if ( !OpenFile(exception_on_error))
return;
- Parse();
- LoadHeaderEntries();
+ if (ParseHeader()) {
+ LoadHeaderEntries();
+ }
CloseFile();
wasUpdated = 0; // will be set to 1 if user adds an entry
* 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);
}
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);
}
*/
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
free(a);
return NULL;
}
+
return a;
}
* \ 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!)
* @param type type of the File to be written
* (ACR-NEMA, ExplicitVR, ImplicitVR)
* @param _fp already open file pointer
std::string vr;
guint32 val_uint32;
guint16 val_uint16;
-
+ guint16 valZero =0;
+ void *voidArea;
std::vector<std::string> tokens;
+ // TODO : function CheckHeaderCoherence to be written
+
// 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;
-
+
// TODO (?) tester les echecs en ecriture (apres chaque fwrite)
-
+ int compte =0;
+
for (ListTag::iterator tag2=listEntries.begin();
tag2 != listEntries.end();
++tag2)
{
gr = (*tag2)->GetGroup();
el = (*tag2)->GetElement();
- lgr = (*tag2)->GetLength();
+ lgr = (*tag2)->GetReadLength();
val = (*tag2)->GetValue().c_str();
vr = (*tag2)->GetVR();
-//cout << hex << gr << " " << el << " "<< vr << " " << val << endl; // JPR
+ voidArea = (*tag2)->GetVoidArea();
if ( type == ACR )
{
{
// 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
- {
+ if (vr == "unkn") { // Unknown was 'written'
shortLgr=lgr;
fwrite ( &shortLgr,(size_t)2 ,(size_t)1 ,_fp);
- }
+ fwrite ( &z, (size_t)2 ,(size_t)1 ,_fp);
+ } else {
+ if (gr != 0xfffe) { // NO value for 'delimiters'
+ if (vr == "unkn") // Unknown was 'written'
+ 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") || gr == 0xfffe)
+ {
+ if (gr != 0xfffe)
+ fwrite ( &z, (size_t)2 ,(size_t)1 ,_fp);
+ fwrite ( &lgr,(size_t)4 ,(size_t)1 ,_fp);
+ }
+ else
+ {
+ shortLgr=lgr;
+ fwrite ( &shortLgr,(size_t)2 ,(size_t)1 ,_fp);
+ }
+ }
}
else // IMPLICIT VR
{
if (vr == "SQ") continue; // no "value" to write for the SEQuences
if (gr == 0xfffe)continue;
+ if (voidArea != NULL) { // there is a 'non string' LUT, overlay, etc
+ fwrite ( voidArea,(size_t)lgr ,(size_t)1 ,_fp); // Elem value
+ continue;
+ }
+
if (vr == "US" || vr == "SS")
{
tokens.erase(tokens.begin(),tokens.end()); // clean any previous value
}
tokens.clear();
continue;
- }
+ }
+
// 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
+ break;
+ }
fwrite ( val,(size_t)lgr ,(size_t)1 ,_fp); // Elem value
}
}
/**
* \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);
}
* \brief add a new Dicom Element pointer to
* the H Table and to the chained List
* \warning push_bash in listEntries ONLY during ParseHeader
- * \todo something to allow further Elements addition,
+ * \TODO something to allow further Elements addition,
* \ when position to be taken care of
* @param newHeaderEntry
*/
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.Verbose(2, "gdcmParser::FindLength: ",
- "we reached 7fe0 0010");
+ "we reached (GrPixel,NumPixel)");
}
if ( (filetype == ExplicitVR) && (! Entry->IsImplicitVR()) )
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))
{
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::cout << "Warning : Tag with uneven length " << FoundLength
+ << "in x(" << std::hex << gr << "," << el <<")" << std::endl;
+ }
// 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
}
// 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());
}
* \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;
}
}
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)
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