2 //-----------------------------------------------------------------------------
5 #include "jpeg/ljpg/jpegless.h"
7 typedef std::pair<TagHeaderEntryHT::iterator,TagHeaderEntryHT::iterator> IterHT;
9 //-----------------------------------------------------------------------------
10 // Constructor / Destructor
13 * \brief Constructor dedicated to writing a new DICOMV3 part10 compliant
14 * file (see SetFileName, SetDcmTag and Write)
15 * Opens (in read only and when possible) an existing file and checks
16 * for DICOM compliance. Returns NULL on failure.
17 * \note the in-memory representation of all available tags found in
18 * the DICOM header is post-poned to first header information access.
19 * This avoid a double parsing of public part of the header when
20 * one sets an a posteriori shadow dictionary (efficiency can be
21 * seen as a side effect).
22 * @param header file to be opened for reading datas
25 gdcmFile::gdcmFile(gdcmHeader *header) {
28 PixelRead=-1; // no ImageData read yet.
30 if (Header->IsReadable())
31 SetPixelDataSizeFromHeader();
36 * \brief Constructor dedicated to writing a new DICOMV3 part10 compliant
37 * file (see SetFileName, SetDcmTag and Write)
38 * Opens (in read only and when possible) an existing file and checks
39 * for DICOM compliance. Returns NULL on failure.
40 * \note the in-memory representation of all available tags found in
41 * the DICOM header is post-poned to first header information access.
42 * This avoid a double parsing of public part of the header when
43 * one sets an a posteriori shadow dictionary (efficiency can be
44 * seen as a side effect).
45 * @param filename file to be opened for parsing
46 * @param exception_on_error whether we throw an exception or not
47 * @param enable_sequences = true to allow the header
48 * to be parsed *inside* the SeQuences,
49 * when they have an actual length
50 * \warning enable_sequences *has to be* true for reading PAPYRUS 3.0 files
51 * @param ignore_shadow to allow skipping the shadow elements,
52 * to save memory space.
53 * \warning The TRUE value for this param has to be used
54 * with a FALSE value for the 'enable_sequence' param.
55 * ('public elements' may be embedded in 'shadow Sequences')
57 gdcmFile::gdcmFile(std::string & filename,
58 bool exception_on_error,
59 bool enable_sequences,
61 Header=new gdcmHeader(filename.c_str(),
66 PixelRead=-1; // no ImageData read yet.
68 if (Header->IsReadable())
69 SetPixelDataSizeFromHeader();
74 * \brief Constructor dedicated to writing a new DICOMV3 part10 compliant
75 * file (see SetFileName, SetDcmTag and Write)
76 * Opens (in read only and when possible) an existing file and checks
77 * for DICOM compliance. Returns NULL on failure.
78 * \note the in-memory representation of all available tags found in
79 * the DICOM header is post-poned to first header information access.
80 * This avoid a double parsing of public part of the header when
81 * one sets an a posteriori shadow dictionary (efficiency can be
82 * seen as a side effect).
83 * @param filename file to be opened for parsing
84 * @param exception_on_error whether we throw an exception or not
85 * @param enable_sequences = true to allow the header
86 * to be parsed *inside* the SeQuences,
87 * when they have an actual length
88 * \warning enable_sequences *has to be* true for reading PAPYRUS 3.0 files
89 * @param ignore_shadow to allow skipping the shadow elements,
90 * to save memory space.
91 * \warning The TRUE value for this param has to be used
92 * with a FALSE value for the 'enable_sequence' param.
93 * ('public elements' may be embedded in 'shadow Sequences')
95 gdcmFile::gdcmFile(const char *filename,
96 bool exception_on_error,
97 bool enable_sequences,
99 Header=new gdcmHeader(filename,
104 PixelRead=-1; // no ImageData read yet.
106 if (Header->IsReadable())
107 SetPixelDataSizeFromHeader();
112 * \brief canonical destructor
113 * \note If the gdcmHeader is created by the gdcmFile, it is destroyed
116 gdcmFile::~gdcmFile(void) {
122 //-----------------------------------------------------------------------------
125 //-----------------------------------------------------------------------------
129 * \brief returns the gdcmHeader *Header
132 gdcmHeader *gdcmFile::GetHeader(void) {
138 * \brief computes the length (in bytes) to ALLOCATE to receive the
139 * image(s) pixels (multiframes taken into account)
140 * \warning : it is NOT the group 7FE0 length
141 * (no interest for compressed images).
142 * @return length to allocate
144 void gdcmFile::SetPixelDataSizeFromHeader(void) {
145 // see PS 3.3-2003 : C.7.6.3.2.1
155 // YBR_FULL_422 (no LUT, no Palette)
161 // ex : gdcm-US-ALOKA-16.dcm
162 // 0028|1221 [OW] [Segmented Red Palette Color Lookup Table Data]
163 // 0028|1222 [OW] [Segmented Green Palette Color Lookup Table Data]
164 // 0028|1223 [OW] [Segmented Blue Palette Color Lookup Table Data]
166 // ex : OT-PAL-8-face.dcm
167 // 0028|1201 [US] [Red Palette Color Lookup Table Data]
168 // 0028|1202 [US] [Green Palette Color Lookup Table Data]
169 // 0028|1203 [US] [Blue Palette Color Lookup Table Data]
173 str_nb=Header->GetEntryByNumber(0x0028,0x0100);
174 if (str_nb == GDCM_UNFOUND ) {
177 nb = atoi(str_nb.c_str() );
178 if (nb == 12) nb =16;
180 lgrTotale = lgrTotaleRaw = Header->GetXSize() * Header->GetYSize()
181 * Header->GetZSize() * (nb/8)* Header->GetSamplesPerPixel();
182 std::string str_PhotometricInterpretation =
183 Header->GetEntryByNumber(0x0028,0x0004);
185 /*if ( str_PhotometricInterpretation == "PALETTE COLOR " )*/
186 // pb when undealt Segmented Palette Color
188 if (Header->HasLUT()) {
195 * \brief Returns the size (in bytes) of required memory to hold
196 * the pixel data represented in this file.
197 * @return The size of pixel data in bytes.
199 size_t gdcmFile::GetImageDataSize(void) {
205 * \brief Returns the size (in bytes) of required memory to hold
206 * the pixel data represented in this file, when user DOESN'T want
207 * to get RGB pixels image when it's stored as a PALETTE COLOR image
208 * -the (vtk) user is supposed to know how deal with LUTs-
209 * \warning to be used with GetImagePixelsRaw()
210 * @return The size of pixel data in bytes.
212 size_t gdcmFile::GetImageDataSizeRaw(void) {
213 return (lgrTotaleRaw);
218 * \brief Allocates necessary memory, copies the pixel data
219 * (image[s]/volume[s]) to newly allocated zone.
220 * Transforms YBR pixels into RGB pixels if any
221 * Transforms 3 planes R, G, B into a single RGB Plane
222 * Transforms single Grey plane + 3 Palettes into a RGB Plane
223 * @return Pointer to newly allocated pixel data.
224 * NULL if alloc fails
226 void * gdcmFile::GetImageData (void) {
227 PixelData = new char[lgrTotale];
229 GetImageDataIntoVector(PixelData, lgrTotale);
231 PixelRead=0; // no PixelRaw
237 * \brief Copies at most MaxSize bytes of pixel data to caller's
239 * \warning This function was designed to avoid people that want to build
240 * a volume from an image stack to need first to get the image pixels
241 * and then move them to the volume area.
242 * It's absolutely useless for any VTK user since vtk chooses
243 * to invert the lines of an image, that is the last line comes first
244 * (for some axis related reasons?). Hence he will have
245 * to load the image line by line, starting from the end.
246 * VTK users have to call GetImageData
248 * @param destination Address (in caller's memory space) at which the
249 * pixel data should be copied
250 * @param MaxSize Maximum number of bytes to be copied. When MaxSize
251 * is not sufficient to hold the pixel data the copy is not
252 * executed (i.e. no partial copy).
253 * @return On success, the number of bytes actually copied. Zero on
254 * failure e.g. MaxSize is lower than necessary.
256 size_t gdcmFile::GetImageDataIntoVector (void* destination, size_t MaxSize) {
257 //size_t l = GetImageDataIntoVectorRaw (destination, MaxSize);
258 GetImageDataIntoVectorRaw (destination, MaxSize);
259 PixelRead=0 ; // no PixelRaw
260 if (!Header->HasLUT())
263 // from Lut R + Lut G + Lut B
264 unsigned char *newDest = new unsigned char[lgrTotale];
265 unsigned char *a = (unsigned char *)destination;
266 unsigned char *lutRGBA = Header->GetLUTRGBA();
268 int l = lgrTotaleRaw;
269 memmove(newDest, destination, l);// move Gray pixels to temp area
271 for (int i=0;i<l; i++) { // Build RGB Pixels
279 // now, it's an RGB image
280 // Lets's write it in the Header
282 // CreateOrReplaceIfExist ?
284 std::string spp = "3"; // Samples Per Pixel
285 Header->SetEntryByNumber(spp,0x0028,0x0002);
286 std::string rgb= "RGB "; // Photometric Interpretation
287 Header->SetEntryByNumber(rgb,0x0028,0x0004);
288 std::string planConfig = "0"; // Planar Configuration
289 Header->SetEntryByNumber(planConfig,0x0028,0x0006);
292 // need to make RGB Pixels (?)
293 // from grey Pixels (?!)
294 // and Gray Lut (!?!)
295 // or Segmented xxx Palette Color Lookup Table Data and so on
297 // Oops! I get one (gdcm-US-ALOKA-16.dcm)
298 // No idea how to manage such an image
299 // It seems that *no Dicom Viewer* has any idea :-(
300 // Segmented xxx Palette Color are *more* than 65535 long ?!?
302 std::string rgb= "MONOCHROME1 "; // Photometric Interpretation
303 Header->SetEntryByNumber(rgb,0x0028,0x0004);
305 /// \todo Drop Palette Color out of the Header?
311 * \brief Allocates necessary memory, copies the pixel data
312 * (image[s]/volume[s]) to newly allocated zone.
313 * Transforms YBR pixels into RGB pixels if any
314 * Transforms 3 planes R, G, B into a single RGB Plane
315 * DOES NOT transform Grey plane + 3 Palettes into a RGB Plane
316 * @return Pointer to newly allocated pixel data.
317 * \ NULL if alloc fails
319 void * gdcmFile::GetImageDataRaw (void) {
320 if (Header->HasLUT())
321 /// \todo Let gdcmHeadar user a chance to get the right value
322 /// Create a member lgrTotaleRaw ???
324 PixelData = new char[lgrTotale];
326 GetImageDataIntoVectorRaw(PixelData, lgrTotale);
327 PixelRead=1; // PixelRaw
333 * \brief Copies at most MaxSize bytes of pixel data to caller's
335 * \warning This function was designed to avoid people that want to build
336 * a volume from an image stack to need first to get the image pixels
337 * and then move them to the volume area.
338 * It's absolutely useless for any VTK user since vtk chooses
339 * to invert the lines of an image, that is the last line comes first
340 * (for some axis related reasons?). Hence he will have
341 * to load the image line by line, starting from the end.
342 * VTK users hace to call GetImageData
343 * \warning DOES NOT transform the Grey Plane + Palette Color (if any)
344 * into a single RGB Pixels Plane
345 * the (VTK) user will manage the palettes
347 * @param destination Address (in caller's memory space) at which the
348 * pixel data should be copied
349 * @param MaxSize Maximum number of bytes to be copied. When MaxSize
350 * is not sufficient to hold the pixel data the copy is not
351 * executed (i.e. no partial copy).
352 * @return On success, the number of bytes actually copied. Zero on
353 * failure e.g. MaxSize is lower than necessary.
355 size_t gdcmFile::GetImageDataIntoVectorRaw (void *destination, size_t MaxSize) {
357 int nb, nbu, highBit, signe;
358 std::string str_nbFrames, str_nb, str_nbu, str_highBit, str_signe;
359 PixelRead=1 ; // PixelRaw
361 if ( lgrTotale > MaxSize ) {
362 dbg.Verbose(0, "gdcmFile::GetImageDataIntoVector: pixel data bigger"
363 "than caller's expected MaxSize");
367 (void)ReadPixelData(destination);
369 // Number of Bits Allocated for storing a Pixel
370 str_nb = Header->GetEntryByNumber(0x0028,0x0100);
371 if (str_nb == GDCM_UNFOUND ) {
374 nb = atoi(str_nb.c_str() );
376 // Number of Bits actually used
377 str_nbu=Header->GetEntryByNumber(0x0028,0x0101);
378 if (str_nbu == GDCM_UNFOUND ) {
381 nbu = atoi(str_nbu.c_str() );
384 str_highBit=Header->GetEntryByNumber(0x0028,0x0102);
385 if (str_highBit == GDCM_UNFOUND ) {
388 highBit = atoi(str_highBit.c_str() );
393 str_signe=Header->GetEntryByNumber(0x0028,0x0103);
394 if (str_signe == GDCM_UNFOUND ) {
395 signe = 0; // default is unsigned
397 signe = atoi(str_signe.c_str() );
400 // re arange bytes inside the integer (processor endianity)
402 SwapZone(destination, Header->GetSwapCode(), lgrTotale, nb);
404 // to avoid pb with some xmedcon breakers images
405 if (nb==16 && nbu<nb && signe==0) {
406 int l = (int)lgrTotale / (nb/8);
407 guint16 *deb = (guint16 *)destination;
408 for(int i = 0; i<l; i++) {
414 // re arange bits inside the bytes
416 int l = (int)lgrTotale / (nb/8);
418 guint16 mask = 0xffff;
419 mask = mask >> (nb-nbu);
420 guint16 *deb = (guint16 *)destination;
421 for(int i = 0; i<l; i++) {
422 *deb = (*deb >> (nbu-highBit-1)) & mask;
425 } else if (nb == 32 ) {
426 guint32 mask = 0xffffffff;
427 mask = mask >> (nb-nbu);
428 guint32 *deb = (guint32 *)destination;
429 for(int i = 0; i<l; i++) {
430 *deb = (*deb >> (nbu-highBit-1)) & mask;
434 dbg.Verbose(0, "gdcmFile::GetImageDataIntoVector: wierd image");
438 // DO NOT remove this commented out code .
439 // Nobody knows what's expecting you ...
440 // Just to 'see' what was actually read on disk :-(
443 // f2 = fopen("SpuriousFile.RAW","wb");
444 // fwrite(destination,lgrTotale,1,f2);
447 // Deal with the color
448 // -------------------
450 std::string str_PhotometricInterpretation =
451 Header->GetEntryByNumber(0x0028,0x0004);
453 if ( (str_PhotometricInterpretation == "MONOCHROME1 ")
454 || (str_PhotometricInterpretation == "MONOCHROME2 ") ) {
458 // Planar configuration = 0 : Pixels are already RGB
459 // Planar configuration = 1 : 3 planes : R, G, B
460 // Planar configuration = 2 : 1 gray Plane + 3 LUT
462 // Well ... supposed to be !
463 // See US-PAL-8-10x-echo.dcm: PlanarConfiguration=0,
464 // PhotometricInterpretation=PALETTE COLOR
465 // and heuristic has to be found :-(
467 int planConf=Header->GetPlanarConfiguration(); // 0028,0006
469 // Whatever Planar Configuration is,
470 // "PALETTE COLOR " implies that we deal with the palette.
471 if (str_PhotometricInterpretation == "PALETTE COLOR ")
476 // Pixels are already RGB
482 if (str_PhotometricInterpretation == "YBR_FULL") {
484 // Warning : YBR_FULL_422 acts as RGB
485 // : we need to make RGB Pixels from Planes Y,cB,cR
487 // to see the tricks about YBR_FULL, YBR_FULL_422,
488 // YBR_PARTIAL_422, YBR_ICT, YBR_RCT have a look at :
489 // ftp://medical.nema.org/medical/dicom/final/sup61_ft.pdf
490 // and be *very* affraid
492 int l = Header->GetXSize()*Header->GetYSize();
493 int nbFrames = Header->GetZSize();
495 unsigned char *newDest = new unsigned char[lgrTotale];
496 unsigned char *x = newDest;
497 unsigned char *a = (unsigned char *)destination;
498 unsigned char *b = a + l;
499 unsigned char *c = b + l;
502 /// \todo : Replace by the 'well known' integer computation
504 /// see http://lestourtereaux.free.fr/papers/data/yuvrgb.pdf
505 /// for code optimisation
507 for (int i=0;i<nbFrames;i++) {
508 for (int j=0;j<l; j++) {
509 R= 1.164 *(*a-16) + 1.596 *(*c -128) + 0.5;
510 G= 1.164 *(*a-16) - 0.813 *(*c -128) - 0.392 *(*b -128) + 0.5;
511 B= 1.164 *(*a-16) + 2.017 *(*b -128) + 0.5;
516 if (R>255.0) R=255.0;
517 if (G>255.0) G=255.0;
518 if (B>255.0) B=255.0;
520 *(x++) = (unsigned char)R;
521 *(x++) = (unsigned char)G;
522 *(x++) = (unsigned char)B;
526 memmove(destination,newDest,lgrTotale);
531 // need to make RGB Pixels from R,G,B Planes
532 // (all the Frames at a time)
534 int l = Header->GetXSize()*Header->GetYSize()*Header->GetZSize();
536 char *newDest = new char[lgrTotale];
538 char *a = (char *)destination;
542 for (int j=0;j<l; j++) {
547 memmove(destination,newDest,lgrTotale);
553 // Palettes were found
554 // Let the user deal with them !
557 // now, it's an RGB image
558 // Lets's write it in the Header
560 // CreateOrReplaceIfExist ?
562 std::string spp = "3"; // Samples Per Pixel
563 Header->SetEntryByNumber(spp,0x0028,0x0002);
564 std::string rgb="RGB "; // Photometric Interpretation
565 Header->SetEntryByNumber(rgb,0x0028,0x0004);
567 std::string planConfig = "0"; // Planar Configuration
568 Header->SetEntryByNumber(planConfig,0x0028,0x0006);
570 /// \todo Drop Palette Color out of the Header?
576 * \brief performs a shadow copy (not a deep copy) of the user given
578 * 'image' Pixels are presented as C-like 2D arrays : line per line.
579 * 'volume'Pixels are presented as C-like 3D arrays : lane per plane
580 * \warning user is kindly requested NOT TO 'free' the Pixel area
581 * @param inData user supplied pixel area
582 * @param ExpectedSize total image size, in Bytes
586 bool gdcmFile::SetImageData(void *inData, size_t ExpectedSize) {
587 Header->SetImageDataSize(ExpectedSize);
589 lgrTotale = ExpectedSize;
596 * \brief Writes on disk A SINGLE Dicom file
597 * NO test is performed on processor "Endiannity".
598 * It's up to the user to call his Reader properly
599 * @param fileName name of the file to be created
600 * (any already existing file is over written)
601 * @return false if write fails
604 bool gdcmFile::WriteRawData (std::string fileName) {
606 fp1 = fopen(fileName.c_str(),"wb");
608 printf("Fail to open (write) file [%s] \n",fileName.c_str());
611 fwrite (PixelData,lgrTotale, 1, fp1);
618 * \brief Writes on disk A SINGLE Dicom file,
619 * using the Implicit Value Representation convention
620 * NO test is performed on processor "Endiannity".
621 * @param fileName name of the file to be created
622 * (any already existing file is overwritten)
623 * @return false if write fails
626 bool gdcmFile::WriteDcmImplVR (std::string fileName) {
627 return WriteBase(fileName, gdcmImplicitVR);
632 * \brief Writes on disk A SINGLE Dicom file,
633 * using the Implicit Value Representation convention
634 * NO test is performed on processor "Endiannity". * @param fileName name of the file to be created
635 * (any already existing file is overwritten)
636 * @return false if write fails
639 bool gdcmFile::WriteDcmImplVR (const char *fileName) {
640 return WriteDcmImplVR (std::string (fileName));
645 * \brief Writes on disk A SINGLE Dicom file,
646 * using the Explicit Value Representation convention
647 * NO test is performed on processor "Endiannity". * @param fileName name of the file to be created
648 * (any already existing file is overwritten)
649 * @return false if write fails
652 bool gdcmFile::WriteDcmExplVR (std::string fileName) {
653 return WriteBase(fileName, gdcmExplicitVR);
658 * \brief Writes on disk A SINGLE Dicom file,
659 * using the ACR-NEMA convention
660 * NO test is performed on processor "Endiannity".
661 * (a l'attention des logiciels cliniques
662 * qui ne prennent en entrée QUE des images ACR ...
663 * \warning if a DICOM_V3 header is supplied,
664 * groups < 0x0008 and shadow groups are ignored
665 * \warning NO TEST is performed on processor "Endiannity".
666 * @param fileName name of the file to be created
667 * (any already existing file is overwritten)
668 * @return false if write fails
671 bool gdcmFile::WriteAcr (std::string fileName) {
672 return WriteBase(fileName, gdcmACR);
675 //-----------------------------------------------------------------------------
679 * \brief NOT a end user inteded function
680 * (used by WriteDcmExplVR, WriteDcmImplVR, WriteAcr, etc)
681 * @param fileName name of the file to be created
682 * (any already existing file is overwritten)
683 * @param type file type (ExplicitVR, ImplicitVR, ...)
684 * @return false if write fails
686 bool gdcmFile::WriteBase (std::string fileName, FileType type) {
690 if (PixelRead==-1 && type != gdcmExplicitVR) {
694 fp1 = fopen(fileName.c_str(),"wb");
696 printf("Failed to open (write) File [%s] \n",fileName.c_str());
700 if ( (type == gdcmImplicitVR) || (type == gdcmExplicitVR) ) {
702 // writing Dicom File Preamble
703 filePreamble=new char[128];
704 memset(filePreamble,0,128);
705 fwrite(filePreamble,128,1,fp1);
706 fwrite("DICM",4,1,fp1);
707 delete[] filePreamble;
710 // --------------------------------------------------------------
711 // Special Patch to allow gdcm to re-write ACR-LibIDO formated images
713 // if recognition code tells us we dealt with a LibIDO image
714 // we reproduce on disk the switch between lineNumber and columnNumber
715 // just before writting ...
717 /// \todo the best trick would be *change* the recognition code
718 /// but pb expected if user deals with, e.g. COMPLEX images
720 std::string rows, columns;
721 if ( Header->GetFileType() == gdcmACR_LIBIDO){
722 rows = Header->GetEntryByNumber(0x0028, 0x0010);
723 columns = Header->GetEntryByNumber(0x0028, 0x0011);
724 Header->SetEntryByNumber(columns, 0x0028, 0x0010);
725 Header->SetEntryByNumber(rows , 0x0028, 0x0011);
727 // ----------------- End of Special Patch ----------------
729 /// \todo get the grPixel, numPixel values (for some ACR-NEMA images only)
731 guint16 grPixel =Header->GetGrPixel();
732 guint16 numPixel=Header->GetNumPixel();;
734 // Update Pixel Data Length
735 // the *last* of the (GrPixel, NumPixel), if many.
737 TagKey key = gdcmDictEntry::TranslateToKey(grPixel, numPixel);
738 TagHeaderEntryHT::iterator p2;
739 gdcmHeaderEntry *PixelElement;
741 IterHT it= Header->GetEntry().equal_range(key); // get a pair of iterators first-last synonym
743 if (Header->GetEntry().count(key) == 1) // only the first is significant
744 p2=it.first; // iterator on the first (unique) synonym
746 p2=it.second;// iterator on the last synonym
748 PixelElement=p2->second; // H Table target column (2-nd col)
749 // PixelElement->SetPrintLevel(2);
750 // PixelElement->Print();
753 PixelElement->SetLength(lgrTotaleRaw);
754 else if (PixelRead==0)
755 PixelElement->SetLength(lgrTotale);
757 //PixelElement->SetPrintLevel(2);
758 //PixelElement->Print();
759 Header->Write(fp1, type);
761 // --------------------------------------------------------------
762 // Special Patch to allow gdcm to re-write ACR-LibIDO formated images
764 // ...and we restore the Header to be Dicom Compliant again
765 // just after writting
767 if (Header->GetFileType() == gdcmACR_LIBIDO){
768 Header->SetEntryByNumber(rows , 0x0028, 0x0010);
769 Header->SetEntryByNumber(columns, 0x0028, 0x0011);
771 // ----------------- End of Special Patch ----------------
773 fwrite(PixelData, lgrTotale, 1, fp1);
778 //-----------------------------------------------------------------------------
782 * \brief Swap the bytes, according to swap code.
783 * \warning not end user intended
784 * @param im area to deal with
785 * @param swap swap code
786 * @param lgr Area Length
787 * @param nb Pixels Bit number
789 void gdcmFile::SwapZone(void *im, int swap, int lgr, int nb) {
806 for(i=0;i<lgr/2;i++) {
807 ((unsigned short int *)im)[i]= ((((unsigned short int *)im)[i])>>8)
808 | ((((unsigned short int *)im)[i])<<8);
813 printf("SWAP value (16 bits) not allowed : %d\n", swap);
823 for(i=0;i<lgr/4;i++) {
824 faible= ((unsigned long int *)im)[i]&0x0000ffff; /* 4321 */
825 fort =((unsigned long int *)im)[i]>>16;
826 fort= (fort>>8) | (fort<<8);
827 faible=(faible>>8) | (faible<<8);
829 ((unsigned long int *)im)[i]=(s32<<16)|fort;
834 for(i=0;i<lgr/4;i++) {
835 faible= ((unsigned long int *)im)[i]&0x0000ffff; /* 2143 */
836 fort=((unsigned long int *)im)[i]>>16;
837 fort= (fort>>8) | (fort<<8);
838 faible=(faible>>8) | (faible<<8);
840 ((unsigned long int *)im)[i]=(s32<<16)|faible;
845 for(i=0;i<lgr/4;i++) {
846 faible= ((unsigned long int *)im)[i]&0x0000ffff; /* 3412 */
847 fort=((unsigned long int *)im)[i]>>16;
849 ((unsigned long int *)im)[i]=(s32<<16)|fort;
854 printf("SWAP value (32 bits) not allowed : %d\n", swap);
861 * \brief Read pixel data from disk (optionaly decompressing) into the
862 * caller specified memory location.
863 * @param destination where the pixel data should be stored.
866 bool gdcmFile::ReadPixelData(void *destination) {
870 if ( !(fp=Header->OpenFile()))
872 if ( fseek(fp, Header->GetPixelOffset(), SEEK_SET) == -1 ) {
876 // ---------------------- Compacted File (12 Bits Per Pixel)
877 /* unpack 12 Bits pixels into 16 Bits pixels */
878 /* 2 pixels 12bit = [0xABCDEF] */
879 /* 2 pixels 16bit = [0x0ABD] + [0x0FCE] */
881 if (Header->GetBitsAllocated()==12) {
882 int nbPixels = Header->GetXSize() * Header->GetYSize();
883 unsigned char b0, b1, b2;
885 unsigned short int *pdestination = (unsigned short int*)destination;
886 for(int p=0;p<nbPixels;p+=2) {
890 //Two steps is necessary to please VC++
891 *pdestination++ = ((b0 >> 4) << 8) + ((b0 & 0x0f) << 4) + (b1 & 0x0f);
892 /* A */ /* B */ /* D */
893 *pdestination++ = ((b2 & 0x0f) << 8) + ((b1 >> 4) << 4) + (b2 >> 4);
894 /* F */ /* C */ /* E */
896 // Troubles expected on Big-Endian processors ?
903 // ---------------------- Uncompressed File
904 if ( !Header->IsDicomV3() ||
905 Header->IsImplicitVRLittleEndianTransferSyntax() ||
906 Header->IsExplicitVRLittleEndianTransferSyntax() ||
907 Header->IsExplicitVRBigEndianTransferSyntax() ||
908 Header->IsDeflatedExplicitVRLittleEndianTransferSyntax() ) {
910 size_t ItemRead = fread(destination, Header->GetPixelAreaLength(), 1, fp);
911 if ( ItemRead != 1 ) {
920 // ---------------------- Run Length Encoding
921 if (Header->IsRLELossLessTransferSyntax()) {
922 bool res = (bool)gdcm_read_RLE_file (fp,destination);
927 // --------------- SingleFrame/Multiframe JPEG Lossless/Lossy/2000
929 std::string str_nb=Header->GetEntryByNumber(0x0028,0x0100);
930 if (str_nb == GDCM_UNFOUND ) {
933 nb = atoi(str_nb.c_str() );
934 if (nb == 12) nb =16; // ?? 12 should be ACR-NEMA only ?
939 int taille = Header->GetXSize() * Header->GetYSize()
940 * Header->GetSamplesPerPixel();
941 long fragmentBegining; // for ftell, fseek
943 bool jpg2000 = Header->IsJPEG2000();
944 bool jpgLossless = Header->IsJPEGLossless();
947 guint16 ItemTagGr,ItemTagEl;
950 // Position on begining of Jpeg Pixels
952 fread(&ItemTagGr,2,1,fp); // Reading (fffe) : Item Tag Gr
953 fread(&ItemTagEl,2,1,fp); // Reading (e000) : Item Tag El
954 if(Header->GetSwapCode()) {
955 ItemTagGr=Header->SwapShort(ItemTagGr);
956 ItemTagEl=Header->SwapShort(ItemTagEl);
959 if(Header->GetSwapCode())
960 ln=Header->SwapLong(ln); // Basic Offset Table Item length
963 // What is it used for ?!?
964 char *BasicOffsetTableItemValue = new char[ln+1];
965 fread(BasicOffsetTableItemValue,ln,1,fp);
968 // first Fragment initialisation
969 fread(&ItemTagGr,2,1,fp); // Reading (fffe) : Item Tag Gr
970 fread(&ItemTagEl,2,1,fp); // Reading (e000) : Item Tag El
971 if(Header->GetSwapCode()) {
972 ItemTagGr=Header->SwapShort(ItemTagGr);
973 ItemTagEl=Header->SwapShort(ItemTagEl);
976 // parsing fragments until Sequence Delim. Tag found
977 while ( ( ItemTagGr == 0xfffe) && (ItemTagEl != 0xe0dd) ) {
978 // --- for each Fragment
981 if(Header->GetSwapCode())
982 ln=Header->SwapLong(ln); // Fragment Item length
984 fragmentBegining=ftell(fp);
986 if (jpg2000) { // JPEG 2000 : call to ???
988 res = (bool)gdcm_read_JPEG2000_file (fp,destination); // Not Yet written
990 } // ------------------------------------- endif (JPEG2000)
992 else if (jpgLossless) { // JPEG LossLess : call to xmedcom JPEG
994 JPEGLosslessDecodeImage (fp, // Reading Fragment pixels
995 (unsigned short *)destination,
996 Header->GetPixelSize() * 8 * Header->GetSamplesPerPixel(),
998 res=1; // in order not to break the loop
1000 } // ------------------------------------- endif (JPEGLossless)
1002 else { // JPEG Lossy : call to IJG 6b
1004 if (Header->GetBitsStored() == 8) {
1005 res = (bool)gdcm_read_JPEG_file (fp,destination); // Reading Fragment pixels
1007 res = (bool)gdcm_read_JPEG_file12 (fp,destination);// Reading Fragment pixels
1009 } // ------------------------------------- endif (JPEGLossy)
1013 destination = (char *)destination + taille * nBytes; // location in user's memory
1014 // for next fragment (if any)
1016 fseek(fp,fragmentBegining,SEEK_SET); // To be sure we start
1017 fseek(fp,ln,SEEK_CUR); // at the begining of next fragment
1019 ItemTagGr = ItemTagEl =0;
1020 fread(&ItemTagGr,2,1,fp); // Reading (fffe) : Item Tag Gr
1021 fread(&ItemTagEl,2,1,fp); // Reading (e000) : Item Tag El
1022 if(Header->GetSwapCode()) {
1023 ItemTagGr=Header->SwapShort(ItemTagGr);
1024 ItemTagEl=Header->SwapShort(ItemTagEl);
1027 } // endWhile parsing fragments until Sequence Delim. Tag found
1029 Header->CloseFile();
1032 //-----------------------------------------------------------------------------