// gdcmFile.cxx
+//This is needed when compiling in debug mode
+#ifdef _MSC_VER
+// 'type' : forcing value to bool 'true' or 'false' (performance warning)
+//#pragma warning ( disable : 4800 )
+// 'identifier' : class 'type' needs to have dll-interface to be used by
+// clients of class 'type2'
+#pragma warning ( disable : 4251 )
+// 'identifier' : identifier was truncated to 'number' characters in the
+// debug information
+#pragma warning ( disable : 4786 )
+#endif //_MSC_VER
+
#include "gdcmFile.h"
+#include "gdcmUtil.h"
+#include "iddcmjpeg.h" // for the 'LibIDO' Jpeg LossLess
+using namespace std;
-static void _Swap(void* im, int swap, int lgr, int nb);
+#define str2num(str, typeNum) *((typeNum *)(str))
/////////////////////////////////////////////////////////////////
/**
gdcmFile::gdcmFile(string & filename)
:gdcmHeader(filename.c_str())
{
+ SetPixelDataSizeFromHeader();
}
gdcmFile::gdcmFile(const char * filename)
:gdcmHeader(filename)
{
+ SetPixelDataSizeFromHeader();
}
-
-/////////////////////////////////////////////////////////////////
/**
* \ingroup gdcmFile
- * \brief Renvoie la longueur A ALLOUER pour recevoir les pixels de l'image
+ * \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
*/
-
-size_t gdcmFile::GetImageDataSize(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() );
+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 lgrTotale = GetXSize() * GetYSize() * GetZSize() *(nb/8);
- return (lgrTotale);
+ }
+ lgrTotale = GetXSize() * GetYSize() * GetZSize() * (nb/8)* GetSamplesPerPixel();
+
+ string str_PhotometricInterpretation = gdcmHeader::GetPubElValByNumber(0x0028,0x0004);
+ if ( str_PhotometricInterpretation == "PALETTE COLOR "
+ || str_PhotometricInterpretation == "YBR_FULL") { // --> some more to be added !!
+ lgrTotale*=3;
+ }
+
+ // remaining to check :
+ // str_PhotometricInterpretation == "YBR_FULL"
+ // str_PhotometricInterpretation == "YBR_FULL_422" (no LUT, no Palette)
+ // -->and some more !!
}
-
-
/////////////////////////////////////////////////////////////////
/**
* \ingroup gdcmFile
- * \brief TODO
- * \warning WARNING
- *
+ * \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.
*/
-void * gdcmFile::GetImageData (void) {
- char * _Pixels;
- // Longueur en Octets des Pixels a lire
- size_t taille = GetImageDataSize();// ne faudrait-il pas la stocker?
- _Pixels = (char *) malloc(taille);
- GetImageDataIntoVector(_Pixels, taille);
-
- // On l'affecte à un champ du dcmFile
- Pixels = _Pixels;
- lgrTotale = taille;
-
- // ca fait double emploi, il faudra nettoyer ça
-
- return(_Pixels);
+size_t gdcmFile::GetImageDataSize(void) {
+ return (lgrTotale);
}
-
/////////////////////////////////////////////////////////////////
/**
- * \ingroup gdcmFile
- * \brief amene en mémoire dans une zone précisee par l'utilisateur
- * les Pixels d'une image NON COMPRESSEE
- * \Warning Aucun test n'est fait pour le moment sur le caractere compresse ou non de l'image
+ * \ingroup gdcmFile
+ * \brief Parse pixel data from disk and *prints* the result
+ * \ For multi-fragment Jpeg files checking purpose *only*
+ * \ Allows to 'see' if the file *does* conform
+ * \ (some of them do not)
+ * \ with Dicom Part 3, Annex A (PS 3.5-2003, page 58)
*
- * @param destination
- * @param MaxSize
+ */
+bool gdcmFile::ParsePixelData(void) {
+ if ( !OpenFile())
+ return false;
+
+ if ( fseek(fp, GetPixelOffset(), SEEK_SET) == -1 ) {
+ CloseFile();
+ return false;
+ }
+
+ if ( !IsDicomV3() ||
+ IsImplicitVRLittleEndianTransferSyntax() ||
+ IsExplicitVRLittleEndianTransferSyntax() ||
+ IsExplicitVRBigEndianTransferSyntax() ||
+ IsDeflatedExplicitVRLittleEndianTransferSyntax() ) {
+
+ printf ("gdcmFile::ParsePixelData : non JPEG File\n");
+ return 0;
+ }
+
+ 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 taille = GetXSize() * GetYSize() * GetZSize() * GetSamplesPerPixel();
+ int taille = GetXSize() * GetYSize() * GetSamplesPerPixel();
+
+ printf ("Checking the Dicom-Jpeg/RLE Pixels\n");
+
+ // ------------------------------- for Parsing : Position on begining of Jpeg Pixels
+ guint16 ItemTagGr,ItemTagEl;
+ int ln;
+ long ftellRes;
+ char * destination = NULL;
+ ftellRes=ftell(fp);
+ fread(&ItemTagGr,2,1,fp); // Reading (fffe) : Basic Offset Table Item Tag Gr
+ fread(&ItemTagEl,2,1,fp); // Reading (e000) : Basic Offset Table Item Tag El
+ if(GetSwapCode()) {
+ ItemTagGr=SwapShort(ItemTagGr);
+ ItemTagEl=SwapShort(ItemTagEl);
+ }
+ printf ("at %x : ItemTag (should be fffe,e000): %04x,%04x\n",
+ ftellRes,ItemTagGr,ItemTagEl );
+ ftellRes=ftell(fp);
+ fread(&ln,4,1,fp);
+ if(GetSwapCode())
+ ln=SwapLong(ln); // Basic Offset Table Item Lentgh
+ printf("at %x : Basic Offset Table Item Lentgh (??) %d x(%08x)\n",
+ ftellRes,ln,ln);
+ if (ln != 0) {
+ // What is it used for ??
+ char * BasicOffsetTableItemValue= (char *)malloc(ln+1);
+ fread(BasicOffsetTableItemValue,ln,1,fp);
+ guint32 a;
+ for (int i=0;i<ln;i+=4){
+ a=str2num(&BasicOffsetTableItemValue[i],guint32);
+ printf(" x(%08x) %d\n",a,a);
+ }
+ }
+
+ ftellRes=ftell(fp);
+ fread(&ItemTagGr,2,1,fp); // Reading (fffe) : Item Tag Gr
+ fread(&ItemTagEl,2,1,fp); // Reading (e000) : Item Tag El
+ if(GetSwapCode()) {
+ ItemTagGr=SwapShort(ItemTagGr);
+ ItemTagEl=SwapShort(ItemTagEl);
+ }
+ printf ("at %x : ItemTag (should be fffe,e000 or e0dd): %04x,%04x\n",
+ ftellRes,ItemTagGr,ItemTagEl );
+
+ while ( ( ItemTagGr == 0xfffe) && (ItemTagEl != 0xe0dd) ) { // Parse fragments
+
+ ftellRes=ftell(fp);
+ fread(&ln,4,1,fp);
+ if(GetSwapCode())
+ ln=SwapLong(ln); // length
+ printf(" at %x : fragment length %d x(%08x)\n",
+ ftellRes, ln,ln);
+
+ destination += taille * nBytes; // location in user's memory
+
+ printf (" Destination will be x(%x) = %d \n",
+ destination,destination );
+
+ fseek(fp,ln,SEEK_CUR); // skipping (not reading) fragment pixels
+
+ ftellRes=ftell(fp);
+ fread(&ItemTagGr,2,1,fp); // Reading (fffe) : Item Tag Gr
+ fread(&ItemTagEl,2,1,fp); // Reading (e000) : Item Tag El
+ if(GetSwapCode()) {
+ ItemTagGr=SwapShort(ItemTagGr);
+ ItemTagEl=SwapShort(ItemTagEl);
+ }
+ printf ("at %x : ItemTag (should be fffe,e000 or e0dd): %04x,%04x\n",
+ ftellRes,ItemTagGr,ItemTagEl );
+
+
+ }
+ return 1;
+}
+
+/////////////////////////////////////////////////////////////////
+/**
+ * \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.
*
- * @return TODO JPR
*/
+bool gdcmFile::ReadPixelData(void* destination) {
-int gdcmFile::GetImageDataIntoVector (void* destination, size_t MaxSize) {
+ if ( !OpenFile())
+ return false;
+
+ if ( fseek(fp, GetPixelOffset(), SEEK_SET) == -1 ) {
+ CloseFile();
+ return false;
+ }
-// Question :
-// dans quel cas la MaxSize sert-elle a quelque chose?
-// que fait-on si la taille de l'image est + gde que Maxize?
-// que fait-on si la taille de l'image est + petite que Maxize?
+// ------------------------------- Uncompressed File
+
+ if ( !IsDicomV3() ||
+ IsImplicitVRLittleEndianTransferSyntax() ||
+ IsExplicitVRLittleEndianTransferSyntax() ||
+ IsExplicitVRBigEndianTransferSyntax() ||
+ IsDeflatedExplicitVRLittleEndianTransferSyntax() ) {
+
+ size_t ItemRead = fread(destination, lgrTotale, 1, fp);
+ if ( ItemRead != 1 ) {
+ CloseFile();
+ return false;
+ } else {
+ CloseFile();
+ return true;
+ }
+ }
+
+ // ----------------------------- JPEG Compressed File .
+
+ 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 taille = GetXSize() * GetYSize() * GetZSize() * GetSamplesPerPixel();
+ int taille = GetXSize() * GetYSize() * GetSamplesPerPixel();
+
+
+ // ------------------------------- JPEG LossLess : call to Jpeg Libido
+
+ if (IsJPEGLossless() && GetZSize() == 1) {
+
+ int ln; // Position on begining of Jpeg Pixels
+ fseek(fp,4,SEEK_CUR); // skipping (fffe,e000) : Basic Offset Table Item
+ fread(&ln,4,1,fp);
+ if(GetSwapCode())
+ ln=SwapLong(ln); // Item length
+ fseek(fp,ln,SEEK_CUR); // skipping Basic Offset Table ('ln' bytes)
+ fseek(fp,4,SEEK_CUR); // skipping (fffe,e000) : First fragment Item Tag
+ fread(&ln,4,1,fp); // First fragment length (just to know)
+ if(GetSwapCode())
+ ln=SwapLong(ln);
+
+ ClbJpeg* jpg = _IdDcmJpegRead(fp); // TODO : find a 'full' one.
+ // (We use the LibIDO one :-(
+ if(jpg == NULL) {
+ CloseFile();
+ return false;
+ }
+ int * dataJpg = jpg->DataImg;
+
+ 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;
+ }
+ _IdDcmJpegFree (jpg);
+ return true;
+ }
+
+ // ------------------------------- JPEG Lossy : call to IJG 6b
+
+ long fragmentBegining; // for ftell, fseek
+
+ bool a=0, b=0;
+
+ a = gdcmHeader::IsRLELossLessTransferSyntax();
+ if (!a)
+ bool b = gdcmHeader::IsJPEG2000();
+
+ bool res;
+ 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(GetSwapCode()) {
+ ItemTagGr=SwapShort(ItemTagGr);
+ ItemTagEl=SwapShort(ItemTagEl);
+ }
+ fread(&ln,4,1,fp);
+ if(GetSwapCode())
+ ln=SwapLong(ln); // Basic Offset Table Item length
+
+ if (ln != 0) {
+ // What is it used for ?!?
+ char *BasicOffsetTableItemValue = (char *)malloc(ln+1);
+ fread(BasicOffsetTableItemValue,ln,1,fp);
+ }
+
+ // first Fragment initialisation
+ fread(&ItemTagGr,2,1,fp); // Reading (fffe) : Item Tag Gr
+ fread(&ItemTagEl,2,1,fp); // Reading (e000) : Item Tag El
+ if(GetSwapCode()) {
+ ItemTagGr=SwapShort(ItemTagGr);
+ ItemTagEl=SwapShort(ItemTagEl);
+ }
+
+ // parsing fragments until Sequence Delim. Tag found
+ //unsigned short *dest = (unsigned short *)destination;
+
+ while ( ( ItemTagGr == 0xfffe) && (ItemTagEl != 0xe0dd) ) {
+ fread(&ln,4,1,fp);
+ if(GetSwapCode())
+ ln=SwapLong(ln); // Fragment Item length
+
+ // FIXME : multi fragments
+ fragmentBegining=ftell(fp);
+
+ if (a)
+ res = (bool)gdcm_read_RLE_file (destination); // Reading Fragment pixels
+ else if (b)
+ res = (bool)gdcm_read_JPEG2000_file (destination); // Reading Fragment pixels
+
+ else if (IsJPEGLossless()) { // ------------- call to LibIDO Jpeg for each Frame/fragment
+
+ // Warning : Works only if there is one fragment per frame
+ // (Or a single fragment for the multiframe file)
+ ClbJpeg* jpg = _IdDcmJpegRead(fp); // TODO : find a 'full' one.
+ // (We use the LibIDO one :-(
+ if(jpg == NULL) {
+ CloseFile();
+ return false;
+ }
+ int * dataJpg = jpg->DataImg;
+ unsigned short *dest = (unsigned short *)destination;
+ switch (nBytes) {
+ case 1:
+ {
+ for (int i=0; i<taille; i++) {
+ *((unsigned char *)dest+i) = *(dataJpg +i);
+ }
+ break;
+ }
+
+ case 2:
+ {
+ for (int i=0; i<taille; i++) {
+ *((unsigned short *)dest+i) = *(dataJpg +i);
+ }
+ break;
+ }
+ }
+ _IdDcmJpegFree (jpg);
+
+ } // ------------------------------------- endif (IsJPEGLossless())
+
+ else
+ if (GetBitsStored() == 8) {
+ res = (bool)gdcm_read_JPEG_file (destination); // Reading Fragment pixels
+ } else {
+ res = (bool)gdcm_read_JPEG_file12 (destination);// Reading Fragment pixels
+ }
+
+ if (!res) break;
+
+ // FIXME : will work only when each fragment corresponds to a Frame :-(
+
+ destination = (char *)destination + taille * nBytes; // location in user's memory
+ // for next fragment (if any)
+ // TODO : find a suitable file (multifragment/single Frame Jpeg file) to check
+
+ 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(GetSwapCode()) {
+ ItemTagGr=SwapShort(ItemTagGr);
+ ItemTagEl=SwapShort(ItemTagEl);
+ }
+
+ //(char *) destination += taille * nBytes;
+ //cout << "destination" << destination << "\n";
+ }
+
+ return res;
+}
-
- void * Pixels = destination; // pour garder le code identique avec GetImageData
+/**
+ * \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.
+ * \ NULL if alloc fails
+ */
+void * gdcmFile::GetImageData (void) {
+ PixelData = (void *) malloc(lgrTotale);
+ if (PixelData)
+ GetImageDataIntoVector(PixelData, lgrTotale);
+ return(PixelData);
+}
- int nb, nbu, highBit, signe;
- string str_nbFrames, str_nb, str_nbu, str_highBit, str_signe;
-
- unsigned short int mask = 0xffff;
-
- // Longueur en Octets des Pixels a lire
- size_t _lgrTotale = GetImageDataSize(); // ne faudrait-il pas la stocker?
-
- // si lgrTotale < MaxSize ==> Gros pb
- // -> on résoud à la goret
-
- if ( _lgrTotale < MaxSize ) MaxSize = _lgrTotale;
+/**
+ * \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;
+ }
- GetPixels(MaxSize, destination);
+ (void)ReadPixelData(destination);
- // Nombre de Bits Alloues pour le stockage d'un Pixel
- str_nb=gdcmHeader::GetPubElValByNumber(0x0028,0x0100);
-
- if (str_nb == "gdcm::Unfound" ) {
- nb = 16;
- } else {
- nb = atoi(str_nb.c_str() );
- }
+ // 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() );
- }
+ // 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() );
- }
+ // 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) {
- int _sw = GetSwapCode();
+ str_signe=GetPubElValByNumber(0x0028,0x0103);
+ if (str_signe == GDCM_UNFOUND ) {
+ signe = 1;
+ } else {
+ signe = atoi(str_signe.c_str() );
+ }
- _Swap (destination, _sw, _lgrTotale, nb);
- }
-
- // On remet les Bits des Octets dans le bon ordre si besoin est
- //
- // ATTENTION : Jamais confronté a des pixels stockes sur 32 bits
- // avec moins de 32 bits utilises
- // et dont le bit de poids fort ne serait pas la ou on l'attend ...
- // --> ne marchera pas dans ce cas
- if (nbu!=nb){
- mask = mask >> (nb-nbu);
- int l=(int)MaxSize/(nb/8);
- unsigned short *deb = (unsigned short *)Pixels;
- for(int i=0;i<l;i++) {
- *deb = (*deb >> (nbu-highBit-1)) & mask;
- deb ++;
- }
- }
-
- // VOIR s'il ne faudrait pas l'affecter à un champ du dcmHeader
-
- return 1;
+ // re arange bytes inside the integer
+ if (nb != 8)
+ SwapZone(destination, GetSwapCode(), lgrTotale, nb);
+
+ // 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: wierd image");
+ return (size_t)0;
+ }
+ }
+
+ // Try to deal with the color
+ // --------------------------
+
+ string str_PhotometricInterpretation = gdcmHeader::GetPubElValByNumber(0x0028,0x0004);
+
+ if ( (str_PhotometricInterpretation == "MONOCHROME1 ")
+ || (str_PhotometricInterpretation == "MONOCHROME2 ")
+ || (str_PhotometricInterpretation == "RGB")) {
+ return lgrTotale;
+ }
+
+ switch ( GetPlanarConfiguration() ) {
+ case 0:
+ // Pixels are already RGB
+ break;
+
+ case 1:
+ // need to make RGB Pixels from Planes R,G,B
+ {
+ 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++);
+ }
+ memmove(destination,newDest,lgrTotale);
+ free(newDest);
+ // now, it's an RGB image
+ string spp = "3";
+ gdcmHeader::SetPubElValByNumber(spp,0x0028,0x0002);
+ string rgb="RGB";
+ gdcmHeader::SetPubElValByNumber(rgb,0x0028,0x0004);
+ break;
+ }
+
+ case 2:
+ // from Lut R + Lut G + Lut B
+
+ // we no longer use gdcmHeader::GetLUTRGB
+ // since a lot of images have wrong info
+ // in the Lookup Table Descriptors (0028,1101),...
+ {
+ unsigned char *lutR =(unsigned char *)GetPubElValVoidAreaByNumber(0x0028,0x1201);
+ unsigned char *lutG =(unsigned char *)GetPubElValVoidAreaByNumber(0x0028,0x1202);
+ unsigned char *lutB =(unsigned char *)GetPubElValVoidAreaByNumber(0x0028,0x1203);
+
+ if (lutR && lutG && lutB ) { // need to make RGB Pixels
+ // from grey Pixels
+ // and Lut R,Lut G,Lut B
+ unsigned char * newDest = (unsigned char*) malloc(lgrTotale);
+ int l = lgrTotale/3;
+ memmove(newDest, destination, l);// move Gray pixels to temp area
+
+ unsigned char * x = newDest;
+ unsigned char * a = (unsigned char *)destination;
+ int j;
+ for (int i=0;i<l; i++) {
+ j=newDest[i]*2; // Who can explain *why* we have to skip bytes
+ *a++ = lutR[j];
+ *a++ = lutG[j];
+ *a++ = lutB[j];
+ }
+ free(newDest);
+
+ // now, it's an RGB image
+ string spp = "3";
+ gdcmHeader::SetPubElValByNumber(spp,0x0028,0x0002);
+ string rgb="RGB";
+ gdcmHeader::SetPubElValByNumber(rgb,0x0028,0x0004);
+
+ } else { // need to make RGB Pixels (?)
+ // from grey Pixels (?!)
+ // and Gray Lut (!?!)
+ unsigned char *lutGray =(unsigned char *)GetPubElValVoidAreaByNumber(0x0028,0x1200);
+ // Well . I'll wait till I find such an image
+ }
+ break;
+ }
+ }
+
+ return lgrTotale;
}
-
//
// Je laisse le code integral, au cas ça puisse etre reutilise ailleurs
//
-static void _Swap(void* im, int swap, int lgr, int nb) {
+/**
+ * \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
+ */
+
+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;
+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;
+ 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);
- }
+ default:
+ printf("valeur de SWAP (16 bits) not allowed : %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;
+ 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;
+ 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);
- }
+ default:
+ printf(" SWAP value (32 bits) not allowed : %d\n", swap);
+ }
return;
}
/**
* \ingroup gdcmFile
* \brief TODO JPR
- * \warning doit-etre etre publique ? FIXME JPR
+ * \warning doit-etre etre publique ?
+ * TODO : y a-t-il un inconvenient à fusioner ces 2 fonctions
*
- * @param Data TODO JPR
- * @param ExpectedSize TODO JPR
+ * @param inData
+ * @param ExpectedSize
*
- * @return TODO JPR
+ * @return integer acts as a boolean
*/
-int gdcmFile::SetImageData(void * Data, size_t ExpectedSize) {
-
- SetImageDataSize(ExpectedSize);
-
- Pixels = Data;
- lgrTotale = ExpectedSize;
-
- return(1);
+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
- *
- * @param ImageDataSize TODO JPR
+ * \brief Sets the Pixel Area size in the Header
+ * --> not-for-rats function
+ *
+ * \warning WARNING doit-etre etre publique ?
+ * TODO : y aurait il un inconvenient à fusionner ces 2 fonctions
*
+ * @param ImageDataSize new Pixel Area Size
+ * warning : nothing else is checked
*/
void gdcmFile::SetImageDataSize(size_t ImageDataSize) {
-
- string content1;
- string content2;
- char car[20];
-
- // suppose que le ElValue (0x7fe0, 0x0010) existe ...
-
- sprintf(car,"%d",ImageDataSize);
- content2=car;
- SetPubElValByNumber(content2, 0x7fe0, 0x0010);
-
- ImageDataSize+=8;
- sprintf(car,"%d",ImageDataSize);
- content1=car;
- SetPubElValByNumber(content1, 0x7fe0, 0x0000);
+ string content1;
+ char car[20];
+ // Assumes ElValue (0x7fe0, 0x0010) exists ...
+ sprintf(car,"%d",ImageDataSize);
+
+ gdcmElValue*a = GetElValueByNumber(0x7fe0, 0x0010);
+ a->SetLength(ImageDataSize);
+
+ ImageDataSize+=8;
+ sprintf(car,"%d",ImageDataSize);
+ content1=car;
+ SetPubElValByNumber(content1, 0x7fe0, 0x0000);
}
* \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
+ * (Equivalent a IdImaWriteRawFile)
*
- * @param nomFichier TODO JPR
- *
- * @return TODO JPR
+ * @param fileName
+ * @return
*/
-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 (Pixels,lgrTotale, 1, fp1);
- fclose (fp1);
- return(1);
+int gdcmFile::WriteRawData (string fileName) {
+ FILE * fp1;
+ fp1 = fopen(fileName.c_str(),"wb");
+ if (fp1 == NULL) {
+ printf("Echec ouverture (ecriture) Fichier [%s] \n",fileName.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
+ * (Equivalent a IdDcmWrite)
*
- * @return TODO JPR
+ * @param fileName
+ * @return int acts as a boolean
*/
-int gdcmFile::WriteDcmImplVR (string nomFichier) {
- return WriteBase(nomFichier, ImplicitVR);
+int gdcmFile::WriteDcmImplVR (string fileName) {
+ return WriteBase(fileName, ImplicitVR);
}
-int gdcmFile::WriteDcmImplVR (const char* nomFichier) {
- return WriteDcmImplVR (string (nomFichier));
+/////////////////////////////////////////////////////////////////
+/**
+ * \ingroup gdcmFile
+ * \brief
+ * @param fileName
+ * @return int acts as a boolean
+ */
+
+int gdcmFile::WriteDcmImplVR (const char* fileName) {
+ return WriteDcmImplVR (string (fileName));
}
/////////////////////////////////////////////////////////////////
/**
* \ingroup gdcmFile
- *
- * @param nomFichier TODO JPR
- *
- * @return TODO JPR
+ * \brief
+ * @param fileName
+ * @return int acts as a boolean
*/
-int gdcmFile::WriteDcmExplVR (string nomFichier) {
- return WriteBase(nomFichier, ExplicitVR);
+int gdcmFile::WriteDcmExplVR (string fileName) {
+ return WriteBase(fileName, ExplicitVR);
}
/////////////////////////////////////////////////////////////////
/**
* \ingroup gdcmFile
- * \brief Ecrit sur disque UNE image ACR-NEMA
+ * \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 ...
- * si un header DICOM est fourni en entree,
+ * \warning si un header DICOM est fourni en entree,
* les groupes < 0x0008 et les groupes impairs sont ignores)
- * Aucun test n'est fait sur l'"Endiannerie" du processeur.
+ * \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
+ * @param fileName
+ * @return int acts as a boolean
*/
-int gdcmFile::WriteAcr (string nomFichier) {
- return WriteBase(nomFichier, ACR);
+int gdcmFile::WriteAcr (string fileName) {
+ return WriteBase(fileName, ACR);
}
-int gdcmFile::WriteBase (string nomFichier, FileType type) {
+/////////////////////////////////////////////////////////////////
+/**
+ * \ingroup gdcmFile
+ *
+ * @param FileName
+ * @param type
+ *
+ * @return int acts as a boolean
+ */
+int gdcmFile::WriteBase (string FileName, FileType type) {
FILE * fp1;
- fp1 = fopen(nomFichier.c_str(),"wb");
+ fp1 = fopen(FileName.c_str(),"wb");
if (fp1 == NULL) {
- printf("Echec ouverture (ecriture) Fichier [%s] \n",nomFichier.c_str());
+ printf("Echec ouverture (ecriture) Fichier [%s] \n",FileName.c_str());
return (0);
}
if ( (type == ImplicitVR) || (type == ExplicitVR) ) {
char * filePreamble;
- // Ecriture Dicom File Preamble
+ // writing Dicom File Preamble
filePreamble=(char*)calloc(128,1);
fwrite(filePreamble,128,1,fp1);
fwrite("DICM",4,1,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 ...
+
+ std::string rows, columns;
+ if ( filetype == ACR_LIBIDO){
+ rows = GetPubElValByNumber(0x0028, 0x0010);
+ columns = GetPubElValByNumber(0x0028, 0x0011);
+ SetPubElValByNumber(columns, 0x0028, 0x0010);
+ SetPubElValByNumber(rows , 0x0028, 0x0011);
+ }
+ // ----------------- End of Special Patch ----------------
+
gdcmHeader::Write(fp1, type);
- fwrite(Pixels, lgrTotale, 1, fp1);
+
+ // --------------------------------------------------------------
+ // 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 (filetype == ACR_LIBIDO){
+ SetPubElValByNumber(rows , 0x0028, 0x0010);
+ SetPubElValByNumber(columns, 0x0028, 0x0011);
+ }
+ // ----------------- End of Special Patch ----------------
+
+ fwrite(PixelData, lgrTotale, 1, fp1);
fclose (fp1);
return(1);
}