-#include "gdcmlib.h"
+// gdcmFile.cxx
+//-----------------------------------------------------------------------------
+#include "gdcmFile.h"
+#include "gdcmUtil.h"
+#include "jpeg/ljpg/jpegless.h"
-gdcmFile::gdcmFile(string & filename) {
+typedef std::pair<TagHeaderEntryHT::iterator,TagHeaderEntryHT::iterator> IterHT;
+
+//-----------------------------------------------------------------------------
+// Constructor / Destructor
+/**
+ * \ingroup gdcmFile
+ * \brief Constructor dedicated to writing a new DICOMV3 part10 compliant
+ * file (see SetFileName, SetDcmTag and Write)
+ * Opens (in read only and when possible) an existing file and checks
+ * for DICOM compliance. Returns NULL on failure.
+ * \note the in-memory representation of all available tags found in
+ * the DICOM header is post-poned to first header information access.
+ * This avoid a double parsing of public part of the header when
+ * one sets an a posteriori shadow dictionary (efficiency can be
+ * seen as a side effect).
+ * @param header file to be opened for reading datas
+ * @return
+ */
+
+gdcmFile::gdcmFile(gdcmHeader *header) {
+ Header=header;
+ SelfHeader=false;
+ PixelRead=-1; // no ImageData read yet.
+
+ if (Header->IsReadable())
+ SetPixelDataSizeFromHeader();
+}
+
+/**
+ * \ingroup gdcmFile
+ * \brief Constructor dedicated to writing a new DICOMV3 part10 compliant
+ * file (see SetFileName, SetDcmTag and Write)
+ * Opens (in read only and when possible) an existing file and checks
+ * for DICOM compliance. Returns NULL on failure.
+ * \note the in-memory representation of all available tags found in
+ * the DICOM header is post-poned to first header information access.
+ * This avoid a double parsing of public part of the header when
+ * one sets an a posteriori shadow dictionary (efficiency can be
+ * seen as a side effect).
+ * @param filename file to be opened for parsing
+ */
+gdcmFile::gdcmFile(std::string & filename) {
+ Header=new gdcmHeader(filename.c_str());
+ SelfHeader=true;
+ PixelRead=-1; // no ImageData read yet.
+
+ if (Header->IsReadable())
+ SetPixelDataSizeFromHeader();
+}
+
+/**
+ * \ingroup gdcmFile
+ * \brief Constructor dedicated to writing a new DICOMV3 part10 compliant
+ * file (see SetFileName, SetDcmTag and Write)
+ * Opens (in read only and when possible) an existing file and checks
+ * for DICOM compliance. Returns NULL on failure.
+ * \note the in-memory representation of all available tags found in
+ * the DICOM header is post-poned to first header information access.
+ * This avoid a double parsing of public part of the header when
+ * one sets an a posteriori shadow dictionary (efficiency can be
+ * seen as a side effect).
+ * @param filename file to be opened for parsing
+ */
+ gdcmFile::gdcmFile(const char * filename) {
+ Header=new gdcmHeader(filename);
+ SelfHeader=true;
+ PixelRead=-1; // no ImageData read yet.
+
+ if (Header->IsReadable())
+ SetPixelDataSizeFromHeader();
+}
+
+/**
+ * \ingroup gdcmFile
+ * \brief canonical destructor
+ * \Note If the gdcmHeader is created by the gdcmFile, it is destroyed
+ * by the gdcmFile
+ */
+gdcmFile::~gdcmFile(void) {
+ if(SelfHeader)
+ delete Header;
+ Header=NULL;
+}
+
+//-----------------------------------------------------------------------------
+// Print
+
+//-----------------------------------------------------------------------------
+// Public
+/**
+ * \ingroup gdcmFile
+ * \brief
+ * @return
+ */
+gdcmHeader *gdcmFile::GetHeader(void) {
+ return(Header);
+}
+
+/**
+ * \ingroup gdcmFile
+ * \brief computes the length (in bytes) to ALLOCATE to receive the
+ * image(s) pixels (multiframes taken into account)
+ * \warning : it is NOT the group 7FE0 length
+ * (no interest for compressed images).
+ * @return length to allocate
+ */
+void gdcmFile::SetPixelDataSizeFromHeader(void) {
+ // see PS 3.3-2003 : C.7.6.3.2.1
+ //
+ // MONOCHROME1
+ // MONOCHROME2
+ // PALETTE COLOR
+ // RGB
+ // HSV (Retired)
+ // ARGB (Retired)
+ // CMYK (Retired)
+ // YBR_FULL
+ // YBR_FULL_422 (no LUT, no Palette)
+ // YBR_PARTIAL_422
+ // YBR_ICT
+ // YBR_RCT
+
+ // LUT's
+ // ex : gdcm-US-ALOKA-16.dcm
+ // 0028|1221 [OW] [Segmented Red Palette Color Lookup Table Data]
+ // 0028|1222 [OW] [Segmented Green Palette Color Lookup Table Data]
+ // 0028|1223 [OW] [Segmented Blue Palette Color Lookup Table Data]
+
+ // ex : OT-PAL-8-face.dcm
+ // 0028|1201 [US] [Red Palette Color Lookup Table Data]
+ // 0028|1202 [US] [Green Palette Color Lookup Table Data]
+ // 0028|1203 [US] [Blue Palette Color Lookup Table Data]
+
+ int nb;
+ std::string str_nb;
+ str_nb=Header->GetEntryByNumber(0x0028,0x0100);
+ if (str_nb == GDCM_UNFOUND ) {
+ nb = 16;
+ } else {
+ nb = atoi(str_nb.c_str() );
+ if (nb == 12) nb =16;
+ }
+ lgrTotale = lgrTotaleRaw = Header->GetXSize() * Header->GetYSize()
+ * Header->GetZSize() * (nb/8)* Header->GetSamplesPerPixel();
+ std::string str_PhotometricInterpretation =
+ Header->GetEntryByNumber(0x0028,0x0004);
+
+ /*if ( str_PhotometricInterpretation == "PALETTE COLOR " )*/
+ // pb when undealt Segmented Palette Color
+
+ if (Header->HasLUT()) {
+ lgrTotale*=3;
+ }
+}
+
+/**
+ * \ingroup gdcmFile
+ * \brief Returns the size (in bytes) of required memory to hold
+ * the pixel data represented in this file.
+ * @return The size of pixel data in bytes.
+ */
+size_t gdcmFile::GetImageDataSize(void) {
+ return (lgrTotale);
+}
+
+/**
+ * \ingroup gdcmFile
+ * \brief Returns the size (in bytes) of required memory to hold
+ * the pixel data represented in this file, when user DOESN'T want
+ * to get RGB pixels image when it's stored as a PALETTE COLOR image
+ * -the (vtk) user is supposed to know how deal with LUTs-
+ * \warning to be used with GetImagePixelsRaw()
+ * @return The size of pixel data in bytes.
+ */
+size_t gdcmFile::GetImageDataSizeRaw(void) {
+ return (lgrTotaleRaw);
+}
+
+/**
+ * \ingroup gdcmFile
+ * \brief Allocates necessary memory, copies the pixel data
+ * (image[s]/volume[s]) to newly allocated zone.
+ * Transforms YBR pixels into RGB pixels if any
+ * Transforms 3 planes R, G, B into a single RGB Plane
+ * Transforms single Grey plane + 3 Palettes into a RGB Plane
+ * @return Pointer to newly allocated pixel data.
+ * NULL if alloc fails
+ */
+void * gdcmFile::GetImageData (void) {
+ PixelData = (void *) malloc(lgrTotale);
+ if (PixelData)
+ GetImageDataIntoVector(PixelData, lgrTotale);
+ PixelRead=0; // no PixelRaw
+ return(PixelData);
+}
+
+/**
+ * \ingroup gdcmFile
+ * \brief Copies at most MaxSize bytes of pixel data to caller's
+ * memory space.
+ * \warning This function was designed to avoid people that want to build
+ * a volume from an image stack to need first to get the image pixels
+ * and then move them to the volume area.
+ * It's absolutely useless for any VTK user since vtk chooses
+ * to invert the lines of an image, that is the last line comes first
+ * (for some axis related reasons?). Hence he will have
+ * to load the image line by line, starting from the end.
+ * VTK users have to call GetImageData
+ *
+ * @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) {
+ size_t l = GetImageDataIntoVectorRaw (destination, MaxSize);
+ PixelRead=0 ; // no PixelRaw
+ if (!Header->HasLUT())
+ return lgrTotale;
+
+ // from Lut R + Lut G + Lut B
+ unsigned char * newDest = (unsigned char *)malloc(lgrTotale);
+ unsigned char * a = (unsigned char *)destination;
+ unsigned char * lutRGBA = Header->GetLUTRGBA();
+ if (lutRGBA) {
+ int l = lgrTotaleRaw;
+ memmove(newDest, destination, l);// move Gray pixels to temp area
+ int j;
+ for (int i=0;i<l; i++) { // Build RGB Pixels
+ j=newDest[i]*4;
+ *a++ = lutRGBA[j];
+ *a++ = lutRGBA[j+1];
+ *a++ = lutRGBA[j+2];
+ }
+ free(newDest);
+
+ // now, it's an RGB image
+ // Lets's write it in the Header
+
+ // CreateOrReplaceIfExist ?
+
+ std::string spp = "3"; // Samples Per Pixel
+ Header->SetEntryByNumber(spp,0x0028,0x0002);
+ std::string rgb= "RGB "; // Photometric Interpretation
+ Header->SetEntryByNumber(rgb,0x0028,0x0004);
+ std::string planConfig = "0"; // Planar Configuration
+ Header->SetEntryByNumber(planConfig,0x0028,0x0006);
+
+ } else {
+ // need to make RGB Pixels (?)
+ // from grey Pixels (?!)
+ // and Gray Lut (!?!)
+ // or Segmented xxx Palette Color Lookup Table Data and so on
+
+ // Oops! I get one (gdcm-US-ALOKA-16.dcm)
+ // No idea how to manage such an image
+ // It seems that *no Dicom Viewer* has any idea :-(
+ // Segmented xxx Palette Color are *more* than 65535 long ?!?
+
+ std::string rgb= "MONOCHROME1 "; // Photometric Interpretation
+ Header->SetEntryByNumber(rgb,0x0028,0x0004);
+ }
+ // TODO : Drop Palette Color out of the Header?
+ return lgrTotale;
+}
+
+/**
+ * \ingroup gdcmFile
+ * \brief Allocates necessary memory, copies the pixel data
+ * (image[s]/volume[s]) to newly allocated zone.
+ * Transforms YBR pixels into RGB pixels if any
+ * Transforms 3 planes R, G, B into a single RGB Plane
+ * DOES NOT transform Grey plane + 3 Palettes into a RGB Plane
+ * @return Pointer to newly allocated pixel data.
+ * \ NULL if alloc fails
+ */
+void * gdcmFile::GetImageDataRaw (void) {
+ if (Header->HasLUT())
+ lgrTotale /= 3; // TODO Let gdcmHeadar user a chance
+ // to get the right value
+ // Create a member lgrTotaleRaw ???
+ PixelData = (void *) malloc(lgrTotale);
+ if (PixelData)
+ GetImageDataIntoVectorRaw(PixelData, lgrTotale);
+ PixelRead=1; // PixelRaw
+ return(PixelData);
+}
+
+/**
+ * \ingroup gdcmFile
+ * \brief Copies at most MaxSize bytes of pixel data to caller's
+ * memory space.
+ * \warning This function was designed to avoid people that want to build
+ * a volume from an image stack to need first to get the image pixels
+ * and then move them to the volume area.
+ * It's absolutely useless for any VTK user since vtk chooses
+ * to invert the lines of an image, that is the last line comes first
+ * (for some axis related reasons?). Hence he will have
+ * to load the image line by line, starting from the end.
+ * VTK users hace to call GetImageData
+ * \warning DOES NOT transform the Grey Plane + Palette Color (if any)
+ * into a single RGB Pixels Plane
+ * the (VTK) user will manage the palettes
+ *
+ * @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::GetImageDataIntoVectorRaw (void* destination, size_t MaxSize) {
+
+ int nb, nbu, highBit, signe;
+ std::string str_nbFrames, str_nb, str_nbu, str_highBit, str_signe;
+ PixelRead=1 ; // PixelRaw
+
+ if ( lgrTotale > MaxSize ) {
+ dbg.Verbose(0, "gdcmFile::GetImageDataIntoVector: pixel data bigger"
+ "than caller's expected MaxSize");
+ return (size_t)0;
+ }
+ (void)ReadPixelData(destination);
+
+ // Number of Bits Allocated for storing a Pixel
+ str_nb = Header->GetEntryByNumber(0x0028,0x0100);
+ if (str_nb == GDCM_UNFOUND ) {
+ nb = 16;
+ } else {
+ nb = atoi(str_nb.c_str() );
+ }
+ // Number of Bits actually used
+ str_nbu=Header->GetEntryByNumber(0x0028,0x0101);
+ if (str_nbu == GDCM_UNFOUND ) {
+ nbu = nb;
+ } else {
+ nbu = atoi(str_nbu.c_str() );
+ }
+ // High Bit Position
+ str_highBit=Header->GetEntryByNumber(0x0028,0x0102);
+ if (str_highBit == GDCM_UNFOUND ) {
+ highBit = nb - 1;
+ } else {
+ highBit = atoi(str_highBit.c_str() );
+ }
+ // Pixel sign
+ // 0 = Unsigned
+ // 1 = Signed
+ str_signe=Header->GetEntryByNumber(0x0028,0x0103);
+ if (str_signe == GDCM_UNFOUND ) {
+ signe = 0; // default is unsigned
+ } else {
+ signe = atoi(str_signe.c_str() );
+ }
+
+ // re arange bytes inside the integer (processor endianity)
+ if (nb != 8)
+ SwapZone(destination, Header->GetSwapCode(), lgrTotale, nb);
+
+ // to avoid pb with some xmedcon breakers images
+ if (nb==16 && nbu<nb && signe==0) {
+ int l = (int)lgrTotale / (nb/8);
+ guint16 *deb = (guint16 *)destination;
+ for(int i = 0; i<l; i++) {
+ if(*deb == 0xffff)
+ *deb=0;
+ deb++;
+ }
+ }
+
+ // 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;
+ }
+ }
+// DO NOT remove this code commented out.
+// Nobody knows what's expecting you ...
+// Just to 'see' what was actually read on disk :-(
+
+// FILE * f2;
+// f2 = fopen("SpuriousFile.RAW","wb");
+// fwrite(destination,lgrTotale,1,f2);
+// fclose(f2);
+
+ // Deal with the color
+ // -------------------
+
+ std::string str_PhotometricInterpretation =
+ Header->GetEntryByNumber(0x0028,0x0004);
+
+ if ( (str_PhotometricInterpretation == "MONOCHROME1 ")
+ || (str_PhotometricInterpretation == "MONOCHROME2 ") ) {
+ return lgrTotale;
+ }
+
+ // Planar configuration = 0 : Pixels are already RGB
+ // Planar configuration = 1 : 3 planes : R, G, B
+ // Planar configuration = 2 : 1 gray Plane + 3 LUT
+
+ // Well ... supposed to be !
+ // See US-PAL-8-10x-echo.dcm: PlanarConfiguration=0,
+ // PhotometricInterpretation=PALETTE COLOR
+ // and heuristic has to be found :-(
+
+ int planConf=Header->GetPlanarConfiguration(); // 0028,0006
+
+ // Whatever Planar Configuration is,
+ // "PALETTE COLOR " implies that we deal with the palette.
+ if (str_PhotometricInterpretation == "PALETTE COLOR ")
+ planConf=2;
+
+ switch (planConf) {
+ case 0:
+ // Pixels are already RGB
+ break;
+
+ case 1:
+
+ {
+ if (str_PhotometricInterpretation == "YBR_FULL") {
+
+ // Warning : YBR_FULL_422 acts as RGB
+ // : we need to make RGB Pixels from Planes Y,cB,cR
+
+ // to see the tricks about YBR_FULL, YBR_FULL_422,
+ // YBR_PARTIAL_422, YBR_ICT, YBR_RCT have a look at :
+ // ftp://medical.nema.org/medical/dicom/final/sup61_ft.pdf
+ // and be *very* affraid
+ //
+ int l = Header->GetXSize()*Header->GetYSize();
+ int nbFrames = Header->GetZSize();
+
+ unsigned char * newDest = (unsigned char*) malloc(lgrTotale);
+ unsigned char *x = newDest;
+ unsigned char * a = (unsigned char *)destination;
+ unsigned char * b = a + l;
+ unsigned char * c = b + l;
+ double R,G,B;
+
+ // TODO : Replace by the 'well known'
+ // integer computation counterpart
+ // see http://lestourtereaux.free.fr/papers/data/yuvrgb.pdf
+ // for code optimisation
+
+ for (int i=0;i<nbFrames;i++) {
+ for (int j=0;j<l; j++) {
+ R= 1.164 *(*a-16) + 1.596 *(*c -128) + 0.5;
+ G= 1.164 *(*a-16) - 0.813 *(*c -128) - 0.392 *(*b -128) + 0.5;
+ B= 1.164 *(*a-16) + 2.017 *(*b -128) + 0.5;
+
+ if (R<0.0) R=0.0;
+ if (G<0.0) G=0.0;
+ if (B<0.0) B=0.0;
+ if (R>255.0) R=255.0;
+ if (G>255.0) G=255.0;
+ if (B>255.0) B=255.0;
+
+ *(x++) = (unsigned char)R;
+ *(x++) = (unsigned char)G;
+ *(x++) = (unsigned char)B;
+ a++; b++; c++;
+ }
+ }
+ memmove(destination,newDest,lgrTotale);
+ free(newDest);
+
+ } else {
+
+ // need to make RGB Pixels from R,G,B Planes
+ // (all the Frames at a time)
+
+ int l = Header->GetXSize()*Header->GetYSize()*Header->GetZSize();
+
+ char * newDest = (char*) malloc(lgrTotale);
+ char * x = newDest;
+ char * a = (char *)destination;
+ char * b = a + l;
+ char * c = b + l;
+
+ for (int j=0;j<l; j++) {
+ *(x++) = *(a++);
+ *(x++) = *(b++);
+ *(x++) = *(c++);
+ }
+ memmove(destination,newDest,lgrTotale);
+ free(newDest);
+ }
+ break;
+ }
+ case 2:
+ // Palettes were found
+ // Let the user deal with them !
+ return lgrTotale;
+ }
+ // now, it's an RGB image
+ // Lets's write it in the Header
+
+ // CreateOrReplaceIfExist ?
+
+ std::string spp = "3"; // Samples Per Pixel
+ Header->SetEntryByNumber(spp,0x0028,0x0002);
+ std::string rgb="RGB "; // Photometric Interpretation
+ Header->SetEntryByNumber(rgb,0x0028,0x0004);
+
+ std::string planConfig = "0"; // Planar Configuration
+ Header->SetEntryByNumber(planConfig,0x0028,0x0006);
+
+ // TODO : Drop Palette Color out of the Header?
+ return lgrTotale;
+}
+
+/**
+ * \ingroup gdcmFile
+ * \brief TODO JPR
+ * \warning doit-etre etre publique ?
+ * \toto : y a-t-il un inconvenient à fusioner ces 2 fonctions
+ *
+ * @param inData
+ * @param ExpectedSize
+ *
+ * @return boolean
+ */
+bool gdcmFile::SetImageData(void * inData, size_t ExpectedSize) {
+ Header->SetImageDataSize(ExpectedSize);
+ PixelData = inData;
+ lgrTotale = ExpectedSize;
+ return(true);
+}
+
+/**
+ * \ingroup gdcmFile
+ * \brief Writes on disk A SINGLE Dicom file
+ * NO test is performed on processor "Endiannity".
+ * It's up to the user to call his Reader properly
+ * @param fileName name of the file to be created
+ * (any already existing file is over written)
+ * @return false if write fails
+ */
+
+bool gdcmFile::WriteRawData (std::string fileName) {
+ FILE * fp1;
+ fp1 = fopen(fileName.c_str(),"wb");
+ if (fp1 == NULL) {
+ printf("Fail to open (write) file [%s] \n",fileName.c_str());
+ return (false);
+ }
+ fwrite (PixelData,lgrTotale, 1, fp1);
+ fclose (fp1);
+ return(true);
+}
+
+/**
+ * \ingroup gdcmFile
+ * \brief Writes on disk A SINGLE Dicom file
+ * NO test is performed on processor "Endiannity".
+ * @param fileName name of the file to be created
+ * (any already existing file is overwritten)
+ * @return false if write fails
+ */
+
+bool gdcmFile::WriteDcmImplVR (std::string fileName) {
+ return WriteBase(fileName, ImplicitVR);
+}
+
+/**
+ * \ingroup gdcmFile
+ * \brief
+ * @param fileName name of the file to be created
+ * (any already existing file is overwritten)
+ * @return false if write fails
+ */
+
+bool gdcmFile::WriteDcmImplVR (const char* fileName) {
+ return WriteDcmImplVR (std::string (fileName));
+}
+
+/**
+ * \ingroup gdcmFile
+ * \brief
+ * @param fileName name of the file to be created
+ * (any already existing file is overwritten)
+ * @return false if write fails
+ */
+
+bool 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 if a DICOM_V3 header is supplied,
+ * groups < 0x0008 and shadow groups are ignored)
+ * \warning NO TEST is performed on processor "Endiannity".
+ * Ca fonctionnera correctement (?) sur processeur Intel
+ * (Equivalent a IdDcmWrite)
+ *
+ * @param fileName name of the file to be created
+ * (any already existing file is overwritten)
+ * @return false if write fails
+ */
+
+bool gdcmFile::WriteAcr (std::string fileName) {
+ return WriteBase(fileName, ACR);
+}
+
+//-----------------------------------------------------------------------------
+// Protected
+/**
+ * \ingroup gdcmFile
+ *
+ * @param fileName name of the file to be created
+ * (any already existing file is overwritten)
+ * @param type file type (ExplicitVR, ImplicitVR, ...)
+ * @return false if write fails
+ */
+bool gdcmFile::WriteBase (std::string fileName, FileType type) {
+
+ FILE * fp1;
+
+ if (PixelRead==-1 && type != DICOMDIR) {
+/* std::cout << "U never Read the pixels; U cannot write the file"
+ << std::endl;*/
+ return false;
+ }
+
+ fp1 = fopen(fileName.c_str(),"wb");
+ if (fp1 == NULL) {
+ printf("Failed to open (write) File [%s] \n",fileName.c_str());
+ return (false);
+ }
+
+ 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);
+ free (filePreamble);
+ }
+
+ // --------------------------------------------------------------
+ // 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 ...
+
+ // TODO : the best trick would be *change* the recognition code
+ // but pb expected if user deals with, e.g. COMPLEX images
+
+ std::string rows, columns;
+ if ( Header->GetFileType() == ACR_LIBIDO){
+ rows = Header->GetEntryByNumber(0x0028, 0x0010);
+ columns = Header->GetEntryByNumber(0x0028, 0x0011);
+ Header->SetEntryByNumber(columns, 0x0028, 0x0010);
+ Header->SetEntryByNumber(rows , 0x0028, 0x0011);
+ }
+ // ----------------- End of Special Patch ----------------
+
+ // TODO : get the grPixel, numPixel values (for some ACR-NEMA images only)
+
+ guint16 grPixel =Header->GetGrPixel();
+ guint16 numPixel=Header->GetNumPixel();;
+
+ // Update Pixel Data Length
+ // the *last* of the (GrPixel, NumPixel), if many.
+
+ TagKey key = gdcmDictEntry::TranslateToKey(grPixel, numPixel);
+ TagHeaderEntryHT::iterator p2;
+ gdcmHeaderEntry * PixelElement;
+
+ IterHT it= Header->GetEntry().equal_range(key); // get a pair of iterators first-last synonym
+
+ if (Header->GetEntry().count(key) == 1) // only the first is significant
+ p2=it.first; // iterator on the first (unique) synonym
+ else
+ p2=it.second;// iterator on the last synonym
+
+ PixelElement=p2->second; // H Table target column (2-nd col)
+ // PixelElement->SetPrintLevel(2);
+ // PixelElement->Print();
+
+ if (PixelRead==1)
+ PixelElement->SetLength(lgrTotaleRaw);
+ else if (PixelRead==0)
+ PixelElement->SetLength(lgrTotale);
+
+ //PixelElement->SetPrintLevel(2);
+ //PixelElement->Print();
+
+ Header->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 (Header->GetFileType() == ACR_LIBIDO){
+ Header->SetEntryByNumber(rows , 0x0028, 0x0010);
+ Header->SetEntryByNumber(columns, 0x0028, 0x0011);
+ }
+ // ----------------- End of Special Patch ----------------
+
+ fwrite(PixelData, lgrTotale, 1, fp1);
+ fclose (fp1);
+ return(true);
+}
+
+//-----------------------------------------------------------------------------
+// Private
+/**
+ * \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;
+
+ 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("SWAP value (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;
+
+ 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("SWAP value (32 bits) not allowed : %d\n", swap);
+ }
+return;
+}
+
+/**
+ * \ingroup gdcmFile
+ * \brief Read pixel data from disk (optionaly decompressing) into the
+ * caller specified memory location.
+ * @param destination where the pixel data should be stored.
+ *
+ */
+bool gdcmFile::ReadPixelData(void* destination) {
+
+ FILE *fp;
+
+ if ( !(fp=Header->OpenFile()))
+ return false;
+ if ( fseek(fp, Header->GetPixelOffset(), SEEK_SET) == -1 ) {
+ Header->CloseFile();
+ return false;
+ }
+ // ---------------------- Compacted File (12 Bits Per Pixel)
+ /* unpack 12 Bits pixels into 16 Bits pixels */
+ /* 2 pixels 12bit = [0xABCDEF] */
+ /* 2 pixels 16bit = [0x0ABD] + [0x0FCE] */
+
+ if (Header->GetBitsAllocated()==12) {
+ int nbPixels = Header->GetXSize() * Header->GetYSize();
+ unsigned char b0, b1, b2;
+
+ unsigned short int* pdestination = (unsigned short int*)destination;
+ for(int p=0;p<nbPixels;p+=2) {
+ fread(&b0,1,1,fp);
+ fread(&b1,1,1,fp);
+ fread(&b2,1,1,fp);
+ //Two steps is necessary to please VC++
+ *pdestination++ = ((b0 >> 4) << 8) + ((b0 & 0x0f) << 4) + (b1 & 0x0f);
+ /* A */ /* B */ /* D */
+ *pdestination++ = ((b2 & 0x0f) << 8) + ((b1 >> 4) << 4) + (b2 >> 4);
+ /* F */ /* C */ /* E */
+
+ // Troubles expected on Big-Endian processors ?
+ }
+
+ Header->CloseFile();
+ return(true);
+ }
+
+ // ---------------------- Uncompressed File
+ if ( !Header->IsDicomV3() ||
+ Header->IsImplicitVRLittleEndianTransferSyntax() ||
+ Header->IsExplicitVRLittleEndianTransferSyntax() ||
+ Header->IsExplicitVRBigEndianTransferSyntax() ||
+ Header->IsDeflatedExplicitVRLittleEndianTransferSyntax() ) {
+
+ size_t ItemRead = fread(destination, Header->GetPixelAreaLength(), 1, fp);
+ if ( ItemRead != 1 ) {
+ Header->CloseFile();
+ return false;
+ } else {
+ Header->CloseFile();
+ return true;
+ }
+ }
+
+ // ---------------------- Run Length Encoding
+ if (Header->IsRLELossLessTransferSyntax()) {
+ bool res = (bool)gdcm_read_RLE_file (fp,destination);
+ Header->CloseFile();
+ return res;
+ }
+
+ // --------------- SingleFrame/Multiframe JPEG Lossless/Lossy/2000
+ int nb;
+ std::string str_nb=Header->GetEntryByNumber(0x0028,0x0100);
+ if (str_nb == GDCM_UNFOUND ) {
+ nb = 16;
+ } else {
+ nb = atoi(str_nb.c_str() );
+ if (nb == 12) nb =16; // ?? 12 should be ACR-NEMA only ?
+ }
+
+ int nBytes= nb/8;
+
+ int taille = Header->GetXSize() * Header->GetYSize()
+ * Header->GetSamplesPerPixel();
+ long fragmentBegining; // for ftell, fseek
+
+ bool jpg2000 = Header->IsJPEG2000();
+ bool jpgLossless = Header->IsJPEGLossless();
+
+ bool res = true;
+ 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(Header->GetSwapCode()) {
+ ItemTagGr=Header->SwapShort(ItemTagGr);
+ ItemTagEl=Header->SwapShort(ItemTagEl);
+ }
+ fread(&ln,4,1,fp);
+ if(Header->GetSwapCode())
+ ln=Header->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(Header->GetSwapCode()) {
+ ItemTagGr=Header->SwapShort(ItemTagGr);
+ ItemTagEl=Header->SwapShort(ItemTagEl);
+ }
+
+ // parsing fragments until Sequence Delim. Tag found
+ while ( ( ItemTagGr == 0xfffe) && (ItemTagEl != 0xe0dd) ) {
+ // --- for each Fragment
+
+ fread(&ln,4,1,fp);
+ if(Header->GetSwapCode())
+ ln=Header->SwapLong(ln); // Fragment Item length
+
+ fragmentBegining=ftell(fp);
+
+ if (jpg2000) { // JPEG 2000 : call to ???
+
+ res = (bool)gdcm_read_JPEG2000_file (fp,destination); // Not Yet written
+
+ } // ------------------------------------- endif (JPEG2000)
+
+ else if (jpgLossless) { // JPEG LossLess : call to xmedcom JPEG
+
+ JPEGLosslessDecodeImage (fp, // Reading Fragment pixels
+ (unsigned short *)destination,
+ Header->GetPixelSize()*8* Header->GetSamplesPerPixel(),
+ ln);
+ res=1; // in order not to break the loop
+
+ } // ------------------------------------- endif (JPEGLossless)
+
+ else { // JPEG Lossy : call to IJG 6b
+
+ if (Header->GetBitsStored() == 8) {
+ res = (bool)gdcm_read_JPEG_file (fp,destination); // Reading Fragment pixels
+ } else {
+ res = (bool)gdcm_read_JPEG_file12 (fp,destination);// Reading Fragment pixels
+ }
+ } // ------------------------------------- endif (JPEGLossy)
+
+ if (!res) break;
+
+ destination = (char *)destination + taille * nBytes; // location in user's memory
+ // for next fragment (if any)
+
+ 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(Header->GetSwapCode()) {
+ ItemTagGr=Header->SwapShort(ItemTagGr);
+ ItemTagEl=Header->SwapShort(ItemTagEl);
+ }
+
+ } // endWhile parsing fragments until Sequence Delim. Tag found
+
+ Header->CloseFile();
+ return res;
}
+//-----------------------------------------------------------------------------