Program: gdcm
Module: $RCSfile: gdcmPixelReadConvert.cxx,v $
Language: C++
- Date: $Date: 2005/01/31 05:24:21 $
- Version: $Revision: 1.41 $
+ Date: $Date: 2005/02/23 09:54:59 $
+ Version: $Revision: 1.53 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
namespace gdcm
{
+//-----------------------------------------------------------------------------
#define str2num(str, typeNum) *((typeNum *)(str))
-
//-----------------------------------------------------------------------------
// Constructor / Destructor
+/// 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;
+}
+
+/// 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();
+ 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();
+
+ 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 LUT data" );
+ }
+
+ // //// Green round:
+ file->LoadEntryBinArea(0x0028, 0x1202);
+ LutGreenData = (uint8_t*)file->GetEntryBinArea(0x0028, 0x1202 );
+ if ( ! LutGreenData)
+ {
+ gdcmWarningMacro( "Unable to read Green LUT data" );
+ }
+
+ // //// Blue round:
+ file->LoadEntryBinArea(0x0028, 0x1203);
+ LutBlueData = (uint8_t*)file->GetEntryBinArea( 0x0028, 0x1203 );
+ if ( ! LutBlueData )
+ {
+ gdcmWarningMacro( "Unable to read Blue LUT data" );
+ }
+ }
+
+ 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 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)
+ {
+ 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
+ {
+ // Default case concerns JPEG family
+ if ( ! ReadAndDecompressJPEGFile( fp ) )
+ {
+ gdcmWarningMacro( "JPEG decompressor failed." );
+ return false;
+ }
+ }
+
+ ////////////////////////////////////////////
+ //// Third stage: twigle the bytes and bits.
+ ConvertReorderEndianity();
+ ConvertReArrangeBits();
+ ConvertFixGreyLevels();
+ ConvertHandleColor();
+
+ return true;
}
+/// Deletes Pixels Area
void PixelReadConvert::Squeeze()
{
if ( RGB )
LutRGBA = 0;
}
-PixelReadConvert::~PixelReadConvert()
+/**
+ * \brief Build the RGB image from the Raw imagage and the LUTs.
+ */
+bool PixelReadConvert::BuildRGBImage()
{
- Squeeze();
-}
+ if ( RGB )
+ {
+ // The job is already done.
+ return true;
+ }
-void PixelReadConvert::AllocateRGB()
-{
- if ( RGB )
- delete [] RGB;
- RGB = new uint8_t[RGBSize];
-}
+ if ( ! Raw )
+ {
+ // The job can't be done
+ return false;
+ }
-void PixelReadConvert::AllocateRaw()
-{
- if ( Raw )
- delete [] Raw;
- Raw = new uint8_t[RawSize];
+ BuildLUTRGBA();
+ if ( ! LutRGBA )
+ {
+ // The job can't be done
+ return false;
+ }
+
+ // Build RGB Pixels
+ AllocateRGB();
+ uint8_t *localRGB = RGB;
+ for (size_t i = 0; i < RawSize; ++i )
+ {
+ int j = Raw[i] * 4;
+ *localRGB++ = LutRGBA[j];
+ *localRGB++ = LutRGBA[j+1];
+ *localRGB++ = LutRGBA[j+2];
+ }
+ return true;
}
+//-----------------------------------------------------------------------------
+// Protected
+
+//-----------------------------------------------------------------------------
+// Private
/**
* \brief Read from file a 12 bits per pixel image and decompress it
* into a 16 bits per pixel image.
throw ( FormatError )
{
int nbPixels = XSize * YSize;
- uint16_t* localDecompres = (uint16_t*)Raw;
+ uint16_t *localDecompres = (uint16_t*)Raw;
for( int p = 0; p < nbPixels; p += 2 )
{
}
}
-
/**
- * \brief Swap the bytes, according to \ref SwapCode.
+ * \brief Reads from disk the Pixel Data of JPEG Dicom encapsulated
+ * file and decompress it.
+ * @param fp File Pointer
+ * @return Boolean
*/
-void PixelReadConvert::ConvertSwapZone()
+bool PixelReadConvert::ReadAndDecompressJPEGFile( std::ifstream *fp )
{
- unsigned int i;
+ if ( IsJPEG2000 )
+ {
+ gdcmWarningMacro( "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( BitsAllocated == 16 )
+ if ( IsJPEGLS )
{
- uint16_t *im16 = (uint16_t*)Raw;
- switch( SwapCode )
- {
- case 1234:
- break;
+ 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 ??
+ // 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 )
+ {
+ 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 )
+ {
+ 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" );
+ }
+
+ ////////////////////////////////////////////////////////
+ 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;
+ }
+}
+
+/**
+ * \brief Swap the bytes, according to \ref SwapCode.
+ */
+void PixelReadConvert::ConvertSwapZone()
+{
+ unsigned int i;
+
+ if( BitsAllocated == 16 )
+ {
+ uint16_t *im16 = (uint16_t*)Raw;
+ switch( SwapCode )
+ {
+ case 1234:
+ break;
case 3412:
case 2143:
case 4321:
}
break;
default:
- gdcmVerboseMacro("SwapCode value (16 bits) not allowed.");
+ gdcmWarningMacro("SwapCode value (16 bits) not allowed.");
}
}
else if( BitsAllocated == 32 )
uint32_t s32;
uint16_t high;
uint16_t low;
- uint32_t* im32 = (uint32_t*)Raw;
+ 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." );
}
}
}
}
/**
- * \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;
- if ( IsJPEGLS )
+ uint32_t i; // to please M$VC6
+ int16_t j;
+
+ 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 )
{
{
uint16_t mask = 0xffff;
mask = mask >> ( BitsAllocated - BitsStored );
- uint16_t* deb = (uint16_t*)Raw;
+ uint16_t *deb = (uint16_t*)Raw;
for(int i = 0; i<l; i++)
{
*deb = (*deb >> (BitsStored - HighBitPosition - 1)) & mask;
{
uint32_t mask = 0xffffffff;
mask = mask >> ( BitsAllocated - BitsStored );
- uint32_t* deb = (uint32_t*)Raw;
+ uint32_t *deb = (uint32_t*)Raw;
for(int i = 0; i<l; i++)
{
*deb = (*deb >> (BitsStored - HighBitPosition - 1)) & mask;
}
else
{
- gdcmVerboseMacro("Weird image");
+ gdcmWarningMacro("Weird image");
throw FormatError( "Weird image !?" );
}
}
return true;
}
+/**
+ * \brief Convert (Red plane, Green plane, Blue plane) to RGB pixels
+ * \warning Works on all the frames at a time
+ */
+void PixelReadConvert::ConvertRGBPlanesToRGBPixels()
+{
+ uint8_t *localRaw = Raw;
+ uint8_t *copyRaw = new uint8_t[ RawSize ];
+ memmove( copyRaw, localRaw, RawSize );
+
+ int l = XSize * YSize * ZSize;
+
+ uint8_t *a = copyRaw;
+ uint8_t *b = copyRaw + l;
+ uint8_t *c = copyRaw + l + l;
+
+ for (int j = 0; j < l; j++)
+ {
+ *(localRaw++) = *(a++);
+ *(localRaw++) = *(b++);
+ *(localRaw++) = *(c++);
+ }
+ delete[] copyRaw;
+}
+
/**
* \brief Convert (cY plane, cB plane, cR plane) to RGB pixels
* \warning Works on all the frames at a time
delete[] copyRaw;
}
-/**
- * \brief Convert (Red plane, Green plane, Blue plane) to RGB pixels
- * \warning Works on all the frames at a time
- */
-void PixelReadConvert::ConvertRGBPlanesToRGBPixels()
-{
- uint8_t *localRaw = Raw;
- uint8_t *copyRaw = new uint8_t[ RawSize ];
- memmove( copyRaw, localRaw, RawSize );
-
- int l = XSize * YSize * ZSize;
-
- uint8_t* a = copyRaw;
- uint8_t* b = copyRaw + l;
- uint8_t* c = copyRaw + l + l;
-
- for (int j = 0; j < l; j++)
- {
- *(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;
- }
-
- AllocateRaw();
-
- //////////////////////////////////////////////////
- //// 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);
- }
-
- if ( fp->fail() || fp->eof())
- {
- gdcmVerboseMacro( "Reading of Raw pixel data failed." );
- return false;
- }
- }
- else if ( IsRLELossless )
- {
- if ( ! RLEInfo->ReadAndDecompressRLEFile( fp, Raw, XSize, YSize, ZSize, BitsAllocated ) )
- {
- gdcmVerboseMacro( "RLE decompressor failed." );
- return false;
- }
- }
- else
- {
- // Default case concerns JPEG family
- if ( ! ReadAndDecompressJPEGFile( fp ) )
- {
- gdcmVerboseMacro( "JPEG decompressor failed." );
- return false;
- }
- }
-
- ////////////////////////////////////////////
- //// Third stage: twigle the bytes and bits.
- ConvertReorderEndianity();
- ConvertReArrangeBits();
- ConvertHandleColor();
-
- return true;
-}
+/// \brief 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()
{
// 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;
-}
-
+/// Computes the Pixels Size
void PixelReadConvert::ComputeRawAndRGBSizes()
{
int bitsAllocated = BitsAllocated;
}
}
-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];
}
+//-----------------------------------------------------------------------------
+// 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.");
}
}
}
+//-----------------------------------------------------------------------------
} // end namespace gdcm
// NOTES on File internal calls
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff