+FileType gdcmHeader::GetFileType(void) {
+ return(filetype);
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Retrieve the number of columns of image.
+ * @return The encountered size when found, 0 by default.
+ * 0 means the file is NOT USABLE. The caller will have to check
+ */
+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 = GetEntryByNumber(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
+ * (The file contains a Signal, not an Image).
+ */
+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 = GetEntryByNumber(0x0028,0x0010);
+ if (StrSize != GDCM_UNFOUND)
+ return atoi(StrSize.c_str());
+ if ( IsDicomV3() )
+ return 0;
+ else
+ // The Rows (0028,0010) entry was 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 (single image).
+ */
+int gdcmHeader::GetZSize(void) {
+ // Both DicomV3 and ACR/Nema consider the "Number of Frames"
+ // as the third dimension.
+ std::string StrSize = GetEntryByNumber(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 = GetEntryByNumber(0x0028,0x0012);
+ if (StrSize != GDCM_UNFOUND)
+ return atoi(StrSize.c_str());
+ return 1;
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Retrieve the number of Bits Stored (actually used)
+ * (as opposite to number of Bits Allocated)
+ *
+ * @return The encountered number of Bits Stored, 0 by default.
+ * 0 means the file is NOT USABLE. The caller has to check it !
+ */
+int gdcmHeader::GetBitsStored(void) {
+ std::string StrSize = GetEntryByNumber(0x0028,0x0101);
+ if (StrSize == GDCM_UNFOUND)
+ return 0; // It's supposed to be mandatory
+ // the caller will have to check
+ 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.
+ * 0 means the file is NOT USABLE. The caller has to check it !
+ */
+int gdcmHeader::GetBitsAllocated(void) {
+ std::string StrSize = GetEntryByNumber(0x0028,0x0100);
+ if (StrSize == GDCM_UNFOUND)
+ return 0; // It's supposed to be mandatory
+ // the caller will have to check
+ 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.
+ * (Gray level Pixels)
+ */
+int gdcmHeader::GetSamplesPerPixel(void) {
+ std::string StrSize = GetEntryByNumber(0x0028,0x0002);
+ if (StrSize == GDCM_UNFOUND)
+ return 1; // Well, it's supposed to be mandatory ...
+ // but sometimes it's missing : we assume Gray pixels
+ 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 = 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;
+ 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 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 == "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 the pixels.
+ */
+size_t gdcmHeader::GetPixelOffset(void) {
+ // If this file complies with the norm we should encounter the
+ // "Image Location" tag (0x0028, 0x0200). This tag contains the
+ // the group that contains the pixel data (hence the "Pixel Data"
+ // is found by indirection through the "Image Location").
+ // Inside the group pointed by "Image Location" the searched element
+ // is conventionally the element 0x0010 (when the norm is respected).
+ // When the "Image Location" is absent we default to group 0x7fe0.
+ guint16 grPixel;
+ guint16 numPixel;
+ std::string ImageLocation = GetEntryByNumber(0x0028, 0x0200);
+
+ if ( ImageLocation == GDCM_UNFOUND ) { // Image Location
+ grPixel = 0x7fe0;
+ } else {
+ grPixel = (guint16) atoi( ImageLocation.c_str() );
+ }
+ if (grPixel != 0x7fe0)
+ // This is a kludge for old dirty Philips imager.
+ numPixel = 0x1010;
+ else
+ numPixel = 0x0010;
+
+ gdcmHeaderEntry* PixelElement = GetHeaderEntryByNumber(grPixel,numPixel);
+ if (PixelElement)
+ return PixelElement->GetOffset();
+ else
+ return 0;
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Recover the pixel area length (in Bytes)
+ * @return 0 by default. NOT USABLE file. The caller has to check.
+ */
+size_t gdcmHeader::GetPixelAreaLength(void) {
+ // If this file complies with the norm we should encounter the
+ // "Image Location" tag (0x0028, 0x0200). This tag contains the
+ // the group that contains the pixel data (hence the "Pixel Data"
+ // is found by indirection through the "Image Location").
+ // Inside the group pointed by "Image Location" the searched element
+ // is conventionally the element 0x0010 (when the norm is respected).
+ // When the "Image Location" is absent we default to group 0x7fe0.
+ guint16 grPixel;
+ guint16 numPixel;
+ std::string ImageLocation = GetEntryByNumber(0x0028, 0x0200);
+ if ( ImageLocation == GDCM_UNFOUND ) {
+ grPixel = 0x7fe0;
+ } else {
+ grPixel = (guint16) atoi( ImageLocation.c_str() );
+ }
+ if (grPixel != 0x7fe0)
+ // This is a kludge for old dirty Philips imager.
+ numPixel = 0x1010;
+ else
+ numPixel = 0x0010;
+
+ gdcmHeaderEntry* PixelElement = GetHeaderEntryByNumber(grPixel,numPixel);
+ if (PixelElement)
+ return PixelElement->GetLength();
+ else
+ 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
+ * @return a Boolean
+ */
+bool gdcmHeader::HasLUT(void) {
+
+ // Check the presence of the LUT Descriptors
+ if ( !GetHeaderEntryByNumber(0x0028,0x1101) )
+ return false;
+ // LutDescriptorGreen
+ if ( !GetHeaderEntryByNumber(0x0028,0x1102) )
+ return false;
+ // LutDescriptorBlue
+ if ( !GetHeaderEntryByNumber(0x0028,0x1103) )
+ return false;
+ // It is not enough
+ // we check also
+ if ( !GetHeaderEntryByNumber(0x0028,0x1201) )
+ return false;
+ if ( !GetHeaderEntryByNumber(0x0028,0x1202) )
+ return false;
+ if ( !GetHeaderEntryByNumber(0x0028,0x1203) )
+ return false;
+ 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 ]
+ */
+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 (gdcmHeader::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());
+ 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 *)
+ GetPubEntryVoidAreaByNumber(0x0028,0x1201);
+ unsigned char *lutG = (unsigned char *)
+ GetPubEntryVoidAreaByNumber(0x0028,0x1202);
+ unsigned char *lutB = (unsigned char *)
+ GetPubEntryVoidAreaByNumber(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 = 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 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); // Seg Fault when used
+ return(LUTRGBA);
+}
+
+/**
+ * \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::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 Searches within the file Header for element value of
+ * a given tag.
+ * @param tagName name of the searched element.
+ * @return Corresponding element value when it exists, and the string
+ * GDCM_UNFOUND ("gdcm::Unfound") otherwise.
+ */
+std::string gdcmHeader::GetPubEntryByName(std::string tagName) {
+ gdcmDictEntry *dictEntry = RefPubDict->GetTagByName(tagName);
+ if( dictEntry == NULL)
+ return GDCM_UNFOUND;
+
+ return(GetEntryByNumber(dictEntry->GetGroup(),dictEntry->GetElement()));
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Searches within the elements parsed with the file Header for
+ * the element value representation of a given tag.
+ *
+ * Obtaining the VR (Value Representation) might be needed by caller
+ * to convert the string typed content to caller's native type
+ * (think of C++ vs Python). The VR is actually of a higher level
+ * of semantics than just the native C++ type.
+ * @param tagName name of the searched element.
+ * @return Corresponding element value representation when it exists,
+ * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise.
+ */
+std::string gdcmHeader::GetPubEntryVRByName(std::string tagName) {
+ gdcmDictEntry *dictEntry = RefPubDict->GetTagByName(tagName);
+ if( dictEntry == NULL)
+ return GDCM_UNFOUND;
+
+ gdcmHeaderEntry* elem = GetHeaderEntryByNumber(dictEntry->GetGroup(),
+ dictEntry->GetElement());
+ return elem->GetVR();
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Searches within the public dictionary for element value of
+ * a given tag.
+ * @param group Group of the researched tag.
+ * @param element Element of the researched tag.
+ * @return Corresponding element value when it exists, and the string
+ * GDCM_UNFOUND ("gdcm::Unfound") otherwise.
+ */
+std::string gdcmHeader::GetPubEntryByNumber(guint16 group, guint16 element) {
+ return PubEntrySet.GetEntryByNumber(group, element);
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Searches within the public dictionary for element value
+ * representation of a given tag.
+ *
+ * Obtaining the VR (Value Representation) might be needed by caller
+ * to convert the string typed content to caller's native type
+ * (think of C++ vs Python). The VR is actually of a higher level
+ * of semantics than just the native C++ type.
+ * @param group Group of the researched tag.
+ * @param element Element of the researched tag.
+ * @return Corresponding element value representation when it exists,
+ * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise.
+ */
+std::string gdcmHeader::GetPubEntryVRByNumber(guint16 group, guint16 element) {
+ gdcmHeaderEntry* elem = GetHeaderEntryByNumber(group, element);
+ if ( !elem )
+ return GDCM_UNFOUND;
+ return elem->GetVR();
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Accesses an existing gdcmHeaderEntry (i.e. a Dicom Element)
+ * in the PubHeaderEntrySet of this instance
+ * through tag name and modifies it's content with the given value.
+ * @param content new value to substitute with
+ * @param tagName name of the Header Entry (Dicom Element) to be modified
+ */
+bool gdcmHeader::SetPubEntryByName(std::string content, std::string tagName) {
+ //return ( PubHeaderEntrySet.SetHeaderEntryByName (content, tagName) );
+ gdcmDictEntry *dictEntry = RefPubDict->GetTagByName(tagName);
+ if( dictEntry == NULL)
+ return false;
+ return(PubEntrySet.SetEntryByNumber(content,
+ dictEntry->GetGroup(),
+ dictEntry->GetElement()));
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Accesses an existing gdcmHeaderEntry (i.e. a Dicom Element)
+ * in the PubHeaderEntrySet of this instance
+ * through it's (group, element) and modifies it's content with
+ * the given value.
+ * @param content new value to substitute with
+ * @param group group of the Dicom Element to modify
+ * @param element element of the Dicom Element to modify
+ */
+bool gdcmHeader::SetPubEntryByNumber(std::string content, guint16 group,
+ guint16 element)
+
+//TODO : homogeneiser les noms : SetPubElValByNumber
+// qui appelle PubHeaderEntrySet.SetHeaderEntryByNumber
+// pourquoi pas SetPubHeaderEntryByNumber ??
+{
+ return ( PubEntrySet.SetEntryByNumber (content, group, element) );