+
+/**
+ * \ingroup gdcmHeader
+ * \brief
+ * @return integer, acts as a Boolean
+ */
+int gdcmHeader::Write(FILE * fp, FileType type) {
+
+ // TODO : move the following lines (and a lot of others, to be written)
+ // to a future function CheckAndCorrectHeader
+
+ if (type == ImplicitVR) {
+ std::string implicitVRTransfertSyntax = "1.2.840.10008.1.2";
+ ReplaceOrCreateByNumber(implicitVRTransfertSyntax,0x0002, 0x0010);
+
+ //FIXME Refer to standards on page 21, chapter 6.2 "Value representation":
+ // values with a VR of UI shall be padded with a single trailing null
+ // Dans le cas suivant on doit pader manuellement avec un 0
+
+ PubElValSet.SetElValueLengthByNumber(18, 0x0002, 0x0010);
+ }
+
+ if (type == ExplicitVR) {
+ std::string explicitVRTransfertSyntax = "1.2.840.10008.1.2.1";
+ ReplaceOrCreateByNumber(explicitVRTransfertSyntax,0x0002, 0x0010);
+
+ //FIXME Refer to standards on page 21, chapter 6.2 "Value representation":
+ // values with a VR of UI shall be padded with a single trailing null
+ // Dans le cas suivant on doit pader manuellement avec un 0
+
+ PubElValSet.SetElValueLengthByNumber(20, 0x0002, 0x0010);
+ }
+
+ return PubElValSet.Write(fp, type);
+}
+
+//
+// ------------------------ 'non string' elements related functions
+//
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Loads (from disk) the element content
+ * when a string is not suitable
+ */
+void * gdcmHeader::LoadElementVoidArea(guint16 Group, guint16 Elem) {
+ gdcmElValue * Element= PubElValSet.GetElementByNumber(Group, Elem);
+ if ( !Element )
+ return NULL;
+ size_t o =(size_t)Element->GetOffset();
+ fseek(fp, o, SEEK_SET);
+ int l=Element->GetLength();
+ void * a = malloc(l);
+ if(!a) {
+ return NULL;
+ }
+ /* int res = */ PubElValSet.SetVoidAreaByNumber(a, Group, Elem);
+ // TODO check the result
+ size_t l2 = fread(a, 1, l ,fp);
+ if(l != l2) {
+ free(a);
+ return NULL;
+ }
+ return a;
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Gets (from Header) the offset of a 'non string' element value
+ * \ (LoadElementValue has already be executed)
+ * @param Group
+ * @param Elem
+ * @return File Offset of the Element Value
+ */
+ size_t gdcmHeader::GetPubElValOffsetByNumber(guint16 Group, guint16 Elem) {
+ gdcmElValue* elValue = PubElValSet.GetElementByNumber(Group, Elem);
+ if (!elValue) {
+ dbg.Verbose(1, "gdcmHeader::GetElValueByNumber",
+ "failed to Locate gdcmElValue");
+ return (size_t)0;
+ }
+ return elValue->GetOffset();
+}
+
+/**
+ * \ingroup gdcmHeader
+* \brief Gets (from Header) a 'non string' element value
+ * \ (LoadElementValue has already be executed)
+ * @param Group
+ * @param Elem
+ * @return Pointer to the 'non string' area
+
+ */
+ void * gdcmHeader::GetPubElValVoidAreaByNumber(guint16 Group, guint16 Elem) {
+ gdcmElValue* elValue = PubElValSet.GetElementByNumber(Group, Elem);
+ if (!elValue) {
+ dbg.Verbose(1, "gdcmHeader::GetElValueByNumber",
+ "failed to Locate gdcmElValue");
+ return (NULL);
+ }
+ return elValue->GetVoidArea();
+}
+
+
+//
+// =============================================================================
+// Heuristics based accessors
+//==============================================================================
+//
+
+// TODO : move to an other file.
+
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Retrieve the number of columns of image.
+ * @return The encountered size when found, 0 by default.
+ */
+int gdcmHeader::GetXSize(void) {
+ // We cannot check for "Columns" because the "Columns" tag is present
+ // both in IMG (0028,0011) and OLY (6000,0011) sections of the dictionary.
+ std::string StrSize = GetPubElValByNumber(0x0028,0x0011);
+ if (StrSize == GDCM_UNFOUND)
+ return 0;
+ return atoi(StrSize.c_str());
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Retrieve the number of lines of image.
+ * \warning The defaulted value is 1 as opposed to gdcmHeader::GetXSize()
+ * @return The encountered size when found, 1 by default.
+ */
+int gdcmHeader::GetYSize(void) {
+ // We cannot check for "Rows" because the "Rows" tag is present
+ // both in IMG (0028,0010) and OLY (6000,0010) sections of the dictionary.
+ std::string StrSize = GetPubElValByNumber(0x0028,0x0010);
+ if (StrSize != GDCM_UNFOUND)
+ return atoi(StrSize.c_str());
+ if ( IsDicomV3() )
+ return 0;
+ else
+ // The Rows (0028,0010) entry is optional for ACR/NEMA. It might
+ // hence be a signal (1d image). So we default to 1:
+ return 1;
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Retrieve the number of planes of volume or the number
+ * of frames of a multiframe.
+ * \warning When present we consider the "Number of Frames" as the third
+ * dimension. When absent we consider the third dimension as
+ * being the "Planes" tag content.
+ * @return The encountered size when found, 1 by default.
+ */
+int gdcmHeader::GetZSize(void) {
+ // Both in DicomV3 and ACR/Nema the consider the "Number of Frames"
+ // as the third dimension.
+ std::string StrSize = GetPubElValByNumber(0x0028,0x0008);
+ if (StrSize != GDCM_UNFOUND)
+ return atoi(StrSize.c_str());
+
+ // We then consider the "Planes" entry as the third dimension [we
+ // cannot retrieve by name since "Planes tag is present both in
+ // IMG (0028,0012) and OLY (6000,0012) sections of the dictionary].
+ StrSize = GetPubElValByNumber(0x0028,0x0012);
+ if (StrSize != GDCM_UNFOUND)
+ return atoi(StrSize.c_str());
+ return 1;
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Retrieve the number of Bits Stored
+ * (as opposite to number of Bits Allocated)
+ *
+ * @return The encountered number of Bits Stored, 0 by default.
+ */
+int gdcmHeader::GetBitsStored(void) {
+ std::string StrSize = GetPubElValByNumber(0x0028,0x0101);
+ if (StrSize == GDCM_UNFOUND)
+ return 1;
+ return atoi(StrSize.c_str());
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Retrieve the number of Bits Allocated
+ * (8, 12 -compacted ACR-NEMA files, 16, ...)
+ *
+ * @return The encountered number of Bits Allocated, 0 by default.
+ */
+int gdcmHeader::GetBitsAllocated(void) {
+ std::string StrSize = GetPubElValByNumber(0x0028,0x0100);
+ if (StrSize == GDCM_UNFOUND)
+ return 1;
+ return atoi(StrSize.c_str());
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Retrieve the number of Samples Per Pixel
+ * (1 : gray level, 3 : RGB -1 or 3 Planes-)
+ *
+ * @return The encountered number of Samples Per Pixel, 1 by default.
+ */
+int gdcmHeader::GetSamplesPerPixel(void) {
+ std::string StrSize = GetPubElValByNumber(0x0028,0x0002);
+ if (StrSize == GDCM_UNFOUND)
+ return 1; // Well, it's supposed to be mandatory ...
+ return atoi(StrSize.c_str());
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Retrieve the Planar Configuration for RGB images
+ * (0 : RGB Pixels , 1 : R Plane + G Plane + B Plane)
+ *
+ * @return The encountered Planar Configuration, 0 by default.
+ */
+int gdcmHeader::GetPlanarConfiguration(void) {
+ std::string StrSize = GetPubElValByNumber(0x0028,0x0006);
+ if (StrSize == GDCM_UNFOUND)
+ return 0;
+ return atoi(StrSize.c_str());
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Return the size (in bytes) of a single pixel of data.
+ * @return The size in bytes of a single pixel of data.
+ *
+ */
+int gdcmHeader::GetPixelSize(void) {
+ std::string PixelType = GetPixelType();
+ if (PixelType == "8U" || PixelType == "8S")
+ return 1;
+ if (PixelType == "16U" || PixelType == "16S")
+ return 2;
+ if (PixelType == "32U" || PixelType == "32S")
+ return 4;
+ dbg.Verbose(0, "gdcmHeader::GetPixelSize: Unknown pixel type");
+ return 0;
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Build the Pixel Type of the image.
+ * Possible values are:
+ * - 8U unsigned 8 bit,
+ * - 8S signed 8 bit,
+ * - 16U unsigned 16 bit,
+ * - 16S signed 16 bit,
+ * - 32U unsigned 32 bit,
+ * - 32S signed 32 bit,
+ * \warning 12 bit images appear as 16 bit.
+ * \ 24 bit images appear as 8 bit
+ * @return
+ */
+std::string gdcmHeader::GetPixelType(void) {
+ std::string BitsAlloc;
+ BitsAlloc = GetElValByName("Bits Allocated");
+ if (BitsAlloc == GDCM_UNFOUND) {
+ dbg.Verbose(0, "gdcmHeader::GetPixelType: unfound Bits Allocated");
+ BitsAlloc = std::string("16");
+ }
+ if (BitsAlloc == "12") // It will be unpacked
+ BitsAlloc = std::string("16");
+ else if (BitsAlloc == "24") // (in order no to be messed up
+ BitsAlloc = std::string("8"); // by old RGB images)
+
+ std::string Signed;
+ Signed = GetElValByName("Pixel Representation");
+ if (Signed == GDCM_UNFOUND) {
+ dbg.Verbose(0, "gdcmHeader::GetPixelType: unfound Pixel Representation");
+ BitsAlloc = std::string("0");
+ }
+ if (Signed == "0")
+ Signed = std::string("U");
+ else
+ Signed = std::string("S");
+
+ return( BitsAlloc + Signed);
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief gets the info from 0002,0010 : Transfert Syntax
+ * \ else 1.
+ * @return Transfert Syntax Name (as oposite to Transfert Syntax UID)
+ */
+std::string gdcmHeader::GetTransferSyntaxName(void) {
+ std::string TransfertSyntax = GetPubElValByNumber(0x0002,0x0010);
+ if (TransfertSyntax == GDCM_UNFOUND) {
+ dbg.Verbose(0, "gdcmHeader::GetTransferSyntaxName: unfound Transfert Syntax (0002,0010)");
+ return "Uncompressed ACR-NEMA";
+ }
+ // we do it only when we need it
+ gdcmTS * ts = gdcmGlobal::GetTS();
+ std::string tsName=ts->GetValue(TransfertSyntax);
+ //delete ts; // Seg Fault when deleted ?!
+ return tsName;
+}
+
+// -------------------------------- Lookup Table related functions ------------
+
+/**
+ * \ingroup gdcmHeader
+ * \brief tells us if LUT are used
+ * \warning Right now, Segmented xxx Palette Color Lookup Table Data
+ * \ are NOT considered as LUT, since nobody knows
+ *\ how to deal with them
+ * @return int acts as a Boolean
+ */
+
+int gdcmHeader::HasLUT(void) {
+
+ // Check the presence of the LUT Descriptors
+ if (GetPubElValByNumber(0x0028,0x1101) == GDCM_UNFOUND)
+ return 0;
+ // LutDescriptorGreen
+ if (GetPubElValByNumber(0x0028,0x1102) == GDCM_UNFOUND)
+ return 0;
+ // LutDescriptorBlue
+ if (GetPubElValByNumber(0x0028,0x1103) == GDCM_UNFOUND)
+ return 0;
+ // It is not enough
+ // we check also
+ if (GetPubElValByNumber(0x0028,0x1201) == GDCM_UNFOUND)
+ return 0;
+ if (GetPubElValByNumber(0x0028,0x1202) == GDCM_UNFOUND)
+ return 0;
+ if (GetPubElValByNumber(0x0028,0x1203) == GDCM_UNFOUND)
+ return 0;
+ return 1;
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief gets the info from 0028,1101 : Lookup Table Desc-Red
+ * \ else 0
+ * @return Lookup Table nBit
+ * \ when (0028,0004),Photometric Interpretation = [PALETTE COLOR ]
+ */
+
+int gdcmHeader::GetLUTNbits(void) {
+ std::vector<std::string> tokens;
+ //int LutLength;
+ //int LutDepth;
+ int LutNbits;
+ //Just hope Lookup Table Desc-Red = Lookup Table Desc-Red = Lookup Table Desc-Blue
+ // Consistency already checked in GetLUTLength
+ std::string LutDescription = GetPubElValByNumber(0x0028,0x1101);
+ if (LutDescription == GDCM_UNFOUND)
+ return 0;
+ tokens.erase(tokens.begin(),tokens.end()); // clean any previous value
+ Tokenize (LutDescription, tokens, "\\");
+ //LutLength=atoi(tokens[0].c_str());
+ //LutDepth=atoi(tokens[1].c_str());
+ LutNbits=atoi(tokens[2].c_str());
+ tokens.clear();
+ return LutNbits;
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief builts Red/Green/Blue/Alpha LUT from Header
+ * \ when (0028,0004),Photometric Interpretation = [PALETTE COLOR ]
+ * \ and (0028,1101),(0028,1102),(0028,1102)
+ * \ - xxx Palette Color Lookup Table Descriptor - are found
+ * \ and (0028,1201),(0028,1202),(0028,1202)
+ * \ - xxx Palette Color Lookup Table Data - are found
+ * \warning does NOT deal with :
+ * \ 0028 1100 Gray Lookup Table Descriptor (Retired)
+ * \ 0028 1221 Segmented Red Palette Color Lookup Table Data
+ * \ 0028 1222 Segmented Green Palette Color Lookup Table Data
+ * \ 0028 1223 Segmented Blue Palette Color Lookup Table Data
+ * \ no known Dicom reader deails with them :-(
+ * @return Lookup Table RGBA
+ */
+
+unsigned char * gdcmHeader::GetLUTRGBA(void) {
+// Not so easy : see
+// http://www.barre.nom.fr/medical/dicom2/limitations.html#Color%20Lookup%20Tables
+// and OT-PAL-8-face.dcm
+
+// if Photometric Interpretation # PALETTE COLOR, no LUT to be done
+
+ if (gdcmHeader::GetPubElValByNumber(0x0028,0x0004) != "PALETTE COLOR ") {
+ return NULL;
+ }
+
+ int lengthR, debR, nbitsR;
+ int lengthG, debG, nbitsG;
+ int lengthB, debB, nbitsB;
+
+// Get info from Lut Descriptors
+// (the 3 LUT descriptors may be different)
+
+ std::string LutDescriptionR = GetPubElValByNumber(0x0028,0x1101);
+ if (LutDescriptionR == GDCM_UNFOUND)
+ return NULL;
+ std::string LutDescriptionG = GetPubElValByNumber(0x0028,0x1102);
+ if (LutDescriptionG == GDCM_UNFOUND)
+ return NULL;
+ std::string LutDescriptionB = GetPubElValByNumber(0x0028,0x1103);
+ if (LutDescriptionB == GDCM_UNFOUND)
+ return NULL;
+
+ std::vector<std::string> tokens;
+
+ tokens.erase(tokens.begin(),tokens.end()); // clean any previous value
+ Tokenize (LutDescriptionR, tokens, "\\");
+ lengthR=atoi(tokens[0].c_str()); // Red LUT length in Bytes
+ debR =atoi(tokens[1].c_str()); // subscript of the first Lut Value
+ nbitsR =atoi(tokens[2].c_str()); // Lut item size (in Bits)
+ tokens.clear();
+
+ tokens.erase(tokens.begin(),tokens.end()); // clean any previous value
+ Tokenize (LutDescriptionG, tokens, "\\");
+ lengthG=atoi(tokens[0].c_str()); // Green LUT length in Bytes
+ debG =atoi(tokens[1].c_str());
+ nbitsG =atoi(tokens[2].c_str());
+ tokens.clear();
+
+ tokens.erase(tokens.begin(),tokens.end()); // clean any previous value
+ Tokenize (LutDescriptionB, tokens, "\\");
+ lengthB=atoi(tokens[0].c_str()); // Blue LUT length in Bytes
+ debB =atoi(tokens[1].c_str());
+ nbitsB =atoi(tokens[2].c_str());
+ tokens.clear();
+
+// Load LUTs into memory, (as they were stored on disk)
+
+ 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 ) {
+ return NULL;
+ }
+ // forge the 4 * 8 Bits Red/Green/Blue/Alpha LUT
+
+ unsigned char *LUTRGBA = (unsigned char *)calloc(1024,1); // 256 * 4 (R, G, B, Alpha)
+ if (!LUTRGBA) {
+ return NULL;
+ }
+ memset(LUTRGBA, 0, 1024);
+ // Bits Allocated
+ int nb;
+ std::string str_nb = GetPubElValByNumber(0x0028,0x0100);
+ if (str_nb == GDCM_UNFOUND ) {
+ nb = 16;
+ } else {
+ nb = atoi(str_nb.c_str() );
+ }
+ int mult;
+
+ if (nbitsR==16 && nb==8) // when LUT item size is different than pixel size
+ mult=2; // high byte must be = low byte
+ else // See PS 3.3-2003 C.11.1.1.2 p 619
+ mult=1;
+
+
+ // if we get a black image, let's just remove the '+1'
+ // from 'i*mult+1' and check again
+ // if it works, we shall have to check the 3 Palettes
+ // to see which byte is ==0 (first one, or second one)
+ // and fix the code
+ // We give up the checking to avoid some overhead
+
+ unsigned char *a;
+ int i;
+ a= LUTRGBA+0;
+ for(i=0;i<lengthR;i++) {
+ *a = lutR[i*mult+1];
+ a+=4;
+ }
+ a= LUTRGBA+1;
+ for(i=0;i<lengthG;i++) {
+ *a = lutG[i*mult+1];
+ a+=4;
+ }
+ a= LUTRGBA+2;
+ for(i=0;i<lengthB;i++) {
+ *a = lutB[i*mult+1];
+ a+=4;
+ }
+ a= LUTRGBA+3;
+ for(i=0;i<256;i++) {
+ *a = 1; // Alpha component
+ a+=4;
+ }
+
+//How to free the now useless LUTs?
+//
+//free(LutR); free(LutB); free(LutG);
+
+ return(LUTRGBA);
+}
+
+/////////////////////////////////////////////////////////////////
+/**
+ * \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 gdcmHeader::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);
+}
+
+