-// gdcmFile.cxx
+ /*=========================================================================
+
+ Program: gdcm
+ Module: $RCSfile: gdcmFile.cxx,v $
+ Language: C++
+ Date: $Date: 2005/01/11 16:44:43 $
+ Version: $Revision: 1.190 $
+
+ 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 "gdcmGlobal.h"
+#include "gdcmTS.h"
+#include "gdcmDocument.h"
+#include "gdcmDebug.h"
#include "gdcmUtil.h"
+#include "gdcmBinEntry.h"
+#include "gdcmHeader.h"
+#include "gdcmPixelReadConvert.h"
+#include "gdcmPixelWriteConvert.h"
+#include "gdcmDocEntryArchive.h"
+#include <fstream>
-// TODO : remove DEBUG
-#define DEBUG 0
+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
+ * one sets an a posteriori shadow dictionary (efficiency can be
+ * seen as a side effect).
+ */
+File::File( )
+{
+ HeaderInternal = new Header( );
+ SelfHeader = true;
+ Initialise();
+}
-#include "iddcmjpeg.h"
-using namespace std;
+/**
+ * \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 canonical destructor
+ * \note If the Header was created by the File constructor,
+ * it is destroyed by the File
+ */
+File::~File()
+{
+ if( PixelReadConverter )
+ {
+ delete PixelReadConverter;
+ }
+ if( PixelWriteConverter )
+ {
+ delete PixelWriteConverter;
+ }
+ if( Archive )
+ {
+ delete Archive;
+ }
+
+ if( SelfHeader )
+ {
+ delete HeaderInternal;
+ }
+ HeaderInternal = 0;
+}
+
+//-----------------------------------------------------------------------------
+// Print
+void File::Print(std::ostream &os)
{
- SetPixelDataSizeFromHeader();
+ HeaderInternal->SetPrintLevel(PrintLevel);
+ HeaderInternal->Print(os);
+
+ PixelReadConverter->SetPrintLevel(PrintLevel);
+ PixelReadConverter->Print(os);
}
+//-----------------------------------------------------------------------------
+// Public
/**
- * \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 Get the size of the image data
+ *
+ * If the image can be RGB (with a lut or by default), the size
+ * corresponds to the RGB image
+ * @return The image size
*/
-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;
+size_t File::GetImageDataSize()
+{
+ if ( PixelWriteConverter->GetUserData() )
+ {
+ return PixelWriteConverter->GetUserDataSize();
}
- lgrTotale = GetXSize() * GetYSize() * GetZSize() * (nb/8)* GetSamplesPerPixel();;
+
+ return PixelReadConverter->GetRGBSize();
}
-/////////////////////////////////////////////////////////////////
/**
- * \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 Get the size of the image data
+ *
+ * If the image can be RGB by transformation in a LUT, this
+ * transformation isn't considered
+ * @return The raw image size
*/
-size_t gdcmFile::GetImageDataSize(void) {
- return (lgrTotale);
-}
+size_t File::GetImageDataRawSize()
+{
+ if ( PixelWriteConverter->GetUserData() )
+ {
+ return PixelWriteConverter->GetUserDataSize();
+ }
+ return PixelReadConverter->GetRawSize();
+}
-/////////////////////////////////////////////////////////////////
/**
- * \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 - 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
*/
-bool gdcmFile::ReadPixelData(void* destination) {
- if ( !OpenFile())
- return false;
-
- printf("GetPixelOffset() %d\n",GetPixelOffset() );
-
- 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
-
- int ln;
- fseek(fp,4,SEEK_CUR);
- fread(&ln,4,1,fp);
- if(GetSwapCode())
- ln=SwapLong(ln);
- if (DEBUG)
- printf ("ln %d\n",ln);
- fseek(fp,ln,SEEK_CUR);
- fseek(fp,4,SEEK_CUR);
- fread(&ln,4,1,fp);
- if(GetSwapCode())
- ln=SwapLong(ln);
- if (DEBUG)
- printf ("ln image comprimée %d\n",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;
- }
-
- _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;
- }
-
- int res = gdcm_read_JPEG_file (destination);
- if (DEBUG)
- printf ("res : %d\n",res);
- return res;
-}
+uint8_t *File::GetImageData()
+{
+ if ( PixelWriteConverter->GetUserData() )
+ {
+ return PixelWriteConverter->GetUserData();
+ }
+
+ if ( ! GetRaw() )
+ {
+ // If the decompression failed nothing can be done.
+ return 0;
+ }
+
+ if ( HeaderInternal->HasLUT() && PixelReadConverter->BuildRGBImage() )
+ {
+ return PixelReadConverter->GetRGB();
+ }
+ else
+ {
+ // When no LUT or LUT conversion fails, return the Raw
+ return PixelReadConverter->GetRaw();
+ }
+}
/**
- * \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 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::GetImageData (void) {
- PixelData = (void *) malloc(lgrTotale);
- GetImageDataIntoVector(PixelData, lgrTotale);
- return(PixelData);
+uint8_t *File::GetImageDataRaw ()
+{
+ return GetRaw();
}
/**
- * \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 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)
+{
+ if ( ! GetRaw() )
+ {
+ // If the decompression failed nothing can be done.
+ return 0;
+ }
-size_t gdcmFile::GetImageDataIntoVector (void* destination, size_t MaxSize) {
-
- 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;
+ if ( HeaderInternal->HasLUT() && PixelReadConverter->BuildRGBImage() )
+ {
+ if ( PixelReadConverter->GetRGBSize() > maxSize )
+ {
+ gdcmVerboseMacro( "Pixel data bigger than caller's expected MaxSize");
+ return 0;
}
+ memcpy( destination,
+ (void*)PixelReadConverter->GetRGB(),
+ PixelReadConverter->GetRGBSize() );
+ return PixelReadConverter->GetRGBSize();
}
-
- // ---
- 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 i=0;i<l; i++) {
- *(x++) = *(a++);
- *(x++) = *(b++);
- *(x++) = *(c++);
- }
- a = (char *)destination;
- x = newDest;
- for (int i=0;i<lgrTotale; i++) {
- *(a++) = *(x++);
- }
- free(newDest);
+
+ // Either no LUT conversion necessary or LUT conversion failed
+ if ( PixelReadConverter->GetRawSize() > maxSize )
+ {
+ gdcmVerboseMacro( "Pixel data bigger than caller's expected MaxSize");
+ return 0;
}
- return lgrTotale;
+ memcpy( destination,
+ (void*)PixelReadConverter->GetRaw(),
+ PixelReadConverter->GetRawSize() );
+ return PixelReadConverter->GetRawSize();
}
+/**
+ * \brief Points the internal 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
+ */
+void File::SetImageData(uint8_t *inData, size_t expectedSize)
+{
+ SetUserData(inData,expectedSize);
+}
-//
-// Je laisse le code integral, au cas ça puisse etre reutilise ailleurs
-//
+/**
+ * \brief Set the image datas defined by the user
+ * \warning When writting the file, this datas are get as default datas to write
+ */
+void File::SetUserData(uint8_t *data, size_t expectedSize)
+{
+ PixelWriteConverter->SetUserData(data,expectedSize);
+}
-void gdcmFile::SwapZone(void* im, int swap, int lgr, int nb) {
-guint32 s32;
-guint16 fort,faible;
-int i;
+/**
+ * \brief Get the image datas defined by the user
+ * \warning When writting the file, this datas are get as default data to write
+ */
+uint8_t *File::GetUserData()
+{
+ return PixelWriteConverter->GetUserData();
+}
-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);
- }
-
-if( nb == 32 )
- switch (swap) {
- case 0:
- case 1234:
- break;
+/**
+ * \brief Get the image data size defined by the user
+ * \warning When writting the file, this datas are get as default data to write
+ */
+size_t File::GetUserDataSize()
+{
+ return PixelWriteConverter->GetUserDataSize();
+}
- 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;
+/**
+ * \brief Get the image datas from the file.
+ * If a LUT is found, the data are expanded to be RGB
+ */
+uint8_t *File::GetRGBData()
+{
+ return PixelReadConverter->GetRGB();
+}
- 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);
- }
-return;
+/**
+ * \brief Get the image data size from the file.
+ * If a LUT is found, the data are expanded to be RGB
+ */
+size_t File::GetRGBDataSize()
+{
+ return PixelReadConverter->GetRGBSize();
}
-/////////////////////////////////////////////////////////////////
/**
- * \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 Get the image datas from the file.
+ * If a LUT is found, the datas are not expanded !
*/
-int gdcmFile::SetImageData(void * inData, size_t ExpectedSize) {
- SetImageDataSize(ExpectedSize);
- PixelData = inData;
- lgrTotale = ExpectedSize;
- return(1);
+uint8_t *File::GetRawData()
+{
+ return PixelReadConverter->GetRaw();
}
+/**
+ * \brief Get the image data size from the file.
+ * If a LUT is found, the data are not expanded !
+ */
+size_t File::GetRawDataSize()
+{
+ return PixelReadConverter->GetRawSize();
+}
-/////////////////////////////////////////////////////////////////
/**
- * \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
- *
+ * \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
*/
-void gdcmFile::SetImageDataSize(size_t ImageDataSize) {
+bool File::WriteRawData(std::string const &fileName)
+{
+ std::ofstream fp1(fileName.c_str(), std::ios::out | std::ios::binary );
+ if (!fp1)
+ {
+ gdcmVerboseMacro( "Fail to open (write) file:" << fileName.c_str());
+ return false;
+ }
- string content1;
- char car[20];
-
- // suppose que le ElValue (0x7fe0, 0x0010) existe ...
-
- sprintf(car,"%d",ImageDataSize);
-
- gdcmElValue*a = GetElValueByNumber(0x7fe0, 0x0010);
- a->SetLength(ImageDataSize);
-
- ImageDataSize+=8;
- sprintf(car,"%d",ImageDataSize);
- content1=car;
- SetPubElValByNumber(content1, 0x7fe0, 0x0000);
-}
+ if( PixelWriteConverter->GetUserData() )
+ {
+ fp1.write( (char*)PixelWriteConverter->GetUserData(),
+ PixelWriteConverter->GetUserDataSize() );
+ }
+ else if ( PixelReadConverter->GetRGB() )
+ {
+ fp1.write( (char*)PixelReadConverter->GetRGB(),
+ PixelReadConverter->GetRGBSize());
+ }
+ else if ( PixelReadConverter->GetRaw() )
+ {
+ fp1.write( (char*)PixelReadConverter->GetRaw(),
+ PixelReadConverter->GetRawSize());
+ }
+ else
+ {
+ gdcmErrorMacro( "Nothing written." );
+ }
+ fp1.close();
+
+ return true;
+}
-/////////////////////////////////////////////////////////////////
/**
- * \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
- *
- * @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::WriteRawData (string nomFichier) {
+bool File::WriteDcmImplVR (std::string const &fileName)
+{
+ SetWriteTypeToDcmImplVR();
+ return Write(fileName);
+}
- 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);
+/**
+* \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
+ */
+
+bool File::WriteDcmExplVR (std::string const &fileName)
+{
+ SetWriteTypeToDcmExplVR();
+ return Write(fileName);
}
+/**
+ * \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 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
+ */
+bool File::WriteAcr (std::string const &fileName)
+{
+ SetWriteTypeToAcr();
+ return Write(fileName);
+}
-/////////////////////////////////////////////////////////////////
/**
- * \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,
+ * @param fileName name of the file to be created
+ * (any already existing file is overwritten)
+ * @return false if write fails
*/
+bool File::Write(std::string const &fileName)
+{
+ switch(WriteType)
+ {
+ case ImplicitVR:
+ SetWriteFileTypeToImplicitVR();
+ break;
+ case ExplicitVR:
+ SetWriteFileTypeToExplicitVR();
+ break;
+ case ACR:
+ case ACR_LIBIDO:
+ SetWriteFileTypeToACR();
+ break;
+ default:
+ SetWriteFileTypeToExplicitVR();
+ }
-int gdcmFile::WriteDcmImplVR (string nomFichier) {
- return WriteBase(nomFichier, ImplicitVR);
+ // --------------------------------------------------------------
+ // 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
+ if( WriteType == ACR_LIBIDO )
+ {
+ SetWriteToLibido();
+ }
+ else
+ {
+ SetWriteToNoLibido();
+ }
+ // ----------------- End of Special Patch ----------------
+
+ switch(WriteMode)
+ {
+ case WMODE_RAW :
+ SetWriteToRaw();
+ break;
+ case WMODE_RGB :
+ SetWriteToRGB();
+ break;
+ }
+
+ bool check = CheckWriteIntegrity();
+ if(check)
+ {
+ check = HeaderInternal->Write(fileName,WriteType);
+ }
+
+ RestoreWrite();
+ RestoreWriteFileType();
+
+ // --------------------------------------------------------------
+ // 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
+ RestoreWriteOfLibido();
+ // ----------------- End of Special Patch ----------------
+
+ return check;
}
-/////////////////////////////////////////////////////////////////
/**
- * \ingroup gdcmFile
- *
- * @param nomFichier TODO JPR
- *
- * @return TODO JPR
+ * \brief Accesses an existing DocEntry (i.e. a Dicom Element)
+ * through it's (group, element) and modifies it's content with
+ * the given value.
+ * @param content new value (string) to substitute with
+ * @param group group number of the Dicom Element to modify
+ * @param elem element number of the Dicom Element to modify
*/
-
-int gdcmFile::WriteDcmImplVR (const char* nomFichier) {
- return WriteDcmImplVR (string (nomFichier));
+bool File::SetEntry(std::string const &content,
+ uint16_t group, uint16_t elem)
+{
+ return HeaderInternal->SetEntry(content,group,elem);
}
-
-/////////////////////////////////////////////////////////////////
+
+
/**
- * \ingroup gdcmFile
- *
- * @param nomFichier TODO JPR
- *
- * @return TODO JPR
+ * \brief Accesses an existing DocEntry (i.e. a Dicom Element)
+ * through it's (group, element) and modifies it's content with
+ * the given value.
+ * @param content new value (void* -> uint8_t*) to substitute with
+ * @param lgth new value length
+ * @param group group number of the Dicom Element to modify
+ * @param elem element number of the Dicom Element to modify
*/
+bool File::SetEntry(uint8_t *content, int lgth,
+ uint16_t group, uint16_t elem)
+{
+ return HeaderInternal->SetEntry(content,lgth,group,elem);
+}
-int gdcmFile::WriteDcmExplVR (string nomFichier) {
- return WriteBase(nomFichier, ExplicitVR);
+/**
+ * \brief Modifies the value of a given Doc Entry (Dicom Element)
+ * when it exists. Create it with the given value when unexistant.
+ * @param content (string) Value to be set
+ * @param group Group number of the Entry
+ * @param elem Element number of the Entry
+ * \return pointer to the modified/created Header Entry (NULL when creation
+ * failed).
+ */
+bool File::ReplaceOrCreate(std::string const &content,
+ uint16_t group, uint16_t elem)
+{
+ return HeaderInternal->ReplaceOrCreate(content,group,elem) != NULL;
}
-
-/////////////////////////////////////////////////////////////////
+
+/*
+ * \brief Modifies the value of a given Header Entry (Dicom Element)
+ * when it exists. Create it with the given value when unexistant.
+ * A copy of the binArea is made to be kept in the Document.
+ * @param binArea (binary) value to be set
+ * @param group Group number of the Entry
+ * @param elem Element number of the Entry
+ * \return pointer to the modified/created Header Entry (NULL when creation
+ * failed).
+ */
+bool File::ReplaceOrCreate(uint8_t *binArea, int lgth,
+ uint16_t group, uint16_t elem)
+{
+ return HeaderInternal->ReplaceOrCreate(binArea,lgth,group,elem) != NULL;
+}
+
/**
- * \ingroup gdcmFile
- * \brief Ecrit au format ACR-NEMA sur disque l'entete et les pixels
- * (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
+ * \brief Access to the underlying \ref PixelReadConverter RGBA LUT
+ */
+uint8_t* File::GetLutRGBA()
+{
+ return PixelReadConverter->GetLutRGBA();
+}
+
+//-----------------------------------------------------------------------------
+// Protected
+
+/**
+ * \brief Check the write integrity
*
- * @return TODO JPR
+ * The tests made are :
+ * - verify the size of the image to write with the possible write
+ * when the user set an image data
+ * @return true if the check successfulls
*/
+bool File::CheckWriteIntegrity()
+{
+ if(PixelWriteConverter->GetUserData())
+ {
+ int numberBitsAllocated = HeaderInternal->GetBitsAllocated();
+ if ( numberBitsAllocated == 0 || numberBitsAllocated == 12 )
+ {
+ numberBitsAllocated = 16;
+ }
+
+ size_t decSize = HeaderInternal->GetXSize()
+ * HeaderInternal->GetYSize()
+ * HeaderInternal->GetZSize()
+ * ( numberBitsAllocated / 8 )
+ * HeaderInternal->GetSamplesPerPixel();
+ size_t rgbSize = decSize;
+ if( HeaderInternal->HasLUT() )
+ rgbSize = decSize * 3;
+
+ switch(WriteMode)
+ {
+ case WMODE_RAW :
+ if( decSize!=PixelWriteConverter->GetUserDataSize() )
+ {
+ gdcmVerboseMacro( "Data size is incorrect (Raw)" << decSize
+ << " / " << PixelWriteConverter->GetUserDataSize() );
+ return false;
+ }
+ break;
+ case WMODE_RGB :
+ if( rgbSize!=PixelWriteConverter->GetUserDataSize() )
+ {
+ gdcmVerboseMacro( "Data size is incorrect (RGB)" << decSize
+ << " / " << PixelWriteConverter->GetUserDataSize() );
+ return false;
+ }
+ break;
+ }
+ }
+
+ return true;
+}
+
+void File::SetWriteToRaw()
+{
+ if( HeaderInternal->GetNumberOfScalarComponents() == 3
+ && !HeaderInternal->HasLUT())
+ {
+ SetWriteToRGB();
+ }
+ else
+ {
+ ValEntry *photInt = CopyValEntry(0x0028,0x0004);
+ if(HeaderInternal->HasLUT())
+ {
+ photInt->SetValue("PALETTE COLOR ");
+ }
+ else
+ {
+ photInt->SetValue("MONOCHROME1 ");
+ }
+
+ PixelWriteConverter->SetReadData(PixelReadConverter->GetRaw(),
+ PixelReadConverter->GetRawSize());
+
+ BinEntry *pixel =
+ CopyBinEntry(GetHeader()->GetGrPixel(),GetHeader()->GetNumPixel());
+ pixel->SetValue(GDCM_BINLOADED);
+ pixel->SetBinArea(PixelWriteConverter->GetData(),false);
+ pixel->SetLength(PixelWriteConverter->GetDataSize());
+
+ Archive->Push(photInt);
+ Archive->Push(pixel);
+ }
+}
+
+void File::SetWriteToRGB()
+{
+ if(HeaderInternal->GetNumberOfScalarComponents()==3)
+ {
+ PixelReadConverter->BuildRGBImage();
+
+ ValEntry *spp = CopyValEntry(0x0028,0x0002);
+ spp->SetValue("3 ");
-int gdcmFile::WriteAcr (string nomFichier) {
- return WriteBase(nomFichier, ACR);
+ ValEntry *planConfig = CopyValEntry(0x0028,0x0006);
+ planConfig->SetValue("0 ");
+
+ ValEntry *photInt = CopyValEntry(0x0028,0x0004);
+ photInt->SetValue("RGB ");
+
+ if(PixelReadConverter->GetRGB())
+ {
+ PixelWriteConverter->SetReadData(PixelReadConverter->GetRGB(),
+ PixelReadConverter->GetRGBSize());
+ }
+ else // Raw data
+ {
+ PixelWriteConverter->SetReadData(PixelReadConverter->GetRaw(),
+ PixelReadConverter->GetRawSize());
+ }
+
+ BinEntry *pixel =
+ CopyBinEntry(GetHeader()->GetGrPixel(),GetHeader()->GetNumPixel());
+ pixel->SetValue(GDCM_BINLOADED);
+ pixel->SetBinArea(PixelWriteConverter->GetData(),false);
+ pixel->SetLength(PixelWriteConverter->GetDataSize());
+
+ Archive->Push(spp);
+ Archive->Push(planConfig);
+ Archive->Push(photInt);
+ Archive->Push(pixel);
+
+ // Remove any LUT
+ Archive->Push(0x0028,0x1101);
+ Archive->Push(0x0028,0x1102);
+ Archive->Push(0x0028,0x1103);
+ Archive->Push(0x0028,0x1201);
+ Archive->Push(0x0028,0x1202);
+ Archive->Push(0x0028,0x1203);
+
+ // For old ACR-NEMA
+ // Thus, we have a RGB image and the bits allocated = 24 and
+ // samples per pixels = 1 (in the read file)
+ if(HeaderInternal->GetBitsAllocated()==24)
+ {
+ ValEntry *bitsAlloc = CopyValEntry(0x0028,0x0100);
+ bitsAlloc->SetValue("8 ");
+
+ ValEntry *bitsStored = CopyValEntry(0x0028,0x0101);
+ bitsStored->SetValue("8 ");
+
+ ValEntry *highBit = CopyValEntry(0x0028,0x0102);
+ highBit->SetValue("7 ");
+
+ Archive->Push(bitsAlloc);
+ Archive->Push(bitsStored);
+ Archive->Push(highBit);
+ }
+ }
+ else
+ {
+ SetWriteToRaw();
+ }
+}
+
+void File::RestoreWrite()
+{
+ Archive->Restore(0x0028,0x0002);
+ Archive->Restore(0x0028,0x0004);
+ Archive->Restore(0x0028,0x0006);
+ Archive->Restore(GetHeader()->GetGrPixel(),GetHeader()->GetNumPixel());
+
+ // For old ACR-NEMA (24 bits problem)
+ Archive->Restore(0x0028,0x0100);
+ Archive->Restore(0x0028,0x0101);
+ Archive->Restore(0x0028,0x0102);
+
+ // For the LUT
+ Archive->Restore(0x0028,0x1101);
+ Archive->Restore(0x0028,0x1102);
+ Archive->Restore(0x0028,0x1103);
+ Archive->Restore(0x0028,0x1201);
+ Archive->Restore(0x0028,0x1202);
+ Archive->Restore(0x0028,0x1203);
+}
+
+void File::SetWriteFileTypeToACR()
+{
+ Archive->Push(0x0002,0x0010);
}
-/////////////////////////////////////////////////////////////////
+void File::SetWriteFileTypeToExplicitVR()
+{
+ std::string ts = Util::DicomString(
+ Global::GetTS()->GetSpecialTransferSyntax(TS::ExplicitVRLittleEndian) );
+
+ ValEntry *tss = CopyValEntry(0x0002,0x0010);
+ tss->SetValue(ts);
+
+ Archive->Push(tss);
+}
+
+void File::SetWriteFileTypeToImplicitVR()
+{
+ std::string ts = Util::DicomString(
+ Global::GetTS()->GetSpecialTransferSyntax(TS::ImplicitVRLittleEndian) );
+
+ ValEntry *tss = CopyValEntry(0x0002,0x0010);
+ tss->SetValue(ts);
+
+ Archive->Push(tss);
+}
+
+void File::RestoreWriteFileType()
+{
+ Archive->Restore(0x0002,0x0010);
+}
+
+void File::SetWriteToLibido()
+{
+ ValEntry *oldRow = dynamic_cast<ValEntry *>
+ (HeaderInternal->GetDocEntry(0x0028, 0x0010));
+ ValEntry *oldCol = dynamic_cast<ValEntry *>
+ (HeaderInternal->GetDocEntry(0x0028, 0x0011));
+
+ if( oldRow && oldCol )
+ {
+ std::string rows, columns;
+
+ ValEntry *newRow=new ValEntry(oldRow->GetDictEntry());
+ ValEntry *newCol=new ValEntry(oldCol->GetDictEntry());
+
+ newRow->Copy(oldCol);
+ newCol->Copy(oldRow);
+
+ newRow->SetValue(oldCol->GetValue());
+ newCol->SetValue(oldRow->GetValue());
+
+ Archive->Push(newRow);
+ Archive->Push(newCol);
+ }
+
+ ValEntry *libidoCode = CopyValEntry(0x0008,0x0010);
+ libidoCode->SetValue("ACRNEMA_LIBIDO_1.1");
+ Archive->Push(libidoCode);
+}
+
+void File::SetWriteToNoLibido()
+{
+ ValEntry *recCode = dynamic_cast<ValEntry *>
+ (HeaderInternal->GetDocEntry(0x0008,0x0010));
+ if( recCode )
+ {
+ if( recCode->GetValue() == "ACRNEMA_LIBIDO_1.1" )
+ {
+ ValEntry *libidoCode = CopyValEntry(0x0008,0x0010);
+ libidoCode->SetValue("");
+ Archive->Push(libidoCode);
+ }
+ }
+}
+
+void File::RestoreWriteOfLibido()
+{
+ Archive->Restore(0x0028,0x0010);
+ Archive->Restore(0x0028,0x0011);
+ Archive->Restore(0x0008,0x0010);
+}
+
+ValEntry *File::CopyValEntry(uint16_t group,uint16_t elem)
+{
+ DocEntry *oldE = HeaderInternal->GetDocEntry(group, elem);
+ ValEntry *newE;
+
+ if(oldE)
+ {
+ newE = new ValEntry(oldE->GetDictEntry());
+ newE->Copy(oldE);
+ }
+ else
+ {
+ newE = GetHeader()->NewValEntry(group,elem);
+ }
+
+ return newE;
+}
+
+BinEntry *File::CopyBinEntry(uint16_t group,uint16_t elem)
+{
+ DocEntry *oldE = HeaderInternal->GetDocEntry(group, elem);
+ BinEntry *newE;
+
+ if(oldE)
+ {
+ newE = new BinEntry(oldE->GetDictEntry());
+ newE->Copy(oldE);
+ }
+ else
+ {
+ newE = GetHeader()->NewBinEntry(group,elem);
+ }
+
+ return newE;
+}
+
+//-----------------------------------------------------------------------------
+// Protected
/**
- * \ingroup gdcmFile
- *
- * @param FileName TODO JPR
- * @param type TODO JPR
- *
- * @return TODO JPR
+ * \brief Factorization for various forms of constructors.
*/
-int gdcmFile::WriteBase (string FileName, FileType type) {
+void File::Initialise()
+{
+ WriteMode = WMODE_RAW;
+ WriteType = ExplicitVR;
+
+ PixelReadConverter = new PixelReadConvert;
+ PixelWriteConverter = new PixelWriteConvert;
+ Archive = new DocEntryArchive( HeaderInternal );
- FILE * fp1;
- fp1 = fopen(FileName.c_str(),"wb");
- if (fp1 == NULL) {
- printf("Echec ouverture (ecriture) Fichier [%s] \n",FileName.c_str());
- return (0);
+ if ( HeaderInternal->IsReadable() )
+ {
+ PixelReadConverter->GrabInformationsFromHeader( HeaderInternal );
}
+}
- 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);
+uint8_t *File::GetRaw()
+{
+ uint8_t *raw = PixelReadConverter->GetRaw();
+ if ( ! raw )
+ {
+ // The Raw image migth not be loaded yet:
+ std::ifstream *fp = HeaderInternal->OpenFile();
+ PixelReadConverter->ReadAndDecompressPixelData( fp );
+ if(fp)
+ HeaderInternal->CloseFile();
+
+ raw = PixelReadConverter->GetRaw();
+ if ( ! raw )
+ {
+ gdcmVerboseMacro( "Read/decompress of pixel data apparently went wrong.");
+ return 0;
+ }
}
- gdcmHeader::Write(fp1, type);
- fwrite(PixelData, lgrTotale, 1, fp1);
- fclose (fp1);
- return(1);
+ return raw;
}
+
+//-----------------------------------------------------------------------------
+// Private
+
+//-----------------------------------------------------------------------------
+} // end namespace gdcm
+
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff