+ return true;
+}
+
+/**
+ * \brief Convert (Y plane, cB plane, cR plane) to RGB pixels
+ * \warning Works on all the frames at a time
+ */
+void PixelConvert::ConvertYcBcRPlanesToRGBPixels()
+{
+ uint8_t* localDecompressed = Decompressed;
+ uint8_t* copyDecompressed = new uint8_t[ DecompressedSize ];
+ memmove( copyDecompressed, localDecompressed, DecompressedSize );
+
+ // to see the tricks about YBR_FULL, YBR_FULL_422,
+ // YBR_PARTIAL_422, YBR_ICT, YBR_RCT have a look at :
+ // ftp://medical.nema.org/medical/dicom/final/sup61_ft.pdf
+ // and be *very* affraid
+ //
+ int l = XSize * YSize;
+ int nbFrames = ZSize;
+
+ uint8_t* a = copyDecompressed;
+ uint8_t* b = copyDecompressed + l;
+ uint8_t* c = copyDecompressed + 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++ )
+ {
+ 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;
+
+ *(localDecompressed++) = (uint8_t)R;
+ *(localDecompressed++) = (uint8_t)G;
+ *(localDecompressed++) = (uint8_t)B;
+ a++;
+ b++;
+ c++;
+ }
+ }
+ delete[] copyDecompressed;
+}
+
+/**
+ * \brief Convert (Red plane, Green plane, Blue plane) to RGB pixels
+ * \warning Works on all the frames at a time
+ */
+void PixelConvert::ConvertRGBPlanesToRGBPixels()
+{
+ uint8_t* localDecompressed = Decompressed;
+ uint8_t* copyDecompressed = new uint8_t[ DecompressedSize ];
+ memmove( copyDecompressed, localDecompressed, DecompressedSize );
+
+ int l = XSize * YSize * ZSize;
+
+ uint8_t* a = copyDecompressed;
+ uint8_t* b = copyDecompressed + l;
+ uint8_t* c = copyDecompressed + l + l;
+
+ for (int j = 0; j < l; j++)
+ {
+ *(localDecompressed++) = *(a++);
+ *(localDecompressed++) = *(b++);
+ *(localDecompressed++) = *(c++);
+ }
+ delete[] copyDecompressed;
+}
+
+bool PixelConvert::ReadAndDecompressPixelData( FILE* fp )
+{
+ ComputeDecompressedAndRGBSizes();
+ AllocateDecompressed();
+ //////////////////////////////////////////////////
+ //// First stage: get our hands on the Pixel Data.
+ if ( !fp )
+ {
+ dbg.Verbose( 0, "PixelConvert::ReadAndDecompressPixelData: "
+ "unavailable file pointer." );
+ return false;
+ }
+
+ if ( fseek( fp, PixelOffset, SEEK_SET ) == -1 )
+ {
+ dbg.Verbose( 0, "PixelConvert::ReadAndDecompressPixelData: "
+ "unable to find PixelOffset in file." );
+ return false;
+ }
+
+ //////////////////////////////////////////////////
+ //// Second stage: read from disk dans decompress.
+ if ( BitsAllocated == 12 )
+ {
+ ReadAndDecompress12BitsTo16Bits( fp);
+ }
+ else if ( IsDecompressed )
+ {
+ size_t ItemRead = fread( Decompressed, PixelDataLength, 1, fp );
+ if ( ItemRead != 1 )
+ {
+ dbg.Verbose( 0, "PixelConvert::ReadAndDecompressPixelData: "
+ "reading of decompressed pixel data failed." );
+ return false;
+ }
+ }
+ else if ( IsRLELossless )
+ {
+ if ( ! ReadAndDecompressRLEFile( fp ) )
+ {
+ dbg.Verbose( 0, "PixelConvert::ReadAndDecompressPixelData: "
+ "RLE decompressor failed." );
+ return false;
+ }
+ }
+ else
+ {
+ // Default case concerns JPEG family
+ if ( ! ReadAndDecompressJPEGFile( fp ) )
+ {
+ dbg.Verbose( 0, "PixelConvert::ReadAndDecompressPixelData: "
+ "JPEG decompressor failed." );
+ return false;
+ }
+ }
+
+ ////////////////////////////////////////////
+ //// Third stage: twigle the bytes and bits.
+ ConvertReorderEndianity();
+ ConvertReArrangeBits();
+ ConvertHandleColor();
+
+ return true;
+}
+
+void PixelConvert::ConvertHandleColor()
+{
+ //////////////////////////////////
+ // Deal with the color decoding i.e. handle:
+ // - R, G, B planes (as opposed to RGB pixels)
+ // - YBR (various) encodings.
+ // - LUT[s] (or "PALETTE COLOR").
+ //
+ // The classification in the color decoding schema is based on the blending
+ // of two Dicom tags values:
+ // * "Photometric Interpretation" for which we have the cases:
+ // - [Photo A] MONOCHROME[1|2] pictures,
+ // - [Photo B] RGB or YBR_FULL_422 (which acts as RGB),
+ // - [Photo C] YBR_* (with the above exception of YBR_FULL_422)
+ // - [Photo D] "PALETTE COLOR" which indicates the presence of LUT[s].
+ // * "Planar Configuration" for which we have the cases:
+ // - [Planar 0] 0 then Pixels are already RGB
+ // - [Planar 1] 1 then we have 3 planes : R, G, B,
+ // - [Planar 2] 2 then we have 1 gray Plane and 3 LUTs
+ //
+ // Now in theory, one could expect some coherence when blending the above
+ // cases. For example we should not encounter files belonging at the
+ // time to case [Planar 0] and case [Photo D].
+ // Alas, this was only theory ! Because in practice some odd (read ill
+ // formated Dicom) files (e.g. gdcmData/US-PAL-8-10x-echo.dcm) we encounter:
+ // - "Planar Configuration" = 0,
+ // - "Photometric Interpretation" = "PALETTE COLOR".
+ // Hence gdcm shall use the folowing "heuristic" in order to be tolerant
+ // towards Dicom-non-conformance files:
+ // << whatever the "Planar Configuration" value might be, a
+ // "Photometric Interpretation" set to "PALETTE COLOR" forces
+ // a LUT intervention >>
+ //
+ // Now we are left with the following handling of the cases:
+ // - [Planar 0] OR [Photo A] no color decoding (since respectively
+ // Pixels are already RGB and monochrome pictures have no color :),
+ // - [Planar 1] AND [Photo B] handled with ConvertRGBPlanesToRGBPixels()
+ // - [Planar 1] AND [Photo C] handled with ConvertYcBcRPlanesToRGBPixels()
+ // - [Planar 2] OR [Photo D] requires LUT intervention.
+
+ if ( ! IsDecompressedRGB() )
+ {
+ // [Planar 2] OR [Photo D]: LUT intervention done outside
+ return;
+ }
+
+ if ( PlanarConfiguration == 1 )
+ {
+ if ( IsYBRFull )
+ {
+ // [Planar 1] AND [Photo C] (remember YBR_FULL_422 acts as RGB)
+ ConvertYcBcRPlanesToRGBPixels();
+ }
+ else
+ {
+ // [Planar 1] AND [Photo C]
+ ConvertRGBPlanesToRGBPixels();
+ }
+ }
+
+ // When planarConf is 0, pixels are allready in RGB
+}
+
+/**
+ * \brief Predicate to know wether the image[s] (once decompressed) is RGB.
+ * \note See comments of \ref ConvertHandleColor
+ */
+bool PixelConvert::IsDecompressedRGB()
+{
+ if ( IsMonochrome
+ || ( PlanarConfiguration == 2 )
+ || IsPaletteColor )
+ {
+ return false;
+ }
+ return true;
+}
+
+void PixelConvert::ComputeDecompressedAndRGBSizes()
+{
+ int bitsAllocated = BitsAllocated;
+ // Number of "Bits Allocated" is fixed to 16 when it's 12, since
+ // in this case we will expand the image to 16 bits (see
+ // \ref ReadAndDecompress12BitsTo16Bits() )
+ if ( BitsAllocated == 12 )
+ {
+ bitsAllocated = 16;
+ }
+
+ DecompressedSize = XSize * YSize * ZSize
+ * ( bitsAllocated / 8 )
+ * SamplesPerPixel;
+ if ( HasLUT )
+ {
+ RGBSize = 3 * DecompressedSize;
+ }
+
+}
+
+void PixelConvert::GrabInformationsFromHeader( Header* header )
+{
+ // Just in case some access to a Header element requires disk access.
+ // Note: gdcmDocument::Fp is leaved open after OpenFile.
+ FILE* fp = header->OpenFile();
+ // 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
+ 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();
+ IsDecompressed =
+ ( ! header->IsDicomV3() )
+ || header->IsImplicitVRLittleEndianTransferSyntax()
+ || header->IsExplicitVRLittleEndianTransferSyntax()
+ || header->IsExplicitVRBigEndianTransferSyntax()
+ || header->IsDeflatedExplicitVRLittleEndianTransferSyntax();
+ IsJPEG2000 = header->IsJPEG2000();
+ IsJPEGLossless = header->IsJPEGLossless();
+ IsRLELossless = header->IsRLELossLessTransferSyntax();
+ 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 )
+ {
+ LutRedDescriptor = header->GetEntryByNumber( 0x0028, 0x1101 );
+ LutGreenDescriptor = header->GetEntryByNumber( 0x0028, 0x1102 );
+ LutBlueDescriptor = header->GetEntryByNumber( 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 header
+ // and when this fails we read the LUTs data directely 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:
+ LutRedData = (uint8_t*)header->GetEntryBinAreaByNumber( 0x0028, 0x1201 );
+ if ( ! LutRedData )
+ {
+ // Read the Lut Data from disk
+ DocEntry* lutRedDataEntry = header->GetDocEntryByNumber( 0x0028,
+ 0x1201 );
+ LutRedData = new uint8_t[ lutRedDataEntry->GetLength() ];
+ fseek( fp, lutRedDataEntry->GetOffset() ,SEEK_SET );
+ int numberItem = fread( LutRedData,
+ (size_t)lutRedDataEntry->GetLength(),
+ 1, fp );
+ if ( numberItem != 1 )
+ {
+ dbg.Verbose(0, "PixelConvert::GrabInformationsFromHeader: "
+ "unable to read red LUT data" );
+ return;
+ }
+ }
+
+ ////// Green round:
+ LutGreenData = (uint8_t*)header->GetEntryBinAreaByNumber(0x0028, 0x1202 );
+ if ( ! LutGreenData)
+ {
+ // Read the Lut Data from disk
+ DocEntry* lutGreenDataEntry = header->GetDocEntryByNumber( 0x0028,
+ 0x1202 );
+ LutGreenData = new uint8_t[ lutGreenDataEntry->GetLength() ];
+ fseek( fp, lutGreenDataEntry->GetOffset() ,SEEK_SET );
+ int numberItem = fread( LutGreenData,
+ (size_t)lutGreenDataEntry->GetLength(),
+ 1, fp );
+ if ( numberItem != 1 )
+ {
+ dbg.Verbose(0, "PixelConvert::GrabInformationsFromHeader: "
+ "unable to read green LUT data" );
+ return;
+ }
+ }
+
+ ////// Blue round:
+ LutBlueData = (uint8_t*)header->GetEntryBinAreaByNumber( 0x0028, 0x1203 );
+ if ( ! LutBlueData )
+ {
+ // Read the Lut Data from disk
+ DocEntry* lutBlueDataEntry = header->GetDocEntryByNumber( 0x0028,
+ 0x1203 );
+ LutBlueData = new uint8_t[ lutBlueDataEntry->GetLength() ];
+ fseek( fp, lutBlueDataEntry->GetOffset() ,SEEK_SET );
+ int numberItem = fread( LutBlueData,
+ (size_t)lutBlueDataEntry->GetLength(),
+ 1, fp );
+ if ( numberItem != 1 )
+ {
+ dbg.Verbose(0, "PixelConvert::GrabInformationsFromHeader: "
+ "unable to read blue LUT data" );
+ return;
+ }
+ }
+ }
+
+ header->CloseFile();