-// $Header: /cvs/public/gdcm/src/Attic/gdcmHeader.cxx,v 1.61 2003/05/05 14:13:59 frog Exp $
+
+// $Header: /cvs/public/gdcm/src/Attic/gdcmHeader.cxx,v 1.78 2003/07/03 14:38:16 jpr Exp $
#include <stdio.h>
#include <cerrno>
#include <sstream>
#include "gdcmUtil.h"
#include "gdcmHeader.h"
+using namespace std;
+
+
+// TODO : remove DEBUG
+#define DEBUG 0
// Refer to gdcmHeader::CheckSwap()
#define HEADER_LENGTH_TO_READ 256
// Refer to gdcmHeader::SetMaxSizeLoadElementValue()
#define _MaxSizeLoadElementValue_ 1024
+/**
+ * \ingroup gdcmHeader
+ * \brief
+ */
void gdcmHeader::Initialise(void) {
dicom_vr = gdcmGlobal::GetVR();
- Dicts = gdcmGlobal::GetDicts();
+ dicom_ts = gdcmGlobal::GetTS();
+ Dicts = gdcmGlobal::GetDicts();
RefPubDict = Dicts->GetDefaultPubDict();
RefShaDict = (gdcmDict*)0;
}
+/**
+ * \ingroup gdcmHeader
+ * \brief
+ * @param InFilename
+ * @param exception_on_error
+ */
gdcmHeader::gdcmHeader(const char *InFilename, bool exception_on_error) {
+ SetMaxSizeLoadElementValue(_MaxSizeLoadElementValue_);
+ filename = InFilename;
+ Initialise();
+ if ( !OpenFile(exception_on_error))
+ return;
+ ParseHeader();
+ LoadElements();
+ CloseFile();
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief
+ * @param exception_on_error
+ */
+gdcmHeader::gdcmHeader(bool exception_on_error) {
SetMaxSizeLoadElementValue(_MaxSizeLoadElementValue_);
- filename = InFilename;
Initialise();
- OpenFile(exception_on_error);
- ParseHeader();
- LoadElements();
- CloseFile();
}
-bool gdcmHeader::OpenFile(bool exception_on_error)
+/**
+ * \ingroup gdcmHeader
+ * \brief
+ * @param exception_on_error
+ * @return
+ */
+ bool gdcmHeader::OpenFile(bool exception_on_error)
throw(gdcmFileError) {
fp=fopen(filename.c_str(),"rb");
if(exception_on_error) {
if(!fp)
throw gdcmFileError("gdcmHeader::gdcmHeader(const char *, bool)");
}
- else
- dbg.Error(!fp, "gdcmHeader::gdcmHeader cannot open file", filename.c_str());
if ( fp )
return true;
+ dbg.Verbose(0, "gdcmHeader::gdcmHeader cannot open file", filename.c_str());
return false;
}
+/**
+ * \ingroup gdcmHeader
+ * \brief
+ * @return
+ */
bool gdcmHeader::CloseFile(void) {
int closed = fclose(fp);
fp = (FILE *)0;
return true;
}
+/**
+ * \ingroup gdcmHeader
+ * \brief Canonical destructor.
+ */
gdcmHeader::~gdcmHeader (void) {
- dicom_vr = (gdcmVR*)0;
- Dicts = (gdcmDictSet*)0;
+ dicom_vr = (gdcmVR*)0;
+ Dicts = (gdcmDictSet*)0;
RefPubDict = (gdcmDict*)0;
RefShaDict = (gdcmDict*)0;
return;
// Use gdcmHeader::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) )
- {
+ (memcmp(entCur, "OB", (size_t)2) == 0) ||
+ (memcmp(entCur, "UI", (size_t)2) == 0) )
+ {
filetype = ExplicitVR;
dbg.Verbose(1, "gdcmHeader::CheckSwap:",
"explicit Value Representation");
dbg.Verbose(1, "gdcmHeader::CheckSwap:",
"not an explicit Value Representation");
}
-
if (net2host) {
sw = 4321;
dbg.Verbose(1, "gdcmHeader::CheckSwap:",
return;
}
+/**
+ * \ingroup gdcmHeader
+ * \brief
+ */
void gdcmHeader::SwitchSwapToBigEndian(void) {
dbg.Verbose(1, "gdcmHeader::SwitchSwapToBigEndian",
"Switching to BigEndian mode.");
/**
* \ingroup gdcmHeader
* \brief Find the value representation of the current tag.
+ * @param ElVal
*/
void gdcmHeader::FindVR( gdcmElValue *ElVal) {
if (filetype != ExplicitVR)
char VR[3];
string vr;
int lgrLue;
+ char msg[100]; // for sprintf. Sorry
+
long PositionOnEntry = ftell(fp);
// Warning: we believe this is explicit VR (Value Representation) because
// we used a heuristic that found "UL" in the first tag. Alas this
}
// We thought this was explicit VR, but we end up with an
- // implicit VR tag. Let's backtrack.
- dbg.Verbose(1, "gdcmHeader::FindVR:", "Falsely explicit vr file");
+ // implicit VR tag. Let's backtrack.
+
+ sprintf(msg,"Falsely explicit vr file (%04x,%04x)\n", ElVal->GetGroup(),ElVal->GetElement());
+ dbg.Verbose(1, "gdcmHeader::FindVR: ",msg);
+
fseek(fp, PositionOnEntry, SEEK_SET);
// When this element is known in the dictionary we shall use, e.g. for
// the semantics (see the usage of IsAnInteger), the vr proposed by the
/**
* \ingroup gdcmHeader
- * \brief Determines if the Transfer Syntax was allready encountered
+ * \brief Determines if the Transfer Syntax was already encountered
* and if it corresponds to a ImplicitVRLittleEndian one.
*
* @return True when ImplicitVRLittleEndian found. False in all other cases.
/**
* \ingroup gdcmHeader
- * \brief Determines if the Transfer Syntax was allready encountered
+ * \brief Determines if the Transfer Syntax was already encountered
* and if it corresponds to a ExplicitVRLittleEndian one.
*
* @return True when ExplicitVRLittleEndian found. False in all other cases.
/**
* \ingroup gdcmHeader
- * \brief Determines if the Transfer Syntax was allready encountered
+ * \brief Determines if the Transfer Syntax was already encountered
* and if it corresponds to a DeflatedExplicitVRLittleEndian one.
*
* @return True when DeflatedExplicitVRLittleEndian found. False in all other cases.
/**
* \ingroup gdcmHeader
- * \brief Determines if the Transfer Syntax was allready encountered
+ * \brief Determines if the Transfer Syntax was already encountered
* and if it corresponds to a Explicit VR Big Endian one.
*
* @return True when big endian found. False in all other cases.
/**
* \ingroup gdcmHeader
- * \brief Determines if the Transfer Syntax was allready encountered
+ * \brief Determines if the Transfer Syntax was already encountered
* and if it corresponds to a JPEGBaseLineProcess1 one.
*
* @return True when JPEGBaseLineProcess1found. False in all other cases.
return false;
}
-// faire qq chose d'intelligent a la place de ça
-
+/**
+ * \ingroup gdcmHeader
+ * \brief
+ *
+ * @return
+ */
bool gdcmHeader::IsJPEGLossless(void) {
gdcmElValue* Element = PubElValSet.GetElementByNumber(0x0002, 0x0010);
+ // faire qq chose d'intelligent a la place de ça
if ( !Element )
return false;
LoadElementValueSafe(Element);
const char * Transfert = Element->GetValue().c_str();
- printf("TransfertSyntx %s\n",Transfert);
if ( memcmp(Transfert+strlen(Transfert)-2 ,"70",2)==0) return true;
if ( memcmp(Transfert+strlen(Transfert)-2 ,"55",2)==0) return true;
return false;
/**
* \ingroup gdcmHeader
- * \brief Determines if the Transfer Syntax was allready encountered
+ * \brief Determines if the Transfer Syntax was already encountered
* and if it corresponds to a JPEGExtendedProcess2-4 one.
*
* @return True when JPEGExtendedProcess2-4 found. False in all other cases.
/**
* \ingroup gdcmHeader
- * \brief Determines if the Transfer Syntax was allready encountered
+ * \brief Determines if the Transfer Syntax was already encountered
* and if it corresponds to a JPEGExtendeProcess3-5 one.
*
* @return True when JPEGExtendedProcess3-5 found. False in all other cases.
/**
* \ingroup gdcmHeader
- * \brief Determines if the Transfer Syntax was allready encountered
+ * \brief Determines if the Transfer Syntax was already encountered
* and if it corresponds to a JPEGSpectralSelectionProcess6-8 one.
*
* @return True when JPEGSpectralSelectionProcess6-8 found. False in all
return true;
return false;
}
+
/**
* \ingroup gdcmHeader
* \brief Predicate for dicom version 3 file.
ElVal->SetLength(FoundLength);
}
-guint32 gdcmHeader::FindLengthOB(void) {
+/**
+ * \ingroup gdcmHeader
+ * \brief
+ *
+ * @return
+ */
+ guint32 gdcmHeader::FindLengthOB(void) {
// See PS 3.5-2001, section A.4 p. 49 on encapsulation of encoded pixel data.
guint16 g;
guint16 n;
while ( ! FoundSequenceDelimiter) {
g = ReadInt16();
n = ReadInt16();
+
+ long l = ftell(fp);
+
if (errno == 1)
return 0;
TotalLength += 4; // We even have to decount the group and element
- if ( g != 0xfffe ) {
- dbg.Verbose(1, "gdcmHeader::FindLengthOB: ",
- "wrong group for an item sequence.");
+
+ if ( g != 0xfffe && g!=0xb00c ) /*for bogus header */ {
+ char msg[100]; // for sprintf. Sorry
+ sprintf(msg,"wrong group (%04x) for an item sequence (%04x,%04x)\n",g, g,n);
+ dbg.Verbose(1, "gdcmHeader::FindLengthOB: ",msg);
+ long l = ftell(fp);
errno = 1;
return 0;
}
- if ( n == 0xe0dd )
+ if ( n == 0xe0dd || ( g==0xb00c && n==0x0eb6 ) ) /* for bogus header */
FoundSequenceDelimiter = true;
- else if ( n != 0xe000) {
- dbg.Verbose(1, "gdcmHeader::FindLengthOB: ",
- "wrong element for an item sequence.");
+ else if ( n != 0xe000 ){
+ char msg[100]; // for sprintf. Sorry
+ sprintf(msg,"wrong element (%04x) for an item sequence (%04x,%04x)\n",n, g,n);
+ dbg.Verbose(1, "gdcmHeader::FindLengthOB: ",msg);
errno = 1;
return 0;
}
ItemLength = ReadInt32();
TotalLength += ItemLength + 4; // We add 4 bytes since we just read
// the ItemLength with ReadInt32
+
SkipBytes(ItemLength);
}
fseek(fp, PositionOnEntry, SEEK_SET);
return TotalLength;
}
-void gdcmHeader::FindLength(gdcmElValue * ElVal) {
+/**
+ * \ingroup gdcmHeader
+ * \brief
+ *
+ * @return
+ */
+ void gdcmHeader::FindLength (gdcmElValue * ElVal) {
guint16 element = ElVal->GetElement();
+ guint16 group = ElVal->GetGroup();
string vr = ElVal->GetVR();
guint16 length16;
+ if( (element == 0x0010) && (group == 0x7fe0) ) {
+ dbg.SetDebug(0);
+ dbg.Verbose(2, "gdcmHeader::FindLength: ",
+ "on est sur 7fe0 0010");
+ }
if ( (filetype == ExplicitVR) && ! ElVal->IsImplicitVr() ) {
-
if ( (vr=="OB") || (vr=="OW") || (vr=="SQ") || (vr=="UN") ) {
+
// The following reserved two bytes (see PS 3.5-2001, section
// 7.1.2 Data element structure with explicit vr p27) must be
// skipped before proceeding on reading the length on 4 bytes.
fseek(fp, 2L, SEEK_CUR);
+
guint32 length32 = ReadInt32();
if ( (vr == "OB") && (length32 == 0xffffffff) ) {
ElVal->SetLength(FindLengthOB());
return;
}
- FixFoundLength(ElVal, length32);
+ FixFoundLength(ElVal, length32);
return;
}
// We shall use this second strategy. In order to make sure that we
// can interpret the presence of an apparently big endian encoded
// length of a "Group Length" without committing a big mistake, we
- // add an additional check: we look in the allready parsed elements
+ // add an additional check: we look in the already parsed elements
// for the presence of a "Transfer Syntax" whose value has to be "big
// endian encoding". When this is the case, chances are we have got our
// hands on a big endian encoded file: we switch the swap code to
// big endian and proceed...
- if ( (element == 0x000) && (length16 == 0x0400) ) {
+ if ( (element == 0x0000) && (length16 == 0x0400) ) {
if ( ! IsExplicitVRBigEndianTransferSyntax() ) {
dbg.Verbose(0, "gdcmHeader::FindLength", "not explicit VR");
errno = 1;
return (a);
}
-void gdcmHeader::SkipBytes(guint32 NBytes) {
+/**
+ * \ingroup gdcmHeader
+ * \brief
+ *
+ * @return
+ */
+ void gdcmHeader::SkipBytes(guint32 NBytes) {
//FIXME don't dump the returned value
(void)fseek(fp, (long)NBytes, SEEK_CUR);
}
-void gdcmHeader::SkipElementValue(gdcmElValue * ElVal) {
+/**
+ * \ingroup gdcmHeader
+ * \brief
+ *
+ * @return
+ */
+ void gdcmHeader::SkipElementValue(gdcmElValue * ElVal) {
SkipBytes(ElVal->GetLength());
}
-void gdcmHeader::SetMaxSizeLoadElementValue(long NewSize) {
+/**
+ * \ingroup gdcmHeader
+ * \brief
+ *
+ * @return
+ */
+ void gdcmHeader::SetMaxSizeLoadElementValue(long NewSize) {
if (NewSize < 0)
return;
if ((guint32)NewSize >= (guint32)0xffffffff) {
void gdcmHeader::LoadElementValue(gdcmElValue * ElVal) {
size_t item_read;
guint16 group = ElVal->GetGroup();
- guint16 elem = ElVal->GetElement();
string vr = ElVal->GetVR();
guint32 length = ElVal->GetLength();
bool SkipLoad = false;
// four bytes properly i.e. as an integer as opposed to a string.
// pour les elements de Value Multiplicity > 1
- // on aura en fait une serie d'entiers
-
+ // on aura en fait une serie d'entiers
// on devrait pouvoir faire + compact (?)
- if ( IsAnInteger(ElVal) ) {
- guint32 NewInt;
- ostringstream s;
- int nbInt;
- if (vr == "US" || vr == "SS") {
- nbInt = length / 2;
- NewInt = ReadInt16();
- s << NewInt;
- if (nbInt > 1) {
- for (int i=1; i < nbInt; i++) {
- s << '\\';
- NewInt = ReadInt16();
- s << NewInt;
- }
- }
+ if ( IsAnInteger(ElVal) ) {
+ guint32 NewInt;
+ ostringstream s;
+ int nbInt;
+ if (vr == "US" || vr == "SS") {
+ nbInt = length / 2;
+ NewInt = ReadInt16();
+ s << NewInt;
+ if (nbInt > 1) {
+ for (int i=1; i < nbInt; i++) {
+ s << '\\';
+ NewInt = ReadInt16();
+ s << NewInt;
+ }
+ }
- } else if (vr == "UL" || vr == "SL") {
- nbInt = length / 4;
- NewInt = ReadInt32();
- s << NewInt;
- if (nbInt > 1) {
- for (int i=1; i < nbInt; i++) {
- s << '\\';
- NewInt = ReadInt32();
- s << NewInt;
- }
- }
- }
- ElVal->SetValue(s.str());
- return;
- }
+ } else if (vr == "UL" || vr == "SL") {
+ nbInt = length / 4;
+ NewInt = ReadInt32();
+ s << NewInt;
+ if (nbInt > 1) {
+ for (int i=1; i < nbInt; i++) {
+ s << '\\';
+ NewInt = ReadInt32();
+ s << NewInt;
+ }
+ }
+ }
+ ElVal->SetValue(s.str());
+ return;
+ }
// We need an additional byte for storing \0 that is not on disk
char* NewValue = (char*)malloc(length+1);
fseek(fp, PositionOnEntry, SEEK_SET);
}
-
+/**
+ * \ingroup gdcmHeader
+ * \brief
+ *
+ * @return
+ */
guint16 gdcmHeader::ReadInt16(void) {
guint16 g;
size_t item_read;
item_read = fread (&g, (size_t)2,(size_t)1, fp);
- errno = 0;
if ( item_read != 1 ) {
- dbg.Verbose(1, "gdcmHeader::ReadInt16", " File read error");
+ // dbg.Verbose(0, "gdcmHeader::ReadInt16", " Failed to read :");
+ // if(feof(fp))
+ // dbg.Verbose(0, "gdcmHeader::ReadInt16", " End of File encountered");
+ if(ferror(fp))
+ dbg.Verbose(0, "gdcmHeader::ReadInt16", " File Error");
errno = 1;
return 0;
}
+ errno = 0;
g = SwapShort(g);
return g;
}
+/**
+ * \ingroup gdcmHeader
+ * \brief
+ *
+ * @return
+ */
guint32 gdcmHeader::ReadInt32(void) {
guint32 g;
size_t item_read;
item_read = fread (&g, (size_t)4,(size_t)1, fp);
- errno = 0;
- if ( item_read != 1 ) {
- dbg.Verbose(1, "gdcmHeader::ReadInt32", " File read error");
+ if ( item_read != 1 ) {
+ //dbg.Verbose(0, "gdcmHeader::ReadInt32", " Failed to read :");
+ //if(feof(fp))
+ // dbg.Verbose(0, "gdcmHeader::ReadInt32", " End of File encountered");
+ if(ferror(fp))
+ dbg.Verbose(0, "gdcmHeader::ReadInt32", " File Error");
errno = 1;
return 0;
}
+ errno = 0;
g = SwapLong(g);
return g;
}
+/**
+ * \ingroup gdcmHeader
+ * \brief
+ *
+ * @return
+ */
+ gdcmElValue* gdcmHeader::GetElValueByNumber(guint16 Group, guint16 Elem) {
+
+ gdcmElValue* elValue = PubElValSet.GetElementByNumber(Group, Elem);
+ if (!elValue) {
+ dbg.Verbose(1, "gdcmHeader::GetElValueByNumber",
+ "failed to Locate gdcmElValue");
+ return (gdcmElValue*)0;
+ }
+ return elValue;
+}
+
/**
* \ingroup gdcmHeader
* \brief Build a new Element Value from all the low level arguments.
/**
* \ingroup gdcmHeader
* \brief TODO
- * @param
+ * @param Value
+ * @param Group
+ * @param Elem
*/
int gdcmHeader::ReplaceOrCreateByNumber(string Value, guint16 Group, guint16 Elem ) {
- gdcmElValue* nvElValue=NewElValueByNumber(Group, Elem);
- PubElValSet.Add(nvElValue);
- PubElValSet.SetElValueByNumber(Value, Group, Elem);
- return(1);
+ // TODO : FIXME JPRx
+ // curieux, non ?
+ // on (je) cree une Elvalue ne contenant pas de valeur
+ // on l'ajoute au ElValSet
+ // on affecte une valeur a cette ElValue a l'interieur du ElValSet
+ // --> devrait pouvoir etre fait + simplement ???
+
+ gdcmElValue* nvElValue=NewElValueByNumber(Group, Elem);
+ PubElValSet.Add(nvElValue);
+ PubElValSet.SetElValueByNumber(Value, Group, Elem);
+ return(1);
}
+/**
+ * \ingroup gdcmHeader
+ * \brief TODO
+ * @param Value
+ * @param Group
+ * @param Elem
+ */
+int gdcmHeader::ReplaceOrCreateByNumber(char* Value, guint16 Group, guint16 Elem ) {
+
+ gdcmElValue* nvElValue=NewElValueByNumber(Group, Elem);
+ PubElValSet.Add(nvElValue);
+ string v = Value;
+ PubElValSet.SetElValueByNumber(v, Group, Elem);
+ return(1);
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief TODO
+ * @param Group
+ * @param Elem
+ */
+
+int gdcmHeader::CheckIfExistByNumber(guint16 Group, guint16 Elem ) {
+ return (PubElValSet.CheckIfExistByNumber(Group, Elem));
+ }
+
+
/**
* \ingroup gdcmHeader
* \brief Build a new Element Value from all the low level arguments.
g = ReadInt16();
n = ReadInt16();
+
+ if ( (g==0x7fe0) && (n==0x0010) )
+ if (DEBUG)
+ printf("in gdcmHeader::ReadNextElement try to read 7fe0 0010 \n");
+
if (errno == 1)
// We reached the EOF (or an error occured) and header parsing
// has to be considered as finished.
NewElVal = NewElValueByNumber(g, n);
FindVR(NewElVal);
FindLength(NewElVal);
- if (errno == 1)
+ if (errno == 1) {
// Call it quits
+ if (DEBUG) printf("in gdcmHeader::ReadNextElement : g %04x n %04x errno %d\n",g, n, errno);
return (gdcmElValue *)0;
- NewElVal->SetOffset(ftell(fp));
+ }
+ NewElVal->SetOffset(ftell(fp));
+ if ( (g==0x7fe0) && (n==0x0010) )
+ if (DEBUG)
+ printf("sortie de gdcmHeader::ReadNextElement 7fe0 0010 \n");
return NewElVal;
}
if (length == 4)
return true;
else {
- printf("Erroneous Group Length element length (%04x , %04x) : %d\n",
+ if (DEBUG) printf("Erroneous Group Length element length (%04x , %04x) : %d\n",
group, element,length);
dbg.Error("gdcmHeader::IsAnInteger",
"Erroneous Group Length element length.");
}
}
-
if ( (vr == "UL") || (vr == "US") || (vr == "SL") || (vr == "SS") )
return true;
numPixel = 0x1010;
else
numPixel = 0x0010;
+
gdcmElValue* PixelElement = PubElValSet.GetElementByNumber(grPixel,
numPixel);
if (PixelElement)
*/
int gdcmHeader::SetPubElValByNumber(string content, guint16 group,
guint16 element)
+
+//TODO : homogeneiser les noms : SetPubElValByNumber qui appelle PubElValSet.SetElValueByNumber
+// pourquoi pas SetPubElValueByNumber ??
{
+
return ( PubElValSet.SetElValueByNumber (content, group, element) );
}
* \brief Accesses an existing gdcmElValue in the ShaElValSet of this instance
* through tag name and modifies it's content with the given value.
* @param content new value to substitute with
- * @param TagName name of the tag to be modified
+ * @param ShadowTagName name of the tag to be modified
*/
-int gdcmHeader::SetShaElValByName(string content, string TagName) {
- return ( ShaElValSet.SetElValueByName (content, TagName) );
+int gdcmHeader::SetShaElValByName(string content, string ShadowTagName) {
+ return ( ShaElValSet.SetElValueByName (content, ShadowTagName) );
}
/**
}
}
+/**
+ * \ingroup gdcmHeader
+ * \brief This predicate, based on hopefully reasonnable heuristics,
+ * decides whether or not the current gdcmHeader was properly parsed
+ * and contains the mandatory information for being considered as
+ * a well formed and usable image.
+ * @return true when gdcmHeader is the one of a reasonable Dicom file,
+ * false otherwise.
+ */
+bool gdcmHeader::IsReadable(void) {
+ if ( GetElValByName("Image Dimensions") != "gdcm::Unfound"
+ && atoi(GetElValByName("Image Dimensions").c_str()) > 4 ) {
+ return false;
+ }
+ if ( GetElValByName("Bits Allocated") == "gdcm::Unfound" )
+ return false;
+ if ( GetElValByName("Bits Stored") == "gdcm::Unfound" )
+ return false;
+ if ( GetElValByName("High Bit") == "gdcm::Unfound" )
+ return false;
+ if ( GetElValByName("Pixel Representation") == "gdcm::Unfound" )
+ return false;
+ return true;
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Small utility function that creates a new manually crafted
+ * (as opposed as read from the file) gdcmElValue with user
+ * specified name and adds it to the public tag hash table.
+ * \note A fake TagKey is generated so the PubDict can keep it's coherence.
+ * @param NewTagName The name to be given to this new tag.
+ * @param VR The Value Representation to be given to this new tag.
+ * @ return The newly hand crafted Element Value.
+ */
+gdcmElValue* gdcmHeader::NewManualElValToPubDict(string NewTagName, string VR) {
+ gdcmElValue* NewElVal = (gdcmElValue*)0;
+ guint32 StuffGroup = 0xffff; // Group to be stuffed with additional info
+ guint32 FreeElem = 0;
+ gdcmDictEntry* NewEntry = (gdcmDictEntry*)0;
+
+ FreeElem = PubElValSet.GenerateFreeTagKeyInGroup(StuffGroup);
+ if (FreeElem == UINT32_MAX) {
+ dbg.Verbose(1, "gdcmHeader::NewManualElValToPubDict",
+ "Group 0xffff in Public Dict is full");
+ return (gdcmElValue*)0;
+ }
+ NewEntry = new gdcmDictEntry(StuffGroup, FreeElem,
+ VR, "GDCM", NewTagName);
+ NewElVal = new gdcmElValue(NewEntry);
+ PubElValSet.Add(NewElVal);
+ return NewElVal;
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Loads the element values of all the elements present in the
+ * public tag based hash table.
+ */
+void gdcmHeader::LoadElements(void) {
+ rewind(fp);
+ TagElValueHT ht = PubElValSet.GetTagHt();
+ for (TagElValueHT::iterator tag = ht.begin(); tag != ht.end(); ++tag) {
+ LoadElementValue(tag->second);
+ }
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief
+ * @return
+ */
+void gdcmHeader::PrintPubElVal(std::ostream & os) {
+ PubElValSet.Print(os);
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief
+ * @return
+ */
+void gdcmHeader::PrintPubDict(std::ostream & os) {
+ RefPubDict->Print(os);
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief
+ * @return
+ */
+int gdcmHeader::Write(FILE * fp, FileType type) {
+ return PubElValSet.Write(fp, type);
+}
+
+//
+// =============================================================================
+// Accesors with euristics
+//==============================================================================
+//
+
+// TODO : move to an other file.
+
+
/**
* \ingroup gdcmHeader
* \brief Retrieve the number of columns of image.
return 1;
}
+/**
+ * \ingroup gdcmHeader
+ * \brief Retrieve the number of Bits Stored
+ * (as opposite to number of Bits Allocated)
+ *
+ * @return The encountered number of Bits Stored, 0 by default.
+ */
+int gdcmHeader::GetBitsStored(void) {
+ string StrSize = GetPubElValByNumber(0x0028,0x0101);
+ if (StrSize == "gdcm::Unfound")
+ return 1;
+ return atoi(StrSize.c_str());
+}
+
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Retrieve the number of Samples Per Pixel
+ * (1 : gray level, 3 : RGB)
+ *
+ * @return The encountered number of Samples Per Pixel, 1 by default.
+ */
+int gdcmHeader::GetSamplesPerPixel(void) {
+ string StrSize = GetPubElValByNumber(0x0028,0x0002);
+ if (StrSize == "gdcm::Unfound")
+ return 1; // Well, it's supposed to be mandatory ...
+ return atoi(StrSize.c_str());
+}
+
+
+/* ================ COMMENT OUT after unfreeze
+**
+ * \ingroup gdcmHeader
+ * \brief Retrieve the Planar Configuration for RGB images
+ * (0 : RGB Pixels , 1 : R Plane + G Plane + B Plane)
+ *
+ * @return The encountered Planar Configuration, 0 by default.
+ *
+int gdcmHeader::GetPlanarConfiguration(void) {
+ string StrSize = GetPubElValByNumber(0x0028,0x0006);
+ if (StrSize == "gdcm::Unfound")
+ return 0;
+ return atoi(StrSize.c_str());
+}
+
+ ======================================= */
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Return the size (in bytes) of a single pixel of data.
+ * @return The size in bytes of a single pixel of data.
+ *
+ */
+int gdcmHeader::GetPixelSize(void) {
+ string PixelType = GetPixelType();
+ if (PixelType == "8U" || PixelType == "8S")
+ return 1;
+ if (PixelType == "16U" || PixelType == "16S")
+ return 2;
+ if (PixelType == "32U" || PixelType == "32S")
+ return 4;
+ dbg.Verbose(0, "gdcmHeader::GetPixelSize: Unknown pixel type");
+ return 0;
+}
+
/**
* \ingroup gdcmHeader
* \brief Build the Pixel Type of the image.
* Possible values are:
- * - U8 unsigned 8 bit,
- * - S8 signed 8 bit,
- * - U16 unsigned 16 bit,
- * - S16 signed 16 bit,
- * - U32 unsigned 32 bit,
- * - S32 signed 32 bit,
+ * - 8U unsigned 8 bit,
+ * - 8S signed 8 bit,
+ * - 16U unsigned 16 bit,
+ * - 16S signed 16 bit,
+ * - 32U unsigned 32 bit,
+ * - 32S signed 32 bit,
* \warning 12 bit images appear as 16 bit.
- * @return
+ * @return
*/
string gdcmHeader::GetPixelType(void) {
string BitsAlloc;
}
/**
- * \ingroup gdcmHeader
- * \brief This predicate, based on hopefully reasonnable heuristics,
- * decides whether or not the current gdcmHeader was properly parsed
- * and contains the mandatory information for being considered as
- * a well formed and usable image.
- * @return true when gdcmHeader is the one of a reasonable Dicom file,
- * false otherwise.
- */
-bool gdcmHeader::IsReadable(void) {
- if ( GetElValByName("Image Dimensions") != "gdcm::Unfound"
- && atoi(GetElValByName("Image Dimensions").c_str()) > 4 ) {
- return false;
- }
- if ( GetElValByName("Bits Allocated") == "gdcm::Unfound" )
- return false;
- if ( GetElValByName("Bits Stored") == "gdcm::Unfound" )
- return false;
- if ( GetElValByName("High Bit") == "gdcm::Unfound" )
- return false;
- if ( GetElValByName("Pixel Representation") == "gdcm::Unfound" )
- return false;
- return true;
+ * \ingroup gdcmHeader
+ * \brief gets the info from 0028,0030 : Pixel Spacing
+ * \ else 1.
+ * @return X dimension of a pixel
+ */
+float gdcmHeader::GetXSpacing(void) {
+ float xspacing, yspacing;
+ string StrSpacing = GetPubElValByNumber(0x0028,0x0030);
+
+ if (StrSpacing == "gdcm::Unfound") {
+ dbg.Verbose(0, "gdcmHeader::GetXSpacing: unfound Pixel Spacing (0028,0030)");
+ return 1.;
+ }
+ if( sscanf( StrSpacing.c_str(), "%f\\%f", &xspacing, &yspacing) != 2)
+ return 0.;
+ //else
+ return xspacing;
}
/**
- * \ingroup gdcmHeader
- * \brief Small utility function that creates a new manually crafted
- * (as opposed as read from the file) gdcmElValue with user
- * specified name and adds it to the public tag hash table.
- * \note A fake TagKey is generated so the PubDict can keep it's coherence.
- * @param NewTagName The name to be given to this new tag.
- * @param VR The Value Representation to be given to this new tag.
- * @ return The newly hand crafted Element Value.
- */
-gdcmElValue* gdcmHeader::NewManualElValToPubDict(string NewTagName, string VR) {
- gdcmElValue* NewElVal = (gdcmElValue*)0;
- guint32 StuffGroup = 0xffff; // Group to be stuffed with additional info
- guint32 FreeElem = 0;
- gdcmDictEntry* NewEntry = (gdcmDictEntry*)0;
+ * \ingroup gdcmHeader
+ * \brief gets the info from 0028,0030 : Pixel Spacing
+ * \ else 1.
+ * @return Y dimension of a pixel
+ */
+float gdcmHeader::GetYSpacing(void) {
+ float xspacing, yspacing;
+ string StrSpacing = GetPubElValByNumber(0x0028,0x0030);
+
+ if (StrSpacing == "gdcm::Unfound") {
+ dbg.Verbose(0, "gdcmHeader::GetYSpacing: unfound Pixel Spacing (0028,0030)");
+ return 1.;
+ }
+ if( sscanf( StrSpacing.c_str(), "%f\\%f", &xspacing, &yspacing) != 2)
+ return 0.;
+ if (yspacing == 0.) {
+ dbg.Verbose(0, "gdcmHeader::GetYSpacing: gdcmData/CT-MONO2-8-abdo.dcm problem");
+ // seems to be a bug in the header ...
+ sscanf( StrSpacing.c_str(), "%f\\0\\%f", &xspacing, &yspacing);
+ }
+ return yspacing;
+}
- FreeElem = PubElValSet.GenerateFreeTagKeyInGroup(StuffGroup);
- if (FreeElem == UINT32_MAX) {
- dbg.Verbose(1, "gdcmHeader::NewManualElValToPubDict",
- "Group 0xffff in Public Dict is full");
- return (gdcmElValue*)0;
- }
- NewEntry = new gdcmDictEntry(StuffGroup, FreeElem,
- VR, "GDCM", NewTagName);
- NewElVal = new gdcmElValue(NewEntry);
- PubElValSet.Add(NewElVal);
- return NewElVal;
+/**
+ *\ingroup gdcmHeader
+ *\brief gets the info from 0018,0088 : Space Between Slices
+ *\ else from 0018,0050 : Slice Thickness
+ *\ else 1.
+ * @return Z dimension of a voxel-to be
+ */
+float gdcmHeader::GetZSpacing(void) {
+ // TODO : translate into English
+ // Spacing Between Slices : distance entre le milieu de chaque coupe
+ // Les coupes peuvent etre :
+ // jointives (Spacing between Slices = Slice Thickness)
+ // chevauchantes (Spacing between Slices < Slice Thickness)
+ // disjointes (Spacing between Slices > Slice Thickness)
+ // Slice Thickness : epaisseur de tissus sur laquelle est acquis le signal
+ // ca interesse le physicien de l'IRM, pas le visualisateur de volumes ...
+ // Si le Spacing Between Slices est absent,
+ // on suppose que les coupes sont jointives
+
+ string StrSpacingBSlices = GetPubElValByNumber(0x0018,0x0088);
+
+ if (StrSpacingBSlices == "gdcm::Unfound") {
+ dbg.Verbose(0, "gdcmHeader::GetZSpacing: unfound StrSpacingBSlices");
+ string StrSliceThickness = GetPubElValByNumber(0x0018,0x0050);
+ if (StrSliceThickness == "gdcm::Unfound")
+ return 1.;
+ else
+ // if no 'Spacing Between Slices' is found,
+ // we assume slices join together
+ // (no overlapping, no interslice gap)
+ // if they don't, we're fucked up
+ return atof(StrSliceThickness.c_str());
+ } else {
+ return atof(StrSpacingBSlices.c_str());
+ }
}
+//
+// Image Position Patient (0020,0032):
+// If not found (ACR_NEMA) we try Image Position (0020,0030)
+// If not found (ACR-NEMA), we consider Slice Location (0020,1041)
+// or Location (0020,0050)
+// as the Z coordinate,
+// 0. for all the coordinates if nothing is found
+
+// TODO : find a way to inform the caller nothing was found
+// TODO : How to tell the caller a wrong number of values was found?
+
/**
- * \ingroup gdcmHeader
- * \brief Loads the element values of all the elements present in the
- * public tag based hash table.
- */
-void gdcmHeader::LoadElements(void) {
- rewind(fp);
- TagElValueHT ht = PubElValSet.GetTagHt();
- for (TagElValueHT::iterator tag = ht.begin(); tag != ht.end(); ++tag) {
- LoadElementValue(tag->second);
- }
+ * \ingroup gdcmHeader
+ * \brief gets the info from 0020,0032 : Image Position Patient
+ *\ else from 0020,0030 : Image Position (RET)
+ *\ else 0.
+ * @return up-left image corner position
+ */
+float gdcmHeader::GetXImagePosition(void) {
+ float xImPos, yImPos, zImPos;
+ string StrImPos = GetPubElValByNumber(0x0020,0x0032);
+
+ if (StrImPos == "gdcm::Unfound") {
+ dbg.Verbose(0, "gdcmHeader::GetXImagePosition: unfound Image Position Patient (0020,0032)");
+ StrImPos = GetPubElValByNumber(0x0020,0x0030); // For ACR-NEMA images
+ if (StrImPos == "gdcm::Unfound") {
+ dbg.Verbose(0, "gdcmHeader::GetXImagePosition: unfound Image Position (RET) (0020,0030)");
+ // How to tell the caller nothing was found ?
+ }
+ return 0.;
+ }
+ if( sscanf( StrImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3)
+ return 0.;
+ return xImPos;
}
-void gdcmHeader::PrintPubElVal(ostream & os) {
- PubElValSet.Print(os);
+/**
+ * \ingroup gdcmHeader
+ * \brief gets the info from 0020,0032 : Image Position Patient
+ * \ else from 0020,0030 : Image Position (RET)
+ * \ else 0.
+ * @return up-left image corner position
+ */
+float gdcmHeader::GetYImagePosition(void) {
+ float xImPos, yImPos, zImPos;
+ string StrImPos = GetPubElValByNumber(0x0020,0x0032);
+
+ if (StrImPos == "gdcm::Unfound") {
+ dbg.Verbose(0, "gdcmHeader::GetYImagePosition: unfound Image Position Patient (0020,0032)");
+ StrImPos = GetPubElValByNumber(0x0020,0x0030); // For ACR-NEMA images
+ if (StrImPos == "gdcm::Unfound") {
+ dbg.Verbose(0, "gdcmHeader::GetYImagePosition: unfound Image Position (RET) (0020,0030)");
+ }
+ return 0.;
+ }
+ if( sscanf( StrImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3)
+ return 0.;
+ return yImPos;
}
-void gdcmHeader::PrintPubDict(ostream & os) {
- RefPubDict->Print(os);
+/**
+ * \ingroup gdcmHeader
+ * \brief gets the info from 0020,0032 : Image Position Patient
+ * \ else from 0020,0030 : Image Position (RET)
+ * \ else from 0020,1041 : Slice Location
+ * \ else from 0020,0050 : Location
+ * \ else 0.
+ * @return up-left image corner position
+ */
+float gdcmHeader::GetZImagePosition(void) {
+ float xImPos, yImPos, zImPos;
+ string StrImPos = GetPubElValByNumber(0x0020,0x0032);
+ if (StrImPos != "gdcm::Unfound") {
+ if( sscanf( StrImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3) {
+ dbg.Verbose(0, "gdcmHeader::GetZImagePosition: wrong Image Position Patient (0020,0032)");
+ return 0.; // bug in the element 0x0020,0x0032
+ } else {
+ return zImPos;
+ }
+ }
+ StrImPos = GetPubElValByNumber(0x0020,0x0030); // For ACR-NEMA images
+ if (StrImPos != "gdcm::Unfound") {
+ if( sscanf( StrImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3) {
+ dbg.Verbose(0, "gdcmHeader::GetZImagePosition: wrong Image Position (RET) (0020,0030)");
+ return 0.; // bug in the element 0x0020,0x0032
+ } else {
+ return zImPos;
+ }
+ }
+ string StrSliceLocation = GetPubElValByNumber(0x0020,0x1041);// for *very* old ACR-NEMA images
+ if (StrSliceLocation != "gdcm::Unfound") {
+ if( sscanf( StrSliceLocation.c_str(), "%f", &zImPos) !=1) {
+ dbg.Verbose(0, "gdcmHeader::GetZImagePosition: wrong Slice Location (0020,1041)");
+ return 0.; // bug in the element 0x0020,0x1041
+ } else {
+ return zImPos;
+ }
+ }
+ dbg.Verbose(0, "gdcmHeader::GetZImagePosition: unfound Slice Location (0020,1041)");
+ string StrLocation = GetPubElValByNumber(0x0020,0x0050);
+ if (StrLocation != "gdcm::Unfound") {
+ if( sscanf( StrLocation.c_str(), "%f", &zImPos) !=1) {
+ dbg.Verbose(0, "gdcmHeader::GetZImagePosition: wrong Location (0020,0050)");
+ return 0.; // bug in the element 0x0020,0x0050
+ } else {
+ return zImPos;
+ }
+ }
+ dbg.Verbose(0, "gdcmHeader::GetYImagePosition: unfound Location (0020,0050)");
+ return 0.; // Hopeless
}
-int gdcmHeader::Write(FILE * fp, FileType type) {
- return PubElValSet.Write(fp, type);
-}
+
+
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff