-/*=========================================================================
+ /*=========================================================================
Program: gdcm
Module: $RCSfile: gdcmFile.cxx,v $
Language: C++
- Date: $Date: 2004/06/25 17:48:45 $
- Version: $Revision: 1.110 $
+ Date: $Date: 2004/11/24 11:17:47 $
+ Version: $Revision: 1.161 $
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"
+#include "gdcmUtil.h"
+#include "gdcmBinEntry.h"
+#include <fstream>
+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) {
- Header=header;
- SelfHeader=false;
- PixelRead=-1; // no ImageData read yet.
-
- if (Header->IsReadable())
- SetPixelDataSizeFromHeader();
+File::File(Header *header)
+{
+ HeaderInternal = header;
+ SelfHeader = false;
+ 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
- * @param enable_sequences = true to allow the header
- * to be parsed *inside* the SeQuences,
- * when they have an actual length
- * \warning enable_sequences *has to be* true for reading PAPYRUS 3.0 files
- * @param ignore_shadow to allow skipping the shadow elements,
- * to save memory space.
- * \warning The TRUE value for this param has to be used
- * with a FALSE value for the 'enable_sequence' param.
- * ('public elements' may be embedded in 'shadow Sequences')
*/
-gdcmFile::gdcmFile(std::string const & filename,
- bool exception_on_error,
- bool enable_sequences,
- bool ignore_shadow) {
- Header=new gdcmHeader(filename.c_str(),
- exception_on_error,
- enable_sequences,
- ignore_shadow);
- SelfHeader=true;
- PixelRead=-1; // no ImageData read yet.
-
- if (Header->IsReadable())
- SetPixelDataSizeFromHeader();
+File::File(std::string const & filename )
+{
+ HeaderInternal = new Header( filename );
+ SelfHeader = true;
+ Initialise();
+}
+
+/**
+ * \brief Factorization for various forms of constructors.
+ */
+void File::Initialise()
+{
+ WriteMode = WMODE_RGB;
+ WriteType = WTYPE_IMPL_VR;
+
+ PixelConverter = new PixelConvert;
+ Archive = new DocEntryArchive( HeaderInternal );
+
+ if ( HeaderInternal->IsReadable() )
+ {
+ ImageDataSizeRaw = ComputeDecompressedPixelDataSizeFromHeader();
+ if ( HeaderInternal->HasLUT() )
+ {
+ ImageDataSize = 3 * ImageDataSizeRaw;
+ }
+ else
+ {
+ ImageDataSize = ImageDataSizeRaw;
+ }
+
+ 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
+ */
+File::~File()
+{
+ if( PixelConverter )
+ {
+ delete PixelConverter;
+ }
+ if( Archive )
+ {
+ delete Archive;
+ }
+
+ if( SelfHeader )
+ {
+ delete HeaderInternal;
+ }
+ HeaderInternal = 0;
+}
+
+/**
+ * \brief Sets some initial values for the Constructor
+ * \warning not end user intended
*/
-gdcmFile::~gdcmFile() {
- if(SelfHeader)
- delete Header;
- Header=NULL;
+void File::SaveInitialValues()
+{
+ PixelRead = -1; // no ImageData read yet.
+ Pixel_Data = 0;
}
//-----------------------------------------------------------------------------
// 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
//
// MONOCHROME1
// 0028|1202 [US] [Green Palette Color Lookup Table Data]
// 0028|1203 [US] [Blue Palette Color Lookup Table Data]
- int nb;
- std::string str_nb;
- 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;
- }
- lgrTotale = lgrTotaleRaw = 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()) {
- lgrTotale*=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 lgrTotale;
-}
+ 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;
+ }
-/**
- * \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 lgrTotaleRaw;
+ 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 () {
- PixelData = new unsigned char[lgrTotale]; //consistant with GetImageDataIntoVector
- if (PixelData) {
- GetImageDataIntoVector(PixelData, lgrTotale);
- GetHeader()->SetEntryVoidAreaByNumber(PixelData,
- GetHeader()->GetGrPixel(),
- GetHeader()->GetNumPixel());
- }
- PixelRead=0; // no PixelRaw
-
- return PixelData;
+uint8_t* File::GetImageData()
+{
+ if ( ! GetDecompressed() )
+ {
+ // 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();
+ }
+
+/* if ( ! GetDecompressed() )
+ {
+ // If the decompression failed nothing can be done.
+ return 0;
+ }
+
+ uint8_t* pixelData;
+ if ( HeaderInternal->HasLUT() && PixelConverter->BuildRGBImage() )
+ {
+ pixelData = PixelConverter->GetRGB();
+ }
+ else
+ {
+ // When no LUT or LUT conversion fails, return the decompressed
+ pixelData = PixelConverter->GetDecompressed();
+ }
+
+// PIXELCONVERT CLEANME
+ // 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();
+ }
+ if ( PixelConverter->GetRGB() )
+ {
+ // now, it's an RGB image
+ // Lets's write it in the Header
+ 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);
+ PixelRead = 0; // no PixelRaw
+ }
+ else
+ {
+ if ( HeaderInternal->HasLUT() )
+ {
+ // The LUT interpretation failed
+ std::string photometricInterpretation = Util::DicomString("MONOCHROME1");
+ HeaderInternal->SetEntryByNumber( photometricInterpretation,
+ 0x0028, 0x0004 );
+ PixelRead = 0; // no PixelRaw
+ }
+ else
+ {
+ if ( PixelConverter->IsDecompressedRGB() )
+ {
+ ///////////////////////////////////////////////////
+ // 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
+ HeaderInternal->SetEntryByNumber(spp,0x0028,0x0002);
+ HeaderInternal->SetEntryByNumber(photInt,0x0028,0x0004);
+ HeaderInternal->SetEntryByNumber(planConfig,0x0028,0x0006);
+ }
+ PixelRead = 1; // PixelRaw
+ }
+ }
+
+ // We say the value *is* loaded.
+ SetPixelData(pixelData);
+// END PIXELCONVERT CLEANME
+
+ return pixelData;*/
}
/**
- * \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
*
* @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
+ * @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::GetImageDataIntoVector (void* destination, size_t MaxSize) {
- //size_t l = GetImageDataIntoVectorRaw (destination, MaxSize);
- GetImageDataIntoVectorRaw (destination, MaxSize);
- PixelRead=0 ; // no PixelRaw
- if (!Header->HasLUT())
- return lgrTotale;
-
- // from Lut R + Lut G + Lut B
- unsigned char *newDest = new unsigned char[lgrTotale];
- unsigned char *a = (unsigned char *)destination;
- unsigned char *lutRGBA = Header->GetLUTRGBA();
-
- if (lutRGBA) {
- int l = lgrTotaleRaw;
- memmove(newDest, destination, l);// move Gray pixels to temp area
- int j;
- for (int i=0;i<l; i++) { // Build RGB Pixels
- j=newDest[i]*4;
- *a++ = lutRGBA[j];
- *a++ = lutRGBA[j+1];
- *a++ = lutRGBA[j+2];
+size_t File::GetImageDataIntoVector (void* destination, size_t maxSize)
+{
+ if ( ! GetDecompressed() )
+ {
+ // If the decompression failed nothing can be done.
+ return 0;
+ }
+
+ if ( HeaderInternal->HasLUT() && PixelConverter->BuildRGBImage() )
+ {
+ if ( PixelConverter->GetRGBSize() > maxSize )
+ {
+ 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
-
- // 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);
-
- } else {
- // 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
- // 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);
- }
- /// \todo Drop Palette Color out of the Header?
- return lgrTotale;
+ memcpy( destination,
+ (void*)PixelConverter->GetRGB(),
+ PixelConverter->GetRGBSize() );
+ return PixelConverter->GetRGBSize();
+ }
+
+ // 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();
}
/**
- * \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 () {
- if (Header->HasLUT())
- /// \todo Let gdcmHeader user a chance to get the right value
- /// Create a member lgrTotaleRaw ???
- lgrTotale /= 3;
- PixelData = new unsigned char[lgrTotale];
-
- if (PixelData) {
- GetImageDataIntoVectorRaw(PixelData, lgrTotale);
- GetHeader()->SetEntryVoidAreaByNumber(PixelData,
- GetHeader()->GetGrPixel(),
- GetHeader()->GetNumPixel());
- }
- PixelRead=1; // PixelRaw
-
- return PixelData;
-}
+uint8_t* File::GetImageDataRaw ()
+{
+ return GetDecompressed();
+/* uint8_t* decompressed = GetDecompressed();
+ if ( ! decompressed )
+ {
+ return 0;
+ }
-/**
- * \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
- * 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) {
+// PIXELCONVERT CLEANME
+ // 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();
+ }
+ if ( PixelConverter->IsDecompressedRGB() )
+ {
+ ///////////////////////////////////////////////////
+ // 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
+ HeaderInternal->SetEntryByNumber(spp,0x0028,0x0002);
+ HeaderInternal->SetEntryByNumber(photInt,0x0028,0x0004);
+ HeaderInternal->SetEntryByNumber(planConfig,0x0028,0x0006);
+ }
- int nb, nbu, highBit, signe;
- std::string str_nbFrames, str_nb, str_nbu, str_highBit, str_signe;
- PixelRead=1 ; // PixelRaw
+ // We say the value *is* loaded.
+ SetPixelData(decompressed);
- if ( lgrTotale > 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
- str_nb = Header->GetEntryByNumber(0x0028,0x0100);
- if (str_nb == GDCM_UNFOUND ) {
- nb = 16;
- } else {
- nb = atoi(str_nb.c_str() );
- }
- // Number of Bits actually used
- str_nbu=Header->GetEntryByNumber(0x0028,0x0101);
- if (str_nbu == GDCM_UNFOUND ) {
- nbu = nb;
- } else {
- nbu = atoi(str_nbu.c_str() );
- }
- // High Bit Position
- 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
- str_signe=Header->GetEntryByNumber(0x0028,0x0103);
- if (str_signe == GDCM_UNFOUND ) {
- signe = 0; // default is unsigned
- } else {
- signe = atoi(str_signe.c_str() );
- }
-
- // re arange bytes inside the integer (processor endianity)
- if (nb != 8)
- SwapZone(destination, Header->GetSwapCode(), lgrTotale, nb);
-
- // to avoid pb with some xmedcon breakers images
- if (nb==16 && nbu<nb && signe==0) {
- int l = (int)lgrTotale / (nb/8);
- guint16 *deb = (guint16 *)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)lgrTotale / (nb/8);
- if (nb == 16) {
- guint16 mask = 0xffff;
- mask = mask >> (nb-nbu);
- guint16 *deb = (guint16 *)destination;
- for(int i = 0; i<l; i++) {
- *deb = (*deb >> (nbu-highBit-1)) & mask;
- deb ++;
- }
- } else if (nb == 32 ) {
- guint32 mask = 0xffffffff;
- mask = mask >> (nb-nbu);
- guint32 *deb = (guint32 *)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 commented out code .
-// Nobody knows what's expecting you ...
-// Just to 'see' what was actually read on disk :-(
+ PixelRead = 1; // PixelRaw
+// END PIXELCONVERT CLEANME
-// FILE * f2;
-// f2 = fopen("SpuriousFile.RAW","wb");
-// fwrite(destination,lgrTotale,1,f2);
-// fclose(f2);
-
- // Deal with the color
- // -------------------
-
- std::string str_PhotometricInterpretation =
- Header->GetEntryByNumber(0x0028,0x0004);
+ return decompressed;*/
+}
- if ( (str_PhotometricInterpretation == "MONOCHROME1 ")
- || (str_PhotometricInterpretation == "MONOCHROME2 ") ) {
- return lgrTotale;
+uint8_t* File::GetDecompressed()
+{
+ 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 )
+ {
+ dbg.Verbose(0, "File::GetDecompressed: read/decompress of "
+ "pixel data apparently went wrong.");
+ return 0;
}
-
- // 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
-
- // Whatever Planar Configuration is,
- // "PALETTE COLOR " implies that we deal with the palette.
- if (str_PhotometricInterpretation == "PALETTE COLOR ")
- planConf=2;
-
- 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();
-
- unsigned char *newDest = new unsigned char[lgrTotale];
- unsigned char *x = newDest;
- unsigned char *a = (unsigned char *)destination;
- unsigned char *b = a + l;
- unsigned char *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++) = (unsigned char)R;
- *(x++) = (unsigned char)G;
- *(x++) = (unsigned char)B;
- a++; b++; c++;
- }
- }
- memmove(destination,newDest,lgrTotale);
- 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();
-
- char *newDest = new char[lgrTotale];
- char *x = newDest;
- char *a = (char *)destination;
- char *b = a + l;
- char *c = b + l;
-
- for (int j=0;j<l; j++) {
- *(x++) = *(a++);
- *(x++) = *(b++);
- *(x++) = *(c++);
- }
- memmove(destination,newDest,lgrTotale);
- delete[] newDest;
- }
- break;
- }
- case 2:
- // Palettes were found
- // Let the user deal with them !
- return lgrTotale;
- }
- // now, it's an RGB image
- // Lets's write it in the Header
-
- // 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);
-
- /// \todo Drop Palette Color out of the Header?
- return lgrTotale;
+ return decompressed;
}
/**
- * \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
+ * @param expectedSize total image size, in Bytes
*
* @return boolean
*/
-bool gdcmFile::SetImageData(void *inData, size_t ExpectedSize) {
- Header->SetImageDataSize(ExpectedSize);
- PixelData = inData;
- lgrTotale = ExpectedSize;
- PixelRead = 1;
-
+bool File::SetImageData(uint8_t* inData, size_t 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) {
- FILE *fp1;
- fp1 = fopen(fileName.c_str(),"wb");
- if (fp1 == NULL) {
- printf("Fail to open (write) file [%s] \n",fileName.c_str());
+bool File::WriteRawData(std::string const & fileName)
+{
+ std::ofstream fp1(fileName.c_str(), std::ios::out | std::ios::binary );
+ if (!fp1)
+ {
+ dbg.Verbose(2, "Fail to open (write) file:", fileName.c_str());
return false;
}
- fwrite (PixelData,lgrTotale, 1, fp1);
- fclose (fp1);
+ fp1.write((char*)Pixel_Data, ImageDataSize);
+ fp1.close();
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) {
- return WriteBase(fileName, gdcmImplicitVR);
+bool File::WriteDcmImplVR (std::string const & fileName)
+{
+ SetWriteTypeToDcmImplVR();
+ return Write(fileName);
}
/**
- * \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) {
- return WriteBase(fileName, gdcmExplicitVR);
+bool File::WriteDcmExplVR (std::string const & fileName)
+{
+ SetWriteTypeToDcmExplVR();
+ return Write(fileName);
}
/**
- * \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) {
- return WriteBase(fileName, gdcmACR);
+bool File::WriteAcr (std::string const & fileName)
+{
+ 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);
}
//-----------------------------------------------------------------------------
// 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 != ExplicitVR)
+ {
+ return false;
+ }*/
- FILE *fp1;
-
- if (PixelRead==-1 && type != gdcmExplicitVR) {
+ std::ofstream* fp1 = new std::ofstream(fileName.c_str(),
+ std::ios::out | std::ios::binary);
+ if (fp1 == NULL)
+ {
+ dbg.Verbose(2, "Failed to open (write) File: " , fileName.c_str());
return false;
}
- fp1 = fopen(fileName.c_str(),"wb");
- if (fp1 == NULL) {
- printf("Failed to open (write) File [%s] \n",fileName.c_str());
- return (false);
+ if ( type == ImplicitVR || type == ExplicitVR )
+ {
+ // writing Dicom File Preamble
+ char filePreamble[128];
+ memset(filePreamble, 0, 128);
+ fp1->write(filePreamble, 128);
+ fp1->write("DICM", 4);
}
- if ( (type == gdcmImplicitVR) || (type == gdcmExplicitVR) ) {
- char *filePreamble;
- // writing Dicom File Preamble
- filePreamble=new char[128];
- memset(filePreamble,0,128);
- fwrite(filePreamble,128,1,fp1);
- fwrite("DICM",4,1,fp1);
- delete[] filePreamble;
+ switch(WriteMode)
+ {
+ case WMODE_NATIVE :
+ SetWriteToNative();
+ break;
+ case WMODE_DECOMPRESSED :
+ SetWriteToDecompressed();
+ break;
+ case WMODE_RGB :
+ SetWriteToRGB();
+ break;
}
// --------------------------------------------------------------
/// but pb expected if user deals with, e.g. COMPLEX images
std::string rows, columns;
- if ( Header->GetFileType() == gdcmACR_LIBIDO){
- rows = Header->GetEntryByNumber(0x0028, 0x0010);
- columns = Header->GetEntryByNumber(0x0028, 0x0011);
- Header->SetEntryByNumber(columns, 0x0028, 0x0010);
- Header->SetEntryByNumber(rows , 0x0028, 0x0011);
+ if ( HeaderInternal->GetFileType() == ACR_LIBIDO)
+ {
+ SetWriteToLibido();
}
// ----------------- End of Special Patch ----------------
-
- /// \todo get the grPixel, numPixel values (for some ACR-NEMA images only)
-
- guint16 grPixel =Header->GetGrPixel();
- guint16 numPixel=Header->GetNumPixel();;
-
- // Update Pixel Data Length
- // the *last* of the (GrPixel, NumPixel), if many.
+
+/* uint16_t grPixel = HeaderInternal->GetGrPixel();
+ uint16_t numPixel = HeaderInternal->GetNumPixel();;
- TagKey key = gdcmDictEntry::TranslateToKey(grPixel, numPixel);
- TagDocEntryHT::iterator p2;
- gdcmDocEntry *PixelElement;
-
- IterHT it= Header->GetEntry().equal_range(key); // get a pair of iterators first-last synonym
-
- if (Header->GetEntry().count(key) == 1) // only the first is significant
- p2=it.first; // iterator on the first (unique) synonym
- else
- p2=it.second;// iterator on the last synonym
-
- PixelElement=p2->second; // H Table target column (2-nd col)
- // PixelElement->SetPrintLevel(2);
- // PixelElement->Print();
+ DocEntry* PixelElement =
+ GetHeader()->GetDocEntryByNumber(grPixel, numPixel);
- if (PixelRead==1)
- PixelElement->SetLength(lgrTotaleRaw);
- else if (PixelRead==0)
- PixelElement->SetLength(lgrTotale);
-
- //PixelElement->SetPrintLevel(2);
- //PixelElement->Print();
- Header->Write(fp1, type);
+ 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 );
+ }*/
+
+ 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){
- Header->SetEntryByNumber(rows , 0x0028, 0x0010);
- Header->SetEntryByNumber(columns, 0x0028, 0x0011);
+ if ( HeaderInternal->GetFileType() == ACR_LIBIDO )
+ {
+ RestoreWriteFromLibido();
}
// ----------------- End of Special Patch ----------------
-
- // fwrite(PixelData, lgrTotale, 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
/**
- * \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 Set the pixel datas in the good entry of the Header
*/
-void gdcmFile::SwapZone(void *im, int swap, int lgr, int nb) {
- guint32 s32;
- guint16 fort,faible;
- int i;
-
- if(nb == 16)
- switch(swap) {
- case 0:
- case 12:
- case 1234:
- break;
-
- case 21:
- case 3412:
- case 2143:
- case 4321:
+void File::SetPixelData(uint8_t* data)
+{
+ GetHeader()->SetEntryByNumber( GDCM_BINLOADED,
+ GetHeader()->GetGrPixel(), GetHeader()->GetNumPixel());
+
+ // Will be 7fe0, 0010 in standard case
+ DocEntry* currentEntry = GetHeader()->GetDocEntryByNumber(GetHeader()->GetGrPixel(), GetHeader()->GetNumPixel());
+ if ( currentEntry )
+ {
+ if ( BinEntry* binEntry = dynamic_cast<BinEntry *>(currentEntry) )
+ // Flag is to false because datas are kept in the gdcmPixelConvert
+ binEntry->SetBinArea( data, false );
+ }
+}
- for(i=0;i<lgr/2;i++) {
- ((unsigned short int *)im)[i]= ((((unsigned short int *)im)[i])>>8)
- | ((((unsigned short int *)im)[i])<<8);
- }
- break;
+void File::SetWriteToNative()
+{
+// Nothing to do
+}
- default:
- std::cout << "SWAP value (16 bits) not allowed :i" << swap << std::endl;
+void File::SetWriteToDecompressed()
+{
+// if (( !HeaderInternal->HasLUT() ) || (!PixelConverter->BuildRGBImage()))
+ if(HeaderInternal->HasLUT() && PixelConverter->BuildRGBImage())
+ {
+ SetWriteToRGB();
}
-
- if( nb == 32 )
- switch (swap) {
- case 0:
- case 1234:
- break;
+ else
+ {
+ ValEntry* photInt = CopyValEntry(0x0028,0x0004);
+ photInt->SetValue("MONOCHROME1 ");
+ photInt->SetLength(12);
+
+ BinEntry* pixel = CopyBinEntry(GetHeader()->GetGrPixel(),GetHeader()->GetNumPixel());
+ pixel->SetValue(GDCM_BINLOADED);
+ pixel->SetBinArea(PixelConverter->GetDecompressed(),false);
+ pixel->SetLength(PixelConverter->GetDecompressedSize());
+
+ Archive->Push(photInt);
+ Archive->Push(pixel);
+ }
+/* else
+ {
+ SetWriteToRGB();
+ } */
+}
- case 4321:
- for(i=0;i<lgr/4;i++) {
- faible= ((unsigned long int *)im)[i]&0x0000ffff; /* 4321 */
- fort =((unsigned long int *)im)[i]>>16;
- fort= (fort>>8) | (fort<<8);
- faible=(faible>>8) | (faible<<8);
- s32=faible;
- ((unsigned long int *)im)[i]=(s32<<16)|fort;
- }
- break;
+void File::SetWriteToRGB()
+{
+ if(PixelConverter->BuildRGBImage())
+ {
+ ValEntry* spp = CopyValEntry(0x0028,0x0002);
+ spp->SetValue("3 ");
+ spp->SetLength(2);
+
+ ValEntry* photInt = CopyValEntry(0x0028,0x0004);
+ photInt->SetValue("RGB ");
+ photInt->SetLength(4);
+
+ ValEntry* planConfig = CopyValEntry(0x0028,0x0006);
+ planConfig->SetValue("0 ");
+ planConfig->SetLength(2);
+
+ BinEntry* pixel = CopyBinEntry(GetHeader()->GetGrPixel(),GetHeader()->GetNumPixel());
+ pixel->SetValue(GDCM_BINLOADED);
+ pixel->SetBinArea(PixelConverter->GetRGB(),false);
+ pixel->SetLength(PixelConverter->GetRGBSize());
+
+ Archive->Push(spp);
+ Archive->Push(photInt);
+ Archive->Push(planConfig);
+ Archive->Push(pixel);
+ }
+ else
+ {
+ SetWriteToDecompressed();
+ }
+}
- case 2143:
- for(i=0;i<lgr/4;i++) {
- faible= ((unsigned long int *)im)[i]&0x0000ffff; /* 2143 */
- fort=((unsigned long int *)im)[i]>>16;
- fort= (fort>>8) | (fort<<8);
- faible=(faible>>8) | (faible<<8);
- s32=fort;
- ((unsigned long int *)im)[i]=(s32<<16)|faible;
- }
- break;
-
- case 3412:
- for(i=0;i<lgr/4;i++) {
- faible= ((unsigned long int *)im)[i]&0x0000ffff; /* 3412 */
- fort=((unsigned long int *)im)[i]>>16;
- s32=faible;
- ((unsigned long int *)im)[i]=(s32<<16)|fort;
- }
- break;
-
- default:
- std::cout << "SWAP value (32 bits) not allowed : " << swap << std::endl;
- }
+void File::RestoreWrite()
+{
+ Archive->Restore(0x0028,0x0002);
+ Archive->Restore(0x0028,0x0004);
+ Archive->Restore(0x0028,0x0006);
+ Archive->Restore(GetHeader()->GetGrPixel(),GetHeader()->GetNumPixel());
}
-/**
- * \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) {
+void File::SetWriteToLibido()
+{
+ ValEntry *oldRow = dynamic_cast<ValEntry *>(HeaderInternal->GetDocEntryByNumber(0x0028, 0x0010));
+ ValEntry *oldCol = dynamic_cast<ValEntry *>(HeaderInternal->GetDocEntryByNumber(0x0028, 0x0011));
+
+ if( oldRow && oldCol )
+ {
+ std::string rows, columns;
- FILE *fp;
+ ValEntry *newRow=new ValEntry(oldRow->GetDictEntry());
+ ValEntry *newCol=new ValEntry(oldCol->GetDictEntry());
- if ( !(fp=Header->OpenFile()))
- return false;
- if ( fseek(fp, Header->GetPixelOffset(), SEEK_SET) == -1 ) {
- Header->CloseFile();
- return false;
+ newRow->Copy(oldCol);
+ newCol->Copy(oldRow);
+
+ newRow->SetValue(oldCol->GetValue());
+ newCol->SetValue(oldRow->GetValue());
+
+ Archive->Push(newRow);
+ Archive->Push(newCol);
}
- // ---------------------- 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();
- unsigned char b0, b1, b2;
-
- unsigned short int *pdestination = (unsigned short int*)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);
- if ( ItemRead != 1 ) {
- Header->CloseFile();
- return false;
- } else {
- Header->CloseFile();
- return true;
- }
- }
+void File::RestoreWriteFromLibido()
+{
+ Archive->Restore(0x0028,0x0010);
+ Archive->Restore(0x0028,0x0011);
+}
- // ---------------------- Run Length Encoding
- if (Header->IsRLELossLessTransferSyntax()) {
- bool res = (bool)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
+ValEntry* File::CopyValEntry(uint16_t group,uint16_t element)
+{
+ DocEntry* oldE = HeaderInternal->GetDocEntryByNumber(group, element);
+ ValEntry* newE;
- bool jpg2000 = Header->IsJPEG2000();
- bool jpgLossless = Header->IsJPEGLossless();
+ if(oldE)
+ {
+ newE = new ValEntry(oldE->GetDictEntry());
+ newE->Copy(oldE);
+ }
+ else
+ {
+ newE = GetHeader()->NewValEntryByNumber(group,element);
+ }
- bool res = true;
- guint16 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 ?!?
- char *BasicOffsetTableItemValue = new char[ln+1];
- fread(BasicOffsetTableItemValue,ln,1,fp);
+ return(newE);
+}
+
+BinEntry* File::CopyBinEntry(uint16_t group,uint16_t element)
+{
+ DocEntry* oldE = HeaderInternal->GetDocEntryByNumber(group, element);
+ BinEntry* newE;
+
+ if(oldE)
+ {
+ newE = new BinEntry(oldE->GetDictEntry());
+ newE->Copy(oldE);
+ }
+ else
+ {
+ newE = GetHeader()->NewBinEntryByNumber(group,element);
}
-
- // 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 = (bool)gdcm_read_JPEG2000_file (fp,destination); // Not Yet written
-
- } // ------------------------------------- endif (JPEG2000)
-
- else if (jpgLossless) { // JPEG LossLess : call to xmedcom JPEG
- JPEGLosslessDecodeImage (fp, // Reading Fragment pixels
- (unsigned short *)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) {
- res = (bool)gdcm_read_JPEG_file (fp,destination); // Reading Fragment pixels
- } else {
- res = (bool)gdcm_read_JPEG_file12 (fp,destination);// Reading Fragment pixels
- }
- } // ------------------------------------- endif (JPEGLossy)
-
- if (!res) break;
-
- destination = (char *)destination + taille * nBytes; // location in user's memory
- // for next fragment (if any)
-
- 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;
+
+ return(newE);
}
+
//-----------------------------------------------------------------------------
+} // end namespace gdcm
+