Program: gdcm
Module: $RCSfile: gdcmFile.cxx,v $
Language: C++
- Date: $Date: 2004/10/08 17:02:53 $
- Version: $Revision: 1.136 $
+ Date: $Date: 2004/11/24 16:39:18 $
+ Version: $Revision: 1.162 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
#include "gdcmFile.h"
#include "gdcmDebug.h"
-#include "gdcmPixelConvert.h"
-#include "jpeg/ljpg/jpegless.h"
+#include "gdcmUtil.h"
+#include "gdcmBinEntry.h"
+#include <fstream>
+namespace gdcm
+{
typedef std::pair<TagDocEntryHT::iterator,TagDocEntryHT::iterator> IterHT;
//-------------------------------------------------------------------------
// Constructor / Destructor
/**
* \brief Constructor dedicated to deal with the *pixels* area of a ACR/DICOMV3
- * file (gdcmHeader only deals with the ... header)
+ * file (Header only deals with the ... header)
* Opens (in read only and when possible) an existing file and checks
* for DICOM compliance. Returns NULL on failure.
* It will be up to the user to load the pixels into memory
* This avoid a double parsing of public part of the header when
* user sets an a posteriori shadow dictionary (efficiency can be
* seen as a side effect).
- * @param header already built gdcmHeader
+ * @param header already built Header
*/
-gdcmFile::gdcmFile(gdcmHeader *header)
+File::File(Header *header)
{
- Header = header;
+ HeaderInternal = header;
SelfHeader = false;
Initialise();
}
/**
* \brief Constructor dedicated to deal with the *pixels* area of a ACR/DICOMV3
- * file (gdcmHeader only deals with the ... header)
+ * file (Header only deals with the ... header)
* Opens (in read only and when possible) an existing file and checks
* for DICOM compliance. Returns NULL on failure.
* It will be up to the user to load the pixels into memory
* seen as a side effect).
* @param filename file to be opened for parsing
*/
-gdcmFile::gdcmFile(std::string const & filename )
+File::File(std::string const & filename )
{
- Header = new gdcmHeader( filename );
+ HeaderInternal = new Header( filename );
SelfHeader = true;
Initialise();
}
/**
* \brief Factorization for various forms of constructors.
*/
-void gdcmFile::Initialise()
+void File::Initialise()
{
- if ( Header->IsReadable() )
+ WriteMode = WMODE_DECOMPRESSED;
+ WriteType = WTYPE_IMPL_VR;
+
+ PixelConverter = new PixelConvert;
+ Archive = new DocEntryArchive( HeaderInternal );
+
+ if ( HeaderInternal->IsReadable() )
{
ImageDataSizeRaw = ComputeDecompressedPixelDataSizeFromHeader();
- if ( Header->HasLUT() )
+ if ( HeaderInternal->HasLUT() )
{
ImageDataSize = 3 * ImageDataSizeRaw;
}
{
ImageDataSize = ImageDataSizeRaw;
}
+
+ PixelConverter->GrabInformationsFromHeader( HeaderInternal );
}
+
SaveInitialValues();
}
/**
* \brief canonical destructor
- * \note If the gdcmHeader was created by the gdcmFile constructor,
- * it is destroyed by the gdcmFile
+ * \note If the Header was created by the File constructor,
+ * it is destroyed by the File
*/
-gdcmFile::~gdcmFile()
+File::~File()
{
- if( SelfHeader )
+ if( PixelConverter )
+ {
+ delete PixelConverter;
+ }
+ if( Archive )
{
- delete Header;
+ delete Archive;
}
- Header = 0;
- DeleteInitialValues();
+ if( SelfHeader )
+ {
+ delete HeaderInternal;
+ }
+ HeaderInternal = 0;
}
/**
* \brief Sets some initial values for the Constructor
* \warning not end user intended
*/
-void gdcmFile::SaveInitialValues()
+void File::SaveInitialValues()
{
-
PixelRead = -1; // no ImageData read yet.
- LastAllocatedPixelDataLength = 0;
Pixel_Data = 0;
-
- InitialSpp = "";
- InitialPhotInt = "";
- InitialPlanConfig = "";
- InitialBitsAllocated = "";
- InitialHighBit = "";
-
- InitialRedLUTDescr = 0;
- InitialGreenLUTDescr = 0;
- InitialBlueLUTDescr = 0;
- InitialRedLUTData = 0;
- InitialGreenLUTData = 0;
- InitialBlueLUTData = 0;
-
- if ( Header->IsReadable() )
- {
- // the following values *may* be modified
- // by gdcmFile::GetImageDataIntoVectorRaw
- // we save their initial value.
- InitialSpp = Header->GetEntryByNumber(0x0028,0x0002);
- InitialPhotInt = Header->GetEntryByNumber(0x0028,0x0004);
- InitialPlanConfig = Header->GetEntryByNumber(0x0028,0x0006);
-
- InitialBitsAllocated = Header->GetEntryByNumber(0x0028,0x0100);
- InitialHighBit = Header->GetEntryByNumber(0x0028,0x0102);
-
- // the following entries *may* be removed from the H table
- // (NOT deleted ...) by gdcmFile::GetImageDataIntoVectorRaw
- // we keep a pointer on them.
- InitialRedLUTDescr = Header->GetDocEntryByNumber(0x0028,0x1101);
- InitialGreenLUTDescr = Header->GetDocEntryByNumber(0x0028,0x1102);
- InitialBlueLUTDescr = Header->GetDocEntryByNumber(0x0028,0x1103);
-
- InitialRedLUTData = Header->GetDocEntryByNumber(0x0028,0x1201);
- InitialGreenLUTData = Header->GetDocEntryByNumber(0x0028,0x1202);
- InitialBlueLUTData = Header->GetDocEntryByNumber(0x0028,0x1203);
- }
-}
-
-/**
- * \brief restores some initial values
- * \warning not end user intended
- */
-void gdcmFile::RestoreInitialValues()
-{
- if ( Header->IsReadable() )
- {
- // the following values *may* have been modified
- // by gdcmFile::GetImageDataIntoVectorRaw
- // we restore their initial value.
- if ( InitialSpp != "")
- Header->SetEntryByNumber(InitialSpp,0x0028,0x0002);
- if ( InitialPhotInt != "")
- Header->SetEntryByNumber(InitialPhotInt,0x0028,0x0004);
- if ( InitialPlanConfig != "")
-
- Header->SetEntryByNumber(InitialPlanConfig,0x0028,0x0006);
- if ( InitialBitsAllocated != "")
- Header->SetEntryByNumber(InitialBitsAllocated,0x0028,0x0100);
- if ( InitialHighBit != "")
- Header->SetEntryByNumber(InitialHighBit,0x0028,0x0102);
-
- // the following entries *may* be have been removed from the H table
- // (NOT deleted ...) by gdcmFile::GetImageDataIntoVectorRaw
- // we restore them.
-
- if (InitialRedLUTDescr)
- Header->AddEntry(InitialRedLUTDescr);
- if (InitialGreenLUTDescr)
- Header->AddEntry(InitialGreenLUTDescr);
- if (InitialBlueLUTDescr)
- Header->AddEntry(InitialBlueLUTDescr);
-
- if (InitialRedLUTData)
- Header->AddEntry(InitialBlueLUTDescr);
- if (InitialGreenLUTData)
- Header->AddEntry(InitialGreenLUTData);
- if (InitialBlueLUTData)
- Header->AddEntry(InitialBlueLUTData);
- }
-}
-
-/**
- * \brief delete initial values (il they were saved)
- * of InitialLutDescriptors and InitialLutData
- */
-void gdcmFile::DeleteInitialValues()
-{
-
-// InitialLutDescriptors and InitialLutData
-// will have to be deleted if the don't belong any longer
-// to the Header H table when the header is deleted...
-
- if ( InitialRedLUTDescr )
- delete InitialRedLUTDescr;
-
- if ( InitialGreenLUTDescr )
- delete InitialGreenLUTDescr;
-
- if ( InitialBlueLUTDescr )
- delete InitialBlueLUTDescr;
-
- if ( InitialRedLUTData )
- delete InitialRedLUTData;
-
- if ( InitialGreenLUTData != NULL)
- delete InitialGreenLUTData;
-
- if ( InitialBlueLUTData != NULL)
- delete InitialBlueLUTData;
}
//-----------------------------------------------------------------------------
* \warning : it is NOT the group 7FE0 length
* (no interest for compressed images).
*/
-int gdcmFile::ComputeDecompressedPixelDataSizeFromHeader()
+int File::ComputeDecompressedPixelDataSizeFromHeader()
{
// see PS 3.3-2003 : C.7.6.3.2.1
//
// 0028|1202 [US] [Green Palette Color Lookup Table Data]
// 0028|1203 [US] [Blue Palette Color Lookup Table Data]
- // Number of "Bits Allocated"
- int numberBitsAllocated = Header->GetBitsAllocated();
- if ( ( numberBitsAllocated == 0 ) || ( numberBitsAllocated == 12 ) )
+ int numberBitsAllocated = HeaderInternal->GetBitsAllocated();
+ // Number of "Bits Allocated" is fixed to 16 when:
+ // - it is not defined (i.e. it's value is 0)
+ // - it's 12, since we will expand the image to 16 bits (see
+ // PixelConvert::ConvertDecompress12BitsTo16Bits() )
+ if ( numberBitsAllocated == 0 || numberBitsAllocated == 12 )
{
numberBitsAllocated = 16;
}
- int DecompressedSize = Header->GetXSize()
- * Header->GetYSize()
- * Header->GetZSize()
+ int DecompressedSize = HeaderInternal->GetXSize()
+ * HeaderInternal->GetYSize()
+ * HeaderInternal->GetZSize()
* ( numberBitsAllocated / 8 )
- * Header->GetSamplesPerPixel();
+ * HeaderInternal->GetSamplesPerPixel();
return DecompressedSize;
}
+/// Accessor to \ref ImageDataSize
+size_t File::GetImageDataSize()
+{
+ if ( ! GetDecompressed() )
+ {
+ // If the decompression failed nothing can be done.
+ return 0;
+ }
+
+ if ( HeaderInternal->HasLUT() && PixelConverter->BuildRGBImage() )
+ {
+ return PixelConverter->GetRGBSize();
+ }
+ else
+ {
+ // When no LUT or LUT conversion fails, return the decompressed
+ return PixelConverter->GetDecompressedSize();
+ }
+}
+
+/// Accessor to \ref ImageDataSizeRaw
+size_t File::GetImageDataSizeRaw()
+{
+ if ( ! GetDecompressed() )
+ {
+ // If the decompression failed nothing can be done.
+ return 0;
+ }
+ return PixelConverter->GetDecompressedSize();
+}
+
/**
* \brief - Allocates necessary memory,
* - Reads the pixels from disk (uncompress if necessary),
* @return Pointer to newly allocated pixel data.
* NULL if alloc fails
*/
-uint8_t* gdcmFile::GetImageData()
+uint8_t* File::GetImageData()
{
- // FIXME (Mathieu)
- // I need to deallocate Pixel_Data before doing any allocation:
-
- if ( Pixel_Data )
- if ( LastAllocatedPixelDataLength != ImageDataSize )
- free(Pixel_Data);
- if ( !Pixel_Data )
- Pixel_Data = new uint8_t[ImageDataSize];
-
- if ( Pixel_Data )
+ if ( ! GetDecompressed() )
{
- LastAllocatedPixelDataLength = ImageDataSize;
-
- // we load the pixels (and transform grey level + LUT into RGB)
- GetImageDataIntoVector(Pixel_Data, ImageDataSize);
-
- // We say the value *is* loaded.
- GetHeader()->SetEntryByNumber( GDCM_BINLOADED,
- GetHeader()->GetGrPixel(), GetHeader()->GetNumPixel());
-
- // Will be 7fe0, 0010 in standard case
- GetHeader()->SetEntryBinAreaByNumber( Pixel_Data,
- GetHeader()->GetGrPixel(), GetHeader()->GetNumPixel());
- }
- PixelRead = 0; // no PixelRaw
-
- return Pixel_Data;
+ // If the decompression failed nothing can be done.
+ return 0;
+ }
+
+ if ( HeaderInternal->HasLUT() && PixelConverter->BuildRGBImage() )
+ {
+ return PixelConverter->GetRGB();
+ }
+ else
+ {
+ // When no LUT or LUT conversion fails, return the decompressed
+ return PixelConverter->GetDecompressed();
+ }
}
/**
* @return On success, the number of bytes actually copied. Zero on
* failure e.g. MaxSize is lower than necessary.
*/
-size_t gdcmFile::GetImageDataIntoVector (void* destination, size_t maxSize)
+size_t File::GetImageDataIntoVector (void* destination, size_t maxSize)
{
- GetImageDataIntoVectorRaw (destination, maxSize);
- PixelRead = 0 ; // =0 : no ImageDataRaw
- if ( !Header->HasLUT() )
+ if ( ! GetDecompressed() )
{
- return ImageDataSize;
+ // If the decompression failed nothing can be done.
+ return 0;
}
-
- // from Lut R + Lut G + Lut B
- uint8_t *newDest = new uint8_t[ImageDataSize];
- uint8_t *a = (uint8_t *)destination;
- uint8_t *lutRGBA = Header->GetLUTRGBA();
- if ( lutRGBA )
+ if ( HeaderInternal->HasLUT() && PixelConverter->BuildRGBImage() )
{
- int j;
- // move Gray pixels to temp area
- memmove(newDest, destination, ImageDataSizeRaw);
- for (size_t i=0; i<ImageDataSizeRaw; ++i)
+ if ( PixelConverter->GetRGBSize() > maxSize )
{
- // Build RGB Pixels
- j = newDest[i]*4;
- *a++ = lutRGBA[j];
- *a++ = lutRGBA[j+1];
- *a++ = lutRGBA[j+2];
+ dbg.Verbose(0, "File::GetImageDataIntoVector: pixel data bigger"
+ "than caller's expected MaxSize");
+ return 0;
}
- delete[] newDest;
-
- // now, it's an RGB image
- // Lets's write it in the Header
-
- // FIXME : Better use CreateOrReplaceIfExist ?
-
- std::string spp = "3"; // Samples Per Pixel
- Header->SetEntryByNumber(spp,0x0028,0x0002);
- std::string rgb = "RGB "; // Photometric Interpretation
- Header->SetEntryByNumber(rgb,0x0028,0x0004);
- std::string planConfig = "0"; // Planar Configuration
- Header->SetEntryByNumber(planConfig,0x0028,0x0006);
-
+ memcpy( destination,
+ (void*)PixelConverter->GetRGB(),
+ PixelConverter->GetRGBSize() );
+ return PixelConverter->GetRGBSize();
}
- else // GetLUTRGBA() failed
- {
- // (gdcm-US-ALOKA-16.dcm), contains Segmented xxx Palette Color
- // that are *more* than 65535 long ?!?
- // No idea how to manage such an image !
- // Need to make RGB Pixels (?) from grey Pixels (?!) and Gray Lut (!?!)
- // It seems that *no Dicom Viewer* has any idea :-(
-
- std::string photomInterp = "MONOCHROME1 "; // Photometric Interpretation
- Header->SetEntryByNumber(photomInterp,0x0028,0x0004);
- }
- /// \todo Drop Palette Color out of the Header?
- return ImageDataSize;
+ // Either no LUT conversion necessary or LUT conversion failed
+ if ( PixelConverter->GetDecompressedSize() > maxSize )
+ {
+ dbg.Verbose(0, "File::GetImageDataIntoVector: pixel data bigger"
+ "than caller's expected MaxSize");
+ return 0;
+ }
+ memcpy( destination,
+ (void*)PixelConverter->GetDecompressed(),
+ PixelConverter->GetDecompressedSize() );
+ return PixelConverter->GetDecompressedSize();
}
/**
* @return Pointer to newly allocated pixel data.
* \ NULL if alloc fails
*/
-uint8_t* gdcmFile::GetImageDataRaw ()
+uint8_t* File::GetImageDataRaw ()
{
- size_t imgDataSize;
- if ( Header->HasLUT() )
- /// \todo Let gdcmHeader user a chance to get the right value
- imgDataSize = ImageDataSizeRaw;
- else
- imgDataSize = ImageDataSize;
-
- // FIXME (Mathieu)
- // I need to deallocate Pixel_Data before doing any allocation:
-
- if ( Pixel_Data )
- if ( LastAllocatedPixelDataLength != imgDataSize )
- free(Pixel_Data);
- if ( !Pixel_Data )
- Pixel_Data = new uint8_t[imgDataSize];
-
- if ( Pixel_Data )
- {
- LastAllocatedPixelDataLength = imgDataSize;
-
- // we load the pixels ( grey level or RGB, but NO transformation)
- GetImageDataIntoVectorRaw(Pixel_Data, imgDataSize);
-
- // We say the value *is* loaded.
- GetHeader()->SetEntryByNumber( GDCM_BINLOADED,
- GetHeader()->GetGrPixel(), GetHeader()->GetNumPixel());
-
- // will be 7fe0, 0010 in standard cases
- GetHeader()->SetEntryBinAreaByNumber(Pixel_Data,
- GetHeader()->GetGrPixel(), GetHeader()->GetNumPixel());
- }
- PixelRead = 1; // PixelRaw
-
- return Pixel_Data;
-}
-
-/**
- * \brief Copies at most MaxSize bytes of pixel data to caller's
- * memory space.
- * \warning This function was designed to avoid people that want to build
- * a volume from an image stack to need first to get the image pixels
- * and then move them to the volume area.
- * It's absolutely useless for any VTK user since vtk chooses
- * to invert the lines of an image, that is the last line comes first
- * (for some axis related reasons?). Hence he will have
- * to load the image line by line, starting from the end.
- * VTK users hace to call GetImageData
- * \warning DOES NOT transform the Grey Plane + Palette Color (if any)
- * into a single RGB Pixels Plane
- * the (VTK) user will manage the palettes
- *
- * @param destination Address (in caller's memory space) at which the
- * pixel data should be copied
- * @param maxSize Maximum number of bytes to be copied. When MaxSize
- * is not sufficient to hold the pixel data the copy is not
- * executed (i.e. no partial copy).
- * @return On success, the number of bytes actually copied. Zero on
- * failure e.g. MaxSize is lower than necessary.
- */
-size_t gdcmFile::GetImageDataIntoVectorRaw (void* destination, size_t maxSize)
-{
- // we save the initial values of the following
- // in order to be able to restore the header in a disk-consistent state
- // (if user asks twice to get the pixels from disk)
-
- if ( PixelRead != -1 ) // File was "read" before
- {
- RestoreInitialValues();
- }
-
- PixelRead = 1 ; // PixelRaw
-
- if ( ImageDataSize > maxSize )
- {
- dbg.Verbose(0, "gdcmFile::GetImageDataIntoVector: pixel data bigger"
- "than caller's expected MaxSize");
- return (size_t)0;
- }
-
- ReadPixelData( destination );
-
- // Number of Bits Allocated for storing a Pixel
- int numberBitsAllocated = Header->GetBitsAllocated();
- if ( numberBitsAllocated == 0 )
- {
- numberBitsAllocated = 16;
- }
-
- // Number of Bits actually used
- int numberBitsStored = Header->GetBitsStored();
- if ( numberBitsStored == 0 )
- {
- numberBitsStored = numberBitsAllocated;
- }
-
- // High Bit Position
- int highBitPosition = Header->GetHighBitPosition();
- if ( highBitPosition == 0 )
- {
- highBitPosition = numberBitsAllocated - 1;
- }
-
- bool signedPixel = Header->IsSignedPixelData();
-
- gdcmPixelConvert::ConvertReorderEndianity(
- (uint8_t*) destination,
- ImageDataSize,
- numberBitsStored,
- numberBitsAllocated,
- Header->GetSwapCode(),
- signedPixel );
-
- ConvertReArrangeBits( (uint8_t*) destination,
- ImageDataSize,
- numberBitsStored,
- numberBitsAllocated,
- highBitPosition );
-
-#ifdef GDCM_DEBUG
- FILE* DebugFile;
- DebugFile = fopen( "SpuriousFile.RAW", "wb" );
- fwrite( PixelConvertor.GetUncompressed(),
- PixelConvertor.GetUncompressedsSize(),
- 1, DebugFile );
- fclose( DebugFile );
-#endif //GDCM_DEBUG
-
-// SPLIT ME
-//////////////////////////////////
-// Deal with the color
-
- // Monochrome pictures don't require color intervention
- if ( Header->IsMonochrome() )
- {
- return ImageDataSize;
- }
-
- // Planar configuration = 0 : Pixels are already RGB
- // Planar configuration = 1 : 3 planes : R, G, B
- // Planar configuration = 2 : 1 gray Plane + 3 LUT
-
- // Well ... supposed to be !
- // See US-PAL-8-10x-echo.dcm: PlanarConfiguration=0,
- // PhotometricInterpretation=PALETTE COLOR
- // and heuristic has to be found :-(
-
- int planConf = Header->GetPlanarConfiguration();
-
- // 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() )
- {
- return ImageDataSize;
- }
-
- // When planConf is 0, pixels are allready in RGB
-
- 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
-
- // Droping Palette Color out of the Header
- // has been moved to the Write process.
-
- // TODO : move 'values' modification to the write process
- // : save also (in order to be able to restore)
- // : 'high bit' -when not equal to 'bits stored' + 1
- // : 'bits allocated', when it's equal to 12 ?!
-
- std::string spp = "3"; // Samples Per Pixel
- std::string photInt = "RGB "; // Photometric Interpretation
- std::string planConfig = "0"; // Planar Configuration
-
- Header->SetEntryByNumber(spp,0x0028,0x0002);
- Header->SetEntryByNumber(photInt,0x0028,0x0004);
- Header->SetEntryByNumber(planConfig,0x0028,0x0006);
-
- 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 !?" );
- }
- }
+ return GetDecompressed();
}
-/**
- * \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)
+uint8_t* File::GetDecompressed()
{
- // 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++)
+ uint8_t* decompressed = PixelConverter->GetDecompressed();
+ if ( ! decompressed )
+ {
+ // The decompressed image migth not be loaded yet:
+ std::ifstream* fp = HeaderInternal->OpenFile();
+ PixelConverter->ReadAndDecompressPixelData( fp );
+ if(fp) HeaderInternal->CloseFile();
+ decompressed = PixelConverter->GetDecompressed();
+ if ( ! decompressed )
{
- 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++;
+ dbg.Verbose(0, "File::GetDecompressed: read/decompress of "
+ "pixel data apparently went wrong.");
+ return 0;
}
}
-}
-
-/**
- * \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++);
- }
+ return decompressed;
}
/**
*
* @return boolean
*/
-bool gdcmFile::SetImageData(uint8_t* inData, size_t expectedSize)
+bool File::SetImageData(uint8_t* inData, size_t expectedSize)
{
- Header->SetImageDataSize( expectedSize );
+ HeaderInternal->SetImageDataSize( expectedSize );
// FIXME : if already allocated, memory leak !
Pixel_Data = inData;
ImageDataSize = ImageDataSizeRaw = expectedSize;
* @return false if write fails
*/
-bool gdcmFile::WriteRawData(std::string const & fileName)
+bool File::WriteRawData(std::string const & fileName)
{
- FILE* fp1 = fopen(fileName.c_str(), "wb");
- if (fp1 == NULL)
+ std::ofstream fp1(fileName.c_str(), std::ios::out | std::ios::binary );
+ if (!fp1)
{
- printf("Fail to open (write) file [%s] \n", fileName.c_str());
+ dbg.Verbose(2, "Fail to open (write) file:", fileName.c_str());
return false;
}
- fwrite (Pixel_Data, ImageDataSize, 1, fp1);
- fclose (fp1);
+ fp1.write((char*)Pixel_Data, ImageDataSize);
+ fp1.close();
return true;
}
* @return false if write fails
*/
-bool gdcmFile::WriteDcmImplVR (std::string const & fileName)
+bool File::WriteDcmImplVR (std::string const & fileName)
{
- return WriteBase(fileName, gdcmImplicitVR);
+ SetWriteTypeToDcmImplVR();
+ return Write(fileName);
}
/**
* @return false if write fails
*/
-bool gdcmFile::WriteDcmExplVR (std::string const & fileName)
+bool File::WriteDcmExplVR (std::string const & fileName)
{
- return WriteBase(fileName, gdcmExplicitVR);
+ SetWriteTypeToDcmExplVR();
+ return Write(fileName);
}
/**
* @return false if write fails
*/
-bool gdcmFile::WriteAcr (std::string const & fileName)
+bool File::WriteAcr (std::string const & fileName)
{
- return WriteBase(fileName, gdcmACR);
+ SetWriteTypeToAcr();
+ return Write(fileName);
+}
+
+bool File::Write(std::string const& fileName)
+{
+ switch(WriteType)
+ {
+ case WTYPE_IMPL_VR:
+ return WriteBase(fileName,ImplicitVR);
+ case WTYPE_EXPL_VR:
+ return WriteBase(fileName,ExplicitVR);
+ case WTYPE_ACR:
+ return WriteBase(fileName,ACR);
+ }
+ return(false);
}
//-----------------------------------------------------------------------------
* @param type file type (ExplicitVR, ImplicitVR, ...)
* @return false if write fails
*/
-bool gdcmFile::WriteBase (std::string const & fileName, FileType type)
+bool File::WriteBase (std::string const & fileName, FileType type)
{
- if ( PixelRead == -1 && type != gdcmExplicitVR)
+/* if ( PixelRead == -1 && type != ExplicitVR)
{
return false;
- }
+ }*/
- FILE* fp1 = fopen(fileName.c_str(), "wb");
+ std::ofstream* fp1 = new std::ofstream(fileName.c_str(),
+ std::ios::out | std::ios::binary);
if (fp1 == NULL)
{
- printf("Failed to open (write) File [%s] \n", fileName.c_str());
+ dbg.Verbose(2, "Failed to open (write) File: " , fileName.c_str());
return false;
}
- if ( type == gdcmImplicitVR || type == gdcmExplicitVR )
+ switch(WriteMode)
{
- // writing Dicom File Preamble
- uint8_t* filePreamble = new uint8_t[128];
- memset(filePreamble, 0, 128);
- fwrite(filePreamble, 128, 1, fp1);
- fwrite("DICM", 4, 1, fp1);
-
- delete[] filePreamble;
+ case WMODE_NATIVE :
+ SetWriteToNative();
+ break;
+ case WMODE_DECOMPRESSED :
+ SetWriteToDecompressed();
+ break;
+ case WMODE_RGB :
+ SetWriteToRGB();
+ break;
}
// --------------------------------------------------------------
// if recognition code tells us we dealt with a LibIDO image
// we reproduce on disk the switch between lineNumber and columnNumber
// just before writting ...
-
/// \todo the best trick would be *change* the recognition code
/// but pb expected if user deals with, e.g. COMPLEX images
-
- std::string rows, columns;
- if ( Header->GetFileType() == gdcmACR_LIBIDO)
+/* if ( HeaderInternal->GetFileType() == ACR_LIBIDO)
{
- rows = Header->GetEntryByNumber(0x0028, 0x0010);
- columns = Header->GetEntryByNumber(0x0028, 0x0011);
-
- Header->SetEntryByNumber(columns, 0x0028, 0x0010);
- Header->SetEntryByNumber(rows , 0x0028, 0x0011);
- }
+ SetWriteToLibido();
+ }*/
// ----------------- End of Special Patch ----------------
-
- uint16_t grPixel = Header->GetGrPixel();
- uint16_t numPixel = Header->GetNumPixel();;
-
- gdcmDocEntry* PixelElement =
- GetHeader()->GetDocEntryByNumber(grPixel, numPixel);
- if ( PixelRead == 1 )
- {
- // we read pixel 'as is' (no tranformation LUT -> RGB)
- PixelElement->SetLength( ImageDataSizeRaw );
- }
- else if ( PixelRead == 0 )
- {
- // we tranformed GrayLevel pixels + LUT into RGB Pixel
- PixelElement->SetLength( ImageDataSize );
- }
-
- Header->Write(fp1, type);
+ HeaderInternal->Write(fp1, type);
// --------------------------------------------------------------
// Special Patch to allow gdcm to re-write ACR-LibIDO formated images
//
// ...and we restore the Header to be Dicom Compliant again
// just after writting
-
- if ( Header->GetFileType() == gdcmACR_LIBIDO )
+/* if ( HeaderInternal->GetFileType() == ACR_LIBIDO )
{
- Header->SetEntryByNumber(rows , 0x0028, 0x0010);
- Header->SetEntryByNumber(columns, 0x0028, 0x0011);
- }
+ RestoreWriteFromLibido();
+ }*/
// ----------------- End of Special Patch ----------------
-
- // fwrite(Pixel_Data, ImageDataSize, 1, fp1); // should be useless, now
- fclose (fp1);
+
+ RestoreWrite();
+
+
+ fp1->close ();
+ delete fp1;
return true;
}
+/**
+ * \brief Access to the underlying \ref PixelConverter RGBA LUT
+ */
+uint8_t* File::GetLutRGBA()
+{
+ return PixelConverter->GetLutRGBA();
+}
+
//-----------------------------------------------------------------------------
// Private
/**
- * \brief Read pixel data from disk (optionaly decompressing) into the
- * caller specified memory location.
- * @param destination where the pixel data should be stored.
- *
+ * \brief Set the pixel datas in the good entry of the Header
*/
-bool gdcmFile::ReadPixelData(void* destination)
+void File::SetPixelData(uint8_t* data)
{
- FILE* fp = Header->OpenFile();
+ GetHeader()->SetEntryByNumber( GDCM_BINLOADED,
+ GetHeader()->GetGrPixel(), GetHeader()->GetNumPixel());
- if ( !fp )
+ // Will be 7fe0, 0010 in standard case
+ DocEntry* currentEntry = GetHeader()->GetDocEntryByNumber(GetHeader()->GetGrPixel(), GetHeader()->GetNumPixel());
+ if ( currentEntry )
{
- return false;
- }
- if ( fseek(fp, Header->GetPixelOffset(), SEEK_SET) == -1 )
- {
- Header->CloseFile();
- return false;
+ if ( BinEntry* binEntry = dynamic_cast<BinEntry *>(currentEntry) )
+ // Flag is to false because datas are kept in the gdcmPixelConvert
+ binEntry->SetBinArea( data, false );
}
+}
- if ( Header->GetBitsAllocated() == 12 )
- {
- gdcmPixelConvert::ConvertDecompress12BitsTo16Bits(
- (uint8_t*)destination,
- Header->GetXSize(),
- Header->GetYSize(),
- fp);
- Header->CloseFile();
- return true;
- }
+void File::SetWriteToNative()
+{
+// Nothing to do
+}
- // ---------------------- Uncompressed File
- if ( !Header->IsDicomV3() ||
- Header->IsImplicitVRLittleEndianTransferSyntax() ||
- Header->IsExplicitVRLittleEndianTransferSyntax() ||
- Header->IsExplicitVRBigEndianTransferSyntax() ||
- Header->IsDeflatedExplicitVRLittleEndianTransferSyntax() )
+void File::SetWriteToDecompressed()
+{
+ if(HeaderInternal->GetNumberOfScalarComponents()==3 && !HeaderInternal->HasLUT())
+ {
+ SetWriteToRGB();
+ }
+ else
{
- size_t ItemRead = fread(destination, Header->GetPixelAreaLength(), 1, fp);
- Header->CloseFile();
- if ( ItemRead != 1 )
+ ValEntry* photInt = CopyValEntry(0x0028,0x0004);
+ if(HeaderInternal->HasLUT())
{
- return false;
+ photInt->SetValue("PALETTE COLOR ");
+ photInt->SetLength(14);
}
else
{
- return true;
+ photInt->SetValue("MONOCHROME1 ");
+ photInt->SetLength(12);
+ }
+
+ BinEntry* pixel = CopyBinEntry(GetHeader()->GetGrPixel(),GetHeader()->GetNumPixel());
+ pixel->SetValue(GDCM_BINLOADED);
+ if(Pixel_Data)
+ {
+ pixel->SetBinArea(Pixel_Data,false);
+ pixel->SetLength(ImageDataSize);
}
+ else
+ {
+ pixel->SetBinArea(PixelConverter->GetDecompressed(),false);
+ pixel->SetLength(PixelConverter->GetDecompressedSize());
+ }
+
+ Archive->Push(photInt);
+ Archive->Push(pixel);
}
+}
- // ---------------------- Run Length Encoding
- if ( Header->IsRLELossLessTransferSyntax() )
- {
- bool res = gdcmPixelConvert::gdcm_read_RLE_file ( destination,
- Header->GetXSize(),
- Header->GetYSize(),
- Header->GetZSize(),
- Header->GetBitsAllocated(),
- &(Header->RLEInfo),
- fp );
- Header->CloseFile();
- return res;
- }
-
- // --------------- SingleFrame/Multiframe JPEG Lossless/Lossy/2000
- int numberBitsAllocated = Header->GetBitsAllocated();
- if ( ( numberBitsAllocated == 0 ) || ( numberBitsAllocated == 12 ) )
+void File::SetWriteToRGB()
+{
+ if(HeaderInternal->GetNumberOfScalarComponents()==3 && !HeaderInternal->HasLUT())
{
- numberBitsAllocated = 16;
- }
+ PixelConverter->BuildRGBImage();
+
+ ValEntry* spp = CopyValEntry(0x0028,0x0002);
+ spp->SetValue("3 ");
+ spp->SetLength(2);
- int nBytes= numberBitsAllocated/8;
- int taille = Header->GetXSize() * Header->GetYSize()
- * Header->GetSamplesPerPixel();
- long fragmentBegining; // for ftell, fseek
+ ValEntry* planConfig = CopyValEntry(0x0028,0x0006);
+ planConfig->SetValue("0 ");
+ planConfig->SetLength(2);
- bool jpg2000 = Header->IsJPEG2000();
- bool jpgLossless = Header->IsJPEGLossless();
+ ValEntry* photInt = CopyValEntry(0x0028,0x0004);
+ photInt->SetValue("RGB ");
+ photInt->SetLength(4);
- bool res = true;
- uint16_t ItemTagGr, ItemTagEl;
- int ln;
-
- // Position on begining of Jpeg Pixels
-
- fread(&ItemTagGr,2,1,fp); // Reading (fffe) : Item Tag Gr
- fread(&ItemTagEl,2,1,fp); // Reading (e000) : Item Tag El
- if(Header->GetSwapCode())
- {
- ItemTagGr = Header->SwapShort(ItemTagGr);
- ItemTagEl = Header->SwapShort(ItemTagEl);
- }
+ BinEntry* pixel = CopyBinEntry(GetHeader()->GetGrPixel(),GetHeader()->GetNumPixel());
+ pixel->SetValue(GDCM_BINLOADED);
+ if(Pixel_Data)
+ {
+ pixel->SetBinArea(Pixel_Data,false);
+ pixel->SetLength(ImageDataSize);
+ }
+ else if(PixelConverter->GetRGB())
+ {
+ pixel->SetBinArea(PixelConverter->GetRGB(),false);
+ pixel->SetLength(PixelConverter->GetRGBSize());
+ }
+ else // Decompressed data
+ {
+ pixel->SetBinArea(PixelConverter->GetDecompressed(),false);
+ pixel->SetLength(PixelConverter->GetDecompressedSize());
+ }
- fread(&ln,4,1,fp);
- if( Header->GetSwapCode() )
+ Archive->Push(spp);
+ Archive->Push(planConfig);
+ Archive->Push(photInt);
+ Archive->Push(pixel);
+
+ // For old ACR-NEMA
+ // Thus, we have a RGB image and the bits allocated = 24 and
+ // samples per pixels = 1 (in the read file)
+ if(HeaderInternal->GetBitsAllocated()==24)
+ {
+ ValEntry* bitsAlloc = CopyValEntry(0x0028,0x0100);
+ bitsAlloc->SetValue("8 ");
+ bitsAlloc->SetLength(2);
+
+ ValEntry* bitsStored = CopyValEntry(0x0028,0x0101);
+ bitsStored->SetValue("8 ");
+ bitsStored->SetLength(2);
+
+ ValEntry* highBit = CopyValEntry(0x0028,0x0102);
+ highBit->SetValue("7 ");
+ highBit->SetLength(2);
+
+ Archive->Push(bitsAlloc);
+ Archive->Push(bitsStored);
+ Archive->Push(highBit);
+ }
+ }
+ else
{
- ln = Header->SwapLong( ln ); // Basic Offset Table Item length
+ SetWriteToDecompressed();
}
+}
+
+void File::RestoreWrite()
+{
+ Archive->Restore(0x0028,0x0002);
+ Archive->Restore(0x0028,0x0004);
+ Archive->Restore(0x0028,0x0006);
+ Archive->Restore(GetHeader()->GetGrPixel(),GetHeader()->GetNumPixel());
+
+ // For old ACR-NEMA (24 bits problem)
+ Archive->Restore(0x0028,0x0100);
+ Archive->Restore(0x0028,0x0101);
+ Archive->Restore(0x0028,0x0102);
+}
- if ( ln != 0 )
+void File::SetWriteToLibido()
+{
+ ValEntry *oldRow = dynamic_cast<ValEntry *>(HeaderInternal->GetDocEntryByNumber(0x0028, 0x0010));
+ ValEntry *oldCol = dynamic_cast<ValEntry *>(HeaderInternal->GetDocEntryByNumber(0x0028, 0x0011));
+
+ if( oldRow && oldCol )
{
- // What is it used for ?!?
- uint8_t* BasicOffsetTableItemValue = new uint8_t[ln+1];
- fread(BasicOffsetTableItemValue,ln,1,fp);
- //delete[] BasicOffsetTableItemValue;
+ std::string rows, columns;
+
+ ValEntry *newRow=new ValEntry(oldRow->GetDictEntry());
+ ValEntry *newCol=new ValEntry(oldCol->GetDictEntry());
+
+ newRow->Copy(oldCol);
+ newCol->Copy(oldRow);
+
+ newRow->SetValue(oldCol->GetValue());
+ newCol->SetValue(oldRow->GetValue());
+
+ Archive->Push(newRow);
+ Archive->Push(newCol);
}
+}
+
+void File::RestoreWriteFromLibido()
+{
+ Archive->Restore(0x0028,0x0010);
+ Archive->Restore(0x0028,0x0011);
+}
+
+ValEntry* File::CopyValEntry(uint16_t group,uint16_t element)
+{
+ DocEntry* oldE = HeaderInternal->GetDocEntryByNumber(group, element);
+ ValEntry* newE;
- // first Fragment initialisation
- fread(&ItemTagGr,2,1,fp); // Reading (fffe) : Item Tag Gr
- fread(&ItemTagEl,2,1,fp); // Reading (e000) : Item Tag El
- if( Header->GetSwapCode() )
+ if(oldE)
{
- ItemTagGr = Header->SwapShort( ItemTagGr );
- ItemTagEl = Header->SwapShort( ItemTagEl );
+ newE = new ValEntry(oldE->GetDictEntry());
+ newE->Copy(oldE);
}
-
- // parsing fragments until Sequence Delim. Tag found
- while ( ItemTagGr == 0xfffe && ItemTagEl != 0xe0dd )
+ else
{
- // --- for each Fragment
- fread(&ln,4,1,fp);
- if( Header->GetSwapCode() )
- {
- ln = Header->SwapLong(ln); // Fragment Item length
- }
- fragmentBegining = ftell( fp );
+ newE = GetHeader()->NewValEntryByNumber(group,element);
+ }
- if ( jpg2000 )
- {
- // JPEG 2000 : call to ???
- res = gdcm_read_JPEG2000_file (fp,destination); // Not Yet written
- // ------------------------------------- endif (JPEG2000)
- }
- else if (jpgLossless)
- {
- // JPEG LossLess : call to xmedcom Lossless JPEG
- // Reading Fragment pixels
- JPEGLosslessDecodeImage (fp, (uint16_t*)destination,
- Header->GetPixelSize() * 8 * Header->GetSamplesPerPixel(), ln);
- res = 1; // in order not to break the loop
-
- } // ------------------------------------- endif (JPEGLossless)
- else
- {
- // JPEG Lossy : call to IJG 6b
- if ( Header->GetBitsStored() == 8)
- {
- // Reading Fragment pixels
- res = gdcm_read_JPEG_file (fp,destination);
- }
- else
- {
- // Reading Fragment pixels
- res = gdcm_read_JPEG_file12 (fp,destination);
- }
- // ------------------------------------- endif (JPEGLossy)
- }
+ return(newE);
+}
- if ( !res )
- {
- break;
- }
-
- // location in user's memory
- // for next fragment (if any)
- destination = (uint8_t*)destination + taille * nBytes;
+BinEntry* File::CopyBinEntry(uint16_t group,uint16_t element)
+{
+ DocEntry* oldE = HeaderInternal->GetDocEntryByNumber(group, element);
+ BinEntry* newE;
- fseek(fp,fragmentBegining, SEEK_SET); // To be sure we start
- fseek(fp,ln,SEEK_CUR); // at the begining of next fragment
-
- ItemTagGr = ItemTagEl = 0;
- fread(&ItemTagGr,2,1,fp); // Reading (fffe) : Item Tag Gr
- fread(&ItemTagEl,2,1,fp); // Reading (e000) : Item Tag El
- if( Header->GetSwapCode() )
- {
- ItemTagGr = Header->SwapShort( ItemTagGr );
- ItemTagEl = Header->SwapShort( ItemTagEl );
- }
+ if(oldE)
+ {
+ newE = new BinEntry(oldE->GetDictEntry());
+ newE->Copy(oldE);
+ }
+ else
+ {
+ newE = GetHeader()->NewBinEntryByNumber(group,element);
}
- // endWhile parsing fragments until Sequence Delim. Tag found
- Header->CloseFile();
- return res;
+
+ return(newE);
}
+//-----------------------------------------------------------------------------
+} // end namespace gdcm
+