-// gdcmHeader.cxx
+// gdcmParser.cxx
//-----------------------------------------------------------------------------
#include "gdcmParser.h"
#include "gdcmUtil.h"
#endif
# include <iomanip>
+#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"
+
+ // 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
+ //
+
+ // Other usefull abreviations :
+ // Radiographic view associated with Patient Position (0018,5100).
+ // Defined Terms:
+ //
+ // AP = Anterior/Posterior
+ // PA = Posterior/Anterior
+ // LL = Left Lateral
+ // RL = Right Lateral
+ // RLD = Right Lateral Decubitus
+ // LLD = Left Lateral Decubitus
+ // RLO = Right Lateral Oblique
+ // LLO = Left Lateral Oblique
+
//-----------------------------------------------------------------------------
// Refer to gdcmParser::CheckSwap()
const unsigned int gdcmParser::HEADER_LENGTH_TO_READ = 256;
-// Refer to gdcmParser::SetMaxSizeLoadElementValue()
+// 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;
+
//-----------------------------------------------------------------------------
// Constructor / Destructor
+
/**
* \ingroup gdcmParser
- * \brief
- * @param InFilename
- * @param exception_on_error
+ * \brief constructor
+ * @param inFilename
+ * @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,
* when they have an actual length
- *\TODO may be we need one more bool,
- * to allow skipping the private elements while parsing the header
- * in order to save space
+ * @param ignore_shadow to allow skipping the shadow elements,
+ * to save memory space.
+ * \warning The TRUE value for this param has to be used
+ * with a FALSE value for the 'enable_sequence' param.
+ * ('public elements' may be embedded in 'shadow Sequences')
*/
-gdcmParser::gdcmParser(const char *InFilename,
+gdcmParser::gdcmParser(const char *inFilename,
bool exception_on_error,
- bool enable_sequences )
-{
+ bool enable_sequences,
+ bool ignore_shadow) {
enableSequences=enable_sequences;
+ ignoreShadow =ignore_shadow;
SetMaxSizeLoadEntry(MAX_SIZE_LOAD_ELEMENT_VALUE);
- filename = InFilename;
+ filename = inFilename;
Initialise();
if ( !OpenFile(exception_on_error))
return;
-
- Parse();
- LoadHeaderEntries();
-
+ if (ParseHeader()) {
+ LoadHeaderEntries();
+ }
CloseFile();
wasUpdated = 0; // will be set to 1 if user adds an entry
- printLevel = 1; // 'Medium' header print by default
+ printLevel = 1; // 'Medium' print level by default
}
/**
* \ingroup gdcmParser
- * \brief
+ * \brief constructor
* @param exception_on_error
*/
-gdcmParser::gdcmParser(bool exception_on_error)
-{
- //enableSequences=0;
+gdcmParser::gdcmParser(bool exception_on_error) {
+ enableSequences=0;
SetMaxSizeLoadEntry(MAX_SIZE_LOAD_ELEMENT_VALUE);
Initialise();
wasUpdated = 0; // will be set to 1 if user adds an entry
- printLevel = 1; // 'Heavy' header print by default
+ printLevel = 1; // 'Medium' print level by default
}
/**
* \ingroup gdcmParser
* \brief Canonical destructor.
*/
-gdcmParser::~gdcmParser (void)
-{
+gdcmParser::~gdcmParser (void) {
RefPubDict = NULL;
RefShaDict = NULL;
}
* both from the H Table and the chained list
* @return
*/
-void gdcmParser::PrintEntry(std::ostream & os)
-{
+void gdcmParser::PrintEntry(std::ostream & os) {
std::ostringstream s;
- s << "------------ gdcmParser::Print, using listEntries ----------------" << std::endl;
for (ListTag::iterator i = listEntries.begin();
i != listEntries.end();
++i)
* \brief Prints The Dict Entries of THE public Dicom Dictionnry
* @return
*/
-void gdcmParser::PrintPubDict(std::ostream & os)
-{
+void gdcmParser::PrintPubDict(std::ostream & os) {
RefPubDict->Print(os);
}
/**
* \ingroup gdcmParser
- * \brief Prints The Dict Entries of the current shadow Dicom Dictionnry
+ * \brief Prints The Dict Entries of THE shadow Dicom Dictionnry
* @return
*/
-void gdcmParser::PrintShaDict(std::ostream & os)
-{
+void gdcmParser::PrintShaDict(std::ostream & os) {
RefShaDict->Print(os);
}
// Public
/**
* \ingroup gdcmParser
- * \brief Get THE public dictionary used
+ * \brief Get the public dictionary used
*/
-gdcmDict *gdcmParser::GetPubDict(void)
-{
+gdcmDict *gdcmParser::GetPubDict(void) {
return(RefPubDict);
}
/**
* \ingroup gdcmParser
- * \brief Get the current shadow dictionary
+ * \brief Get the shadow dictionary used
*/
-gdcmDict *gdcmParser::GetShaDict(void)
-{
+gdcmDict *gdcmParser::GetShaDict(void) {
return(RefShaDict);
}
* \brief Set the shadow dictionary used
* \param dict dictionary to use in shadow
*/
-bool gdcmParser::SetShaDict(gdcmDict *dict)
-{
+bool gdcmParser::SetShaDict(gdcmDict *dict){
RefShaDict=dict;
return(!RefShaDict);
}
* \brief Set the shadow dictionary used
* \param dictName name of the dictionary to use in shadow
*/
-bool gdcmParser::SetShaDict(DictKey dictName) {
+bool gdcmParser::SetShaDict(DictKey dictName){
RefShaDict=gdcmGlobal::GetDicts()->GetDict(dictName);
return(!RefShaDict);
}
* @return true when gdcmParser is the one of a reasonable Dicom/Acr file,
* false otherwise.
*/
-bool gdcmParser::IsReadable(void)
-{
- std::string res = GetEntryByNumber(0x0028, 0x0005);
- if ( res != GDCM_UNFOUND && atoi(res.c_str()) > 4 ) {
- //std::cout << "error on : 28 5" << std::endl;
- return false; // Image Dimensions
- }
-
- if ( !GetHeaderEntryByNumber(0x0028, 0x0100) ) {
- //std::cout << "error on : 28 100" << std::endl;
- return false; // "Bits Allocated"
- }
- if ( !GetHeaderEntryByNumber(0x0028, 0x0101) ){
- // std::cout << "error on : 28 101" << std::endl;
- return false; // "Bits Stored"
- }
- if ( !GetHeaderEntryByNumber(0x0028, 0x0102) ) {
- //std::cout << "error on : 28 102" << std::endl;
- return false; // "High Bit"
+bool gdcmParser::IsReadable(void) {
+ if(filetype==Unknown) {
+ return(false);
}
- if ( !GetHeaderEntryByNumber(0x0028, 0x0103) ) {
- //std::cout << "error on : 28 103" << std::endl;
- return false; // "Pixel Representation"
+ if(listEntries.size()<=0) {
+ return(false);
}
- return true;
+
+ return(true);
}
/**
* \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.
*/
bool gdcmParser::IsImplicitVRLittleEndianTransferSyntax(void) {
LoadHeaderEntrySafe(Element);
std::string Transfer = Element->GetValue();
- if ( Transfer == "1.2.840.10008.1.2" )
+ if ( Transfer == UI1_2_840_10008_1_2 )
return true;
return false;
}
* \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.
*/
-bool gdcmParser::IsExplicitVRLittleEndianTransferSyntax(void)
-{
+bool gdcmParser::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" )
+ if ( Transfer == UI1_2_840_10008_1_2_1 )
return true;
return false;
}
* \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.
*/
-bool gdcmParser::IsDeflatedExplicitVRLittleEndianTransferSyntax(void)
-{
+bool gdcmParser::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" )
+ if ( Transfer == UI1_2_840_10008_1_2_1_99 )
return true;
return false;
}
* \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.
*/
-bool gdcmParser::IsExplicitVRBigEndianTransferSyntax(void)
-{
+bool gdcmParser::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 !
+ if ( Transfer == UI1_2_840_10008_1_2_2 ) //1.2.2 ??? A verifier !
return true;
return false;
}
* \ingroup gdcmParser
* \brief returns the File Type
* (ACR, ACR_LIBIDO, ExplicitVR, ImplicitVR, Unknown)
- * @return
+ * @return the FileType code
*/
FileType gdcmParser::GetFileType(void) {
return(filetype);
return(fp);
fclose(fp);
- dbg.Verbose(0, "gdcmParser::gdcmParser not DICOM/ACR", filename.c_str());
+ dbg.Verbose(0, "gdcmParser::OpenFile not DICOM/ACR", filename.c_str());
}
else {
- dbg.Verbose(0, "gdcmParser::gdcmParser cannot open file", filename.c_str());
+ dbg.Verbose(0, "gdcmParser::OpenFile cannot open file", filename.c_str());
}
return(NULL);
}
* \brief closes the file
* @return TRUE if the close was successfull
*/
-bool gdcmParser::CloseFile(void)
-{
+bool gdcmParser::CloseFile(void) {
int closed = fclose(fp);
fp = (FILE *)0;
if (! closed)
/**
* \ingroup gdcmParser
- * \brief
+ * \brief writes on disc 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
* (ACR-NEMA, ExplicitVR, ImplicitVR)
* @return always "True" ?!
*/
-bool gdcmParser::Write(FILE *fp, FileType type)
-{
+bool gdcmParser::Write(FILE *fp, FileType type) {
// ==============
-// TODO The stuff has been rewritten using the chained list instead
+// 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
if (type == ImplicitVR)
{
- std::string implicitVRTransfertSyntax = "1.2.840.10008.1.2";
+ 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":
if (type == ExplicitVR)
{
- std::string explicitVRTransfertSyntax = "1.2.840.10008.1.2.1";
+ 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":
SetEntryLengthByNumber(20, 0x0002, 0x0010);
}
+/* TODO : rewrite later
if ( (type == ImplicitVR) || (type == ExplicitVR) )
UpdateGroupLength(false,type);
if ( type == ACR)
UpdateGroupLength(true,ACR);
+*/
- WriteEntries(type, fp);
+ 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
- * @param Elem
- * \return boolean
- */
-bool gdcmParser::ReplaceOrCreateByNumber(std::string Value,
- guint16 Group, guint16 Elem )
-{
- if (CheckIfEntryExistByNumber(Group, Elem) == 0) {
+ * @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(
+ std::string Value,
+ guint16 Group,
+ guint16 Elem ){
+ gdcmHeaderEntry* a;
+ a = GetHeaderEntryByNumber( Group, Elem);
+ if (a == NULL) {
gdcmHeaderEntry *a =NewHeaderEntryByNumber(Group, Elem);
if (a == NULL)
- return false;
+ return NULL;
AddHeaderEntry(a);
}
- SetEntryByNumber(Value, Group, Elem);
- return(true);
+ //SetEntryByNumber(Value, Group, Elem);
+ a->SetValue(Value);
+ return(a);
}
/**
* \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
+ * @param Group group of the Entry
+ * @param Elem element of the Entry
+ * \return pointer to the created Header Entry
+ * NULL if creation failed
*
*/
-bool gdcmParser::ReplaceOrCreateByNumber(char* Value, guint16 Group, guint16 Elem )
-{
+gdcmHeaderEntry * gdcmParser::ReplaceOrCreateByNumber(
+ char* Value,
+ guint16 Group,
+ guint16 Elem ) {
gdcmHeaderEntry* nvHeaderEntry=NewHeaderEntryByNumber(Group, Elem);
if(!nvHeaderEntry)
- return(false);
+ return(NULL);
AddHeaderEntry(nvHeaderEntry);
std::string v = Value;
SetEntryByNumber(v, Group, Elem);
- return(true);
+ return(nvHeaderEntry);
}
/**
* \ingroup gdcmParser
* \brief Set a new value if the invoked element exists
* Seems to be useless !!!
- * @param Value
- * @param Group
- * @param Elem
+ * @param Value new element value
+ * @param Group group of the Entry
+ * @param Elem element of the Entry
* \return boolean
*/
bool gdcmParser::ReplaceIfExistByNumber(char* Value, guint16 Group, guint16 Elem )
//-----------------------------------------------------------------------------
// Protected
+
/**
* \ingroup gdcmParser
* \brief Checks if a given Dicom Element exists
- * \ within the H table
+ * 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 gdcmParser::CheckIfEntryExistByNumber(guint16 group, guint16 element )
-{
+int gdcmParser::CheckIfEntryExistByNumber(guint16 group, guint16 element ) {
std::string key = gdcmDictEntry::TranslateToKey(group, element );
return (tagHT.count(key));
}
* \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 gdcmParser::GetEntryByName(std::string tagName)
-{
+std::string gdcmParser::GetEntryByName(std::string tagName) {
gdcmDictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName);
if( dictEntry == NULL)
return GDCM_UNFOUND;
* @return Corresponding element value representation when it exists,
* and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise.
*/
-std::string gdcmParser::GetEntryVRByName(std::string tagName)
-{
+std::string gdcmParser::GetEntryVRByName(std::string tagName) {
gdcmDictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName);
if( dictEntry == NULL)
return GDCM_UNFOUND;
return elem->GetVR();
}
+
/**
* \ingroup gdcmParser
* \brief Searches within Header Entries (Dicom Elements) parsed with
* @return Corresponding element value representation when it exists,
* and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise.
*/
-std::string gdcmParser::GetEntryByNumber(guint16 group, guint16 element)
-{
+std::string gdcmParser::GetEntryByNumber(guint16 group, guint16 element){
TagKey key = gdcmDictEntry::TranslateToKey(group, element);
if ( ! tagHT.count(key))
return GDCM_UNFOUND;
* @return Corresponding element value representation when it exists,
* and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise.
*/
-std::string gdcmParser::GetEntryVRByNumber(guint16 group, guint16 element)
-{
+std::string gdcmParser::GetEntryVRByNumber(guint16 group, guint16 element) {
gdcmHeaderEntry* elem = GetHeaderEntryByNumber(group, element);
if ( !elem )
return GDCM_UNFOUND;
return elem->GetVR();
}
+/**
+ * \ingroup gdcmParser
+ * \brief Searches within Header Entries (Dicom Elements) parsed with
+ * the public and private dictionaries
+ * for the value length of a given tag..
+ * @param group Group of the searched tag.
+ * @param element Element of the searched tag.
+ * @return Corresponding element length; -2 if not found
+ */
+int gdcmParser::GetEntryLengthByNumber(guint16 group, guint16 element) {
+ gdcmHeaderEntry* elem = GetHeaderEntryByNumber(group, element);
+ if ( !elem )
+ return -2;
+ return elem->GetLength();
+}
/**
* \ingroup gdcmParser
* \brief Sets the value (string) of the Header Entry (Dicom Element)
* @param tagName name of the searched Dicom Element.
* @return true when found
*/
-bool gdcmParser::SetEntryByName(std::string content,std::string tagName)
-{
+bool gdcmParser::SetEntryByName(std::string content,std::string tagName) {
gdcmDictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName);
if( dictEntry == NULL)
return false;
if ( ! tagHT.count(key))
return false;
int l = content.length();
- if(l%2) // Odd length are padded with a space (020H).
+ if(l%2) // Non even length are padded with a space (020H).
{
l++;
content = content + '\0';
}
- //tagHT[key]->SetValue(content);
gdcmHeaderEntry * a;
IterHT p;
TagHeaderEntryHT::iterator p2;
a-> SetValue(content);
- //std::string vr = tagHT[key]->GetVR();
std::string vr = a->GetVR();
guint32 lgr;
else
lgr = l;
- //tagHT[key]->SetLength(lgr);
a->SetLength(lgr);
return true;
}
* 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 entry to modify
- * @param element element of the Entry to modify
- * @return 1 on success, 0 otherwise.
+ * @param l new length to substitute with
+ * @param group group of the Entry to modify
+ * @param element element of the Entry to modify
+ * @return true on success, false otherwise.
*/
-
-bool gdcmParser::SetEntryLengthByNumber(guint32 length,
- guint16 group, guint16 element)
+bool gdcmParser::SetEntryLengthByNumber(guint32 l,
+ 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);
+ if (l%2) l++; // length must be even
+ ( ((tagHT.equal_range(key)).first)->second )->SetLength(l);
return true ;
}
/**
* \ingroup gdcmParser
* \brief Gets (from Header) the offset of a 'non string' element value
- * \ (LoadElementValues has already be executed)
- * @param Group
- * @param Elem
+ * (LoadElementValues has already be executed)
+ * @param Group group of the Entry
+ * @param Elem element of the Entry
* @return File Offset of the Element Value
*/
size_t gdcmParser::GetEntryOffsetByNumber(guint16 Group, guint16 Elem)
/**
* \ingroup gdcmParser
* \brief Gets (from Header) a 'non string' element value
- * \ (LoadElementValues has already be executed)
- * @param Group
- * @param Elem
+ * (LoadElementValues has already be executed)
+ * @param Group group of the Entry
+ * @param Elem element of the Entry
* @return Pointer to the 'non string' area
*/
void * gdcmParser::GetEntryVoidAreaByNumber(guint16 Group, guint16 Elem)
* \ingroup gdcmParser
* \brief Loads (from disk) the element content
* when a string is not suitable
+ * @param Group group of the Entry
+ * @param Elem element of the Entry
*/
void *gdcmParser::LoadEntryVoidArea(guint16 Group, guint16 Elem)
{
free(a);
return NULL;
}
+
return a;
}
* @param element Element number of the searched Dicom Element
* @return
*/
-bool gdcmParser::SetEntryVoidAreaByNumber(void * area,guint16 group, guint16 element)
+bool gdcmParser::SetEntryVoidAreaByNumber(void * area,
+ guint16 group,
+ guint16 element)
{
TagKey key = gdcmDictEntry::TranslateToKey(group, element);
if ( ! tagHT.count(key))
return false;
- //tagHT[key]->SetVoidArea(area);
( ((tagHT.equal_range(key)).first)->second )->SetVoidArea(area);
return true;
}
/**
* \ingroup gdcmParser
- * \brief Update the entries with the shadow dictionary. Only odd entries are
- * analized
+ * \brief Update the entries with the shadow dictionary.
+ * Only non even entries are analyzed
*/
-void gdcmParser::UpdateShaEntries(void)
-{
+void gdcmParser::UpdateShaEntries(void) {
gdcmDictEntry *entry;
std::string vr;
vr=(*it)->GetVR();
(*it)->SetValue(GetHeaderEntryUnvalue(*it));
- if(entry)
- {
+ if(entry){
// Set the new entry and the new value
(*it)->SetDictEntry(entry);
CheckHeaderEntryVR(*it,vr);
* @return Corresponding Dicom Element when it exists, and NULL
* otherwise.
*/
- gdcmHeaderEntry *gdcmParser::GetHeaderEntryByName(std::string tagName)
- {
+ gdcmHeaderEntry *gdcmParser::GetHeaderEntryByName(std::string tagName) {
gdcmDictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName);
if( dictEntry == NULL)
return NULL;
/**
* \ingroup gdcmParser
* \brief retrieves a Dicom Element (the first one) using (group, element)
- * \ warning (group, element) IS NOT an identifier inside the Dicom Header
+ * \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)
*/
gdcmHeaderEntry* gdcmParser::GetHeaderEntryByNumber(guint16 group, guint16 element)
{
- TagKey key = gdcmDictEntry::TranslateToKey(group, element);
+ TagKey key = gdcmDictEntry::TranslateToKey(group, element);
if ( ! tagHT.count(key))
return NULL;
return tagHT.find(key)->second;
}
+/**
+ * \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.
+ * @return a range (i.e.pair<,>) containing all elements whose key is group|element)
+ */
+
+IterHT gdcmParser::GetHeaderEntrySameNumber(guint16 group, guint16 element){
+ TagKey key = gdcmDictEntry::TranslateToKey(group, element);
+ return (tagHT.equal_range(key));
+}
+
/**
* \ingroup gdcmParser
* \brief Loads the element while preserving the current
* @param entry Header Entry whose value shall be loaded.
* @return
*/
-void gdcmParser::LoadHeaderEntrySafe(gdcmHeaderEntry * entry)
-{
+void gdcmParser::LoadHeaderEntrySafe(gdcmHeaderEntry * entry) {
long PositionOnEntry = ftell(fp);
LoadHeaderEntry(entry);
fseek(fp, PositionOnEntry, SEEK_SET);
* @param SkipSequence TRUE if we don't want to write Sequences (ACR-NEMA Files)
* @param type Type of the File (ExplicitVR,ImplicitVR, ACR, ...)
*/
-void gdcmParser::UpdateGroupLength(bool SkipSequence, FileType type)
-{
+void gdcmParser::UpdateGroupLength(bool SkipSequence, FileType type) {
guint16 gr, el;
std::string vr;
/**
* \ingroup gdcmParser
* \brief writes on disc according to the requested format
- * \ (ACR-NEMA, ExplicitVR, ImplicitVR) the image
- * \ warning does NOT add the missing elements in the header :
- * \ it's up to the user doing it !
- * \ (function CheckHeaderCoherence to be written)
+ * (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
*/
-void gdcmParser::WriteEntries(FileType type, FILE * _fp)
+void gdcmParser::WriteEntry(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;
-
- // uses now listEntries to iterate, not TagHt!
- //
- // pb : gdcmParser.Add does NOT update listEntries
- // TODO : find a trick (in STL?) to do it, at low cost !
void *ptr;
-
+ int ff=0xffffffff;
// TODO (?) tester les echecs en ecriture (apres chaque fwrite)
-
- for (ListTag::iterator tag2=listEntries.begin();
- tag2 != listEntries.end();
- ++tag2)
- {
- gr = (*tag2)->GetGroup();
- el = (*tag2)->GetElement();
- lgr = (*tag2)->GetLength();
- val = (*tag2)->GetValue().c_str();
- vr = (*tag2)->GetVR();
+ 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);
+ }
if ( type == ACR )
{
- if (gr < 0x0008) continue; // ignore pure DICOM V3 groups
- if (gr %2) continue; // ignore shadow groups
- if (vr == "SQ" ) continue; // ignore Sequences
+ 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 ) continue; // ignore delimiters
+ 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) && (gr <= 0x0002) )
- {
+
+ if ( (type == ExplicitVR) || (type == DICOMDIR) ) {
// EXPLICIT VR
guint16 z=0, shortLgr;
- fwrite (vr.c_str(),(size_t)2 ,(size_t)1 ,_fp);
-
- if ( (vr == "OB") || (vr == "OW") || (vr == "SQ") )
- {
- fwrite ( &z, (size_t)2 ,(size_t)1 ,_fp);
- fwrite ( &lgr,(size_t)4 ,(size_t)1 ,_fp);
-
- }
- else
- {
- shortLgr=lgr;
+
+ if (gr == 0xfffe) { // NO Value Representation for 'delimiters'
+ // no length : write ffffffff
+
+ // special patch to make some MR PHILIPS
+ if (el == 0x0000) return; // 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 !
+
+ fwrite (&ff,(size_t)4 ,(size_t)1 ,_fp);
+ return; // NO value for 'delimiters'
+ }
+
+ shortLgr=lgr;
+ if (vr == "unkn") { // Unknown was 'written'
+ // deal with Little Endian
fwrite ( &shortLgr,(size_t)2 ,(size_t)1 ,_fp);
+ fwrite ( &z, (size_t)2 ,(size_t)1 ,_fp);
+ } else {
+ fwrite (vr.c_str(),(size_t)2 ,(size_t)1 ,_fp);
+ if ( (vr == "OB") || (vr == "OW") || (vr == "SQ") ){
+ fwrite ( &z, (size_t)2 ,(size_t)1 ,_fp);
+ fwrite ( &lgr,(size_t)4 ,(size_t)1 ,_fp);
+ } else {
+ fwrite ( &shortLgr,(size_t)2 ,(size_t)1 ,_fp);
+ }
}
}
- else // IMPLICIT VR
+ else // IMPLICIT VR
{
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
+
+ if (voidArea != NULL)
+ { // there is a 'non string' LUT, overlay, etc
+ fwrite ( voidArea,(size_t)lgr ,(size_t)1 ,_fp); // Elem value
+ return;
+ }
+
if (vr == "US" || vr == "SS")
{
tokens.erase(tokens.begin(),tokens.end()); // clean any previous value
- Tokenize ((*tag2)->GetValue(), tokens, "\\");
+ Tokenize (tag->GetValue(), tokens, "\\");
for (unsigned int i=0; i<tokens.size();i++)
{
val_uint16 = atoi(tokens[i].c_str());
fwrite ( ptr,(size_t)2 ,(size_t)1 ,_fp);
}
tokens.clear();
- continue;
+ return;
}
if (vr == "UL" || vr == "SL")
{
tokens.erase(tokens.begin(),tokens.end()); // clean any previous value
- Tokenize ((*tag2)->GetValue(), tokens, "\\");
+ Tokenize (tag->GetValue(), tokens, "\\");
for (unsigned int i=0; i<tokens.size();i++)
{
val_uint32 = atoi(tokens[i].c_str());
fwrite ( ptr,(size_t)4 ,(size_t)1 ,_fp);
}
tokens.clear();
- continue;
- }
+ return;
+ }
+
// Pixels are never loaded in the element !
- if ((gr == 0x7fe0) && (el == 0x0010) )
- break;
-
+ // 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
+}
+
+/**
+ * \ingroup gdcmParser
+ * \brief writes on disc according to the requested format
+ * (ACR-NEMA, ExplicitVR, ImplicitVR) the image
+ * using the Chained List
+ * \warning does NOT add the missing elements in the header :
+ * it's up to the user doing it !
+ * (function CheckHeaderCoherence to be written)
+ * \warning DON'T try, right now, to write a DICOM image
+ * from an ACR Header (meta elements will be missing!)
+ * \sa WriteEntriesDeprecated (Special temporary method for Theralys)
+ * @param type type of the File to be written
+ * (ACR-NEMA, ExplicitVR, ImplicitVR)
+ * @param _fp already open file pointer
+ */
+
+void gdcmParser::WriteEntries(FILE *_fp,FileType type)
+{
+ // TODO (?) tester les echecs en ecriture (apres chaque fwrite)
+
+ for (ListTag::iterator tag2=listEntries.begin();
+ tag2 != listEntries.end();
+ ++tag2)
+ {
+ WriteEntry(*tag2,_fp,type);
+ if (itsTimeToWritePixels)
+ break;
+ }
+}
+
+/**
+ * \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.
+ * \warning Uses the H Table, instead of the Chained List
+ * in order to be compliant with the old way to proceed
+ * (added elements taken in to account)
+ * Only THERALYS, during a transitory phase is supposed
+ * to use this method !!!
+ * \warning DON'T try, right now, to write a DICOM image
+ * from an ACR Header (meta elements will be missing!)
+ * \sa WriteEntries
+ * @param _fp already open file pointer
+ * @param type type of the File to be written
+ * (ACR-NEMA, ExplicitVR, ImplicitVR)
+ */
+void gdcmParser::WriteEntriesDeprecated(FILE *_fp,FileType type) {
+
+ // restent a tester les echecs en ecriture (apres chaque fwrite)
+
+ for (TagHeaderEntryHT::iterator tag2=tagHT.begin();
+ tag2 != tagHT.end();
+ ++tag2){
+ WriteEntry(tag2->second,_fp,type);
+ if (itsTimeToWritePixels)
+ break;
}
}
* processor order.
* @return The properly swaped 32 bits integer.
*/
-guint32 gdcmParser::SwapLong(guint32 a)
-{
- switch (sw)
- {
+guint32 gdcmParser::SwapLong(guint32 a) {
+ switch (sw) {
case 0 :
break;
case 4321 :
* processor order.
* @return The properly unswaped 32 bits integer.
*/
-guint32 gdcmParser::UnswapLong(guint32 a)
-{
+guint32 gdcmParser::UnswapLong(guint32 a) {
return (SwapLong(a));
}
* \brief Swaps the bytes so they agree with the processor order
* @return The properly swaped 16 bits integer.
*/
-guint16 gdcmParser::SwapShort(guint16 a)
-{
+guint16 gdcmParser::SwapShort(guint16 a) {
if ( (sw==4321) || (sw==2143) )
a =(((a<<8) & 0x0ff00) | ((a>>8)&0x00ff));
return (a);
* \brief Unswaps the bytes so they agree with the processor order
* @return The properly unswaped 16 bits integer.
*/
-guint16 gdcmParser::UnswapShort(guint16 a)
-{
+guint16 gdcmParser::UnswapShort(guint16 a) {
return (SwapShort(a));
}
/**
* \ingroup gdcmParser
* \brief Parses the header of the file but WITHOUT loading element values.
+ * @return false if file is not ACR-NEMA / DICOM
*/
-void gdcmParser::Parse(bool exception_on_error) throw(gdcmFormatError)
-{
- gdcmHeaderEntry *newHeaderEntry = (gdcmHeaderEntry *)0;
+bool gdcmParser::ParseHeader(bool exception_on_error) throw(gdcmFormatError) {
rewind(fp);
- CheckSwap();
- while ( (newHeaderEntry = ReadNextHeaderEntry()) )
- {
- SkipHeaderEntry(newHeaderEntry);
- AddHeaderEntry(newHeaderEntry);
+ if (!CheckSwap())
+ return false;
+
+ gdcmHeaderEntry *newHeaderEntry = (gdcmHeaderEntry *)0;
+ while ( (newHeaderEntry = ReadNextHeaderEntry()) ) {
+ SkipHeaderEntry(newHeaderEntry);
+ if ( (ignoreShadow==0) || (newHeaderEntry->GetGroup()%2) == 0) {
+ AddHeaderEntry(newHeaderEntry);
+ }
}
+ return true;
}
/**
* \brief Loads the element values of all the Header Entries pointed in the
* public Chained List.
*/
-void gdcmParser::LoadHeaderEntries(void)
-{
+void gdcmParser::LoadHeaderEntries(void) {
rewind(fp);
for (ListTag::iterator i = GetListEntry().begin();
i != GetListEntry().end();
// Load 'non string' values
std::string PhotometricInterpretation = GetEntryByNumber(0x0028,0x0004);
- if( PhotometricInterpretation == "PALETTE COLOR " )
- {
+ if( PhotometricInterpretation == "PALETTE COLOR " ) {
LoadEntryVoidArea(0x0028,0x1200); // gray LUT
LoadEntryVoidArea(0x0028,0x1201); // R LUT
LoadEntryVoidArea(0x0028,0x1202); // G 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
- }
-
+ }
+ //FIXME : how to use it?
+ LoadEntryVoidArea(0x0028,0x3006); //LUT Data (CTX dependent)
+
// --------------------------------------------------------------
// Special Patch to allow gdcm to read ACR-LibIDO formated images
//
/**
* \ingroup gdcmParser
- * \brief Loads the element content if it's length is not bigger
- * than the value specified with
- * gdcmParser::SetMaxSizeLoadEntry()
+ * \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
*/
-void gdcmParser::LoadHeaderEntry(gdcmHeaderEntry *Entry)
-{
+void gdcmParser::LoadHeaderEntry(gdcmHeaderEntry *Entry) {
size_t item_read;
guint16 group = Entry->GetGroup();
std::string vr= Entry->GetVR();
if( group == 0xfffe )
SkipLoad = true;
- if ( SkipLoad )
- {
+ if ( SkipLoad ) {
Entry->SetLength(0);
Entry->SetValue("gdcm::Skipped");
return;
}
// When the length is zero things are easy:
- if ( length == 0 )
- {
+ if ( length == 0 ) {
Entry->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 > MaxSizeLoadEntry)
- {
+ if (length > MaxSizeLoadEntry) {
std::ostringstream s;
s << "gdcm::NotLoaded.";
s << " Address:" << (long)Entry->GetOffset();
// 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.
+ // 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) )
- {
+ if ( IsHeaderEntryAnInteger(Entry) ) {
guint32 NewInt;
std::ostringstream s;
int nbInt;
- if (vr == "US" || vr == "SS")
- {
+ if (vr == "US" || vr == "SS") {
nbInt = length / 2;
NewInt = ReadInt16();
s << NewInt;
- if (nbInt > 1)
- {
- for (int i=1; i < nbInt; i++)
- {
+ if (nbInt > 1){
+ for (int i=1; i < nbInt; i++) {
s << '\\';
NewInt = ReadInt16();
s << NewInt;
}
- }
-
+ }
}
- else if (vr == "UL" || vr == "SL")
- {
+ else if (vr == "UL" || vr == "SL") {
nbInt = length / 4;
NewInt = ReadInt32();
s << NewInt;
- if (nbInt > 1)
- {
- for (int i=1; i < nbInt; i++)
- {
+ 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
+
Entry->SetValue(s.str());
return;
}
// We need an additional byte for storing \0 that is not on disk
std::string NewValue(length,0);
item_read = fread(&(NewValue[0]), (size_t)length, (size_t)1, fp);
- if ( item_read != 1 )
- {
+ if ( item_read != 1 ) {
dbg.Verbose(1, "gdcmParser::LoadElementValue","unread element value");
Entry->SetValue("gdcm::UnRead");
return;
}
- Entry->SetValue(NewValue);
+
+ if( (vr == "UI") ) // Because of correspondance with the VR dic
+ Entry->SetValue(NewValue.c_str()); // ??? JPR ???
+ else
+ Entry->SetValue(NewValue);
}
/**
* \ingroup gdcmParser
* \brief add a new Dicom Element pointer to
- * the H Table and to the chained List
+ * the H Table and at the end of the chained List
* \warning push_bash in listEntries ONLY during ParseHeader
* \todo something to allow further Elements addition,
- * \ when position to be taken care of
+ * (at their right place in the chained list)
+ * when position to be taken care of
* @param newHeaderEntry
*/
-void gdcmParser::AddHeaderEntry(gdcmHeaderEntry *newHeaderEntry)
-{
+void gdcmParser::AddHeaderEntry(gdcmHeaderEntry *newHeaderEntry) {
tagHT.insert( PairHT( newHeaderEntry->GetKey(),newHeaderEntry) );
listEntries.push_back(newHeaderEntry);
wasUpdated = 1;
/**
* \ingroup gdcmParser
- * \brief
- * @param Entry Header Entry whose length of the value shall be loaded.
-
- * @return
+ * \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)
- {
+ void gdcmParser::FindHeaderEntryLength (gdcmHeaderEntry *Entry) {
guint16 element = Entry->GetElement();
guint16 group = Entry->GetGroup();
std::string vr = Entry->GetVR();
guint16 length16;
- if( (element == 0x0010) && (group == 0x7fe0) )
+
+ if( (element == NumPixel) && (group == GrPixel) )
{
- dbg.SetDebug(-1);
+ dbg.SetDebug(GDCM_DEBUG);
dbg.Verbose(2, "gdcmParser::FindLength: ",
- "we reached 7fe0 0010");
+ "we reached (GrPixel,NumPixel)");
}
if ( (filetype == ExplicitVR) && (! Entry->IsImplicitVR()) )
// Actually, length= 0xffff means that we deal with
// Unknown Sequence Length
}
-
FixHeaderEntryFoundLength(Entry, (guint32)length16);
return;
}
else
{
- // Either implicit VR or a non DICOM conformal (see not below) explicit
+ // Either implicit VR or a non DICOM conformal (see note 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(Entry, ReadInt32());
return;
}
return;
char VR[3];
- int lgrLue;
long PositionOnEntry = ftell(fp);
// Warning: we believe this is explicit VR (Value Representation) because
// is in explicit VR and try to fix things if it happens not to be
// the case.
- lgrLue=fread (&VR, (size_t)2,(size_t)1, fp);
+ int lgrLue=fread (&VR, (size_t)2,(size_t)1, fp); // lgrLue not used
VR[2]=0;
if(!CheckHeaderEntryVR(Entry,VR))
{
* \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.
- * @param Entry
- * @param VR
+ * @param Entry Header Entry to check
+ * @param vr Dicom Value Representation
* @return false if the VR is incorrect of if the VR isn't referenced
* otherwise, it returns true
*/
sprintf(msg,"Falsely explicit vr file (%04x,%04x)\n",
Entry->GetGroup(),Entry->GetElement());
dbg.Verbose(1, "gdcmParser::FindVR: ",msg);
-
+ if (Entry->GetGroup()%2 && Entry->GetElement() == 0x0000) { // Group length is UL !
+ gdcmDictEntry* NewEntry = NewVirtualDictEntry(
+ Entry->GetGroup(),Entry->GetElement(),
+ "UL","FIXME","Group Length");
+ Entry->SetDictEntry(NewEntry);
+ }
return(false);
}
if ( Entry->IsVRUnknown() )
{
// When not a dictionary entry, we can safely overwrite the VR.
- Entry->SetVR(vr);
+ if (Entry->GetElement() == 0x0000) { // Group length is UL !
+ Entry->SetVR("UL");
+ } else {
+ Entry->SetVR(vr);
+ }
}
else if ( Entry->GetVR() != vr )
{
{
if(i!=0)
s << '\\';
- NewInt32=(val[4*i+0]&0xFF)+((val[4*i+1]&0xFF)<<8)+((val[4*i+2]&0xFF)<<16)+((val[4*i+3]&0xFF)<<24);
+ NewInt32= (val[4*i+0]&0xFF)+((val[4*i+1]&0xFF)<<8)+
+ ((val[4*i+2]&0xFF)<<16)+((val[4*i+3]&0xFF)<<24);
NewInt32=SwapLong(NewInt32);
s << NewInt32;
}
}
-
#ifdef GDCM_NO_ANSI_STRING_STREAM
s << std::ends; // to avoid oddities on Solaris
#endif //GDCM_NO_ANSI_STRING_STREAM
std::string vr=Entry->GetVR();
std::ostringstream s;
std::vector<std::string> tokens;
- unsigned char *ptr;
if (vr == "US" || vr == "SS")
{
{
Entry->SetReadLength(FoundLength); // will be updated only if a bug is found
- if ( FoundLength == 0xffffffff)
- {
+ if ( FoundLength == 0xffffffff) {
FoundLength = 0;
}
+
+ guint16 gr =Entry->GetGroup();
+ guint16 el =Entry->GetElement();
+
+ if (FoundLength%2) {
+ std::ostringstream s;
+ s << "Warning : Tag with uneven length " << FoundLength
+ << " in x(" << std::hex << gr << "," << el <<")" << std::dec;
+ dbg.Verbose(0,s.str().c_str());
+ }
// Sorry for the patch!
// XMedCom did the trick to read some nasty GE images ...
- else if (FoundLength == 13)
- {
+ 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 ( (Entry->GetGroup() != 0x0008) ||
- ( (Entry->GetElement() != 0x0070) && (Entry->GetElement() != 0x0080) ) ) {
+ ( (Entry->GetElement() != 0x0070) && (Entry->GetElement() != 0x0080) ) ){
// end of remove area
FoundLength =10;
Entry->SetReadLength(10); // a bug is to be fixed
// to fix some garbage 'Leonardo' Siemens images
// May be commented out to avoid overhead
else if ( (Entry->GetGroup() == 0x0009) &&
- ( (Entry->GetElement() == 0x1113) || (Entry->GetElement() == 0x1114) ) )
- {
+ ( (Entry->GetElement() == 0x1113) || (Entry->GetElement() == 0x1114) ) ){
FoundLength =4;
Entry->SetReadLength(4); // a bug is to be fixed
}
else if ( Entry->GetVR() == "SQ")
{
if (enableSequences) // only if the user does want to !
- FoundLength =0;
+ FoundLength =0; // ReadLength is unchanged
}
// 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 :-(
-
+ // fffe|e000 is just a marker, its length *should be* zero
else if(Entry->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 :-(
- }
-
+ // *normally, fffe|0000 doesn't exist !
+ if( Entry->GetElement() != 0x0000 ) // gdcm-MR-PHILIPS-16-Multi-Seq.dcm
+ // causes extra troubles :-(
+ FoundLength =0;
+ }
Entry->SetUsableLength(FoundLength);
}
/**
* \ingroup gdcmParser
- * \brief Apply some heuristics to predict wether the considered
+ * \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 The result of the heuristical predicate.
*/
-bool gdcmParser::IsHeaderEntryAnInteger(gdcmHeaderEntry *Entry)
-{
+bool gdcmParser::IsHeaderEntryAnInteger(gdcmHeaderEntry *Entry) {
guint16 element = Entry->GetElement();
guint16 group = Entry->GetGroup();
std::string vr = Entry->GetVR();
guint32 length = Entry->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.
else
{
std::ostringstream s;
- s << "Erroneous Group Length element length on :" \
- << std::hex << group << " , " << element;
- dbg.Error("gdcmParser::IsAnInteger",
- s.str().c_str());
+ int filePosition = ftell(fp);
+ s << "Erroneous Group Length element length on : (" \
+ << std::hex << group << " , " << element
+ << ") -before- position x(" << filePosition << ")"
+ << "lgt : " << length;
+ // These 2 lines commented out : a *very dirty* patch
+ // to go on PrintHeader'ing gdcm-MR-PHILIPS-16-Multi-Seq.dcm.
+ // have a glance at offset x(8336) ...
+ // For *regular* headers, the test is useless..
+ // lets's print a warning message and go on,
+ // instead of giving up with an error message
+
+ //std::cout << s.str().c_str() << std::endl;
+
+ // dbg.Error("gdcmParser::IsHeaderEntryAnInteger",
+ // s.str().c_str());
}
}
if ( (vr == "UL") || (vr == "US") || (vr == "SL") || (vr == "SS") )
return false;
}
-
/**
* \ingroup gdcmParser
- * \brief
- *
+ * \brief Find the Length till the next sequence delimiter
+ * \warning NOT end user intended method !
* @return
*/
- guint32 gdcmParser::FindHeaderEntryLengthOB(void)
- {
+
+ guint32 gdcmParser::FindHeaderEntryLengthOB(void) {
// See PS 3.5-2001, section A.4 p. 49 on encapsulation of encoded pixel data.
guint16 g;
guint16 n;
/**
* \ingroup gdcmParser
* \brief Reads a supposed to be 16 Bits integer
- * \ (swaps it depending on processor endianity)
- *
- * @return integer acts as a boolean
+ * (swaps it depending on processor endianity)
+ * @return read value
*/
-guint16 gdcmParser::ReadInt16(void)
-{
+guint16 gdcmParser::ReadInt16(void) {
guint16 g;
size_t item_read;
item_read = fread (&g, (size_t)2,(size_t)1, fp);
- if ( item_read != 1 )
- {
+ if ( item_read != 1 ) {
if(ferror(fp))
dbg.Verbose(0, "gdcmParser::ReadInt16", " File Error");
errno = 1;
return 0;
}
errno = 0;
- g = SwapShort(g);
+ g = SwapShort(g);
return g;
}
/**
* \ingroup gdcmParser
* \brief Reads a supposed to be 32 Bits integer
- * \ (swaps it depending on processor endianity)
- *
- * @return
+ * (swaps it depending on processor endianity)
+ * @return read value
*/
-guint32 gdcmParser::ReadInt32(void)
-{
+guint32 gdcmParser::ReadInt32(void) {
guint32 g;
size_t item_read;
item_read = fread (&g, (size_t)4,(size_t)1, fp);
- if ( item_read != 1 )
- {
+ if ( item_read != 1 ) {
if(ferror(fp))
dbg.Verbose(0, "gdcmParser::ReadInt32", " File Error");
errno = 1;
/**
* \ingroup gdcmParser
- * \brief
- *
+ * \brief skips bytes inside the source file
+ * \warning NOT end user intended method !
* @return
*/
-void gdcmParser::SkipBytes(guint32 NBytes)
-{
+void gdcmParser::SkipBytes(guint32 NBytes) {
//FIXME don't dump the returned value
(void)fseek(fp, (long)NBytes, SEEK_CUR);
}
/**
* \ingroup gdcmParser
- * \brief
+ * \brief Loads all the needed Dictionaries
+ * \warning NOT end user intended method !
*/
void gdcmParser::Initialise(void)
{
* \ingroup gdcmParser
* \brief Discover what the swap code is (among little endian, big endian,
* bad little endian, bad big endian).
- *
+ * sw is set
+ * @return false when we are absolutely sure
+ * it's neither ACR-NEMA nor DICOM
+ * true when we hope ours assuptions are OK
*/
-void gdcmParser::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
- //
+bool gdcmParser::CheckSwap() {
// 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
-
+ guint32 s32;
+ guint16 s16;
+
int lgrLue;
char *entCur;
char deb[HEADER_LENGTH_TO_READ];
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)
- {
+ if(memcmp(entCur, "DICM", (size_t)4) == 0) {
dbg.Verbose(1, "gdcmParser::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) -,
// * the 4 bytes of the first tag (0002, 0000),or (0002, 0001)
// i.e. a total of 136 bytes.
entCur = deb + 136;
+
+ // FIXME : FIXME:
+ // Sometimes (see : gdcmData/icone.dcm) group 0x0002 *is* Explicit VR,
+ // but elem 0002,0010 (Transfert Syntax) tells us the file is *Implicit* VR.
+ // -and it is !-
+
+ if( (memcmp(entCur, "UL", (size_t)2) == 0) ||
+ (memcmp(entCur, "OB", (size_t)2) == 0) ||
+ (memcmp(entCur, "UI", (size_t)2) == 0) ||
+ (memcmp(entCur, "CS", (size_t)2) == 0) ) // CS, to remove later
+ // when Write DCM *adds*
// FIXME
// Use gdcmParser::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) )
+ // instead of just checking for UL, OB and UI !? // group 0000
+
{
filetype = ExplicitVR;
dbg.Verbose(1, "gdcmParser::CheckSwap:",
dbg.Verbose(1, "gdcmParser::CheckSwap:",
"not an explicit Value Representation");
}
+
if (net2host)
{
sw = 4321;
// after the file preamble and the "DICM" string).
rewind(fp);
fseek (fp, 132L, SEEK_SET);
- return;
+ return true;
} // End of DicomV3
// Alas, this is not a DicomV3 file and whatever happens there is no file
// 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)
- {
+ s32 = *((guint32 *)(entCur));
+
+ switch (s32) {
case 0x00040000 :
sw = 3412;
filetype = ACR;
- return;
+ return true;
case 0x04000000 :
sw = 4321;
filetype = ACR;
- return;
+ return true;
case 0x00000400 :
sw = 2143;
filetype = ACR;
- return;
+ return true;
case 0x00000004 :
sw = 0;
filetype = ACR;
- return;
+ return true;
+ default :
+
+ // 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 check if this file wouldn't happen to be 'dirty' ACR/NEMA,
+ // i.e. the 'group length' element is not present :
+
+ // check the supposed to be 'group number'
+ // 0x0002 or 0x0004 or 0x0008
+ // to determine ' sw' value .
+ // Only 0 or 4321 will be possible
+ // (no oportunity to check for the formerly well known
+ // ACR-NEMA 'Bad Big Endian' or 'Bad Little Endian'
+ // if unsuccessfull (i.e. neither 0x0002 nor 0x0200 etc -4, 8-)
+ // 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 (time to raise bets)");
+ "ACR/NEMA unfound swap info (Really hopeless !)");
+ filetype = Unknown;
+ return false;
+ }
+
+ // Then the only info we have is the net2host one.
+ //if (! net2host )
+ // sw = 0;
+ //else
+ // sw = 4321;
+ //return;
}
-
- // 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 gdcmParser
- * \brief
+ * \brief Restore the unproperly loaded values i.e. the group, the element
+ * and the dictionary entry depending on them.
*/
void gdcmParser::SwitchSwapToBigEndian(void)
{
/**
* \ingroup gdcmParser
- * \brief
+ * \brief during parsing, Header Elements too long are not loaded in memory
* @param NewSize
- * @return
*/
void gdcmParser::SetMaxSizeLoadEntry(long NewSize)
{
MaxSizeLoadEntry = 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)
+ *
+ * @param NewSize
+ */
+void gdcmParser::SetMaxSizePrintEntry(long NewSize)
+{
+ if (NewSize < 0)
+ return;
+ if ((guint32)NewSize >= (guint32)0xffffffff)
+ {
+ MaxSizePrintEntry = 0xffffffff;
+ return;
+ }
+ MaxSizePrintEntry = NewSize;
+}
+
/**
* \ingroup gdcmParser
* \brief Searches both the public and the shadow dictionary (when they
* \brief Read the next tag but WITHOUT loading it's value
* @return On succes the newly created HeaderEntry, NULL on failure.
*/
-gdcmHeaderEntry *gdcmParser::ReadNextHeaderEntry(void)
-{
+gdcmHeaderEntry *gdcmParser::ReadNextHeaderEntry(void) {
guint16 g,n;
gdcmHeaderEntry *NewEntry;
-
g = ReadInt16();
n = ReadInt16();
if (errno == 1)
- // We reached the EOF (or an error occured) and header parsing
- // has to be considered as finished.
+ // We reached the EOF (or an error occured) therefore
+ // header parsing has to be considered as finished.
return (gdcmHeaderEntry *)0;
+
+/* Pb : how to propagate the element length (used in SkipHeaderEntry)
+// direct call to SkipBytes ?
+ if (ignoreShadow == 1 && g%2 ==1) //JPR
+ // if user wants to skip shadow groups
+ // and current element *is* a shadow element
+ // we don't create anything
+ return (gdcmHeaderEntry *)1; // to tell caller it's NOT finished
+*/
NewEntry = NewHeaderEntryByNumber(g, n);
FindHeaderEntryVR(NewEntry);
FindHeaderEntryLength(NewEntry);
- if (errno == 1)
- {
+ if (errno == 1) {
// Call it quits
return NULL;
}
NewEntry->SetOffset(ftell(fp));
- //if ( (g==0x7fe0) && (n==0x0010) )
return NewEntry;
}
{
gdcmDictEntry *NewTag = GetDictEntryByName(Name);
if (!NewTag)
- NewTag = NewVirtualDictEntry(0xffff, 0xffff, "LO", "Unknown", Name);
+ NewTag = NewVirtualDictEntry(0xffff, 0xffff, "LO", "unkn", Name);
gdcmHeaderEntry* NewEntry = new gdcmHeaderEntry(NewTag);
if (!NewEntry)
/**
* \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
- * @param vr VR of the underlying DictEntry
- * @param fourth owner group
- * @param name english name
+ * @param group group of the underlying DictEntry
+ * @param element element of the underlying DictEntry
+ * @param vr VR of the underlying DictEntry
+ * @param fourth owner group
+ * @param name english name
*/
gdcmDictEntry *gdcmParser::NewVirtualDictEntry(guint16 group, guint16 element,
std::string vr,
return NewEntry;
}
+// Never used; commented out, waiting for removal.
/**
* \ingroup gdcmParser
* \brief Small utility function that creates a new manually crafted
* @param VR The Value Representation to be given to this new tag.
* @return The newly hand crafted Element Value.
*/
-gdcmHeaderEntry *gdcmParser::NewManualHeaderEntryToPubDict(std::string NewTagName,
- std::string VR)
-{
- gdcmHeaderEntry *NewEntry = NULL;
- guint32 StuffGroup = 0xffff; // Group to be stuffed with additional info
- guint32 FreeElem = 0;
- gdcmDictEntry *DictEntry = NULL;
-
- FreeElem = GenerateFreeTagKeyInGroup(StuffGroup);
- if (FreeElem == UINT32_MAX)
- {
- dbg.Verbose(1, "gdcmHeader::NewManualHeaderEntryToPubDict",
- "Group 0xffff in Public Dict is full");
- return NULL;
- }
-
- DictEntry = NewVirtualDictEntry(StuffGroup, FreeElem,
- VR, "GDCM", NewTagName);
- NewEntry = new gdcmHeaderEntry(DictEntry);
- AddHeaderEntry(NewEntry);
- return NewEntry;
-}
+//gdcmHeaderEntry *gdcmParser::NewManualHeaderEntryToPubDict(std::string NewTagName,
+// std::string VR)
+//{
+// gdcmHeaderEntry *NewEntry = NULL;
+// guint32 StuffGroup = 0xffff; // Group to be stuffed with additional info
+// guint32 FreeElem = 0;
+// gdcmDictEntry *DictEntry = NULL;
+//
+// FreeElem = GenerateFreeTagKeyInGroup(StuffGroup);
+// if (FreeElem == UINT32_MAX)
+// {
+// dbg.Verbose(1, "gdcmHeader::NewManualHeaderEntryToPubDict",
+// "Group 0xffff in Public Dict is full");
+// return NULL;
+// }
+//
+// DictEntry = NewVirtualDictEntry(StuffGroup, FreeElem,
+// VR, "GDCM", NewTagName);
+// NewEntry = new gdcmHeaderEntry(DictEntry);
+// AddHeaderEntry(NewEntry);
+// return NewEntry;
+//}
/**
* \ingroup gdcmParser
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff