5 #include "iddcmjpeg.h" // for the 'LibIDO' Jpeg LossLess
7 /////////////////////////////////////////////////////////////////
10 * \brief Constructor dedicated to writing a new DICOMV3 part10 compliant
11 * file (see SetFileName, SetDcmTag and Write)
12 * Opens (in read only and when possible) an existing file and checks
13 * for DICOM compliance. Returns NULL on failure.
14 * \Note the in-memory representation of all available tags found in
15 * the DICOM header is post-poned to first header information access.
16 * This avoid a double parsing of public part of the header when
17 * one sets an a posteriori shadow dictionary (efficiency can be
18 * seen as a side effect).
20 * @param filename file to be opened for parsing
25 gdcmFile::gdcmFile(std::string & filename)
26 :gdcmHeader(filename.c_str())
28 SetPixelDataSizeFromHeader();
31 gdcmFile::gdcmFile(const char * filename)
34 SetPixelDataSizeFromHeader();
39 * \brief calcule la longueur (in bytes) A ALLOUER pour recevoir les
41 * ou DES images dans le cas d'un multiframe
42 * ATTENTION : il ne s'agit PAS de la longueur du groupe des Pixels
43 * (dans le cas d'images compressees, elle n'a pas de sens).
45 * @return longueur a allouer
47 void gdcmFile::SetPixelDataSizeFromHeader(void) {
51 str_nb=gdcmHeader::GetPubElValByNumber(0x0028,0x0100);
52 if (str_nb == GDCM_UNFOUND ) {
55 nb = atoi(str_nb.c_str() );
58 lgrTotale = GetXSize() * GetYSize() * GetZSize() * (nb/8)* GetSamplesPerPixel();
59 std::string str_PhotometricInterpretation = gdcmHeader::GetPubElValByNumber(0x0028,0x0004);
60 if ( str_PhotometricInterpretation == "PALETTE COLOR " ) {
64 // see PS 3.3-2003 : C.7.6.3.2.1
74 // YBR_FULL_422 (no LUT, no Palette)
80 // ex : gdcm-US-ALOKA-16.dcm
81 // 0028|1221 [OW] [Segmented Red Palette Color Lookup Table Data]
82 // 0028|1222 [OW] [Segmented Green Palette Color Lookup Table Data]
83 // 0028|1223 [OW] [Segmented Blue Palette Color Lookup Table Data]
85 // ex : US-PAL-8-10x-echo.dcm, 8BitsRunLengthColor.dcm
86 // 0028|1201 [OW] [Red Palette Color Lookup Table Data]
87 // 0028|1202 [OW] [Green Palette Color Lookup Table Data]
88 // 0028|1203 [OW] [Blue Palette Color Lookup Table Data]
90 // ex : OT-PAL-8-face.dcm
91 // 0028|1201 [US] [Red Palette Color Lookup Table Data]
92 // 0028|1202 [US] [Green Palette Color Lookup Table Data]
93 // 0028|1203 [US] [Blue Palette Color Lookup Table Data]
96 /////////////////////////////////////////////////////////////////
99 * \brief Returns the size (in bytes) of required memory to hold
100 * the pixel data represented in this file.
101 * @return The size of pixel data in bytes.
104 size_t gdcmFile::GetImageDataSize(void) {
109 /////////////////////////////////////////////////////////////////
112 * \brief Read pixel data from disk (optionaly decompressing) into the
113 * caller specified memory location.
114 * @param destination where the pixel data should be stored.
117 bool gdcmFile::ReadPixelData(void* destination) {
122 if ( fseek(fp, GetPixelOffset(), SEEK_SET) == -1 ) {
127 // ------------------------- Uncompressed File
130 IsImplicitVRLittleEndianTransferSyntax() ||
131 IsExplicitVRLittleEndianTransferSyntax() ||
132 IsExplicitVRBigEndianTransferSyntax() ||
133 IsDeflatedExplicitVRLittleEndianTransferSyntax() ) {
135 size_t ItemRead = fread(destination, lgrTotale, 1, fp);
136 if ( ItemRead != 1 ) {
145 // ------------------------ Compressed File .
148 std::string str_nb=gdcmHeader::GetPubElValByNumber(0x0028,0x0100);
149 if (str_nb == GDCM_UNFOUND ) {
152 nb = atoi(str_nb.c_str() );
153 if (nb == 12) nb =16;
157 int taille = GetXSize() * GetYSize() * GetSamplesPerPixel();
160 // ------------------------------- JPEG LossLess : call to Jpeg Libido
162 if (IsJPEGLossless() && GetZSize() == 1) {
164 int ln; // Position on begining of Jpeg Pixels
165 fseek(fp,4,SEEK_CUR); // skipping (fffe,e000) : Basic Offset Table Item
168 ln=SwapLong(ln); // Item length
169 fseek(fp,ln,SEEK_CUR); // skipping Basic Offset Table ('ln' bytes)
170 fseek(fp,4,SEEK_CUR); // skipping (fffe,e000) : First fragment Item Tag
171 fread(&ln,4,1,fp); // First fragment length (just to know)
175 ClbJpeg* jpg = _IdDcmJpegRead(fp); // TODO : find a 'full' one.
176 // (We use the LibIDO one :-(
181 int * dataJpg = jpg->DataImg;
186 unsigned short *dest = (unsigned short *)destination;
187 for (int i=0; i<taille; i++) {
188 *((unsigned char *)dest+i) = *(dataJpg +i);
195 unsigned short *dest = (unsigned short *)destination;
196 for (int i=0; i<taille; i++) {
197 *((unsigned short *)dest+i) = *(dataJpg +i);
202 _IdDcmJpegFree (jpg);
206 // ------------------------------- RLE
208 if (gdcmHeader::IsRLELossLessTransferSyntax()) {
209 int res = (bool)gdcm_read_RLE_file (destination);
213 // ------------------------------- Multiframe JPEG
215 long fragmentBegining; // for ftell, fseek
216 bool b = gdcmHeader::IsJPEG2000();
219 guint16 ItemTagGr,ItemTagEl;
220 int ln; // Position on begining of Jpeg Pixels
222 fread(&ItemTagGr,2,1,fp); // Reading (fffe) : Item Tag Gr
223 fread(&ItemTagEl,2,1,fp); // Reading (e000) : Item Tag El
225 ItemTagGr=SwapShort(ItemTagGr);
226 ItemTagEl=SwapShort(ItemTagEl);
230 ln=SwapLong(ln); // Basic Offset Table Item length
233 // What is it used for ?!?
234 char *BasicOffsetTableItemValue = (char *)malloc(ln+1);
235 fread(BasicOffsetTableItemValue,ln,1,fp);
238 // first Fragment initialisation
239 fread(&ItemTagGr,2,1,fp); // Reading (fffe) : Item Tag Gr
240 fread(&ItemTagEl,2,1,fp); // Reading (e000) : Item Tag El
242 ItemTagGr=SwapShort(ItemTagGr);
243 ItemTagEl=SwapShort(ItemTagEl);
246 // parsing fragments until Sequence Delim. Tag found
247 //unsigned short *dest = (unsigned short *)destination;
249 while ( ( ItemTagGr == 0xfffe) && (ItemTagEl != 0xe0dd) ) {
252 ln=SwapLong(ln); // Fragment Item length
254 // FIXME : multi fragments
255 fragmentBegining=ftell(fp);
258 res = (bool)gdcm_read_JPEG2000_file (destination); // Not Yet written
260 else if (IsJPEGLossless()) { // JPEG LossLess : call to LibIDO Jpeg
262 // ------------- for each Fragment
264 // Warning : Works only if there is one fragment per frame
265 // (Or a single fragment for the multiframe file)
266 ClbJpeg* jpg = _IdDcmJpegRead(fp); // TODO : find a 'full' one.
267 // (We use the LibIDO one :-(
272 int * dataJpg = jpg->DataImg;
273 unsigned short *dest = (unsigned short *)destination;
277 for (int i=0; i<taille; i++) {
278 *((unsigned char *)dest+i) = *(dataJpg +i);
285 for (int i=0; i<taille; i++) {
286 *((unsigned short *)dest+i) = *(dataJpg +i);
291 _IdDcmJpegFree (jpg);
293 res=1; // in order not to break the loop
295 } // ------------------------------------- endif (IsJPEGLossless())
297 else // JPEG Lossy : call to IJG 6b
298 if (GetBitsStored() == 8) {
299 res = (bool)gdcm_read_JPEG_file (destination); // Reading Fragment pixels
301 res = (bool)gdcm_read_JPEG_file12 (destination);// Reading Fragment pixels
306 destination = (char *)destination + taille * nBytes; // location in user's memory
307 // for next fragment (if any)
309 fseek(fp,fragmentBegining,SEEK_SET); // To be sure we start
310 fseek(fp,ln,SEEK_CUR); // at the begining of next fragment
312 ItemTagGr = ItemTagEl =0;
313 fread(&ItemTagGr,2,1,fp); // Reading (fffe) : Item Tag Gr
314 fread(&ItemTagEl,2,1,fp); // Reading (e000) : Item Tag El
316 ItemTagGr=SwapShort(ItemTagGr);
317 ItemTagEl=SwapShort(ItemTagEl);
320 } // endWhile parsing fragments until Sequence Delim. Tag found
327 * \brief Allocates necessary memory, copies the pixel data
328 * (image[s]/volume[s]) to newly allocated zone.
329 * @return Pointer to newly allocated pixel data.
330 * \ NULL if alloc fails
332 void * gdcmFile::GetImageData (void) {
333 PixelData = (void *) malloc(lgrTotale);
335 GetImageDataIntoVector(PixelData, lgrTotale);
341 * \brief Copies at most MaxSize bytes of pixel data to caller's
343 * @param destination Address (in caller's memory space) at which the
344 * pixel data should be copied
345 * @param MaxSize Maximum number of bytes to be copied. When MaxSize
346 * is not sufficient to hold the pixel data the copy is not
347 * executed (i.e. no partial copy).
348 * @return On success, the number of bytes actually copied. Zero on
349 * failure e.g. MaxSize is lower than necessary.
352 size_t gdcmFile::GetImageDataIntoVector (void* destination, size_t MaxSize) {
354 int nb, nbu, highBit, signe;
355 std::string str_nbFrames, str_nb, str_nbu, str_highBit, str_signe;
357 if ( lgrTotale > MaxSize ) {
358 dbg.Verbose(0, "gdcmFile::GetImageDataIntoVector: pixel data bigger"
359 "than caller's expected MaxSize");
363 (void)ReadPixelData(destination);
365 // Nombre de Bits Alloues pour le stockage d'un Pixel
366 str_nb = GetPubElValByNumber(0x0028,0x0100);
367 if (str_nb == GDCM_UNFOUND ) {
370 nb = atoi(str_nb.c_str() );
373 // Nombre de Bits Utilises
374 str_nbu=GetPubElValByNumber(0x0028,0x0101);
375 if (str_nbu == GDCM_UNFOUND ) {
378 nbu = atoi(str_nbu.c_str() );
381 // Position du Bit de Poids Fort
382 str_highBit=GetPubElValByNumber(0x0028,0x0102);
383 if (str_highBit == GDCM_UNFOUND ) {
386 highBit = atoi(str_highBit.c_str() );
390 str_signe=GetPubElValByNumber(0x0028,0x0103);
391 if (str_signe == GDCM_UNFOUND ) {
394 signe = atoi(str_signe.c_str() );
397 // re arange bytes inside the integer
399 SwapZone(destination, GetSwapCode(), lgrTotale, nb);
401 // re arange bits inside the bytes
403 int l = (int)lgrTotale / (nb/8);
405 guint16 mask = 0xffff;
406 mask = mask >> (nb-nbu);
407 guint16 *deb = (guint16 *)destination;
408 for(int i = 0; i<l; i++) {
409 *deb = (*deb >> (nbu-highBit-1)) & mask;
412 } else if (nb == 32 ) {
413 guint32 mask = 0xffffffff;
414 mask = mask >> (nb-nbu);
415 guint32 *deb = (guint32 *)destination;
416 for(int i = 0; i<l; i++) {
417 *deb = (*deb >> (nbu-highBit-1)) & mask;
421 dbg.Verbose(0, "gdcmFile::GetImageDataIntoVector: wierd image");
426 // Just to 'see' was was actually read on disk :-(
427 // Some troubles expected
429 // *Try* to deal with the color
430 // ----------------------------
432 // Planar configuration = 0 : Pixels are already RGB
433 // Planar configuration = 1 : 3 planes : R, G, B
434 // Planar configuration = 2 : 1 gray Plane + 3 LUT
436 // Well ... supposed to be !
437 // See US-PAL-8-10x-echo.dcm: PlanarConfiguration=0,PhotometricInterpretation=PALETTE COLOR
438 // and heuristic has to be found :-(
440 std::string str_PhotometricInterpretation = gdcmHeader::GetPubElValByNumber(0x0028,0x0004);
442 if ( (str_PhotometricInterpretation == "MONOCHROME1 ")
443 || (str_PhotometricInterpretation == "MONOCHROME2 ")
444 || (str_PhotometricInterpretation == "RGB")) {
447 int planConf=GetPlanarConfiguration();
449 // Whatever Planar Configuration is, "PALETTE COLOR " implies that we deal with the palette.
450 if (str_PhotometricInterpretation == "PALETTE COLOR ")
455 // Pixels are already RGB
461 if (str_PhotometricInterpretation == "YBR_FULL") { // Warning : YBR_FULL_422 acts as RGB (?!)
463 // need to make RGB Pixels from Planes Y,cB,cR
464 // see http://lestourtereaux.free.fr/papers/data/yuvrgb.pdf
465 // for code optimisation
467 int l = GetXSize()*GetYSize();
468 int nbFrames = GetZSize();
470 unsigned char * newDest = (unsigned char*) malloc(lgrTotale);
471 unsigned char *x = newDest;
472 unsigned char * a = (unsigned char *)destination;
473 unsigned char * b = a + l;
474 unsigned char * c = b + l;
478 // TODO : Replace by the 'well known'
479 // integer computation counterpart
480 for (int i=0;i<nbFrames;i++) {
481 for (int j=0;j<l; j++) {
482 R= 1.164 *( *a-16) + 1.596 *( *c -128) + 0.5;
483 G= 1.164 *( *a-16) - 0.813 *( *c -128) - 0.392 *(*b -128) + 0.5;
484 B= 1.164 *( *a-16) + 2.017 *( *b -128) + 0.5;
489 if (R>255.0) R=255.0;
490 if (G>255.0) G=255.0;
491 if (B>255.0) B=255.0;
493 *(x++) = (unsigned char)R;
494 *(x++) = (unsigned char)G;
495 *(x++) = (unsigned char)B;
499 memmove(destination,newDest,lgrTotale);
504 // need to make RGB Pixels from Planes R,G,B
506 int l = GetXSize()*GetYSize();
507 int nbFrames = GetZSize();
509 char * newDest = (char*) malloc(lgrTotale);
511 char * a = (char *)destination;
516 // any trick not to have to allocate temporary buffer is welcome ...
518 for (int i=0;i<nbFrames;i++) {
519 for (int j=0;j<l; j++) {
525 memmove(destination,newDest,lgrTotale);
529 // now, it's an RGB image
530 // Lets's write it in the Header
531 std::string spp = "3";
532 gdcmHeader::SetPubElValByNumber(spp,0x0028,0x0002);
533 std::string rgb="RGB";
534 gdcmHeader::SetPubElValByNumber(rgb,0x0028,0x0004);
539 // from Lut R + Lut G + Lut B
541 // we no longer use gdcmHeader::GetLUTRGB
542 // since a lot of images have strange info
543 // in the Lookup Table Descriptors (0028,1101),...
545 unsigned char * newDest = (unsigned char*) malloc(lgrTotale);
546 unsigned char * a = (unsigned char *)destination;
548 unsigned char *lutR =(unsigned char *)GetPubElValVoidAreaByNumber(0x0028,0x1201);
549 unsigned char *lutG =(unsigned char *)GetPubElValVoidAreaByNumber(0x0028,0x1202);
550 unsigned char *lutB =(unsigned char *)GetPubElValVoidAreaByNumber(0x0028,0x1203);
552 if (lutR && lutG && lutB ) { // need to make RGB Pixels
554 // and Lut R,Lut G,Lut B
556 unsigned char * newDest = (unsigned char*) malloc(lgrTotale);
558 memmove(newDest, destination, l);// move Gray pixels to temp area
560 unsigned char * x = newDest;
563 // See PS 3.3-2003 C.11.1.1.2 p 619
566 if ( GetLUTNbits()==16 && nb==8) mult=2; // See PS 3.3
569 // if we get a black image, let's just remove the '+1'
571 // if it works, we shall have to check the 3 Palettes
572 // to see which byte is ==0 (first one, on second one)
574 for (int i=0;i<l; i++) {
575 j=newDest[i]*mult +1;
583 // now, it's an RGB image
584 std::string spp = "3";
585 gdcmHeader::SetPubElValByNumber(spp,0x0028,0x0002);
586 std::string rgb="RGB";
587 gdcmHeader::SetPubElValByNumber(rgb,0x0028,0x0004);
589 } else { // need to make RGB Pixels (?)
590 // from grey Pixels (?!)
591 // and Gray Lut (!?!)
592 unsigned char *lutGray =(unsigned char *)GetPubElValVoidAreaByNumber(0x0028,0x1200);
593 // Well . I'll wait till I find such an image
603 // Je laisse le code integral, au cas ça puisse etre reutilise ailleurs
608 * \brief Swap the bytes, according to swap code.
609 * \warning not end user intended
610 * @param im area to deal with
611 * @param swap swap code
612 * @param lgr Area Length
613 * @param nb Pixels Bit number
616 void gdcmFile::SwapZone(void* im, int swap, int lgr, int nb) {
634 ((unsigned short int*)im)[i]= ((((unsigned short int*)im)[i])>>8)
635 | ((((unsigned short int*)im)[i])<<8);
639 printf("valeur de SWAP (16 bits) not allowed : %d\n", swap);
650 faible= ((unsigned long int*)im)[i]&0x0000ffff; /* 4321 */
651 fort =((unsigned long int*)im)[i]>>16;
652 fort= (fort>>8) | (fort<<8);
653 faible=(faible>>8) | (faible<<8);
655 ((unsigned long int*)im)[i]=(s32<<16)|fort;
661 faible= ((unsigned long int*)im)[i]&0x0000ffff; /* 2143 */
662 fort=((unsigned long int*)im)[i]>>16;
663 fort= (fort>>8) | (fort<<8);
664 faible=(faible>>8) | (faible<<8);
666 ((unsigned long int*)im)[i]=(s32<<16)|faible;
672 faible= ((unsigned long int*)im)[i]&0x0000ffff; /* 3412 */
673 fort=((unsigned long int*)im)[i]>>16;
675 ((unsigned long int*)im)[i]=(s32<<16)|fort;
680 printf(" SWAP value (32 bits) not allowed : %d\n", swap);
685 /////////////////////////////////////////////////////////////////
689 * \warning doit-etre etre publique ?
690 * TODO : y a-t-il un inconvenient à fusioner ces 2 fonctions
693 * @param ExpectedSize
695 * @return integer acts as a boolean
697 int gdcmFile::SetImageData(void * inData, size_t ExpectedSize) {
698 SetImageDataSize(ExpectedSize);
700 lgrTotale = ExpectedSize;
705 /////////////////////////////////////////////////////////////////
708 * \brief Sets the Pixel Area size in the Header
709 * --> not-for-rats function
711 * \warning WARNING doit-etre etre publique ?
712 * TODO : y aurait il un inconvenient à fusionner ces 2 fonctions
714 * @param ImageDataSize new Pixel Area Size
715 * warning : nothing else is checked
718 void gdcmFile::SetImageDataSize(size_t ImageDataSize) {
719 std::string content1;
721 // Assumes ElValue (0x7fe0, 0x0010) exists ...
722 sprintf(car,"%d",ImageDataSize);
724 gdcmElValue*a = GetElValueByNumber(0x7fe0, 0x0010);
725 a->SetLength(ImageDataSize);
728 sprintf(car,"%d",ImageDataSize);
730 SetPubElValByNumber(content1, 0x7fe0, 0x0000);
734 /////////////////////////////////////////////////////////////////
737 * \brief Ecrit sur disque les pixels d'UNE image
738 * Aucun test n'est fait sur l'"Endiannerie" du processeur.
739 * Ca sera à l'utilisateur d'appeler son Reader correctement
740 * (Equivalent a IdImaWriteRawFile)
746 int gdcmFile::WriteRawData (std::string fileName) {
748 fp1 = fopen(fileName.c_str(),"wb");
750 printf("Echec ouverture (ecriture) Fichier [%s] \n",fileName.c_str());
753 fwrite (PixelData,lgrTotale, 1, fp1);
758 /////////////////////////////////////////////////////////////////
761 * \brief Ecrit sur disque UNE image Dicom
762 * Aucun test n'est fait sur l'"Endiannerie" du processeur.
763 * Ca fonctionnera correctement (?) sur processeur Intel
764 * (Equivalent a IdDcmWrite)
767 * @return int acts as a boolean
770 int gdcmFile::WriteDcmImplVR (std::string fileName) {
771 return WriteBase(fileName, ImplicitVR);
774 /////////////////////////////////////////////////////////////////
779 * @return int acts as a boolean
782 int gdcmFile::WriteDcmImplVR (const char* fileName) {
783 return WriteDcmImplVR (std::string (fileName));
786 /////////////////////////////////////////////////////////////////
791 * @return int acts as a boolean
794 int gdcmFile::WriteDcmExplVR (std::string fileName) {
795 return WriteBase(fileName, ExplicitVR);
798 /////////////////////////////////////////////////////////////////
801 * \brief Ecrit au format ACR-NEMA sur disque l'entete et les pixels
802 * (a l'attention des logiciels cliniques
803 * qui ne prennent en entrée QUE des images ACR ...
804 * \warning si un header DICOM est fourni en entree,
805 * les groupes < 0x0008 et les groupes impairs sont ignores)
806 * \warning Aucun test n'est fait sur l'"Endiannerie" du processeur.
807 * Ca fonctionnera correctement (?) sur processeur Intel
808 * (Equivalent a IdDcmWrite)
811 * @return int acts as a boolean
814 int gdcmFile::WriteAcr (std::string fileName) {
815 return WriteBase(fileName, ACR);
818 /////////////////////////////////////////////////////////////////
825 * @return int acts as a boolean
827 int gdcmFile::WriteBase (std::string FileName, FileType type) {
830 fp1 = fopen(FileName.c_str(),"wb");
832 printf("Echec ouverture (ecriture) Fichier [%s] \n",FileName.c_str());
836 if ( (type == ImplicitVR) || (type == ExplicitVR) ) {
838 // writing Dicom File Preamble
839 filePreamble=(char*)calloc(128,1);
840 fwrite(filePreamble,128,1,fp1);
841 fwrite("DICM",4,1,fp1);
844 // --------------------------------------------------------------
845 // Special Patch to allow gdcm to re-write ACR-LibIDO formated images
847 // if recognition code tells us we dealt with a LibIDO image
848 // we reproduce on disk the switch between lineNumber and columnNumber
849 // just before writting ...
851 std::string rows, columns;
852 if ( filetype == ACR_LIBIDO){
853 rows = GetPubElValByNumber(0x0028, 0x0010);
854 columns = GetPubElValByNumber(0x0028, 0x0011);
855 SetPubElValByNumber(columns, 0x0028, 0x0010);
856 SetPubElValByNumber(rows , 0x0028, 0x0011);
858 // ----------------- End of Special Patch ----------------
860 gdcmHeader::Write(fp1, type);
862 // --------------------------------------------------------------
863 // Special Patch to allow gdcm to re-write ACR-LibIDO formated images
865 // ...and we restore the Header to be Dicom Compliant again
866 // just after writting
868 if (filetype == ACR_LIBIDO){
869 SetPubElValByNumber(rows , 0x0028, 0x0010);
870 SetPubElValByNumber(columns, 0x0028, 0x0011);
872 // ----------------- End of Special Patch ----------------
874 fwrite(PixelData, lgrTotale, 1, fp1);