-#include "gdcmlib.h"
+// gdcmFile.cxx
-gdcmFile::gdcmFile(string & filename) {
+#include "gdcmFile.h"
+#include "gdcmUtil.h"
+
+
+// TODO : remove DEBUG
+#define DEBUG 0
+
+
+#include "iddcmjpeg.h"
+using namespace std;
+
+/////////////////////////////////////////////////////////////////
+/**
+ * \ingroup gdcmFile
+ * \brief Constructor dedicated to writing a new DICOMV3 part10 compliant
+ * file (see SetFileName, SetDcmTag and Write)
+ * 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
+ * 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())
+{
+ SetPixelDataSizeFromHeader();
+}
+
+gdcmFile::gdcmFile(const char * filename)
+ :gdcmHeader(filename)
+{
+ SetPixelDataSizeFromHeader();
+}
+
+/**
+ * \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
+ */
+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;
+ }
+ lgrTotale = GetXSize() * GetYSize() * GetZSize() * (nb/8)* GetSamplesPerPixel();;
+}
+
+/////////////////////////////////////////////////////////////////
+/**
+ * \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(void) {
+ return (lgrTotale);
+}
+
+
+/////////////////////////////////////////////////////////////////
+/**
+ * \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) {
+ 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;
+}
+
+/**
+ * \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.
+ */
+void * gdcmFile::GetImageData (void) {
+ PixelData = (void *) malloc(lgrTotale);
+ GetImageDataIntoVector(PixelData, lgrTotale);
+ return(PixelData);
+}
+
+/**
+ * \ingroup gdcmFile
+ * \brief Copies at most MaxSize bytes of pixel data to caller's
+ * memory space.
+ * @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::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;
+ }
+ }
+
+ // ---
+ 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);
+ }
+ return lgrTotale;
+}
+
+
+//
+// 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);
+ }
+
+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);
+ }
+return;
+}
+
+/////////////////////////////////////////////////////////////////
+/**
+ * \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
+ */
+int gdcmFile::SetImageData(void * inData, size_t ExpectedSize) {
+ SetImageDataSize(ExpectedSize);
+ PixelData = inData;
+ lgrTotale = ExpectedSize;
+ return(1);
+}
+
+
+/////////////////////////////////////////////////////////////////
+/**
+ * \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
+ *
+ */
+
+void gdcmFile::SetImageDataSize(size_t ImageDataSize) {
+
+ 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);
+}
+
+
+/////////////////////////////////////////////////////////////////
+/**
+ * \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
+ */
+
+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);
+}
+
+
+
+/////////////////////////////////////////////////////////////////
+/**
+ * \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
+ */
+
+int gdcmFile::WriteDcmImplVR (string nomFichier) {
+ return WriteBase(nomFichier, ImplicitVR);
+}
+
+/////////////////////////////////////////////////////////////////
+/**
+ * \ingroup gdcmFile
+ *
+ * @param nomFichier TODO JPR
+ *
+ * @return TODO JPR
+ */
+
+int gdcmFile::WriteDcmImplVR (const char* nomFichier) {
+ return WriteDcmImplVR (string (nomFichier));
+}
+
+/////////////////////////////////////////////////////////////////
+/**
+ * \ingroup gdcmFile
+ *
+ * @param nomFichier TODO JPR
+ *
+ * @return TODO JPR
+ */
+
+int gdcmFile::WriteDcmExplVR (string nomFichier) {
+ return WriteBase(nomFichier, ExplicitVR);
+}
+/////////////////////////////////////////////////////////////////
+/**
+ * \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
+ *
+ * @return TODO JPR
+ */
+
+int gdcmFile::WriteAcr (string nomFichier) {
+ return WriteBase(nomFichier, ACR);
+}
+
+/////////////////////////////////////////////////////////////////
+/**
+ * \ingroup gdcmFile
+ *
+ * @param FileName TODO JPR
+ * @param type TODO JPR
+ *
+ * @return TODO JPR
+ */
+int gdcmFile::WriteBase (string FileName, FileType type) {
+
+ FILE * fp1;
+ fp1 = fopen(FileName.c_str(),"wb");
+ if (fp1 == NULL) {
+ printf("Echec ouverture (ecriture) Fichier [%s] \n",FileName.c_str());
+ return (0);
+ }
+
+ 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);
+ }
+
+ gdcmHeader::Write(fp1, type);
+ fwrite(PixelData, lgrTotale, 1, fp1);
+ fclose (fp1);
+ return(1);
}
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff