- }
-
- // ---------------------- Run Length Encoding
-
- if (Header->IsRLELossLessTransferSyntax()) {
- bool res = (bool)gdcm_read_RLE_file (fp,destination);
- return res;
- }
-
- // --------------- SingleFrame/Multiframe JPEG Lossless/Lossy/2000
-
- int nb;
- std::string str_nb=Header->GetPubElValByNumber(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;
-}
-
-/**
- * \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);
- return(PixelData);
-}
-
-/**
- * \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);
- 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);
-
- 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];
+ }
+
+ // beware of trailing space at end of string
+ // DICOM tags are never of odd length
+ if ( strPhotometricInterpretation == GDCM_UNFOUND ||
+ Util::DicomStringEqual(strPhotometricInterpretation, "MONOCHROME1") ||
+ Util::DicomStringEqual(strPhotometricInterpretation, "MONOCHROME2") )
+ {
+ return 1;
+ }
+ else
+ {
+ // we assume that *all* kinds of YBR are dealt with
+ return 3;
+ }
+}
+
+/**
+ * \brief This function is intended to user that 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 1 if Gray level, 3 if Color (RGB or YBR - NOT 'PALETTE COLOR' -)
+ */
+int File::GetNumberOfScalarComponentsRaw()
+{
+ // 0028 0100 US IMG Bits Allocated
+ // (in order no to be messed up by old RGB images)
+ if ( File::GetEntryString(0x0028,0x0100) == "24" )
+ {
+ return 3;
+ }
+
+ // we assume that *all* kinds of YBR are dealt with
+ return GetSamplesPerPixel();
+}
+
+/**
+ * \brief Recover the offset (from the beginning of the file)
+ * of *image* pixels (not *icone image* pixels, if any !)
+ * @return Pixel Offset
+ */
+size_t File::GetPixelOffset()
+{
+ DocEntry *pxlElement = GetDocEntry(GrPixel, NumPixel);
+ if ( pxlElement )
+ {
+ return pxlElement->GetOffset();
+ }
+ else
+ {
+ gdcmDebugMacro( "Big trouble : Pixel Element ("
+ << std::hex << GrPixel<<","<< NumPixel<< ") NOT found" );
+ return 0;
+ }
+}
+
+/**
+ * \brief Recover the pixel area length (in Bytes)
+ * @return Pixel Element Length, as stored in the header
+ * (NOT the memory space necessary to hold the Pixels
+ * -in case of embeded compressed image-)
+ * 0 : NOT USABLE file. The caller has to check.
+ */
+size_t File::GetPixelAreaLength()
+{
+ DocEntry *pxlElement = GetDocEntry(GrPixel, NumPixel);
+ if ( pxlElement )
+ {
+ return pxlElement->GetLength();
+ }
+ else
+ {
+ gdcmDebugMacro( "Big trouble : Pixel Element ("
+ << std::hex << GrPixel<<","<< NumPixel<< ") NOT found" );
+ return 0;
+ }
+}
+
+/**
+ * \brief Adds the characteristics of a new element we want to anonymize
+ * @param group Group number of the target tag.
+ * @param elem Element number of the target tag.
+ * @param value new value (string) to substitute with
+ */
+void File::AddAnonymizeElement (uint16_t group, uint16_t elem,
+ std::string const &value)
+{
+ DicomElement el;
+ el.Group = group;
+ el.Elem = elem;
+ el.Value = value;
+ UserAnonymizeList.push_back(el);
+}
+
+/**
+ * \brief Overwrites in the file the values of the DicomElements
+ * held in the list
+ */
+void File::AnonymizeNoLoad()
+{
+ std::fstream *fp = new std::fstream(Filename.c_str(),
+ std::ios::in | std::ios::out | std::ios::binary);
+ gdcm::DocEntry *d;
+ uint32_t offset;
+ uint32_t lgth;
+ uint32_t valLgth = 0;
+ std::string *spaces;
+ for (ListElements::iterator it = UserAnonymizeList.begin();
+ it != UserAnonymizeList.end();
+ ++it)
+ {
+ d = GetDocEntry( (*it).Group, (*it).Elem);
+
+ if ( d == NULL)
+ continue;
+
+ if ( dynamic_cast<SeqEntry *>(d) )
+ {
+ gdcmWarningMacro( "You cannot 'Anonymize' a SeqEntry ");
+ continue;