Program: gdcm
Module: $RCSfile: gdcmFile.cxx,v $
Language: C++
- Date: $Date: 2004/09/29 17:33:17 $
- Version: $Revision: 1.132 $
+ Date: $Date: 2004/10/01 12:40:57 $
+ Version: $Revision: 1.134 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
bool signedPixel = Header->IsSignedPixelData();
-// SPLIT ME
-////////////////////////////////////////////////////////
-// ENDIANITY SECTION: re-arange bytes inside the integer
- if ( numberBitsAllocated != 8 )
- {
- SwapZone( destination, Header->GetSwapCode(), ImageDataSize,
- numberBitsAllocated );
- }
-
- // to avoid pb with some xmedcon breakers images
- if ( ( numberBitsAllocated == 16 )
- && ( numberBitsStored < numberBitsAllocated )
- && ( ! signedPixel ) )
- {
- int l = (int)(ImageDataSize / (numberBitsAllocated/8));
- uint16_t *deb = (uint16_t *)destination;
- for(int i = 0; i<l; i++)
- {
- if( *deb == 0xffff )
- {
- *deb = 0;
- }
- deb++;
- }
- }
+ ConvertReorderEndianity( (uint8_t*) destination,
+ ImageDataSize,
+ numberBitsStored,
+ numberBitsAllocated,
+ signedPixel );
-// SPLIT ME
-//////////////////////////////////
-// re arange bits inside the bytes
- if ( numberBitsStored != numberBitsAllocated )
- {
- int l = (int)(ImageDataSize / (numberBitsAllocated/8));
- if ( numberBitsAllocated == 16 )
- {
- uint16_t mask = 0xffff;
- mask = mask >> ( numberBitsAllocated - numberBitsStored );
- uint16_t *deb = (uint16_t *)destination;
- for(int i = 0; i<l; i++)
- {
- *deb = (*deb >> (numberBitsStored - highBitPosition - 1)) & mask;
- deb++;
- }
- }
- else if ( numberBitsAllocated == 32 )
- {
- uint32_t mask = 0xffffffff;
- mask = mask >> ( numberBitsAllocated - numberBitsStored );
- uint32_t *deb = (uint32_t *)destination;
- for(int i = 0; i<l; i++)
- {
- *deb = (*deb >> (numberBitsStored - highBitPosition - 1)) & mask;
- deb++;
- }
- }
- else
- {
- dbg.Verbose(0, "gdcmFile::GetImageDataIntoVector: weird image");
- return 0;
- }
- }
+ ConvertReArrangeBits( (uint8_t*) destination,
+ ImageDataSize,
+ numberBitsStored,
+ numberBitsAllocated,
+ highBitPosition );
#ifdef GDCM_DEBUG
FILE* DebugFile;
// PhotometricInterpretation=PALETTE COLOR
// and heuristic has to be found :-(
- int planConf = Header->GetPlanarConfiguration(); // 0028,0006
+ int planConf = Header->GetPlanarConfiguration();
- // Whatever Planar Configuration is,
- // "PALETTE COLOR " implies that we deal with the palette.
- if ( Header->IsPaletteColor() )
+ // Planar configuration = 2 ==> 1 gray Plane + 3 LUT
+ // ...and...
+ // whatever the Planar Configuration might be, "PALETTE COLOR "
+ // implies that we deal with the palette.
+ if ( ( planConf == 2 ) || Header->IsPaletteColor() )
{
- planConf = 2;
+ return ImageDataSize;
}
- switch ( planConf )
- {
- case 0:
- // Pixels are already RGB
- break;
- case 1:
- if ( Header->IsYBRFull() )
- {
- // Warning : YBR_FULL_422 acts as RGB
- // : we need to make RGB Pixels from Planes Y,cB,cR
-
- // 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 = Header->GetXSize() * Header->GetYSize();
- int nbFrames = Header->GetZSize();
-
- uint8_t* newDest = new uint8_t[ImageDataSize];
- uint8_t* x = newDest;
- uint8_t* a = (uint8_t*)destination;
- uint8_t* b = a + l;
- uint8_t* c = b + l;
- double R,G,B;
-
- /// \todo : Replace by the 'well known' integer computation
- /// counterpart
- /// see 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;
-
- *(x++) = (uint8_t)R;
- *(x++) = (uint8_t)G;
- *(x++) = (uint8_t)B;
- a++; b++; c++;
- }
- }
- memmove(destination, newDest, ImageDataSize);
- delete[] newDest;
- }
- else
- {
- // need to make RGB Pixels from R,G,B Planes
- // (all the Frames at a time)
+ // When planConf is 0, pixels are allready in RGB
- int l = Header->GetXSize() * Header->GetYSize() * Header->GetZSize();
-
- uint8_t *newDest = new uint8_t[ImageDataSize];
- uint8_t *x = newDest;
- uint8_t *a = (uint8_t *)destination;
- uint8_t *b = a + l;
- uint8_t *c = b + l;
-
- for (int j = 0; j < l; j++)
- {
- *(x++) = *(a++);
- *(x++) = *(b++);
- *(x++) = *(c++);
- }
- memmove(destination, newDest, ImageDataSize);
- delete[] newDest;
- }
- break;
- case 2:
- // Palettes were found
- // Let the user deal with them !
- return ImageDataSize;
+ if ( planConf == 1 )
+ {
+ uint8_t* newDest = new uint8_t[ImageDataSize];
+ // Warning : YBR_FULL_422 acts as RGB
+ if ( Header->IsYBRFull() )
+ {
+ ConvertYcBcRPlanesToRGBPixels((uint8_t*)destination, newDest);
+ }
+ else
+ {
+ ConvertRGBPlanesToRGBPixels((uint8_t*)destination, newDest);
+ }
+ memmove(destination, newDest, ImageDataSize);
+ delete[] newDest;
}
+
+///////////////////////////////////////////////////
// now, it's an RGB image
// Lets's write it in the Header
return ImageDataSize;
}
+/**
+ * \brief Re-arrange the bits within the bytes.
+ */
+void gdcmFile::ConvertReArrangeBits( uint8_t* pixelZone,
+ size_t imageDataSize,
+ int numberBitsStored,
+ int numberBitsAllocated,
+ int highBitPosition)
+ throw ( gdcmFormatError )
+{
+ if ( numberBitsStored != numberBitsAllocated )
+ {
+ int l = (int)(imageDataSize / (numberBitsAllocated/8));
+ if ( numberBitsAllocated == 16 )
+ {
+ uint16_t mask = 0xffff;
+ mask = mask >> ( numberBitsAllocated - numberBitsStored );
+ uint16_t* deb = (uint16_t*)pixelZone;
+ for(int i = 0; i<l; i++)
+ {
+ *deb = (*deb >> (numberBitsStored - highBitPosition - 1)) & mask;
+ deb++;
+ }
+ }
+ else if ( numberBitsAllocated == 32 )
+ {
+ uint32_t mask = 0xffffffff;
+ mask = mask >> ( numberBitsAllocated - numberBitsStored );
+ uint32_t* deb = (uint32_t*)pixelZone;
+ for(int i = 0; i<l; i++)
+ {
+ *deb = (*deb >> (numberBitsStored - highBitPosition - 1)) & mask;
+ deb++;
+ }
+ }
+ else
+ {
+ dbg.Verbose(0, "gdcmFile::ConvertReArrangeBits: weird image");
+ throw gdcmFormatError( "gdcmFile::ConvertReArrangeBits()",
+ "weird image !?" );
+ }
+ }
+}
+
+/**
+ * \brief Deal with endianity i.e. re-arange bytes inside the integer
+ */
+void gdcmFile::ConvertReorderEndianity( uint8_t* pixelZone,
+ size_t imageDataSize,
+ int numberBitsStored,
+ int numberBitsAllocated,
+ bool signedPixel)
+{
+ if ( numberBitsAllocated != 8 )
+ {
+ SwapZone( pixelZone, Header->GetSwapCode(), ImageDataSize,
+ numberBitsAllocated );
+ }
+
+ // Special kludge in order to deal with xmedcon broken images:
+ if ( ( numberBitsAllocated == 16 )
+ && ( numberBitsStored < numberBitsAllocated )
+ && ( ! signedPixel ) )
+ {
+ int l = (int)(ImageDataSize / (numberBitsAllocated/8));
+ uint16_t *deb = (uint16_t *)pixelZone;
+ for(int i = 0; i<l; i++)
+ {
+ if( *deb == 0xffff )
+ {
+ *deb = 0;
+ }
+ deb++;
+ }
+ }
+}
+
+/**
+ * \brief Convert (Y plane, cB plane, cR plane) to RGB pixels
+ * \warning Works on all the frames at a time
+ */
+void gdcmFile::ConvertYcBcRPlanesToRGBPixels(uint8_t* source,
+ uint8_t* destination)
+{
+ // 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 = Header->GetXSize() * Header->GetYSize();
+ int nbFrames = Header->GetZSize();
+
+ uint8_t* a = source;
+ uint8_t* b = source + l;
+ uint8_t* c = source + 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;
+
+ *(destination++) = (uint8_t)R;
+ *(destination++) = (uint8_t)G;
+ *(destination++) = (uint8_t)B;
+ a++;
+ b++;
+ c++;
+ }
+ }
+}
+
+/**
+ * \brief Convert (Red plane, Green plane, Blue plane) to RGB pixels
+ * \warning Works on all the frames at a time
+ */
+void gdcmFile::ConvertRGBPlanesToRGBPixels(uint8_t* source,
+ uint8_t* destination)
+{
+ int l = Header->GetXSize() * Header->GetYSize() * Header->GetZSize();
+
+ uint8_t* a = source;
+ uint8_t* b = source + l;
+ uint8_t* c = source + l + l;
+
+ for (int j = 0; j < l; j++)
+ {
+ *(destination++) = *(a++);
+ *(destination++) = *(b++);
+ *(destination++) = *(c++);
+ }
+}
+
/**
* \brief Points the internal Pixel_Data pointer to the callers inData
* image representation, BUT WITHOUT COPYING THE DATA.
return false;
}
- // ---------------------- Compacted File (12 Bits Per Pixel)
- // unpack 12 Bits pixels into 16 Bits pixels
- // 2 pixels 12bit = [0xABCDEF]
- // 2 pixels 16bit = [0x0ABD] + [0x0FCE]
-
if ( Header->GetBitsAllocated() == 12 )
{
- int nbPixels = Header->GetXSize() * Header->GetYSize();
- uint8_t b0, b1, b2;
-
- uint16_t* pdestination = (uint16_t*)destination;
- for(int p = 0; p < nbPixels; p += 2 )
- {
- fread(&b0,1,1,fp);
- fread(&b1,1,1,fp);
- fread(&b2,1,1,fp);
-
- //Two steps is necessary to please VC++
- *pdestination++ = ((b0 >> 4) << 8) + ((b0 & 0x0f) << 4) + (b1 & 0x0f);
- // A B D
- *pdestination++ = ((b2 & 0x0f) << 8) + ((b1 >> 4) << 4) + (b2 >> 4);
- // F C E
-
- // Troubles expected on Big-Endian processors ?
- }
-
+ ConvertDecompress12BitsTo16Bits( (uint8_t*)destination,
+ Header->GetXSize(),
+ Header->GetYSize(),
+ fp);
Header->CloseFile();
return true;
}
}
// --------------- SingleFrame/Multiframe JPEG Lossless/Lossy/2000
- int nb;
- std::string str_nb = Header->GetEntryByNumber(0x0028,0x0100);
- if ( str_nb == GDCM_UNFOUND )
- {
- nb = 16;
- }
- else
+ int numberBitsAllocated = Header->GetBitsAllocated();
+ if ( ( numberBitsAllocated == 0 ) || ( numberBitsAllocated == 12 ) )
{
- nb = atoi( str_nb.c_str() );
- if ( nb == 12 )
- {
- nb = 16; // ?? 12 should be ACR-NEMA only
- }
+ numberBitsAllocated = 16;
}
- int nBytes= nb/8;
+ int nBytes= numberBitsAllocated/8;
int taille = Header->GetXSize() * Header->GetYSize()
* Header->GetSamplesPerPixel();
long fragmentBegining; // for ftell, fseek
Header->CloseFile();
return res;
}
+
+/**
+ * \brief Read from file a 12 bits per pixel image and uncompress it
+ * into a 16 bits per pixel image.
+ */
+void gdcmFile::ConvertDecompress12BitsTo16Bits(
+ uint8_t* pixelZone,
+ int sizeX,
+ int sizeY,
+ FILE* filePtr)
+ throw ( gdcmFormatError )
+{
+ int nbPixels = sizeX * sizeY;
+ uint16_t* destination = (uint16_t*)pixelZone;
+
+ for( int p = 0; p < nbPixels; p += 2 )
+ {
+ uint8_t b0, b1, b2;
+ size_t ItemRead;
+
+ ItemRead = fread( &b0, 1, 1, filePtr);
+ if ( ItemRead != 1 )
+ {
+ throw gdcmFormatError( "gdcmFile::ConvertDecompress12BitsTo16Bits()",
+ "Unfound first block" );
+ }
+
+ ItemRead = fread( &b1, 1, 1, filePtr);
+ if ( ItemRead != 1 )
+ {
+ throw gdcmFormatError( "gdcmFile::ConvertDecompress12BitsTo16Bits()",
+ "Unfound second block" );
+ }
+
+ ItemRead = fread( &b2, 1, 1, filePtr);
+ if ( ItemRead != 1 )
+ {
+ throw gdcmFormatError( "gdcmFile::ConvertDecompress12BitsTo16Bits()",
+ "Unfound second block" );
+ }
+
+ // Two steps are necessary to please VC++
+ //
+ // 2 pixels 12bit = [0xABCDEF]
+ // 2 pixels 16bit = [0x0ABD] + [0x0FCE]
+ // A B D
+ *destination++ = ((b0 >> 4) << 8) + ((b0 & 0x0f) << 4) + (b1 & 0x0f);
+ // F C E
+ *destination++ = ((b2 & 0x0f) << 8) + ((b1 >> 4) << 4) + (b2 >> 4);
+
+ /// \todo JPR Troubles expected on Big-Endian processors ?
+ }
+}
//-----------------------------------------------------------------------------
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff