-#include "gdcmlib.h"
+// gdcmHeader.cxx
+//-----------------------------------------------------------------------------
+#include "gdcmHeader.h"
-/* =======================================================================
+#include <stdio.h>
+#include <cerrno>
+#include <cctype> // for isalpha
- _IdDcmCheckSwap
- La seule maniere sure que l'on aie pour determiner
- si on est en LITTLE_ENDIAN, BIG-ENDIAN,
- BAD-LITTLE-ENDIAN, BAD-BIG-ENDIAN
- est de trouver l'element qui donne la longueur d'un 'GROUP'
- (on sait que la longueur de cet element vaut 0x00000004)
- et de regarder comment cette longueur est codee en memoire
+#include "gdcmUtil.h"
+#include "gdcmTS.h"
- Le probleme vient de ce que parfois, il n'y en a pas ...
- On fait alors le pari qu'on a a faire a du LITTLE_ENDIAN propre.
- (Ce qui est la norme -pas respectee- depuis ACR-NEMA)
- Si ce n'est pas le cas, on ne peut rien faire.
+//-----------------------------------------------------------------------------
+// Constructor / Destructor
+/**
+ * \ingroup gdcmHeader
+ * \brief Constructor
+ * @param InFilename
+ * @param exception_on_error
+ * @param enable_sequences = true to allow the header
+ * to be parsed *inside* the SeQuences,
+ * when they have an actual length
+ * @param ignore_shadow = true if user wants to skip shadow groups
+ * during parsing, to save memory space
+ */
+gdcmHeader::gdcmHeader(const char *InFilename,
+ bool exception_on_error,
+ bool enable_sequences,
+ bool ignore_shadow):
+ gdcmParser(InFilename,exception_on_error,enable_sequences,ignore_shadow)
+{
+
+ // for some ACR-NEMA images GrPixel, NumPixel is *not* 7fe0,0010
+ // We may encounter the 'RETired' (0x0028, 0x0200) tag
+ // (Image Location") . This Element contains the number of
+ // 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.
+
+ // This IS the right place for the code
+
+ std::string ImageLocation = GetEntryByNumber(0x0028, 0x0200);
+ if ( ImageLocation == GDCM_UNFOUND ) { // Image Location
+ GrPixel = 0x7fe0; // default value
+ } else {
+ GrPixel = (guint16) atoi( ImageLocation.c_str() );
+ }
+ if (GrPixel == 0xe07f) // sometimes Image Location value doesn't follow
+ GrPixel = 0x7fe0; // the supposed processor endianity.
+ // see gdcmData/cr172241.dcm
+ if (GrPixel != 0x7fe0)
+ // This is a kludge for old dirty Philips imager.
+ NumPixel = 0x1010;
+ else
+ NumPixel = 0x0010;
+
+ TagKey key = gdcmDictEntry::TranslateToKey(GrPixel, NumPixel);
+ countGrPixel = GetEntry().count(key);
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Constructor
+ * @param exception_on_error
+ */
+gdcmHeader::gdcmHeader(bool exception_on_error) :
+ gdcmParser(exception_on_error)
+{
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Canonical destructor.
+ */
+gdcmHeader::~gdcmHeader (void) {
+}
- (il faudrait avoir des fonctions auxquelles
- on passe le code Swap en parametre, pour faire des essais 'manuels')
+//-----------------------------------------------------------------------------
+// Print
- ======================================================================= */
+// see gdcmParser.cxx
+//-----------------------------------------------------------------------------
+// Public
-EndianType gdcmHeader::gdcmHeader()
-{
- //guint32 s;
- guint32 x=4; // x : pour ntohs
- bool net2host; // true when HostByteOrder is the same as NetworkByteOrder
-
- int sw;
- int lgrLue;
- char * entCur;
- char deb[LGR_ENTETE_A_LIRE];
-
- // On teste le processeur
- if (x==ntohs(x)) {
- net2host = true;
- } else {
- net2host = false;
+/**
+ * \ingroup gdcmHeader
+ * \brief This predicate, based on hopefully reasonable heuristics,
+ * decides whether or not the current gdcmParser was properly parsed
+ * and contains the mandatory information for being considered as
+ * a well formed and usable Dicom/Acr File.
+ * @return true when gdcmParser is the one of a reasonable Dicom/Acr file,
+ * false otherwise.
+ */
+bool gdcmHeader::IsReadable(void) {
+ if(!gdcmParser::IsReadable()) {
+ return(false);
}
+ std::string res = GetEntryByNumber(0x0028, 0x0005);
+ if ( res != GDCM_UNFOUND && atoi(res.c_str()) > 4 )
+ return false; // Image Dimensions
+ if ( !GetHeaderEntryByNumber(0x0028, 0x0100) )
+ return false; // "Bits Allocated"
+ if ( !GetHeaderEntryByNumber(0x0028, 0x0101) )
+ return false; // "Bits Stored"
+ if ( !GetHeaderEntryByNumber(0x0028, 0x0102) )
+ return false; // "High Bit"
+ if ( !GetHeaderEntryByNumber(0x0028, 0x0103) )
+ return false; // "Pixel Representation" i.e. 'Sign'
+ return true;
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Determines if the Transfer Syntax was already encountered
+ * and if it corresponds to a JPEGBaseLineProcess1 one.
+ * @return True when JPEGBaseLineProcess1found. False in all other cases.
+ */
+bool gdcmHeader::IsJPEGBaseLineProcess1TransferSyntax(void) {
+ gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010);
+ if ( !Element )
+ return false;
+ LoadHeaderEntrySafe(Element);
+
+ std::string Transfer = Element->GetValue();
+ if ( Transfer == "1.2.840.10008.1.2.4.50" )
+ return true;
+ return false;
+}
- // On commence par verifier si c'est du DICOM 'actuel'
- // -------------
+/**
+ * \ingroup gdcmHeader
+ * \brief Determines if the Transfer Syntax was already encountered
+ * and if it corresponds to a JPEGExtendedProcess2-4 one.
+ * @return True when JPEGExtendedProcess2-4 found. False in all other cases.
+ */
+bool gdcmHeader::IsJPEGExtendedProcess2_4TransferSyntax(void) {
+ gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010);
+ if ( !Element )
+ return false;
+ LoadHeaderEntrySafe(Element);
+ return ( Element->GetValue() == "1.2.840.10008.1.2.4.51" );
+}
- lgrLue = fread(deb,1,LGR_ENTETE_A_LIRE,e->fp);
+/**
+ * \ingroup gdcmHeader
+ * \brief Determines if the Transfer Syntax was already encountered
+ * and if it corresponds to a JPEGExtendeProcess3-5 one.
+ * @return True when JPEGExtendedProcess3-5 found. False in all other cases.
+ */
+bool gdcmHeader::IsJPEGExtendedProcess3_5TransferSyntax(void) {
+ gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010);
+ if ( !Element )
+ return false;
+ LoadHeaderEntrySafe(Element);
+
+ std::string Transfer = Element->GetValue();
+ if ( Transfer == "1.2.840.10008.1.2.4.52" )
+ return true;
+ return false;
+}
- entCur = deb+128;
- if(memcmp(entCur, "DICM", (size_t)4) == 0) {
- filetype = TrueDicom;
- if (DEBUG) printf ("_IdDcmCheckSwap : C est du DICOM actuel \n");
- } else {
- filetype = Unknown;
- if (DEBUG) printf ("_IdDcmCheckSwap : Ce n'est PAS du DICOM actuel\n");
+/**
+ * \ingroup gdcmHeader
+ * \brief Determines if the Transfer Syntax was already encountered
+ * and if it corresponds to a JPEGSpectralSelectionProcess6-8 one.
+ * @return True when JPEGSpectralSelectionProcess6-8 found. False in all
+ * other cases.
+ */
+bool gdcmHeader::IsJPEGSpectralSelectionProcess6_8TransferSyntax(void) {
+ gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010);
+ if ( !Element )
+ return false;
+ LoadHeaderEntrySafe(Element);
+
+ std::string Transfer = Element->GetValue();
+ if ( Transfer == "1.2.840.10008.1.2.4.53" )
+ return true;
+ return false;
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Determines if the Transfer Syntax was already encountered
+ * and if it corresponds to a RLE Lossless one.
+ * @return True when RLE Lossless found. False in all
+ * other cases.
+ */
+bool gdcmHeader::IsRLELossLessTransferSyntax(void) {
+ gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010);
+ if ( !Element )
+ return false;
+ LoadHeaderEntrySafe(Element);
+
+ std::string Transfer = Element->GetValue();
+ if ( Transfer == "1.2.840.10008.1.2.5" ) {
+ return true;
+ }
+ return false;
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Determines if Transfer Syntax was already encountered
+ * and if it corresponds to a JPEG Lossless one.
+ * @return True when RLE Lossless found. False in all
+ * other cases.
+ */
+bool gdcmHeader::IsJPEGLossless(void) {
+ gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010);
+ // faire qq chose d'intelligent a la place de ça
+ if ( !Element )
+ return false;
+ LoadHeaderEntrySafe(Element);
+
+ const char * Transfert = Element->GetValue().c_str();
+ if ( memcmp(Transfert+strlen(Transfert)-2 ,"70",2)==0) return true;
+ if ( memcmp(Transfert+strlen(Transfert)-2 ,"55",2)==0) return true;
+ if (Element->GetValue() == "1.2.840.10008.1.2.4.57") return true;
+
+ return false;
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Determines if the Transfer Syntax was already encountered
+ * and if it corresponds to a JPEG2000 one
+ * @return True when JPEG2000 (Lossly or LossLess) found. False in all
+ * other cases.
+ */
+bool gdcmHeader::IsJPEG2000(void) {
+ gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010);
+ if ( !Element )
+ return false;
+ LoadHeaderEntrySafe(Element);
+
+ std::string Transfer = Element->GetValue();
+ if ( (Transfer == "1.2.840.10008.1.2.4.90")
+ || (Transfer == "1.2.840.10008.1.2.4.91") )
+ return true;
+ return false;
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Predicate for dicom version 3 file.
+ * @return True when the file is a dicom version 3.
+ */
+bool gdcmHeader::IsDicomV3(void) {
+ // Checking if Transfert Syntax exists is enough
+ // Anyway, it's to late check if the 'Preamble' was found ...
+ // And ... would it be a rich idea to check ?
+ // (some 'no Preamble' DICOM images exist !)
+ return (GetHeaderEntryByNumber(0x0002, 0x0010) != NULL);
+}
+
+/**
+ * \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) {
+ std::string StrSize;
+ 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 ACR-MEMA file contains a Signal, not an Image).
+ */
+int gdcmHeader::GetYSize(void) {
+ 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 ACR-NEMA "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
+ 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;
+ 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");
- if(filetype == TrueDicom) {
- // on saute le File Preamble (souvent a ZERO) : 128 Octets
- // + le DICM (4), et le (0002, 0000) soit 4 (136 = 128 + 4 + 4)
- entCur = deb+136;
- if(memcmp(entCur, "UL", (size_t)2) == 0) {
- // les 2 premiers octets de la lgr peuvent valoir UL --> Explicit VR
- filetype = ExplicitVR;
- if (DEBUG) printf ("_IdDcmCheckSwap : Explicit VR\n");
- } else {
- filetype = ImplicitVR;
- if (DEBUG) printf ("_IdDcmCheckSwap : PAS Explicit VR\n");
- }
+ return( BitsAlloc + Signed);
+}
- if (net2host) { // HostByteOrder is different from NetworkByteOrder
- sw = 0; // on est sur PC ou DEC --> LITTLE-ENDIAN -> Rien a faire
- if (DEBUG) printf("HostByteOrder = NetworkByteOrder\n");
- } else { /* on est sur une Sun ou une SGI */
- sw = 4321;
- if (DEBUG) printf("HostByteOrder != NetworkByteOrder\n");
- }
+/**
+ * \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 ...
+
+ //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 {
+/* std::cout << "Big trouble : Pixel Element ("
+ << std::hex << GrPixel<<","<< NumPixel<< ") NOT found"
+ << std::endl; */
+ 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;
- rewind(e->fp);
- fseek (e->fp, 132L, SEEK_SET); //On se positionne sur le debut des info
- e->offsetCourant=132;
- return sw;
-
- } /* fin TrueDicom */
-
- // Pas du TrueDicom : permiere hypothese c'est de l'ACR 'propre', auquel
- // cas la lgr du premier element du groupe est FORCEMENT 4
-
- entCur=deb + 4;
- s=str2num(entCur,int);
-
- switch (s) {
- case 0x00040000 :
- sw=3412; if(DEBUG) printf("s : %08x sw : %d\n",s,sw);
- filetype = ACR;
- break;
- case 0x04000000 :
- sw=4321; if(DEBUG) printf("s : %08x sw : %d\n",s,sw);
- filetype = ACR;
- break;
- case 0x00000400 :
- sw=2143; if(DEBUG) printf("s : %08x sw : %d\n",s,sw);
- filetype = ACR;
- break;
- case 0x00000004 :
- sw=0; if(DEBUG) printf("s : %08x sw : %d\n",s,sw);
- filetype = ACR;
- break;
- default :
- sw = -1;
- if (DEBUG) printf (" Pas trouve l info de Swap; On va parier\n");
- }
-
- // Deuxieme hypothese : c'est de l'ACR 'pas propre' i.e. il manque
- // la lgr du groupe
-
- if(sw==-1) {
- /* On n'a pas trouve l'info de swap 28/11/2000 JPR */
- // Si c'est du VRAI ACR NEMA si on est sur une DEC ou un PC swap=0,
- // SUN ou SGI SWAP=4321
- /* si c'est du RAW, ca degagera + tard */
-
- if (DEBUG) printf("On force la chance \n");
-
- if (x!=ntohs(x)) // HostByteOrder is different from NetworkByteOrder
- sw = 0; // on est sur PC ou DEC --> LITTLE-ENDIAN -> Rien a faire
- else
- sw = 4321; // on est sur Sun ou SGI
- }
+ if (PixelElement) {
+ return PixelElement->GetLength();
+ } else {
+/* std::cout << "Big trouble : Pixel Element ("
+ << std::hex << GrPixel<<","<< NumPixel<< ") NOT found"
+ << std::endl;*/
+ return 0;
+ }
+}
- rewind(e->fp); // les info commencent au debut
- e->offsetCourant=0;
- return (sw);
+/**
+ * \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;
+ return true;
}
-void gdcmHeader::_setAcrLibido() {
-
- _ID_DCM_ELEM * ple;
- PLIST_ELEMENT plelem;
- PLIST pl;
-
- // Positionnement ACR_LIBIDO
- if(DEBUG) printf("Entree ds _setAcrLibido\n");
-
- filetype = ACR_LIBIDO = 0;
- if ( filetype != TrueDicom) {
- // Recognition Code --> n'existe plus en DICOM V3 ...
-
- pl = e->plist;
- plelem = IdLstFirst(pl);
- while (plelem) {
- ple= IdLstPtrObj(plelem);
- if(DEBUG) printf("gr %04x Num %04x\n", ple->Gr, ple->Num);
- if(ple->Gr > 0x0008) break; // On a depasse
- if(ple->Gr == 0x0008) {
- if(ple->Num > 0x0010) break; // On a depasse
- if(ple->Num == 0x0010) {
- if ( (memcmp(ple->valeurElem,"ACRNEMA_LIBIDO",14)==0)
- // si c'est egal
- || (memcmp(ple->valeurElem,"CANRME_AILIBOD",14)==0)) {
- // en cas d'objet ACRLibido fait sr 1 autre machine)
- e->ACR_LIBIDO =1;
- } // fin if memcmp
- break;
- } // fin if ple->Num==0x0010
- } // fin ple->Gr==0x0008
- plelem = IdLstNext(plelem);
- } // fin while
- } // fin if TrueDicom
-
- return;
+/**
+ * \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;
}
-/* =======================================================================
-* _IdDcmRecupLgr
-*
-* ACR-NEMA : On a toujours
-* GroupNumber (2 Octets)
-* ElementNumber (2 Octets)
-* ElementSize (4 Octets)
-*
-*
-* DICOM : On peut avoir (implicit Value Representation)
-* GroupNumber (2 Octets)
-* ElementNumber (2 Octets)
-* ElementSize (4 Octets)
-*
-* On peut avoir (explicit Value Representation)
-* GroupNumber (2 Octets)
-* ElementNumber (2 Octets)
-* ValueRepresentation (2 Octets)
-* ElementSize (2 Octets)
-*
-* ATTENTION : dans le cas ou ValueRepresentation = OB, OW, SQ, UN
-* GroupNumber (2 Octets)
-* ElementNumber (2 Octets)
-* ValueRepresentation (2 Octets)
-* zone reservee (2 Octets)
-* ElementSize (4 Octets)
-*
-*
-* ======================================================================= */
/**
- * \ingroup dcm
- * \brief recupere la longueur d'un champ DICOM.
- * (le fichier doit deja avoir ete ouvert,
- * _IdAcrCheckSwap(ID_DCM_HDR *e) avoir ete appele)
- * et la partie 'group' ainsi que la partie 'elem'
- * de l'acr_element doivent avoir ete lues.
- * @param sw code swap
- * @param skippedLength pointeur sur nombre d'octets que l'on a saute qd la lecture est finie
- * @param longueurLue pointeur sur longueur (en nombre d'octets) effectivement lue
-
- * @return longueur retenue pour le champ
+ * \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 = (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 (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;
+}
-static guint32 _IdDcmRecupLgr(ID_DCM_HDR *e, int sw, int *skippedLength, int *longueurLue) {
-guint32 l_gr;
-unsigned short int l_gr_2;
-int i, trouve;
-char VR[5];
-int lgrLue;
-
-/*
- * ATTENTION :
-*/
-
-int nbCode=26; // nombre d'elements dans la table de type DICOM_VR definie dans dicom.c
-
-/* ================ */
-
-// ID_DCM_HDR *e sert uniquement de passe-plat pour __ExplicitVR
-
-
-if (e->__ExplicitVR == 1) {
- lgrLue=fread (&VR, (size_t)2,(size_t)1, e->fp);
- VR[2]=0;
-
- // ATTENTION :
- // Ce n'est pas parce qu'on a trouve UL la premiere fois qu'on respecte
- // Explicit VR tout le temps
- // (cf e=film ...)
-
- for(i=0,trouve=0;i<nbCode;i++) {
- if(memcmp(_ID_dicom_vr[i].dicom_VR,VR,(size_t)2)==0) {
- (e->pleCourant)->VR=_ID_dicom_vr[i].dicom_VR;
- trouve=1;
- break;
- }
- }
-
- if ( trouve == 0) {
-
- // On est mal : implicit VR repere
- // mais ce n'est pas un code connu ...
- // On reconstitue la longueur
-
- if(DEBUG) printf("IdDcmRecupLgr : Explicit VR, mais pas trouve de code connu\n");
- memcpy(&l_gr, VR,(size_t)2);
-
- lgrLue=fread ( ((char*)&l_gr)+2, (size_t)2, (size_t)1, e->fp);
-
- if(sw) l_gr = _IdDcmSWAP_LONG(((guint32)l_gr),sw);
-
- if(DEBUG) printf("IdDcmRecupLgr : lgr deduite : %08x , %d\n",l_gr,l_gr);
-
- *longueurLue=l_gr;
- if ( (int)l_gr == -1) {
- l_gr=0;
- }
- *skippedLength = 4;
- if (DEBUG) printf(" 1 : lgr %08x (%d )skippedLength %d\n",l_gr,l_gr, *skippedLength);
- return(l_gr);
- }
-
- // On repart dans la sequence 'sensee'
-
- if(DEBUG) printf("VR : [%01x , %01x] (%c%c) en position %d du tableau\n", VR[0],VR[1],VR[0],VR[1],i);
- //printf(" %d , %s\n", i,_ID_dicom_vr[i].dicom_VR);
-
- if (
- (!memcmp( VR,"OB",(size_t)2 )) ||
- (!memcmp( VR,"OW",(size_t)2 )) ||
- (!memcmp( VR,"SQ",(size_t)2 )) ||
- (!memcmp( VR,"UN",(size_t)2 )) ) {
-
- // les 2 octets suivants sont reserves
-
- if(DEBUG) printf("IdDcmRecupLgr : les 2 octets suivants sont reserves\n");
- //on les saute
- fseek(e->fp, 2L,SEEK_CUR);
-
- //on lit la lgr sur QUATRE octets
-
- lgrLue=fread (&l_gr, (size_t)4,(size_t)1, e->fp);
-
- if(sw) l_gr = _IdDcmSWAP_LONG(((guint32)l_gr),sw);
- *skippedLength = 8;
-
- } else {
- //on lit la lgr sur DEUX octets
-
- lgrLue=fread (&l_gr_2, (size_t)2,(size_t)1, e->fp);
-
- if(sw) l_gr_2 = _IdDcmSWAP_SHORT((unsigned short)l_gr_2,sw);
-
- *longueurLue=l_gr_2;
-
-
- if ( l_gr_2 == 0xffff) {
- l_gr = 0;
- } else {
- l_gr = l_gr_2;
- }
- *skippedLength = 4;
- }
- } else { // Explicit VR = 0
-
- //on lit la lgr sur QUATRE octets
-
- lgrLue=fread (&l_gr, (size_t)4,(size_t)1, e->fp);
+/**
+ * \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);
+}
- if(sw)l_gr=_IdDcmSWAP_LONG(((long)l_gr),sw);
- *skippedLength = 4;
- }
+
+/**
+ * \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);
+}
+
+//-----------------------------------------------------------------------------
+// Protected
+
+/**
+ * \ingroup gdcmHeader
+ * \brief anonymize a Header (removes Patient's personal info)
+ * (read the code to see which ones ...)
+ * @param
+ */
+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
- *longueurLue=l_gr;
+ if (patientNameHE) {
+ std::string StudyInstanceUID = GetEntryByNumber (0x0020, 0x000d);
+ if (StudyInstanceUID !=GDCM_UNFOUND)
+ ReplaceOrCreateByNumber(StudyInstanceUID, 0x0010, 0x0010);
+ else
+ ReplaceOrCreateByNumber("anonymised", 0x0010, 0x0010);
+ }
- // Traitement des curiosites sur la longueur
+ // Just for fun :-(
+ // (if any) remove or replace all the stuff that contains a Date
- if ( (int)l_gr == 0xffffffff)
- l_gr=0;
-
- if(!memcmp( VR,"SQ",(size_t)2 )) { // ca annonce une SEQUENCE d'items ?!
- l_gr=0; // on lira donc les items de la sequence
- if (DEBUG) printf(" SQ trouve : lgr %d \n",l_gr);
- }
-
-if (DEBUG) printf(" 2 : lgr %08x (%d) skippedLength %d\n",l_gr,l_gr, *skippedLength);
- return(l_gr);
-}
+//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
+
+//-----------------------------------------------------------------------------
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff