ }
-/**
- * \brief Reads from disk the Pixel Data of JPEG Dicom encapsulated
- * file and decompress it.
- * @param fp File Pointer
- * @return Boolean
- */
-bool PixelReadConvert::ReadAndDecompressJPEGFile( std::ifstream *fp )
-{
- if ( IsJPEG2000 )
+ uint16_t *deb = (uint16_t *)Raw;
+ for (i=0; i<RawSize/2; i++)
+ {
+ *deb = mask - *deb;
+ deb++;
+ }
+ return;
+ }
+ }
+ else
{
- fp->seekg( (*JPEGInfo->Fragments.begin())->Offset, std::ios::beg);
-// if ( ! gdcm_read_JPEG2000_file( fp,Raw ) )
- return false;
+ if ( BitsAllocated == 8 )
+ {
+ uint8_t smask8 = 255;
+ uint8_t *deb = (uint8_t *)Raw;
+ for (i=0; i<RawSize; i++)
+ {
+ *deb = smask8 - *deb;
+ deb++;
+ }
+ return;
+ }
+ if ( BitsAllocated == 16 )
+ {
+ uint16_t smask16 = 65535;
+ uint16_t *deb = (uint16_t *)Raw;
+ for (i=0; i<RawSize/2; i++)
+ {
+ *deb = smask16 - *deb;
+ deb++;
+ }
+ return;
+ }
}
-
-// if ( ( ZSize == 1 ) && ( JPEGInfo->Fragments.size() > 1 ) )
-// {
-// // we have one frame split into several fragments
-// // we will pack those fragments into a single buffer and
-// // read from it
-// return ReadAndDecompressJPEGSingleFrameFragmentsFromFile( fp );
-// }
-// else if (JPEGInfo->Fragments.size() == (size_t)ZSize)
-// {
- // suppose each fragment is a frame
- return ReadAndDecompressJPEGFramesFromFile( fp );
-// }
-// else
-// {
-// // The dicom image contains frames containing fragments of images
-// // a more complex algorithm :-)
-// return ReadAndDecompressJPEGFragmentedFramesFromFile( fp );
-// }
}
/**
* \brief Re-arrange the bits within the bytes.
- * @return Boolean
+ * @return Boolean always true
*/
bool PixelReadConvert::ConvertReArrangeBits() throw ( FormatError )
{
+
if ( BitsStored != BitsAllocated )
{
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++)
+ // pmask : to mask the 'unused bits' (may contain overlays)
+ uint16_t pmask = 0xffff;
+
+ // It's up to the user to decide if he wants to ignore overlays (if any),
+ // not to gdcm, without asking.
+ // default is NOT TO LOAD, in order not to confuse ITK users (and others!).
+
+ if ( !FH->GetKeepOverlays() ) // mask spurious bits ! (overlay are NOT loaded!)
{
- *deb = (*deb >> (BitsStored - HighBitPosition - 1)) & mask;
- deb++;
+ pmask = pmask >> ( BitsAllocated - BitsStored );
+ }
+ // else : it's up to the user to manage the 'pixels + overlays' he just loaded!
+
+ uint16_t *deb = (uint16_t*)Raw;
+
+ if ( !PixelSign ) // Pixels are unsigned
+ {
+ for(int i = 0; i<l; i++)
+ {
+ *deb = (*deb >> (BitsStored - HighBitPosition - 1)) & pmask;
+ deb++;
+ }
+ }
+ else // Pixels are signed
+ {
+ // Hope there is never ACR-NEMA-like overlays within signed pixels (?!?)
+
+ // smask : to check the 'sign' when BitsStored != BitsAllocated
+ uint16_t smask = 0x0001;
+ smask = smask << ( 16 - (BitsAllocated - BitsStored + 1) );
+ // nmask : to propagate sign bit on negative values
+ int16_t nmask = (int16_t)0x8000;
+ nmask = nmask >> ( BitsAllocated - BitsStored - 1 );
+
+ for(int i = 0; i<l; i++)
+ {
+ *deb = *deb >> (BitsStored - HighBitPosition - 1);
+ if ( *deb & smask )
+ {
+ *deb = *deb | nmask;
+ }
+ else
+ {
+ *deb = *deb & pmask;
+ }
+ 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++)
+ // pmask : to mask the 'unused bits' (may contain overlays)
+ uint32_t pmask = 0xffffffff;
+ pmask = pmask >> ( BitsAllocated - BitsStored );
+
+ uint32_t *deb = (uint32_t*)Raw;
+
+ if ( !PixelSign )
{
- *deb = (*deb >> (BitsStored - HighBitPosition - 1)) & mask;
- deb++;
+ for(int i = 0; i<l; i++)
+ {
+ *deb = (*deb >> (BitsStored - HighBitPosition - 1)) & pmask;
+ deb++;
+ }
+ }
+ else
+ {
+ // smask : to check the 'sign' when BitsStored != BitsAllocated
+ uint32_t smask = 0x00000001;
+ smask = smask >> ( 32 - (BitsAllocated - BitsStored +1 ));
+ // nmask : to propagate sign bit on negative values
+ int32_t nmask = 0x80000000;
+ nmask = nmask >> ( BitsAllocated - BitsStored -1 );
+
+ for(int i = 0; i<l; i++)
+ {
+ *deb = *deb >> (BitsStored - HighBitPosition - 1);
+ if ( *deb & smask )
+ *deb = *deb | nmask;
+ else
+ *deb = *deb & pmask;
+ deb++;
+ }
}
}
else
{
- gdcmVerboseMacro("Weird image");
+ gdcmWarningMacro("Weird image (BitsAllocated !=8, 12, 16, 32)");
throw FormatError( "Weird image !?" );
}
}
}
/**
- * \brief Convert (cY plane, cB plane, cR plane) to RGB pixels
+ * \brief Convert (Red plane, Green plane, Blue plane) to RGB pixels
* \warning Works on all the frames at a time
*/
-void PixelReadConvert::ConvertYcBcRPlanesToRGBPixels()
+void PixelReadConvert::ConvertRGBPlanesToRGBPixels()
{
+ gdcmWarningMacro("--> ConvertRGBPlanesToRGBPixels");
+
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;
+ int l = XSize * YSize * 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++ )
+ for (int j = 0; j < l; j++)
{
- 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++;
- }
+ *(localRaw++) = *(a++);
+ *(localRaw++) = *(b++);
+ *(localRaw++) = *(c++);
}
delete[] copyRaw;
}
/**
- * \brief Convert (Red plane, Green plane, Blue plane) to RGB pixels
+ * \brief Convert (cY plane, cB plane, cR plane) to RGB pixels
* \warning Works on all the frames at a time
*/
-void PixelReadConvert::ConvertRGBPlanesToRGBPixels()
+void PixelReadConvert::ConvertYcBcRPlanesToRGBPixels()
{
+ // Remarks for YBR newbees :
+ // YBR_FULL works very much like RGB, i.e. three samples per pixel,
+ // just the color space is YCbCr instead of RGB. This is particularly useful
+ // for doppler ultrasound where most of the image is grayscale
+ // (i.e. only populates the Y components) and Cb and Cr are mostly zero,
+ // except for the few patches of color on the image.
+ // On such images, RLE achieves a compression ratio that is much better
+ // than the compression ratio on an equivalent RGB image.
+
+ gdcmWarningMacro("--> ConvertYcBcRPlanesToRGBPixels");
+
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++)
- {
- *(localRaw++) = *(a++);
- *(localRaw++) = *(b++);
- *(localRaw++) = *(c++);
- }
- delete[] copyRaw;
-}
-
-bool PixelReadConvert::ReadAndDecompressPixelData( std::ifstream *fp )
-{
- // ComputeRawAndRGBSizes is already made by
- // ::GrabInformationsFromHeader. So, the structure sizes are
- // correct
- Squeeze();
+ // 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
+ //
- //////////////////////////////////////////////////
- //// First stage: get our hands on the Pixel Data.
- if ( !fp )
- {
- gdcmVerboseMacro( "Unavailable file pointer." );
- return false;
- }
+ /// \todo : find an example to see how 3rd dim and 4th dim work together
+ int l = XSize * YSize * TSize;
+ int nbFrames = ZSize;
- fp->seekg( PixelOffset, std::ios::beg );
- if( fp->fail() || fp->eof())
- {
- gdcmVerboseMacro( "Unable to find PixelOffset in file." );
- return false;
- }
+ uint8_t *a = copyRaw + 0;
+ uint8_t *b = copyRaw + l;
+ uint8_t *c = copyRaw + l+ l;
+ int32_t R, G, B;
- AllocateRaw();
+ /// We replaced easy to understand but time consuming floating point
+ /// computations by the 'well known' integer computation counterpart
+ /// Refer to :
+ /// http://lestourtereaux.free.fr/papers/data/yuvrgb.pdf
+ /// for code optimisation.
- //////////////////////////////////////////////////
- //// Second stage: read from disk dans decompress.
- if ( BitsAllocated == 12 )
- {
- ReadAndDecompress12BitsTo16Bits( fp);
- }
- else if ( IsRaw )
+ for ( int i = 0; i < nbFrames; i++ )
{
- // 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
+ for ( int j = 0; j < l; j++ )
{
- fp->read( (char*)Raw, PixelDataLength);
- }
+ R = 38142 *(*a-16) + 52298 *(*c -128);
+ G = 38142 *(*a-16) - 26640 *(*c -128) - 12845 *(*b -128);
+ B = 38142 *(*a-16) + 66093 *(*b -128);
- if ( fp->fail() || fp->eof())
- {
- gdcmVerboseMacro( "Reading of Raw pixel data failed." );
- return false;
- }
- }
- else if ( IsRLELossless )
- {
- if ( ! ReadAndDecompressRLEFile( fp ) )
- {
- gdcmVerboseMacro( "RLE decompressor failed." );
- return false;
- }
- }
- else
- {
- // Default case concerns JPEG family
- if ( ! ReadAndDecompressJPEGFile( fp ) )
- {
- gdcmVerboseMacro( "JPEG decompressor failed." );
- return false;
- }
- }
+ R = (R+16384)>>15;
+ G = (G+16384)>>15;
+ B = (B+16384)>>15;
- ////////////////////////////////////////////
- //// Third stage: twigle the bytes and bits.
- ConvertReorderEndianity();
- ConvertReArrangeBits();
- ConvertHandleColor();
+ if (R < 0) R = 0;
+ if (G < 0) G = 0;
+ if (B < 0) B = 0;
+ if (R > 255) R = 255;
+ if (G > 255) G = 255;
+ if (B > 255) B = 255;
- return true;
+ *(localRaw++) = (uint8_t)R;
+ *(localRaw++) = (uint8_t)G;
+ *(localRaw++) = (uint8_t)B;
+ a++;
+ b++;
+ c++;
+ }
+ }
+ delete[] copyRaw;
}
+/// \brief Deals with the color decoding i.e. handle:
+/// - R, G, B planes (as opposed to RGB pixels)
+/// - YBR (various) encodings.
+/// - LUT[s] (or "PALETTE COLOR").
+
void PixelReadConvert::ConvertHandleColor()
{
//////////////////////////////////
// - "Planar Configuration" = 0,
// - "Photometric Interpretation" = "PALETTE COLOR".
// Hence gdcm will use the folowing "heuristic" in order to be tolerant
- // towards Dicom-non-conformance files:
+ // towards Dicom-non-conformant files:
// << whatever the "Planar Configuration" value might be, a
// "Photometric Interpretation" set to "PALETTE COLOR" forces
// a LUT intervention >>
// - [Planar 1] AND [Photo C] handled with ConvertYcBcRPlanesToRGBPixels()
// - [Planar 2] OR [Photo D] requires LUT intervention.
+ gdcmDebugMacro("--> ConvertHandleColor "
+ << "Planar Configuration " << PlanarConfiguration );
+
if ( ! IsRawRGB() )
{
// [Planar 2] OR [Photo D]: LUT intervention done outside
+ gdcmDebugMacro("--> RawRGB : LUT intervention done outside");
return;
}
if ( IsYBRFull )
{
// [Planar 1] AND [Photo C] (remember YBR_FULL_422 acts as RGB)
+ gdcmDebugMacro("--> YBRFull");
ConvertYcBcRPlanesToRGBPixels();
}
else
{
// [Planar 1] AND [Photo C]
+ gdcmDebugMacro("--> YBRFull");
ConvertRGBPlanesToRGBPixels();
}
return;
}
// When planarConf is 0, and RLELossless (forbidden by Dicom norm)
- // pixels need to be RGB-fied anyway
+ // pixels need to be RGB-fyied anyway
+
if (IsRLELossless)
- {
+ {
+ gdcmDebugMacro("--> RLE Lossless");
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
- */
-bool PixelReadConvert::IsRawRGB()
-{
- if ( IsMonochrome
- || PlanarConfiguration == 2
- || IsPaletteColor )
- {
- return false;
- }
- return true;
+ // In *normal *case, when planarConf is 0, pixels are already in RGB
}
+/// Computes the Pixels Size
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() )
+ // ReadAndDecompress12BitsTo16Bits() )
if ( BitsAllocated == 12 )
{
bitsAllocated = 16;
}
- RawSize = XSize * YSize * ZSize
+ RawSize = XSize * YSize * ZSize * TSize
* ( bitsAllocated / 8 )
* SamplesPerPixel;
if ( HasLUT )
{
- RGBSize = 3 * RawSize;
+ RGBSize = 3 * RawSize; // works for 8 and 16 bits per Pixel
}
else
{
RGBSize = RawSize;
}
+ RawSize += RawSize%2;
+ RGBSize += RGBSize%2;
}
-void PixelReadConvert::GrabInformationsFromHeader( File *header )
-{
- // 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, defaulted to "Bits Allocated" - 1
- 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();
- std::string ts = header->GetTransferSyntax();
- IsRaw =
- ( ! header->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 = 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 )
- {
- // Just in case some access to a File element requires disk access.
- LutRedDescriptor = header->GetEntry( 0x0028, 0x1101 );
- LutGreenDescriptor = header->GetEntry( 0x0028, 0x1102 );
- LutBlueDescriptor = header->GetEntry( 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
- header->LoadEntryBinArea(0x0028, 0x1201);
- LutRedData = (uint8_t*)header->GetEntryBinArea( 0x0028, 0x1201 );
- if ( ! LutRedData )
- {
- gdcmVerboseMacro( "Unable to read Red LUT data" );
- }
-
- ////// Green round:
- header->LoadEntryBinArea(0x0028, 0x1202);
- LutGreenData = (uint8_t*)header->GetEntryBinArea(0x0028, 0x1202 );
- if ( ! LutGreenData)
- {
- gdcmVerboseMacro( "Unable to read Green LUT data" );
- }
-
- ////// Blue round:
- header->LoadEntryBinArea(0x0028, 0x1203);
- LutBlueData = (uint8_t*)header->GetEntryBinArea( 0x0028, 0x1203 );
- if ( ! LutBlueData )
- {
- gdcmVerboseMacro( "Unable to read Blue LUT data" );
- }
- }
-
- ComputeRawAndRGBSizes();
-}
-
-/**
- * \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()
+/// Allocates room for RGB Pixels
+void PixelReadConvert::AllocateRGB()
{
- 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 )
- {
- 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 ) )
- {
- 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;
- }
+ if ( RGB )
+ delete [] RGB;
+ RGB = new uint8_t[RGBSize];
}
-/**
- * \brief Build the RGB image from the Raw imagage and the LUTs.
- */
-bool PixelReadConvert::BuildRGBImage()
+/// Allocates room for RAW Pixels
+void PixelReadConvert::AllocateRaw()
{
- if ( RGB )
- {
- // The job is already done.
- return true;
- }
-
- if ( ! Raw )
- {
- // 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 < RawSize; ++i )
- {
- int j = Raw[i] * 4;
- *localRGB++ = LutRGBA[j];
- *localRGB++ = LutRGBA[j+1];
- *localRGB++ = LutRGBA[j+2];
- }
- return true;
+ 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 -------------------------"
}
else
{
- gdcmVerboseMacro("Set as RLE file but NO RLEinfo present.");
+ gdcmWarningMacro("Set as RLE file but NO RLEinfo present.");
}
}
}
else
{
- gdcmVerboseMacro("Set as JPEG file but NO JPEGinfo present.");
+ gdcmWarningMacro("Set as JPEG file but NO JPEGinfo present.");
}
}
}
+/**
+ * \brief CallStartMethod
+ */
+void PixelReadConvert::CallStartMethod()
+{
+ Progress = 0.0f;
+ Abort = false;
+ CommandManager::ExecuteCommand(FH,CMD_STARTPROGRESS);
+}
+
+/**
+ * \brief CallProgressMethod
+ */
+void PixelReadConvert::CallProgressMethod()
+{
+ CommandManager::ExecuteCommand(FH,CMD_PROGRESS);
+}
+
+/**
+ * \brief CallEndMethod
+ */
+void PixelReadConvert::CallEndMethod()
+{
+ Progress = 1.0f;
+ CommandManager::ExecuteCommand(FH,CMD_ENDPROGRESS);
+}
+
+//-----------------------------------------------------------------------------
} // end namespace gdcm
-// NOTES on File internal calls
-// User
-// ---> GetImageData
-// ---> GetImageDataIntoVector
-// |---> GetImageDataIntoVectorRaw
-// | lut intervention
-// User
-// ---> GetImageDataRaw
-// ---> GetImageDataIntoVectorRaw
+// Note to developpers :
+// Here is a very detailled post from David Clunie, on the troubles caused
+// 'non standard' LUT and LUT description
+// We shall have to take it into accound in our code.
+// Some day ...
+
+
+/*
+Subject: Problem with VOI LUTs in Agfa and Fuji CR and GE DX images, was Re: VOI LUT issues
+Date: Sun, 06 Feb 2005 17:13:40 GMT
+From: David Clunie <dclunie@dclunie.com>
+Reply-To: dclunie@dclunie.com
+Newsgroups: comp.protocols.dicom
+References: <1107553502.040221.189550@o13g2000cwo.googlegroups.com>
+
+> THE LUT that comes with [my] image claims to be 16-bit, but none of the
+> values goes higher than 4095. That being said, though, none of my
+> original pixel values goes higher than that, either. I have read
+> elsewhere on this group that when that happens you are supposed to
+> adjust the LUT. Can someone be more specific? There was a thread from
+> 2002 where Marco and David were mentioning doing precisely that.
+>
+> Thanks
+>
+> -carlos rodriguez
+
+
+You have encountered the well known "we know what the standard says but
+we are going to ignore it and do what we have been doing for almost
+a decade regardless" CR vendor bug. Agfa started this, but they are not
+the only vendor doing this now; GE and Fuji may have joined the club.
+
+Sadly, one needs to look at the LUT Data, figure out what the maximum
+value actually encoded is, and find the next highest power of 2 (e.g.
+212 in this case), to figure out what the range of the data is
+supposed to be. I have assumed that if the maximum value in the LUT
+data is less than a power of 2 minus 1 (e.g. 0xebc) then the intent
+of the vendor was not to use the maximum available grayscale range
+of the display (e.g. the maximum is 0xfff in this case). An alternative
+would be to scale to the actual maximum rather than a power of two.
+
+Very irritating, and in theory not totally reliable if one really
+intended the full 16 bits and only used, say 15, but that is extremely
+unlikely since everything would be too dark, and this heuristic
+seems to work OK.
+
+There has never been anything in the standard that describes having
+to go through these convolutions. Since the only value in the
+standard that describes the bit depth of the LUT values is LUT
+Descriptor value 3 and that is (usually) always required to be
+either 8 or 16, it mystifies me how the creators' of these images
+imagine that the receiver is going to divine the range that is intended. Further, the standard is quite explicit that this 3rd
+value defines the range of LUT values, but as far as I am aware, all
+the vendors are ignoring the standard and indeed sending a third value
+of 16 in all cases.
+
+This problem is not confined to CR, and is also seen with DX products.
+
+Typically I have seen:
+
+- Agfa CR, which usually (always ?) sends LUTs, values up to 0x0fff
+- Fuji CR, which occasionally send LUTs, values up to 0x03ff
+- GE DX, for presentation, which always have LUTs, up to 0x3fff
+
+Swissray, Siemens, Philips, Canon and Kodak never seem to send VOI LUTs
+at this point (which is a whole other problem). Note that the presence
+or absence of a VOI LUT as opposed to window values may be configurable
+on the modality in some cases, and I have just looked at what I happen
+to have received from a myriad of sites over whose configuration I have
+no control. This may be why the majority of Fuji images have no VOI LUTs,
+but a few do (or it may be the Siemens system that these Fuji images went
+through that perhaps added it). I do have some test Hologic DX images that
+are not from a clinical site that do actually get this right (a value
+of 12 for the third value and a max of 0xfff).
+
+Since almost every vendor that I have encountered that encodes LUTs
+makes this mistake, perhaps it is time to amend the standard to warn
+implementor's of receivers and/or sanction this bad behavior. We have
+talked about this in the past in WG 6 but so far everyone has been
+reluctant to write into the standard such a comment. Maybe it is time
+to try again, since if one is not aware of this problem, one cannot
+effectively implement display using VOI LUTs, and there is a vast
+installed base to contend with.
+
+I did not check presentation states, in which VOI LUTs could also be
+encountered, for the prevalence of this mistake, nor did I look at the
+encoding of Modality LUT's, which are unusual. Nor did I check digital
+mammography images. I would be interested to hear from anyone who has.
+
+David
+
+PS. The following older thread in this newsgroup discusses this:
+
+"http://groups-beta.google.com/group/comp.protocols.dicom/browse_frm/t hread/6a033444802a35fc/0f0a9a1e35c1468e?q=voi+lut&_done=%2Fgroup%2Fcom p.protocols.dicom%2Fsearch%3Fgroup%3Dcomp.protocols.dicom%26q%3Dvoi+lu t%26qt_g%3D1%26searchnow%3DSearch+this+group%26&_doneTitle=Back+to+Sea rch&&d#0f0a9a1e35c1468e"
+
+PPS. From a historical perspective, the following may be of interest.
+
+In the original standard in 1993, all that was said about this was a
+reference to the corresponding such where Modality LUTs are described
+that said:
+
+"The third value specifies the number of bits for each entry in the
+LUT Data. It shall take the value 8 or 16. The LUT Data shall be stored
+in a format equivalent to 8 or 16 bits allocated and high bit equal
+1-bits allocated."
+
+Since the high bit hint was not apparently explicit enough, a very
+early CP, CP 15 (submitted by Agfa as it happens), replaced this with:
+
+"The third value conveys the range of LUT entry values. It shall take
+the value 8 or 16, corresponding with the LUT entry value range of
+256 or 65536.
+
+Note: The third value is not required for describing the
+ LUT data and is only included for informational usage
+ and for maintaining compatibility with ACRNEMA 2.0.
+
+The LUT Data contains the LUT entry values."
+
+That is how it read in the 1996, 1998 and 1999 editions.
+
+By the 2000 edition, Supplement 33 that introduced presentation states
+extensively reworked this entire section and tried to explain this in
+different words:
+
+"The output range is from 0 to 2^n-1 where n is the third value of LUT
+Descriptor. This range is always unsigned."
+
+and also added a note to spell out what the output range meant in the
+VOI LUT section:
+
+"9. The output of the Window Center/Width or VOI LUT transformation
+is either implicitly scaled to the full range of the display device
+if there is no succeeding transformation defined, or implicitly scaled
+to the full input range of the succeeding transformation step (such as
+the Presentation LUT), if present. See C.11.6.1."
+
+It still reads this way in the 2004 edition.
+
+Note that LUTs in other applications than the general VOI LUT allow for
+values other than 8 or 16 in the third value of LUT descriptor to permit
+ranges other than 0 to 255 or 65535.
+
+In addition, the DX Image Module specializes the VOI LUT
+attributes as follows, in PS 3.3 section C.8.11.3.1.5 (added in Sup 32):
+
+"The third value specifies the number of bits for each entry in the LUT
+Data (analogous to ìbits storedî). It shall be between 10-16. The LUT
+Data shall be stored in a format equivalent to 16 ìbits allocatedî and
+ìhigh bitî equal to ìbits storedî - 1. The third value conveys the range
+of LUT entry values. These unsigned LUT entry values shall range between
+0 and 2^n-1, where n is the third value of the LUT Descriptor."
+
+So in the case of the GE DX for presentation images, the third value of
+LUT descriptor is allowed to be and probably should be 14 rather than 16.
+*/
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