+/**
+ * \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
+ * Seems to be useless !!!
+ * @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
+ */
+
+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 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);
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief
+ * @return integer, acts as a Boolean
+ */
+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);
+}
+
+//
+// ------------------------ '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;
+ }
+ return a;
+}
+
+/**
+ * \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 Bits Allocated
+ * (8, 12 -compacted ACR-NEMA files, 16, ...)
+ *
+ * @return The encountered number of Bits Allocated, 0 by default.
+ */
+int gdcmHeader::GetBitsAllocated(void) {
+ std::string StrSize = GetPubElValByNumber(0x0028,0x0100);
+ 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]);
+//}