// gdcmParser.cxx
//-----------------------------------------------------------------------------
+//#define UINT32_MAX (4294967295U)
+
+
+#include "gdcmParser.h"
+#include "gdcmGlobal.h"
+#include "gdcmUtil.h"
+#include "gdcmDebug.h"
+
#include <errno.h>
#include <vector>
#include <netinet/in.h>
#endif
-#ifdef GDCM_NO_ANSI_STRING_STREAM
-# include <strstream>
-# define ostringstream ostrstream
-# else
-# include <sstream>
-#endif
# include <iomanip>
-#include "gdcmParser.h"
-#include "gdcmGlobal.h"
-#include "gdcmUtil.h"
-#include "gdcmDebug.h"
-
#define UI1_2_840_10008_1_2 "1.2.840.10008.1.2"
#define UI1_2_840_10008_1_2_1 "1.2.840.10008.1.2.1"
#define UI1_2_840_10008_1_2_2 "1.2.840.10008.1.2.2"
#define UI1_2_840_10008_1_2_1_99 "1.2.840.10008.1.2.1.99"
+typedef struct {
+ guint32 totalSQlength;
+ guint32 alreadyParsedlength;
+} pileElem;
+
//-----------------------------------------------------------------------------
// Refer to gdcmParser::CheckSwap()
const unsigned int gdcmParser::HEADER_LENGTH_TO_READ = 256;
// Refer to gdcmParser::SetMaxSizeLoadEntry()
const unsigned int gdcmParser::MAX_SIZE_LOAD_ELEMENT_VALUE = 4096;
-// Refer to gdcmParser::SetMaxSizePrintEntry()
-// TODO : Right now, better see "define, in gdcmHederEntry.cxx
const unsigned int gdcmParser::MAX_SIZE_PRINT_ELEMENT_VALUE = 64;
//-----------------------------------------------------------------------------
/**
* \brief constructor
- * @param inFilename
+ * @param inFilename file to be opened for parsing
* @param exception_on_error whether we throw an exception or not
* @param enable_sequences = true to allow the header
- * to be parsed *inside* the SeQuences,
+ * to be parsed *inside* the SeQuences,
* when they have an actual length
+ * \warning enable_sequences *has to be* true for reading PAPYRUS 3.0 files
* @param ignore_shadow to allow skipping the shadow elements,
* to save memory space.
* \warning The TRUE value for this param has to be used
if ( !OpenFile(exception_on_error))
return;
- if (ParseHeader()) {
- LoadHeaderEntries();
- }
+
+ LoadHeaderEntries();
CloseFile();
wasUpdated = 0; // will be set to 1 if user adds an entry
}
/**
- * \ingroup gdcmParser
* \brief constructor
* @param exception_on_error
*/
gdcmParser::gdcmParser(bool exception_on_error) {
+ (void)exception_on_error;
enableSequences=0;
SetMaxSizeLoadEntry(MAX_SIZE_LOAD_ELEMENT_VALUE);
}
/**
- * \ingroup gdcmParser
* \brief Canonical destructor.
*/
gdcmParser::~gdcmParser (void) {
//-----------------------------------------------------------------------------
// Print
/**
- * \ingroup gdcmParser
* \brief Prints the Header Entries (Dicom Elements)
- * both from the H Table and the chained list
+ * from the chained list
* @return
*/
void gdcmParser::PrintEntry(std::ostream & os) {
- std::ostringstream s;
for (ListTag::iterator i = listEntries.begin();
i != listEntries.end();
(*i)->SetPrintLevel(printLevel);
(*i)->Print(os);
}
- os<<s.str();
}
+
/**
- * \ingroup gdcmParser
- * \brief Prints The Dict Entries of THE public Dicom Dictionnry
+ * \brief Prints The Dict Entries of THE public Dicom Dictionary
* @return
*/
void gdcmParser::PrintPubDict(std::ostream & os) {
}
/**
- * \ingroup gdcmParser
- * \brief Prints The Dict Entries of THE shadow Dicom Dictionnary
+ * \brief Prints The Dict Entries of THE shadow Dicom Dictionary
* @return
*/
void gdcmParser::PrintShaDict(std::ostream & os) {
//-----------------------------------------------------------------------------
// Public
/**
- * \ingroup gdcmParser
* \brief Get the public dictionary used
*/
gdcmDict *gdcmParser::GetPubDict(void) {
}
/**
- * \ingroup gdcmParser
* \brief Get the shadow dictionary used
*/
gdcmDict *gdcmParser::GetShaDict(void) {
}
/**
- * \ingroup gdcmParser
* \brief Set the shadow dictionary used
* \param dict dictionary to use in shadow
*/
}
/**
- * \ingroup gdcmParser
* \brief Set the shadow dictionary used
* \param dictName name of the dictionary to use in shadow
*/
}
/**
- * \ingroup gdcmParser
* \brief This predicate, based on hopefully reasonable heuristics,
* decides whether or not the current gdcmParser was properly parsed
* and contains the mandatory information for being considered as
* false otherwise.
*/
bool gdcmParser::IsReadable(void) {
- if(filetype==Unknown) {
+ if(filetype==gdcmUnknown) {
return(false);
}
if(listEntries.size()<=0) {
}
/**
- * \ingroup gdcmParser
* \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.
}
/**
- * \ingroup gdcmParser
* \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.
}
/**
- * \ingroup gdcmParser
* \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.
}
/**
- * \ingroup gdcmParser
* \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.
}
/**
- * \ingroup gdcmParser
* \brief returns the File Type
- * (ACR, ACR_LIBIDO, ExplicitVR, ImplicitVR, Unknown)
+ * (ACR, ACR_LIBIDO, ExplicitVR, ImplicitVR, Unfound)
* @return the FileType code
*/
FileType gdcmParser::GetFileType(void) {
}
/**
- * \ingroup gdcmParser
* \brief opens the file
* @param exception_on_error
* @return
}
/**
- * \ingroup gdcmParser
* \brief closes the file
* @return TRUE if the close was successfull
*/
}
/**
- * \ingroup gdcmParser
- * \brief writes on disc all the Header Entries (Dicom Elements)
+ * \brief Writes in a file all the Header Entries (Dicom Elements)
* of the Chained List
* @param fp file pointer on an already open file
- * @param type type of the File to be written
+ * @param type Type of the File to be written
* (ACR-NEMA, ExplicitVR, ImplicitVR)
- * @return always "True" ?!
+ * \return Always true.
*/
bool gdcmParser::Write(FILE *fp, FileType type) {
-// ==============
-// TODO The stuff was rewritten using the chained list instead
-// of the H table
-// so we could remove the GroupHT from the gdcmParser
-// To be checked
-// =============
-
- // TODO : move the following lines (and a lot of others, to be written)
- // to a future function CheckAndCorrectHeader
+/// \todo
+/// ==============
+/// The stuff will have to be rewritten using the SeQuence based
+/// tree-like stucture instead of the chained list .
+/// (so we shall remove the GroupHT from the gdcmParser)
+/// 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 gdcmParser ...)
- // 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)
+ /// \todo
+ /// Question :
+ /// Comment pourrait-on savoir si le DcmHeader vient d'un fichier
+ /// DicomV3 ou non (FileType est un champ de gdcmParser ...)
+ /// 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 == gdcmImplicitVR)
{
std::string implicitVRTransfertSyntax = UI1_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
+ /// \todo 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)
+ if (type == gdcmExplicitVR)
{
std::string explicitVRTransfertSyntax = UI1_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
+ /// \todo 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);
}
-/* TODO : rewrite later, if really usefull
-
- if ( (type == ImplicitVR) || (type == ExplicitVR) )
- UpdateGroupLength(false,type);
- if ( type == ACR)
- UpdateGroupLength(true,ACR);
-*/
+/**
+ * \todo rewrite later, if really usefull
+ *
+ * --> Warning : un-updated odd groups lengths can causes pb
+ * --> (xmedcon breaks)
+ * --> to be re- written with future org.
+ *
+ * if ( (type == ImplicitVR) || (type == ExplicitVR) )
+ * UpdateGroupLength(false,type);
+ * if ( type == ACR)
+ * UpdateGroupLength(true,ACR);
+ */
WriteEntries(fp,type);
return(true);
- }
+}
/**
- * \ingroup gdcmParser
* \brief Modifies the value of a given Header Entry (Dicom Element)
- * if it exists; Creates it with the given value if it doesn't
- * \warning : adds the Header Entry to the HTable, NOT to the chained List
- * @param Value passed as a std::string
- * @param Group group of the Entry
- * @param Elem element of the Entry
- * \return pointer to the created Header Entry
- * NULL if creation failed
+ * when it exists. Create it with the given value when unexistant.
+ * \warning Adds the Header Entry to the HTable, NOT to the chained List
+ * @param Value Value to be set
+ * @param Group Group of the Entry
+ * @param Elem Element of the Entry
+ * \return pointer to the modified/created Header Entry (NULL when creation
+ * failed).
*/
gdcmHeaderEntry * gdcmParser::ReplaceOrCreateByNumber(
std::string Value,
gdcmHeaderEntry* a;
a = GetHeaderEntryByNumber( Group, Elem);
if (a == NULL) {
- gdcmHeaderEntry *a =NewHeaderEntryByNumber(Group, Elem);
+ a =NewHeaderEntryByNumber(Group, Elem);
if (a == NULL)
return NULL;
AddHeaderEntry(a);
}
- //SetEntryByNumber(Value, Group, Elem);
+ //CLEANME SetEntryByNumber(Value, Group, Elem);
a->SetValue(Value);
return(a);
}
/**
- * \ingroup gdcmParser
- * \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 group of the Entry
- * @param Elem element of the Entry
- * \return pointer to the created Header Entry
- * NULL if creation failed
- *
- */
-gdcmHeaderEntry * gdcmParser::ReplaceOrCreateByNumber(
- char* Value,
- guint16 Group,
- guint16 Elem ) {
- gdcmHeaderEntry* nvHeaderEntry=NewHeaderEntryByNumber(Group, Elem);
-
- if(!nvHeaderEntry)
- return(NULL);
-
- AddHeaderEntry(nvHeaderEntry);
-
- std::string v = Value;
- SetEntryByNumber(v, Group, Elem);
- return(nvHeaderEntry);
-}
-
-/**
- * \ingroup gdcmParser
- * \brief Set a new value if the invoked element exists
- * Seems to be useless !!!
+ * \brief Set a new value if the invoked element exists
+ * Seems to be useless !!!
* @param Value new element value
* @param Group group of the Entry
* @param Elem element of the Entry
// Protected
/**
- * \ingroup gdcmParser
* \brief Checks if a given Dicom Element exists
* within the H table
* @param group Group number of the searched Dicom Element
}
/**
- * \ingroup gdcmParser
* \brief Searches within Header Entries (Dicom Elements) parsed with
* the public and private dictionaries
* for the element value of a given tag.
}
/**
- * \ingroup gdcmParser
* \brief Searches within Header Entries (Dicom Elements) parsed with
* the public and private dictionaries
* for the element value representation of a given tag.
/**
- * \ingroup gdcmParser
* \brief Searches within Header Entries (Dicom Elements) parsed with
* the public and private dictionaries
* for the element value representation of a given tag.
}
/**
- * \ingroup gdcmParser
* \brief Searches within Header Entries (Dicom Elements) parsed with
* the public and private dictionaries
* for the element value representation of a given tag..
}
/**
- * \ingroup gdcmParser
* \brief Searches within Header Entries (Dicom Elements) parsed with
* the public and private dictionaries
* for the value length of a given tag..
return elem->GetLength();
}
/**
- * \ingroup gdcmParser
* \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.
}
/**
- * \ingroup gdcmParser
* \brief Accesses an existing gdcmHeaderEntry (i.e. a Dicom Element)
* through it's (group, element) and modifies it's content with
* the given value.
}
/**
- * \ingroup gdcmParser
* \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
}
/**
- * \ingroup gdcmParser
* \brief Gets (from Header) the offset of a 'non string' element value
* (LoadElementValues has already be executed)
* @param Group group of the Entry
}
/**
- * \ingroup gdcmParser
* \brief Gets (from Header) a 'non string' element value
* (LoadElementValues has already be executed)
* @param Group group of the Entry
}
/**
- * \ingroup gdcmParser
* \brief Loads (from disk) the element content
* when a string is not suitable
* @param Group group of the Entry
return NULL;
size_t o =(size_t)Element->GetOffset();
fseek(fp, o, SEEK_SET);
- int l=Element->GetLength();
- void * a = malloc(l);
+ size_t l=Element->GetLength();
+ char* a = new char[l];
if(!a)
return NULL;
SetEntryVoidAreaByNumber(a, Group, Elem);
- // TODO check the result
+ /// \todo check the result
size_t l2 = fread(a, 1, l ,fp);
if(l != l2)
{
- free(a);
+ delete[] a;
return NULL;
}
}
/**
- * \ingroup gdcmParser
* \brief Sets a 'non string' value to a given Dicom Element
* @param area
* @param group Group number of the searched Dicom Element
}
/**
- * \ingroup gdcmParser
* \brief Update the entries with the shadow dictionary.
* Only non even entries are analyzed
*/
}
/**
- * \ingroup gdcmParser
* \brief Searches within the Header Entries for a Dicom Element of
* a given tag.
* @param tagName name of the searched Dicom Element.
}
/**
- * \ingroup gdcmParser
* \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
}
/**
- * \ingroup gdcmParser
* \brief retrieves the Dicom Elements (all of them) using (group, element)
* @param group Group number of the searched Dicom Element.
* @param element Element number of the searched Dicom Element.
}
/**
- * \ingroup gdcmParser
* \brief Loads the element while preserving the current
* underlying file position indicator as opposed to
* to LoadHeaderEntry that modifies it.
}
/**
- * \ingroup gdcmParser
* \brief Re-computes the length of a ACR-NEMA/Dicom group from a DcmHeader
* \warning : to be re-written using the chained list instead of the H table.
* \warning : DO NOT use (doesn't work any longer because of the multimap)
// since it's at the end of the Hash Table
// (fffe,e0dd)
- // pas SEQUENCE en ACR-NEMA
+ // there is SEQUENCE in ACR-NEMA
// WARNING :
// --> la descente a l'interieur' des SQ
// devrait etre faite avec une liste chainee, pas avec une HTable...
}
else // any elem but the first
{
- if (type == ExplicitVR)
+ if (type == gdcmExplicitVR)
{
if ( (vr == "OB") || (vr == "OW") || (vr == "SQ") )
{
{
// FIXME: g++ -Wall -Wstrict-prototypes reports on following line:
// warning: unsigned int format, different type arg
- sscanf(g->first.c_str(),"%x",&gr_bid);
+ sscanf(g->first.c_str(),"%x",&gr_bid); //FIXME
tk = g->first + "|0000"; // generate the element full tag
if ( tagHT.count(tk) == 0) // if element 0x0000 not found
}
/**
- * \ingroup gdcmParser
- * \brief writes on disc according to the requested format
- * (ACR-NEMA, ExplicitVR, ImplicitVR) ONE
- * gdcmHeaderEntry
- * @param tag pointer on the gdcmHeaderEntry to be written
- * @param type type of the File to be written
- * (ACR-NEMA, ExplicitVR, ImplicitVR)
- * @param _fp already open file pointer
+ * \brief Writes in a file (according to the requested format)
+ * the group, the element, the value representation and the length
+ * of a single gdcmHeaderEntry passed as argument.
+ * @param tag pointer on the gdcmHeaderEntry to be written
+ * @param _fp already open file pointer
+ * @param type type of the File to be written
*/
-void gdcmParser::WriteEntry(gdcmHeaderEntry *tag, FILE *_fp,FileType type)
+void gdcmParser::WriteEntryTagVRLength(gdcmHeaderEntry *tag,
+ FILE *_fp,
+ FileType type)
{
- guint16 gr, el;
- guint32 lgr;
- std::string value;
- const char * val;
- std::string vr;
- guint32 val_uint32;
- guint16 val_uint16;
- guint16 valZero =0;
- void *voidArea;
- std::vector<std::string> tokens;
-
- void *ptr;
- int ff=0xffffffff;
- // TODO (?) tester les echecs en ecriture (apres chaque fwrite)
- int compte =0;
- itsTimeToWritePixels = false;
-
- gr = tag->GetGroup();
- el = tag->GetElement();
- lgr = tag->GetReadLength();
- val = tag->GetValue().c_str();
- vr = tag->GetVR();
- voidArea = tag->GetVoidArea();
-
- // === Deal with the length
- // --------------------
- if((tag->GetLength())%2==1)
- {
- tag->SetValue(tag->GetValue()+"\0");
- tag->SetLength(tag->GetReadLength()+1);
- }
+ guint16 group = tag->GetGroup();
+ std::string vr = tag->GetVR();
+ guint16 el = tag->GetElement();
+ guint32 lgr = tag->GetReadLength();
+
+ if ( (group == 0xfffe) && (el == 0x0000) )
+ // Fix in order to make some MR PHILIPS images e-film readable
+ // see gdcmData/gdcm-MR-PHILIPS-16-Multi-Seq.dcm:
+ // we just *always* ignore spurious fffe|0000 tag !
+ return;
+
+ fwrite ( &group,(size_t)2 ,(size_t)1 ,_fp); //group
+ fwrite ( &el,(size_t)2 ,(size_t)1 ,_fp); //element
- if ( type == ACR )
- {
- if (gr < 0x0008) return; // ignore pure DICOM V3 groups
- if (gr %2) return; // ignore shadow groups
- if (vr == "SQ" ) return; // ignore Sequences
- // TODO : find a trick to *skip* the SeQuences !
- // Not only ignore the SQ element
- if (gr == 0xfffe ) return; // ignore delimiters
- }
-
- fwrite ( &gr,(size_t)2 ,(size_t)1 ,_fp); //group
- fwrite ( &el,(size_t)2 ,(size_t)1 ,_fp); //element
-
- if ( (type == ExplicitVR) || (type == DICOMDIR) ) {
- // EXPLICIT VR
- guint16 z=0, shortLgr;
-
- if (gr == 0xfffe) { // NO Value Representation for 'delimiters'
- // no length : write ffffffff
+ if ( type == gdcmExplicitVR ) {
- // special patch to make some MR PHILIPS images e-film readable
- // see gdcmData/gdcm-MR-PHILIPS-16-Multi-Seq.dcm
- // from Hospital Guy de Chauliac, Montpellier
- // we just ignore spurious fffe|0000 tag !
- if (el == 0x0000) return;
+ // Special case of delimiters:
+ if (group == 0xfffe) {
+ // Delimiters have NO Value Representation and have NO length.
+ // Hence we skip writing the VR and length and we pad by writing
+ // 0xffffffff
+ int ff=0xffffffff;
fwrite (&ff,(size_t)4 ,(size_t)1 ,_fp);
- return; // NO value for 'delimiters'
+ return;
}
- shortLgr=lgr;
- if (vr == "unkn") { // Unknown was 'written'
+ guint16 z=0;
+ guint16 shortLgr = lgr;
+ if (vr == "unkn") { // Unfound was 'written'
// deal with Little Endian
fwrite ( &shortLgr,(size_t)2 ,(size_t)1 ,_fp);
fwrite ( &z, (size_t)2 ,(size_t)1 ,_fp);
{
fwrite ( &lgr,(size_t)4 ,(size_t)1 ,_fp);
}
+}
- // === Deal with the value
- // -------------------
- if (vr == "SQ") return; // no "value" to write for the SEQuences
- if (gr == 0xfffe)return; // no "value" to write for the delimiters
+/**
+ * \brief Writes in a file (according to the requested format)
+ * the value of a single gdcmHeaderEntry passed as argument.
+ * @param tag Pointer on the gdcmHeaderEntry to be written
+ * @param _fp Already open file pointer
+ * @param type type of the File to be written
+ */
+void gdcmParser::WriteEntryValue(gdcmHeaderEntry *tag, FILE *_fp,FileType type)
+{
+ (void)type;
+ guint16 group = tag->GetGroup();
+ std::string vr = tag->GetVR();
+ guint32 lgr = tag->GetReadLength();
+
+ if (vr == "SQ")
+ // SeQuences have no value:
+ return;
+ if (group == 0xfffe)
+ // Delimiters have no associated value:
+ return;
+ void *voidArea;
+ voidArea = tag->GetVoidArea();
if (voidArea != NULL)
{ // there is a 'non string' LUT, overlay, etc
fwrite ( voidArea,(size_t)lgr ,(size_t)1 ,_fp); // Elem value
if (vr == "US" || vr == "SS")
{
+ // some 'Short integer' fields may be mulivaluated
+ // each single value is separated from the next one by '\'
+ // we split the string and write each value as a short int
+ std::vector<std::string> tokens;
tokens.erase(tokens.begin(),tokens.end()); // clean any previous value
Tokenize (tag->GetValue(), tokens, "\\");
for (unsigned int i=0; i<tokens.size();i++)
{
- val_uint16 = atoi(tokens[i].c_str());
- ptr = &val_uint16;
+ guint16 val_uint16 = atoi(tokens[i].c_str());
+ void *ptr = &val_uint16;
fwrite ( ptr,(size_t)2 ,(size_t)1 ,_fp);
}
tokens.clear();
return;
}
-
+ // some 'Integer' fields may be mulivaluated
+ // each single value is separated from the next one by '\'
+ // we split the string and write each value as an int
if (vr == "UL" || vr == "SL")
{
+ std::vector<std::string> tokens;
tokens.erase(tokens.begin(),tokens.end()); // clean any previous value
Tokenize (tag->GetValue(), tokens, "\\");
for (unsigned int i=0; i<tokens.size();i++)
{
- val_uint32 = atoi(tokens[i].c_str());
- ptr = &val_uint32;
+ guint32 val_uint32 = atoi(tokens[i].c_str());
+ void *ptr = &val_uint32;
fwrite ( ptr,(size_t)4 ,(size_t)1 ,_fp);
}
tokens.clear();
return;
- }
-
- // Pixels are never loaded in the element !
- // we stop writting when Pixel are processed
- // FIX : we loose trailing elements (RAB, right now)
-
- if ((gr == GrPixel) && (el == NumPixel) ) {
- compte++;
- if (compte == countGrPixel) {// we passed *all* the GrPixel,NumPixel
- itsTimeToWritePixels = true;
- return;
- }
- }
- fwrite ( val,(size_t)lgr ,(size_t)1 ,_fp); // Elem value
+ }
+ fwrite (tag->GetValue().c_str(), (size_t)lgr ,(size_t)1, _fp); // Elem value
+}
+
+/**
+ * \brief Writes in a file (according to the requested format)
+ * a single gdcmHeaderEntry passed as argument.
+ * \sa WriteEntryValue, WriteEntryTagVRLength.
+ * @param tag Pointer on the gdcmHeaderEntry to be written
+ * @param _fp Already open file pointer
+ * @param type type of the File to be written
+ */
+
+bool gdcmParser::WriteEntry(gdcmHeaderEntry *tag, FILE *_fp,FileType type)
+{
+ guint32 length = tag->GetLength();
+
+ // The value of a tag MUST (see the DICOM norm) be an odd number of
+ // bytes. When this is not the case, pad with an additional byte:
+ if(length%2==1)
+ {
+ tag->SetValue(tag->GetValue()+"\0");
+ tag->SetLength(tag->GetReadLength()+1);
+ }
+
+ WriteEntryTagVRLength(tag, _fp, type);
+ WriteEntryValue(tag, _fp, type);
+ return true;
}
/**
- * \ingroup gdcmParser
* \brief writes on disc according to the requested format
* (ACR-NEMA, ExplicitVR, ImplicitVR) the image
* using the Chained List
* @param _fp already open file pointer
*/
-void gdcmParser::WriteEntries(FILE *_fp,FileType type)
+bool gdcmParser::WriteEntries(FILE *_fp,FileType type)
{
- // TODO (?) tester les echecs en ecriture (apres chaque fwrite)
-
+ /// \todo (?) check write failures (after *each* fwrite)
+
for (ListTag::iterator tag2=listEntries.begin();
tag2 != listEntries.end();
++tag2)
{
- WriteEntry(*tag2,_fp,type);
- if (itsTimeToWritePixels)
- break;
+ if ( type == gdcmACR ){
+ if ((*tag2)->GetGroup() < 0x0008)
+ // Ignore pure DICOM V3 groups
+ continue;
+ if ((*tag2)->GetElement() %2)
+ // Ignore the "shadow" groups
+ continue;
+ if ((*tag2)->GetVR() == "SQ" ) // ignore Sequences
+ continue;
+ if ((*tag2)->GetSQDepthLevel() != 0) // Not only ignore the SQ element
+ continue;
+ }
+ if (! WriteEntry(*tag2,_fp,type) )
+ return false;
}
+ return true;
}
/**
- * \ingroup gdcmParser
* \brief writes on disc according to the requested format
* (ACR-NEMA, ExplicitVR, ImplicitVR) the image,
* using only the last synonym of each mutimap H Table post.
for (TagHeaderEntryHT::iterator tag2=tagHT.begin();
tag2 != tagHT.end();
++tag2){
- WriteEntry(tag2->second,_fp,type);
- if (itsTimeToWritePixels)
+ if ( type == gdcmACR ){
+ if ((*tag2->second).GetGroup() < 0x0008) continue; // ignore pure DICOM V3 groups
+ if ((*tag2->second).GetElement() %2) continue; // ignore shadow groups
+ if ((*tag2->second).GetVR() == "SQ" ) continue; // ignore Sequences
+ if ((*tag2->second).GetSQDepthLevel() != 0) continue; // Not only ignore the SQ element
+ }
+ if ( ! WriteEntry(tag2->second,_fp,type))
break;
}
}
/**
- * \ingroup gdcmParser
* \brief Swaps back the bytes of 4-byte long integer accordingly to
* processor order.
* @return The properly swaped 32 bits integer.
}
/**
- * \ingroup gdcmParser
* \brief Unswaps back the bytes of 4-byte long integer accordingly to
* processor order.
* @return The properly unswaped 32 bits integer.
}
/**
- * \ingroup gdcmParser
* \brief Swaps the bytes so they agree with the processor order
* @return The properly swaped 16 bits integer.
*/
}
/**
- * \ingroup gdcmParser
* \brief Unswaps the bytes so they agree with the processor order
* @return The properly unswaped 16 bits integer.
*/
//-----------------------------------------------------------------------------
// Private
/**
- * \ingroup gdcmParser
- * \brief Parses the header of the file but WITHOUT loading element values.
- * @return false if file is not ACR-NEMA / DICOM
+ * \brief Parses the header of the file and load element values.
+ * @return false if file is not ACR-NEMA / PAPYRUS / DICOM
*/
-bool gdcmParser::ParseHeader(bool exception_on_error) throw(gdcmFormatError) {
-
+bool gdcmParser::LoadHeaderEntries(bool exception_on_error) throw(gdcmFormatError) {
+ (void)exception_on_error;
rewind(fp);
if (!CheckSwap())
return false;
if ( (ignoreShadow==0) || (newHeaderEntry->GetGroup()%2) == 0) {
AddHeaderEntry(newHeaderEntry);
}
- }
- return true;
-}
-
-/**
- * \ingroup gdcmParser
- * \brief Loads the element values of all the Header Entries pointed in the
- * public Chained List.
- */
-void gdcmParser::LoadHeaderEntries(void) {
- rewind(fp);
- for (ListTag::iterator i = GetListEntry().begin();
- i != GetListEntry().end();
- ++i)
- {
- LoadHeaderEntry(*i);
- }
-
+ }
rewind(fp);
-
- // Load 'non string' values
+ // Be carefull : merging this two loops may cause troubles ...
+ for (ListTag::iterator i = GetListEntry().begin();
+ i != GetListEntry().end();
+ ++i)
+ {
+ LoadHeaderEntry(*i);
+ }
+ rewind(fp);
+
+ // Load 'non string' values
+
std::string PhotometricInterpretation = GetEntryByNumber(0x0028,0x0004);
if( PhotometricInterpretation == "PALETTE COLOR " ) {
LoadEntryVoidArea(0x0028,0x1200); // gray LUT
LoadEntryVoidArea(0x0028,0x1222); // Segmented Green Palette Color LUT Data
LoadEntryVoidArea(0x0028,0x1223); // Segmented Blue Palette Color LUT Data
}
- //FIXME : how to use it?
+ //FIXME later : how to use it?
LoadEntryVoidArea(0x0028,0x3006); //LUT Data (CTX dependent)
// --------------------------------------------------------------
std::string RecCode;
RecCode = GetEntryByNumber(0x0008, 0x0010); // recognition code
if (RecCode == "ACRNEMA_LIBIDO_1.1" ||
- RecCode == "CANRME_AILIBOD1_1." )
+ RecCode == "CANRME_AILIBOD1_1." ) // for brain-damaged softwares
+ // with "little-endian strings"
{
- filetype = ACR_LIBIDO;
+ filetype = gdcmACR_LIBIDO;
std::string rows = GetEntryByNumber(0x0028, 0x0010);
std::string columns = GetEntryByNumber(0x0028, 0x0011);
SetEntryByNumber(columns, 0x0028, 0x0010);
SetEntryByNumber(rows , 0x0028, 0x0011);
}
- // ----------------- End of Special Patch ----------------
+ // ----------------- End of Special Patch ----------------
+ return true;
}
/**
- * \ingroup gdcmParser
* \brief Loads the element content if its length doesn't exceed
* the value specified with gdcmParser::SetMaxSizeLoadEntry()
* @param Entry Header Entry (Dicom Element) to be dealt with
guint16 group = Entry->GetGroup();
std::string vr= Entry->GetVR();
guint32 length = Entry->GetLength();
- bool SkipLoad = false;
fseek(fp, (long)Entry->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 ) {
- Entry->SetLength(0);
+ if( group == 0xfffe ) {
Entry->SetValue("gdcm::Skipped");
return;
}
Entry->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 strings.
- // Elements with Value Multiplicity > 1
- // contain a set of integers (not a single one)
// Any compacter code suggested (?)
if ( IsHeaderEntryAnInteger(Entry) ) {
guint32 NewInt;
std::ostringstream s;
int nbInt;
+ // When short integer(s) are expected, read and convert the following
+ // n *two characters properly i.e. as short integers as opposed to strings.
+ // Elements with Value Multiplicity > 1
+ // contain a set of integers (not a single one)
if (vr == "US" || vr == "SS") {
nbInt = length / 2;
NewInt = ReadInt16();
}
}
}
+ // When integer(s) are expected, read and convert the following
+ // n * four characters properly i.e. as integers as opposed to strings.
+ // Elements with Value Multiplicity > 1
+ // contain a set of integers (not a single one)
else if (vr == "UL" || vr == "SL") {
nbInt = length / 4;
NewInt = ReadInt32();
}
/**
- * \ingroup gdcmParser
* \brief add a new Dicom Element pointer to
* the H Table and at the end of the chained List
* \warning push_bash in listEntries ONLY during ParseHeader
}
/**
- * \ingroup gdcmParser
* \brief Find the value Length of the passed Header Entry
* @param Entry Header Entry whose length of the value shall be loaded.
*/
void gdcmParser::FindHeaderEntryLength (gdcmHeaderEntry *Entry) {
guint16 element = Entry->GetElement();
- guint16 group = Entry->GetGroup();
+ //guint16 group = Entry->GetGroup(); //FIXME
std::string vr = Entry->GetVR();
guint16 length16;
+
- if( (element == NumPixel) && (group == GrPixel) )
- {
- dbg.SetDebug(GDCM_DEBUG);
- dbg.Verbose(2, "gdcmParser::FindLength: ",
- "we reached (GrPixel,NumPixel)");
- }
-
- if ( (filetype == ExplicitVR) && (! Entry->IsImplicitVR()) )
+ if ( (filetype == gdcmExplicitVR) && (! Entry->IsImplicitVR()) )
{
if ( (vr=="OB") || (vr=="OW") || (vr=="SQ") || (vr=="UN") )
{
//dbg.Verbose(0, "gdcmParser::FindLength",
// "Erroneous element length fixed.");
// Actually, length= 0xffff means that we deal with
- // Unknown Sequence Length
+ // Unfound Sequence Length
}
FixHeaderEntryFoundLength(Entry, (guint32)length16);
return;
}
/**
- * \ingroup gdcmParser
* \brief Find the Value Representation of the current Dicom Element.
* @param Entry
*/
void gdcmParser::FindHeaderEntryVR( gdcmHeaderEntry *Entry)
{
- if (filetype != ExplicitVR)
+ if (filetype != gdcmExplicitVR)
return;
char VR[3];
// is in explicit VR and try to fix things if it happens not to be
// the case.
- int lgrLue=fread (&VR, (size_t)2,(size_t)1, fp); // lgrLue not used
+ (void)fread (&VR, (size_t)2,(size_t)1, fp);
VR[2]=0;
if(!CheckHeaderEntryVR(Entry,VR))
{
}
/**
- * \ingroup gdcmParser
* \brief Check the correspondance between the VR of the header entry
* and the taken VR. If they are different, the header entry is
* updated with the new VR.
}
/**
- * \ingroup gdcmParser
* \brief Get the transformed value of the header entry. The VR value
* is used to define the transformation to operate on the value
* \warning NOT end user intended method !
std::ostringstream s;
int nbInt;
+ // When short integer(s) are expected, read and convert the following
+ // n * 2 bytes properly i.e. as a multivaluated strings
+ // (each single value is separated fromthe next one by '\'
+ // as usual for standard multivaluated filels
+ // Elements with Value Multiplicity > 1
+ // contain a set of short integers (not a single one)
+
if (vr == "US" || vr == "SS")
{
guint16 NewInt16;
}
}
+ // When integer(s) are expected, read and convert the following
+ // n * 4 bytes properly i.e. as a multivaluated strings
+ // (each single value is separated fromthe next one by '\'
+ // as usual for standard multivaluated filels
+ // Elements with Value Multiplicity > 1
+ // contain a set of integers (not a single one)
else if (vr == "UL" || vr == "SL")
{
guint32 NewInt32;
}
/**
- * \ingroup gdcmParser
* \brief Get the reverse transformed value of the header entry. The VR
* value is used to define the reverse transformation to operate on
* the value
}
/**
- * \ingroup gdcmParser
* \brief Skip a given Header Entry
* \warning NOT end user intended method !
* @param entry
}
/**
- * \ingroup gdcmParser
* \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 gdcmParser::FixHeaderEntryFoundLength(gdcmHeaderEntry *Entry, guint32 FoundLength)
{
- Entry->SetReadLength(FoundLength); // will be updated only if a bug is found
-
+ Entry->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 ...
+ // XMedCom did the trick to read some naughty GE images ...
if (FoundLength == 13) {
// The following 'if' will be removed when there is no more
// images on Creatis HDs with a 13 length for Manufacturer...
FoundLength =0; // ReadLength is unchanged
}
- // a SeQuence Element is beginning
- // fffe|e000 is just a marker, its length *should be* zero
+ // we found a 'delimiter' element
+ // fffe|xxxx is just a marker, we don't take its length into account
else if(Entry->GetGroup() == 0xfffe)
- {
+ {
// *normally, fffe|0000 doesn't exist !
if( Entry->GetElement() != 0x0000 ) // gdcm-MR-PHILIPS-16-Multi-Seq.dcm
- // causes extra troubles :-(
- FoundLength =0;
- }
+ // causes extra troubles :-(
+ FoundLength =0;
+ }
+
Entry->SetUsableLength(FoundLength);
}
/**
- * \ingroup gdcmParser
* \brief Apply some heuristics to predict whether the considered
* element value contains/represents an integer or not.
* @param Entry The element value on which to apply the predicate.
return false;
}
/**
- * \ingroup gdcmParser
* \brief Find the Length till the next sequence delimiter
* \warning NOT end user intended method !
* @return
}
/**
- * \ingroup gdcmParser
* \brief Reads a supposed to be 16 Bits integer
* (swaps it depending on processor endianity)
* @return read value
}
/**
- * \ingroup gdcmParser
* \brief Reads a supposed to be 32 Bits integer
* (swaps it depending on processor endianity)
* @return read value
}
/**
- * \ingroup gdcmParser
* \brief skips bytes inside the source file
* \warning NOT end user intended method !
* @return
}
/**
- * \ingroup gdcmParser
* \brief Loads all the needed Dictionaries
* \warning NOT end user intended method !
*/
}
/**
- * \ingroup gdcmParser
* \brief Discover what the swap code is (among little endian, big endian,
* bad little endian, bad big endian).
* sw is set
// Use gdcmParser::dicom_vr to test all the possibilities
// instead of just checking for UL, OB and UI !? group 0000
{
- filetype = ExplicitVR;
+ filetype = gdcmExplicitVR;
dbg.Verbose(1, "gdcmParser::CheckSwap:",
"explicit Value Representation");
}
else
{
- filetype = ImplicitVR;
+ filetype = gdcmImplicitVR;
dbg.Verbose(1, "gdcmParser::CheckSwap:",
"not an explicit Value Representation");
}
switch (s32) {
case 0x00040000 :
sw = 3412;
- filetype = ACR;
+ filetype = gdcmACR;
return true;
case 0x04000000 :
sw = 4321;
- filetype = ACR;
+ filetype = gdcmACR;
return true;
case 0x00000400 :
sw = 2143;
- filetype = ACR;
+ filetype = gdcmACR;
return true;
case 0x00000004 :
sw = 0;
- filetype = ACR;
+ filetype = gdcmACR;
return true;
default :
// the file IS NOT ACR-NEMA nor DICOM V3
// Find a trick to tell it the caller...
- s16 = *((guint16 *)(deb));
-
- switch (s16) {
- case 0x0002 :
- case 0x0004 :
- case 0x0008 :
- sw = 0;
- filetype = ACR;
- return true;
- case 0x0200 :
- case 0x0400 :
- case 0x0800 :
- sw = 4321;
- filetype = ACR;
- return true;
- default :
- dbg.Verbose(0, "gdcmParser::CheckSwap:",
- "ACR/NEMA unfound swap info (Really hopeless !)");
- filetype = Unknown;
- return false;
- }
+ s16 = *((guint16 *)(deb));
+
+ switch (s16) {
+ case 0x0002 :
+ case 0x0004 :
+ case 0x0008 :
+ sw = 0;
+ filetype = gdcmACR;
+ return true;
+ case 0x0200 :
+ case 0x0400 :
+ case 0x0800 :
+ sw = 4321;
+ filetype = gdcmACR;
+ return true;
+ default :
+ dbg.Verbose(0, "gdcmParser::CheckSwap:",
+ "ACR/NEMA unfound swap info (Really hopeless !)");
+ filetype = gdcmUnknown;
+ return false;
+ }
// Then the only info we have is the net2host one.
//if (! net2host )
}
/**
- * \ingroup gdcmParser
* \brief Restore the unproperly loaded values i.e. the group, the element
* and the dictionary entry depending on them.
*/
}
/**
- * \ingroup gdcmParser
* \brief during parsing, Header Elements too long are not loaded in memory
* @param NewSize
*/
/**
- * \ingroup gdcmParser
* \brief Header Elements too long will not be printed
- * \warning
- * \todo : not yet usable
- * (see MAX_SIZE_PRINT_ELEMENT_VALUE
- * in gdcmHeaderEntry gdcmLoadEntry)
- *
+ * \todo See comments of \ref gdcmParser::MAX_SIZE_PRINT_ELEMENT_VALUE
* @param NewSize
*/
void gdcmParser::SetMaxSizePrintEntry(long NewSize)
}
/**
- * \ingroup gdcmParser
* \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.
}
/**
- * \ingroup gdcmParser
* \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
}
/**
- * \ingroup gdcmParser
* \brief Read the next tag but WITHOUT loading it's value
* @return On succes the newly created HeaderEntry, NULL on failure.
*/
}
/**
- * \ingroup gdcmParser
* \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.
}
/**
- * \ingroup gdcmParser
* \brief Request a new virtual dict entry to the dict set
* @param group group of the underlying DictEntry
* @param element element of the underlying DictEntry
}
/**
- * \ingroup gdcmParser
* \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.
return NewEntry;
}
-// Never used; commented out, waiting for removal.
+/// \todo Never used; commented out, waiting for removal.
/**
- * \ingroup gdcmParser
* \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.
//}
/**
- * \ingroup gdcmParser
* \brief Generate a free TagKey i.e. a TagKey that is not present
* in the TagHt dictionary.
* @param group The generated tag must belong to this group.
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff