-// gdcmHeader.cxx
+// gdcmParser.cxx
//-----------------------------------------------------------------------------
#include "gdcmParser.h"
#include "gdcmUtil.h"
// 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
* 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 ignore_shadow) {
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
/**
* \ingroup gdcmParser
- * \brief
+ * \brief constructor
* @param exception_on_error
*/
gdcmParser::gdcmParser(bool exception_on_error) {
* false otherwise.
*/
bool gdcmParser::IsReadable(void) {
-cout << "filetype [" << filetype <<"]" << endl;
- if(filetype==Unknown)
+ if(filetype==Unknown) {
return(false);
-cout << "trouv filetype" << endl;
- if(listEntries.size()<=0)
+ }
+ if(listEntries.size()<=0) {
return(false);
+ }
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) {
* \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) {
* \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) {
* \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) {
* \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);
}
/**
* \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)
*/
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
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
+ * @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(std::string Value,
+gdcmHeaderEntry * gdcmParser::ReplaceOrCreateByNumber(
+ std::string Value,
guint16 Group,
- guint16 Elem ){
- if (CheckIfEntryExistByNumber(Group, Elem) == 0) {
+ 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
return elem->GetVR();
}
+
/**
* \ingroup gdcmParser
* \brief Searches within Header Entries (Dicom Elements) parsed with
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)
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';
* 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,
+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.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
- * @param Elem
+ * @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;
}
/**
* \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) {
gdcmDictEntry *entry;
/**
* \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 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();
-//cout << hex << gr << " " << el << " "<< vr << " " << val << endl; // JPR
+ 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
- // === Deal with the length
- // --------------------
-
- // if ( (type == ExplicitVR) && (gr <= 0x0002) ) // ?!? < 2
- if ( (type == ExplicitVR) || (type == DICOMDIR) )
- {
+ if ( (type == ExplicitVR) || (type == DICOMDIR) ) {
// EXPLICIT VR
guint16 z=0, shortLgr;
- if (gr != 0xfffe) // JPR
- fwrite (vr.c_str(),(size_t)2 ,(size_t)1 ,_fp);
-
- if ( (vr == "OB") || (vr == "OW") || (vr == "SQ") || gr == 0xfffe) // JPR
- {
- if (gr != 0xfffe)
- 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
// === Deal with the value
// -------------------
- if (vr == "SQ") continue; // vo "value" to write for the SEQuences
- if (gr == 0xfffe)continue;
+ 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;
}
}
/**
* \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();
+ if (!CheckSwap())
+ return false;
+
+ gdcmHeaderEntry *newHeaderEntry = (gdcmHeaderEntry *)0;
while ( (newHeaderEntry = ReadNextHeaderEntry()) ) {
SkipHeaderEntry(newHeaderEntry);
- if ( (ignoreShadow==0) || (newHeaderEntry->GetGroup()%2) == 0) { //JPR
+ if ( (ignoreShadow==0) || (newHeaderEntry->GetGroup()%2) == 0) {
AddHeaderEntry(newHeaderEntry);
}
}
+ return true;
}
/**
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) {
// 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)
}
if( (vr == "UI") ) // Because of correspondance with the VR dic
- Entry->SetValue(NewValue.c_str());
+ 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) {
/**
* \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) {
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 )
{
s << NewInt32;
}
}
-
#ifdef GDCM_NO_ANSI_STRING_STREAM
s << std::ends; // to avoid oddities on Solaris
#endif //GDCM_NO_ANSI_STRING_STREAM
{
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
}
}
// 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.
// 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;
+
+ //std::cout << s.str().c_str() << std::endl;
+
// dbg.Error("gdcmParser::IsHeaderEntryAnInteger",
// s.str().c_str());
}
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) {
// See PS 3.5-2001, section A.4 p. 49 on encapsulation of encoded pixel data.
guint16 g;
/**
* \ingroup gdcmParser
* \brief Reads a supposed to be 16 Bits integer
- * \ (swaps it depending on processor endianity)
- *
+ * (swaps it depending on processor endianity)
* @return read value
*/
guint16 gdcmParser::ReadInt16(void) {
/**
* \ingroup gdcmParser
* \brief Reads a supposed to be 32 Bits integer
- * \ (swaps it depending on processor endianity)
- *
+ * (swaps it depending on processor endianity)
* @return read value
*/
guint32 gdcmParser::ReadInt32(void) {
/**
* \ingroup gdcmParser
- * \brief
- *
+ * \brief skips bytes inside the source file
+ * \warning NOT end user intended method !
* @return
*/
void gdcmParser::SkipBytes(guint32 NBytes) {
/**
* \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() {
+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];
// * the 4 bytes of the first tag (0002, 0000),or (0002, 0001)
// i.e. a total of 136 bytes.
entCur = deb + 136;
- // FIXME
- // Use gdcmParser::dicom_vr to test all the possibilities
- // instead of just checking for UL, OB and UI !?
+
+ // 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, "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 !? // 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));
+ s32 = *((guint32 *)(entCur));
- switch (s) {
+ 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 :
- dbg.Verbose(0, "gdcmParser::CheckSwap:",
- "ACR/NEMA unfound swap info (time to raise bets)");
// We are out of luck. It is not a DicomV3 nor a 'clean' ACR/NEMA file.
// It is time for despaired wild guesses.
- // So, let's assume this file happens to be 'dirty' ACR/NEMA,
- // i.e. the length of the group is not present.
+ // 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;
- // Then the only info we have is the net2host one.
- if (! net2host )
- sw = 0;
- else
+ return true;
+ case 0x0200 :
+ case 0x0400 :
+ case 0x0800 :
sw = 4321;
- return;
+ filetype = ACR;
+ return true;
+ default :
+ dbg.Verbose(0, "gdcmParser::CheckSwap:",
+ "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;
}
}
/**
* \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
gdcmHeaderEntry *gdcmParser::ReadNextHeaderEntry(void) {
guint16 g,n;
gdcmHeaderEntry *NewEntry;
-
g = ReadInt16();
n = ReadInt16();
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 elem element 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
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