+//-----------------------------------------------------------------------------
+// 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();
+
+ if (! file->IsDicomV3() ) // Should be ACR-NEMA file
+ {
+ IsRaw = true;
+ // Don't loose time checking unexistant Transfer Syntax !
+ IsPrivateGETransferSyntax = IsMPEG
+ = IsJPEG2000 = IsJPEGLS = IsJPEGLossy
+ = IsJPEGLossless = IsRLELossless
+ = false;
+ }
+ else
+ {
+ std::string ts = file->GetTransferSyntax();
+
+ IsRaw = false;
+ while (true)
+ {
+ // 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;
+ if( IsRaw = Global::GetTS()->GetSpecialTransferSyntax(ts) == TS::DeflatedExplicitVRLittleEndian) break;
+ break;
+ }
+
+ 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;
+ gdcmWarningMacro("Unexepected 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 )
+ {
+ // 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 );
+
+ // 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");
+ }
+ }
+ 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 ( 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()
+{
+
+ // 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" );
+ }
+
+ 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 :-(