-#include "gdcmlib.h"
-extern "C" {
-#include "glib.h"
-}
+// $Header: /cvs/public/gdcm/src/Attic/gdcmHeader.cxx,v 1.96 2003/10/09 13:22:54 jpr Exp $
+
+#include "gdcmHeader.h"
+
#include <stdio.h>
+#include <cerrno>
// For nthos:
#ifdef _MSC_VER
#include <winsock.h>
#else
#include <netinet/in.h>
#endif
-#include <map>
+#include <cctype> // for isalpha
#include <sstream>
#include "gdcmUtil.h"
+#include "gdcmTS.h"
-#define HEADER_LENGHT_TO_READ 256 // on ne lit plus que le debut
+// Refer to gdcmHeader::CheckSwap()
+#define HEADER_LENGTH_TO_READ 256
+// Refer to gdcmHeader::SetMaxSizeLoadElementValue()
+//#define _MaxSizeLoadElementValue_ 1024
+#define _MaxSizeLoadElementValue_ 4096
+/**
+ * \ingroup gdcmHeader
+ * \brief
+ */
+void gdcmHeader::Initialise(void) {
+ dicom_vr = gdcmGlobal::GetVR();
+ dicom_ts = gdcmGlobal::GetTS();
+ Dicts = gdcmGlobal::GetDicts();
+ RefPubDict = Dicts->GetDefaultPubDict();
+ RefShaDict = (gdcmDict*)0;
+}
-//FIXME: this looks dirty to me...
-#define str2num(str, typeNum) *((typeNum *)(str))
+/**
+ * \ingroup gdcmHeader
+ * \brief
+ * @param InFilename
+ * @param exception_on_error
+ */
+gdcmHeader::gdcmHeader(const char *InFilename, bool exception_on_error) {
+ SetMaxSizeLoadElementValue(_MaxSizeLoadElementValue_);
+ filename = InFilename;
+ Initialise();
+ if ( !OpenFile(exception_on_error))
+ return;
+ ParseHeader();
+ LoadElements();
+ CloseFile();
+}
-VRHT * gdcmHeader::dicom_vr = (VRHT*)0;
-gdcmDictSet* gdcmHeader::Dicts = new gdcmDictSet();
+/**
+ * \ingroup gdcmHeader
+ * \brief
+ * @param exception_on_error
+ */
+gdcmHeader::gdcmHeader(bool exception_on_error) {
+ SetMaxSizeLoadElementValue(_MaxSizeLoadElementValue_);
+ Initialise();
+}
-void gdcmHeader::Initialise(void) {
- if (!gdcmHeader::dicom_vr)
- InitVRDict();
- PixelPosition = (size_t)0;
- PixelsTrouves = false;
- RefPubDict = gdcmHeader::Dicts->GetDefaultPublicDict();
- RefShaDict = (gdcmDict*)0;
+/**
+ * \ingroup gdcmHeader
+ * \brief
+ * @param exception_on_error
+ * @return
+ */
+ bool gdcmHeader::OpenFile(bool exception_on_error)
+ throw(gdcmFileError) {
+ fp=fopen(filename.c_str(),"rb");
+ if(exception_on_error) {
+ if(!fp)
+ throw gdcmFileError("gdcmHeader::gdcmHeader(const char *, bool)");
+ }
+ if ( fp )
+ return true;
+ dbg.Verbose(0, "gdcmHeader::gdcmHeader cannot open file", filename.c_str());
+ return false;
}
-gdcmHeader::gdcmHeader (char* InFilename) {
- filename = InFilename;
- Initialise();
- fp=fopen(InFilename,"rw");
- dbg.Error(!fp, "gdcmHeader::gdcmHeader cannot open file", InFilename);
- BuildHeader();
- fclose(fp);
+/**
+ * \ingroup gdcmHeader
+ * \brief
+ * @return TRUE if the close was successfull
+ */
+bool gdcmHeader::CloseFile(void) {
+ int closed = fclose(fp);
+ fp = (FILE *)0;
+ if (! closed)
+ return false;
+ return true;
}
+/**
+ * \ingroup gdcmHeader
+ * \brief Canonical destructor.
+ */
gdcmHeader::~gdcmHeader (void) {
- return;
-}
-
-void gdcmHeader::InitVRDict (void) {
- if (dicom_vr) {
- dbg.Verbose(0, "gdcmHeader::InitVRDict:", "VR dictionary allready set");
- return;
- }
- VRHT *vr = new VRHT;
- (*vr)["AE"] = "Application Entity"; // 16 car max
- (*vr)["AS"] = "Age String"; // 4 car fixe
- (*vr)["AT"] = "Attribute Tag"; // 2 unsigned short int
- (*vr)["CS"] = "Code String"; // 16 car max
- (*vr)["DA"] = "Date"; // 8 car fixe
- (*vr)["DS"] = "Decimal String"; // Decimal codé Binaire 16 max
- (*vr)["DT"] = "Date Time"; // 26 car max
- (*vr)["FL"] = "Floating Point Single"; // 4 octets IEEE 754:1985
- (*vr)["FD"] = "Floating Point Double"; // 8 octets IEEE 754:1985
- (*vr)["IS"] = "Integer String"; // en format externe 12 max
- (*vr)["LO"] = "Long String"; // 64 octets max
- (*vr)["LT"] = "Long Text"; // 10240 max
- (*vr)["OB"] = "Other Byte String";
- (*vr)["OW"] = "Other Word String";
- (*vr)["PN"] = "Person Name";
- (*vr)["SH"] = "Short String"; // 16 car max
- (*vr)["SL"] = "Signed Long";
- (*vr)["SQ"] = "Sequence of Items"; // Not Applicable
- (*vr)["SS"] = "Signed Short"; // 2 octets
- (*vr)["ST"] = "Short Text"; // 1024 car max
- (*vr)["TM"] = "Time"; // 16 car max
- (*vr)["UI"] = "Unique Identifier"; // 64 car max
- (*vr)["UN"] = "Unknown";
- (*vr)["UT"] = "Unlimited Text"; // 2 puissance 32 -1 car max
- (*vr)["UL"] = "Unsigned Long "; // 4 octets fixe
- (*vr)["US"] = "Unsigned Short "; // 2 octets fixe
- dicom_vr = vr;
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief 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
- *
- * 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.
+ dicom_vr = (gdcmVR*)0;
+ Dicts = (gdcmDictSet*)0;
+ RefPubDict = (gdcmDict*)0;
+ RefShaDict = (gdcmDict*)0;
+ return;
+}
+
+// Fourth semantics:
+//
+// ---> Warning : This fourth fiels is NOT part
+// of the 'official' Dicom Dictionnary
+// and should NOT be used.
+// (Not defined for all the groups
+// may be removed in a future release)
+//
+// CMD Command
+// META Meta Information
+// DIR Directory
+// ID
+// PAT Patient
+// ACQ Acquisition
+// REL Related
+// IMG Image
+// SDY Study
+// VIS Visit
+// WAV Waveform
+// PRC
+// DEV Device
+// NMI Nuclear Medicine
+// MED
+// BFS Basic Film Session
+// BFB Basic Film Box
+// BIB Basic Image Box
+// BAB
+// IOB
+// PJ
+// PRINTER
+// RT Radio Therapy
+// DVH
+// SSET
+// RES Results
+// CRV Curve
+// OLY Overlays
+// PXL Pixels
+// DL Delimiters
+//
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Discover what the swap code is (among little endian, big endian,
+ * bad little endian, bad big endian).
*
- * (il faudrait avoir des fonctions auxquelles
- * on passe le code Swap en parametre, pour faire des essais 'manuels')
*/
void gdcmHeader::CheckSwap()
{
- guint32 s;
- guint32 x=4; // x : pour ntohs
- bool net2host; // true when HostByteOrder is the same as NetworkByteOrder
-
- int lgrLue;
- char * entCur;
- char deb[HEADER_LENGHT_TO_READ];
-
- // First, compare HostByteOrder and NetworkByteOrder in order to
- // determine if we shall need to swap bytes (i.e. the Endian type).
- if (x==ntohs(x))
- net2host = true;
- else
- net2host = false;
-
- // The easiest case is the one of a DICOM header, since it possesses a
- // file preamble where it suffice to look for the sting "DICM".
- lgrLue = fread(deb, 1, HEADER_LENGHT_TO_READ, fp);
-
- entCur = deb + 128;
- if(memcmp(entCur, "DICM", (size_t)4) == 0) {
- filetype = TrueDicom;
- dbg.Verbose(0, "gdcmHeader::CheckSwap:", "looks like DICOM Version3");
- } else {
- filetype = Unknown;
- dbg.Verbose(0, "gdcmHeader::CheckSwap:", "not a DICOM Version3 file");
- }
-
- if(filetype == TrueDicom) {
- // Next, determine the value representation (VR). Let's skip to the
- // first element (0002, 0000) and check there if we find "UL", in
- // which case we (almost) know it is explicit VR.
- // WARNING: if it happens to be implicit VR then what we will read
- // is the length of the group. If this ascii representation of this
- // length happens to be "UL" then we shall believe it is explicit VR.
- // FIXME: in order to fix the above warning, we could read the next
- // element value (or a couple of elements values) in order to make
- // sure we are not commiting a big mistake.
- // We need to skip :
- // * the 128 bytes of File Preamble (often padded with zeroes),
- // * the 4 bytes of "DICM" string,
- // * the 4 bytes of the first tag (0002, 0000),
- // i.e. a total of 136 bytes.
- entCur = deb + 136;
- if(memcmp(entCur, "UL", (size_t)2) == 0) {
- filetype = ExplicitVR;
- dbg.Verbose(0, "gdcmHeader::CheckSwap:",
- "explicit Value Representation");
- } else {
- filetype = ImplicitVR;
- dbg.Verbose(0, "gdcmHeader::CheckSwap:",
- "not an explicit Value Representation");
- }
-
- if (net2host) {
- sw = 4321;
- dbg.Verbose(0, "gdcmHeader::CheckSwap:",
- "HostByteOrder != NetworkByteOrder");
- } else {
- sw = 0;
- dbg.Verbose(0, "gdcmHeader::CheckSwap:",
- "HostByteOrder = NetworkByteOrder");
- }
-
- // Position the file position indicator at first tag (i.e.
- // after the file preamble and the "DICM" string).
- rewind(fp);
- fseek (fp, 132L, SEEK_SET);
- return;
- } // End of TrueDicom
-
- // Alas, this is not a DicomV3 file and whatever happens there is no file
- // preamble. We can reset the file position indicator to where the data
- // is (i.e. the beginning of the file).
- rewind(fp);
-
- // Our next best chance would be to be considering a 'clean' ACR/NEMA file.
- // By clean we mean that the length of the first tag is written down.
- // If this is the case and since the length of the first group HAS to be
- // four (bytes), then determining the proper swap code is straightforward.
-
- entCur = deb + 4;
- s = str2num(entCur, int);
-
- switch (s) {
- case 0x00040000 :
- sw=3412;
- filetype = ACR;
- return;
- case 0x04000000 :
- sw=4321;
- filetype = ACR;
- return;
- case 0x00000400 :
- sw=2143;
- filetype = ACR;
- return;
- case 0x00000004 :
- sw=0;
- filetype = ACR;
- return;
- default :
- dbg.Verbose(0, "gdcmHeader::CheckSwap:",
- "ACE/NEMA unfound swap info (time to raise bets)");
- }
-
- // We are out of luck. It is not a DicomV3 nor a 'clean' ACR/NEMA file.
- // It is time for despaired wild guesses. So, let's assume this file
- // happens to be 'dirty' ACR/NEMA, i.e. the length of the group it
- // not present. Then the only info we have is the net2host one.
- //FIXME Si c'est du RAW, ca degagera + tard
-
- if (! net2host )
- sw = 0;
- else
- sw = 4321;
- return;
+ // The only guaranted way of finding the swap code is to find a
+ // group tag since we know it's length has to be of four bytes i.e.
+ // 0x00000004. Finding the swap code in then straigthforward. Trouble
+ // occurs when we can't find such group...
+ guint32 s;
+ guint32 x=4; // x : for ntohs
+ bool net2host; // true when HostByteOrder is the same as NetworkByteOrder
+
+ int lgrLue;
+ char * entCur;
+ char deb[HEADER_LENGTH_TO_READ];
+
+ // First, compare HostByteOrder and NetworkByteOrder in order to
+ // determine if we shall need to swap bytes (i.e. the Endian type).
+ if (x==ntohs(x))
+ net2host = true;
+ else
+ net2host = false;
+
+ // The easiest case is the one of a DICOM header, since it possesses a
+ // file preamble where it suffice to look for the string "DICM".
+ lgrLue = fread(deb, 1, HEADER_LENGTH_TO_READ, fp);
+
+ entCur = deb + 128;
+ if(memcmp(entCur, "DICM", (size_t)4) == 0) {
+ dbg.Verbose(1, "gdcmHeader::CheckSwap:", "looks like DICOM Version3");
+ // Next, determine the value representation (VR). Let's skip to the
+ // first element (0002, 0000) and check there if we find "UL"
+ // - or "OB" if the 1st one is (0002,0001) -,
+ // in which case we (almost) know it is explicit VR.
+ // WARNING: if it happens to be implicit VR then what we will read
+ // is the length of the group. If this ascii representation of this
+ // length happens to be "UL" then we shall believe it is explicit VR.
+ // FIXME: in order to fix the above warning, we could read the next
+ // element value (or a couple of elements values) in order to make
+ // sure we are not commiting a big mistake.
+ // We need to skip :
+ // * the 128 bytes of File Preamble (often padded with zeroes),
+ // * the 4 bytes of "DICM" string,
+ // * the 4 bytes of the first tag (0002, 0000),or (0002, 0001)
+ // i.e. a total of 136 bytes.
+ entCur = deb + 136;
+ // FIXME
+ // Use gdcmHeader::dicom_vr to test all the possibilities
+ // instead of just checking for UL, OB and UI !?
+ if( (memcmp(entCur, "UL", (size_t)2) == 0) ||
+ (memcmp(entCur, "OB", (size_t)2) == 0) ||
+ (memcmp(entCur, "UI", (size_t)2) == 0) )
+ {
+ filetype = ExplicitVR;
+ dbg.Verbose(1, "gdcmHeader::CheckSwap:",
+ "explicit Value Representation");
+ } else {
+ filetype = ImplicitVR;
+ dbg.Verbose(1, "gdcmHeader::CheckSwap:",
+ "not an explicit Value Representation");
+ }
+ if (net2host) {
+ sw = 4321;
+ dbg.Verbose(1, "gdcmHeader::CheckSwap:",
+ "HostByteOrder != NetworkByteOrder");
+ } else {
+ sw = 0;
+ dbg.Verbose(1, "gdcmHeader::CheckSwap:",
+ "HostByteOrder = NetworkByteOrder");
+ }
+
+ // Position the file position indicator at first tag (i.e.
+ // after the file preamble and the "DICM" string).
+ rewind(fp);
+ fseek (fp, 132L, SEEK_SET);
+ return;
+ } // End of DicomV3
+
+ // Alas, this is not a DicomV3 file and whatever happens there is no file
+ // preamble. We can reset the file position indicator to where the data
+ // is (i.e. the beginning of the file).
+ dbg.Verbose(1, "gdcmHeader::CheckSwap:", "not a DICOM Version3 file");
+ rewind(fp);
+
+ // Our next best chance would be to be considering a 'clean' ACR/NEMA file.
+ // By clean we mean that the length of the first tag is written down.
+ // If this is the case and since the length of the first group HAS to be
+ // four (bytes), then determining the proper swap code is straightforward.
+
+ entCur = deb + 4;
+ // We assume the array of char we are considering contains the binary
+ // representation of a 32 bits integer. Hence the following dirty
+ // trick :
+ s = *((guint32 *)(entCur));
+
+ switch (s) {
+ case 0x00040000 :
+ sw = 3412;
+ filetype = ACR;
+ return;
+ case 0x04000000 :
+ sw = 4321;
+ filetype = ACR;
+ return;
+ case 0x00000400 :
+ sw = 2143;
+ filetype = ACR;
+ return;
+ case 0x00000004 :
+ sw = 0;
+ filetype = ACR;
+ return;
+ default :
+ dbg.Verbose(0, "gdcmHeader::CheckSwap:",
+ "ACR/NEMA unfound swap info (time to raise bets)");
+ }
+
+ // We are out of luck. It is not a DicomV3 nor a 'clean' ACR/NEMA file.
+ // It is time for despaired wild guesses. So, let's assume this file
+ // happens to be 'dirty' ACR/NEMA, i.e. the length of the group is
+ // not present. Then the only info we have is the net2host one.
+ filetype = Unknown;
+ if (! net2host )
+ sw = 0;
+ else
+ sw = 4321;
+ return;
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief
+ */
+void gdcmHeader::SwitchSwapToBigEndian(void) {
+ dbg.Verbose(1, "gdcmHeader::SwitchSwapToBigEndian",
+ "Switching to BigEndian mode.");
+ if ( sw == 0 ) {
+ sw = 4321;
+ return;
+ }
+ if ( sw == 4321 ) {
+ sw = 0;
+ return;
+ }
+ if ( sw == 3412 ) {
+ sw = 2143;
+ return;
+ }
+ if ( sw == 2143 )
+ sw = 3412;
}
/**
* \ingroup gdcmHeader
- * \brief recupere la longueur d'un champ DICOM.
- * Preconditions:
- * 1/ le fichier doit deja avoir ete ouvert,
- * 2/ CheckSwap() doit avoir ete appele
- * 3/ la partie 'group' ainsi que la partie 'elem'
- * de l'acr_element doivent avoir ete lues.
+ * \brief Find the value representation of the current tag.
+ * @param ElVal
+ */
+void gdcmHeader::FindVR( gdcmElValue *ElVal) {
+ if (filetype != ExplicitVR)
+ return;
+
+ char VR[3];
+ std::string vr;
+ int lgrLue;
+ char msg[100]; // for sprintf. Sorry
+
+ long PositionOnEntry = ftell(fp);
+ // Warning: we believe this is explicit VR (Value Representation) because
+ // we used a heuristic that found "UL" in the first tag. Alas this
+ // doesn't guarantee that all the tags will be in explicit VR. In some
+ // cases (see e-film filtered files) one finds implicit VR tags mixed
+ // within an explicit VR file. Hence we make sure the present tag
+ // is in explicit VR and try to fix things if it happens not to be
+ // the case.
+ bool RealExplicit = true;
+
+ lgrLue=fread (&VR, (size_t)2,(size_t)1, fp);
+ VR[2]=0;
+ vr = std::string(VR);
+
+ // Assume we are reading a falsely explicit VR file i.e. we reached
+ // a tag where we expect reading a VR but are in fact we read the
+ // first to bytes of the length. Then we will interogate (through find)
+ // the dicom_vr dictionary with oddities like "\004\0" which crashes
+ // both GCC and VC++ implementations of the STL map. Hence when the
+ // expected VR read happens to be non-ascii characters we consider
+ // we hit falsely explicit VR tag.
+
+ if ( (!isalpha(VR[0])) && (!isalpha(VR[1])) )
+ RealExplicit = false;
+
+ // CLEANME searching the dicom_vr at each occurence is expensive.
+ // PostPone this test in an optional integrity check at the end
+ // of parsing or only in debug mode.
+ if ( RealExplicit && !dicom_vr->Count(vr) )
+ RealExplicit= false;
+
+ if ( RealExplicit ) {
+ if ( ElVal->IsVrUnknown() ) {
+ // When not a dictionary entry, we can safely overwrite the vr.
+ ElVal->SetVR(vr);
+ return;
+ }
+ if ( ElVal->GetVR() == vr ) {
+ // The vr we just read and the dictionary agree. Nothing to do.
+ return;
+ }
+ // The vr present in the file and the dictionary disagree. We assume
+ // the file writer knew best and use the vr of the file. Since it would
+ // be unwise to overwrite the vr of a dictionary (since it would
+ // compromise it's next user), we need to clone the actual DictEntry
+ // and change the vr for the read one.
+ gdcmDictEntry* NewTag = new gdcmDictEntry(ElVal->GetGroup(),
+ ElVal->GetElement(),
+ vr,
+ "FIXME",
+ ElVal->GetName());
+ ElVal->SetDictEntry(NewTag);
+ return;
+ }
+
+ // We thought this was explicit VR, but we end up with an
+ // implicit VR tag. Let's backtrack.
+
+ sprintf(msg,"Falsely explicit vr file (%04x,%04x)\n",
+ ElVal->GetGroup(),ElVal->GetElement());
+ dbg.Verbose(1, "gdcmHeader::FindVR: ",msg);
+
+ fseek(fp, PositionOnEntry, SEEK_SET);
+ // When this element is known in the dictionary we shall use, e.g. for
+ // the semantics (see the usage of IsAnInteger), the vr proposed by the
+ // dictionary entry. Still we have to flag the element as implicit since
+ // we know now our assumption on expliciteness is not furfilled.
+ // avoid .
+ if ( ElVal->IsVrUnknown() )
+ ElVal->SetVR("Implicit");
+ ElVal->SetImplicitVr();
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Determines if the Transfer Syntax was already encountered
+ * and if it corresponds to a ImplicitVRLittleEndian one.
*
- * ACR-NEMA : we allways get
- * GroupNumber (2 Octets)
- * ElementNumber (2 Octets)
- * ElementSize (4 Octets)
- * DICOM en implicit Value Representation :
- * GroupNumber (2 Octets)
- * ElementNumber (2 Octets)
- * ElementSize (4 Octets)
+ * @return True when ImplicitVRLittleEndian found. False in all other cases.
+ */
+bool gdcmHeader::IsImplicitVRLittleEndianTransferSyntax(void) {
+ gdcmElValue* Element = PubElValSet.GetElementByNumber(0x0002, 0x0010);
+ if ( !Element )
+ return false;
+ LoadElementValueSafe(Element);
+ std::string Transfer = Element->GetValue();
+ if ( Transfer == "1.2.840.10008.1.2" )
+ return true;
+ return false;
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Determines if the Transfer Syntax was already encountered
+ * and if it corresponds to a ExplicitVRLittleEndian one.
*
- * DICOM en explicit Value Representation :
- * GroupNumber (2 Octets)
- * ElementNumber (2 Octets)
- * ValueRepresentation (2 Octets)
- * ElementSize (2 Octets)
+ * @return True when ExplicitVRLittleEndian found. False in all other cases.
+ */
+bool gdcmHeader::IsExplicitVRLittleEndianTransferSyntax(void) {
+ gdcmElValue* Element = PubElValSet.GetElementByNumber(0x0002, 0x0010);
+ if ( !Element )
+ return false;
+ LoadElementValueSafe(Element);
+ std::string Transfer = Element->GetValue();
+ if ( Transfer == "1.2.840.10008.1.2.1" )
+ return true;
+ return false;
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Determines if the Transfer Syntax was already encountered
+ * and if it corresponds to a DeflatedExplicitVRLittleEndian one.
*
- * 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)
+ * @return True when DeflatedExplicitVRLittleEndian found. False in all other cases.
+ */
+bool gdcmHeader::IsDeflatedExplicitVRLittleEndianTransferSyntax(void) {
+ gdcmElValue* Element = PubElValSet.GetElementByNumber(0x0002, 0x0010);
+ if ( !Element )
+ return false;
+ LoadElementValueSafe(Element);
+ std::string Transfer = Element->GetValue();
+ if ( Transfer == "1.2.840.10008.1.2.1.99" )
+ return true;
+ return false;
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Determines if the Transfer Syntax was already encountered
+ * and if it corresponds to a Explicit VR Big Endian one.
*
- * @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
- */
-
-void gdcmHeader::FindVR( ElValue *pleCourant) {
- char VR[3];
- int lgrLue;
- long PositionOnEntry = ftell(fp);
-
- if (filetype != ExplicitVR)
- return;
+ * @return True when big endian found. False in all other cases.
+ */
+bool gdcmHeader::IsExplicitVRBigEndianTransferSyntax(void) {
+ gdcmElValue* Element = PubElValSet.GetElementByNumber(0x0002, 0x0010);
+ if ( !Element )
+ return false;
+ LoadElementValueSafe(Element);
+ std::string Transfer = Element->GetValue();
+ if ( Transfer == "1.2.840.10008.1.2.2" ) //1.2.2 ??? A verifier !
+ return true;
+ return false;
+}
- lgrLue=fread (&VR, (size_t)2,(size_t)1, fp);
- VR[2]=0;
-
- // Warning: we believe this is explicit VR (Value Representation) because
- // we used a heuristic that found "UL" in the first tag. Alas this
- // doesn't guarantee that all the tags will be in explicit VR. In some
- // cases (see e-film filtered files) one finds implicit VR tags mixed
- // within an explicit VR file. Hence we make sure the present tag
- // is in explicit VR and try to fix things if it happens not to be
- // the case.
-
- // FIXME There should be only one occurence returned. Avoid the
- // first extraction by calling proper method.
- VRAtr FoundVR = dicom_vr->find(string(VR))->first;
- if ( ! FoundVR.empty()) {
- pleCourant->SetVR(FoundVR);
- return;
- }
-
- // We thought this was explicit VR, but we end up with an
- // implicit VR tag. Let's backtrack.
- pleCourant->SetVR("Implicit");
- fseek(fp, PositionOnEntry, SEEK_SET);
+/**
+ * \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) {
+ gdcmElValue* Element = PubElValSet.GetElementByNumber(0x0002, 0x0010);
+ if ( !Element )
+ return false;
+ LoadElementValueSafe(Element);
+ std::string Transfer = Element->GetValue();
+ if ( Transfer == "1.2.840.10008.1.2.4.50" )
+ return true;
+ return false;
}
-void gdcmHeader::FindLength( ElValue *pleCourant) {
- int lgrLue;
- guint32 l_gr;
- unsigned short int l_gr_2;
-
- string vr = pleCourant->GetVR();
-
- if ( (filetype == ExplicitVR) && (vr != "Implicit") ) {
- if ( ( vr == "OB" ) || ( vr == "OW" )
- || ( vr == "SQ" ) || ( vr == "UN" ) ) {
-
- // The following two bytes are reserved, so we skip them,
- // and we proceed on reading the length on 4 bytes.
- fseek(fp, 2L,SEEK_CUR);
- lgrLue=fread (&l_gr, (size_t)4,(size_t)1, fp);
- l_gr = SwapLong((guint32)l_gr);
-
- } else {
- // Length is encoded on 2 bytes.
- lgrLue=fread (&l_gr_2, (size_t)2,(size_t)1, fp);
-
- l_gr_2 = SwapShort((unsigned short)l_gr_2);
-
- if ( l_gr_2 == 0xffff) {
- l_gr = 0;
- } else {
- l_gr = l_gr_2;
- }
- }
- } else {
- // Either implicit VR or an explicit VR that (at least for this
- // element) lied a little bit. Length is on 4 bytes.
- lgrLue=fread (&l_gr, (size_t)4,(size_t)1, fp);
- l_gr= SwapLong((long)l_gr);
- }
-
- // Traitement des curiosites sur la longueur
- if ( l_gr == 0xffffffff)
- l_gr=0;
-
- pleCourant->SetLength(l_gr);
+/**
+ * \ingroup gdcmHeader
+ * \brief
+ *
+ * @return
+ */
+bool gdcmHeader::IsJPEGLossless(void) {
+ gdcmElValue* Element = PubElValSet.GetElementByNumber(0x0002, 0x0010);
+ // faire qq chose d'intelligent a la place de ça
+ if ( !Element )
+ return false;
+ LoadElementValueSafe(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 JPEGExtendedProcess2-4 one.
+ *
+ * @return True when JPEGExtendedProcess2-4 found. False in all other cases.
+ */
+bool gdcmHeader::IsJPEGExtendedProcess2_4TransferSyntax(void) {
+ gdcmElValue* Element = PubElValSet.GetElementByNumber(0x0002, 0x0010);
+ if ( !Element )
+ return false;
+ LoadElementValueSafe(Element);
+ std::string Transfer = Element->GetValue();
+ if ( Transfer == "1.2.840.10008.1.2.4.51" )
+ return true;
+ return false;
+}
+
+/**
+ * \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) {
+ gdcmElValue* Element = PubElValSet.GetElementByNumber(0x0002, 0x0010);
+ if ( !Element )
+ return false;
+ LoadElementValueSafe(Element);
+ std::string Transfer = Element->GetValue();
+ if ( Transfer == "1.2.840.10008.1.2.4.52" )
+ return true;
+ return false;
+}
+
+/**
+ * \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) {
+ gdcmElValue* Element = PubElValSet.GetElementByNumber(0x0002, 0x0010);
+ if ( !Element )
+ return false;
+ LoadElementValueSafe(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) {
+ gdcmElValue* Element = PubElValSet.GetElementByNumber(0x0002, 0x0010);
+ if ( !Element )
+ return false;
+ LoadElementValueSafe(Element);
+ std::string Transfer = Element->GetValue();
+ if ( Transfer == "1.2.840.10008.1.2.5" )
+ return true;
+ return false;
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Determines if the Transfer Syntax was already encountered
+ * and if it corresponds to a JPEG200 one.0
+ *
+ * @return True when JPEG2000 (Lossly or LossLess) found. False in all
+ * other cases.
+ */
+bool gdcmHeader::IsJPEG2000(void) {
+ gdcmElValue* Element = PubElValSet.GetElementByNumber(0x0002, 0x0010);
+ if ( !Element )
+ return false;
+ LoadElementValueSafe(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) {
+ if ( (filetype == ExplicitVR)
+ || (filetype == ImplicitVR) )
+ return true;
+ return false;
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief When the length of an element value is obviously wrong (because
+ * the parser went Jabberwocky) one can hope improving things by
+ * applying this heuristic.
+ */
+void gdcmHeader::FixFoundLength(gdcmElValue * ElVal, guint32 FoundLength) {
+ if ( FoundLength == 0xffffffff)
+ FoundLength = 0;
+ // Sorry for the patch!
+ // XMedCom did the trick to read some nasty GE images ...
+ if (FoundLength == 13)
+ // The following 'if' will be removed when there is no more
+ // images on Creatis HD with a 13 length for Manufacturer...
+ if ( (ElVal->GetGroup() != 0x0008) || (ElVal->GetElem() )
+ // end of remove area
+ FoundLength =10;
+
+ ElVal->SetLength(FoundLength);
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief
+ *
+ * @return
+ */
+ guint32 gdcmHeader::FindLengthOB(void) {
+ // See PS 3.5-2001, section A.4 p. 49 on encapsulation of encoded pixel data.
+ guint16 g;
+ guint16 n;
+ long PositionOnEntry = ftell(fp);
+ bool FoundSequenceDelimiter = false;
+ guint32 TotalLength = 0;
+ guint32 ItemLength;
+
+ while ( ! FoundSequenceDelimiter) {
+ g = ReadInt16();
+ n = ReadInt16();
+
+ long l = ftell(fp);
+
+ if (errno == 1)
+ return 0;
+ TotalLength += 4; // We even have to decount the group and element
+
+ if ( g != 0xfffe && g!=0xb00c ) /*for bogus header */ {
+ char msg[100]; // for sprintf. Sorry
+ sprintf(msg,"wrong group (%04x) for an item sequence (%04x,%04x)\n",g, g,n);
+ dbg.Verbose(1, "gdcmHeader::FindLengthOB: ",msg);
+ long l = ftell(fp);
+ errno = 1;
+ return 0;
+ }
+ if ( n == 0xe0dd || ( g==0xb00c && n==0x0eb6 ) ) /* for bogus header */
+ FoundSequenceDelimiter = true;
+ else if ( n != 0xe000 ){
+ char msg[100]; // for sprintf. Sorry
+ sprintf(msg,"wrong element (%04x) for an item sequence (%04x,%04x)\n",
+ n, g,n);
+ dbg.Verbose(1, "gdcmHeader::FindLengthOB: ",msg);
+ errno = 1;
+ return 0;
+ }
+ ItemLength = ReadInt32();
+ TotalLength += ItemLength + 4; // We add 4 bytes since we just read
+ // the ItemLength with ReadInt32
+
+ SkipBytes(ItemLength);
+ }
+ fseek(fp, PositionOnEntry, SEEK_SET);
+ return TotalLength;
}
/**
* \ingroup gdcmHeader
- * \brief remet les octets dans un ordre compatible avec celui du processeur
+ * \brief
+ *
+ * @return
+ */
+ void gdcmHeader::FindLength (gdcmElValue * ElVal) {
+ guint16 element = ElVal->GetElement();
+ guint16 group = ElVal->GetGroup();
+ std::string vr = ElVal->GetVR();
+ guint16 length16;
+ if( (element == 0x0010) && (group == 0x7fe0) ) {
+ dbg.SetDebug(0);
+ dbg.Verbose(2, "gdcmHeader::FindLength: ",
+ "we reached 7fe0 0010");
+ }
+
+ if ( (filetype == ExplicitVR) && ! ElVal->IsImplicitVr() ) {
+ if ( (vr=="OB") || (vr=="OW") || (vr=="SQ") || (vr=="UN") ) {
+
+ // The following reserved two bytes (see PS 3.5-2001, section
+ // 7.1.2 Data element structure with explicit vr p27) must be
+ // skipped before proceeding on reading the length on 4 bytes.
+ fseek(fp, 2L, SEEK_CUR);
+
+ guint32 length32 = ReadInt32();
+
+ if ( (vr == "OB") && (length32 == 0xffffffff) ) {
+ ElVal->SetLength(FindLengthOB());
+ return;
+ }
+ FixFoundLength(ElVal, length32);
+ return;
+ }
+
+ // Length is encoded on 2 bytes.
+ length16 = ReadInt16();
+
+ // We can tell the current file is encoded in big endian (like
+ // Data/US-RGB-8-epicard) when we find the "Transfer Syntax" tag
+ // and it's value is the one of the encoding of a big endian file.
+ // In order to deal with such big endian encoded files, we have
+ // (at least) two strategies:
+ // * when we load the "Transfer Syntax" tag with value of big endian
+ // encoding, we raise the proper flags. Then we wait for the end
+ // of the META group (0x0002) among which is "Transfer Syntax",
+ // before switching the swap code to big endian. We have to postpone
+ // the switching of the swap code since the META group is fully encoded
+ // in little endian, and big endian coding only starts at the next
+ // group. The corresponding code can be hard to analyse and adds
+ // many additional unnecessary tests for regular tags.
+ // * the second strategy consists in waiting for trouble, that shall
+ // appear when we find the first group with big endian encoding. This
+ // is easy to detect since the length of a "Group Length" tag (the
+ // ones with zero as element number) has to be of 4 (0x0004). When we
+ // encouter 1024 (0x0400) chances are the encoding changed and we
+ // found a group with big endian encoding.
+ // We shall use this second strategy. In order to make sure that we
+ // can interpret the presence of an apparently big endian encoded
+ // length of a "Group Length" without committing a big mistake, we
+ // add an additional check: we look in the already parsed elements
+ // for the presence of a "Transfer Syntax" whose value has to be "big
+ // endian encoding". When this is the case, chances are we have got our
+ // hands on a big endian encoded file: we switch the swap code to
+ // big endian and proceed...
+ if ( (element == 0x0000) && (length16 == 0x0400) ) {
+ if ( ! IsExplicitVRBigEndianTransferSyntax() ) {
+ dbg.Verbose(0, "gdcmHeader::FindLength", "not explicit VR");
+ errno = 1;
+ return;
+ }
+ length16 = 4;
+ SwitchSwapToBigEndian();
+ // Restore the unproperly loaded values i.e. the group, the element
+ // and the dictionary entry depending on them.
+ guint16 CorrectGroup = SwapShort(ElVal->GetGroup());
+ guint16 CorrectElem = SwapShort(ElVal->GetElement());
+ gdcmDictEntry * NewTag = GetDictEntryByNumber(CorrectGroup,
+ CorrectElem);
+ if (!NewTag) {
+ // This correct tag is not in the dictionary. Create a new one.
+ NewTag = new gdcmDictEntry(CorrectGroup, CorrectElem);
+ }
+ // FIXME this can create a memory leaks on the old entry that be
+ // left unreferenced.
+ ElVal->SetDictEntry(NewTag);
+ }
+
+ // Heuristic: well some files are really ill-formed.
+ if ( length16 == 0xffff) {
+ length16 = 0;
+ //dbg.Verbose(0, "gdcmHeader::FindLength",
+ // "Erroneous element length fixed.");
+ // Actually, length= 0xffff means that we deal with
+ // Unknown Sequence Length
+ }
+
+ FixFoundLength(ElVal, (guint32)length16);
+ return;
+ }
+
+ // Either implicit VR or a non DICOM conformal (see not below) explicit
+ // VR that ommited the VR of (at least) this element. Farts happen.
+ // [Note: according to the part 5, PS 3.5-2001, section 7.1 p25
+ // on Data elements "Implicit and Explicit VR Data Elements shall
+ // not coexist in a Data Set and Data Sets nested within it".]
+ // Length is on 4 bytes.
+ FixFoundLength(ElVal, ReadInt32());
+}
- * @return longueur retenue pour le champ
+/**
+ * \ingroup gdcmHeader
+ * \brief Swaps back the bytes of 4-byte long integer accordingly to
+ * processor order.
+ *
+ * @return The suggested integer.
*/
guint32 gdcmHeader::SwapLong(guint32 a) {
- // FIXME: il pourrait y avoir un pb pour les entiers negatifs ...
- switch (sw) {
- case 0 :
- break;
- case 4321 :
- a=( ((a<<24) & 0xff000000) | ((a<<8) & 0x00ff0000) |
- ((a>>8) & 0x0000ff00) | ((a>>24) & 0x000000ff) );
- break;
-
- case 3412 :
- a=( ((a<<16) & 0xffff0000) | ((a>>16) & 0x0000ffff) );
- break;
-
- case 2143 :
- a=( ((a<<8) & 0xff00ff00) | ((a>>8) & 0x00ff00ff) );
- break;
- default :
- dbg.Error(" gdcmHeader::SwapLong : unset swap code");
- a=0;
- }
- return(a);
+ switch (sw) {
+ case 0 :
+ break;
+ case 4321 :
+ a=( ((a<<24) & 0xff000000) | ((a<<8) & 0x00ff0000) |
+ ((a>>8) & 0x0000ff00) | ((a>>24) & 0x000000ff) );
+ break;
+
+ case 3412 :
+ a=( ((a<<16) & 0xffff0000) | ((a>>16) & 0x0000ffff) );
+ break;
+
+ case 2143 :
+ a=( ((a<<8) & 0xff00ff00) | ((a>>8) & 0x00ff00ff) );
+ break;
+ default :
+ dbg.Error(" gdcmHeader::SwapLong : unset swap code");
+ a=0;
+ }
+ return(a);
}
/**
* \ingroup gdcmHeader
- * \brief remet les octets dans un ordre compatible avec celui du processeur
+ * \brief Swaps the bytes so they agree with the processor order
+ * @return The properly swaped 16 bits integer.
+ */
+guint16 gdcmHeader::SwapShort(guint16 a) {
+ if ( (sw==4321) || (sw==2143) )
+ a =(((a<<8) & 0x0ff00) | ((a>>8)&0x00ff));
+ return (a);
+}
- * @return longueur retenue pour le champ
+/**
+ * \ingroup gdcmHeader
+ * \brief
+ *
+ * @return
+ */
+ void gdcmHeader::SkipBytes(guint32 NBytes) {
+ //FIXME don't dump the returned value
+ (void)fseek(fp, (long)NBytes, SEEK_CUR);
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief
+ * @param ElVal
+ * @return
+ */
+ void gdcmHeader::SkipElementValue(gdcmElValue * ElVal) {
+ SkipBytes(ElVal->GetLength());
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief
+ * @param NewSize
+ * @return
*/
-short int gdcmHeader::SwapShort(short int a) {
- if ( (sw==4321) || (sw==2143) )
- a =(((a<<8) & 0x0ff00) | ((a>>8)&0x00ff));
- return (a);
+ void gdcmHeader::SetMaxSizeLoadElementValue(long NewSize) {
+ if (NewSize < 0)
+ return;
+ if ((guint32)NewSize >= (guint32)0xffffffff) {
+ MaxSizeLoadElementValue = 0xffffffff;
+ return;
+ }
+ MaxSizeLoadElementValue = NewSize;
}
/**
* \ingroup gdcmHeader
- * \brief lit le dicom_element suivant.
- * (le fichier doit deja avoir ete ouvert,
- * _IdAcrCheckSwap(ID_DCM_HDR *e) avoir ete appele)
- * @param e ID_DCM_HDR dans lequel effectuer la recherche.
- * @param sw code swap.
- * @return En cas de succes, 1
- * 0 en cas d'echec.
- */
-
-ElValue * gdcmHeader::ReadNextElement(void) {
- guint16 g;
- guint16 n;
- guint32 l;
- size_t lgrLue;
- ElValue * nouvDcmElem;
-
- // ------------------------- Lecture Num group : g
- lgrLue=fread (&g, (size_t)2,(size_t)1, fp);
-
- if (feof(fp)) {
- dbg.Verbose(1, "ReadNextElement: EOF encountered");
- return (NULL);
- }
- if (ferror(fp)){
- dbg.Verbose(1, "ReadNextElement: failed to read NumGr");
- return (NULL);
- }
-
- if (sw) g= SwapShort(((short)g));
-
- // ------------------------- Lecture Num Elem : n
- lgrLue=fread (&n, (size_t)2,(size_t)1, fp);
-
- if (feof(fp)) {
- dbg.Verbose(1, "ReadNextElement: EOF encountered");
- return (NULL);
- }
- if (ferror(fp)){
- dbg.Verbose(1, "ReadNextElement: failed to read NumElem");
- return (NULL);
- }
-
- if(sw) n= SwapShort(((short)n));
-
- // Find out if the tag we encountered is in the dictionaries:
- gdcmDictEntry * NewTag = IsInDicts(g, n);
- if (!NewTag)
- NewTag = new gdcmDictEntry(g, n, "Unknown", "Unknown", "Unkown");
-
- nouvDcmElem = new ElValue(NewTag);
- if (!nouvDcmElem) {
- dbg.Verbose(1, "ReadNextElement: failed to allocate ElValue");
- return(NULL);
- }
-
- FindVR(nouvDcmElem);
- FindLength(nouvDcmElem);
- nouvDcmElem->SetOffset(ftell(fp));
- l = nouvDcmElem->GetLength();
-
- //FIXMEif(!memcmp( VR,"SQ",(size_t)2 )) { // ca annonce une SEQUENCE d'items ?!
- //FIXME l_gr=0; // on lira donc les items de la sequence
- //FIXME}
- //FIXMEreturn(l_gr);
-
- // Une sequence contient un ensemble de group element repetes n fois
- // et g=fffe indique la fin (contient une longueur bidon).
- if(g==0xfffe) l=0; // pour sauter les indicateurs de 'SQ'
-
-
- // ------------------------- Lecture Valeur element
-
- // FIXME The exact size should be l if we move to strings or whatever
- // CLEAN ME NEWValue used to be nouvDcmElem->valeurElem
- char* NewValue = (char*)g_malloc(l+1);
- if(NewValue) {
- NewValue[l]= 0;
- } else {
- return (NULL);
- }
-
- // FIXME les elements trop long (seuil a fixer a la main) ne devraient
- // pas etre charge's !!!! Voir TODO.
- lgrLue=fread (NewValue, (size_t)l,(size_t)1, fp);
-
- if ( IsAnInteger(g, n, NewTag->GetVR(), l) ) {
- // CLEANME THe following is really UGLY !
- if( l == 4 ) {
- *(guint32 *) NewValue = SwapLong ((*(guint32 *) NewValue));
- } else {
- if( l == 2 )
- *(guint16 *) NewValue = SwapShort ((*(guint16 *)NewValue));
- }
- //FIXME: don't we have to distinguish guin16 and guint32
- //FIXME: make the following an util fonction
- ostringstream s;
- s << *(guint32 *) NewValue;
- nouvDcmElem->value = s.str();
- g_free(NewValue);
- } else
- nouvDcmElem->value = NewValue;
- return nouvDcmElem;
-}
-
-bool gdcmHeader::IsAnInteger(guint16 group, guint16 element,
- string vr, guint32 length ) {
- // When we have some semantics on the element we just read, and we
- // a priori now we are dealing with an integer, then we can swap it's
- // element value properly.
- if ( element == 0 ) { // This is the group length of the group
- if (length != 4)
- dbg.Error("gdcmHeader::ShouldBeSwaped", "should be four");
- return true;
- }
-
- if ( group % 2 != 0 )
- // We only have some semantics on documented elements, which are
- // the even ones.
- return false;
-
- if ( (length != 4) && ( length != 2) )
- // Swapping only make sense on integers which are 2 or 4 bytes long.
- return false;
-
- if ( (vr == "UL") || (vr == "US") || (vr == "SL") || (vr == "SS") )
- return true;
-
- if ( (group == 0x0028) && (element == 0x0005) )
- // This tag is retained from ACR/NEMA
- // CHECKME Why should "Image Dimensions" be a single integer ?
- return true;
-
- if ( (group == 0x0028) && (element == 0x0200) )
- // This tag is retained from ACR/NEMA
- return true;
+ * \brief Loads the element content if it's length is not bigger
+ * than the value specified with
+ * gdcmHeader::SetMaxSizeLoadElementValue()
+ */
+void gdcmHeader::LoadElementValue(gdcmElValue * ElVal) {
+ size_t item_read;
+ guint16 group = ElVal->GetGroup();
+ std::string vr= ElVal->GetVR();
+ guint32 length = ElVal->GetLength();
+ bool SkipLoad = false;
+
+ fseek(fp, (long)ElVal->GetOffset(), SEEK_SET);
+
+ // FIXME Sequences not treated yet !
+ //
+ // Ne faudrait-il pas au contraire trouver immediatement
+ // une maniere 'propre' de traiter les sequences (vr = SQ)
+ // car commencer par les ignorer risque de conduire a qq chose
+ // qui pourrait ne pas etre generalisable
+ // Well, I'm expecting your code !!!
+
+ if( vr == "SQ" )
+ SkipLoad = true;
+
+ // Heuristic : a sequence "contains" a set of tags (called items). It looks
+ // like the last tag of a sequence (the one that terminates the sequence)
+ // has a group of 0xfffe (with a dummy length).
+ // Well ...
+ // Actually (fffe e000) tells us an Element is beginning
+ // (fffe e00d) tells us an Element just ended
+ // (fffe e0dd) tells us the current SEQuence just ended
+
+ if( group == 0xfffe )
+ SkipLoad = true;
+
+ if ( SkipLoad ) {
+ ElVal->SetLength(0);
+ ElVal->SetValue("gdcm::Skipped");
+ return;
+ }
+
+ // When the length is zero things are easy:
+ if ( length == 0 ) {
+ ElVal->SetValue("");
+ return;
+ }
+
+ // The elements whose length is bigger than the specified upper bound
+ // are not loaded. Instead we leave a short notice of the offset of
+ // the element content and it's length.
+ if (length > MaxSizeLoadElementValue) {
+ std::ostringstream s;
+ s << "gdcm::NotLoaded.";
+ s << " Address:" << (long)ElVal->GetOffset();
+ s << " Length:" << ElVal->GetLength();
+ ElVal->SetValue(s.str());
+ return;
+ }
+
+ // When an integer is expected, read and convert the following two or
+ // four bytes properly i.e. as an integer as opposed to a string.
- return false;
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief If we encountered the offset of the pixels in the file
- * (Pixel Data) then keep the info aside.
- */
-void gdcmHeader::SetAsidePixelData(ElValue* elem) {
- // They are two cases :
- // * the pixel data (i.e. the image or the volume) is pointed by it's
- // default official tag (0x7fe0,0x0010),
- // * the writer of this file decided to put the image "address" (i.e the
- // offset from the begining of the file) at a different tag.
- // Then the "Pixel Data" offset might be found by indirection through
- // the "Image Location" tag (0x0028, 0x0200). In other terms the Image
- // Location tag contains the group where the "Pixel Data" offset is and
- // inside this group the element is conventionally at element 0x0010
- // (when the norm is respected).
- //
- // Hence getting our hands on the Pixel Data is a two stage process:
- // 1/ * find if the "Pixel Data" tag exists.
- // * if it does not exist, look for the "Pixel Location" tag.
- // 2/ look at the proper tag ("Pixel Data" or "Pixel Location" when
- // it exists) what the offset is.
- cout << "aaaaaaaaaaaaaaaaaaaaa";
- // PubElVals.PrintByName(cout);
- ostringstream val;
- val << hex << GetPubElValByName("Image Location");
- cout << GetPubElValByName("Image Location") << endl;
- cout <<hex << GetPubElValByName("Image Location") << dec << endl;
- cout << "aaaa" << hex << val << dec << endl;
- if (val)
- //grPixel = val.hex().str();
- grPixel = 0;
- else
- grPixel = 0x7FE0;
- return;
-
- guint16 g;
- guint16 n;
- g = elem->GetGroup();
- n = elem->GetElement();
- if (!grPixelTrouve) { // on n a pas encore trouve les pixels
- if (g > 0x0028) {
- if (n > 0x0200 || g == 0x7FE0 ) { // on a depasse (28,200)
- grPixel = 0x7FE0;
- numPixel = 0x0010;
- grPixelTrouve = true;
- }
- } else { // on est sur (28,200)
- if (g == 0x0028) {
- if (n == 0x0200) {
- grPixelTrouve = 1;
- char* NewValue = (char*)g_malloc(elem->GetLength()+1);
- // FIXME: not very elegant conversion
- for(int i=0;i<4;i++)
- *((char*)(&grPixel)+i) = *(NewValue+i);
- elem->SetValue(NewValue);
-
- if (grPixel != 0x7FE0) // Vieux pb Philips
- numPixel = 0x1010; // encore utile ??
- else
- numPixel = 0x0010;
- }
- }
- }
- } else { // on vient de trouver les pixels
- if (g == grPixel) {
- if (n == numPixel) {
- PixelPosition = elem->Offset;
- PixelsTrouves = true;
- dbg.Verbose(0, "gdcmHeader::SetAsidePixelData:",
- "Pixel data found");
- }
- }
- }
-}
-
-gdcmDictEntry * gdcmHeader::IsInDicts(guint32 group, guint32 element) {
- gdcmDictEntry * found = (gdcmDictEntry*)0;
- if (!RefPubDict && !RefShaDict) {
- //FIXME build a default dictionary !
- printf("FIXME in gdcmHeader::IsInDicts\n");
- }
- if (RefPubDict) {
- found = RefPubDict->GetTag(group, element);
- if (found)
- return found;
- }
- if (RefShaDict) {
- found = RefShaDict->GetTag(group, element);
- if (found)
- return found;
- }
- return found;
-}
-
-string gdcmHeader::GetPubElValByNumber(guint16 group, guint16 element) {
- return PubElVals.GetElValue(group, element);
-}
-
-string gdcmHeader::GetPubElValByName(string TagName) {
- return PubElVals.GetElValue(TagName);
+ // pour les elements de Value Multiplicity > 1
+ // on aura en fait une serie d'entiers
+ // on devrait pouvoir faire + compact (?)
+
+ if ( IsAnInteger(ElVal) ) {
+ guint32 NewInt;
+ std::ostringstream s;
+ int nbInt;
+ if (vr == "US" || vr == "SS") {
+ nbInt = length / 2;
+ NewInt = ReadInt16();
+ s << NewInt;
+ if (nbInt > 1) {
+ for (int i=1; i < nbInt; i++) {
+ s << '\\';
+ NewInt = ReadInt16();
+ s << NewInt;
+ }
+ }
+
+ } else if (vr == "UL" || vr == "SL") {
+ nbInt = length / 4;
+ NewInt = ReadInt32();
+ s << NewInt;
+ if (nbInt > 1) {
+ for (int i=1; i < nbInt; i++) {
+ s << '\\';
+ NewInt = ReadInt32();
+ s << NewInt;
+ }
+ }
+ }
+ ElVal->SetValue(s.str());
+ return;
+ }
+
+ // We need an additional byte for storing \0 that is not on disk
+ char* NewValue = (char*)malloc(length+1);
+ if( !NewValue) {
+ dbg.Verbose(1, "LoadElementValue: Failed to allocate NewValue");
+ return;
+ }
+ NewValue[length]= 0;
+
+ item_read = fread(NewValue, (size_t)length, (size_t)1, fp);
+ if ( item_read != 1 ) {
+ free(NewValue);
+ dbg.Verbose(1, "gdcmHeader::LoadElementValue","unread element value");
+ ElVal->SetValue("gdcm::UnRead");
+ return;
+ }
+ ElVal->SetValue(NewValue);
+ free(NewValue);
}
/**
* \ingroup gdcmHeader
- * \brief renvoie un pointeur sur le ID_DCM_HDR correspondant au fichier
- * @param filename Nom du fichier ACR / LibIDO / DICOM
- * @return le ID_DCM_HDR
+ * \brief Loads the element while preserving the current
+ * underlying file position indicator as opposed to
+ * to LoadElementValue that modifies it.
+ * @param ElVal Element whose value shall be loaded.
+ * @return
+ */
+void gdcmHeader::LoadElementValueSafe(gdcmElValue * ElVal) {
+ long PositionOnEntry = ftell(fp);
+ LoadElementValue(ElVal);
+ fseek(fp, PositionOnEntry, SEEK_SET);
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Reads a supposed to be 16 Bits integer
+ * \ (swaps it depending on processor endianity)
+ *
+ * @return integer acts as a boolean
+ */
+guint16 gdcmHeader::ReadInt16(void) {
+ guint16 g;
+ size_t item_read;
+ item_read = fread (&g, (size_t)2,(size_t)1, fp);
+ if ( item_read != 1 ) {
+ // dbg.Verbose(0, "gdcmHeader::ReadInt16", " Failed to read :");
+ // if(feof(fp))
+ // dbg.Verbose(0, "gdcmHeader::ReadInt16", " End of File encountered");
+ if(ferror(fp))
+ dbg.Verbose(0, "gdcmHeader::ReadInt16", " File Error");
+ errno = 1;
+ return 0;
+ }
+ errno = 0;
+ g = SwapShort(g);
+ return g;
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Reads a supposed to be 32 Bits integer
+ * \ (swaps it depending on processor endianity)
+ *
+ * @return
+ */
+guint32 gdcmHeader::ReadInt32(void) {
+ guint32 g;
+ size_t item_read;
+ item_read = fread (&g, (size_t)4,(size_t)1, fp);
+ if ( item_read != 1 ) {
+ //dbg.Verbose(0, "gdcmHeader::ReadInt32", " Failed to read :");
+ //if(feof(fp))
+ // dbg.Verbose(0, "gdcmHeader::ReadInt32", " End of File encountered");
+ if(ferror(fp))
+ dbg.Verbose(0, "gdcmHeader::ReadInt32", " File Error");
+ errno = 1;
+ return 0;
+ }
+ errno = 0;
+ g = SwapLong(g);
+ return g;
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief
+ *
+ * @return
+ */
+ gdcmElValue* gdcmHeader::GetElValueByNumber(guint16 Group, guint16 Elem) {
+
+ gdcmElValue* elValue = PubElValSet.GetElementByNumber(Group, Elem);
+ if (!elValue) {
+ dbg.Verbose(1, "gdcmHeader::GetElValueByNumber",
+ "failed to Locate gdcmElValue");
+ return (gdcmElValue*)0;
+ }
+ return elValue;
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Build a new Element Value from all the low level arguments.
+ * Check for existence of dictionary entry, and build
+ * a default one when absent.
+ * @param Group group of the underlying DictEntry
+ * @param Elem element of the underlying DictEntry
+ */
+gdcmElValue* gdcmHeader::NewElValueByNumber(guint16 Group, guint16 Elem) {
+ // Find out if the tag we encountered is in the dictionaries:
+ gdcmDictEntry * NewTag = GetDictEntryByNumber(Group, Elem);
+ if (!NewTag)
+ NewTag = new gdcmDictEntry(Group, Elem);
+
+ gdcmElValue* NewElVal = new gdcmElValue(NewTag);
+ if (!NewElVal) {
+ dbg.Verbose(1, "gdcmHeader::NewElValueByNumber",
+ "failed to allocate gdcmElValue");
+ return (gdcmElValue*)0;
+ }
+ return NewElVal;
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief TODO
+ * @param Value
+ * @param Group
+ * @param Elem
+ * \return integer acts as a boolean
+ */
+int gdcmHeader::ReplaceOrCreateByNumber(std::string Value,
+ guint16 Group, guint16 Elem ) {
+
+ // TODO : FIXME JPRx
+ // curieux, non ?
+ // on (je) cree une Elvalue ne contenant pas de valeur
+ // on l'ajoute au ElValSet
+ // on affecte une valeur a cette ElValue a l'interieur du ElValSet
+ // --> devrait pouvoir etre fait + simplement ???
+ if (CheckIfExistByNumber(Group, Elem) == 0) {
+ gdcmElValue* a =NewElValueByNumber(Group, Elem);
+ if (a == NULL)
+ return 0;
+ PubElValSet.Add(a);
+ }
+ PubElValSet.SetElValueByNumber(Value, Group, Elem);
+ return(1);
+}
+
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Modify (or Creates if not found) an element
+ * @param Value new value
+ * @param Group
+ * @param Elem
+ * \return integer acts as a boolean
+ *
+ */
+int gdcmHeader::ReplaceOrCreateByNumber(char* Value, guint16 Group, guint16 Elem ) {
+
+ gdcmElValue* nvElValue=NewElValueByNumber(Group, Elem);
+ PubElValSet.Add(nvElValue);
+ std::string v = Value;
+ PubElValSet.SetElValueByNumber(v, Group, Elem);
+ return(1);
+}
+
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Set a new value if the invoked element exists
+ * @param Value
+ * @param Group
+ * @param Elem
+ * \return integer acts as a boolean
+ */
+int gdcmHeader::ReplaceIfExistByNumber(char* Value, guint16 Group, guint16 Elem ) {
+
+ gdcmElValue* elValue = PubElValSet.GetElementByNumber(Group, Elem);
+ std::string v = Value;
+ PubElValSet.SetElValueByNumber(v, Group, Elem);
+ return 1;
+}
+
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Checks if a given ElValue (group,number)
+ * \ exists in the Public ElValSet
+ * @param Group
+ * @param Elem
+ * @return integer acts as a boolean
*/
-void gdcmHeader::BuildHeader(void) {
- ElValue * newElValue = (ElValue *)0;
-
- rewind(fp);
- CheckSwap();
- while ( (newElValue = ReadNextElement()) ) {
- PubElVals.Add(newElValue);
- }
- SetAsidePixelData((ElValue*)0);
+int gdcmHeader::CheckIfExistByNumber(guint16 Group, guint16 Elem ) {
+ return (PubElValSet.CheckIfExistByNumber(Group, Elem));
+ }
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Build a new Element Value from all the low level arguments.
+ * Check for existence of dictionary entry, and build
+ * a default one when absent.
+ * @param Name Name of the underlying DictEntry
+ */
+gdcmElValue* gdcmHeader::NewElValueByName(std::string Name) {
+
+ gdcmDictEntry * NewTag = GetDictEntryByName(Name);
+ if (!NewTag)
+ NewTag = new gdcmDictEntry(0xffff, 0xffff, "LO", "Unknown", Name);
+
+ gdcmElValue* NewElVal = new gdcmElValue(NewTag);
+ if (!NewElVal) {
+ dbg.Verbose(1, "gdcmHeader::ObtainElValueByName",
+ "failed to allocate gdcmElValue");
+ return (gdcmElValue*)0;
+ }
+ return NewElVal;
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Read the next tag but WITHOUT loading it's value
+ * @return On succes the newly created ElValue, NULL on failure.
+ */
+gdcmElValue * gdcmHeader::ReadNextElement(void) {
+
+ guint16 g,n;
+ gdcmElValue * NewElVal;
+
+ g = ReadInt16();
+ n = ReadInt16();
+
+ if (errno == 1)
+ // We reached the EOF (or an error occured) and header parsing
+ // has to be considered as finished.
+ return (gdcmElValue *)0;
+
+ NewElVal = NewElValueByNumber(g, n);
+ FindVR(NewElVal);
+ FindLength(NewElVal);
+ if (errno == 1) {
+ // Call it quits
+ return (gdcmElValue *)0;
+ }
+ NewElVal->SetOffset(ftell(fp));
+ //if ( (g==0x7fe0) && (n==0x0010) )
+ return NewElVal;
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Apply some heuristics to predict wether the considered
+ * element value contains/represents an integer or not.
+ * @param ElVal The element value on which to apply the predicate.
+ * @return The result of the heuristical predicate.
+ */
+bool gdcmHeader::IsAnInteger(gdcmElValue * ElVal) {
+ guint16 group = ElVal->GetGroup();
+ guint16 element = ElVal->GetElement();
+ std::string vr = ElVal->GetVR();
+ guint32 length = ElVal->GetLength();
+
+ // When we have some semantics on the element we just read, and if we
+ // a priori know we are dealing with an integer, then we shall be
+ // able to swap it's element value properly.
+ if ( element == 0 ) { // This is the group length of the group
+ if (length == 4)
+ return true;
+ else {
+ dbg.Error("gdcmHeader::IsAnInteger",
+ "Erroneous Group Length element length.");
+ }
+ }
+ if ( (vr == "UL") || (vr == "US") || (vr == "SL") || (vr == "SS") )
+ return true;
+
+ return false;
+}
+
+/**
+ * \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 = GetPubElValByName("Image Location");
+ 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;
+
+ gdcmElValue* PixelElement = PubElValSet.GetElementByNumber(grPixel,
+ numPixel);
+ if (PixelElement)
+ return PixelElement->GetOffset();
+ else
+ return 0;
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Searches both the public and the shadow dictionary (when they
+ * exist) for the presence of the DictEntry with given
+ * group and element. The public dictionary has precedence on the
+ * shadow one.
+ * @param group group of the searched DictEntry
+ * @param element element of the searched DictEntry
+ * @return Corresponding DictEntry when it exists, NULL otherwise.
+ */
+gdcmDictEntry * gdcmHeader::GetDictEntryByNumber(guint16 group,
+ guint16 element) {
+ gdcmDictEntry * found = (gdcmDictEntry*)0;
+ if (!RefPubDict && !RefShaDict) {
+ dbg.Verbose(0, "gdcmHeader::GetDictEntry",
+ "we SHOULD have a default dictionary");
+ }
+ if (RefPubDict) {
+ found = RefPubDict->GetTagByNumber(group, element);
+ if (found)
+ return found;
+ }
+ if (RefShaDict) {
+ found = RefShaDict->GetTagByNumber(group, element);
+ if (found)
+ return found;
+ }
+ return found;
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Searches both the public and the shadow dictionary (when they
+ * exist) for the presence of the DictEntry with given name.
+ * The public dictionary has precedence on the shadow one.
+ * @param Name name of the searched DictEntry
+ * @return Corresponding DictEntry when it exists, NULL otherwise.
+ */
+gdcmDictEntry * gdcmHeader::GetDictEntryByName(std::string Name) {
+ gdcmDictEntry * found = (gdcmDictEntry*)0;
+ if (!RefPubDict && !RefShaDict) {
+ dbg.Verbose(0, "gdcmHeader::GetDictEntry",
+ "we SHOULD have a default dictionary");
+ }
+ if (RefPubDict) {
+ found = RefPubDict->GetTagByName(Name);
+ if (found)
+ return found;
+ }
+ if (RefShaDict) {
+ found = RefShaDict->GetTagByName(Name);
+ if (found)
+ return found;
+ }
+ return found;
+}
+
+/**
+ * \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::GetPubElValByNumber(guint16 group, guint16 element) {
+ return PubElValSet.GetElValueByNumber(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::GetPubElValRepByNumber(guint16 group, guint16 element) {
+ gdcmElValue* elem = PubElValSet.GetElementByNumber(group, element);
+ if ( !elem )
+ return GDCM_UNFOUND;
+ return elem->GetVR();
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Searches within the public dictionary for element value of
+ * a given tag.
+ * @param TagName name of the researched element.
+ * @return Corresponding element value when it exists, and the string
+ * GDCM_UNFOUND ("gdcm::Unfound") otherwise.
+ */
+std::string gdcmHeader::GetPubElValByName(std::string TagName) {
+ return PubElValSet.GetElValueByName(TagName);
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Searches within the elements parsed with the public dictionary 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 researched element.
+ * @return Corresponding element value representation when it exists,
+ * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise.
+ */
+std::string gdcmHeader::GetPubElValRepByName(std::string TagName) {
+ gdcmElValue* elem = PubElValSet.GetElementByName(TagName);
+ if ( !elem )
+ return GDCM_UNFOUND;
+ return elem->GetVR();
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Searches within elements parsed with the SHADOW dictionary
+ * for the element value of a given tag.
+ * @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::GetShaElValByNumber(guint16 group, guint16 element) {
+ return ShaElValSet.GetElValueByNumber(group, element);
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Searches within the elements parsed with the SHADOW dictionary
+ * 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 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::GetShaElValRepByNumber(guint16 group, guint16 element) {
+ gdcmElValue* elem = ShaElValSet.GetElementByNumber(group, element);
+ if ( !elem )
+ return GDCM_UNFOUND;
+ return elem->GetVR();
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Searches within the elements parsed with the shadow dictionary
+ * for an element value of given tag.
+ * @param TagName name of the researched element.
+ * @return Corresponding element value when it exists, and the string
+ * GDCM_UNFOUND ("gdcm::Unfound") otherwise.
+ */
+std::string gdcmHeader::GetShaElValByName(std::string TagName) {
+ return ShaElValSet.GetElValueByName(TagName);
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Searches within the elements parsed with the shadow dictionary 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 researched element.
+ * @return Corresponding element value representation when it exists,
+ * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise.
+ */
+std::string gdcmHeader::GetShaElValRepByName(std::string TagName) {
+ gdcmElValue* elem = ShaElValSet.GetElementByName(TagName);
+ if ( !elem )
+ return GDCM_UNFOUND;
+ return elem->GetVR();
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Searches within elements parsed with the public dictionary
+ * and then within the elements parsed with the shadow dictionary
+ * for the element value of a given tag.
+ * @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::GetElValByNumber(guint16 group, guint16 element) {
+ std::string pub = GetPubElValByNumber(group, element);
+ if (pub.length())
+ return pub;
+ return GetShaElValByNumber(group, element);
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Searches within elements parsed with the public dictionary
+ * and then within the elements parsed with the shadow dictionary
+ * 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 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::GetElValRepByNumber(guint16 group, guint16 element) {
+ std::string pub = GetPubElValRepByNumber(group, element);
+ if (pub.length())
+ return pub;
+ return GetShaElValRepByNumber(group, element);
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Searches within elements parsed with the public dictionary
+ * and then within the elements parsed with the shadow dictionary
+ * for the element value of a given tag.
+ * @param TagName name of the researched element.
+ * @return Corresponding element value when it exists,
+ * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise.
+ */
+std::string gdcmHeader::GetElValByName(std::string TagName) {
+ std::string pub = GetPubElValByName(TagName);
+ if (pub.length())
+ return pub;
+ return GetShaElValByName(TagName);
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Searches within elements parsed with the public dictionary
+ * and then within the elements parsed with the shadow dictionary
+ * 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 researched element.
+ * @return Corresponding element value representation when it exists,
+ * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise.
+ */
+std::string gdcmHeader::GetElValRepByName(std::string TagName) {
+ std::string pub = GetPubElValRepByName(TagName);
+ if (pub.length())
+ return pub;
+ return GetShaElValRepByName(TagName);
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Accesses an existing gdcmElValue in the PubElValSet 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 ElVal to modify
+ * @param element element of the ElVal to modify
+ */
+int gdcmHeader::SetPubElValByNumber(std::string content, guint16 group,
+ guint16 element)
+
+//TODO : homogeneiser les noms : SetPubElValByNumber
+// qui appelle PubElValSet.SetElValueByNumber
+// pourquoi pas SetPubElValueByNumber ??
+{
+
+ return ( PubElValSet.SetElValueByNumber (content, group, element) );
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Accesses an existing gdcmElValue in the PubElValSet 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 tag to be modified
+ */
+int gdcmHeader::SetPubElValByName(std::string content, std::string TagName) {
+ return ( PubElValSet.SetElValueByName (content, TagName) );
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Accesses an existing gdcmElValue in the PubElValSet of this instance
+ * through it's (group, element) and modifies it's length with
+ * the given value.
+ * \warning Use with extreme caution.
+ * @param length new length to substitute with
+ * @param group group of the ElVal to modify
+ * @param element element of the ElVal to modify
+ * @return 1 on success, 0 otherwise.
+ */
+
+int gdcmHeader::SetPubElValLengthByNumber(guint32 length, guint16 group,
+ guint16 element) {
+ return ( PubElValSet.SetElValueLengthByNumber (length, group, element) );
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Accesses an existing gdcmElValue in the ShaElValSet 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 ElVal to modify
+ * @param element element of the ElVal to modify
+ * @return 1 on success, 0 otherwise.
+ */
+int gdcmHeader::SetShaElValByNumber(std::string content,
+ guint16 group, guint16 element) {
+ return ( ShaElValSet.SetElValueByNumber (content, group, element) );
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Accesses an existing gdcmElValue in the ShaElValSet of this instance
+ * through tag name and modifies it's content with the given value.
+ * @param content new value to substitute with
+ * @param ShadowTagName name of the tag to be modified
+ */
+int gdcmHeader::SetShaElValByName(std::string content, std::string ShadowTagName) {
+ return ( ShaElValSet.SetElValueByName (content, ShadowTagName) );
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Parses the header of the file but WITHOUT loading element values.
+ */
+void gdcmHeader::ParseHeader(bool exception_on_error) throw(gdcmFormatError) {
+ gdcmElValue * newElValue = (gdcmElValue *)0;
+
+ rewind(fp);
+ CheckSwap();
+ while ( (newElValue = ReadNextElement()) ) {
+ SkipElementValue(newElValue);
+ PubElValSet.Add(newElValue);
+ }
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief This predicate, based on hopefully reasonnable heuristics,
+ * decides whether or not the current gdcmHeader was properly parsed
+ * and contains the mandatory information for being considered as
+ * a well formed and usable image.
+ * @return true when gdcmHeader is the one of a reasonable Dicom file,
+ * false otherwise.
+ */
+bool gdcmHeader::IsReadable(void) {
+ if ( GetElValByName("Image Dimensions") != GDCM_UNFOUND
+ && atoi(GetElValByName("Image Dimensions").c_str()) > 4 ) {
+ return false;
+ }
+ if ( GetElValByName("Bits Allocated") == GDCM_UNFOUND )
+ return false;
+ if ( GetElValByName("Bits Stored") == GDCM_UNFOUND )
+ return false;
+ if ( GetElValByName("High Bit") == GDCM_UNFOUND )
+ return false;
+ if ( GetElValByName("Pixel Representation") == GDCM_UNFOUND )
+ return false;
+ return true;
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Small utility function that creates a new manually crafted
+ * (as opposed as read from the file) gdcmElValue with user
+ * specified name and adds it to the public tag hash table.
+ * \note A fake TagKey is generated so the PubDict can keep it's coherence.
+ * @param NewTagName The name to be given to this new tag.
+ * @param VR The Value Representation to be given to this new tag.
+ * @ return The newly hand crafted Element Value.
+ */
+gdcmElValue* gdcmHeader::NewManualElValToPubDict(std::string NewTagName,
+ std::string VR) {
+ gdcmElValue* NewElVal = (gdcmElValue*)0;
+ guint32 StuffGroup = 0xffff; // Group to be stuffed with additional info
+ guint32 FreeElem = 0;
+ gdcmDictEntry* NewEntry = (gdcmDictEntry*)0;
+
+ FreeElem = PubElValSet.GenerateFreeTagKeyInGroup(StuffGroup);
+ if (FreeElem == UINT32_MAX) {
+ dbg.Verbose(1, "gdcmHeader::NewManualElValToPubDict",
+ "Group 0xffff in Public Dict is full");
+ return (gdcmElValue*)0;
+ }
+ NewEntry = new gdcmDictEntry(StuffGroup, FreeElem,
+ VR, "GDCM", NewTagName);
+ NewElVal = new gdcmElValue(NewEntry);
+ PubElValSet.Add(NewElVal);
+ return NewElVal;
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Loads the element values of all the elements present in the
+ * public tag based hash table.
+ */
+void gdcmHeader::LoadElements(void) {
+ rewind(fp);
+ TagElValueHT ht = PubElValSet.GetTagHt();
+ for (TagElValueHT::iterator tag = ht.begin(); tag != ht.end(); ++tag) {
+ LoadElementValue(tag->second);
+ }
+ rewind(fp);
+
+ // Load 'non string' values
+ std::string PhotometricInterpretation = GetPubElValByNumber(0x0028,0x0004);
+ if( PhotometricInterpretation == "PALETTE COLOR " ){
+ LoadElementVoidArea(0x0028,0x1200); // gray LUT
+ LoadElementVoidArea(0x0028,0x1201); // R LUT
+ LoadElementVoidArea(0x0028,0x1202); // G LUT
+ LoadElementVoidArea(0x0028,0x1203); // B LUT
+
+ LoadElementVoidArea(0x0028,0x1221); // Segmented Red Palette Color LUT Data
+ LoadElementVoidArea(0x0028,0x1222); // Segmented Green Palette Color LUT Data
+ LoadElementVoidArea(0x0028,0x1223); // Segmented Blue Palette Color LUT Data
+ }
+
+ // --------------------------------------------------------------
+ // Special Patch to allow gdcm to read ACR-LibIDO formated images
+ //
+ // if recognition code tells us we deal with a LibIDO image
+ // we switch lineNumber and columnNumber
+ //
+ std::string RecCode;
+ RecCode = GetPubElValByNumber(0x0008, 0x0010);
+ if (RecCode == "ACRNEMA_LIBIDO_1.1" ||
+ RecCode == "CANRME_AILIBOD1_1." ) {
+ filetype = ACR_LIBIDO;
+ std::string rows = GetPubElValByNumber(0x0028, 0x0010);
+ std::string columns = GetPubElValByNumber(0x0028, 0x0011);
+ SetPubElValByNumber(columns, 0x0028, 0x0010);
+ SetPubElValByNumber(rows , 0x0028, 0x0011);
+ }
+ // ----------------- End of Special Patch ----------------
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief
+ * @return
+ */
+void gdcmHeader::PrintPubElVal(std::ostream & os) {
+ PubElValSet.Print(os);
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief
+ * @return
+ */
+void gdcmHeader::PrintPubDict(std::ostream & os) {
+ RefPubDict->Print(os);
}
-void gdcmHeader::PrintPubElVal(ostream & os) {
- PubElVals.Print(os);
+/**
+ * \ingroup gdcmHeader
+ * \brief
+ * @return
+ */
+int gdcmHeader::Write(FILE * fp, FileType type) {
+
+
+ // TODO : move the following lines (and a lot of others)
+ // to a future function CheckAndCorrectHeader
+
+ if (type == ImplicitVR) {
+ std::string implicitVRTransfertSyntax = "1.2.840.10008.1.2";
+ ReplaceOrCreateByNumber(implicitVRTransfertSyntax,0x0002, 0x0010);
+
+ //FIXME Refer to standards on page 21, chapter 6.2 "Value representation":
+ // values with a VR of UI shall be padded with a single trailing null
+ // Dans le cas suivant on doit pader manuellement avec un 0
+
+ PubElValSet.SetElValueLengthByNumber(18, 0x0002, 0x0010);
+ }
+
+ if (type == ExplicitVR) {
+ std::string explicitVRTransfertSyntax = "1.2.840.10008.1.2.1";
+ ReplaceOrCreateByNumber(explicitVRTransfertSyntax,0x0002, 0x0010);
+
+ //FIXME Refer to standards on page 21, chapter 6.2 "Value representation":
+ // values with a VR of UI shall be padded with a single trailing null
+ // Dans le cas suivant on doit pader manuellement avec un 0
+
+ PubElValSet.SetElValueLengthByNumber(20, 0x0002, 0x0010);
+ }
+
+ return PubElValSet.Write(fp, type);
}
-void gdcmHeader::PrintPubDict(ostream & os) {
- RefPubDict->Print(os);
+//
+// ------------------------ 'non string' elements related functions
+//
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Loads (from disk) the element content
+ * when a string is not suitable
+ */
+void * gdcmHeader::LoadElementVoidArea(guint16 Group, guint16 Elem) {
+ gdcmElValue * Element= PubElValSet.GetElementByNumber(Group, Elem);
+ if ( !Element )
+ return NULL;
+ size_t o =(size_t)Element->GetOffset();
+ fseek(fp, o, SEEK_SET);
+ int l=Element->GetLength();
+ void * a = malloc(l);
+ if(!a) {
+ std::cout << "Big Broblem (LoadElementVoidArea, malloc) "
+ << std::hex << Group << " " << Elem << std::endl;
+ return NULL;
+ }
+ int res = PubElValSet.SetVoidAreaByNumber(a, Group, Elem);
+ // TODO check the result
+ size_t l2 = fread(a, 1, l ,fp);
+ if(l != l2) {
+ std::cout << "Big Broblem (LoadElementVoidArea, fread) "
+ << std::hex << Group << " " << Elem << std::endl;
+ free(a);
+ return NULL;
+ }
}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Gets (from Header) the offset of a 'non string' element value
+ * \ (LoadElementValue has already be executed)
+ * @param Group
+ * @param Elem
+ * @return File Offset of the Element Value
+ */
+ size_t gdcmHeader::GetPubElValOffsetByNumber(guint16 Group, guint16 Elem) {
+ gdcmElValue* elValue = PubElValSet.GetElementByNumber(Group, Elem);
+ if (!elValue) {
+ dbg.Verbose(1, "gdcmHeader::GetElValueByNumber",
+ "failed to Locate gdcmElValue");
+ return (size_t)0;
+ }
+ return elValue->GetOffset();
+}
+
+/**
+ * \ingroup gdcmHeader
+* \brief Gets (from Header) a 'non string' element value
+ * \ (LoadElementValue has already be executed)
+ * @param Group
+ * @param Elem
+ * @return Pointer to the 'non string' area
+
+ */
+ void * gdcmHeader::GetPubElValVoidAreaByNumber(guint16 Group, guint16 Elem) {
+ gdcmElValue* elValue = PubElValSet.GetElementByNumber(Group, Elem);
+ if (!elValue) {
+ dbg.Verbose(1, "gdcmHeader::GetElValueByNumber",
+ "failed to Locate gdcmElValue");
+ return (NULL);
+ }
+ return elValue->GetVoidArea();
+}
+
+
+//
+// =============================================================================
+// Heuristics based accessors
+//==============================================================================
+//
+
+// TODO : move to an other file.
+
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Retrieve the number of columns of image.
+ * @return The encountered size when found, 0 by default.
+ */
+int gdcmHeader::GetXSize(void) {
+ // We cannot check for "Columns" because the "Columns" tag is present
+ // both in IMG (0028,0011) and OLY (6000,0011) sections of the dictionary.
+ std::string StrSize = GetPubElValByNumber(0x0028,0x0011);
+ if (StrSize == GDCM_UNFOUND)
+ return 0;
+ return atoi(StrSize.c_str());
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Retrieve the number of lines of image.
+ * \warning The defaulted value is 1 as opposed to gdcmHeader::GetXSize()
+ * @return The encountered size when found, 1 by default.
+ */
+int gdcmHeader::GetYSize(void) {
+ // We cannot check for "Rows" because the "Rows" tag is present
+ // both in IMG (0028,0010) and OLY (6000,0010) sections of the dictionary.
+ std::string StrSize = GetPubElValByNumber(0x0028,0x0010);
+ if (StrSize != GDCM_UNFOUND)
+ return atoi(StrSize.c_str());
+ if ( IsDicomV3() )
+ return 0;
+ else
+ // The Rows (0028,0010) entry is optional for ACR/NEMA. It might
+ // hence be a signal (1d image). So we default to 1:
+ return 1;
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Retrieve the number of planes of volume or the number
+ * of frames of a multiframe.
+ * \warning When present we consider the "Number of Frames" as the third
+ * dimension. When absent we consider the third dimension as
+ * being the "Planes" tag content.
+ * @return The encountered size when found, 1 by default.
+ */
+int gdcmHeader::GetZSize(void) {
+ // Both in DicomV3 and ACR/Nema the consider the "Number of Frames"
+ // as the third dimension.
+ std::string StrSize = GetPubElValByNumber(0x0028,0x0008);
+ if (StrSize != GDCM_UNFOUND)
+ return atoi(StrSize.c_str());
+
+ // We then consider the "Planes" entry as the third dimension [we
+ // cannot retrieve by name since "Planes tag is present both in
+ // IMG (0028,0012) and OLY (6000,0012) sections of the dictionary].
+ StrSize = GetPubElValByNumber(0x0028,0x0012);
+ if (StrSize != GDCM_UNFOUND)
+ return atoi(StrSize.c_str());
+ return 1;
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Retrieve the number of Bits Stored
+ * (as opposite to number of Bits Allocated)
+ *
+ * @return The encountered number of Bits Stored, 0 by default.
+ */
+int gdcmHeader::GetBitsStored(void) {
+ std::string StrSize = GetPubElValByNumber(0x0028,0x0101);
+ if (StrSize == GDCM_UNFOUND)
+ return 1;
+ return atoi(StrSize.c_str());
+}
+
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Retrieve the number of Samples Per Pixel
+ * (1 : gray level, 3 : RGB)
+ *
+ * @return The encountered number of Samples Per Pixel, 1 by default.
+ */
+int gdcmHeader::GetSamplesPerPixel(void) {
+ std::string StrSize = GetPubElValByNumber(0x0028,0x0002);
+ if (StrSize == GDCM_UNFOUND)
+ return 1; // Well, it's supposed to be mandatory ...
+ return atoi(StrSize.c_str());
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Retrieve the Planar Configuration for RGB images
+ * (0 : RGB Pixels , 1 : R Plane + G Plane + B Plane)
+ *
+ * @return The encountered Planar Configuration, 0 by default.
+ */
+int gdcmHeader::GetPlanarConfiguration(void) {
+ std::string StrSize = GetPubElValByNumber(0x0028,0x0006);
+ if (StrSize == GDCM_UNFOUND)
+ return 0;
+ return atoi(StrSize.c_str());
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Return the size (in bytes) of a single pixel of data.
+ * @return The size in bytes of a single pixel of data.
+ *
+ */
+int gdcmHeader::GetPixelSize(void) {
+ std::string PixelType = GetPixelType();
+ if (PixelType == "8U" || PixelType == "8S")
+ return 1;
+ if (PixelType == "16U" || PixelType == "16S")
+ return 2;
+ if (PixelType == "32U" || PixelType == "32S")
+ return 4;
+ dbg.Verbose(0, "gdcmHeader::GetPixelSize: Unknown pixel type");
+ return 0;
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Build the Pixel Type of the image.
+ * Possible values are:
+ * - 8U unsigned 8 bit,
+ * - 8S signed 8 bit,
+ * - 16U unsigned 16 bit,
+ * - 16S signed 16 bit,
+ * - 32U unsigned 32 bit,
+ * - 32S signed 32 bit,
+ * \warning 12 bit images appear as 16 bit.
+ * @return
+ */
+std::string gdcmHeader::GetPixelType(void) {
+ std::string BitsAlloc;
+ BitsAlloc = GetElValByName("Bits Allocated");
+ if (BitsAlloc == GDCM_UNFOUND) {
+ dbg.Verbose(0, "gdcmHeader::GetPixelType: unfound Bits Allocated");
+ BitsAlloc = std::string("16");
+ }
+ if (BitsAlloc == "12")
+ BitsAlloc = std::string("16");
+
+ std::string Signed;
+ Signed = GetElValByName("Pixel Representation");
+ if (Signed == GDCM_UNFOUND) {
+ dbg.Verbose(0, "gdcmHeader::GetPixelType: unfound Pixel Representation");
+ BitsAlloc = std::string("0");
+ }
+ if (Signed == "0")
+ Signed = std::string("U");
+ else
+ Signed = std::string("S");
+
+ return( BitsAlloc + Signed);
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief gets the info from 0002,0010 : Transfert Syntax
+ * \ else 1.
+ * @return Transfert Syntax Name (as oposite to Transfert Syntax UID)
+ */
+std::string gdcmHeader::GetTransferSyntaxName(void) {
+ std::string TransfertSyntax = GetPubElValByNumber(0x0002,0x0010);
+ if (TransfertSyntax == GDCM_UNFOUND) {
+ dbg.Verbose(0, "gdcmHeader::GetTransferSyntaxName: unfound Transfert Syntax (0002,0010)");
+ return "Uncompressed ACR-NEMA";
+ }
+ // we do it only when we need it
+ gdcmTS * ts = gdcmGlobal::GetTS();
+ std::string tsName=ts->GetValue(TransfertSyntax);
+ //delete ts; // Seg Fault when deleted ?!
+ return tsName;
+}
+
+// -------------------------------- Lookup Table related functions ------------
+
+/**
+ * \ingroup gdcmHeader
+ * \brief gets the info from 0028,1101 : Lookup Table Desc-Red
+ * \ else 0
+ * @return Lookup Table Length
+ * \ when (0028,0004),Photometric Interpretation = [PALETTE COLOR ]
+ */
+
+int gdcmHeader::GetLUTLength(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
+ std::string LutDescriptionR = GetPubElValByNumber(0x0028,0x1101);
+ if (LutDescriptionR == GDCM_UNFOUND)
+ return 0;
+ std::string LutDescriptionG = GetPubElValByNumber(0x0028,0x1102);
+ if (LutDescriptionG == GDCM_UNFOUND)
+ return 0;
+ std::string LutDescriptionB = GetPubElValByNumber(0x0028,0x1103);
+ if (LutDescriptionB == GDCM_UNFOUND)
+ return 0;
+ if( (LutDescriptionR != LutDescriptionG) || (LutDescriptionR != LutDescriptionB) ) {
+ dbg.Verbose(0, "gdcmHeader::GetLUTLength: The CLUT R,G,B are not equal");
+ return 0;
+ }
+ std::cout << "Lut Description " << LutDescriptionR <<std::endl;
+ tokens.erase(tokens.begin(),tokens.end()); // clean any previous value
+ Tokenize (LutDescriptionR, tokens, "\\");
+ LutLength=atoi(tokens[0].c_str());
+ //LutDepth=atoi(tokens[1].c_str());
+ //LutNbits=atoi(tokens[2].c_str());
+ tokens.clear();
+ return LutLength;
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief gets the info from 0028,1101 : Lookup Table Desc-Red
+ * \ else 0
+ * @return Lookup Table nBit
+ * \ when (0028,0004),Photometric Interpretation = [PALETTE COLOR ]
+ */
+
+int gdcmHeader::GetLUTNbits(void) {
+ std::vector<std::string> tokens;
+ //int LutLength;
+ //int LutDepth;
+ int LutNbits;
+ //Just hope Lookup Table Desc-Red = Lookup Table Desc-Red = Lookup Table Desc-Blue
+ // Consistency already checked in GetLUTLength
+ std::string LutDescription = GetPubElValByNumber(0x0028,0x1101);
+ if (LutDescription == GDCM_UNFOUND)
+ return 0;
+ tokens.erase(tokens.begin(),tokens.end()); // clean any previous value
+ Tokenize (LutDescription, tokens, "\\");
+ //LutLength=atoi(tokens[0].c_str());
+ //LutDepth=atoi(tokens[1].c_str());
+ LutNbits=atoi(tokens[2].c_str());
+ tokens.clear();
+ return LutNbits;
+}
+
+
+/**
+ * \ingroup gdcmHeader
+ * \brief gets the info from 0028,1201 : Lookup Table Red
+ * \ else 0
+ * @return Lookup Table Red
+ * \ when (0028,0004),Photometric Interpretation = [PALETTE COLOR ]
+ */
+void * gdcmHeader::GetLUTRed(void) {
+ return GetPubElValVoidAreaByNumber(0x0028,0x1201);
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief gets the info from 0028,1202 : Lookup Table Green
+ * \ else 0
+ * @return Lookup Table Red
+ * \ when (0028,0004),Photometric Interpretation = [PALETTE COLOR ]
+ */
+ void * gdcmHeader::GetLUTGreen(void) {
+ return GetPubElValVoidAreaByNumber(0x0028,0x1202);
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief gets the info from 0028,1202 : Lookup Table Blue
+ * \ else 0
+ * @return Lookup Table Blue
+ * \ when (0028,0004),Photometric Interpretation = [PALETTE COLOR ]
+ */
+void * gdcmHeader::GetLUTBlue(void) {
+ return GetPubElValVoidAreaByNumber(0x0028,0x1203);
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief
+ * @return Lookup Table RGB
+ * \ when (0028,0004),Photometric Interpretation = [PALETTE COLOR ]
+ * \ and (0028,1201),(0028,1202),(0028,1202) are found
+ * \warning : hazardous ! Use better GetPubElValVoidAreaByNumber
+ */
+void * gdcmHeader::GetLUTRGB(void) {
+// Not so easy : see
+// http://www.barre.nom.fr/medical/dicom2/limitations.html#Color%20Lookup%20Tables
+// and OT-PAL-8-face.dcm
+
+ if (GetPubElValByNumber(0x0028,0x0004) == GDCM_UNFOUND) {
+ dbg.Verbose(0, "gdcmHeader::GetLUTRGB: unfound Photometric Interpretation");
+ return NULL;
+ }
+ void * LutR,*LutG,*LutB;
+ int l;
+
+ // Maybe, some day we get an image
+ // that respects the definition ...
+ // Let's consider no ones does.
+
+ l= GetLUTLength();
+ if(l==0)
+ return (NULL);
+ int nBits=GetLUTNbits();
+
+ // a virer quand on aura trouve UNE image
+ // qui correspond VRAIMENT à la definition !
+ std::cout << "l " << l << " nBits " << nBits;
+
+ l= l/(nBits/8);
+
+ LutR =GetPubElValVoidAreaByNumber(0x0028,0x1201);
+ LutG =GetPubElValVoidAreaByNumber(0x0028,0x1202);
+ LutB =GetPubElValVoidAreaByNumber(0x0028,0x1203);
+
+ // Warning : Any value for nBits as to be considered as 8
+ // Any value for Length as to be considered as 256
+ // That's DICOM ...
+
+ // Just wait before removing the following code
+ /*
+ if (nBits == 16) {
+ guint16 * LUTRGB, *rgb;
+ LUTRGB = rgb = (guint16 *) malloc(3*l*sizeof( guint16));
+ guint16 * r = (guint16 *)LutR;
+ guint16 * g = (guint16 *)LutG;
+ guint16 * b = (guint16 *)LutB;
+ for(int i=0;i<l;i++) {
+ *rgb++ = *r++;
+ *rgb++ = *g++;
+ *rgb++ = *b++;
+ }
+ return(LUTRGB);
+ } else
+
+ */ { // we assume it's always 8 Bits
+ l=256; // we assume ...
+ unsigned char * LUTRGB, *rgb;
+ LUTRGB = rgb = (unsigned char *) malloc(3*l*sizeof( char));
+ unsigned char * r = (unsigned char *)LutR;
+ unsigned char * g = (unsigned char *)LutG;
+ unsigned char * b = (unsigned char *)LutB;
+ for(int i=0;i<l;i++) {
+ //std::cout << "lut16 " << i << " : " << *r << " " << *g << " " << *b
+ // << std::endl;
+ printf("lut 8 %d : %d %d %d \n",i,*r,*g,*b);
+ *rgb++ = *r++;
+ *rgb++ = *g++;
+ *rgb++ = *b++;
+ }
+ free(LutR); free(LutB); free(LutG);
+ return(LUTRGB);
+ }
+
+/* Sorry for the comments. The code will be moved in a fonction
+
+ std::string x=GetPubElValByNumber(0x0028,0x1201);
+ unsigned short int * lutR = (unsigned short int *)malloc((size_t)200*sizeof(short int));
+ unsigned short int * lutG = (unsigned short int *)malloc((size_t)200*sizeof(short int));
+ unsigned short int * lutB = (unsigned short int *)malloc((size_t)200*sizeof(short int));
+
+ std::vector<std::string> tokens;
+ tokens.erase(tokens.begin(),tokens.end()); // clean any previous value
+ Tokenize ((const std::string)x, tokens, "\\");
+ for (unsigned int i=0; i<tokens.size();i++) {
+ lutR[i] = atoi(tokens[i].c_str());
+ printf("%d (%x)\n",lutR[i],lutR[i]);
+ }
+
+ std::string y=GetPubElValByNumber(0x0028,0x1202);
+ tokens.erase(tokens.begin(),tokens.end()); // clean any previous value
+ Tokenize ((const std::string)y, tokens, "\\");
+ for (unsigned int i=0; i<tokens.size();i++) {
+ lutG[i] = atoi(tokens[i].c_str());
+ }
+
+ std::string z=GetPubElValByNumber(0x0028,0x1203);
+ tokens.erase(tokens.begin(),tokens.end()); // clean any previous value
+ Tokenize ((const std::string)z, tokens, "\\");
+ for (unsigned int i=0; i<tokens.size();i++) {
+ lutB[i] = atoi(tokens[i].c_str());
+ }
+ tokens.erase(tokens.begin(),tokens.end()); // clean any previous value
+ Tokenize ((const std::string)x, tokens, "\\");
+ for (unsigned int i=0; i<tokens.size();i++) {
+ lutB[i] = atoi(tokens[i].c_str());
+ }
+
+ */
+
+//int lgth=GetLUTLength();
+//cout << "lgth " << lgth << std::endl;;
+//for (int j=0;j<lgth;j++){
+//printf ("%d : %d (%x) %d (%x) %d (%x)\n",j,lutR[j],lutR[j],lutG[j],lutG[j],lutB[j],lutB[j]);
+//}
+
+
+}
+