-// $Header: /cvs/public/gdcm/src/Attic/gdcmHeader.cxx,v 1.69 2003/06/17 17:44:48 jpr Exp $
+// $Header: /cvs/public/gdcm/src/Attic/gdcmHeader.cxx,v 1.81 2003/09/05 11:53:39 malaterre Exp $
+
+//This is needed when compiling in debug mode
+#ifdef _MSC_VER
+//'identifier' : not all control paths return a value
+//#pragma warning ( disable : 4715 )
+// 'identifier' : class 'type' needs to have dll-interface to be used by
+// clients of class 'type2'
+#pragma warning ( disable : 4251 )
+// 'identifier' : identifier was truncated to 'number' characters in the
+// debug information
+#pragma warning ( disable : 4786 )
+#endif //_MSC_VER
#include <stdio.h>
#include <cerrno>
#include "gdcmUtil.h"
#include "gdcmHeader.h"
using namespace std;
+#include "gdcmTS.h"
// TODO : remove DEBUG
// Refer to gdcmHeader::CheckSwap()
#define HEADER_LENGTH_TO_READ 256
// Refer to gdcmHeader::SetMaxSizeLoadElementValue()
-#define _MaxSizeLoadElementValue_ 1024
-
+//#define _MaxSizeLoadElementValue_ 1024
+#define _MaxSizeLoadElementValue_ 4096
+/**
+ * \ingroup gdcmHeader
+ * \brief
+ */
void gdcmHeader::Initialise(void) {
dicom_vr = gdcmGlobal::GetVR();
dicom_ts = gdcmGlobal::GetTS();
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();
+ 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_);
Initialise();
}
-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) {
return false;
}
+/**
+ * \ingroup gdcmHeader
+ * \brief
+ * @return TRUE if the close was successfull
+ */
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;
// CRV Curve
// OLY Overlays
// PXL Pixels
+// DL Delimiters
//
/**
// 0x00000004. Finding the swap code in then straigthforward. Trouble
// occurs when we can't find such group...
guint32 s;
- guint32 x=4; // x : pour ntohs
+ guint32 x=4; // x : for ntohs
bool net2host; // true when HostByteOrder is the same as NetworkByteOrder
int lgrLue;
// 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)
/**
* \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.
/**
* \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 false;
}
+/**
+ * \ingroup gdcmHeader
+ * \brief Determines if the Transfer Syntax was already encountered
+ * and if it corresponds to a RLE Lossless one.
+ *
+ * @return True when RLE Lossless found. False in all
+ * other cases.
+ */
+bool gdcmHeader::IsRLELossLessTransferSyntax(void) {
+ gdcmElValue* Element = PubElValSet.GetElementByNumber(0x0002, 0x0010);
+ if ( !Element )
+ return false;
+ LoadElementValueSafe(Element);
+ string Transfer = Element->GetValue();
+ if ( Transfer == "1.2.840.10008.1.2.5" )
+ return true;
+ return false;
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Determines if the Transfer Syntax was already encountered
+ * and if it corresponds to a JPEG200 one.0
+ *
+ * @return True when JPEG2000 (Lossly or LossLess) found. False in all
+ * other cases.
+ */
+bool gdcmHeader::IsJPEG2000(void) {
+ gdcmElValue* Element = PubElValSet.GetElementByNumber(0x0002, 0x0010);
+ if ( !Element )
+ return false;
+ LoadElementValueSafe(Element);
+ string Transfer = Element->GetValue();
+ if ( (Transfer == "1.2.840.10008.1.2.4.90")
+ || (Transfer == "1.2.840.10008.1.2.4.91") )
+ return true;
+ return false;
+}
+
/**
* \ingroup gdcmHeader
* \brief Predicate for dicom version 3 file.
g = ReadInt16();
n = ReadInt16();
- if (DEBUG) printf ("dans FindLengthOB (%04x,%04x)\n",g,n);
- long l = ftell(fp);
- if (DEBUG) printf("en %d o(%o) x(%x)\n",l,l,l);
+ long l = ftell(fp);
if (errno == 1)
return 0;
TotalLength += 4; // We even have to decount the group and element
- if ( g != 0xfffe && g!=0xb00c ) /*for bogus headerJPR */ {
+ 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);
- if (DEBUG) printf("en %d o(%o) x(%x)\n",l,l,l);
errno = 1;
return 0;
}
-
- if ( n == 0xe0dd || ( g==0xb00c && n==0x0eb6 ) ) /* for bogus header JPR */
+ if ( n == 0xe0dd || ( g==0xb00c && n==0x0eb6 ) ) /* for bogus header */
FoundSequenceDelimiter = true;
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);
- if (DEBUG) printf("wrong element (%04x) for an item sequence (%04x,%04x)\n",n, g,n);
errno = 1;
return 0;
}
TotalLength += ItemLength + 4; // We add 4 bytes since we just read
// the ItemLength with ReadInt32
- if (DEBUG) printf("TotalLength %d\n",TotalLength);
SkipBytes(ItemLength);
}
fseek(fp, PositionOnEntry, SEEK_SET);
*/
void gdcmHeader::FindLength (gdcmElValue * ElVal) {
guint16 element = ElVal->GetElement();
- guint16 group = ElVal->GetGroup(); // JPR a virer
+ guint16 group = ElVal->GetGroup();
string vr = ElVal->GetVR();
guint16 length16;
- if( (element == 0x0010) && (group == 0x7fe0) ) {// JPR
-
- dbg.SetDebug(1);
- dbg.Verbose(2, "gdcmHeader::FindLength: ", // JPR
+ if( (element == 0x0010) && (group == 0x7fe0) ) {
+ dbg.SetDebug(0);
+ dbg.Verbose(2, "gdcmHeader::FindLength: ",
"on est sur 7fe0 0010");
}
// 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
/**
* \ingroup gdcmHeader
* \brief
- *
+ * @param ElVal
* @return
*/
void gdcmHeader::SkipElementValue(gdcmElValue * ElVal) {
/**
* \ingroup gdcmHeader
* \brief
- *
+ * @param NewSize
* @return
*/
void gdcmHeader::SetMaxSizeLoadElementValue(long NewSize) {
// Heuristic : a sequence "contains" a set of tags (called items). It looks
// like the last tag of a sequence (the one that terminates the sequence)
// has a group of 0xfffe (with a dummy length).
+ // Well ...
+ // Actually (fffe e000) tells us an Element is beginning
+ // (fffe e00d) tells us an Element just ended
+ // (fffe e0dd) tells us the current SEQuence just ended
+
if( group == 0xfffe )
SkipLoad = true;
// 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) ) {
/**
* \ingroup gdcmHeader
- * \brief
+ * \brief Reads a supposed to be 16 Bits integer
+ * \ (swaps it depending on processor endianity)
*
- * @return
+ * @return integer acts as a boolean
*/
guint16 gdcmHeader::ReadInt16(void) {
guint16 g;
size_t item_read;
item_read = fread (&g, (size_t)2,(size_t)1, fp);
if ( item_read != 1 ) {
- dbg.Verbose(1, "gdcmHeader::ReadInt16", " Failed to read :");
- if(feof(fp))
- dbg.Verbose(1, "gdcmHeader::ReadInt16", " End of File encountered");
- if(ferror(fp))
- dbg.Verbose(1, "gdcmHeader::ReadInt16", " File 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;
}
/**
* \ingroup gdcmHeader
- * \brief
+ * \brief Reads a supposed to be 32 Bits integer
+ * \ (swaps it depending on processor endianity)
*
* @return
*/
guint32 g;
size_t item_read;
item_read = fread (&g, (size_t)4,(size_t)1, fp);
- if ( item_read != 1 ) {
-
- dbg.Verbose(1, "gdcmHeader::ReadInt32", " Failed to read :");
- if(feof(fp))
- dbg.Verbose(1, "gdcmHeader::ReadInt32", " End of File encountered");
+ 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(1, "gdcmHeader::ReadInt32", " File Error");
+ dbg.Verbose(0, "gdcmHeader::ReadInt32", " File Error");
errno = 1;
return 0;
}
/**
* \ingroup gdcmHeader
* \brief TODO
- * @param
+ * @param Value
+ * @param Group
+ * @param Elem
+ * \return integer acts as a boolean
*/
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 Modify or (Creates if not found) an element
+ * @param Value new value
+ * @param Group
+ * @param Elem
+ * \return integer acts as a boolean
+ *
+ */
+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 Set a new value if the invoked element exists
+ * @param Value
+ * @param Group
+ * @param Elem
+ * \return integer acts as a boolean
+ */
+int gdcmHeader::ReplaceIfExistByNumber(char* Value, guint16 Group, guint16 Elem ) {
+
+ gdcmElValue* elValue = PubElValSet.GetElementByNumber(Group, Elem);
+ string v = Value;
+ PubElValSet.SetElValueByNumber(v, Group, Elem);
+ return 1;
+}
+
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Checks if a given ElValue (group,number)
+ * \ exists in the Public ElValSet
+ * @param Group
+ * @param Elem
+ * @return integer acts as a boolean
+ */
+
+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.
if ( (g==0x7fe0) && (n==0x0010) )
if (DEBUG)
- printf("in gdcmHeader::ReadNextElement try to read 7fe0 0010 \n");
+ printf("in gdcmHeader::ReadNextElement try to read 7fe0 0010 \n");
if (errno == 1)
// We reached the EOF (or an error occured) and header parsing
}
NewElVal->SetOffset(ftell(fp));
if ( (g==0x7fe0) && (n==0x0010) )
- if (DEBUG)
- printf("sortie de gdcmHeader::ReadNextElement 7fe0 0010 \n");
+ if (DEBUG)
+ printf("sortie de gdcmHeader::ReadNextElement 7fe0 0010 \n");
return NewElVal;
}
* \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);
+ }
+ // Load 'non string' values
+ rewind(fp);
+ string PhotometricInterpretation = GetPubElValByNumber(0x0028,0x0004);
+ if( PhotometricInterpretation == "PALETTE COLOR " ){
+ LoadElementVoidArea(0x0028,0x1200); // gray LUT
+ LoadElementVoidArea(0x0028,0x1201); // R LUT
+ LoadElementVoidArea(0x0028,0x1202); // G LUT
+ LoadElementVoidArea(0x0028,0x1203); // B LUT
+
+ LoadElementVoidArea(0x0028,0x1221); // Segmented Red Palette Color LUT Data
+ LoadElementVoidArea(0x0028,0x1222); // Segmented Green Palette Color LUT Data
+ LoadElementVoidArea(0x0028,0x1223); // Segmented Blue Palette Color LUT Data
+ }
+}
+
+/**
+ * \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);
+}
//
-// TODO : JPR
-// des que les element values sont chargees, stocker,
-// en une seule fois, dans des entiers
-// NX, NY, NZ, Bits allocated, Bits Stored, High Bit, Samples Per Pixel
-// (TODO : preciser les autres)
-// et refaire ceux des accesseurs qui renvoient les entiers correspondants
+// ------------------------ 'non string' elements related functions
//
-// --> peut etre dangereux ?
-// si l'utilisateur modifie 'manuellement' l'un des paramètres
-// l'entier de sera pas modifié ...
-// (pb de la mise à jour en cas de redondance :-(
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Loads (from disk) the element content
+ * when a string is not suitable
+ */
+void * gdcmHeader::LoadElementVoidArea(guint16 Group, guint16 Elem) {
+ gdcmElValue * Element= PubElValSet.GetElementByNumber(Group, Elem);
+ if ( !Element )
+ return NULL;
+ size_t o =(size_t)Element->GetOffset();
+ fseek(fp, o, SEEK_SET);
+ int l=Element->GetLength();
+ void * a = malloc(l);
+ if(!a) {
+ cout << "Big Broblem (LoadElementVoidArea, malloc) "
+ << hex << Group << " " << Elem << "\n";
+ return NULL;
+ }
+ int res = PubElValSet.SetVoidAreaByNumber(a, Group, Elem);
+ // TODO check the result
+ size_t l2 = fread(a, 1, l ,fp);
+ if(l != l2) {
+ cout << "Big Broblem (LoadElementVoidArea, fread) "
+ << hex << Group << " " << Elem << "\n";
+ free(a);
+ return NULL;
+ }
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Gets (from Header) the offset of a 'non string' element value
+ * \ (LoadElementValue has already be executed)
+ * @param Group
+ * @param Elem
+ * @return File Offset of the Element Value
+ */
+ size_t gdcmHeader::GetPubElValOffsetByNumber(guint16 Group, guint16 Elem) {
+ gdcmElValue* elValue = PubElValSet.GetElementByNumber(Group, Elem);
+ if (!elValue) {
+ dbg.Verbose(1, "gdcmHeader::GetElValueByNumber",
+ "failed to Locate gdcmElValue");
+ return (size_t)0;
+ }
+ return elValue->GetOffset();
+}
+
+/**
+ * \ingroup gdcmHeader
+* \brief Gets (from Header) a 'non string' element value
+ * \ (LoadElementValue has already be executed)
+ * @param Group
+ * @param Elem
+ * @return Pointer to the 'non string' area
+
+ */
+ void * gdcmHeader::GetPubElValVoidAreaByNumber(guint16 Group, guint16 Elem) {
+ gdcmElValue* elValue = PubElValSet.GetElementByNumber(Group, Elem);
+ if (!elValue) {
+ dbg.Verbose(1, "gdcmHeader::GetElValueByNumber",
+ "failed to Locate gdcmElValue");
+ return (NULL);
+ }
+ return elValue->GetVoidArea();
+}
+
+
+//
+// =============================================================================
+// Heuristics based accessors
+//==============================================================================
+//
+
+// TODO : move to an other file.
+
/**
* \ingroup gdcmHeader
return 1;
}
-
/**
* \ingroup gdcmHeader
* \brief Retrieve the number of Bits Stored
return 1; // Well, it's supposed to be mandatory ...
return atoi(StrSize.c_str());
}
+
+/**
+ * \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( BitsAlloc + Signed);
}
-
-/**
- * \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);
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief
- * @return
+ * \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");
+ dbg.Verbose(0, "gdcmHeader::GetXSpacing: unfound Pixel Spacing (0028,0030)");
return 1.;
}
if( sscanf( StrSpacing.c_str(), "%f\\%f", &xspacing, &yspacing) != 2)
/**
* \ingroup gdcmHeader
- * \brief
- * @return
+ * \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");
+ 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.)
- {
+ 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);
/**
- * \ingroup gdcmHeader
- * \brief
- * @return
+ *\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
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 :
-// If not found (AVR-NEMA), we consider Slice Location (20,1041)
-// or Location (20,50) as the Z coordinate,
-// 0. for all the coordinates if Slice Location not found
+// 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
- * @return
+ * \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;
- // 0020,0032 : Image Position Patient
- // 0020,1041 : Slice Location
+ float xImPos, yImPos, zImPos;
string StrImPos = GetPubElValByNumber(0x0020,0x0032);
if (StrImPos == "gdcm::Unfound") {
- dbg.Verbose(0, "gdcmHeader::GetXImagePosition: unfound Image Position Patient");
- string StrSliceLoc = GetPubElValByNumber(0x0020,0x1041);
- if (StrSliceLoc == "gdcm::Unfound") {
- dbg.Verbose(0, "gdcmHeader::GetXImagePosition: unfound Slice Location");
- // How to tell the caller nothing was found?
- }
- return 0.;
+ 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)
- // How to tell the caller a wrong number of values was found?
return 0.;
- //else
return xImPos;
}
/**
* \ingroup gdcmHeader
- * \brief
- * @return
+ * \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;
- // 0020,0032 : Image Position Patient
- // 0020,1041 : Slice Location
- // 0020,0050 : Location
string StrImPos = GetPubElValByNumber(0x0020,0x0032);
if (StrImPos == "gdcm::Unfound") {
- dbg.Verbose(0, "gdcmHeader::GetYImagePosition: unfound Image Position Patient");
- string StrSliceLoc = GetPubElValByNumber(0x0020,0x1041);
- if (StrSliceLoc == "gdcm::Unfound") {
- dbg.Verbose(0, "gdcmHeader::GetYImagePosition: unfound Slice Location");
- // How to tell the caller nothing was found?
- string StrLocation = GetPubElValByNumber(0x0020,0x0050);
- if (StrSliceLoc == "gdcm::Unfound") {
- dbg.Verbose(0, "gdcmHeader::GetYImagePosition: unfound Slice Location");
- }
- }
- return 0.;
+ 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)");
+ // How to tell the caller nothing was found ?
+ return 0.;
+ }
}
if( sscanf( StrImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3)
- // How to tell the caller a wrong number of values was found?
return 0.;
- //else
return yImPos;
}
/**
* \ingroup gdcmHeader
- * \brief
- * @return
+ * \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;
- // 0020,0032 : Image Position Patient
- // 0020,1041 : Slice Location
- // 0020,0050 : Location
-
- // TODO : How to tell the caller nothing was found?
- // TODO : How to tell the caller a wrong number of values was found?
-
+ 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");
+ dbg.Verbose(0, "gdcmHeader::GetZImagePosition: wrong Image Position Patient (0020,0032)");
return 0.; // bug in the element 0x0020,0x0032
} else {
return zImPos;
}
- }
- dbg.Verbose(0, "gdcmHeader::GetYImagePosition: unfound Image Position Patient");
-
- string StrSliceLocation = GetPubElValByNumber(0x0020,0x1041);
+ }
+ 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");
+ 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::GetYImagePosition: unfound Slice Location");
-
+ 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");
+ 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 Slice Location");
-
+ dbg.Verbose(0, "gdcmHeader::GetYImagePosition: unfound Location (0020,0050)");
return 0.; // Hopeless
}
+/**
+ * \ingroup gdcmHeader
+ * \brief gets the info from 0002,0010 : Transfert Syntax
+ * \ else 1.
+ * @return Transfert Syntax Name (as oposite to Transfert Syntax UID)
+ */
+string gdcmHeader::GetTransferSyntaxName(void) {
+ string TransfertSyntax = GetPubElValByNumber(0x0002,0x0010);
+ if (TransfertSyntax == "gdcm::Unfound") {
+ dbg.Verbose(0, "gdcmHeader::GetTransferSyntaxName: unfound Transfert Syntax (0002,0010)");
+ return "Uncompressed ACR-NEMA";
+ }
+ // we do it only when we need it
+ gdcmTS * ts = gdcmGlobal::GetTS();
+ string tsName=ts->GetValue(TransfertSyntax);
+ //delete ts; // Seg Fault when deleted ?!
+ return tsName;
+}
+
+// -------------------------------- Lookup Table related functions ------------
+
+/**
+ * \ingroup gdcmHeader
+ * \brief gets the info from 0028,1101 : Lookup Table Desc-Red
+ * \ else 0
+ * @return Lookup Table Length
+ * \ when (0028,0004),Photometric Interpretation = [PALETTE COLOR ]
+ */
+
+int gdcmHeader::GetLUTLength(void) {
+ vector<string> tokens;
+ int LutLength;
+ //int LutDepth;
+ //int LutNbits;
+ // Just hope Lookup Table Desc-Red = Lookup Table Desc-Red = Lookup Table Desc-Blue
+ string LutDescriptionR = GetPubElValByNumber(0x0028,0x1101);
+ if (LutDescriptionR == "gdcm::Unfound")
+ return 0;
+ string LutDescriptionG = GetPubElValByNumber(0x0028,0x1102);
+ if (LutDescriptionG == "gdcm::Unfound")
+ return 0;
+ string LutDescriptionB = GetPubElValByNumber(0x0028,0x1103);
+ if (LutDescriptionB == "gdcm::Unfound")
+ return 0;
+ if( (LutDescriptionR != LutDescriptionG) || (LutDescriptionR != LutDescriptionB) ) {
+ dbg.Verbose(0, "gdcmHeader::GetLUTLength: The CLUT R,G,B are not equal");
+ return 0;
+ }
+ cout << "Lut Description " << LutDescriptionR <<"\n";
+ tokens.erase(tokens.begin(),tokens.end()); // clean any previous value
+ Tokenize (LutDescriptionR, tokens, "\\");
+ LutLength=atoi(tokens[0].c_str());
+ //LutDepth=atoi(tokens[1].c_str());
+ //LutNbits=atoi(tokens[2].c_str());
+ tokens.clear();
+ return LutLength;
+}
+/**
+ * \ingroup gdcmHeader
+ * \brief gets the info from 0028,1101 : Lookup Table Desc-Red
+ * \ else 0
+ * @return Lookup Table nBit
+ * \ when (0028,0004),Photometric Interpretation = [PALETTE COLOR ]
+ */
+
+int gdcmHeader::GetLUTNbits(void) {
+ vector<string> tokens;
+ //int LutLength;
+ //int LutDepth;
+ int LutNbits;
+ // Just hope Lookup Table Desc-Red = Lookup Table Desc-Red = Lookup Table Desc-Blue
+ // Consistency already checked in GetLUTLength
+ string LutDescription = GetPubElValByNumber(0x0028,0x1101);
+ if (LutDescription == "gdcm::Unfound")
+ return 0;
+ tokens.erase(tokens.begin(),tokens.end()); // clean any previous value
+ Tokenize (LutDescription, tokens, "\\");
+ //LutLength=atoi(tokens[0].c_str());
+ //LutDepth=atoi(tokens[1].c_str());
+ LutNbits=atoi(tokens[2].c_str());
+ tokens.clear();
+ return LutNbits;
+}
+
+
+/**
+ * \ingroup gdcmHeader
+ * \brief gets the info from 0028,1201 : Lookup Table Red
+ * \ else 0
+ * @return Lookup Table Red
+ * \ when (0028,0004),Photometric Interpretation = [PALETTE COLOR ]
+ */
+void * gdcmHeader::GetLUTRed(void) {
+ return GetPubElValVoidAreaByNumber(0x0028,0x1201);
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief gets the info from 0028,1202 : Lookup Table Green
+ * \ else 0
+ * @return Lookup Table Red
+ * \ when (0028,0004),Photometric Interpretation = [PALETTE COLOR ]
+ */
+ void * gdcmHeader::GetLUTGreen(void) {
+ return GetPubElValVoidAreaByNumber(0x0028,0x1202);
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief gets the info from 0028,1202 : Lookup Table Blue
+ * \ else 0
+ * @return Lookup Table Blue
+ * \ when (0028,0004),Photometric Interpretation = [PALETTE COLOR ]
+ */
+void * gdcmHeader::GetLUTBlue(void) {
+ return GetPubElValVoidAreaByNumber(0x0028,0x1203);
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief
+ * @return Lookup Table RGB
+ * \ when (0028,0004),Photometric Interpretation = [PALETTE COLOR ]
+ * \ and (0028,1201),(0028,1202),(0028,1202) are found
+ * \warning : hazardous ! Use better GetPubElValVoidAreaByNumber
+ */
+void * gdcmHeader::GetLUTRGB(void) {
+// Not so easy : see
+// http://www.barre.nom.fr/medical/dicom2/limitations.html#Color%20Lookup%20Tables
+// and OT-PAL-8-face.dcm
+
+ if (GetPubElValByNumber(0x0028,0x0004) == "gdcm::Unfound") {
+ dbg.Verbose(0, "gdcmHeader::GetLUTRGB: unfound Photometric Interpretation");
+ return NULL;
+ }
+ void * LutR,*LutG,*LutB;
+ int l;
+
+ // Maybe, some day we get an image
+ // that respects the definition ...
+ // Let's consider no ones does.
+
+ l= GetLUTLength();
+ if(l==0)
+ return (NULL);
+ int nBits=GetLUTNbits();
+ // a virer quand on aura trouve UNE image
+ // qui correspond VRAIMENT à la definition !
+ cout << "l " << l << " nBits " << nBits;
+
+ l= l/(nBits/8);
+
+ LutR =GetPubElValVoidAreaByNumber(0x0028,0x1201);
+ LutG =GetPubElValVoidAreaByNumber(0x0028,0x1202);
+ LutB =GetPubElValVoidAreaByNumber(0x0028,0x1203);
+
+ // Warning : Any value for nBits as to be considered as 8
+ // Any value for Length as to be considered as 256
+ // That's DICOM ...
+
+ // Just wait before removing the following code
+ /*
+ if (nBits == 16) {
+ guint16 * LUTRGB, *rgb;
+ LUTRGB = rgb = (guint16 *) malloc(3*l*sizeof( guint16));
+ guint16 * r = (guint16 *)LutR;
+ guint16 * g = (guint16 *)LutG;
+ guint16 * b = (guint16 *)LutB;
+ for(int i=0;i<l;i++) {
+ *rgb++ = *r++;
+ *rgb++ = *g++;
+ *rgb++ = *b++;
+ }
+ return(LUTRGB);
+ } else
+
+ */ { // we assume it's always 8 Bits
+ l=256; // we assume ...
+ unsigned char * LUTRGB, *rgb;
+ LUTRGB = rgb = (unsigned char *) malloc(3*l*sizeof( char));
+ unsigned char * r = (unsigned char *)LutR;
+ unsigned char * g = (unsigned char *)LutG;
+ unsigned char * b = (unsigned char *)LutB;
+ for(int i=0;i<l;i++) {
+ //cout << "lut16 " << i << " : " << *r << " " << *g << " " << *b << "\n";
+ printf("lut 8 %d : %d %d %d \n",i,*r,*g,*b);
+ *rgb++ = *r++;
+ *rgb++ = *g++;
+ *rgb++ = *b++;
+ }
+ free(LutR); free(LutB); free(LutG);
+ return(LUTRGB);
+ }
+}
+
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff