#include <stdio.h>
#include <cerrno>
-// For nthos:
+/*// For nthos:
#ifdef _MSC_VER
-#include <winsock.h>
+ #include <winsock.h>
#else
-#include <netinet/in.h>
-#endif
+ #include <netinet/in.h>
+#endif*/
#include <cctype> // for isalpha
-#ifdef GDCM_NO_ANSI_STRING_STREAM
+/*#ifdef GDCM_NO_ANSI_STRING_STREAM
# include <strstream>
# define ostringstream ostrstream
# else
# include <sstream>
-#endif
+#endif*/
#include "gdcmUtil.h"
#include "gdcmTS.h"
//-----------------------------------------------------------------------------
// Refer to gdcmHeader::CheckSwap()
-const unsigned int gdcmHeader::HEADER_LENGTH_TO_READ = 256;
+//const unsigned int gdcmHeader::HEADER_LENGTH_TO_READ = 256;
-// Refer to gdcmHeader::SetMaxSizeLoadElementValue()
-const unsigned int gdcmHeader::MAX_SIZE_LOAD_ELEMENT_VALUE = 4096;
+// Refer to gdcmHeader::SetMaxSizeLoadEntry()
+//const unsigned int gdcmHeader::MAX_SIZE_LOAD_ELEMENT_VALUE = 4096;
//-----------------------------------------------------------------------------
// Constructor / Destructor
*/
gdcmHeader::gdcmHeader(const char *InFilename,
bool exception_on_error,
- bool enable_sequences ) {
- if (enable_sequences)
- enableSequences = 1;
- else
- enableSequences = 0;
-
- SetMaxSizeLoadElementValue(MAX_SIZE_LOAD_ELEMENT_VALUE);
- filename = InFilename;
- Initialise();
- if ( !OpenFile(exception_on_error))
- return;
- ParseHeader();
- LoadHeaderEntries();
- CloseFile();
- wasUpdated = 0; // will be set to 1 if user adds an entry
- printLevel = 1; // 'Heavy' header print by default
+ bool enable_sequences ):
+ gdcmParser(InFilename,exception_on_error,enable_sequences)
+{
}
/**
* \brief
* @param exception_on_error
*/
-gdcmHeader::gdcmHeader(bool exception_on_error) {
- SetMaxSizeLoadElementValue(MAX_SIZE_LOAD_ELEMENT_VALUE);
- Initialise();
+gdcmHeader::gdcmHeader(bool exception_on_error) :
+ gdcmParser(exception_on_error)
+{
}
/**
* \brief Canonical destructor.
*/
gdcmHeader::~gdcmHeader (void) {
- dicom_vr = (gdcmVR*)0;
- Dicts = (gdcmDictSet*)0;
- RefPubDict = (gdcmDict*)0;
- RefShaDict = (gdcmDict*)0;
- return;
}
//-----------------------------------------------------------------------------
// Print
-/**
- * \ingroup gdcmHeader
- * \brief Prints the Header Entries (Dicom Elements)
- * both from the H Table and the chained list
- * @return
- */
-void gdcmHeader::PrintPubEntry(std::ostream & os) {
- Print(os);
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief Prints The Dict Entries of THE public Dicom Dictionnry
- * @return
- */
-void gdcmHeader::PrintPubDict(std::ostream & os) {
- RefPubDict->Print(os);
-}
-
//-----------------------------------------------------------------------------
// Public
-/**
- * \ingroup gdcmHeader
- * \brief This predicate, based on hopefully reasonable 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 Dicom/Acr File.
- * @return true when gdcmHeader is the one of a reasonable Dicom/Acr file,
- * false otherwise.
- */
-bool gdcmHeader::IsReadable(void) {
- std::string res = GetEntryByNumber(0x0028, 0x0005);
- if ( res != GDCM_UNFOUND && atoi(res.c_str()) > 4 ) {
- return false; // Image Dimensions
- }
-
- if ( !GetHeaderEntryByNumber(0x0028, 0x0100) )
- return false; // "Bits Allocated"
- if ( !GetHeaderEntryByNumber(0x0028, 0x0101) )
- return false; // "Bits Stored"
- if ( !GetHeaderEntryByNumber(0x0028, 0x0102) )
- return false; // "High Bit"
- if ( !GetHeaderEntryByNumber(0x0028, 0x0103) )
- return false; // "Pixel Representation"
- return true;
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief Determines if the Transfer Syntax was already encountered
- * and if it corresponds to a ImplicitVRLittleEndian one.
- *
- * @return True when ImplicitVRLittleEndian found. False in all other cases.
- */
-bool gdcmHeader::IsImplicitVRLittleEndianTransferSyntax(void) {
- gdcmHeaderEntry *Element = GetHeaderEntryByNumber(0x0002, 0x0010);
- if ( !Element )
- return false;
- LoadHeaderEntrySafe(Element);
-
- std::string Transfer = Element->GetValue();
- if ( Transfer == "1.2.840.10008.1.2" )
- return true;
- return false;
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief Determines if the Transfer Syntax was already encountered
- * and if it corresponds to a ExplicitVRLittleEndian one.
- *
- * @return True when ExplicitVRLittleEndian found. False in all other cases.
- */
-bool gdcmHeader::IsExplicitVRLittleEndianTransferSyntax(void) {
- gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010);
- if ( !Element )
- return false;
- LoadHeaderEntrySafe(Element);
-
- std::string Transfer = Element->GetValue();
- if ( Transfer == "1.2.840.10008.1.2.1" )
- return true;
- return false;
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief Determines if the Transfer Syntax was already encountered
- * and if it corresponds to a DeflatedExplicitVRLittleEndian one.
- *
- * @return True when DeflatedExplicitVRLittleEndian found. False in all other cases.
- */
-bool gdcmHeader::IsDeflatedExplicitVRLittleEndianTransferSyntax(void) {
- gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010);
- if ( !Element )
- return false;
- LoadHeaderEntrySafe(Element);
-
- std::string Transfer = Element->GetValue();
- if ( Transfer == "1.2.840.10008.1.2.1.99" )
- 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.
- *
- * @return True when big endian found. False in all other cases.
- */
-bool gdcmHeader::IsExplicitVRBigEndianTransferSyntax(void) {
- gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010);
- if ( !Element )
- return false;
- LoadHeaderEntrySafe(Element);
-
- std::string Transfer = Element->GetValue();
- if ( Transfer == "1.2.840.10008.1.2.2" ) //1.2.2 ??? A verifier !
- return true;
- return false;
-}
-
/**
* \ingroup gdcmHeader
* \brief Determines if the Transfer Syntax was already encountered
return (GetHeaderEntryByNumber(0x0002, 0x0010) != NULL);
}
-/**
- * \ingroup gdcmHeader
- * \brief returns the File Type
- * (ACR, ACR_LIBIDO, ExplicitVR, ImplicitVR, Unknown)
- * @return
- */
-FileType gdcmHeader::GetFileType(void) {
- return(filetype);
-}
-
/**
* \ingroup gdcmHeader
* \brief Retrieve the number of columns of image.
nbitsB =atoi(tokens[2].c_str());
tokens.clear();
-// Load LUTs into memory, (as they were stored on disk)
+ // Load LUTs into memory, (as they were stored on disk)
unsigned char *lutR = (unsigned char *)
- GetPubEntryVoidAreaByNumber(0x0028,0x1201);
+ GetEntryVoidAreaByNumber(0x0028,0x1201);
unsigned char *lutG = (unsigned char *)
- GetPubEntryVoidAreaByNumber(0x0028,0x1202);
+ GetEntryVoidAreaByNumber(0x0028,0x1202);
unsigned char *lutB = (unsigned char *)
- GetPubEntryVoidAreaByNumber(0x0028,0x1203);
+ GetEntryVoidAreaByNumber(0x0028,0x1203);
if (!lutR || !lutG || !lutB ) {
return NULL;
}
- // forge the 4 * 8 Bits Red/Green/Blue/Alpha LUT
+ // forge the 4 * 8 Bits Red/Green/Blue/Alpha LUT
- unsigned char *LUTRGBA = (unsigned char *)calloc(1024,1); // 256 * 4 (R, G, B, Alpha)
- if (!LUTRGBA) {
- return NULL;
- }
- memset(LUTRGBA, 0, 1024);
+ unsigned char *LUTRGBA = (unsigned char *)calloc(1024,1); // 256 * 4 (R, G, B, Alpha)
+ if (!LUTRGBA) {
+ return NULL;
+ }
+ memset(LUTRGBA, 0, 1024);
// Bits Allocated
int nb;
std::string str_nb = GetEntryByNumber(0x0028,0x0100);
} else {
nb = atoi(str_nb.c_str() );
}
- int mult;
-
- if (nbitsR==16 && nb==8) // when LUT item size is different than pixel size
- mult=2; // high byte must be = low byte
- else // See PS 3.3-2003 C.11.1.1.2 p 619
- mult=1;
+ int mult;
+
+ if (nbitsR==16 && nb==8) // when LUT item size is different than pixel size
+ mult=2; // high byte must be = low byte
+ else // See PS 3.3-2003 C.11.1.1.2 p 619
+ mult=1;
// if we get a black image, let's just remove the '+1'
// from 'i*mult+1' and check again
// to see which byte is ==0 (first one, or second one)
// and fix the code
// We give up the checking to avoid some overhead
- unsigned char *a;
- int i;
-
- a = LUTRGBA+0;
- for(i=0;i<lengthR;i++) {
- *a = lutR[i*mult+1];
- a+=4;
- }
- a = LUTRGBA+1;
- for(i=0;i<lengthG;i++) {
- *a = lutG[i*mult+1];
- a+=4;
- }
- a = LUTRGBA+2;
- for(i=0;i<lengthB;i++) {
- *a = lutB[i*mult+1];
- a+=4;
- }
- a = LUTRGBA+3;
- for(i=0;i<256;i++) {
- *a = 1; // Alpha component
- a+=4;
- }
-
-//How to free the now useless LUTs?
+ unsigned char *a;
+ int i;
+
+ a = LUTRGBA+0;
+ for(i=0;i<lengthR;i++) {
+ *a = lutR[i*mult+1];
+ a+=4;
+ }
+ a = LUTRGBA+1;
+ for(i=0;i<lengthG;i++) {
+ *a = lutG[i*mult+1];
+ a+=4;
+ }
+ a = LUTRGBA+2;
+ for(i=0;i<lengthB;i++) {
+ *a = lutB[i*mult+1];
+ a+=4;
+ }
+ a = LUTRGBA+3;
+ for(i=0;i<256;i++) {
+ *a = 1; // Alpha component
+ a+=4;
+ }
+
+ //How to free the now useless LUTs?
-//free(LutR); free(LutB); free(LutG); // Seg Fault when used
- return(LUTRGBA);
+ //free(LutR); free(LutB); free(LutG); // Seg Fault when used
+ return(LUTRGBA);
}
/**
return tsName;
}
-/**
- * \ingroup gdcmHeader
- * \brief Searches within the file Header for element value of
- * a given tag.
- * @param tagName name of the searched element.
- * @return Corresponding element value when it exists, and the string
- * GDCM_UNFOUND ("gdcm::Unfound") otherwise.
- */
-std::string gdcmHeader::GetPubEntryByName(std::string tagName) {
- gdcmDictEntry *dictEntry = RefPubDict->GetTagByName(tagName);
- if( dictEntry == NULL)
- return GDCM_UNFOUND;
-
- return(GetEntryByNumber(dictEntry->GetGroup(),dictEntry->GetElement()));
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief Searches within the elements parsed with the file Header for
- * the element value representation of a given tag.
- *
- * Obtaining the VR (Value Representation) might be needed by caller
- * to convert the string typed content to caller's native type
- * (think of C++ vs Python). The VR is actually of a higher level
- * of semantics than just the native C++ type.
- * @param tagName name of the searched element.
- * @return Corresponding element value representation when it exists,
- * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise.
- */
-std::string gdcmHeader::GetPubEntryVRByName(std::string tagName) {
- gdcmDictEntry *dictEntry = RefPubDict->GetTagByName(tagName);
- if( dictEntry == NULL)
- return GDCM_UNFOUND;
-
- gdcmHeaderEntry* elem = GetHeaderEntryByNumber(dictEntry->GetGroup(),
- dictEntry->GetElement());
- return elem->GetVR();
-}
-
-
-/**
- * \ingroup gdcmHeader
- * \brief Searches within the public dictionary for element value
- * representation of a given tag.
- *
- * Obtaining the VR (Value Representation) might be needed by caller
- * to convert the string typed content to caller's native type
- * (think of C++ vs Python). The VR is actually of a higher level
- * of semantics than just the native C++ type.
- * @param group Group of the researched tag.
- * @param element Element of the researched tag.
- * @return Corresponding element value representation when it exists,
- * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise.
- */
-std::string gdcmHeader::GetPubEntryVRByNumber(guint16 group, guint16 element) {
- gdcmHeaderEntry* elem = GetHeaderEntryByNumber(group, element);
- if ( !elem )
- return GDCM_UNFOUND;
- return elem->GetVR();
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief Accesses an existing gdcmHeaderEntry (i.e. a Dicom Element)
- * in the PubHeaderEntrySet of this instance
- * through tag name and modifies it's content with the given value.
- * @param content new value to substitute with
- * @param tagName name of the Header Entry (Dicom Element) to be modified
- */
-bool gdcmHeader::SetPubEntryByName(std::string content, std::string tagName) {
- //return ( PubHeaderEntrySet.SetHeaderEntryByName (content, tagName) );
- gdcmDictEntry *dictEntry = RefPubDict->GetTagByName(tagName);
- if( dictEntry == NULL)
- return false;
- return(SetEntryByNumber(content,
- dictEntry->GetGroup(),
- dictEntry->GetElement()));
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief Accesses an existing gdcmHeaderEntry (i.e. a Dicom Element)
- * through it's (group, element) and modifies it's content with
- * the given value.
- * @param content new value to substitute with
- * @param group group of the Dicom Element to modify
- * @param element element of the Dicom Element to modify
- */
-bool gdcmHeader::SetPubEntryByNumber(std::string content,
- guint16 group,
- guint16 element) {
- TagKey key = gdcmDictEntry::TranslateToKey(group, element);
- if ( ! tagHT.count(key))
- return false;
- int l = content.length();
- if(l%2) { // Odd length are padded with a space (020H).
- l++;
- content = content + '\0';
- }
-
- //tagHT[key]->SetValue(content);
- gdcmHeaderEntry * a;
- IterHT p;
- TagHeaderEntryHT::iterator p2;
- // DO NOT remove the following lines : they explain the stuff
- //p= tagHT.equal_range(key); // get a pair of iterators first-last synonym
- //p2=p.first; // iterator on the first synonym
- //a=p2->second; // H Table target column (2-nd col)
-
- // or, easier :
- a = ((tagHT.equal_range(key)).first)->second;
-
- a-> SetValue(content);
-
- //std::string vr = tagHT[key]->GetVR();
- std::string vr = a->GetVR();
-
- guint32 lgr;
- if( (vr == "US") || (vr == "SS") )
- lgr = 2;
- else if( (vr == "UL") || (vr == "SL") )
- lgr = 4;
- else
- lgr = l;
- //tagHT[key]->SetLength(lgr);
- a->SetLength(lgr);
- return true;
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief Accesses an existing gdcmHeaderEntry (i.e. a Dicom Element)
- * through it's (group, element) and modifies it's content with
- * the given value.
- * \warning Don't use any longer : use SetPubEntryByNumber
- * @param content new value to substitute with
- * @param group group of the Dicom Element to modify
- * @param element element of the Dicom Element to modify
- */
-bool gdcmHeader::SetEntryByNumber(std::string content,
- guint16 group,
- guint16 element) {
- return SetPubEntryByNumber(content, group, element);
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief Accesses an existing gdcmHeaderEntry (i.e. a Dicom Element)
- * in the PubHeaderEntrySet of this instance
- * through it's (group, element) and modifies it's 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.
- */
-
-bool gdcmHeader::SetPubEntryLengthByNumber(guint32 length,
- guint16 group, guint16 element) {
- TagKey key = gdcmDictEntry::TranslateToKey(group, element);
- if ( ! tagHT.count(key))
- return false;
- if (length%2) length++; // length must be even
- //tagHT[key]->SetLength(length);
- ( ((tagHT.equal_range(key)).first)->second )->SetLength(length);
-
- return true ;
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief Accesses an existing gdcmHeaderEntry (i.e. a Dicom Element)
- * in the PubHeaderEntrySet of this instance
- * through it's (group, element) and modifies it's length with
- * the given value.
- * \warning Don't use any longer : use SetPubEntryLengthByNumber
- * @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.
- */
-
-bool gdcmHeader::SetEntryLengthByNumber(guint32 length,
- guint16 group, guint16 element) {
- return SetPubEntryLengthByNumber( length, group,element);
-}
-/**
- * \ingroup gdcmHeader
- * \brief Searches within Header Entries (Dicom Elements) parsed with
- * the public and private dictionaries
- * for the element value of a given tag.
- * \warning Don't use any longer : use GetPubEntryByName
- * @param tagName name of the searched element.
- * @return Corresponding element value when it exists,
- * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise.
- */
-std::string gdcmHeader::GetEntryByName(std::string tagName) {
- return GetPubEntryByName(tagName);
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief Searches within Header Entries (Dicom Elements) parsed with
- * the public and private dictionaries
- * for the element value representation of a given tag.
- *
- * Obtaining the VR (Value Representation) might be needed by caller
- * to convert the string typed content to caller's native type
- * (think of C++ vs Python). The VR is actually of a higher level
- * of semantics than just the native C++ type.
- * @param tagName name of the searched element.
- * @return Corresponding element value representation when it exists,
- * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise.
- */
-std::string gdcmHeader::GetEntryVRByName(std::string tagName) {
- return GetPubEntryVRByName(tagName);
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief Searches within Header Entries (Dicom Elements) parsed with
- * the public and private dictionaries
- * for the element value representation of a given tag.
- * @param group Group of the searched tag.
- * @param element Element of the searched tag.
- * @return Corresponding element value representation when it exists,
- * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise.
- */
-std::string gdcmHeader::GetEntryByNumber(guint16 group, guint16 element) {
- TagKey key = gdcmDictEntry::TranslateToKey(group, element);
- if ( ! tagHT.count(key))
- return GDCM_UNFOUND;
- return tagHT.find(key)->second->GetValue();
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief Searches within the public dictionary for element value of
- * a given tag.
- * @param group Group of the researched tag.
- * @param element Element of the researched tag.
- * @return Corresponding element value when it exists, and the string
- * GDCM_UNFOUND ("gdcm::Unfound") otherwise.
- */
-std::string gdcmHeader::GetPubEntryByNumber(guint16 group, guint16 element) {
- return GetEntryByNumber(group, element);
-}
-
-
-/**
- * \ingroup gdcmHeader
- * \brief Searches within Header Entries (Dicom Elements) parsed with
- * the public and private dictionaries
- * 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 searched tag.
- * @param element Element of the searched tag.
- * @return Corresponding element value representation when it exists,
- * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise.
- */
-std::string gdcmHeader::GetEntryVRByNumber(guint16 group, guint16 element) {
- return GetPubEntryVRByNumber(group, element);
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief Sets the value (string) of the Header Entry (Dicom Element)
- * @param content string value of the Dicom Element
- * @param tagName name of the searched Dicom Element.
- * @return true when found
- */
-bool gdcmHeader::SetEntryByName(std::string content,std::string tagName) {
- gdcmDictEntry *dictEntry = RefPubDict->GetTagByName(tagName);
- if( dictEntry == NULL)
- return false;
-
-
- TagKey key = gdcmDictEntry::TranslateToKey(dictEntry->GetGroup(),
- dictEntry->GetElement());
- if ( GetPubEntry().count(key) == 0 )
- return false;
- int l = content.length();
- if(l%2) { // Odd length are padded with a space (020H).
- l++;
- content = content + '\0';
- }
-
- //tagHt[key]->SetValue(content);
- gdcmHeaderEntry * a;
- IterHT p;
- TagHeaderEntryHT::iterator p2;
- // DO NOT remove the following lines : they explain how the stuff works
- //p= tagHt.equal_range(key); // get a pair of iterators first-last synonym
- //p2=p.first; // iterator on the first synonym
- //a=p2->second; // H Table target column (2-nd col)
- // or, easier :
- a = ((GetPubEntry().equal_range(key)).first)->second;
- a-> SetValue(content);
- std::string vr = a->GetVR();
-
- guint32 lgr;
- if( (vr == "US") || (vr == "SS") )
- lgr = 2;
- else if( (vr == "UL") || (vr == "SL") )
- lgr = 4;
- else
- lgr = l;
- a->SetLength(lgr);
- return true;
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief opens the file
- * @param exception_on_error
- * @return
- */
-FILE *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 ) {
- guint16 zero;
- fread(&zero, (size_t)2, (size_t)1, fp);
-
- //ACR -- or DICOM with no Preamble --
- if( zero == 0x0008 || zero == 0x0800 || zero == 0x0002 || zero == 0x0200)
- return(fp);
-
- //DICOM
- fseek(fp, 126L, SEEK_CUR);
- char dicm[4];
- fread(dicm, (size_t)4, (size_t)1, fp);
- if( memcmp(dicm, "DICM", 4) == 0 )
- return(fp);
-
- fclose(fp);
- dbg.Verbose(0, "gdcmHeader::gdcmHeader not DICOM/ACR", filename.c_str());
- }
- else {
- dbg.Verbose(0, "gdcmHeader::gdcmHeader cannot open file", filename.c_str());
- }
- return(NULL);
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief closes the file
- * @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 Parses the header of the file but WITHOUT loading element values.
- */
-void gdcmHeader::ParseHeader(bool exception_on_error) throw(gdcmFormatError) {
- gdcmHeaderEntry * newHeaderEntry = (gdcmHeaderEntry *)0;
-
- rewind(fp);
- CheckSwap();
- while ( (newHeaderEntry = ReadNextHeaderEntry()) ) {
- SkipHeaderEntry(newHeaderEntry);
- Add(newHeaderEntry);
- }
-}
-
-
-
-/**
- * \ingroup gdcmHeader
- * \brief
- * @param fp file pointer on an already open file
- * @param type type of the File to be written
- * (ACR-NEMA, ExplicitVR, ImplicitVR)
- * @return always "True" ?!
- */
-bool gdcmHeader::Write(FILE * fp, FileType type) {
-
-// ==============
-// TODO The stuff has been rewritten using the chained list instead
-// of the H table
-// so we could remove the GroupHT from the gdcmHeader
-// To be checked
-// =============
-
- // TODO : move the following lines (and a lot of others, to be written)
- // to a future function CheckAndCorrectHeader
-
- // Question :
- // Comment pourrait-on savoir si le DcmHeader vient d'un fichier DicomV3 ou non
- // (FileType est un champ de gdcmHeader ...)
- // WARNING : Si on veut ecrire du DICOM V3 a partir d'un DcmHeader ACR-NEMA
- // no way
- // a moins de se livrer a un tres complique ajout des champs manquants.
- // faire un 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
-
- SetEntryLengthByNumber(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
-
- SetEntryLengthByNumber(20, 0x0002, 0x0010);
- }
-
-
- if ( (type == ImplicitVR) || (type == ExplicitVR) )
- UpdateGroupLength(false,type);
- if ( type == ACR)
- UpdateGroupLength(true,ACR);
-
- WriteEntries(type, fp);
- return(true);
- }
-
/**
* \ingroup gdcmFile
* \brief Sets the Pixel Area size in the Header
ImageDataSize+=8;
sprintf(car,"%d",ImageDataSize);
content1=car;
- SetPubEntryByNumber(content1, 0x7fe0, 0x0000);
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief Modifies the value of a given Header Entry (Dicom Element)
- * if it exists; Creates it with the given value if it doesn't
- * @param Value passed as a std::string
- * @param Group
- * @param Elem
- * \return boolean
- */
-bool gdcmHeader::ReplaceOrCreateByNumber(std::string Value,
- guint16 Group, guint16 Elem ) {
-
- if (CheckIfExistByNumber(Group, Elem) == 0) {
- gdcmHeaderEntry* a =NewHeaderEntryByNumber(Group, Elem);
- if (a == NULL)
- return false;
- Add(a);
- }
- SetPubEntryByNumber(Value, Group, Elem);
- return(true);
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief Modifies the value of a given Header Entry (Dicom Element)
- * if it exists; Creates it with the given value if it doesn't
- * @param Value passed as a char*
- * @param Group
- * @param Elem
- * \return boolean
- *
- */
-bool gdcmHeader::ReplaceOrCreateByNumber(char* Value, guint16 Group, guint16 Elem ) {
-
- gdcmHeaderEntry* nvHeaderEntry=NewHeaderEntryByNumber(Group, Elem);
- // TODO : check if fails
- Add(nvHeaderEntry);
- std::string v = Value;
- SetEntryByNumber(v, Group, Elem);
- return(true);
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief Set a new value if the invoked element exists
- * Seems to be useless !!!
- * @param Value
- * @param Group
- * @param Elem
- * \return boolean
- */
-bool gdcmHeader::ReplaceIfExistByNumber(char* Value, guint16 Group, guint16 Elem ) {
-
- std::string v = Value;
- SetEntryByNumber(v, Group, Elem);
- return true;
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief Swaps back the bytes of 4-byte long integer accordingly to
- * processor order.
- * @return The properly swaped 32 bits integer.
- */
-guint32 gdcmHeader::SwapLong(guint32 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 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);
+ SetEntryByNumber(content1, 0x7fe0, 0x0000);
}
//-----------------------------------------------------------------------------
// Protected
-/**
- * \ingroup gdcmHeader
- * \brief retrieves a Dicom Element (the first one) using (group, element)
- * \ warning (group, element) IS NOT an identifier inside the Dicom Header
- * if you think it's NOT UNIQUE, check the count number
- * and use iterators to retrieve ALL the Dicoms Elements within
- * a given couple (group, element)
- * @param group Group number of the searched Dicom Element
- * @param element Element number of the searched Dicom Element
- * @return
- */
-gdcmHeaderEntry* gdcmHeader::GetHeaderEntryByNumber(guint16 group, guint16 element) {
- TagKey key = gdcmDictEntry::TranslateToKey(group, element);
- if ( ! tagHT.count(key))
- return NULL;
- return tagHT.find(key)->second;
-}
-
-
-/**
- * \ingroup gdcmHeader
- * \brief Searches within the Header Entries for a Dicom Element of
- * a given tag.
- * @param tagName name of the searched Dicom Element.
- * @return Corresponding Dicom Element when it exists, and NULL
- * otherwise.
- */
- gdcmHeaderEntry *gdcmHeader::GetHeaderEntryByName(std::string tagName) {
- gdcmDictEntry *dictEntry = RefPubDict->GetTagByName(tagName);
- if( dictEntry == NULL)
- return NULL;
-
- return(GetHeaderEntryByNumber(dictEntry->GetGroup(),dictEntry->GetElement()));
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief Checks if a given Dicom Element exists
- * \ within the H table
- * @param group Group number of the searched Dicom Element
- * @param element Element number of the searched Dicom Element
- * @return number of occurences
- */
-int gdcmHeader::CheckIfExistByNumber(guint16 group, guint16 element ) {
- std::string key = gdcmDictEntry::TranslateToKey(group, element );
- return (tagHT.count(key));
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief Gets (from Header) the offset of a 'non string' element value
- * \ (LoadElementValues has already be executed)
- * @param Group
- * @param Elem
- * @return File Offset of the Element Value
- */
-size_t gdcmHeader::GetPubEntryOffsetByNumber(guint16 Group, guint16 Elem) {
- gdcmHeaderEntry* Entry = GetHeaderEntryByNumber(Group, Elem);
- if (!Entry) {
- dbg.Verbose(1, "gdcmHeader::GetHeaderEntryByNumber",
- "failed to Locate gdcmHeaderEntry");
- return (size_t)0;
- }
- return Entry->GetOffset();
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief Gets (from Header) a 'non string' element value
- * \ (LoadElementValues has already be executed)
- * @param Group
- * @param Elem
- * @return Pointer to the 'non string' area
- */
-void * gdcmHeader::GetPubEntryVoidAreaByNumber(guint16 Group, guint16 Elem) {
- gdcmHeaderEntry* Entry = GetHeaderEntryByNumber(Group, Elem);
- if (!Entry) {
- dbg.Verbose(1, "gdcmHeader::GetHeaderEntryByNumber",
- "failed to Locate gdcmHeaderEntry");
- return (NULL);
- }
- return Entry->GetVoidArea();
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief Loads (from disk) the element content
- * when a string is not suitable
- */
-void * gdcmHeader::LoadEntryVoidArea(guint16 Group, guint16 Elem) {
- gdcmHeaderEntry * Element= GetHeaderEntryByNumber(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) {
- return NULL;
- }
-
- SetVoidAreaByNumber(a, Group, Elem);
- // TODO check the result
- size_t l2 = fread(a, 1, l ,fp);
- if(l != l2) {
- free(a);
- return NULL;
- }
- return a;
-}
-
//-----------------------------------------------------------------------------
// Private
-/**
- * \ingroup gdcmHeader
- * \brief Loads the element values of all the Header Entries pointed in the
- * public Chained List.
- */
-void gdcmHeader::LoadHeaderEntries(void) {
- rewind(fp);
- for (ListTag::iterator i = GetPubListEntry().begin();
- i != GetPubListEntry().end();
- ++i){
- LoadHeaderEntry(*i);
- }
-
- rewind(fp);
-
- // Load 'non string' values
- std::string PhotometricInterpretation = GetPubEntryByNumber(0x0028,0x0004);
- if( PhotometricInterpretation == "PALETTE COLOR " ){
- LoadEntryVoidArea(0x0028,0x1200); // gray LUT
- LoadEntryVoidArea(0x0028,0x1201); // R LUT
- LoadEntryVoidArea(0x0028,0x1202); // G LUT
- LoadEntryVoidArea(0x0028,0x1203); // B LUT
-
- LoadEntryVoidArea(0x0028,0x1221); // Segmented Red Palette Color LUT Data
- LoadEntryVoidArea(0x0028,0x1222); // Segmented Green Palette Color LUT Data
- LoadEntryVoidArea(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 = GetPubEntryByNumber(0x0008, 0x0010); // recognition code
- if (RecCode == "ACRNEMA_LIBIDO_1.1" ||
- RecCode == "CANRME_AILIBOD1_1." ) {
- filetype = ACR_LIBIDO;
- std::string rows = GetPubEntryByNumber(0x0028, 0x0010);
- std::string columns = GetPubEntryByNumber(0x0028, 0x0011);
- SetPubEntryByNumber(columns, 0x0028, 0x0010);
- SetPubEntryByNumber(rows , 0x0028, 0x0011);
- }
- // ----------------- End of Special Patch ----------------
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief Loads the element content if it's length is not bigger
- * than the value specified with
- * gdcmHeader::SetMaxSizeLoadElementValue()
- * @param ElVal Header Entry (Dicom Element) to be dealt with
- */
-void gdcmHeader::LoadHeaderEntry(gdcmHeaderEntry * 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);
-
- // the test was commented out to 'go inside' the SeQuences
- // we don't any longer skip them !
-
- // if( vr == "SQ" ) // (DO NOT remove this comment)
- // SkipLoad = true;
-
- // A SeQuence "contains" a set of Elements.
- // (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();
- s << " x(" << std::hex << ElVal->GetLength() << ")";
- ElVal->SetValue(s.str());
- return;
- }
-
- // When integer(s) are expected, read and convert the following
- // n *(two or four bytes)
- // properly i.e. as integers as opposed to a strings.
- // Elements with Value Multiplicity > 1
- // contain a set of integers (not a single one)
-
- // Any compacter code suggested (?)
- if ( IsHeaderEntryAnInteger(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;
- }
- }
- }
-#ifdef GDCM_NO_ANSI_STRING_STREAM
- s << std::ends; // to avoid oddities on Solaris
-#endif //GDCM_NO_ANSI_STRING_STREAM
- 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 Loads the element while preserving the current
- * underlying file position indicator as opposed to
- * to LoadHeaderEntry that modifies it.
- * @param entry Header Entry whose value shall be loaded.
- * @return
- */
-void gdcmHeader::LoadHeaderEntrySafe(gdcmHeaderEntry * entry) {
- long PositionOnEntry = ftell(fp);
- LoadHeaderEntry(entry);
- fseek(fp, PositionOnEntry, SEEK_SET);
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief
- * @param ElVal Header Entry whose length of the value shall be loaded.
-
- * @return
- */
- void gdcmHeader::FindHeaderEntryLength (gdcmHeaderEntry * ElVal) {
- guint16 element = ElVal->GetElement();
- guint16 group = ElVal->GetGroup();
- std::string vr = ElVal->GetVR();
- guint16 length16;
- if( (element == 0x0010) && (group == 0x7fe0) ) {
- dbg.SetDebug(-1);
- 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(FindHeaderEntryLengthOB());
- return;
- }
- FixHeaderEntryFoundLength(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
- // encounter 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 = Dicts->NewVirtualDictEntry(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
- }
-
- FixHeaderEntryFoundLength(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.
- FixHeaderEntryFoundLength(ElVal, ReadInt32());
- return;
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief Find the Value Representation of the current Dicom Element.
- * @param ElVal
- */
-void gdcmHeader::FindHeaderEntryVR( gdcmHeaderEntry *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 = Dicts->NewVirtualDictEntry(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 Skip a given Header Entry
- * \warning NOT end user intended method !
- * @param entry
- * @return
- */
-void gdcmHeader::SkipHeaderEntry(gdcmHeaderEntry * entry) {
- SkipBytes(entry->GetLength());
-}
-
-/**
- * \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::FixHeaderEntryFoundLength(gdcmHeaderEntry * ElVal, guint32 FoundLength) {
-
- ElVal->SetReadLength(FoundLength); // will be updated only if a bug is found
-
- if ( FoundLength == 0xffffffff) {
- FoundLength = 0;
- }
-
- // Sorry for the patch!
- // XMedCom did the trick to read some nasty GE images ...
- else if (FoundLength == 13) {
- // The following 'if' will be removed when there is no more
- // images on Creatis HDs with a 13 length for Manufacturer...
- if ( (ElVal->GetGroup() != 0x0008) ||
- ( (ElVal->GetElement() != 0x0070) && (ElVal->GetElement() != 0x0080) ) ) {
- // end of remove area
- FoundLength =10;
- ElVal->SetReadLength(10); // a bug is to be fixed
- }
- }
- // to fix some garbage 'Leonardo' Siemens images
- // May be commented out to avoid overhead
- else if ( (ElVal->GetGroup() == 0x0009) &&
- ( (ElVal->GetElement() == 0x1113) || (ElVal->GetElement() == 0x1114) ) ){
- FoundLength =4;
- ElVal->SetReadLength(4); // a bug is to be fixed
- }
- // end of fix
-
- // to try to 'go inside' SeQuences (with length), and not to skip them
- else if ( ElVal->GetVR() == "SQ") {
- if (enableSequences) // only if the user does want to !
- FoundLength =0;
- }
-
- // a SeQuence Element is beginning
- // Let's forget it's length
- // (we want to 'go inside')
-
- // Pb : *normaly* fffe|e000 is just a marker, its length *should be* zero
- // in gdcm-MR-PHILIPS-16-Multi-Seq.dcm we find lengthes as big as 28800
- // if we set the length to zero IsHeaderEntryAnInteger() breaks...
- // if we don't, we lost 28800 characters from the Header :-(
-
- else if(ElVal->GetGroup() == 0xfffe){
- // sometimes, length seems to be wrong
- FoundLength =0; // some more clever checking to be done !
- // I give up!
- // only gdcm-MR-PHILIPS-16-Multi-Seq.dcm
- // causes troubles :-(
- }
-
- ElVal->SetUsableLength(FoundLength);
-}
-
-/**
- * \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::IsHeaderEntryAnInteger(gdcmHeaderEntry * ElVal) {
- guint16 element = ElVal->GetElement();
- guint16 group = ElVal->GetGroup();
- 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 {
- std::ostringstream s;
- s << "Erroneous Group Length element length on :" \
- << std::hex << group << " , " << element;
- dbg.Error("gdcmHeader::IsAnInteger",
- s.str().c_str());
- }
- }
- if ( (vr == "UL") || (vr == "US") || (vr == "SL") || (vr == "SS") )
- return true;
-
- return false;
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief
- *
- * @return
- */
- guint32 gdcmHeader::FindHeaderEntryLengthOB(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();
- 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);
- 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 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
- */
-void gdcmHeader::SkipBytes(guint32 NBytes) {
- //FIXME don't dump the returned value
- (void)fseek(fp, (long)NBytes, SEEK_CUR);
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief
- */
-void gdcmHeader::Initialise(void) {
- dicom_vr = gdcmGlobal::GetVR();
- dicom_ts = gdcmGlobal::GetTS();
- Dicts = gdcmGlobal::GetDicts();
- RefPubDict = Dicts->GetDefaultPubDict();
- RefShaDict = (gdcmDict*)0;
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief Discover what the swap code is (among little endian, big endian,
- * bad little endian, bad big endian).
- *
- */
-void gdcmHeader::CheckSwap()
-{
- // Fourth semantics:
- //
- // ---> Warning : This fourth field 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
- //
-
- // 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;
- //cout << net2host << endl;
-
- // 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
- * @param NewSize
- * @return
- */
-void gdcmHeader::SetMaxSizeLoadElementValue(long NewSize) {
- if (NewSize < 0)
- return;
- if ((guint32)NewSize >= (guint32)0xffffffff) {
- MaxSizeLoadElementValue = 0xffffffff;
- return;
- }
- MaxSizeLoadElementValue = NewSize;
-}
-
-/**
- * \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 Read the next tag but WITHOUT loading it's value
- * @return On succes the newly created HeaderEntry, NULL on failure.
- */
-gdcmHeaderEntry * gdcmHeader::ReadNextHeaderEntry(void) {
-
- guint16 g,n;
- gdcmHeaderEntry * 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 (gdcmHeaderEntry *)0;
-
- NewElVal = NewHeaderEntryByNumber(g, n);
- FindHeaderEntryVR(NewElVal);
- FindHeaderEntryLength(NewElVal);
-
- if (errno == 1) {
- // Call it quits
- return (gdcmHeaderEntry *)0;
- }
- NewElVal->SetOffset(ftell(fp));
- //if ( (g==0x7fe0) && (n==0x0010) )
- return NewElVal;
-}
-
-/**
- * \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
- */
-gdcmHeaderEntry* gdcmHeader::NewHeaderEntryByName(std::string Name) {
-
- gdcmDictEntry * NewTag = GetDictEntryByName(Name);
- if (!NewTag)
- NewTag = Dicts->NewVirtualDictEntry(0xffff, 0xffff, "LO", "Unknown", Name);
-
- gdcmHeaderEntry* NewElVal = new gdcmHeaderEntry(NewTag);
- if (!NewElVal) {
- dbg.Verbose(1, "gdcmHeader::ObtainHeaderEntryByName",
- "failed to allocate gdcmHeaderEntry");
- return (gdcmHeaderEntry*)0;
- }
- return NewElVal;
-}
-
-/**
- * \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
- */
-gdcmHeaderEntry* gdcmHeader::NewHeaderEntryByNumber(guint16 Group, guint16 Elem) {
- // Find out if the tag we encountered is in the dictionaries:
- gdcmDictEntry * NewTag = GetDictEntryByNumber(Group, Elem);
- if (!NewTag)
- NewTag = Dicts->NewVirtualDictEntry(Group, Elem);
-
- gdcmHeaderEntry* NewElVal = new gdcmHeaderEntry(NewTag);
- if (!NewElVal) {
- dbg.Verbose(1, "gdcmHeader::NewHeaderEntryByNumber",
- "failed to allocate gdcmHeaderEntry");
- return (gdcmHeaderEntry*)0;
- }
- return NewElVal;
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief Small utility function that creates a new manually crafted
- * (as opposed as read from the file) gdcmHeaderEntry 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.
- */
-gdcmHeaderEntry* gdcmHeader::NewManualHeaderEntryToPubDict(std::string NewTagName,
- std::string VR) {
- gdcmHeaderEntry* NewElVal = (gdcmHeaderEntry*)0;
- guint32 StuffGroup = 0xffff; // Group to be stuffed with additional info
- guint32 FreeElem = 0;
- gdcmDictEntry* NewEntry = (gdcmDictEntry*)0;
-
- FreeElem = GenerateFreeTagKeyInGroup(StuffGroup);
- if (FreeElem == UINT32_MAX) {
- dbg.Verbose(1, "gdcmHeader::NewManualElValToPubDict",
- "Group 0xffff in Public Dict is full");
- return (gdcmHeaderEntry*)0;
- }
- NewEntry = Dicts->NewVirtualDictEntry(StuffGroup, FreeElem,
- VR, "GDCM", NewTagName);
- NewElVal = new gdcmHeaderEntry(NewEntry);
- Add(NewElVal);
- return NewElVal;
-}
//-----------------------------------------------------------------------------
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff