-/*=========================================================================
+ /*=========================================================================
Program: gdcm
Module: $RCSfile: gdcmFile.cxx,v $
Language: C++
- Date: $Date: 2004/07/30 11:40:13 $
- Version: $Revision: 1.117 $
+ Date: $Date: 2004/10/08 17:24:54 $
+ Version: $Revision: 1.137 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
- http://www.creatis.insa-lyon.fr/Public/Gdcm/License.htm for details.
+ http://www.creatis.insa-lyon.fr/Public/Gdcm/License.html for details.
This software is distributed WITHOUT ANY WARRANTY; without even
the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
#include "gdcmFile.h"
#include "gdcmDebug.h"
+#include "gdcmPixelConvert.h"
#include "jpeg/ljpg/jpegless.h"
typedef std::pair<TagDocEntryHT::iterator,TagDocEntryHT::iterator> IterHT;
-//-----------------------------------------------------------------------------
+//-------------------------------------------------------------------------
// Constructor / Destructor
/**
- * \ingroup gdcmFile
- * \brief Constructor dedicated to writing a new DICOMV3 part10 compliant
- * file (see SetFileName, SetDcmTag and Write)
+ * \brief Constructor dedicated to deal with the *pixels* area of a ACR/DICOMV3
+ * file (gdcmHeader 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
+ * (see GetImageData, GetImageDataRaw)
* \note the in-memory representation of all available tags found in
* the DICOM header is post-poned to first header information access.
* This avoid a double parsing of public part of the header when
- * one sets an a posteriori shadow dictionary (efficiency can be
+ * user sets an a posteriori shadow dictionary (efficiency can be
* seen as a side effect).
- * @param header file to be opened for reading datas
- * @return
+ * @param header already built gdcmHeader
*/
gdcmFile::gdcmFile(gdcmHeader *header)
{
Header = header;
SelfHeader = false;
- PixelRead = -1; // no ImageData read yet.
-
- if (Header->IsReadable())
- {
- SetPixelDataSizeFromHeader();
- }
+ Initialise();
}
/**
- * \ingroup gdcmFile
- * \brief Constructor dedicated to writing a new DICOMV3 part10 compliant
- * file (see SetFileName, SetDcmTag and Write)
+ * \brief Constructor dedicated to deal with the *pixels* area of a ACR/DICOMV3
+ * file (gdcmHeader 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
+ * (see GetImageData, GetImageDataRaw)
* \note the in-memory representation of all available tags found in
* the DICOM header is post-poned to first header information access.
* This avoid a double parsing of public part of the header when
* one sets an a posteriori shadow dictionary (efficiency can be
* seen as a side effect).
* @param filename file to be opened for parsing
- * @param exception_on_error whether we throw an exception or not
- * @param ignore_shadow to allow skipping the shadow elements,
- * to save memory space.
*/
-gdcmFile::gdcmFile(std::string const & filename,
- bool exception_on_error,
- bool ignore_shadow)
+gdcmFile::gdcmFile(std::string const & filename )
{
- Header = new gdcmHeader( filename,
- exception_on_error,
- ignore_shadow );
+ Header = new gdcmHeader( filename );
SelfHeader = true;
- PixelRead = -1; // no ImageData read yet.
+ Initialise();
+}
+/**
+ * \brief Factorization for various forms of constructors.
+ */
+void gdcmFile::Initialise()
+{
if ( Header->IsReadable() )
{
- SetPixelDataSizeFromHeader();
+ ImageDataSizeRaw = ComputeDecompressedPixelDataSizeFromHeader();
+ if ( Header->HasLUT() )
+ {
+ ImageDataSize = 3 * ImageDataSizeRaw;
+ }
+ else
+ {
+ ImageDataSize = ImageDataSizeRaw;
+ }
}
+ SaveInitialValues();
}
/**
- * \ingroup gdcmFile
* \brief canonical destructor
- * \note If the gdcmHeader is created by the gdcmFile, it is destroyed
- * by the gdcmFile
+ * \note If the gdcmHeader was created by the gdcmFile constructor,
+ * it is destroyed by the gdcmFile
*/
gdcmFile::~gdcmFile()
-{
+{
if( SelfHeader )
{
delete Header;
}
Header = 0;
+
+ DeleteInitialValues();
+}
+
+/**
+ * \brief Sets some initial values for the Constructor
+ * \warning not end user intended
+ */
+void gdcmFile::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;
}
//-----------------------------------------------------------------------------
// Public
/**
- * \ingroup gdcmFile
- * \brief computes the length (in bytes) to ALLOCATE to receive the
+ * \brief computes the length (in bytes) we must ALLOCATE to receive the
* image(s) pixels (multiframes taken into account)
* \warning : it is NOT the group 7FE0 length
* (no interest for compressed images).
- * @return length to allocate
*/
-void gdcmFile::SetPixelDataSizeFromHeader()
+int gdcmFile::ComputeDecompressedPixelDataSizeFromHeader()
{
// see PS 3.3-2003 : C.7.6.3.2.1
//
// 0028|1203 [US] [Blue Palette Color Lookup Table Data]
// Number of "Bits Allocated"
- int nb;
- std::string str_nb = Header->GetEntryByNumber(0x0028,0x0100);
-
- if ( str_nb == GDCM_UNFOUND )
+ int numberBitsAllocated = Header->GetBitsAllocated();
+ if ( ( numberBitsAllocated == 0 ) || ( numberBitsAllocated == 12 ) )
{
- nb = 16;
+ numberBitsAllocated = 16;
}
- else
- {
- nb = atoi( str_nb.c_str() );
- if (nb == 12)
- {
- nb =16;
- }
- }
- ImageDataSize = ImageDataSizeRaw = Header->GetXSize() * Header->GetYSize()
- * Header->GetZSize() * (nb/8) * Header->GetSamplesPerPixel();
- std::string str_PhotometricInterpretation =
- Header->GetEntryByNumber(0x0028,0x0004);
-
- /*if ( str_PhotometricInterpretation == "PALETTE COLOR " )*/
- // pb when undealt Segmented Palette Color
-
- if ( Header->HasLUT() )
- {
- ImageDataSize *= 3;
- }
-}
-
-/**
- * \ingroup gdcmFile
- * \brief Returns the size (in bytes) of required memory to hold
- * the pixel data represented in this file.
- * @return The size of pixel data in bytes.
- */
-size_t gdcmFile::GetImageDataSize()
-{
- return ImageDataSize;
-}
-/**
- * \ingroup gdcmFile
- * \brief Returns the size (in bytes) of required memory to hold
- * the pixel data represented in this file, when user DOESN'T want
- * to get RGB pixels image when it's stored as a PALETTE COLOR image
- * -the (vtk) user is supposed to know how deal with LUTs-
- * \warning to be used with GetImagePixelsRaw()
- * @return The size of pixel data in bytes.
- */
-size_t gdcmFile::GetImageDataSizeRaw()
-{
- return ImageDataSizeRaw;
+ int DecompressedSize = Header->GetXSize()
+ * Header->GetYSize()
+ * Header->GetZSize()
+ * ( numberBitsAllocated / 8 )
+ * Header->GetSamplesPerPixel();
+
+ return DecompressedSize;
}
/**
- * \ingroup gdcmFile
- * \brief Allocates necessary memory, copies the pixel data
- * (image[s]/volume[s]) to newly allocated zone.
- * Transforms YBR pixels into RGB pixels if any
- * Transforms 3 planes R, G, B into a single RGB Plane
- * Transforms single Grey plane + 3 Palettes into a RGB Plane
+ * \brief - Allocates necessary memory,
+ * - Reads the pixels from disk (uncompress if necessary),
+ * - Transforms YBR pixels, if any, into RGB pixels
+ * - Transforms 3 planes R, G, B, if any, into a single RGB Plane
+ * - Transforms single Grey plane + 3 Palettes into a RGB Plane
+ * - Copies the pixel data (image[s]/volume[s]) to newly allocated zone.
* @return Pointer to newly allocated pixel data.
* NULL if alloc fails
*/
-void *gdcmFile::GetImageData()
+uint8_t* gdcmFile::GetImageData()
{
- // FIXME
- // I need to deallocate PixelData before doing any allocation:
- PixelData = new uint8_t[ImageDataSize];
- if ( PixelData )
+ // 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 )
{
- GetImageDataIntoVector(PixelData, ImageDataSize);
- GetHeader()->SetEntryVoidAreaByNumber( PixelData,
+ 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 PixelData;
+ return Pixel_Data;
}
/**
- * \ingroup gdcmFile
- * \brief Copies at most MaxSize bytes of pixel data to caller's
+ * \brief
+ * Read the pixels from disk (uncompress if necessary),
+ * Transforms YBR pixels, if any, into RGB pixels
+ * Transforms 3 planes R, G, B, if any, into a single RGB Plane
+ * Transforms single Grey plane + 3 Palettes into a RGB Plane
+ * Copies at most MaxSize bytes of pixel data to caller allocated
* 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
+ * \warning This function allows people that want to build a volume
+ * from an image stack *not to* have, 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
*/
size_t gdcmFile::GetImageDataIntoVector (void* destination, size_t maxSize)
{
- //size_t l = GetImageDataIntoVectorRaw (destination, maxSize);
GetImageDataIntoVectorRaw (destination, maxSize);
- PixelRead = 0 ; // no PixelRaw
+ PixelRead = 0 ; // =0 : no ImageDataRaw
if ( !Header->HasLUT() )
{
return ImageDataSize;
if ( lutRGBA )
{
int j;
- //int l = ImageDataSizeRaw; //loss of precision
// move Gray pixels to temp area
memmove(newDest, destination, ImageDataSizeRaw);
for (size_t i=0; i<ImageDataSizeRaw; ++i)
// now, it's an RGB image
// Lets's write it in the Header
- // CreateOrReplaceIfExist ?
+ // FIXME : Better use CreateOrReplaceIfExist ?
std::string spp = "3"; // Samples Per Pixel
Header->SetEntryByNumber(spp,0x0028,0x0002);
- std::string rgb = "RGB "; // Photometric Interpretation
+ std::string rgb = "RGB "; // Photometric Interpretation
Header->SetEntryByNumber(rgb,0x0028,0x0004);
std::string planConfig = "0"; // Planar Configuration
Header->SetEntryByNumber(planConfig,0x0028,0x0006);
}
- else //why is there a 'else' when an allocation failed ?
- {
- // need to make RGB Pixels (?)
- // from grey Pixels (?!)
- // and Gray Lut (!?!)
- // or Segmented xxx Palette Color Lookup Table Data and so on
-
- // Oops! I get one (gdcm-US-ALOKA-16.dcm)
- // No idea how to manage such an image
+ 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 :-(
- // Segmented xxx Palette Color are *more* than 65535 long ?!?
-
- std::string rgb = "MONOCHROME1 "; // Photometric Interpretation
- Header->SetEntryByNumber(rgb,0x0028,0x0004);
+
+ std::string photomInterp = "MONOCHROME1 "; // Photometric Interpretation
+ Header->SetEntryByNumber(photomInterp,0x0028,0x0004);
}
/// \todo Drop Palette Color out of the Header?
}
/**
- * \ingroup gdcmFile
- * \brief Allocates necessary memory, copies the pixel data
- * (image[s]/volume[s]) to newly allocated zone.
- * Transforms YBR pixels into RGB pixels if any
- * Transforms 3 planes R, G, B into a single RGB Plane
+ * \brief Allocates necessary memory,
+ * Transforms YBR pixels (if any) into RGB pixels
+ * Transforms 3 planes R, G, B (if any) into a single RGB Plane
+ * Copies the pixel data (image[s]/volume[s]) to newly allocated zone.
* DOES NOT transform Grey plane + 3 Palettes into a RGB Plane
* @return Pointer to newly allocated pixel data.
* \ NULL if alloc fails
*/
-void * gdcmFile::GetImageDataRaw ()
+uint8_t* gdcmFile::GetImageDataRaw ()
{
- size_t imgDataSize = ImageDataSize;
+ 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];
- // FIXME
- // I need to deallocate PixelData before doing any allocation:
- PixelData = new uint8_t[imgDataSize];
- if ( PixelData )
+ if ( Pixel_Data )
{
- GetImageDataIntoVectorRaw(PixelData, ImageDataSize);
- GetHeader()->SetEntryVoidAreaByNumber(PixelData,
- GetHeader()->GetGrPixel(), GetHeader()->GetNumPixel());
+ 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 PixelData;
+ return Pixel_Data;
}
/**
- * \ingroup gdcmFile
* \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
* @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)
+size_t gdcmFile::GetImageDataIntoVectorRaw (void* destination, size_t maxSize)
{
- int nb, nbu, highBit, sign;
+ // 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"
ReadPixelData( destination );
// Number of Bits Allocated for storing a Pixel
- std::string str_nb = Header->GetEntryByNumber(0x0028,0x0100);
- if ( str_nb == GDCM_UNFOUND )
+ int numberBitsAllocated = Header->GetBitsAllocated();
+ if ( numberBitsAllocated == 0 )
{
- nb = 16;
- }
- else
- {
- nb = atoi( str_nb.c_str() );
- // FIXME
- // From reading SetPixelDataSizeFromHeader, it seems 12 should be treated
- // separately, correct ?
+ numberBitsAllocated = 16;
}
// Number of Bits actually used
- std::string str_nbu = Header->GetEntryByNumber(0x0028,0x0101);
- if ( str_nbu == GDCM_UNFOUND )
+ int numberBitsStored = Header->GetBitsStored();
+ if ( numberBitsStored == 0 )
{
- nbu = nb;
- }
- else
- {
- nbu = atoi( str_nbu.c_str() );
+ numberBitsStored = numberBitsAllocated;
}
// High Bit Position
- std::string str_highBit = Header->GetEntryByNumber(0x0028,0x0102);
- if ( str_highBit == GDCM_UNFOUND )
+ int highBitPosition = Header->GetHighBitPosition();
+ if ( highBitPosition == 0 )
{
- highBit = nb - 1;
+ highBitPosition = numberBitsAllocated - 1;
}
- else
- {
- highBit = atoi( str_highBit.c_str() );
- }
- // Pixel sign
- // 0 = Unsigned
- // 1 = Signed
- std::string str_sign = Header->GetEntryByNumber(0x0028,0x0103);
- if ( str_sign == GDCM_UNFOUND )
- {
- sign = 0; // default is unsigned
- }
- else
+ 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() )
{
- sign = atoi( str_sign.c_str() );
+ 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 :-(
- // re arange bytes inside the integer (processor endianity)
- if ( nb != 8 )
+ 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() )
{
- SwapZone(destination, Header->GetSwapCode(), ImageDataSize, nb);
+ return ImageDataSize;
}
-
- // to avoid pb with some xmedcon breakers images
- if ( nb == 16 && nbu < nb && sign == 0)
+
+ // When planConf is 0, pixels are allready in RGB
+
+ if ( planConf == 1 )
{
- int l = (int)(ImageDataSize / (nb/8));
- uint16_t *deb = (uint16_t *)destination;
- for(int i = 0; i<l; i++)
+ uint8_t* newDest = new uint8_t[ImageDataSize];
+ // Warning : YBR_FULL_422 acts as RGB
+ if ( Header->IsYBRFull() )
{
- if( *deb == 0xffff )
- {
- *deb = 0;
- }
- deb++;
+ ConvertYcBcRPlanesToRGBPixels((uint8_t*)destination, newDest);
+ }
+ else
+ {
+ ConvertRGBPlanesToRGBPixels((uint8_t*)destination, newDest);
}
+ memmove(destination, newDest, ImageDataSize);
+ delete[] newDest;
}
- // re arange bits inside the bytes
- if ( nbu != nb )
+///////////////////////////////////////////////////
+ // 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 / (nb/8));
- if ( nb == 16 )
+ int l = (int)(imageDataSize / (numberBitsAllocated/8));
+ if ( numberBitsAllocated == 16 )
{
uint16_t mask = 0xffff;
- mask = mask >> (nb-nbu);
- uint16_t *deb = (uint16_t *)destination;
+ mask = mask >> ( numberBitsAllocated - numberBitsStored );
+ uint16_t* deb = (uint16_t*)pixelZone;
for(int i = 0; i<l; i++)
{
- *deb = (*deb >> (nbu - highBit - 1)) & mask;
+ *deb = (*deb >> (numberBitsStored - highBitPosition - 1)) & mask;
deb++;
}
}
- else if ( nb == 32 )
+ else if ( numberBitsAllocated == 32 )
{
uint32_t mask = 0xffffffff;
- mask = mask >> (nb - nbu);
- uint32_t *deb = (uint32_t *)destination;
+ mask = mask >> ( numberBitsAllocated - numberBitsStored );
+ uint32_t* deb = (uint32_t*)pixelZone;
for(int i = 0; i<l; i++)
{
- *deb = (*deb >> (nbu - highBit - 1)) & mask;
+ *deb = (*deb >> (numberBitsStored - highBitPosition - 1)) & mask;
deb++;
}
}
else
{
- dbg.Verbose(0, "gdcmFile::GetImageDataIntoVector: weird image");
- return 0;
+ dbg.Verbose(0, "gdcmFile::ConvertReArrangeBits: weird image");
+ throw gdcmFormatError( "gdcmFile::ConvertReArrangeBits()",
+ "weird image !?" );
}
}
-// DO NOT remove this code commented out.
-// Nobody knows what's expecting you ...
-// Just to 'see' what was actually read on disk :-(
-
-// FILE * f2;
-// f2 = fopen("SpuriousFile.RAW","wb");
-// fwrite(destination,ImageDataSize,1,f2);
-// fclose(f2);
-
- // Deal with the color
- // -------------------
-
- std::string str_PhotometricInterpretation =
- Header->GetEntryByNumber(0x0028,0x0004);
+}
- if ( str_PhotometricInterpretation == "MONOCHROME1 "
- || str_PhotometricInterpretation == "MONOCHROME2 " )
+/**
+ * \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++)
{
- return ImageDataSize;
+ 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++;
+ }
}
-
- // 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(); // 0028,0006
+/**
+ * \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();
- // Whatever Planar Configuration is,
- // "PALETTE COLOR " implies that we deal with the palette.
- if ( str_PhotometricInterpretation == "PALETTE COLOR ")
- {
- planConf = 2;
- }
+ uint8_t* a = source;
+ uint8_t* b = source + l;
+ uint8_t* c = source + l + l;
- switch ( planConf )
+ for (int j = 0; j < l; j++)
{
- case 0:
- // Pixels are already RGB
- break;
- case 1:
- if (str_PhotometricInterpretation == "YBR_FULL")
- {
- // 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)
-
- 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;
+ *(destination++) = *(a++);
+ *(destination++) = *(b++);
+ *(destination++) = *(c++);
}
- // now, it's an RGB image
- // Lets's write it in the Header
-
- // CreateOrReplaceIfExist ?
-
- std::string spp = "3"; // Samples Per Pixel
- std::string rgb = "RGB "; // Photometric Interpretation
- std::string planConfig = "0"; // Planar Configuration
-
- Header->SetEntryByNumber(spp,0x0028,0x0002);
- Header->SetEntryByNumber(rgb,0x0028,0x0004);
- Header->SetEntryByNumber(planConfig,0x0028,0x0006);
-
- /// \todo Drop Palette Color out of the Header?
- return ImageDataSize;
}
/**
- * \ingroup gdcmFile
- * \brief performs a shalow copy (not a deep copy) of the user given
- * pixel area.
- * 'image' Pixels are presented as C-like 2D arrays : line per line.
- * 'volume'Pixels are presented as C-like 3D arrays : lane per plane
- * \warning user is kindly requested NOT TO 'free' the Pixel area
+ * \brief Points the internal Pixel_Data pointer to the callers inData
+ * image representation, BUT WITHOUT COPYING THE DATA.
+ * 'image' Pixels are presented as C-like 2D arrays : line per line.
+ * 'volume'Pixels are presented as C-like 3D arrays : plane per plane
+ * \warning Since the pixels are not copied, it is the caller's responsability
+ * not to deallocate it's data before gdcm uses them (e.g. with
+ * the Write() method.
* @param inData user supplied pixel area
* @param expectedSize total image size, in Bytes
*
* @return boolean
*/
-bool gdcmFile::SetImageData(void *inData, size_t expectedSize)
+bool gdcmFile::SetImageData(uint8_t* inData, size_t expectedSize)
{
Header->SetImageDataSize( expectedSize );
- PixelData = inData;
- ImageDataSize = expectedSize;
+// FIXME : if already allocated, memory leak !
+ Pixel_Data = inData;
+ ImageDataSize = ImageDataSizeRaw = expectedSize;
PixelRead = 1;
-
+// FIXME : 7fe0, 0010 IS NOT set ...
return true;
}
/**
- * \ingroup gdcmFile
* \brief Writes on disk A SINGLE Dicom file
* NO test is performed on processor "Endiannity".
* It's up to the user to call his Reader properly
bool gdcmFile::WriteRawData(std::string const & fileName)
{
- FILE *fp1 = fopen(fileName.c_str(), "wb");
+ FILE* fp1 = fopen(fileName.c_str(), "wb");
if (fp1 == NULL)
{
printf("Fail to open (write) file [%s] \n", fileName.c_str());
return false;
}
- fwrite (PixelData, ImageDataSize, 1, fp1);
+ fwrite (Pixel_Data, ImageDataSize, 1, fp1);
fclose (fp1);
return true;
}
/**
- * \ingroup gdcmFile
* \brief Writes on disk A SINGLE Dicom file,
* using the Implicit Value Representation convention
* NO test is performed on processor "Endiannity".
}
/**
- * \ingroup gdcmFile
* \brief Writes on disk A SINGLE Dicom file,
* using the Explicit Value Representation convention
* NO test is performed on processor "Endiannity". * @param fileName name of the file to be created
}
/**
- * \ingroup gdcmFile
* \brief Writes on disk A SINGLE Dicom file,
* using the ACR-NEMA convention
* NO test is performed on processor "Endiannity".
//-----------------------------------------------------------------------------
// Protected
/**
- * \ingroup gdcmFile
* \brief NOT a end user inteded function
* (used by WriteDcmExplVR, WriteDcmImplVR, WriteAcr, etc)
* @param fileName name of the file to be created
return false;
}
- FILE *fp1 = fopen(fileName.c_str(), "wb");
+ FILE* fp1 = fopen(fileName.c_str(), "wb");
if (fp1 == NULL)
{
printf("Failed to open (write) File [%s] \n", fileName.c_str());
}
// ----------------- End of Special Patch ----------------
- // fwrite(PixelData, ImageDataSize, 1, fp1); // should be useless, now
+ // fwrite(Pixel_Data, ImageDataSize, 1, fp1); // should be useless, now
fclose (fp1);
return true;
//-----------------------------------------------------------------------------
// Private
/**
- * \ingroup gdcmFile
- * \brief Swap the bytes, according to swap code.
- * \warning not end user intended
- * @param im area to deal with
- * @param swap swap code
- * @param lgr Area Length
- * @param nb Pixels Bit number
- */
-void gdcmFile::SwapZone(void *im, int swap, int lgr, int nb)
-{
- int i;
-
- if( nb == 16 )
- {
- uint16_t* im16 = (uint16_t*)im;
- switch( swap )
- {
- case 0:
- case 12:
- case 1234:
- break;
- case 21:
- case 3412:
- case 2143:
- case 4321:
- for(i=0; i < lgr/2; i++)
- {
- im16[i]= (im16[i] >> 8) | (im16[i] << 8 );
- }
- break;
- default:
- std::cout << "SWAP value (16 bits) not allowed :i" << swap <<
- std::endl;
- }
- }
- else if( nb == 32 )
- {
- uint32_t s32;
- uint16_t fort, faible;
- uint32_t* im32 = (uint32_t*)im;
- switch ( swap )
- {
- case 0:
- case 1234:
- break;
- case 4321:
- for(i = 0; i < lgr/4; i++)
- {
- faible = im32[i] & 0x0000ffff; // 4321
- fort = im32[i] >> 16;
- fort = ( fort >> 8 ) | ( fort << 8 );
- faible = ( faible >> 8 ) | ( faible << 8);
- s32 = faible;
- im32[i] = ( s32 << 16 ) | fort;
- }
- break;
- case 2143:
- for(i = 0; i < lgr/4; i++)
- {
- faible = im32[i] & 0x0000ffff; // 2143
- fort = im32[i] >> 16;
- fort = ( fort >> 8 ) | ( fort << 8 );
- faible = ( faible >> 8) | ( faible << 8);
- s32 = fort;
- im32[i] = ( s32 << 16 ) | faible;
- }
- break;
- case 3412:
- for(i = 0; i < lgr/4; i++)
- {
- faible = im32[i] & 0x0000ffff; // 3412
- fort = im32[i] >> 16;
- s32 = faible;
- im32[i] = ( s32 << 16 ) | fort;
- }
- break;
- default:
- std::cout << "SWAP value (32 bits) not allowed : " << swap <<
- std::endl;
- }
- }
-}
-
-/**
- * \ingroup gdcmFile
* \brief Read pixel data from disk (optionaly decompressing) into the
* caller specified memory location.
* @param destination where the pixel data should be stored.
*
*/
-bool gdcmFile::ReadPixelData(void *destination)
+bool gdcmFile::ReadPixelData(void* destination)
{
- FILE *fp = Header->OpenFile();
+ FILE* fp = Header->OpenFile();
if ( !fp )
{
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 ?
- }
-
+ gdcmPixelConvert::ConvertDecompress12BitsTo16Bits(
+ (uint8_t*)destination,
+ Header->GetXSize(),
+ Header->GetYSize(),
+ fp);
Header->CloseFile();
return true;
}
// ---------------------- Run Length Encoding
if ( Header->IsRLELossLessTransferSyntax() )
{
- bool res = gdcm_read_RLE_file (fp,destination);
+ 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 nb;
- std::string str_nb = Header->GetEntryByNumber(0x0028,0x0100);
- if ( str_nb == GDCM_UNFOUND )
+ int numberBitsAllocated = Header->GetBitsAllocated();
+ if ( ( numberBitsAllocated == 0 ) || ( numberBitsAllocated == 12 ) )
{
- nb = 16;
- }
- else
- {
- 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
if ( jpg2000 )
{
// JPEG 2000 : call to ???
- res = (bool)gdcm_read_JPEG2000_file (fp,destination); // Not Yet written
+ res = gdcm_read_JPEG2000_file (fp,destination); // Not Yet written
// ------------------------------------- endif (JPEG2000)
}
else if (jpgLossless)
if ( Header->GetBitsStored() == 8)
{
// Reading Fragment pixels
- res = (bool)gdcm_read_JPEG_file (fp,destination);
+ res = gdcm_read_JPEG_file (fp,destination);
}
- else
+ else if ( Header->GetBitsStored() == 12)
{
// Reading Fragment pixels
- res = (bool)gdcm_read_JPEG_file12 (fp,destination);
+ res = gdcm_read_JPEG_file12 (fp,destination);
+ }
+ else
+ {
+ // other JPEG lossy not supported
+ dbg.Error(" gdcmFile::ReadPixelData : unknown jpeg lossy compression");
+ return 0;
}
// ------------------------------------- endif (JPEGLossy)
}
Header->CloseFile();
return res;
}
-//-----------------------------------------------------------------------------
+
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff