-#include "gdcmlib.h"
+/*=========================================================================
+
+ Program: gdcm
+ Module: $RCSfile: gdcmHeader.cxx,v $
+ Language: C++
+ Date: $Date: 2005/01/06 20:03:28 $
+ Version: $Revision: 1.222 $
+
+ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
+ l'Image). All rights reserved. See Doc/License.txt or
+ http://www.creatis.insa-lyon.fr/Public/Gdcm/License.html for details.
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the above copyright notices for more information.
+
+=========================================================================*/
-/* =======================================================================
+#include "gdcmHeader.h"
+#include "gdcmGlobal.h"
+#include "gdcmUtil.h"
+#include "gdcmDebug.h"
+#include "gdcmTS.h"
+#include "gdcmValEntry.h"
+#include <stdio.h> //sscanf
- _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 <vector>
- Le probleme vient de ce que parfois, il n'y en a pas ...
+namespace gdcm
+{
+//-----------------------------------------------------------------------------
+// Constructor / Destructor
+/**
+ * \brief Constructor
+ * @param filename name of the file whose header we want to analyze
+ */
+Header::Header( std::string const &filename ):
+ Document( filename )
+{
+ // 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.
+ // Note: this IS the right place for the code
+
+ // Image Location
+ const std::string &imgLocation = GetEntryByNumber(0x0028, 0x0200);
+ if ( imgLocation == GDCM_UNFOUND )
+ {
+ // default value
+ GrPixel = 0x7fe0;
+ }
+ else
+ {
+ GrPixel = (uint16_t) atoi( imgLocation.c_str() );
+ }
+
+ // sometimes Image Location value doesn't follow
+ // the supposed processor endianity.
+ // see gdcmData/cr172241.dcm
+ if ( GrPixel == 0xe07f )
+ {
+ GrPixel = 0x7fe0;
+ }
- 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.
+ if ( GrPixel != 0x7fe0 )
+ {
+ // This is a kludge for old dirty Philips imager.
+ NumPixel = 0x1010;
+ }
+ else
+ {
+ NumPixel = 0x0010;
+ }
+
+ // Now, we know GrPixel and NumPixel.
+ // Let's create a VirtualDictEntry to allow a further VR modification
+ // and force VR to match with BitsAllocated.
- (il faudrait avoir des fonctions auxquelles
- on passe le code Swap en parametre, pour faire des essais 'manuels')
+ DocEntry *entry = GetDocEntryByNumber(GrPixel, NumPixel);
+ if ( entry != 0 )
+ {
- ======================================================================= */
+ std::string PixelVR;
+ // 8 bits allocated is a 'O Bytes' , as well as 24 (old ACR-NEMA RGB)
+ // more than 8 (i.e 12, 16) is a 'O Words'
+ if ( GetBitsAllocated() == 8 || GetBitsAllocated() == 24 )
+ PixelVR = "OB";
+ else
+ PixelVR = "OW";
+
+ DictEntry* newEntry = NewVirtualDictEntry(
+ GrPixel, NumPixel,
+ PixelVR, "PXL", "Pixel Data");
+
+ entry->SetDictEntry( newEntry );
+ }
+}
-EndianType gdcmHeader::gdcmHeader()
+/**
+ * \brief Constructor used when we want to generate dicom files from scratch
+ */
+Header::Header()
+ :Document()
{
- //guint32 s;
- guint32 x=4; // x : pour ntohs
- bool net2host; // true when HostByteOrder is the same as NetworkByteOrder
+ InitializeDefaultHeader();
+}
- int sw;
- int lgrLue;
- char * entCur;
- char deb[LGR_ENTETE_A_LIRE];
+/**
+ * \brief Canonical destructor.
+ */
+Header::~Header ()
+{
+}
- // On teste le processeur
- if (x==ntohs(x)) {
- net2host = true;
- } else {
- net2host = false;
+/**
+ * \brief Performs some consistency checking on various 'File related'
+ * (as opposed to 'DicomDir related') entries
+ * then writes in a file all the (Dicom Elements) included the Pixels
+ * @param fileName file name to write to
+ * @param filetype Type of the File to be written
+ * (ACR-NEMA, ExplicitVR, ImplicitVR)
+ */
+bool Header::Write(std::string fileName, FileType filetype)
+{
+ std::ofstream *fp = new std::ofstream(fileName.c_str(),
+ std::ios::out | std::ios::binary);
+ if (*fp == NULL)
+ {
+ dbg.Verbose(2, "Failed to open (write) File: " , fileName.c_str());
+ return false;
}
- // On commence par verifier si c'est du DICOM 'actuel'
- // -------------
+ // Bits Allocated
+ if ( GetEntryByNumber(0x0028,0x0100) == "12")
+ {
+ SetEntryByNumber("16", 0x0028,0x0100);
+ }
- lgrLue = fread(deb,1,LGR_ENTETE_A_LIRE,e->fp);
+ /// \todo correct 'Pixel group' Length if necessary
- 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");
+ int i_lgPix = GetEntryLengthByNumber(GrPixel, NumPixel);
+ if (i_lgPix != -2)
+ {
+ // no (GrPixel, NumPixel) element
+ std::string s_lgPix = Util::Format("%d", i_lgPix+12);
+ s_lgPix = Util::DicomString( s_lgPix.c_str() );
+ ReplaceOrCreateByNumber(s_lgPix,GrPixel, 0x0000);
}
- 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");
+ // FIXME : should be nice if we could move it to File
+ // (or in future gdcmPixelData class)
+
+ // Drop Palette Color, if necessary
+
+ if ( GetEntryByNumber(0x0028,0x0002).c_str()[0] == '3' )
+ {
+ // if SamplesPerPixel = 3, sure we don't need any LUT !
+ // Drop 0028|1101, 0028|1102, 0028|1103
+ // Drop 0028|1201, 0028|1202, 0028|1203
+
+ DocEntry *e = GetDocEntryByNumber(0x0028,0x01101);
+ if (e)
+ {
+ RemoveEntryNoDestroy(e);
+ }
+ e = GetDocEntryByNumber(0x0028,0x1102);
+ if (e)
+ {
+ RemoveEntryNoDestroy(e);
+ }
+ e = GetDocEntryByNumber(0x0028,0x1103);
+ if (e)
+ {
+ RemoveEntryNoDestroy(e);
+ }
+ e = GetDocEntryByNumber(0x0028,0x01201);
+ if (e)
+ {
+ RemoveEntryNoDestroy(e);
+ }
+ e = GetDocEntryByNumber(0x0028,0x1202);
+ if (e)
+ {
+ RemoveEntryNoDestroy(e);
+ }
+ e = GetDocEntryByNumber(0x0028,0x1203);
+ if (e)
+ {
+ RemoveEntryNoDestroy(e);
}
+ }
+ Document::WriteContent(fp,filetype);
+
+ fp->close();
+ delete fp;
+
+ return true;
+}
+
+//-----------------------------------------------------------------------------
+// Print
+
+
+//-----------------------------------------------------------------------------
+// Public
+
+/**
+ * \brief This predicate, based on hopefully reasonable heuristics,
+ * decides whether or not the current Header was properly parsed
+ * and contains the mandatory information for being considered as
+ * a well formed and usable Dicom/Acr File.
+ * @return true when Header is the one of a reasonable Dicom/Acr file,
+ * false otherwise.
+ */
+bool Header::IsReadable()
+{
+ if( !Document::IsReadable() )
+ {
+ return false;
+ }
+
+ const std::string &res = GetEntryByNumber(0x0028, 0x0005);
+ if ( res != GDCM_UNFOUND && atoi(res.c_str()) > 4 )
+ {
+ return false; // Image Dimensions
+ }
+ if ( !GetDocEntryByNumber(0x0028, 0x0100) )
+ {
+ return false; // "Bits Allocated"
+ }
+ if ( !GetDocEntryByNumber(0x0028, 0x0101) )
+ {
+ return false; // "Bits Stored"
+ }
+ if ( !GetDocEntryByNumber(0x0028, 0x0102) )
+ {
+ return false; // "High Bit"
+ }
+ if ( !GetDocEntryByNumber(0x0028, 0x0103) )
+ {
+ return false; // "Pixel Representation" i.e. 'Sign'
+ }
+
+ return true;
+}
+
+/**
+ * \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 Header::GetXSize()
+{
+ const std::string &strSize = GetEntryByNumber(0x0028,0x0011);
+ if ( strSize == GDCM_UNFOUND )
+ {
+ return 0;
+ }
+
+ return atoi( strSize.c_str() );
+}
+
+/**
+ * \brief Retrieve the number of lines of image.
+ * \warning The defaulted value is 1 as opposed to Header::GetXSize()
+ * @return The encountered size when found, 1 by default
+ * (The ACR-NEMA file contains a Signal, not an Image).
+ */
+int Header::GetYSize()
+{
+ const std::string &strSize = GetEntryByNumber(0x0028,0x0010);
+ if ( strSize != GDCM_UNFOUND )
+ {
+ return atoi( strSize.c_str() );
+ }
+ if ( IsDicomV3() )
+ {
+ return 0;
+ }
+
+ // 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;
+}
- 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");
+/**
+ * \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 Header::GetZSize()
+{
+ // Both DicomV3 and ACR/Nema consider the "Number of Frames"
+ // as the third dimension.
+ const 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
+ const std::string &strSize2 = GetEntryByNumber(0x0028,0x0012);
+ if ( strSize2 != GDCM_UNFOUND )
+ {
+ return atoi( strSize2.c_str() );
+ }
- } else { /* on est sur une Sun ou une SGI */
- sw = 4321;
- if (DEBUG) printf("HostByteOrder != NetworkByteOrder\n");
+ return 1;
+}
+
+/**
+ * \brief gets the info from 0028,0030 : Pixel Spacing
+ * else 1.0
+ * @return X dimension of a pixel
+ */
+float Header::GetXSpacing()
+{
+ float xspacing, yspacing;
+ const std::string &strSpacing = GetEntryByNumber(0x0028,0x0030);
+
+ if ( strSpacing == GDCM_UNFOUND )
+ {
+ dbg.Verbose(0, "Header::GetXSpacing: unfound Pixel Spacing (0028,0030)");
+ return 1.;
+ }
+
+ int nbValues;
+ if( ( nbValues = sscanf( strSpacing.c_str(),
+ "%f\\%f", &yspacing, &xspacing)) != 2 )
+ {
+ // if single value is found, xspacing is defaulted to yspacing
+ if ( nbValues == 1 )
+ {
+ xspacing = yspacing;
}
- 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
- }
-
- rewind(e->fp); // les info commencent au debut
- e->offsetCourant=0;
- return (sw);
-}
-
-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;
-}
-
-/* =======================================================================
-* _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
- */
-
-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);
-
- if(sw)l_gr=_IdDcmSWAP_LONG(((long)l_gr),sw);
- *skippedLength = 4;
- }
-
- *longueurLue=l_gr;
+ if ( xspacing == 0.0 )
+ xspacing = 1.0;
+
+ return xspacing;
+
+ }
+
+ // to avoid troubles with David Clunie's-like images
+ if ( xspacing == 0. && yspacing == 0.)
+ return 1.;
+
+ if ( xspacing == 0.)
+ {
+ dbg.Verbose(0, "Header::GetXSpacing: gdcmData/CT-MONO2-8-abdo.dcm problem");
+ // seems to be a bug in the header ...
+ nbValues = sscanf( strSpacing.c_str(), "%f\\0\\%f", &yspacing, &xspacing);
+ assert( nbValues == 2 );
+ }
+
+ return xspacing;
+}
+
+/**
+ * \brief gets the info from 0028,0030 : Pixel Spacing
+ * else 1.0
+ * @return Y dimension of a pixel
+ */
+float Header::GetYSpacing()
+{
+ float yspacing = 1.;
+ std::string strSpacing = GetEntryByNumber(0x0028,0x0030);
- // Traitement des curiosites sur la longueur
+ if ( strSpacing == GDCM_UNFOUND )
+ {
+ dbg.Verbose(0, "Header::GetYSpacing: unfound Pixel Spacing (0028,0030)");
+ return 1.;
+ }
+
+ // if sscanf cannot read any float value, it won't affect yspacing
+ sscanf( strSpacing.c_str(), "%f", &yspacing);
+
+ if ( yspacing == 0.0 )
+ yspacing = 1.0;
+
+ return yspacing;
+}
+
+/**
+ * \brief gets the info from 0018,0088 : Space Between Slices
+ * else from 0018,0050 : Slice Thickness
+ * else 1.0
+ * @return Z dimension of a voxel-to be
+ */
+float Header::GetZSpacing()
+{
+ // Spacing Between Slices : distance entre le milieu de chaque coupe
+ // Les coupes peuvent etre :
+ // jointives (Spacing between Slices = Slice Thickness)
+ // chevauchantes (Spacing between Slices < Slice Thickness)
+ // disjointes (Spacing between Slices > Slice Thickness)
+ // Slice Thickness : epaisseur de tissus sur laquelle est acquis le signal
+ // ca interesse le physicien de l'IRM, pas le visualisateur de volumes ...
+ // Si le Spacing Between Slices est absent,
+ // on suppose que les coupes sont jointives
+
+ const std::string &strSpacingBSlices = GetEntryByNumber(0x0018,0x0088);
+
+ if ( strSpacingBSlices == GDCM_UNFOUND )
+ {
+ dbg.Verbose(0, "Header::GetZSpacing: unfound StrSpacingBSlices");
+ const std::string &strSliceThickness = GetEntryByNumber(0x0018,0x0050);
+ if ( strSliceThickness == GDCM_UNFOUND )
+ {
+ return 1.;
+ }
+ else
+ {
+ // if no 'Spacing Between Slices' is found,
+ // we assume slices join together
+ // (no overlapping, no interslice gap)
+ // if they don't, we're fucked up
+ return (float)atof( strSliceThickness.c_str() );
+ }
+ }
+ //else
+ return (float)atof( strSpacingBSlices.c_str() );
+}
+
+/**
+ *\brief gets the info from 0028,1052 : Rescale Intercept
+ * @return Rescale Intercept
+ */
+float Header::GetRescaleIntercept()
+{
+ float resInter = 0.;
+ /// 0028 1052 DS IMG Rescale Intercept
+ const std::string &strRescInter = GetEntryByNumber(0x0028,0x1052);
+ if ( strRescInter != GDCM_UNFOUND )
+ {
+ if( sscanf( strRescInter.c_str(), "%f", &resInter) != 1 )
+ {
+ // bug in the element 0x0028,0x1052
+ dbg.Verbose(0, "Header::GetRescaleIntercept: Rescale Slope "
+ "is empty");
+ }
+ }
+
+ return resInter;
+}
+
+/**
+ *\brief gets the info from 0028,1053 : Rescale Slope
+ * @return Rescale Slope
+ */
+float Header::GetRescaleSlope()
+{
+ float resSlope = 1.;
+ //0028 1053 DS IMG Rescale Slope
+ std::string strRescSlope = GetEntryByNumber(0x0028,0x1053);
+ if ( strRescSlope != GDCM_UNFOUND )
+ {
+ if( sscanf( strRescSlope.c_str(), "%f", &resSlope) != 1)
+ {
+ // bug in the element 0x0028,0x1053
+ dbg.Verbose(0, "Header::GetRescaleSlope: Rescale Slope is empty");
+ }
+ }
+
+ return resSlope;
+}
+
+/**
+ * \brief This function is intended to user who doesn't want
+ * to have to manage a LUT and expects to get an RBG Pixel image
+ * (or a monochrome one ...)
+ * \warning to be used with GetImagePixels()
+ * @return 1 if Gray level, 3 if Color (RGB, YBR or PALETTE COLOR)
+ */
+int Header::GetNumberOfScalarComponents()
+{
+ if ( GetSamplesPerPixel() == 3 )
+ {
+ return 3;
+ }
+
+ // 0028 0100 US IMG Bits Allocated
+ // (in order no to be messed up by old RGB images)
+ if ( GetEntryByNumber(0x0028,0x0100) == "24" )
+ {
+ return 3;
+ }
+
+ std::string strPhotometricInterpretation = GetEntryByNumber(0x0028,0x0004);
+
+ if ( ( strPhotometricInterpretation == "PALETTE COLOR ") )
+ {
+ if ( HasLUT() )// PALETTE COLOR is NOT enough
+ {
+ return 3;
+ }
+ else
+ {
+ return 1;
+ }
+ }
+
+ // 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 Header::GetNumberOfScalarComponentsRaw()
+{
+ // 0028 0100 US IMG Bits Allocated
+ // (in order no to be messed up by old RGB images)
+ if ( Header::GetEntryByNumber(0x0028,0x0100) == "24" )
+ {
+ return 3;
+ }
+
+ // we assume that *all* kinds of YBR are dealt with
+ return GetSamplesPerPixel();
+}
+
+//
+// -------------- Remember ! ----------------------------------
+//
+// Image Position Patient (0020,0032):
+// If not found (ACR_NEMA) we try Image Position (0020,0030)
+// If not found (ACR-NEMA), we consider Slice Location (0020,1041)
+// or Location (0020,0050)
+// as the Z coordinate,
+// 0. for all the coordinates if nothing is found
+
+// \todo find a way to inform the caller nothing was found
+// \todo How to tell the caller a wrong number of values was found?
+//
+// ---------------------------------------------------------------
+//
+
+/**
+ * \brief gets the info from 0020,0032 : Image Position Patient
+ * else from 0020,0030 : Image Position (RET)
+ * else 0.
+ * @return up-left image corner X position
+ */
+float Header::GetXOrigin()
+{
+ float xImPos, yImPos, zImPos;
+ std::string strImPos = GetEntryByNumber(0x0020,0x0032);
+
+ if ( strImPos == GDCM_UNFOUND )
+ {
+ dbg.Verbose(0, "Header::GetXImagePosition: unfound Image "
+ "Position Patient (0020,0032)");
+ strImPos = GetEntryByNumber(0x0020,0x0030); // For ACR-NEMA images
+ if ( strImPos == GDCM_UNFOUND )
+ {
+ dbg.Verbose(0, "Header::GetXImagePosition: unfound Image "
+ "Position (RET) (0020,0030)");
+ /// \todo How to tell the caller nothing was found ?
+ return 0.;
+ }
+ }
+
+ if( sscanf( strImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3 )
+ {
+ return 0.;
+ }
+
+ return xImPos;
+}
+
+/**
+ * \brief gets the info from 0020,0032 : Image Position Patient
+ * else from 0020,0030 : Image Position (RET)
+ * else 0.
+ * @return up-left image corner Y position
+ */
+float Header::GetYOrigin()
+{
+ float xImPos, yImPos, zImPos;
+ std::string strImPos = GetEntryByNumber(0x0020,0x0032);
+
+ if ( strImPos == GDCM_UNFOUND)
+ {
+ dbg.Verbose(0, "Header::GetYImagePosition: unfound Image "
+ "Position Patient (0020,0032)");
+ strImPos = GetEntryByNumber(0x0020,0x0030); // For ACR-NEMA images
+ if ( strImPos == GDCM_UNFOUND )
+ {
+ dbg.Verbose(0, "Header::GetYImagePosition: unfound Image "
+ "Position (RET) (0020,0030)");
+ /// \todo How to tell the caller nothing was found ?
+ return 0.;
+ }
+ }
+
+ if( sscanf( strImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3 )
+ {
+ return 0.;
+ }
+
+ return yImPos;
+}
+
+/**
+ * \brief gets the info from 0020,0032 : Image Position Patient
+ * else from 0020,0030 : Image Position (RET)
+ * else from 0020,1041 : Slice Location
+ * else from 0020,0050 : Location
+ * else 0.
+ * @return up-left image corner Z position
+ */
+float Header::GetZOrigin()
+{
+ float xImPos, yImPos, zImPos;
+ std::string strImPos = GetEntryByNumber(0x0020,0x0032);
+
+ if ( strImPos != GDCM_UNFOUND )
+ {
+ if( sscanf( strImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3)
+ {
+ dbg.Verbose(0, "Header::GetZImagePosition: wrong Image "
+ "Position Patient (0020,0032)");
+ return 0.; // bug in the element 0x0020,0x0032
+ }
+ else
+ {
+ return zImPos;
+ }
+ }
+
+ strImPos = GetEntryByNumber(0x0020,0x0030); // For ACR-NEMA images
+ if ( strImPos != GDCM_UNFOUND )
+ {
+ if( sscanf( strImPos.c_str(),
+ "%f\\%f\\%f", &xImPos, &yImPos, &zImPos ) != 3 )
+ {
+ dbg.Verbose(0, "Header::GetZImagePosition: wrong Image Position (RET) (0020,0030)");
+ return 0.; // bug in the element 0x0020,0x0032
+ }
+ else
+ {
+ return zImPos;
+ }
+ }
+
+ std::string strSliceLocation = GetEntryByNumber(0x0020,0x1041); // for *very* old ACR-NEMA images
+ if ( strSliceLocation != GDCM_UNFOUND )
+ {
+ if( sscanf( strSliceLocation.c_str(), "%f", &zImPos) != 1)
+ {
+ dbg.Verbose(0, "Header::GetZImagePosition: wrong Slice Location (0020,1041)");
+ return 0.; // bug in the element 0x0020,0x1041
+ }
+ else
+ {
+ return zImPos;
+ }
+ }
+ dbg.Verbose(0, "Header::GetZImagePosition: unfound Slice Location (0020,1041)");
+
+ std::string strLocation = GetEntryByNumber(0x0020,0x0050);
+ if ( strLocation != GDCM_UNFOUND )
+ {
+ if( sscanf( strLocation.c_str(), "%f", &zImPos) != 1)
+ {
+ dbg.Verbose(0, "Header::GetZImagePosition: wrong Location (0020,0050)");
+ return 0.; // bug in the element 0x0020,0x0050
+ }
+ else
+ {
+ return zImPos;
+ }
+ }
+ dbg.Verbose(0, "Header::GetYImagePosition: unfound Location (0020,0050)");
+
+ return 0.; // Hopeless
+}
+
+/**
+ * \brief gets the info from 0020,0013 : Image Number else 0.
+ * @return image number
+ */
+int Header::GetImageNumber()
+{
+ // The function i atoi() takes the address of an area of memory as
+ // parameter and converts the string stored at that location to an integer
+ // using the external decimal to internal binary conversion rules. This may
+ // be preferable to sscanf() since atoi() is a much smaller, simpler and
+ // faster function. sscanf() can do all possible conversions whereas
+ // atoi() can only do single decimal integer conversions.
+ //0020 0013 IS REL Image Number
+ std::string strImNumber = GetEntryByNumber(0x0020,0x0013);
+ if ( strImNumber != GDCM_UNFOUND )
+ {
+ return atoi( strImNumber.c_str() );
+ }
+ return 0; //Hopeless
+}
+
+/**
+ * \brief gets the info from 0008,0060 : Modality
+ * @return Modality Type
+ */
+ModalityType Header::GetModality()
+{
+ // 0008 0060 CS ID Modality
+ std::string strModality = GetEntryByNumber(0x0008,0x0060);
+ if ( strModality != GDCM_UNFOUND )
+ {
+ if ( strModality.find("AU") < strModality.length()) return AU;
+ else if ( strModality.find("AS") < strModality.length()) return AS;
+ else if ( strModality.find("BI") < strModality.length()) return BI;
+ else if ( strModality.find("CF") < strModality.length()) return CF;
+ else if ( strModality.find("CP") < strModality.length()) return CP;
+ else if ( strModality.find("CR") < strModality.length()) return CR;
+ else if ( strModality.find("CT") < strModality.length()) return CT;
+ else if ( strModality.find("CS") < strModality.length()) return CS;
+ else if ( strModality.find("DD") < strModality.length()) return DD;
+ else if ( strModality.find("DF") < strModality.length()) return DF;
+ else if ( strModality.find("DG") < strModality.length()) return DG;
+ else if ( strModality.find("DM") < strModality.length()) return DM;
+ else if ( strModality.find("DS") < strModality.length()) return DS;
+ else if ( strModality.find("DX") < strModality.length()) return DX;
+ else if ( strModality.find("ECG") < strModality.length()) return ECG;
+ else if ( strModality.find("EPS") < strModality.length()) return EPS;
+ else if ( strModality.find("FA") < strModality.length()) return FA;
+ else if ( strModality.find("FS") < strModality.length()) return FS;
+ else if ( strModality.find("HC") < strModality.length()) return HC;
+ else if ( strModality.find("HD") < strModality.length()) return HD;
+ else if ( strModality.find("LP") < strModality.length()) return LP;
+ else if ( strModality.find("LS") < strModality.length()) return LS;
+ else if ( strModality.find("MA") < strModality.length()) return MA;
+ else if ( strModality.find("MR") < strModality.length()) return MR;
+ else if ( strModality.find("NM") < strModality.length()) return NM;
+ else if ( strModality.find("OT") < strModality.length()) return OT;
+ else if ( strModality.find("PT") < strModality.length()) return PT;
+ else if ( strModality.find("RF") < strModality.length()) return RF;
+ else if ( strModality.find("RG") < strModality.length()) return RG;
+ else if ( strModality.find("RTDOSE") < strModality.length()) return RTDOSE;
+ else if ( strModality.find("RTIMAGE") < strModality.length()) return RTIMAGE;
+ else if ( strModality.find("RTPLAN") < strModality.length()) return RTPLAN;
+ else if ( strModality.find("RTSTRUCT") < strModality.length()) return RTSTRUCT;
+ else if ( strModality.find("SM") < strModality.length()) return SM;
+ else if ( strModality.find("ST") < strModality.length()) return ST;
+ else if ( strModality.find("TG") < strModality.length()) return TG;
+ else if ( strModality.find("US") < strModality.length()) return US;
+ else if ( strModality.find("VF") < strModality.length()) return VF;
+ else if ( strModality.find("XA") < strModality.length()) return XA;
+ else if ( strModality.find("XC") < strModality.length()) return XC;
+
+ else
+ {
+ /// \todo throw error return value ???
+ /// specified <> unknow in our database
+ return Unknow;
+ }
+ }
+
+ return Unknow;
+}
+
+/**
+ * \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 Header::GetBitsStored()
+{
+ std::string strSize = GetEntryByNumber( 0x0028, 0x0101 );
+ if ( strSize == GDCM_UNFOUND )
+ {
+ dbg.Verbose(0, "Header::GetBitsStored: this is supposed to "
+ "be mandatory");
+ return 0; // It's supposed to be mandatory
+ // the caller will have to check
+ }
+ return atoi( strSize.c_str() );
+}
+
+/**
+ * \brief Retrieve the high bit position.
+ * \warning The method defaults to 0 when information is absent.
+ * The responsability of checking this value is left to the caller.
+ * @return The high bit positin when present. 0 when absent.
+ */
+int Header::GetHighBitPosition()
+{
+ std::string strSize = GetEntryByNumber( 0x0028, 0x0102 );
+ if ( strSize == GDCM_UNFOUND )
+ {
+ dbg.Verbose(0, "Header::GetHighBitPosition: this is supposed "
+ "to be mandatory");
+ return 0;
+ }
+ return atoi( strSize.c_str() );
+}
+
+/**
+ * \brief Check wether the pixels are signed or UNsigned data.
+ * \warning The method defaults to false (UNsigned) when information is absent.
+ * The responsability of checking this value is left to the caller.
+ * @return True when signed, false when UNsigned
+ */
+bool Header::IsSignedPixelData()
+{
+ std::string strSize = GetEntryByNumber( 0x0028, 0x0103 );
+ if ( strSize == GDCM_UNFOUND )
+ {
+ dbg.Verbose(0, "Header::IsSignedPixelData: this is supposed "
+ "to be mandatory");
+ return false;
+ }
+ int sign = atoi( strSize.c_str() );
+ if ( sign == 0 )
+ {
+ return false;
+ }
+ return true;
+}
+
+/**
+ * \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 Header::GetBitsAllocated()
+{
+ std::string strSize = GetEntryByNumber(0x0028,0x0100);
+ if ( strSize == GDCM_UNFOUND )
+ {
+ dbg.Verbose(0, "Header::GetBitsStored: this is supposed to "
+ "be mandatory");
+ return 0; // It's supposed to be mandatory
+ // the caller will have to check
+ }
+ return atoi( strSize.c_str() );
+}
+
+/**
+ * \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 Header::GetSamplesPerPixel()
+{
+ const std::string& strSize = GetEntryByNumber(0x0028,0x0002);
+ if ( strSize == GDCM_UNFOUND )
+ {
+ dbg.Verbose(0, "Header::GetBitsStored: this is supposed to "
+ "be mandatory");
+ return 1; // Well, it's supposed to be mandatory ...
+ // but sometimes it's missing : *we* assume Gray pixels
+ }
+ return atoi( strSize.c_str() );
+}
+
+/**
+ * \brief Check wether this a monochrome picture or not by accessing
+ * the "Photometric Interpretation" tag ( 0x0028, 0x0004 ).
+ * @return true when "MONOCHROME1" or "MONOCHROME2". False otherwise.
+ */
+bool Header::IsMonochrome()
+{
+ const std::string& PhotometricInterp = GetEntryByNumber( 0x0028, 0x0004 );
+ if ( Util::DicomStringEqual(PhotometricInterp, "MONOCHROME1")
+ || Util::DicomStringEqual(PhotometricInterp, "MONOCHROME2") )
+ {
+ return true;
+ }
+ if ( PhotometricInterp == GDCM_UNFOUND )
+ {
+ dbg.Verbose(0, "Header::IsMonochrome: absent Photometric "
+ "Interpretation");
+ }
+ return false;
+}
+
+/**
+ * \brief Check wether this a "PALETTE COLOR" picture or not by accessing
+ * the "Photometric Interpretation" tag ( 0x0028, 0x0004 ).
+ * @return true when "PALETTE COLOR". False otherwise.
+ */
+bool Header::IsPaletteColor()
+{
+ std::string PhotometricInterp = GetEntryByNumber( 0x0028, 0x0004 );
+ if ( PhotometricInterp == "PALETTE COLOR " )
+ {
+ return true;
+ }
+ if ( PhotometricInterp == GDCM_UNFOUND )
+ {
+ dbg.Verbose(0, "Header::IsPaletteColor: absent Photometric "
+ "Interpretation");
+ }
+ return false;
+}
+
+/**
+ * \brief Check wether this a "YBR_FULL" color picture or not by accessing
+ * the "Photometric Interpretation" tag ( 0x0028, 0x0004 ).
+ * @return true when "YBR_FULL". False otherwise.
+ */
+bool Header::IsYBRFull()
+{
+ std::string PhotometricInterp = GetEntryByNumber( 0x0028, 0x0004 );
+ if ( PhotometricInterp == "YBR_FULL" )
+ {
+ return true;
+ }
+ if ( PhotometricInterp == GDCM_UNFOUND )
+ {
+ dbg.Verbose(0, "Header::IsYBRFull: absent Photometric "
+ "Interpretation");
+ }
+ return false;
+}
+
+/**
+ * \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 Header::GetPlanarConfiguration()
+{
+ std::string strSize = GetEntryByNumber(0x0028,0x0006);
+ if ( strSize == GDCM_UNFOUND )
+ {
+ return 0;
+ }
+ return atoi( strSize.c_str() );
+}
+
+/**
+ * \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 Header::GetPixelSize()
+{
+ // 0028 0100 US IMG Bits Allocated
+ // (in order no to be messed up by old RGB images)
+ // if (Header::GetEntryByNumber(0x0028,0x0100) == "24")
+ // return 3;
+
+ 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, "Header::GetPixelSize: Unknown pixel type");
+ return 0;
+}
+
+/**
+ * \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 Header::GetPixelType()
+{
+ std::string bitsAlloc = GetEntryByNumber(0x0028, 0x0100); // Bits Allocated
+ if ( bitsAlloc == GDCM_UNFOUND )
+ {
+ dbg.Verbose(0, "Header::GetPixelType: unfound Bits Allocated");
+ bitsAlloc = "16";
+ }
+
+ if ( bitsAlloc == "64" )
+ {
+ return "FD";
+ }
+ else if ( bitsAlloc == "12" )
+ {
+ // It will be unpacked
+ bitsAlloc = "16";
+ }
+ else if ( bitsAlloc == "24" )
+ {
+ // (in order no to be messed up
+ bitsAlloc = "8"; // by old RGB images)
+ }
+
+ std::string sign = GetEntryByNumber(0x0028, 0x0103);//"Pixel Representation"
+
+ if (sign == GDCM_UNFOUND )
+ {
+ dbg.Verbose(0, "Header::GetPixelType: unfound Pixel Representation");
+ bitsAlloc = "0";
+ }
+ else if ( sign == "0" )
+ {
+ sign = "U";
+ }
+ else
+ {
+ sign = "S";
+ }
+ return bitsAlloc + sign;
+}
+
+
+/**
+ * \brief Recover the offset (from the beginning of the file)
+ * of *image* pixels (not *icone image* pixels, if any !)
+ * @return Pixel Offset
+ */
+size_t Header::GetPixelOffset()
+{
+ DocEntry* pxlElement = GetDocEntryByNumber(GrPixel,NumPixel);
+ if ( pxlElement )
+ {
+ return pxlElement->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 TODO : unify those two (previous one and next one)
+/**
+ * \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 Header::GetPixelAreaLength()
+{
+ DocEntry* pxlElement = GetDocEntryByNumber(GrPixel,NumPixel);
+ if ( pxlElement )
+ {
+ return pxlElement->GetLength();
+ }
+ else
+ {
+#ifdef GDCM_DEBUG
+ std::cout << "Big trouble : Pixel Element ("
+ << std::hex << GrPixel<<","<< NumPixel<< ") NOT found"
+ << std::endl;
+#endif //GDCM_DEBUG
+ return 0;
+ }
+}
+
+/**
+ * \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 Header::HasLUT()
+{
+ // Check the presence of the LUT Descriptors, and LUT Tables
+ // LutDescriptorRed
+ if ( !GetDocEntryByNumber(0x0028,0x1101) )
+ {
+ return false;
+ }
+ // LutDescriptorGreen
+ if ( !GetDocEntryByNumber(0x0028,0x1102) )
+ {
+ return false;
+ }
+ // LutDescriptorBlue
+ if ( !GetDocEntryByNumber(0x0028,0x1103) )
+ {
+ return false;
+ }
+ // Red Palette Color Lookup Table Data
+ if ( !GetDocEntryByNumber(0x0028,0x1201) )
+ {
+ return false;
+ }
+ // Green Palette Color Lookup Table Data
+ if ( !GetDocEntryByNumber(0x0028,0x1202) )
+ {
+ return false;
+ }
+ // Blue Palette Color Lookup Table Data
+ if ( !GetDocEntryByNumber(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;
+}
+
+/**
+ * \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 Header::GetLUTNbits()
+{
+ std::vector<std::string> tokens;
+ 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.clear(); // clean any previous value
+ Util::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;
+}
+
+/**
+ * \brief Accesses the info from 0002,0010 : Transfert Syntax and TS
+ * else 1.
+ * @return The full Transfert Syntax Name (as opposed to Transfert Syntax UID)
+ */
+std::string Header::GetTransfertSyntaxName()
+{
+ // use the TS (TS : Transfert Syntax)
+ std::string transfertSyntax = GetEntryByNumber(0x0002,0x0010);
+
+ if ( transfertSyntax == GDCM_NOTLOADED )
+ {
+ std::cout << "Transfert Syntax not loaded. " << std::endl
+ << "Better you increase MAX_SIZE_LOAD_ELEMENT_VALUE"
+ << std::endl;
+ return "Uncompressed ACR-NEMA";
+ }
+ if ( transfertSyntax == GDCM_UNFOUND )
+ {
+ dbg.Verbose(0, "Header::GetTransfertSyntaxName:"
+ " unfound Transfert Syntax (0002,0010)");
+ return "Uncompressed ACR-NEMA";
+ }
+
+ while ( ! isdigit((unsigned char)transfertSyntax[transfertSyntax.length()-1]) )
+ {
+ transfertSyntax.erase(transfertSyntax.length()-1, 1);
+ }
+ // we do it only when we need it
+ TS* ts = Global::GetTS();
+ std::string tsName = ts->GetValue( transfertSyntax );
+
+ //delete ts; /// \todo Seg Fault when deleted ?!
+ return tsName;
+}
+
+//-----------------------------------------------------------------------------
+// Protected
+
+/**
+ * \brief anonymize a Header (removes Patient's personal info)
+ * (read the code to see which ones ...)
+ */
+bool Header::AnonymizeHeader()
+{
+ // If exist, replace by spaces
+ SetEntryByNumber (" ",0x0010, 0x2154); // Telephone
+ SetEntryByNumber (" ",0x0010, 0x1040); // Adress
+ SetEntryByNumber (" ",0x0010, 0x0020); // Patient ID
+
+ DocEntry* patientNameHE = GetDocEntryByNumber (0x0010, 0x0010);
- 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);
+ if ( patientNameHE ) // we replace it by Study Instance UID (why not)
+ {
+ std::string studyInstanceUID = GetEntryByNumber (0x0020, 0x000d);
+ if ( studyInstanceUID != GDCM_UNFOUND )
+ {
+ ReplaceOrCreateByNumber(studyInstanceUID, 0x0010, 0x0010);
+ }
+ else
+ {
+ ReplaceOrCreateByNumber("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;
}
+
+/**
+ * \brief gets the info from 0020,0037 : Image Orientation Patient
+ * @param iop adress of the (6)float aray to receive values
+ * @return cosines of image orientation patient
+ */
+void Header::GetImageOrientationPatient( float iop[6] )
+{
+ std::string strImOriPat;
+ //iop is supposed to be float[6]
+ iop[0] = iop[1] = iop[2] = iop[3] = iop[4] = iop[5] = 0.;
+
+ // 0020 0037 DS REL Image Orientation (Patient)
+ if ( (strImOriPat = GetEntryByNumber(0x0020,0x0037)) != GDCM_UNFOUND )
+ {
+ if( sscanf( strImOriPat.c_str(), "%f\\%f\\%f\\%f\\%f\\%f",
+ &iop[0], &iop[1], &iop[2], &iop[3], &iop[4], &iop[5]) != 6 )
+ {
+ dbg.Verbose(0, "Header::GetImageOrientationPatient: "
+ "wrong Image Orientation Patient (0020,0037)");
+ }
+ }
+ //For ACR-NEMA
+ // 0020 0035 DS REL Image Orientation (RET)
+ else if ( (strImOriPat = GetEntryByNumber(0x0020,0x0035)) != GDCM_UNFOUND )
+ {
+ if( sscanf( strImOriPat.c_str(), "%f\\%f\\%f\\%f\\%f\\%f",
+ &iop[0], &iop[1], &iop[2], &iop[3], &iop[4], &iop[5]) != 6 )
+ {
+ dbg.Verbose(0, "Header::GetImageOrientationPatient: "
+ "wrong Image Orientation Patient (0020,0035)");
+ }
+ }
+}
+
+/**
+ * \brief Initialize a default DICOM header that should contain all the
+ * field require by other reader. DICOM standard does not
+ * explicitely defines those fields, heuristic has been choosen.
+ * This is not perfect as we are writting a CT image...
+ */
+void Header::InitializeDefaultHeader()
+{
+ typedef struct
+ {
+ const char *value;
+ uint16_t group;
+ uint16_t elem;
+ } DICOM_DEFAULT_VALUE;
+
+ std::string date = Util::GetCurrentDate();
+ std::string time = Util::GetCurrentTime();
+ std::string uid = Util::CreateUniqueUID();
+ std::string uidMedia = uid;
+ std::string uidClass = uid + ".1";
+ std::string uidInst = uid + ".10";
+ std::string uidStudy = uid + ".100";
+ std::string uidSerie = uid + ".1000";
+
+ static DICOM_DEFAULT_VALUE defaultvalue[] = {
+ { "146 ", 0x0002, 0x0000}, // Meta Element Group Length // FIXME: how to recompute ?
+ { "1.2.840.10008.5.1.4.1.1.2", 0x0002, 0x0002}, // Media Storage SOP Class UID (CT Image Storage)
+ { uidClass.c_str(), 0x0002, 0x0003}, // Media Storage SOP Instance UID
+ { uidClass.c_str(), 0x0002, 0x0012}, // META Implementation Class UID
+ { "GDCM", 0x0002, 0x0016}, // Source Application Entity Title
+
+ { date.c_str(), 0x0008, 0x0012}, // Instance Creation Date
+ { time.c_str(), 0x0008, 0x0013}, // Instance Creation Time
+ { "1.2.840.10008.5.1.4.1.1.2", 0x0008, 0x0016}, // SOP Class UID
+ { uidInst.c_str(), 0x0008, 0x0018}, // SOP Instance UID
+ { "CT", 0x0008, 0x0060}, // Modality
+ { "GDCM", 0x0008, 0x0070}, // Manufacturer
+ { "GDCM", 0x0008, 0x0080}, // Institution Name
+ { "http://www-creatis.insa-lyon.fr/Public/Gdcm", 0x0008, 0x0081}, // Institution Address
+
+ { "GDCM", 0x0010, 0x0010}, // Patient's Name
+ { "GDCMID", 0x0010, 0x0020}, // Patient ID
+
+ { uidStudy.c_str(), 0x0020, 0x000d}, // Study Instance UID
+ { uidSerie.c_str(), 0x0020, 0x000e}, // Series Instance UID
+ { "1", 0x0020, 0x0010}, // StudyID
+ { "1", 0x0020, 0x0011}, // SeriesNumber
+
+ { "1", 0x0028, 0x0002}, // Samples per pixel 1 or 3
+ { "MONOCHROME1", 0x0028, 0x0004}, // photochromatic interpretation
+ { "0", 0x0028, 0x0010}, // nbRows
+ { "0", 0x0028, 0x0011}, // nbCols
+ { "8", 0x0028, 0x0100}, // BitsAllocated 8 or 12 or 16
+ { "8", 0x0028, 0x0101}, // BitsStored <= BitsAllocated
+ { "7", 0x0028, 0x0102}, // HighBit <= BitsAllocated - 1
+ { "0", 0x0028, 0x0103}, // Pixel Representation 0(unsigned) or 1(signed)
+ { 0, 0, 0 }
+ };
+
+ // default value
+ // Special case this is the image (not a string)
+ GrPixel = 0x7fe0;
+ NumPixel = 0x0010;
+ ReplaceOrCreateByNumber(0, 0, GrPixel, NumPixel);
+
+ // All remaining strings:
+ unsigned int i = 0;
+ DICOM_DEFAULT_VALUE current = defaultvalue[i];
+ while( current.value )
+ {
+ ReplaceOrCreateByNumber(current.value, current.group, current.elem);
+ current = defaultvalue[++i];
+ }
+}
+
+
+//-----------------------------------------------------------------------------
+// Private
+
+//-----------------------------------------------------------------------------
+
+} // end namespace gdcm
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff