-// gdcmFile.cxx
+ /*=========================================================================
+
+ Program: gdcm
+ Module: $RCSfile: gdcmFile.cxx,v $
+ Language: C++
+ 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.html for details.
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the above copyright notices for more information.
+
+=========================================================================*/
#include "gdcmFile.h"
-#include "gdcmUtil.h"
-#include "iddcmjpeg.h"
-using namespace std;
+#include "gdcmDebug.h"
+
+namespace gdcm
+{
+typedef std::pair<TagDocEntryHT::iterator,TagDocEntryHT::iterator> IterHT;
+
+//-------------------------------------------------------------------------
+// Constructor / Destructor
+/**
+ * \brief Constructor dedicated to deal with the *pixels* area of a ACR/DICOMV3
+ * file (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
+ * user sets an a posteriori shadow dictionary (efficiency can be
+ * seen as a side effect).
+ * @param header already built Header
+ */
+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.
- * \Note the in-memory representation of all available tags found in
+ * 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
- *
- * @return
*/
-
-gdcmFile::gdcmFile(string & filename)
- :gdcmHeader(filename.c_str())
+File::File(std::string const & filename )
{
- SetPixelDataSizeFromHeader();
+ HeaderInternal = new Header( filename );
+ SelfHeader = true;
+ Initialise();
}
-gdcmFile::gdcmFile(const char * filename)
- :gdcmHeader(filename)
+/**
+ * \brief Factorization for various forms of constructors.
+ */
+void File::Initialise()
{
- SetPixelDataSizeFromHeader();
+ if ( HeaderInternal->IsReadable() )
+ {
+ ImageDataSizeRaw = ComputeDecompressedPixelDataSizeFromHeader();
+ if ( HeaderInternal->HasLUT() )
+ {
+ ImageDataSize = 3 * ImageDataSizeRaw;
+ }
+ else
+ {
+ ImageDataSize = ImageDataSizeRaw;
+ }
+
+ PixelConverter = new PixelConvert;
+ PixelConverter->GrabInformationsFromHeader( HeaderInternal );
+ }
+ SaveInitialValues();
}
/**
- * \ingroup gdcmFile
- * \brief calcule la longueur (in bytes) A ALLOUER pour recevoir les
- * pixels de l'image
- * ou DES images dans le cas d'un multiframe
- * ATTENTION : il ne s'agit PAS de la longueur du groupe des Pixels
- * (dans le cas d'images compressees, elle n'a pas de sens).
- *
- * @return longueur a allouer
+ * \brief canonical destructor
+ * \note If the Header was created by the File constructor,
+ * it is destroyed by the File
*/
-void gdcmFile::SetPixelDataSizeFromHeader(void) {
- int nb;
- string str_nb;
-
- str_nb=gdcmHeader::GetPubElValByNumber(0x0028,0x0100);
- if (str_nb == "gdcm::Unfound" ) {
- nb = 16;
- } else {
- nb = atoi(str_nb.c_str() );
- if (nb == 12) nb =16;
+File::~File()
+{
+ if( SelfHeader )
+ {
+ delete HeaderInternal;
}
- lgrTotale = GetXSize() * GetYSize() * GetZSize() * (nb/8)* GetSamplesPerPixel();;
+ HeaderInternal = 0;
+
+ DeleteInitialValues();
}
-/////////////////////////////////////////////////////////////////
/**
- * \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.
+ * \brief Sets some initial values for the Constructor
+ * \warning not end user intended
*/
-size_t gdcmFile::GetImageDataSize(void) {
- return (lgrTotale);
+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);
+ }
+}
-/////////////////////////////////////////////////////////////////
/**
- * \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.
- *
+ * \brief delete initial values (il they were saved)
+ * of InitialLutDescriptors and InitialLutData
*/
-bool gdcmFile::ReadPixelData(void* destination) {
- if ( !OpenFile())
- return false;
-
- if ( fseek(fp, GetPixelOffset(), SEEK_SET) == -1 ) {
- CloseFile();
- return false;
- }
-
- if ( !IsDicomV3() ||
- IsImplicitVRLittleEndianTransferSyntax() ||
- IsExplicitVRLittleEndianTransferSyntax() ||
- IsExplicitVRBigEndianTransferSyntax() ||
- IsDeflatedExplicitVRLittleEndianTransferSyntax() ) {
-
- size_t ItemRead = fread(destination, lgrTotale, 1, fp);
- if ( ItemRead != 1 ) {
- CloseFile();
- return false;
- } else {
- CloseFile();
- return true;
- }
- }
-
- // ------------------------------- Position on begining of Jpeg Pixels
+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;
- int ln;
- fseek(fp,4,SEEK_CUR);
- fread(&ln,4,1,fp);
- if(GetSwapCode())
- ln=SwapLong(ln);
- fseek(fp,ln,SEEK_CUR);
- fseek(fp,4,SEEK_CUR);
- fread(&ln,4,1,fp);
- if(GetSwapCode())
- ln=SwapLong(ln);
-
- // ------------------------------- JPEG LossLess : call to Jpeg Libido
-
- if (IsJPEGLossless()) {
-
- ClbJpeg* jpg = _IdDcmJpegRead(fp);
- if(jpg == NULL) {
- CloseFile();
- return false;
- }
-
- int nb;
- string str_nb=gdcmHeader::GetPubElValByNumber(0x0028,0x0100);
- if (str_nb == "gdcm::Unfound" ) {
- nb = 16;
- } else {
- nb = atoi(str_nb.c_str() );
- if (nb == 12) nb =16;
- }
- int nBytes= nb/8;
- int * dataJpg = jpg->DataImg;
- int taille = GetXSize() * GetYSize() * GetZSize() * GetSamplesPerPixel();
-
- switch (nBytes) {
- case 1:
- {
- unsigned short *dest = (unsigned short *)destination;
- for (int i=0; i<taille; i++) {
- *((unsigned char *)dest+i) = *(dataJpg +i);
- }
- }
- break;
-
- case 2:
- {
- unsigned short *dest = (unsigned short *)destination;
- for (int i=0; i<taille; i++) {
- *((unsigned short *)dest+i) = *(dataJpg +i);
- }
- }
- break;
-
- case 4:
- {
- unsigned int *dest=(unsigned int *)destination;
- for (int i=0;i<taille; i++) {
- *((unsigned int *)dest+i) = *(dataJpg +i);
- }
- }
- break;
- }
+ if ( InitialGreenLUTDescr )
+ delete InitialGreenLUTDescr;
- _IdDcmJpegFree (jpg);
- return true;
- }
-
- // ------------------------------- JPEG Lossy : call to IJG 6b
-
- // TODO : faire qq chose d'intelligent pour limiter
- // la duplication du code JPEG <bits=8 / bits=12>
- // TODO : eplucher icelui pour traiter *egalement* bits=16
-
- int nBS;
- if ((nBS = GetBitsStored()) != 12) {
- printf("Sorry, Bits Stored = %d not yet taken into account\n",nBS);
- return false;
- }
+ if ( InitialBlueLUTDescr )
+ delete InitialBlueLUTDescr;
+
+ if ( InitialRedLUTData )
+ delete InitialRedLUTData;
+
+ if ( InitialGreenLUTData != NULL)
+ delete InitialGreenLUTData;
- bool res = (bool)gdcm_read_JPEG_file (destination);
- return res;
-}
+ if ( InitialBlueLUTData != NULL)
+ delete InitialBlueLUTData;
+}
+
+//-----------------------------------------------------------------------------
+// Print
+
+//-----------------------------------------------------------------------------
+// Public
/**
- * \ingroup gdcmFile
- * \brief Allocates necessary memory, copies the pixel data
- * (image[s]/volume[s]) to newly allocated zone.
- * @return Pointer to newly allocated pixel data.
+ * \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).
*/
-void * gdcmFile::GetImageData (void) {
- PixelData = (void *) malloc(lgrTotale);
- GetImageDataIntoVector(PixelData, lgrTotale);
- return(PixelData);
+int File::ComputeDecompressedPixelDataSizeFromHeader()
+{
+ // see PS 3.3-2003 : C.7.6.3.2.1
+ //
+ // MONOCHROME1
+ // MONOCHROME2
+ // PALETTE COLOR
+ // RGB
+ // HSV (Retired)
+ // ARGB (Retired)
+ // CMYK (Retired)
+ // YBR_FULL
+ // YBR_FULL_422 (no LUT, no Palette)
+ // YBR_PARTIAL_422
+ // YBR_ICT
+ // YBR_RCT
+
+ // LUT's
+ // ex : gdcm-US-ALOKA-16.dcm
+ // 0028|1221 [OW] [Segmented Red Palette Color Lookup Table Data]
+ // 0028|1222 [OW] [Segmented Green Palette Color Lookup Table Data]
+ // 0028|1223 [OW] [Segmented Blue Palette Color Lookup Table Data]
+
+ // ex : OT-PAL-8-face.dcm
+ // 0028|1201 [US] [Red Palette Color Lookup Table Data]
+ // 0028|1202 [US] [Green Palette Color Lookup Table Data]
+ // 0028|1203 [US] [Blue Palette Color Lookup Table Data]
+
+ int numberBitsAllocated = HeaderInternal->GetBitsAllocated();
+ // Number of "Bits Allocated" is fixed to 16 when:
+ // - it is not defined (i.e. it's value is 0)
+ // - it's 12, since we will expand the image to 16 bits (see
+ // PixelConvert::ConvertDecompress12BitsTo16Bits() )
+ if ( ( numberBitsAllocated == 0 ) || ( numberBitsAllocated == 12 ) )
+ {
+ numberBitsAllocated = 16;
+ }
+
+ int DecompressedSize = HeaderInternal->GetXSize()
+ * HeaderInternal->GetYSize()
+ * HeaderInternal->GetZSize()
+ * ( numberBitsAllocated / 8 )
+ * HeaderInternal->GetSamplesPerPixel();
+
+ return DecompressedSize;
}
/**
- * \ingroup gdcmFile
- * \brief Copies at most MaxSize bytes of pixel data to caller's
+ * \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
+ */
+uint8_t* File::GetImageData()
+{
+ // FIXME (Mathieu)
+ // I need to deallocate Pixel_Data before doing any allocation:
+
+ if ( Pixel_Data )
+ if ( LastAllocatedPixelDataLength != ImageDataSize )
+ free(Pixel_Data);
+ if ( !Pixel_Data )
+ Pixel_Data = new uint8_t[ImageDataSize];
+
+ if ( Pixel_Data )
+ {
+ LastAllocatedPixelDataLength = ImageDataSize;
+
+ // we load the pixels (and transform grey level + LUT into RGB)
+ GetImageDataIntoVector(Pixel_Data, ImageDataSize);
+
+ // We say the value *is* loaded.
+ GetHeader()->SetEntryByNumber( GDCM_BINLOADED,
+ GetHeader()->GetGrPixel(), GetHeader()->GetNumPixel());
+
+ // Will be 7fe0, 0010 in standard case
+ GetHeader()->SetEntryBinAreaByNumber( Pixel_Data,
+ GetHeader()->GetGrPixel(), GetHeader()->GetNumPixel());
+ }
+ PixelRead = 0; // no PixelRaw
+
+ return Pixel_Data;
+}
+
+/**
+ * \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 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
+ * (for some axis related reasons?). Hence he will have
+ * to load the image line by line, starting from the end.
+ * VTK users have to call GetImageData
+ *
* @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 File::GetImageDataIntoVector (void* destination, size_t maxSize)
+{
+ GetImageDataIntoVectorRaw (destination, maxSize);
+ PixelRead = 0 ; // =0 : no ImageDataRaw
+ if ( !HeaderInternal->HasLUT() )
+ {
+ return ImageDataSize;
+ }
+
+ FILE* fp = HeaderInternal->OpenFile();
+ if ( PixelConverter->BuildRGBImage( fp ) )
+ {
+ memmove( destination,
+ (void*)PixelConverter->GetRGB(),
+ PixelConverter->GetRGBSize() );
+
+ // now, it's an RGB image
+ // Lets's write it in the Header
-size_t gdcmFile::GetImageDataIntoVector (void* destination, size_t MaxSize) {
+ // FIXME : Better use CreateOrReplaceIfExist ?
+
+ 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);
- int nb, nbu, highBit, signe;
- string str_nbFrames, str_nb, str_nbu, str_highBit, str_signe;
-
- if ( lgrTotale > MaxSize ) {
- dbg.Verbose(0, "gdcmFile::GetImageDataIntoVector: pixel data bigger"
- "than caller's expected MaxSize");
- return (size_t)0;
- }
-
- (void)ReadPixelData(destination);
-
- // Nombre de Bits Alloues pour le stockage d'un Pixel
- str_nb = GetPubElValByNumber(0x0028,0x0100);
- if (str_nb == "gdcm::Unfound" ) {
- nb = 16;
- } else {
- nb = atoi(str_nb.c_str() );
- }
-
- // Nombre de Bits Utilises
- str_nbu=GetPubElValByNumber(0x0028,0x0101);
- if (str_nbu == "gdcm::Unfound" ) {
- nbu = nb;
- } else {
- nbu = atoi(str_nbu.c_str() );
- }
-
- // Position du Bit de Poids Fort
- str_highBit=GetPubElValByNumber(0x0028,0x0102);
- if (str_highBit == "gdcm::Unfound" ) {
- highBit = nb - 1;
- } else {
- highBit = atoi(str_highBit.c_str() );
- }
-
- // Signe des Pixels
- str_signe=GetPubElValByNumber(0x0028,0x0103);
- if (str_signe == "gdcm::Unfound" ) {
- signe = 1;
- } else {
- signe = atoi(str_signe.c_str() );
- }
-
- // On remet les Octets dans le bon ordre si besoin est
- if (nb != 8)
- SwapZone(destination, GetSwapCode(), lgrTotale, nb);
-
- // On remet les Bits des Octets dans le bon ordre si besoin est
- 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: wierd image");
- return (size_t)0;
- }
- }
-
- // ---
- string str_PlanarConfiguration = GetPubElValByNumber(0x0028,0x0006);
- int PlanarConfiguration;
- if (str_PlanarConfiguration == "gdcm::Unfound" ) {
- PlanarConfiguration = 0;
- } else {
- PlanarConfiguration = atoi(str_PlanarConfiguration.c_str() );
- }
- // ---
-
- // TODO : replace by
- // if (GetPlanarConfiguration() == 1) {
- // after unfreeze
-
- if (PlanarConfiguration == 1) { // need to make RGB Pixels
- int l = lgrTotale/3 ;
-
- char * a = (char *)destination;
- char * b = a + l;
- char * c = b + l;
- char * newDest = (char*) malloc(lgrTotale);
- // TODO :
- // any trick not to have to allocate temporary buffer is welcome ...
- char *x = newDest;
- for (int j=0;j<l; j++) {
- *(x++) = *(a++);
- *(x++) = *(b++);
- *(x++) = *(c++);
- }
- a = (char *)destination;
- x = newDest;
- for (int i=0;i<lgrTotale; i++) {
- *(a++) = *(x++);
- }
- free(newDest);
}
- return lgrTotale;
+ 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 :-(
+
+ std::string photomInterp = "MONOCHROME1 "; // Photometric Interpretation
+ HeaderInternal->SetEntryByNumber(photomInterp,0x0028,0x0004);
+ }
+ HeaderInternal->CloseFile();
+
+ /// \todo Drop Palette Color out of the Header?
+ return ImageDataSize;
}
+/**
+ * \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
+ */
+uint8_t* File::GetImageDataRaw ()
+{
+ 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];
+
+ if ( Pixel_Data )
+ {
+ LastAllocatedPixelDataLength = imgDataSize;
+
+ // we load the pixels ( grey level or RGB, but NO transformation)
+ GetImageDataIntoVectorRaw(Pixel_Data, imgDataSize);
-//
-// Je laisse le code integral, au cas ça puisse etre reutilise ailleurs
-//
-
-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:
-
- for(i=0;i<lgr;i++)
- ((unsigned short int*)im)[i]= ((((unsigned short int*)im)[i])>>8)
- | ((((unsigned short int*)im)[i])<<8);
- break;
-
- default:
- printf("valeur de SWAP (16 bits) non autorisee : %d\n", swap);
- }
+ // We say the value *is* loaded.
+ GetHeader()->SetEntryByNumber( GDCM_BINLOADED,
+ GetHeader()->GetGrPixel(), GetHeader()->GetNumPixel());
-if( nb == 32 )
- switch (swap) {
- case 0:
- case 1234:
- break;
-
- case 4321:
- for(i=0;i<lgr;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;
-
- case 2143:
- for(i=0;i<lgr;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;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:
- printf("valeur de SWAP (32 bits) non autorisee : %d\n", swap);
+ // will be 7fe0, 0010 in standard cases
+ GetHeader()->SetEntryBinAreaByNumber(Pixel_Data,
+ GetHeader()->GetGrPixel(), GetHeader()->GetNumPixel());
}
-return;
+ PixelRead = 1; // PixelRaw
+
+ return Pixel_Data;
}
-/////////////////////////////////////////////////////////////////
/**
- * \ingroup gdcmFile
- * \brief TODO JPR
- * \warning doit-etre etre publique ? FIXME JPR
- * TODO : y a-t-il un inconvenient à fusioner ces 2 fonctions
- *
- * @param inData TODO JPR
- * @param ExpectedSize TODO JPR
- *
- * @return TODO JPR
+ * \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.
*/
-int gdcmFile::SetImageData(void * inData, size_t ExpectedSize) {
- SetImageDataSize(ExpectedSize);
- PixelData = inData;
- lgrTotale = ExpectedSize;
- return(1);
-}
+void File::GetImageDataIntoVectorRaw (void* destination, size_t maxSize)
+{
+ // we save the initial values of the following
+ // in order to be able to restore the header in a disk-consistent state
+ // (if user asks twice to get the pixels from disk)
+
+ if ( PixelRead != -1 ) // File was "read" before
+ {
+ RestoreInitialValues();
+ }
+
+ PixelRead = 1 ; // PixelRaw
+
+ if ( ImageDataSize > maxSize )
+ {
+ dbg.Verbose(0, "File::GetImageDataIntoVector: pixel data bigger"
+ "than caller's expected MaxSize");
+ return;
+ }
+ FILE* fp = HeaderInternal->OpenFile();
+ PixelConverter->ReadAndDecompressPixelData( fp );
+ HeaderInternal->CloseFile();
+ memmove( destination,
+ (void*)PixelConverter->GetDecompressed(),
+ PixelConverter->GetDecompressedSize() );
-/////////////////////////////////////////////////////////////////
-/**
- * \ingroup gdcmFile
- * \brief TODO JPR
- * \
- * \warning WARNING doit-etre etre publique ? FIXME JPR
- * TODO : y aurait il un inconvenient à fusionner ces 2 fonctions
- *
- * @param ImageDataSize TODO JPR
- *
- */
+ if ( ! PixelConverter->IsDecompressedRGB() )
+ {
+ return;
+ }
+
+///////////////////////////////////////////////////
+ // 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.
-void gdcmFile::SetImageDataSize(size_t ImageDataSize) {
+ // 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 ?!
- string content1;
- char car[20];
-
- // suppose que le ElValue (0x7fe0, 0x0010) existe ...
-
- sprintf(car,"%d",ImageDataSize);
+ 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);
- gdcmElValue*a = GetElValueByNumber(0x7fe0, 0x0010);
- a->SetLength(ImageDataSize);
-
- ImageDataSize+=8;
- sprintf(car,"%d",ImageDataSize);
- content1=car;
- SetPubElValByNumber(content1, 0x7fe0, 0x0000);
+ return;
}
-
-/////////////////////////////////////////////////////////////////
/**
- * \ingroup gdcmFile
- * \brief Ecrit sur disque les pixels d'UNE image
- * Aucun test n'est fait sur l'"Endiannerie" du processeur.
- * Ca sera à l'utilisateur d'appeler son Reader correctement
- * (Equivalent a IdImaWriteRawFile) FIXME JPR
+ * \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 nomFichier TODO JPR
- *
- * @return TODO JPR
+ * @return boolean
*/
-
-int gdcmFile::WriteRawData (string nomFichier) {
-
- FILE * fp1;
- fp1 = fopen(nomFichier.c_str(),"wb");
- if (fp1 == NULL) {
- printf("Echec ouverture (ecriture) Fichier [%s] \n",nomFichier.c_str());
- return (0);
- }
-
- fwrite (PixelData,lgrTotale, 1, fp1);
- fclose (fp1);
- return(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 Ecrit sur disque UNE image Dicom
- * Aucun test n'est fait sur l'"Endiannerie" du processeur.
- * Ca fonctionnera correctement (?) sur processeur Intel
- * (Equivalent a IdDcmWrite) FIXME JPR
- *
- * @param nomFichier TODO JPR
- *
- * @return TODO JPR
+ * \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
+ * @param fileName name of the file to be created
+ * (any already existing file is over written)
+ * @return false if write fails
*/
-int gdcmFile::WriteDcmImplVR (string nomFichier) {
- return WriteBase(nomFichier, ImplicitVR);
+bool File::WriteRawData(std::string const & fileName)
+{
+ FILE* fp1 = fopen(fileName.c_str(), "wb");
+ if (fp1 == NULL)
+ {
+ printf("Fail to open (write) file [%s] \n", fileName.c_str());
+ return false;
+ }
+ fwrite (Pixel_Data, ImageDataSize, 1, fp1);
+ fclose (fp1);
+
+ return true;
}
-/////////////////////////////////////////////////////////////////
/**
- * \ingroup gdcmFile
- *
- * @param nomFichier TODO JPR
- *
- * @return TODO JPR
+ * \brief Writes on disk A SINGLE Dicom file,
+ * using the Implicit Value Representation convention
+ * NO test is performed on processor "Endiannity".
+ * @param fileName name of the file to be created
+ * (any already existing file is overwritten)
+ * @return false if write fails
*/
-
-int gdcmFile::WriteDcmImplVR (const char* nomFichier) {
- return WriteDcmImplVR (string (nomFichier));
+
+bool File::WriteDcmImplVR (std::string const & fileName)
+{
+ return WriteBase(fileName, ImplicitVR);
}
-
-/////////////////////////////////////////////////////////////////
+
/**
- * \ingroup gdcmFile
- *
- * @param nomFichier TODO JPR
- *
- * @return TODO JPR
+* \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
+ * (any already existing file is overwritten)
+ * @return false if write fails
*/
-int gdcmFile::WriteDcmExplVR (string nomFichier) {
- return WriteBase(nomFichier, ExplicitVR);
+bool File::WriteDcmExplVR (std::string const & fileName)
+{
+ return WriteBase(fileName, ExplicitVR);
}
-
-/////////////////////////////////////////////////////////////////
+
/**
- * \ingroup gdcmFile
- * \brief Ecrit au format ACR-NEMA sur disque l'entete et les pixels
+ * \brief Writes on disk A SINGLE Dicom file,
+ * using the ACR-NEMA convention
+ * NO test is performed on processor "Endiannity".
* (a l'attention des logiciels cliniques
* qui ne prennent en entrée QUE des images ACR ...
- * \warning si un header DICOM est fourni en entree,
- * les groupes < 0x0008 et les groupes impairs sont ignores)
- * \warning Aucun test n'est fait sur l'"Endiannerie" du processeur.
- * Ca fonctionnera correctement (?) sur processeur Intel
- * (Equivalent a IdDcmWrite)
- *
- * @param nomFichier TODO JPR
- *
- * @return TODO JPR
+ * \warning if a DICOM_V3 header is supplied,
+ * groups < 0x0008 and shadow groups are ignored
+ * \warning NO TEST is performed on processor "Endiannity".
+ * @param fileName name of the file to be created
+ * (any already existing file is overwritten)
+ * @return false if write fails
*/
-int gdcmFile::WriteAcr (string nomFichier) {
- return WriteBase(nomFichier, ACR);
+bool File::WriteAcr (std::string const & fileName)
+{
+ return WriteBase(fileName, ACR);
}
-/////////////////////////////////////////////////////////////////
+//-----------------------------------------------------------------------------
+// Protected
/**
- * \ingroup gdcmFile
- *
- * @param FileName TODO JPR
- * @param type TODO JPR
- *
- * @return TODO JPR
+ * \brief NOT a end user inteded function
+ * (used by WriteDcmExplVR, WriteDcmImplVR, WriteAcr, etc)
+ * @param fileName name of the file to be created
+ * (any already existing file is overwritten)
+ * @param type file type (ExplicitVR, ImplicitVR, ...)
+ * @return false if write fails
*/
-int gdcmFile::WriteBase (string FileName, FileType type) {
+bool File::WriteBase (std::string const & fileName, FileType type)
+{
+ if ( PixelRead == -1 && type != ExplicitVR)
+ {
+ return false;
+ }
- FILE * fp1;
- fp1 = fopen(FileName.c_str(),"wb");
- if (fp1 == NULL) {
- printf("Echec ouverture (ecriture) Fichier [%s] \n",FileName.c_str());
- return (0);
+ 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 == ImplicitVR) || (type == ExplicitVR) ) {
- char * filePreamble;
- // Ecriture Dicom File Preamble
- filePreamble=(char*)calloc(128,1);
- fwrite(filePreamble,128,1,fp1);
- fwrite("DICM",4,1,fp1);
+ if ( type == ImplicitVR || type == ExplicitVR )
+ {
+ // writing Dicom File Preamble
+ uint8_t* filePreamble = new uint8_t[128];
+ memset(filePreamble, 0, 128);
+ fwrite(filePreamble, 128, 1, fp1);
+ fwrite("DICM", 4, 1, fp1);
+
+ delete[] filePreamble;
}
- gdcmHeader::Write(fp1, type);
- fwrite(PixelData, lgrTotale, 1, fp1);
+ // --------------------------------------------------------------
+ // Special Patch to allow gdcm to re-write ACR-LibIDO formated images
+ //
+ // if recognition code tells us we dealt with a LibIDO image
+ // we reproduce on disk the switch between lineNumber and columnNumber
+ // just before writting ...
+
+ /// \todo the best trick would be *change* the recognition code
+ /// but pb expected if user deals with, e.g. COMPLEX images
+
+ std::string rows, columns;
+ if ( HeaderInternal->GetFileType() == ACR_LIBIDO)
+ {
+ rows = HeaderInternal->GetEntryByNumber(0x0028, 0x0010);
+ columns = HeaderInternal->GetEntryByNumber(0x0028, 0x0011);
+
+ HeaderInternal->SetEntryByNumber(columns, 0x0028, 0x0010);
+ HeaderInternal->SetEntryByNumber(rows , 0x0028, 0x0011);
+ }
+ // ----------------- End of Special Patch ----------------
+
+ uint16_t grPixel = HeaderInternal->GetGrPixel();
+ uint16_t numPixel = HeaderInternal->GetNumPixel();;
+
+ DocEntry* PixelElement =
+ GetHeader()->GetDocEntryByNumber(grPixel, numPixel);
+
+ if ( PixelRead == 1 )
+ {
+ // we read pixel 'as is' (no tranformation LUT -> RGB)
+ PixelElement->SetLength( ImageDataSizeRaw );
+ }
+ else if ( PixelRead == 0 )
+ {
+ // we tranformed GrayLevel pixels + LUT into RGB Pixel
+ PixelElement->SetLength( ImageDataSize );
+ }
+
+ 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 ( HeaderInternal->GetFileType() == ACR_LIBIDO )
+ {
+ HeaderInternal->SetEntryByNumber(rows , 0x0028, 0x0010);
+ HeaderInternal->SetEntryByNumber(columns, 0x0028, 0x0011);
+ }
+ // ----------------- End of Special Patch ----------------
+
+ // fwrite(Pixel_Data, ImageDataSize, 1, fp1); // should be useless, now
fclose (fp1);
- return(1);
+
+ return true;
}
+
+/**
+ * \brief Access to the underlying \ref PixelConverter RGBA LUT
+ */
+uint8_t* File::GetLutRGBA()
+{
+ return PixelConverter->GetLutRGBA();
+}
+
+} // end namespace gdcm
+
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff