+
+/**
+ * \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 = GetEntryByNumber(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; 0 by default
+ * 0 means the file is NOT USABLE; the caller will have to check
+ */
+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;
+ if (PixelType == "FD")
+ return 8;
+ 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,
+ * - FD floating double 64 bits (Not kosher DICOM, but so usefull!)
+ * \warning 12 bit images appear as 16 bit.
+ * 24 bit images appear as 8 bit
+ * @return 0S if nothing found. NOT USABLE file. The caller has to check
+ */
+std::string gdcmHeader::GetPixelType(void) {
+ std::string BitsAlloc = GetEntryByNumber(0x0028, 0x0100); // Bits Allocated
+ if (BitsAlloc == GDCM_UNFOUND) {
+ dbg.Verbose(0, "gdcmHeader::GetPixelType: unfound Bits Allocated");
+ BitsAlloc = std::string("16");
+ }
+ if (BitsAlloc == "64") // )
+ return ("FD");
+ 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 = GetEntryByNumber(0x0028, 0x0103); // "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 Recover the offset (from the beginning of the file)
+ * of *image* pixels (not *icone image* pixels, if any !)
+ * @return Pixel Offset
+ */
+size_t gdcmHeader::GetPixelOffset(void) {
+ //
+ // If the element (0x0088,0x0200) 'icone image sequence' is found
+ // (grPixel,numPixel) is stored twice : the first one for the icon
+ // the second one for the image ...
+ // pb : sometimes , (0x0088,0x0200) exists, but doesn't contain *anything*
+ // see gdcmData/MxTwinLossLess.dcm ...
+
+ /**
+ * \todo Clean me
+ *std::string icone = GetEntryByNumber(0x0088,0x0200); //icone image sequence
+ */
+
+ IterHT it = GetHeaderEntrySameNumber(GrPixel,NumPixel);
+ TagKey key = gdcmDictEntry::TranslateToKey(GrPixel,NumPixel);
+ gdcmHeaderEntry* PixelElement;
+ if (countGrPixel == 1)
+ PixelElement = (it.first)->second;
+ else {
+ PixelElement = (++it.first)->second; // hope there are no more than 2 !
+ }
+ if (PixelElement) {
+ return PixelElement->GetOffset();
+ } else {
+#ifdef GDCM_DEBUG
+ std::cout << "Big trouble : Pixel Element ("
+ << std::hex << GrPixel<<","<< NumPixel<< ") NOT found"
+ << std::endl;
+#endif //GDCM_DEBUG
+ return 0;
+ }
+}
+// TODO : unify those two (previous one and next one)
+/**
+ * \ingroup gdcmHeader
+ * \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 gdcmHeader::GetPixelAreaLength(void) {
+
+ IterHT it = GetHeaderEntrySameNumber(GrPixel,NumPixel);
+ TagKey key = gdcmDictEntry::TranslateToKey(GrPixel,NumPixel);
+ gdcmHeaderEntry* PixelElement;
+
+ if (countGrPixel==1)
+ PixelElement = (it.first)->second;
+ else
+ PixelElement = (++it.first)->second;
+
+ if (PixelElement) {
+ return PixelElement->GetLength();
+ } else {
+#ifdef GDCM_DEBUG
+ std::cout << "Big trouble : Pixel Element ("
+ << std::hex << GrPixel<<","<< NumPixel<< ") NOT found"
+ << std::endl;
+#endif //GDCM_DEBUG
+ return 0;
+ }
+}
+
+/**
+ * \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
+ * Please warn me if you know sbdy that *does* know ... jprx
+ * @return true if LUT Descriptors and LUT Tables were found
+ */
+bool gdcmHeader::HasLUT(void) {
+
+ // Check the presence of the LUT Descriptors, and LUT Tables
+ // LutDescriptorRed
+ if ( !GetHeaderEntryByNumber(0x0028,0x1101) )
+ return false;
+ // LutDescriptorGreen
+ if ( !GetHeaderEntryByNumber(0x0028,0x1102) )
+ return false;
+ // LutDescriptorBlue
+ if ( !GetHeaderEntryByNumber(0x0028,0x1103) )
+ return false;
+ // Red Palette Color Lookup Table Data
+ if ( !GetHeaderEntryByNumber(0x0028,0x1201) )
+ return false;
+ // Green Palette Color Lookup Table Data
+ if ( !GetHeaderEntryByNumber(0x0028,0x1202) )
+ return false;
+ // Blue Palette Color Lookup Table Data
+ if ( !GetHeaderEntryByNumber(0x0028,0x1203) )
+ return false;
+ // FIXME : (0x0028,0x3006) : LUT Data (CTX dependent)
+ // NOT taken into account, but we don't know how to use it ...
+ return true;
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief gets the info from 0028,1101 : Lookup Table Desc-Red
+ * else 0
+ * @return Lookup Table number of Bits , 0 by default
+ * when (0028,0004),Photometric Interpretation = [PALETTE COLOR ]
+ * @ return bit number of each LUT item
+ */
+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 = GetEntryByNumber(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 deals with them :-(
+ * @return a RGBA Lookup Table
+ */
+unsigned char * gdcmHeader::GetLUTRGBA(void) {
+// Not so easy : see
+// http://www.barre.nom.fr/medical/dicom2/limitations.html#Color%20Lookup%20Tables
+
+// if Photometric Interpretation # PALETTE COLOR, no LUT to be done
+ if (GetEntryByNumber(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 = GetEntryByNumber(0x0028,0x1101);
+ if (LutDescriptionR == GDCM_UNFOUND)
+ return NULL;
+ std::string LutDescriptionG = GetEntryByNumber(0x0028,0x1102);
+ if (LutDescriptionG == GDCM_UNFOUND)
+ return NULL;
+ std::string LutDescriptionB = GetEntryByNumber(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()); // subscript of the first Lut Value
+ nbitsG =atoi(tokens[2].c_str()); // Lut item size (in Bits)
+ 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()); // subscript of the first Lut Value
+ nbitsB =atoi(tokens[2].c_str()); // Lut item size (in Bits)
+ tokens.clear();
+
+ // Load LUTs into memory, (as they were stored on disk)
+ unsigned char *lutR = (unsigned char *)
+ GetEntryVoidAreaByNumber(0x0028,0x1201);
+ unsigned char *lutG = (unsigned char *)
+ GetEntryVoidAreaByNumber(0x0028,0x1202);
+ unsigned char *lutB = (unsigned char *)
+ GetEntryVoidAreaByNumber(0x0028,0x1203);
+
+ if (!lutR || !lutG || !lutB ) {
+ return NULL;
+ }
+ // forge the 4 * 8 Bits Red/Green/Blue/Alpha LUT
+
+ unsigned char *LUTRGBA = new (unsigned char)[1024]; // 256 * 4 (R, G, B, Alpha)
+ if (!LUTRGBA) {
+ return NULL;
+ }
+ memset(LUTRGBA, 0, 1024);
+ // Bits Allocated
+ int nb;
+ std::string str_nb = GetEntryByNumber(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 (useless ?)overhead
+ // (optimistic asumption)
+ 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); // Seg Fault when used
+ return(LUTRGBA);
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief gets the info from 0002,0010 : Transfert Syntax and gdcmTS
+ * else 1.
+ * @return the full Transfert Syntax Name (as oposite to Transfert Syntax UID)
+ */
+std::string gdcmHeader::GetTransfertSyntaxName(void) {
+ // use the gdcmTS (TS : Transfert Syntax)
+ std::string TransfertSyntax = GetEntryByNumber(0x0002,0x0010);
+ if (TransfertSyntax == GDCM_UNFOUND) {
+ dbg.Verbose(0, "gdcmHeader::GetTransfertSyntaxName: 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;
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Sets the Pixel Area size in the Header
+ * --> not-for-rats function
+ * @param ImageDataSize new Pixel Area Size
+ * warning : nothing else is checked
+ */
+void gdcmHeader::SetImageDataSize(size_t ImageDataSize) {
+ std::string content1;
+ char car[20];
+
+ // Assumes HeaderEntry (GrPixel, NumPixel) is unique ...
+ //\todo deal with multiplicity (see gdcmData/icone.dcm)
+ sprintf(car,"%d",ImageDataSize);
+
+ gdcmHeaderEntry *a = GetHeaderEntryByNumber(GrPixel, NumPixel);
+ a->SetLength(ImageDataSize);
+
+ ImageDataSize+=8;
+ sprintf(car,"%d",ImageDataSize);
+ content1=car;
+ SetEntryByNumber(content1, GrPixel, NumPixel);
+}
+
+
+/**
+ * \ingroup gdcmHeader
+ * \brief compares 2 Headers, according to DICOMDIR rules
+ * --> not-for-rats function
+ * \warning does NOT work with ACR-NEMA files
+ * \todo find a trick to solve the pb (use RET fields ?)
+ * @param header
+ * @return true if 'smaller'
+ */
+ bool gdcmHeader::operator<(gdcmHeader &header){
+ std::string s1,s2;
+
+ // Patient Name
+ s1=this->GetEntryByNumber(0x0010,0x0010);
+ s2=header.GetEntryByNumber(0x0010,0x0010);
+ if(s1 < s2)
+ return(true);
+ else if(s1 > s2)
+ return(false);
+ else
+ {
+ // Patient ID
+ s1=this->GetEntryByNumber(0x0010,0x0020);
+ s2=header.GetEntryByNumber(0x0010,0x0020);
+ if (s1 < s2)
+ return(true);
+ else if (s1 > s2)
+ return(1);
+ else
+ {
+ // Study Instance UID
+ s1=this->GetEntryByNumber(0x0020,0x000d);
+ s2=header.GetEntryByNumber(0x0020,0x000d);
+ if (s1 < s2)
+ return(true);
+ else if(s1 > s2)
+ return(false);
+ else
+ {
+ // Serie Instance UID
+ s1=this->GetEntryByNumber(0x0020,0x000e);
+ s2=header.GetEntryByNumber(0x0020,0x000e);
+ if (s1 < s2)
+ return(true);
+ else if(s1 > s2)
+ return(false);
+ }
+ }
+ }
+ return(false);
+}
+
+bool gdcmHeader::WriteEntry(gdcmHeaderEntry *tag, FILE *_fp,FileType type)
+{
+ guint32 length = tag->GetLength();
+
+ // The value of a tag MUST (see the DICOM norm) be an odd number of
+ // bytes. When this is not the case, pad with an additional byte:
+ if(length%2==1)
+ {
+ tag->SetValue(tag->GetValue()+"\0");
+ tag->SetLength(tag->GetReadLength()+1);
+ }
+
+ WriteEntryTagVRLength(tag, _fp, type);
+
+ // Pixels are never loaded in the element !
+ // we stop writting when Pixel are processed
+ // FIX : we loose trailing elements (RAB, right now)
+ guint16 el = tag->GetElement();
+ guint16 group = tag->GetGroup();
+ int compte =0;
+ if ((group == GrPixel) && (el == NumPixel) ) {
+ compte++;
+ if (compte == countGrPixel) {// we passed *all* the GrPixel,NumPixel
+ return false;
+ }
+ }
+ WriteEntryValue(tag, _fp, type);
+ return true;
+}
+
+//-----------------------------------------------------------------------------
+// Protected
+
+/**
+ * \ingroup gdcmHeader
+ * \brief anonymize a Header (removes Patient's personal info)
+ * (read the code to see which ones ...)
+ */
+bool gdcmHeader::anonymizeHeader() {
+
+ gdcmHeaderEntry *patientNameHE = GetHeaderEntryByNumber (0x0010, 0x0010);
+ // gdcmHeaderEntry *patientIDHE = GetHeaderEntryByNumber (0x0010, 0x0020);
+
+ ReplaceIfExistByNumber (" ",0x0010, 0x2154); // Telephone
+ ReplaceIfExistByNumber (" ",0x0010, 0x1040); // Adress
+ ReplaceIfExistByNumber (" ",0x0010, 0x0020); // Patient ID
+
+ if (patientNameHE) {
+ std::string StudyInstanceUID = GetEntryByNumber (0x0020, 0x000d);
+ if (StudyInstanceUID !=GDCM_UNFOUND)
+ ReplaceOrCreateByNumber(StudyInstanceUID, 0x0010, 0x0010);
+ else
+ ReplaceOrCreateByNumber(std::string("anonymised"), 0x0010, 0x0010);
+ }
+
+ // Just for fun :-(
+ // (if any) remove or replace all the stuff that contains a Date
+
+//0008 0012 DA ID Instance Creation Date
+//0008 0020 DA ID Study Date
+//0008 0021 DA ID Series Date
+//0008 0022 DA ID Acquisition Date
+//0008 0023 DA ID Content Date
+//0008 0024 DA ID Overlay Date
+//0008 0025 DA ID Curve Date
+//0008 002a DT ID Acquisition Datetime
+//0018 9074 DT ACQ Frame Acquisition Datetime
+//0018 9151 DT ACQ Frame Reference Datetime
+//0018 a002 DT ACQ Contribution Date Time
+//0020 3403 SH REL Modified Image Date (RET)
+//0032 0032 DA SDY Study Verified Date
+//0032 0034 DA SDY Study Read Date
+//0032 1000 DA SDY Scheduled Study Start Date
+//0032 1010 DA SDY Scheduled Study Stop Date
+//0032 1040 DA SDY Study Arrival Date
+//0032 1050 DA SDY Study Completion Date
+//0038 001a DA VIS Scheduled Admission Date
+//0038 001c DA VIS Scheduled Discharge Date
+//0038 0020 DA VIS Admitting Date
+//0038 0030 DA VIS Discharge Date
+//0040 0002 DA PRC Scheduled Procedure Step Start Date
+//0040 0004 DA PRC Scheduled Procedure Step End Date
+//0040 0244 DA PRC Performed Procedure Step Start Date
+//0040 0250 DA PRC Performed Procedure Step End Date
+//0040 2004 DA PRC Issue Date of Imaging Service Request
+//0040 4005 DT PRC Scheduled Procedure Step Start Date and Time
+//0040 4011 DT PRC Expected Completion Date and Time
+//0040 a030 DT PRC Verification Date Time
+//0040 a032 DT PRC Observation Date Time
+//0040 a120 DT PRC DateTime
+//0040 a121 DA PRC Date
+//0040 a13a DT PRC Referenced Datetime
+//0070 0082 DA ??? Presentation Creation Date
+//0100 0420 DT ??? SOP Autorization Date and Time
+//0400 0105 DT ??? Digital Signature DateTime
+//2100 0040 DA PJ Creation Date
+//3006 0008 DA SSET Structure Set Date
+//3008 0024 DA ??? Treatment Control Point Date
+//3008 0054 DA ??? First Treatment Date
+//3008 0056 DA ??? Most Recent Treatment Date
+//3008 0162 DA ??? Safe Position Exit Date
+//3008 0166 DA ??? Safe Position Return Date
+//3008 0250 DA ??? Treatment Date
+//300a 0006 DA RT RT Plan Date
+//300a 022c DA RT Air Kerma Rate Reference Date
+//300e 0004 DA RT Review Date
+ return true;
+}
+//-----------------------------------------------------------------------------
+// Private
+
+//-----------------------------------------------------------------------------