/*=========================================================================
-
+
Program: gdcm
Module: $RCSfile: gdcmPixelReadConvert.cxx,v $
Language: C++
- Date: $Date: 2005/02/01 10:29:55 $
- Version: $Revision: 1.43 $
+ Date: $Date: 2005/08/19 13:15:05 $
+ Version: $Revision: 1.76 $
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"
namespace gdcm
{
+
+//bool ReadMPEGFile (std::ifstream *fp, void *image_buffer, size_t lenght);
+bool gdcm_read_JPEG2000_file (void* raw,
+ char *inputdata, size_t inputlength);
//-----------------------------------------------------------------------------
#define str2num(str, typeNum) *((typeNum *)(str))
//-----------------------------------------------------------------------------
// Constructor / Destructor
+/// 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;
}
+/// Canonical Destructor
PixelReadConvert::~PixelReadConvert()
{
Squeeze();
//-----------------------------------------------------------------------------
// Public
+/**
+ * \brief Predicate to know whether 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;
+}
+/**
+ * \brief Gets various usefull informations from the file header
+ * @param file gdcm::File pointer
+ */
+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;
+ }
+
+ // Number of "Bits Stored", defaulted to number of "Bits Allocated"
+ // when absent from the file.
+ BitsStored = file->GetBitsStored();
+ if ( BitsStored == 0 )
+ {
+ BitsStored = BitsAllocated;
+ }
+
+ // 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();
+ SamplesPerPixel = file->GetSamplesPerPixel();
+ //PixelSize = file->GetPixelSize(); Useless
+ 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;
+
+ IsMPEG = Global::GetTS()->IsMPEG(ts);
+ 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();
+
+ IsMonochrome = file->IsMonochrome();
+ IsMonochrome1 = file->IsMonochrome1();
+ IsPaletteColor = file->IsPaletteColor();
+ IsYBRFull = file->IsYBRFull();
+
+ PlanarConfiguration = file->GetPlanarConfiguration();
+
+ /////////////////////////////////////////////////////////////////
+ // 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 )
+ {
+ 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" );
+ }
+ }
+ FileInternal = file;
+
+ ComputeRawAndRGBSizes();
+}
+
+/// \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();
+
+ //////////////////////////////////////////////////
+ //// Second stage: read from disk and decompress.
+ if ( BitsAllocated == 12 )
+ {
+ 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 );
+ }
+ if ( PixelDataLength > RawSize )
+ {
+ fp->read( (char*)Raw, RawSize);
+ }
+ else
+ {
+ fp->read( (char*)Raw, PixelDataLength);
+ }
+
+ 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, 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, Raw, PixelDataLength);
+ return true;
+ }
+ else
+ {
+ // Default case concerns JPEG family
+ if ( ! ReadAndDecompressJPEGFile( fp ) )
+ {
+ gdcmWarningMacro( "JPEG decompressor 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;
+}
+
+/// Deletes Pixels Area
void PixelReadConvert::Squeeze()
{
if ( RGB )
delete [] RGB;
RGB = 0;
- if ( Raw )
- delete [] Raw;
- Raw = 0;
+ if ( Raw )
+ delete [] Raw;
+ Raw = 0;
+
+ if ( LutRGBA )
+ delete [] LutRGBA;
+ LutRGBA = 0;
+}
+
+/**
+ * \brief Build the RGB image from the Raw image and the LUTs.
+ */
+bool PixelReadConvert::BuildRGBImage()
+{
+ 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;
+ }
+
+ gdcmWarningMacro( "--> 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;
+
+ for( int p = 0; p < nbPixels; p += 2 )
+ {
+ uint8_t b0, b1, b2;
+
+ fp->read( (char*)&b0, 1);
+ if ( fp->fail() || fp->eof() )
+ {
+ throw FormatError( "PixelReadConvert::ReadAndDecompress12BitsTo16Bits()",
+ "Unfound first block" );
+ }
+
+ fp->read( (char*)&b1, 1 );
+ if ( fp->fail() || fp->eof())
+ {
+ throw FormatError( "PixelReadConvert::ReadAndDecompress12BitsTo16Bits()",
+ "Unfound second block" );
+ }
+
+ fp->read( (char*)&b2, 1 );
+ if ( fp->fail() || fp->eof())
+ {
+ throw FormatError( "PixelReadConvert::ReadAndDecompress12BitsTo16Bits()",
+ "Unfound second block" );
+ }
+
+ // 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 ?
+ }
+}
+
+/**
+ * \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 )
+ {
+ // 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
+
+ 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 delete in the function
+ if ( ! gdcm_read_JPEG2000_file( Raw,
+ (char*)inputdata, inputlength ) )
+ {
+ return true;
+ }
+ // wow what happen, must be an error
+ return false;
+ }
+ 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 )
+ {
+ 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();
+ }
+
+ //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
+ {
+ // make sure this is the right JPEG compression
+ assert( !IsJPEGLS || !IsJPEG2000 );
+ // 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 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()
+{
+ 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" );
+ }
+
+ gdcmWarningMacro(" lengthR " << lengthR << " debR "
+ << debR << " nbitsR " << nbitsR);
+ gdcmWarningMacro(" lengthG " << lengthG << " debG "
+ << debG << " nbitsG " << nbitsG);
+ gdcmWarningMacro(" 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 )
+ {
+ // 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 ) )
+ {
+ // 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;
+
+ //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 )
+ {
+ *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;
+ }
+ }
+ else
+ {
+ // Probabely the same stuff is to be done for 16 Bits Pixels
+ // with 65536 entries LUT ?!?
+ // Still looking for accurate info on the web :-(
- if ( LutRGBA )
- delete [] LutRGBA;
- LutRGBA = 0;
-}
+ gdcmWarningMacro( "Sorry Palette Color Lookup Tables not yet dealt with"
+ << " for 16 Bits Per Pixel images" );
-void PixelReadConvert::AllocateRGB()
-{
- if ( RGB )
- delete [] RGB;
- RGB = new uint8_t[RGBSize];
-}
+ // forge the 4 * 16 Bits Red/Green/Blue/Alpha LUT
-void PixelReadConvert::AllocateRaw()
-{
- if ( Raw )
- delete [] Raw;
- Raw = new uint8_t[RawSize];
-}
+ 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 ;-)
-/**
- * \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;
+ LutItemNumber = 65536;
+ LutItemSize = 16;
- for( int p = 0; p < nbPixels; p += 2 )
- {
- uint8_t b0, b1, b2;
+ int i;
+ uint16_t *a16;
- fp->read( (char*)&b0, 1);
- if ( fp->fail() || fp->eof() )
+ //take "Subscript of the first Lut Value" (debR,debG,debB) into account!
+
+ a16 = (uint16_t*)LutRGBA + 0 + debR;
+ for( i=0; i < lengthR; ++i )
{
- throw FormatError( "PixelReadConvert::ReadAndDecompress12BitsTo16Bits()",
- "Unfound first block" );
+ *a16 = ((uint16_t*)LutRedData)[i];
+ a16 += 4;
}
-
- fp->read( (char*)&b1, 1 );
- if ( fp->fail() || fp->eof())
+
+ a16 = (uint16_t*)LutRGBA + 1 + debG;
+ for( i=0; i < lengthG; ++i)
{
- throw FormatError( "PixelReadConvert::ReadAndDecompress12BitsTo16Bits()",
- "Unfound second block" );
+ *a16 = ((uint16_t*)LutGreenData)[i];
+ a16 += 4;
}
-
- fp->read( (char*)&b2, 1 );
- if ( fp->fail() || fp->eof())
+
+ a16 = (uint16_t*)LutRGBA + 2 + debB;
+ for(i=0; i < lengthB; ++i)
{
- throw FormatError( "PixelReadConvert::ReadAndDecompress12BitsTo16Bits()",
- "Unfound second block" );
+ *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
- // 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 ?
+ a16=(uint16_t*)LutRGBA;
+ for (int j=0;j<65536;j++)
+ {
+ std::cout << *a16 << " " << *(a16+1) << " "
+ << *(a16+2) << " " << *(a16+3) << std::endl;
+ a16+=4;
+ }
+*/
}
}
-
/**
* \brief Swap the bytes, according to \ref SwapCode.
*/
{
unsigned int i;
- if( BitsAllocated == 16 )
+ if ( BitsAllocated == 16 )
{
uint16_t *im16 = (uint16_t*)Raw;
switch( SwapCode )
}
break;
default:
- gdcmVerboseMacro("SwapCode value (16 bits) not allowed.");
+ gdcmWarningMacro("SwapCode value (16 bits) not allowed.");
}
}
- else if( BitsAllocated == 32 )
+ else if ( BitsAllocated == 32 )
{
uint32_t s32;
uint16_t high;
uint16_t low;
- uint32_t* im32 = (uint32_t*)Raw;
+ uint32_t *im32 = (uint32_t*)Raw;
switch ( SwapCode )
{
case 1234:
}
break;
default:
- gdcmVerboseMacro("SwapCode value (32 bits) not allowed." );
+ gdcmWarningMacro("SwapCode value (32 bits) not allowed." );
}
}
}
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.
- * @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::ReadAndDecompressJPEGFile( std::ifstream *fp )
+void PixelReadConvert::ConvertFixGreyLevels()
{
- if ( IsJPEG2000 )
- {
- gdcmVerboseMacro( "Sorry, JPEG2000 not yet taken into account" );
- fp->seekg( JPEGInfo->GetFirstFragment()->GetOffset(), std::ios::beg);
-// if ( ! gdcm_read_JPEG2000_file( fp,Raw ) )
- return false;
- }
+ if (!IsMonochrome1)
+ return;
+
+ uint32_t i; // to please M$VC6
+ int16_t j;
- if ( IsJPEGLS )
+ if (!PixelSign)
{
- gdcmVerboseMacro( "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;
- }
+ if ( BitsAllocated == 8 )
+ {
+ uint8_t *deb = (uint8_t *)Raw;
+ for (i=0; i<RawSize; i++)
+ {
+ *deb = 255 - *deb;
+ deb++;
+ }
+ return;
+ }
- // else ??
- // Precompute the offset localRaw will be shifted with
- int length = XSize * YSize * SamplesPerPixel;
- int numberBytes = BitsAllocated / 8;
+ if ( BitsAllocated == 16 )
+ {
+ uint16_t mask =1;
+ for (j=0; j<BitsStored-1; j++)
+ {
+ mask = (mask << 1) +1; // will be fff when BitsStored=12
+ }
- JPEGInfo->DecompressFromFile(fp, Raw, BitsStored, numberBytes, length );
- return true;
+ uint16_t *deb = (uint16_t *)Raw;
+ for (i=0; i<RawSize/2; i++)
+ {
+ *deb = mask - *deb;
+ deb++;
+ }
+ return;
+ }
+ }
+ else
+ {
+ 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;
+ }
+ }
}
/**
* \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;
+ pmask = pmask >> ( BitsAllocated - BitsStored );
+
+ uint16_t *deb = (uint16_t*)Raw;
+
+ if ( !PixelSign ) // Pixels are unsigned
{
- *deb = (*deb >> (BitsStored - HighBitPosition - 1)) & mask;
- deb++;
+ for(int i = 0; i<l; i++)
+ {
+ *deb = (*deb >> (BitsStored - HighBitPosition - 1)) & pmask;
+ deb++;
+ }
+ }
+ else // Pixels are signed
+ {
+ // 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 );
+/*
+std::cout << "BitsStored " << BitsStored
+ << " BitsAllocated " << BitsAllocated
+ << std::endl;
+std::cout << std::hex << "pmask " << pmask
+ << " smask " << smask
+ << " nmask " << nmask
+ << std::endl;
+*/
+ 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
- // ::GrabInformationsFromfile. So, the structure sizes are
- // correct
- Squeeze();
-
- //////////////////////////////////////////////////
- //// First stage: get our hands on the Pixel Data.
- if ( !fp )
- {
- gdcmVerboseMacro( "Unavailable file pointer." );
- return false;
- }
-
- fp->seekg( PixelOffset, std::ios::beg );
- if( fp->fail() || fp->eof())
- {
- gdcmVerboseMacro( "Unable to find PixelOffset in file." );
- return false;
- }
+ // 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;
- AllocateRaw();
+ uint8_t *a = copyRaw + 0;
+ uint8_t *b = copyRaw + l;
+ uint8_t *c = copyRaw + l+ l;
+ int32_t R, G, B;
- //////////////////////////////////////////////////
- //// Second stage: read from disk dans decompress.
- if ( BitsAllocated == 12 )
- {
- 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)
- {
- gdcmVerboseMacro( "Mismatch between PixelReadConvert and RawSize." );
- }
- if( PixelDataLength > RawSize)
- {
- fp->read( (char*)Raw, RawSize);
- }
- else
- {
- fp->read( (char*)Raw, PixelDataLength);
- }
+ /// 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.
- if ( fp->fail() || fp->eof())
- {
- gdcmVerboseMacro( "Reading of Raw pixel data failed." );
- return false;
- }
- }
- else if ( IsRLELossless )
- {
- if ( ! RLEInfo->DecompressRLEFile( fp, Raw, XSize, YSize, ZSize, BitsAllocated ) )
- {
- gdcmVerboseMacro( "RLE decompressor failed." );
- return false;
- }
- }
- else
+ for ( int i = 0; i < nbFrames; i++ )
{
- // Default case concerns JPEG family
- if ( ! ReadAndDecompressJPEGFile( fp ) )
+ for ( int j = 0; j < l; j++ )
{
- gdcmVerboseMacro( "JPEG decompressor failed." );
- return false;
- }
- }
+ R = 38142 *(*a-16) + 52298 *(*c -128);
+ G = 38142 *(*a-16) - 26640 *(*c -128) - 12845 *(*b -128);
+ B = 38142 *(*a-16) + 66093 *(*b -128);
- ////////////////////////////////////////////
- //// Third stage: twigle the bytes and bits.
- ConvertReorderEndianity();
- ConvertReArrangeBits();
- ConvertHandleColor();
+ R = (R+16384)>>15;
+ G = (G+16384)>>15;
+ B = (B+16384)>>15;
- return true;
+ 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;
+
+ *(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.
+ gdcmWarningMacro("--> ConvertHandleColor"
+ << "Planar Configuration " << PlanarConfiguration );
+
if ( ! IsRawRGB() )
{
// [Planar 2] OR [Photo D]: LUT intervention done outside
+ gdcmWarningMacro("--> RawRGB : LUT intervention done outside");
return;
}
if ( IsYBRFull )
{
// [Planar 1] AND [Photo C] (remember YBR_FULL_422 acts as RGB)
+ gdcmWarningMacro("--> YBRFull");
ConvertYcBcRPlanesToRGBPixels();
}
else
{
// [Planar 1] AND [Photo C]
+ gdcmWarningMacro("--> 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)
- {
+ {
+ gdcmWarningMacro("--> 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;
* SamplesPerPixel;
if ( HasLUT )
{
- RGBSize = 3 * RawSize;
+ RGBSize = 3 * RawSize; // works for 8 and 16 bits per Pixel
}
else
{
}
}
-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;
- }
-
- // Number of "Bits Stored", defaulted to number of "Bits Allocated"
- // when absent from the file.
- BitsStored = file->GetBitsStored();
- if ( BitsStored == 0 )
- {
- BitsStored = BitsAllocated;
- }
-
- // 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();
- 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 )
- {
- gdcmVerboseMacro( "Unable to read Red LUT data" );
- }
-
- ////// Green round:
- file->LoadEntryBinArea(0x0028, 0x1202);
- LutGreenData = (uint8_t*)file->GetEntryBinArea(0x0028, 0x1202 );
- if ( ! LutGreenData)
- {
- gdcmVerboseMacro( "Unable to read Green LUT data" );
- }
-
- ////// Blue round:
- file->LoadEntryBinArea(0x0028, 0x1203);
- LutBlueData = (uint8_t*)file->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];
}
-//-----------------------------------------------------------------------------
-// Protected
-
-//-----------------------------------------------------------------------------
-// Private
-
//-----------------------------------------------------------------------------
// Print
/**
* @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.");
}
}
}
//-----------------------------------------------------------------------------
} // end namespace gdcm
-
-// NOTES on File internal calls
-// User
-// ---> GetImageData
-// ---> GetImageDataIntoVector
-// |---> GetImageDataIntoVectorRaw
-// | lut intervention
-// User
-// ---> GetImageDataRaw
-// ---> GetImageDataIntoVectorRaw
-