// 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"
// 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;
//-----------------------------------------------------------------------------
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
*/
}
/**
- * \ingroup gdcmParser
* \brief Canonical destructor.
*/
gdcmParser::~gdcmParser (void) {
//-----------------------------------------------------------------------------
// Print
/**
- * \ingroup gdcmParser
* \brief Prints the Header Entries (Dicom Elements)
* from the chained list
* @return
}
}
-/**
- * \ingroup gdcmParser
- * \brief Prints the Header Entries (Dicom Elements)
- * from the chained list
- * and skips the elements belonging to a 'no length' SeQuence
- * @return
- */
-void gdcmParser::PrintEntryNoSQ(std::ostream & os) {
- int countSQ = 0;
- for (ListTag::iterator i = listEntries.begin();
- i != listEntries.end();
- ++i)
- {
- if ( (*i)->GetVR() == "SQ"){
- countSQ ++;
- }
-
- if ( (*i)->GetGroup() == 0xfffe && (*i)->GetElement() == 0xe0dd){
- countSQ --;
- continue;
- }
-
- if (countSQ == 0) {
- (*i)->SetPrintLevel(printLevel);
- (*i)->Print(os);
- }
- }
-}
-
-/**
- * \ingroup gdcmParser
- * \brief Prints the Header Entries (Dicom Elements)
- * from the chained list
- * and indents the elements belonging to any SeQuence
- * \warning : will be removed
- * @return
- */
-void gdcmParser::PrintEntryNiceSQ(std::ostream & os) {
- pileElem pile[50]; // Hope embedded sequence depth is no more than 50
- int top =-1;
- int countSQ = 0;
- int currentParsedlength = 0;
- int totalElementlength;
- std::ostringstream tab;
- tab << " ";
-
- int DEBUG = 0; // Sorry; Dealing with e-film breaker images
- // will (certainly) cause a lot of troubles ...
- // I prefer keeping my 'trace' on .
-
- for (ListTag::iterator i = listEntries.begin();
- i != listEntries.end();
- ++i) {
- if ( (*i)->GetVR() == "SQ" && (*i)->GetReadLength() != 0) { // SQ found
- countSQ++;
- top ++;
- if ( top >= 50) {
- std::cout << "Kaie ! Kaie! SQ stack overflow" << std::endl;
- return;
- }
- if (DEBUG) cout << "\n >>>>> empile niveau " << top
- << "; Lgr SeQ: " << (*i)->GetReadLength()
- << "\n" <<endl;
-
- pile[top].totalSQlength = (*i)->GetReadLength();
- pile[top].alreadyParsedlength = 0;
- currentParsedlength = 0;
-
- } else { // non SQ found
-
- if (countSQ != 0) { // we are 'inside a SeQuence'
- if ( (*i)->GetGroup()==0xfffe && (*i)->GetElement()==0xe0dd){
- // we just found 'end of SeQuence'
-
- if (DEBUG)
- std::cout << "fffe,e0dd : depile" << std::endl;
- currentParsedlength += 8; // gr:2 elem:2 vr:2 lgt:2
- countSQ --;
- top --;
- pile[top].alreadyParsedlength += currentParsedlength;
- } else {
- // we are on a 'standard' elem
- // or a Zero-length SeQuence
-
- totalElementlength = (*i)->GetFullLength();
- currentParsedlength += totalElementlength;
- pile[top].alreadyParsedlength += totalElementlength;
-
- if (pile[top].totalSQlength == 0xffffffff) {
- if (DEBUG)
- std::cout << "totalSeQlength == 0xffffffff"
- << std::endl;
- } else {
- if (DEBUG)
- cout << "alrdyPseLgt:"
- << pile[top].alreadyParsedlength << " totSeQlgt: "
- << pile[top].totalSQlength << " curPseLgt: "
- << currentParsedlength
- << endl;
- while (pile[top].alreadyParsedlength==pile[top].totalSQlength) {
-
- if (DEBUG)
- std::cout << " \n<<<<<< On depile niveau " << top
- << "\n" << std::endl;
-
- currentParsedlength = pile[top].alreadyParsedlength;
- countSQ --;
- top --;
- if (top >=0) {
-
- pile[top].alreadyParsedlength += currentParsedlength +12;
- // 12 : length of 'SQ embedded' SQ element
- currentParsedlength += 8; // gr:2 elem:2 vr:2 lgt:2
-
- if (DEBUG)
- std::cout << pile[top].alreadyParsedlength << " "
- << pile[top].totalSQlength << " "
- << currentParsedlength
- << std::endl;
- }
- if (top == -1) {
- currentParsedlength = 0;
- break;
- }
- }
- }
- }
- } // end : 'inside a SeQuence'
- }
-
- if (countSQ != 0) {
- for (int i=0;i<countSQ;i++)
- os << tab.str();
- }
- (*i)->SetPrintLevel(printLevel);
- (*i)->Print(os);
-
- } // end for
-}
-
-
/**
* \brief Prints The Dict Entries of THE public Dicom Dictionary
}
/**
- * \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.
* \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 (?)
+ /// \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 == ImplicitVR)
{
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);
}
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
-
---> 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);
-*/
+/**
+ * \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 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
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)
{
}
/**
- * \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.
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();
if ((*tag2)->GetElement() %2)
// Ignore the "shadow" groups
continue;
- if ((*tag2)->GetVR() == "SQ" )
- // For the time being sequences are simply ignored
- // TODO : find a trick not to *skip* the SeQuences !
- continue;
- if ((*tag2)->GetGroup() == 0xfffe )
- // Ignore the documented delimiter
+ 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;
}
/**
- * \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.
tag2 != tagHT.end();
++tag2){
if ( type == ACR ){
- 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
- // TODO : find a trick to *skip* the SeQuences !
- // Not only ignore the SQ element
- // --> will be done with the next organization
- if ((*tag2->second).GetGroup() == 0xfffe ) continue; // ignore delimiters
+ 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())
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;
std::string rows = GetEntryByNumber(0x0028, 0x0010);
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
}
/**
- * \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.
*/
}
/**
- * \ingroup gdcmParser
* \brief Find the Value Representation of the current Dicom Element.
* @param Entry
*/
}
/**
- * \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 !
}
/**
- * \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.
}
/**
- * \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
}
/**
- * \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