// gdcmFile.cxx
-#include "gdcm.h"
-
-static void _Swap(void* im, int swap, int lgr, int nb);
+//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
+
+#define str2num(str, typeNum) *((typeNum *)(str))
/////////////////////////////////////////////////////////////////
/**
* \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).
+ * 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
+ * @param filename file to be opened for parsing
*
* @return
*/
-gdcmFile::gdcmFile(string & filename)
- :gdcmHeader(filename.c_str())
+gdcmFile::gdcmFile(std::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
- * \ 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).
- *
- * @param void Rien en entree
+ * \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;
+ std::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();
+
+ std::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 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) {
- int nbLignes, nbCol, nbFrames, nb;
- string str_nbFrames, str_nb;
- // Nombre de Lignes
- nbLignes=atoi(gdcmHeader::GetPubElValByNumber(0x0028,0x0010).c_str());
- // Nombre de Colonnes
- nbCol =atoi(gdcmHeader::GetPubElValByNumber(0x0028,0x0011).c_str());
-
- // Nombre de Frames
- str_nbFrames=gdcmHeader::GetPubElValByNumber(0x0028,0x0008);
-
- if (str_nbFrames == "UNFOUND" ) {
- nbFrames = 1;
- } else {
- nbFrames = atoi(str_nbFrames.c_str() );
- }
-
- // Nombre de Bits Alloues pour le stockage d'un Pixel
- str_nb=gdcmHeader::GetPubElValByNumber(0x0028,0x0100);
-
- if (str_nb == "UNFOUND" ) {
- nb = 16;
- } else {
- nb = atoi(str_nb.c_str() );
- }
+ return (lgrTotale);
+}
- size_t lgrTotale = nbFrames*nbLignes*nbCol*(nb/8);
- return (lgrTotale);
+/////////////////////////////////////////////////////////////////
+/**
+ * \ingroup gdcmFile
+ * \brief Parse pixel data from disk and *prints* the result
+ * \ For multi-fragment Jpeg/Rle 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, page 85)
+ *
+ */
+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/RLE File\n");
+ return 0;
+ }
+
+ int nb;
+ std::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");
+
+ guint16 ItemTagGr,ItemTagEl;
+ int ln;
+ long ftellRes;
+ char * destination = NULL;
+
+ // ------------------------------- for Parsing : Position on begining of Jpeg/RLE Pixels
+
+ if( !IsRLELossLessTransferSyntax()) {
+
+ // JPEG Image
+
+ cout << "JPEG image" << std::endl;
+ 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 );
+ }
+
+ } else {
+
+ // RLE Image
+
+ cout << "RLE image" << std::endl;
+ long RleSegmentLength[15],fragmentLength;
+ guint32 nbRleSegments;
+ guint32 RleSegmentOffsetTable[15];
+ ftellRes=ftell(fp);
+ // Basic Offset Table with Item Value
+ // Item Tag
+ 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 );
+ // Item Length
+ 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 'Sequence Delimiter Item' (fffe,e0dd) not found
+ while ( ( ItemTagGr == 0xfffe) && (ItemTagEl != 0xe0dd) ) {
+ // Parse fragments of the current Fragment (Frame)
+ ftellRes=ftell(fp);
+ fread(&fragmentLength,4,1,fp);
+ if(GetSwapCode())
+ fragmentLength=SwapLong(fragmentLength); // length
+ printf(" at %x : 'fragment' length %d x(%08x)\n",
+ ftellRes, fragmentLength,fragmentLength);
+
+// destination += taille * nBytes; // location in user's memory
+// printf (" Destination will be x(%x) = %d \n",
+// destination,destination );
+
+ //------------------ scanning (not reading) fragment pixels
+
+ fread(&nbRleSegments,4,1,fp); // Reading : Number of RLE Segments
+ if(GetSwapCode())
+ nbRleSegments=SwapLong(nbRleSegments);
+ printf(" Nb of RLE Segments : %d\n",nbRleSegments);
+
+ for(int k=1; k<=15; k++) { // Reading RLE Segments Offset Table
+ ftellRes=ftell(fp);
+ fread(&RleSegmentOffsetTable[k],4,1,fp);
+ if(GetSwapCode())
+ RleSegmentOffsetTable[k]=SwapLong(RleSegmentOffsetTable[k]);
+ printf(" at : %x Offset Segment %d : %d (%x)\n",
+ ftellRes,k,RleSegmentOffsetTable[k],RleSegmentOffsetTable[k]);
+ }
+ if (nbRleSegments>1) {
+ for(int k=1; k<=nbRleSegments-1; k++) { // skipping (not reading) RLE Segments
+ RleSegmentLength[k]=RleSegmentOffsetTable[k+1]-RleSegmentOffsetTable[k];
+ ftellRes=ftell(fp);
+ printf (" Segment %d : Length = %d Start at %x\n",
+ k,RleSegmentLength[k], ftellRes);
+ fseek(fp,RleSegmentLength[k],SEEK_CUR);
+ }
+ }
+ RleSegmentLength[nbRleSegments] = fragmentLength - RleSegmentOffsetTable[nbRleSegments] ;
+ // TODO : Check the value
+ ftellRes=ftell(fp);
+ printf (" Segment %d : Length = %d Start at %x\n",
+ nbRleSegments,RleSegmentLength[nbRleSegments],ftellRes);
+
+ fseek(fp,RleSegmentLength[nbRleSegments],SEEK_CUR);
+
+ // ------------------ end of scanning 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 amene en mémoire les Pixels d'une image NON COMPRESSEE
- * \Aucun test n'est fait pour le moment sur le caractere compresse ou non de l'image
- *
- * @param rien
+ * \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 Pointeur sur la zone mémoire contenant les Pixels lus
*/
+bool gdcmFile::ReadPixelData(void* destination) {
-void * gdcmFile::GetImageData (void) {
-
- char* Pixels;
- int nbLignes, nbCol;
+ if ( !OpenFile())
+ return false;
+
+ if ( fseek(fp, GetPixelOffset(), SEEK_SET) == -1 ) {
+ CloseFile();
+ return false;
+ }
- int nbFrames, nb, nbu, highBit, signe;
- string str_nbFrames, str_nb, str_nbu, str_highBit, str_signe;
-
- unsigned short int mask = 0xffff;
-
- // Nombre de Lignes
- nbLignes=atoi(GetPubElValByNumber(0x0028,0x0010).c_str());
- // Nombre de Colonnes
- nbCol =atoi(GetPubElValByNumber(0x0028,0x0011).c_str());
+// ------------------------- 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;
+ }
+ }
+
+ // ------------------------ Compressed File .
+
+ int nb;
+ std::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;
+ }
+
+ // ------------------------------- RLE
- // Nombre de Frames
- str_nbFrames=GetPubElValByNumber(0x0028,0x0008);
+ if (gdcmHeader::IsRLELossLessTransferSyntax()) {
+ int res = (bool)gdcm_read_RLE_file (destination);
+ return res;
+ }
-
- if (str_nbFrames == "UNFOUND" ) {
- nbFrames = 1;
- } else {
- nbFrames = atoi(str_nbFrames.c_str() );
- }
-
- // Nombre de Bits Alloues
- str_nb=GetPubElValByNumber(0x0028,0x0100);
-
- if (str_nb == "UNFOUND" ) {
- nb = 16;
- } else {
- nb = atoi(str_nb.c_str() );
- }
-
- // Nombre de Bits Utilises
- str_nbu=GetPubElValByNumber(0x0028,0x0101);
-
- if (str_nbu == "UNFOUND" ) {
- nbu = nb;
- } else {
- nbu = atoi(str_nbu.c_str() );
- }
-
- // Position du Bit de Poids Fort
- str_highBit=GetPubElValByNumber(0x0028,0x0102);
-
- if (str_highBit == "UNFOUND" ) {
- highBit = nb - 1;
- } else {
- highBit = atoi(str_highBit.c_str() );
- }
-
- // Signe des Pixels
- str_signe=GetPubElValByNumber(0x0028,0x0103);
+ // ------------------------------- JPEG Lossy : call to IJG 6b
+
+ long fragmentBegining; // for ftell, fseek
+ 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 (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 << std::endl;
+ }
+
+ return res;
+}
- if (str_signe == "UNFOUND" ) {
- signe = 1;
- } else {
- signe = atoi(str_signe.c_str() );
- }
-
- // Longueur en Octets des Pixels a lire
- size_t lgrTotale = nbFrames*nbLignes*nbCol*(nb/8);
-
- //Pixels = (char *) g_malloc(lgrTotale);
- Pixels = (char *) malloc(lgrTotale);
-
- GetPixels(lgrTotale, Pixels);
+/**
+ * \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);
+}
- // On remet les Octets dans le bon ordre si besoin est
- if (nb != 8) {
- int _sw = GetSwapCode();
+/**
+ * \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.
+ */
- _Swap (Pixels, _sw, lgrTotale, nb); // A REMETTRE
- }
+size_t gdcmFile::GetImageDataIntoVector (void* destination, size_t MaxSize) {
+
+ int nb, nbu, highBit, signe;
+ std::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;
+ }
- // 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)lgrTotale/(nb/8);
- unsigned short *deb = (unsigned short *)Pixels;
- for(int i=0;i<l;i++) {
- *deb = (*deb >> (nbu-highBit-1)) & mask;
- deb ++;
- }
- }
-
- printf ("on est sorti\n");
+ (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() );
+ }
- // VOIR s'il ne faudrait pas l'affecter à un champ du dcmHeader
+ // Nombre de Bits Utilises
+ str_nbu=GetPubElValByNumber(0x0028,0x0101);
+ if (str_nbu == GDCM_UNFOUND ) {
+ nbu = nb;
+ } else {
+ nbu = atoi(str_nbu.c_str() );
+ }
- return (Pixels);
+ // 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() );
+ }
+
+ // 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
+ // --------------------------
+
+ std::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
+ std::string spp = "3";
+ gdcmHeader::SetPubElValByNumber(spp,0x0028,0x0002);
+ std::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
+ std::string spp = "3";
+ gdcmHeader::SetPubElValByNumber(spp,0x0028,0x0002);
+ std::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 ?
+ * TODO : y a-t-il un inconvenient à fusioner ces 2 fonctions
+ *
+ * @param inData
+ * @param ExpectedSize
+ *
+ * @return integer acts as a boolean
+ */
+int gdcmFile::SetImageData(void * inData, size_t ExpectedSize) {
+ SetImageDataSize(ExpectedSize);
+ PixelData = inData;
+ lgrTotale = ExpectedSize;
+ return(1);
+}
+
+
+/////////////////////////////////////////////////////////////////
+/**
+ * \ingroup gdcmFile
+ * \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) {
+ std::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);
+}
+
+/////////////////////////////////////////////////////////////////
+/**
+ * \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)
+ *
+ * @param fileName
+ * @return
+ */
+
+int gdcmFile::WriteRawData (std::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)
+ *
+ * @param fileName
+ * @return int acts as a boolean
+ */
+
+int gdcmFile::WriteDcmImplVR (std::string fileName) {
+ return WriteBase(fileName, ImplicitVR);
+}
+
+/////////////////////////////////////////////////////////////////
+/**
+ * \ingroup gdcmFile
+ * \brief
+ * @param fileName
+ * @return int acts as a boolean
+ */
+
+int gdcmFile::WriteDcmImplVR (const char* fileName) {
+ return WriteDcmImplVR (std::string (fileName));
+}
+
+/////////////////////////////////////////////////////////////////
+/**
+ * \ingroup gdcmFile
+ * \brief
+ * @param fileName
+ * @return int acts as a boolean
+ */
+
+int gdcmFile::WriteDcmExplVR (std::string fileName) {
+ return WriteBase(fileName, 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 fileName
+ * @return int acts as a boolean
+ */
+
+int gdcmFile::WriteAcr (std::string fileName) {
+ return WriteBase(fileName, ACR);
+}
+
+/////////////////////////////////////////////////////////////////
+/**
+ * \ingroup gdcmFile
+ *
+ * @param FileName
+ * @param type
+ *
+ * @return int acts as a boolean
+ */
+int gdcmFile::WriteBase (std::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;
+ // 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);
+
+ // --------------------------------------------------------------
+ // 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);
+}
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff