-/*=========================================================================
+ /*=========================================================================
Program: gdcm
Module: $RCSfile: gdcmFile.cxx,v $
Language: C++
- Date: $Date: 2004/07/31 23:30:04 $
- Version: $Revision: 1.119 $
+ Date: $Date: 2004/10/20 14:30:40 $
+ Version: $Revision: 1.146 $
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 "jpeg/ljpg/jpegless.h"
+namespace gdcm
+{
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 (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
+ * (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 Header
*/
-gdcmFile::gdcmFile(gdcmHeader *header)
+File::File(Header *header)
{
- Header = header;
+ HeaderInternal = 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 (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
+ * (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
*/
-gdcmFile::gdcmFile(std::string const & filename,
- bool exception_on_error )
+File::File(std::string const & filename )
{
- Header = new gdcmHeader( filename, exception_on_error );
+ HeaderInternal = new Header( filename );
SelfHeader = true;
- PixelRead = -1; // no ImageData read yet.
+ Initialise();
+}
- if ( Header->IsReadable() )
+/**
+ * \brief Factorization for various forms of constructors.
+ */
+void File::Initialise()
+{
+ if ( HeaderInternal->IsReadable() )
{
- SetPixelDataSizeFromHeader();
+ ImageDataSizeRaw = ComputeDecompressedPixelDataSizeFromHeader();
+ if ( HeaderInternal->HasLUT() )
+ {
+ ImageDataSize = 3 * ImageDataSizeRaw;
+ }
+ else
+ {
+ ImageDataSize = ImageDataSizeRaw;
+ }
+
+ PixelConverter = new PixelConvert;
+ PixelConverter->GrabInformationsFromHeader( HeaderInternal );
}
+ SaveInitialValues();
}
/**
- * \ingroup gdcmFile
* \brief canonical destructor
- * \note If the gdcmHeader is created by the gdcmFile, 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 )
{
- delete Header;
+ delete HeaderInternal;
+ }
+ HeaderInternal = 0;
+
+ DeleteInitialValues();
+}
+
+/**
+ * \brief Sets some initial values for the Constructor
+ * \warning not end user intended
+ */
+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 ( HeaderInternal->IsReadable() )
+ {
+ // the following values *may* be modified
+ // by File::GetImageDataIntoVectorRaw
+ // we save their initial value.
+ InitialSpp = HeaderInternal->GetEntryByNumber(0x0028,0x0002);
+ InitialPhotInt = HeaderInternal->GetEntryByNumber(0x0028,0x0004);
+ InitialPlanConfig = HeaderInternal->GetEntryByNumber(0x0028,0x0006);
+
+ InitialBitsAllocated = HeaderInternal->GetEntryByNumber(0x0028,0x0100);
+ InitialHighBit = HeaderInternal->GetEntryByNumber(0x0028,0x0102);
+
+ // the following entries *may* be removed from the H table
+ // (NOT deleted ...) by File::GetImageDataIntoVectorRaw
+ // we keep a pointer on them.
+ InitialRedLUTDescr = HeaderInternal->GetDocEntryByNumber(0x0028,0x1101);
+ InitialGreenLUTDescr = HeaderInternal->GetDocEntryByNumber(0x0028,0x1102);
+ InitialBlueLUTDescr = HeaderInternal->GetDocEntryByNumber(0x0028,0x1103);
+
+ InitialRedLUTData = HeaderInternal->GetDocEntryByNumber(0x0028,0x1201);
+ InitialGreenLUTData = HeaderInternal->GetDocEntryByNumber(0x0028,0x1202);
+ InitialBlueLUTData = HeaderInternal->GetDocEntryByNumber(0x0028,0x1203);
+ }
+}
+
+/**
+ * \brief restores some initial values
+ * \warning not end user intended
+ */
+void File::RestoreInitialValues()
+{
+ if ( HeaderInternal->IsReadable() )
+ {
+ // the following values *may* have been modified
+ // by File::GetImageDataIntoVectorRaw
+ // we restore their initial value.
+ if ( InitialSpp != "")
+ HeaderInternal->SetEntryByNumber(InitialSpp,0x0028,0x0002);
+ if ( InitialPhotInt != "")
+ HeaderInternal->SetEntryByNumber(InitialPhotInt,0x0028,0x0004);
+ if ( InitialPlanConfig != "")
+
+ HeaderInternal->SetEntryByNumber(InitialPlanConfig,0x0028,0x0006);
+ if ( InitialBitsAllocated != "")
+ HeaderInternal->SetEntryByNumber(InitialBitsAllocated,0x0028,0x0100);
+ if ( InitialHighBit != "")
+ HeaderInternal->SetEntryByNumber(InitialHighBit,0x0028,0x0102);
+
+ // the following entries *may* be have been removed from the H table
+ // (NOT deleted ...) by File::GetImageDataIntoVectorRaw
+ // we restore them.
+
+ if (InitialRedLUTDescr)
+ HeaderInternal->AddEntry(InitialRedLUTDescr);
+ if (InitialGreenLUTDescr)
+ HeaderInternal->AddEntry(InitialGreenLUTDescr);
+ if (InitialBlueLUTDescr)
+ HeaderInternal->AddEntry(InitialBlueLUTDescr);
+
+ if (InitialRedLUTData)
+ HeaderInternal->AddEntry(InitialBlueLUTDescr);
+ if (InitialGreenLUTData)
+ HeaderInternal->AddEntry(InitialGreenLUTData);
+ if (InitialBlueLUTData)
+ HeaderInternal->AddEntry(InitialBlueLUTData);
}
- Header = 0;
+}
+
+/**
+ * \brief delete initial values (il they were saved)
+ * of InitialLutDescriptors and InitialLutData
+ */
+void File::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 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 nb;
- std::string str_nb = Header->GetEntryByNumber(0x0028,0x0100);
-
- if ( str_nb == GDCM_UNFOUND )
+ 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 ) )
{
- 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 = HeaderInternal->GetXSize()
+ * HeaderInternal->GetYSize()
+ * HeaderInternal->GetZSize()
+ * ( numberBitsAllocated / 8 )
+ * HeaderInternal->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* File::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
* @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)
{
- //size_t l = GetImageDataIntoVectorRaw (destination, maxSize);
GetImageDataIntoVectorRaw (destination, maxSize);
- PixelRead = 0 ; // no PixelRaw
- if ( !Header->HasLUT() )
+ PixelRead = 0 ; // =0 : no ImageDataRaw
+ if ( !HeaderInternal->HasLUT() )
{
return ImageDataSize;
}
- // 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 )
+ FILE* fp = HeaderInternal->OpenFile();
+ if ( PixelConverter->BuildRGBImage( fp ) )
{
- 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)
- {
- // Build RGB Pixels
- j = newDest[i]*4;
- *a++ = lutRGBA[j];
- *a++ = lutRGBA[j+1];
- *a++ = lutRGBA[j+2];
- }
- delete[] newDest;
+ memmove( destination,
+ (void*)PixelConverter->GetRGB(),
+ PixelConverter->GetRGBSize() );
- // now, it's an RGB image
- // Lets's write it in the Header
+ // 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
- Header->SetEntryByNumber(rgb,0x0028,0x0004);
- std::string planConfig = "0"; // Planar Configuration
- Header->SetEntryByNumber(planConfig,0x0028,0x0006);
+ std::string spp = "3"; // Samples Per Pixel
+ HeaderInternal->SetEntryByNumber(spp,0x0028,0x0002);
+ std::string rgb = "RGB "; // Photometric Interpretation
+ HeaderInternal->SetEntryByNumber(rgb,0x0028,0x0004);
+ std::string planConfig = "0"; // Planar Configuration
+ HeaderInternal->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
+ {
+ // PixelConverter->BuildRGBImage() failed probably because
+ // PixelConverter->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
+ HeaderInternal->SetEntryByNumber(photomInterp,0x0028,0x0004);
}
+ HeaderInternal->CloseFile();
/// \todo Drop Palette Color out of the Header?
return ImageDataSize;
}
/**
- * \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* File::GetImageDataRaw ()
{
- size_t imgDataSize = ImageDataSize;
- if ( Header->HasLUT() )
- {
- /// \todo Let gdcmHeader user a chance to get the right value
+ size_t imgDataSize;
+ if ( HeaderInternal->HasLUT() )
+ /// \todo Let Header 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)
+void File::GetImageDataIntoVectorRaw (void* destination, size_t maxSize)
{
- int nb, nbu, highBit, sign;
- PixelRead = 1 ; // PixelRaw
-
- if ( ImageDataSize > maxSize )
- {
- dbg.Verbose(0, "gdcmFile::GetImageDataIntoVector: pixel data bigger"
- "than caller's expected MaxSize");
- return (size_t)0;
- }
+ // 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)
- ReadPixelData( destination );
-
- // Number of Bits Allocated for storing a Pixel
- std::string str_nb = Header->GetEntryByNumber(0x0028,0x0100);
- if ( str_nb == GDCM_UNFOUND )
- {
- nb = 16;
- }
- else
- {
- nb = atoi( str_nb.c_str() );
- // FIXME
- // From reading SetPixelDataSizeFromHeader, it seems 12 should be treated
- // separately, correct ?
- }
-
- // Number of Bits actually used
- std::string str_nbu = Header->GetEntryByNumber(0x0028,0x0101);
- if ( str_nbu == GDCM_UNFOUND )
- {
- nbu = nb;
- }
- else
- {
- nbu = atoi( str_nbu.c_str() );
- }
-
- // High Bit Position
- std::string str_highBit = Header->GetEntryByNumber(0x0028,0x0102);
- if ( str_highBit == GDCM_UNFOUND )
- {
- highBit = nb - 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
- {
- sign = atoi( str_sign.c_str() );
+ if ( PixelRead != -1 ) // File was "read" before
+ {
+ RestoreInitialValues();
}
-
- // re arange bytes inside the integer (processor endianity)
- if ( nb != 8 )
- {
- SwapZone(destination, Header->GetSwapCode(), ImageDataSize, nb);
- }
-
- // to avoid pb with some xmedcon breakers images
- if ( nb == 16 && nbu < nb && sign == 0)
- {
- int l = (int)(ImageDataSize / (nb/8));
- uint16_t *deb = (uint16_t *)destination;
- for(int i = 0; i<l; i++)
- {
- if( *deb == 0xffff )
- {
- *deb = 0;
- }
- deb++;
- }
- }
-
- // re arange bits inside the bytes
- if ( nbu != nb )
- {
- int l = (int)(ImageDataSize / (nb/8));
- if ( nb == 16 )
- {
- uint16_t mask = 0xffff;
- mask = mask >> (nb-nbu);
- uint16_t *deb = (uint16_t *)destination;
- for(int i = 0; i<l; i++)
- {
- *deb = (*deb >> (nbu - highBit - 1)) & mask;
- deb++;
- }
- }
- else if ( nb == 32 )
- {
- uint32_t mask = 0xffffffff;
- mask = mask >> (nb - nbu);
- uint32_t *deb = (uint32_t *)destination;
- for(int i = 0; i<l; i++)
- {
- *deb = (*deb >> (nbu - highBit - 1)) & mask;
- deb++;
- }
- }
- else
- {
- dbg.Verbose(0, "gdcmFile::GetImageDataIntoVector: weird image");
- return 0;
- }
- }
-// 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 " )
+ PixelRead = 1 ; // PixelRaw
+
+ if ( ImageDataSize > maxSize )
{
- return ImageDataSize;
+ dbg.Verbose(0, "File::GetImageDataIntoVector: pixel data bigger"
+ "than caller's expected MaxSize");
+ return;
}
-
- // 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 :-(
+ FILE* fp = HeaderInternal->OpenFile();
+ PixelConverter->ReadAndDecompressPixelData( fp );
+ HeaderInternal->CloseFile();
+ memmove( destination,
+ (void*)PixelConverter->GetDecompressed(),
+ PixelConverter->GetDecompressedSize() );
- int planConf = Header->GetPlanarConfiguration(); // 0028,0006
-
- // Whatever Planar Configuration is,
- // "PALETTE COLOR " implies that we deal with the palette.
- if ( str_PhotometricInterpretation == "PALETTE COLOR ")
+ if ( ! PixelConverter->IsDecompressedRGB() )
{
- planConf = 2;
+ return;
}
- switch ( planConf )
- {
- 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;
- }
+///////////////////////////////////////////////////
// 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.
- // CreateOrReplaceIfExist ?
-
- std::string spp = "3"; // Samples Per Pixel
- std::string rgb = "RGB "; // Photometric Interpretation
- std::string planConfig = "0"; // Planar Configuration
+ // 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 ?!
- Header->SetEntryByNumber(spp,0x0028,0x0002);
- Header->SetEntryByNumber(rgb,0x0028,0x0004);
- Header->SetEntryByNumber(planConfig,0x0028,0x0006);
+ std::string spp = "3"; // Samples Per Pixel
+ std::string photInt = "RGB "; // Photometric Interpretation
+ std::string planConfig = "0"; // Planar Configuration
+
+ HeaderInternal->SetEntryByNumber(spp,0x0028,0x0002);
+ HeaderInternal->SetEntryByNumber(photInt,0x0028,0x0004);
+ HeaderInternal->SetEntryByNumber(planConfig,0x0028,0x0006);
- /// \todo Drop Palette Color out of the Header?
- return ImageDataSize;
+ return;
}
/**
- * \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 File::SetImageData(uint8_t* inData, size_t expectedSize)
{
- Header->SetImageDataSize( expectedSize );
- PixelData = inData;
- ImageDataSize = expectedSize;
+ HeaderInternal->SetImageDataSize( 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
* @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");
+ 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".
* @return false if write fails
*/
-bool gdcmFile::WriteDcmImplVR (std::string const & fileName)
+bool File::WriteDcmImplVR (std::string const & fileName)
{
- return WriteBase(fileName, gdcmImplicitVR);
+ return WriteBase(fileName, ImplicitVR);
}
/**
- * \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
* @return false if write fails
*/
-bool gdcmFile::WriteDcmExplVR (std::string const & fileName)
+bool File::WriteDcmExplVR (std::string const & fileName)
{
- return WriteBase(fileName, gdcmExplicitVR);
+ return WriteBase(fileName, ExplicitVR);
}
/**
- * \ingroup gdcmFile
* \brief Writes on disk A SINGLE Dicom file,
* using the ACR-NEMA convention
* NO test is performed on processor "Endiannity".
* @return false if write fails
*/
-bool gdcmFile::WriteAcr (std::string const & fileName)
+bool File::WriteAcr (std::string const & fileName)
{
- return WriteBase(fileName, gdcmACR);
+ return WriteBase(fileName, ACR);
}
//-----------------------------------------------------------------------------
// 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
* @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");
+ FILE* fp1 = fopen(fileName.c_str(), "wb");
if (fp1 == NULL)
{
printf("Failed to open (write) File [%s] \n", fileName.c_str());
return false;
}
- if ( type == gdcmImplicitVR || type == gdcmExplicitVR )
+ if ( type == ImplicitVR || type == ExplicitVR )
{
// writing Dicom File Preamble
uint8_t* filePreamble = new uint8_t[128];
/// 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);
+ rows = HeaderInternal->GetEntryByNumber(0x0028, 0x0010);
+ columns = HeaderInternal->GetEntryByNumber(0x0028, 0x0011);
- Header->SetEntryByNumber(columns, 0x0028, 0x0010);
- Header->SetEntryByNumber(rows , 0x0028, 0x0011);
+ HeaderInternal->SetEntryByNumber(columns, 0x0028, 0x0010);
+ HeaderInternal->SetEntryByNumber(rows , 0x0028, 0x0011);
}
// ----------------- End of Special Patch ----------------
- uint16_t grPixel = Header->GetGrPixel();
- uint16_t numPixel = Header->GetNumPixel();;
+ uint16_t grPixel = HeaderInternal->GetGrPixel();
+ uint16_t numPixel = HeaderInternal->GetNumPixel();;
- gdcmDocEntry* PixelElement =
+ DocEntry* PixelElement =
GetHeader()->GetDocEntryByNumber(grPixel, numPixel);
if ( PixelRead == 1 )
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);
+ HeaderInternal->SetEntryByNumber(rows , 0x0028, 0x0010);
+ HeaderInternal->SetEntryByNumber(columns, 0x0028, 0x0011);
}
// ----------------- 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
+ * \brief Access to the underlying \ref PixelConverter RGBA LUT
*/
-void gdcmFile::SwapZone(void *im, int swap, int lgr, int nb)
+uint8_t* File::GetLutRGBA()
{
- 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;
- }
- }
+ return PixelConverter->GetLutRGBA();
}
-/**
- * \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)
-{
- FILE *fp = Header->OpenFile();
+} // end namespace gdcm
- if ( !fp )
- {
- return false;
- }
- if ( fseek(fp, Header->GetPixelOffset(), SEEK_SET) == -1 )
- {
- Header->CloseFile();
- 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 ?
- }
-
- Header->CloseFile();
- return true;
- }
-
- // ---------------------- Uncompressed File
- if ( !Header->IsDicomV3() ||
- Header->IsImplicitVRLittleEndianTransferSyntax() ||
- Header->IsExplicitVRLittleEndianTransferSyntax() ||
- Header->IsExplicitVRBigEndianTransferSyntax() ||
- Header->IsDeflatedExplicitVRLittleEndianTransferSyntax() )
- {
- size_t ItemRead = fread(destination, Header->GetPixelAreaLength(), 1, fp);
- Header->CloseFile();
- if ( ItemRead != 1 )
- {
- return false;
- }
- else
- {
- return true;
- }
- }
-
- // ---------------------- Run Length Encoding
- if ( Header->IsRLELossLessTransferSyntax() )
- {
- bool res = gdcm_read_RLE_file (fp,destination);
- 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 )
- {
- nb = 16;
- }
- else
- {
- nb = atoi( str_nb.c_str() );
- if ( nb == 12 )
- {
- nb = 16; // ?? 12 should be ACR-NEMA only
- }
- }
-
- int nBytes= nb/8;
- int taille = Header->GetXSize() * Header->GetYSize()
- * Header->GetSamplesPerPixel();
- long fragmentBegining; // for ftell, fseek
-
- bool jpg2000 = Header->IsJPEG2000();
- bool jpgLossless = Header->IsJPEGLossless();
-
- 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);
- }
-
- fread(&ln,4,1,fp);
- if( Header->GetSwapCode() )
- {
- ln = Header->SwapLong( ln ); // Basic Offset Table Item length
- }
-
- if ( ln != 0 )
- {
- // What is it used for ?!?
- uint8_t* BasicOffsetTableItemValue = new uint8_t[ln+1];
- fread(BasicOffsetTableItemValue,ln,1,fp);
- //delete[] BasicOffsetTableItemValue;
- }
-
- // 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() )
- {
- ItemTagGr = Header->SwapShort( ItemTagGr );
- ItemTagEl = Header->SwapShort( ItemTagEl );
- }
-
- // parsing fragments until Sequence Delim. Tag found
- while ( ItemTagGr == 0xfffe && ItemTagEl != 0xe0dd )
- {
- // --- for each Fragment
- fread(&ln,4,1,fp);
- if( Header->GetSwapCode() )
- {
- ln = Header->SwapLong(ln); // Fragment Item length
- }
- fragmentBegining = ftell( fp );
-
- 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)
- }
-
- if ( !res )
- {
- break;
- }
-
- // location in user's memory
- // for next fragment (if any)
- destination = (uint8_t*)destination + taille * nBytes;
-
- 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 );
- }
- }
- // endWhile parsing fragments until Sequence Delim. Tag found
-
- Header->CloseFile();
- return res;
-}
-//-----------------------------------------------------------------------------
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff