-// $Header: /cvs/public/gdcm/src/Attic/gdcmHeader.cxx,v 1.70 2003/06/20 14:17:47 jpr Exp $
+// $Header: /cvs/public/gdcm/src/Attic/gdcmHeader.cxx,v 1.117 2003/11/13 18:08:34 jpr Exp $
+
+#include "gdcmHeader.h"
#include <stdio.h>
#include <cerrno>
#include <cctype> // for isalpha
#include <sstream>
#include "gdcmUtil.h"
-#include "gdcmHeader.h"
-using namespace std;
-
-
-// TODO : remove DEBUG
-#define DEBUG 0
+#include "gdcmTS.h"
// 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
- * @param none
- * @return
*/
- void gdcmHeader::Initialise(void) {
+void gdcmHeader::Initialise(void) {
dicom_vr = gdcmGlobal::GetVR();
dicom_ts = gdcmGlobal::GetTS();
- Dicts = gdcmGlobal::GetDicts();
+ Dicts = gdcmGlobal::GetDicts();
RefPubDict = Dicts->GetDefaultPubDict();
RefShaDict = (gdcmDict*)0;
}
/**
* \ingroup gdcmHeader
* \brief
- * @param
- * @return
- */
- gdcmHeader::gdcmHeader(const char *InFilename, bool exception_on_error) {
- SetMaxSizeLoadElementValue(_MaxSizeLoadElementValue_);
- filename = InFilename;
- Initialise();
- if ( !OpenFile(exception_on_error))
- return;
- ParseHeader();
- LoadElements();
- CloseFile();
+ * @param InFilename
+ * @param exception_on_error
+ */
+gdcmHeader::gdcmHeader(const char *InFilename,
+ bool exception_on_error,
+ bool enable_sequences ) {
+ if (enable_sequences)
+ enableSequences = 1;
+ else
+ enableSequences = 0;
+
+ SetMaxSizeLoadElementValue(_MaxSizeLoadElementValue_);
+ filename = InFilename;
+ Initialise();
+ if ( !OpenFile(exception_on_error))
+ return;
+ ParseHeader();
+ LoadElements();
+ CloseFile();
}
/**
* \ingroup gdcmHeader
* \brief
- * @param
- * @return
+ * @param exception_on_error
*/
- gdcmHeader::gdcmHeader(bool exception_on_error) {
+gdcmHeader::gdcmHeader(bool exception_on_error) {
SetMaxSizeLoadElementValue(_MaxSizeLoadElementValue_);
Initialise();
}
/**
* \ingroup gdcmHeader
* \brief
- * @param
+ * @param exception_on_error
* @return
*/
bool gdcmHeader::OpenFile(bool exception_on_error)
if(!fp)
throw gdcmFileError("gdcmHeader::gdcmHeader(const char *, bool)");
}
- if ( fp )
- return true;
- dbg.Verbose(0, "gdcmHeader::gdcmHeader cannot open file", filename.c_str());
+
+ if ( fp ) {
+ guint16 zero;
+ fread(&zero, (size_t)2, (size_t)1, fp);
+
+ //ACR -- or DICOM with no Preamble
+ if( zero == 0x0008 || zero == 0x0800 || zero == 0x0002 || zero == 0x0200)
+ return true;
+ //DICOM
+ fseek(fp, 126L, SEEK_CUR);
+ char dicm[4];
+ fread(dicm, (size_t)4, (size_t)1, fp);
+ if( memcmp(dicm, "DICM", 4) == 0 )
+ return true;
+ fclose(fp);
+ dbg.Verbose(0, "gdcmHeader::gdcmHeader not DICOM/ACR", filename.c_str());
+ }
+ else {
+ dbg.Verbose(0, "gdcmHeader::gdcmHeader cannot open file", filename.c_str());
+ }
return false;
}
/**
* \ingroup gdcmHeader
* \brief
- * @param
- * @return
+ * @return TRUE if the close was successfull
*/
- bool gdcmHeader::CloseFile(void) {
+bool gdcmHeader::CloseFile(void) {
int closed = fclose(fp);
fp = (FILE *)0;
if (! closed)
/**
* \ingroup gdcmHeader
- * \brief
- * @param
- * @return
+ * \brief Canonical destructor.
*/
- gdcmHeader::~gdcmHeader (void) {
- dicom_vr = (gdcmVR*)0;
- Dicts = (gdcmDictSet*)0;
- RefPubDict = (gdcmDict*)0;
- RefShaDict = (gdcmDict*)0;
- return;
+gdcmHeader::~gdcmHeader (void) {
+ dicom_vr = (gdcmVR*)0;
+ Dicts = (gdcmDictSet*)0;
+ RefPubDict = (gdcmDict*)0;
+ RefShaDict = (gdcmDict*)0;
+ return;
}
// Fourth semantics:
+//
+// ---> Warning : This fourth field is NOT part
+// of the 'official' Dicom Dictionnary
+// and should NOT be used.
+// (Not defined for all the groups
+// may be removed in a future release)
+//
// CMD Command
// META Meta Information
// DIR Directory
// 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:",
/**
* \ingroup gdcmHeader
* \brief
- * @param
- * @return
*/
- void gdcmHeader::SwitchSwapToBigEndian(void) {
+void gdcmHeader::SwitchSwapToBigEndian(void) {
dbg.Verbose(1, "gdcmHeader::SwitchSwapToBigEndian",
"Switching to BigEndian mode.");
if ( sw == 0 ) {
/**
* \ingroup gdcmHeader
* \brief Find the value representation of the current tag.
+ * @param ElVal
*/
void gdcmHeader::FindVR( gdcmElValue *ElVal) {
if (filetype != ExplicitVR)
return;
char VR[3];
- string vr;
+ std::string vr;
int lgrLue;
char msg[100]; // for sprintf. Sorry
lgrLue=fread (&VR, (size_t)2,(size_t)1, fp);
VR[2]=0;
- vr = string(VR);
+ vr = std::string(VR);
// Assume we are reading a falsely explicit VR file i.e. we reached
// a tag where we expect reading a VR but are in fact we read the
// We thought this was explicit VR, but we end up with an
// implicit VR tag. Let's backtrack.
- sprintf(msg,"Falsely explicit vr file (%04x,%04x)\n", ElVal->GetGroup(),ElVal->GetElement());
+ 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
+ // the semantics (see the usage of IsAnInteger), the vr proposed by the
// dictionary entry. Still we have to flag the element as implicit since
// we know now our assumption on expliciteness is not furfilled.
// avoid .
/**
* \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.
if ( !Element )
return false;
LoadElementValueSafe(Element);
- string Transfer = Element->GetValue();
+ std::string Transfer = Element->GetValue();
if ( Transfer == "1.2.840.10008.1.2" )
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 ExplicitVRLittleEndian one.
*
* @return True when ExplicitVRLittleEndian found. False in all other cases.
if ( !Element )
return false;
LoadElementValueSafe(Element);
- string Transfer = Element->GetValue();
+ std::string Transfer = Element->GetValue();
if ( Transfer == "1.2.840.10008.1.2.1" )
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 DeflatedExplicitVRLittleEndian one.
*
* @return True when DeflatedExplicitVRLittleEndian found. False in all other cases.
if ( !Element )
return false;
LoadElementValueSafe(Element);
- string Transfer = Element->GetValue();
+ std::string Transfer = Element->GetValue();
if ( Transfer == "1.2.840.10008.1.2.1.99" )
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 Explicit VR Big Endian one.
*
* @return True when big endian found. False in all other cases.
if ( !Element )
return false;
LoadElementValueSafe(Element);
- string Transfer = Element->GetValue();
+ std::string Transfer = Element->GetValue();
if ( Transfer == "1.2.840.10008.1.2.2" ) //1.2.2 ??? A verifier !
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 JPEGBaseLineProcess1 one.
*
* @return True when JPEGBaseLineProcess1found. False in all other cases.
if ( !Element )
return false;
LoadElementValueSafe(Element);
- string Transfer = Element->GetValue();
+ std::string Transfer = Element->GetValue();
if ( Transfer == "1.2.840.10008.1.2.4.50" )
return true;
return false;
const char * Transfert = Element->GetValue().c_str();
if ( memcmp(Transfert+strlen(Transfert)-2 ,"70",2)==0) return true;
if ( memcmp(Transfert+strlen(Transfert)-2 ,"55",2)==0) return true;
+ if (Element->GetValue() == "1.2.840.10008.1.2.4.57") 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.
if ( !Element )
return false;
LoadElementValueSafe(Element);
- string Transfer = Element->GetValue();
+ std::string Transfer = Element->GetValue();
if ( Transfer == "1.2.840.10008.1.2.4.51" )
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 JPEGExtendeProcess3-5 one.
*
* @return True when JPEGExtendedProcess3-5 found. False in all other cases.
if ( !Element )
return false;
LoadElementValueSafe(Element);
- string Transfer = Element->GetValue();
+ std::string Transfer = Element->GetValue();
if ( Transfer == "1.2.840.10008.1.2.4.52" )
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 JPEGSpectralSelectionProcess6-8 one.
*
* @return True when JPEGSpectralSelectionProcess6-8 found. False in all
if ( !Element )
return false;
LoadElementValueSafe(Element);
- string Transfer = Element->GetValue();
+ std::string Transfer = Element->GetValue();
if ( Transfer == "1.2.840.10008.1.2.4.53" )
return true;
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);
+ std::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);
+ std::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.
* applying this heuristic.
*/
void gdcmHeader::FixFoundLength(gdcmElValue * ElVal, guint32 FoundLength) {
- if ( FoundLength == 0xffffffff)
+
+ ElVal->SetReadLength(FoundLength); // will be updated only if a bug is found
+
+ if ( FoundLength == 0xffffffff) {
FoundLength = 0;
- ElVal->SetLength(FoundLength);
+ }
+
+ // Sorry for the patch!
+ // XMedCom did the trick to read some nasty GE images ...
+ else 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 ( (ElVal->GetGroup() != 0x0008) &&
+ ( (ElVal->GetElement() != 0x0070) || (ElVal->GetElement() != 0x0080) ) ) {
+ // end of remove area
+ FoundLength =10;
+ ElVal->SetReadLength(10); // a bug is to be fixed
+ }
+ }
+ // to fix some garbage 'Leonardo' Siemens images
+ // May be commented out to avoid overhead
+ else if ( (ElVal->GetGroup() == 0x0009)
+ &&
+ ( (ElVal->GetElement() == 0x1113) || (ElVal->GetElement() == 0x1114) ) ){
+ FoundLength =4;
+ ElVal->SetReadLength(4); // a bug is to be fixed
+ }
+ // end of fix
+
+ // to try to 'go inside' SeQuences (with length), and not to skip them
+ else if ( ElVal->GetVR() == "SQ") {
+ if (enableSequences) // only if the user does want to !
+ FoundLength =0;
+ }
+
+ // a SeQuence Element is beginning
+ // Let's forget it's length
+ // (we want to 'go inside')
+ else if(ElVal->GetGroup() == 0xfffe){
+ FoundLength =0;
+ }
+
+ ElVal->SetUsableLength(FoundLength);
}
/**
while ( ! FoundSequenceDelimiter) {
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);
-
+ n = ReadInt16();
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);
+ 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;
}
ItemLength = ReadInt32();
TotalLength += ItemLength + 4; // We add 4 bytes since we just read
- // the ItemLength with ReadInt32
-
- if (DEBUG) printf("TotalLength %d\n",TotalLength);
+ // the ItemLength with ReadInt32
SkipBytes(ItemLength);
}
fseek(fp, PositionOnEntry, SEEK_SET);
*/
void gdcmHeader::FindLength (gdcmElValue * ElVal) {
guint16 element = ElVal->GetElement();
- guint16 group = ElVal->GetGroup(); // JPR a virer
- string vr = ElVal->GetVR();
+ guint16 group = ElVal->GetGroup();
+ std::string vr = ElVal->GetVR();
guint16 length16;
- if( (element == 0x0010) && (group == 0x7fe0) ) {// JPR
-
- dbg.SetDebug(1);
- dbg.Verbose(2, "gdcmHeader::FindLength: ", // JPR
- "on est sur 7fe0 0010");
+ if( (element == 0x0010) && (group == 0x7fe0) ) {
+ dbg.SetDebug(0);
+ dbg.Verbose(2, "gdcmHeader::FindLength: ",
+ "we reached 7fe0 0010");
}
if ( (filetype == ExplicitVR) && ! ElVal->IsImplicitVr() ) {
fseek(fp, 2L, SEEK_CUR);
guint32 length32 = ReadInt32();
+
if ( (vr == "OB") && (length32 == 0xffffffff) ) {
ElVal->SetLength(FindLengthOB());
return;
}
- FixFoundLength(ElVal, length32);
+ FixFoundLength(ElVal, length32);
return;
}
// appear when we find the first group with big endian encoding. This
// is easy to detect since the length of a "Group Length" tag (the
// ones with zero as element number) has to be of 4 (0x0004). When we
- // encouter 1024 (0x0400) chances are the encoding changed and we
+ // encounter 1024 (0x0400) chances are the encoding changed and we
// found a group with big endian encoding.
// 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
// Heuristic: well some files are really ill-formed.
if ( length16 == 0xffff) {
length16 = 0;
- dbg.Verbose(0, "gdcmHeader::FindLength",
- "Erroneous element length fixed.");
+ //dbg.Verbose(0, "gdcmHeader::FindLength",
+ // "Erroneous element length fixed.");
+ // Actually, length= 0xffff means that we deal with
+ // Unknown Sequence Length
}
+
FixFoundLength(ElVal, (guint32)length16);
return;
}
// not coexist in a Data Set and Data Sets nested within it".]
// Length is on 4 bytes.
FixFoundLength(ElVal, ReadInt32());
+ return;
}
/**
* \ingroup gdcmHeader
* \brief Swaps back the bytes of 4-byte long integer accordingly to
* processor order.
- *
- * @return The suggested integer.
+ * @return The properly swaped 32 bits integer.
*/
guint32 gdcmHeader::SwapLong(guint32 a) {
switch (sw) {
/**
* \ingroup gdcmHeader
* \brief
- *
+ * @param ElVal
* @return
*/
void gdcmHeader::SkipElementValue(gdcmElValue * ElVal) {
- SkipBytes(ElVal->GetLength());
+ SkipBytes(ElVal->GetLength());
}
/**
* \ingroup gdcmHeader
* \brief
- *
+ * @param NewSize
* @return
*/
void gdcmHeader::SetMaxSizeLoadElementValue(long NewSize) {
void gdcmHeader::LoadElementValue(gdcmElValue * ElVal) {
size_t item_read;
guint16 group = ElVal->GetGroup();
- string vr = ElVal->GetVR();
+ std::string vr= ElVal->GetVR();
guint32 length = ElVal->GetLength();
bool SkipLoad = false;
// car commencer par les ignorer risque de conduire a qq chose
// qui pourrait ne pas etre generalisable
// Well, I'm expecting your code !!!
+
+ // the test was commented out to 'go inside' the SeQuences
+ // we don't any longer skip them !
- if( vr == "SQ" )
- SkipLoad = true;
+ // if( vr == "SQ" )
+ // SkipLoad = true;
- // 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).
+ // A SeQuence "contains" a set of Elements.
+ // (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;
// are not loaded. Instead we leave a short notice of the offset of
// the element content and it's length.
if (length > MaxSizeLoadElementValue) {
- ostringstream s;
+ std::ostringstream s;
s << "gdcm::NotLoaded.";
s << " Address:" << (long)ElVal->GetOffset();
s << " Length:" << ElVal->GetLength();
+ s << " x(" << std::hex << ElVal->GetLength() << ")";
ElVal->SetValue(s.str());
return;
}
// When an integer is expected, read and convert the following two or
// 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 devrait pouvoir faire + compact (?)
+ // Actually, elements with Value Multiplicity > 1
+ // contain a set of integers (not a single one)
+ // Any compacter code suggested (?)
if ( IsAnInteger(ElVal) ) {
guint32 NewInt;
- ostringstream s;
+ std::ostringstream s;
int nbInt;
if (vr == "US" || vr == "SS") {
nbInt = length / 2;
s << NewInt;
}
}
- }
+ }
+ s << '\0'; // to avoid oddities on Solaris
ElVal->SetValue(s.str());
return;
}
/**
* \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
- */
-int gdcmHeader::ReplaceOrCreateByNumber(string Value, guint16 Group, guint16 Elem ) {
-
- gdcmElValue* nvElValue=NewElValueByNumber(Group, Elem);
- PubElValSet.Add(nvElValue);
- PubElValSet.SetElValueByNumber(Value, Group, Elem);
- return(1);
+ * @param Value
+ * @param Group
+ * @param Elem
+ * \return integer acts as a boolean
+ */
+int gdcmHeader::ReplaceOrCreateByNumber(std::string Value,
+ guint16 Group, guint16 Elem ) {
+ // 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 ???
+ if (CheckIfExistByNumber(Group, Elem) == 0) {
+ gdcmElValue* a =NewElValueByNumber(Group, Elem);
+ if (a == NULL)
+ return 0;
+ PubElValSet.Add(a);
+ }
+ PubElValSet.SetElValueByNumber(Value, Group, Elem);
+ return(1);
}
/**
* \ingroup gdcmHeader
- * \brief TODO
- * @param
+ * \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);
-}
+ gdcmElValue* nvElValue=NewElValueByNumber(Group, Elem);
+ PubElValSet.Add(nvElValue);
+ std::string v = Value;
+ PubElValSet.SetElValueByNumber(v, Group, Elem);
+ return(1);
+}
+
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Set a new value if the invoked element exists
+ * Seems to be useless !!!
+ * @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);
+ std::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.
* a default one when absent.
* @param Name Name of the underlying DictEntry
*/
-gdcmElValue* gdcmHeader::NewElValueByName(string Name) {
+gdcmElValue* gdcmHeader::NewElValueByName(std::string Name) {
gdcmDictEntry * NewTag = GetDictEntryByName(Name);
if (!NewTag)
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) {
// 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));
- if ( (g==0x7fe0) && (n==0x0010) )
- if (DEBUG)
- printf("sortie de gdcmHeader::ReadNextElement 7fe0 0010 \n");
+ //if ( (g==0x7fe0) && (n==0x0010) )
return NewElVal;
}
* @return The result of the heuristical predicate.
*/
bool gdcmHeader::IsAnInteger(gdcmElValue * ElVal) {
- guint16 group = ElVal->GetGroup();
guint16 element = ElVal->GetElement();
- string vr = ElVal->GetVR();
+ std::string vr = ElVal->GetVR();
guint32 length = ElVal->GetLength();
// When we have some semantics on the element we just read, and if we
if (length == 4)
return true;
else {
- if (DEBUG) printf("Erroneous Group Length element length (%04x , %04x) : %d\n",
- group, element,length);
-
dbg.Error("gdcmHeader::IsAnInteger",
"Erroneous Group Length element length.");
}
// When the "Image Location" is absent we default to group 0x7fe0.
guint16 grPixel;
guint16 numPixel;
- string ImageLocation = GetPubElValByName("Image Location");
- if ( ImageLocation == "gdcm::Unfound" ) {
+ std::string ImageLocation = GetPubElValByName("Image Location");
+ if ( ImageLocation == GDCM_UNFOUND ) {
grPixel = 0x7fe0;
} else {
grPixel = (guint16) atoi( ImageLocation.c_str() );
return 0;
}
+/**
+ * \ingroup gdcmHeader
+ * \brief Recover the pixel area length (in Bytes) .
+ */
+size_t gdcmHeader::GetPixelAreaLength(void) {
+ // If this file complies with the norm we should encounter the
+ // "Image Location" tag (0x0028, 0x0200). This tag contains the
+ // the group that contains the pixel data (hence the "Pixel Data"
+ // is found by indirection through the "Image Location").
+ // Inside the group pointed by "Image Location" the searched element
+ // is conventionally the element 0x0010 (when the norm is respected).
+ // When the "Image Location" is absent we default to group 0x7fe0.
+ guint16 grPixel;
+ guint16 numPixel;
+ std::string ImageLocation = GetPubElValByName("Image Location");
+ if ( ImageLocation == GDCM_UNFOUND ) {
+ grPixel = 0x7fe0;
+ } else {
+ grPixel = (guint16) atoi( ImageLocation.c_str() );
+ }
+ if (grPixel != 0x7fe0)
+ // This is a kludge for old dirty Philips imager.
+ numPixel = 0x1010;
+ else
+ numPixel = 0x0010;
+
+ gdcmElValue* PixelElement = PubElValSet.GetElementByNumber(grPixel,
+ numPixel);
+ if (PixelElement)
+ return PixelElement->GetLength();
+ else
+ return 0;
+}
+
/**
* \ingroup gdcmHeader
* \brief Searches both the public and the shadow dictionary (when they
* @param Name name of the searched DictEntry
* @return Corresponding DictEntry when it exists, NULL otherwise.
*/
-gdcmDictEntry * gdcmHeader::GetDictEntryByName(string Name) {
+gdcmDictEntry * gdcmHeader::GetDictEntryByName(std::string Name) {
gdcmDictEntry * found = (gdcmDictEntry*)0;
if (!RefPubDict && !RefShaDict) {
dbg.Verbose(0, "gdcmHeader::GetDictEntry",
* @param group Group of the researched tag.
* @param element Element of the researched tag.
* @return Corresponding element value when it exists, and the string
- * "gdcm::Unfound" otherwise.
+ * GDCM_UNFOUND ("gdcm::Unfound") otherwise.
*/
-string gdcmHeader::GetPubElValByNumber(guint16 group, guint16 element) {
+std::string gdcmHeader::GetPubElValByNumber(guint16 group, guint16 element) {
return PubElValSet.GetElValueByNumber(group, element);
}
* @param group Group of the researched tag.
* @param element Element of the researched tag.
* @return Corresponding element value representation when it exists,
- * and the string "gdcm::Unfound" otherwise.
+ * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise.
*/
-string gdcmHeader::GetPubElValRepByNumber(guint16 group, guint16 element) {
+std::string gdcmHeader::GetPubElValRepByNumber(guint16 group, guint16 element) {
gdcmElValue* elem = PubElValSet.GetElementByNumber(group, element);
if ( !elem )
- return "gdcm::Unfound";
+ return GDCM_UNFOUND;
return elem->GetVR();
}
* \ingroup gdcmHeader
* \brief Searches within the public dictionary for element value of
* a given tag.
- * @param TagName name of the researched element.
+ * @param TagName name of the searched element.
* @return Corresponding element value when it exists, and the string
- * "gdcm::Unfound" otherwise.
+ * GDCM_UNFOUND ("gdcm::Unfound") otherwise.
*/
-string gdcmHeader::GetPubElValByName(string TagName) {
+std::string gdcmHeader::GetPubElValByName(std::string TagName) {
return PubElValSet.GetElValueByName(TagName);
}
* to convert the string typed content to caller's native type
* (think of C++ vs Python). The VR is actually of a higher level
* of semantics than just the native C++ type.
- * @param TagName name of the researched element.
+ * @param TagName name of the searched element.
* @return Corresponding element value representation when it exists,
- * and the string "gdcm::Unfound" otherwise.
+ * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise.
*/
-string gdcmHeader::GetPubElValRepByName(string TagName) {
+std::string gdcmHeader::GetPubElValRepByName(std::string TagName) {
gdcmElValue* elem = PubElValSet.GetElementByName(TagName);
if ( !elem )
- return "gdcm::Unfound";
+ return GDCM_UNFOUND;
return elem->GetVR();
}
* \ingroup gdcmHeader
* \brief Searches within elements parsed with the SHADOW dictionary
* for the element value of a given tag.
- * @param group Group of the researched tag.
- * @param element Element of the researched tag.
+ * @param group Group of the searched tag.
+ * @param element Element of the searched tag.
* @return Corresponding element value representation when it exists,
- * and the string "gdcm::Unfound" otherwise.
+ * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise.
*/
-string gdcmHeader::GetShaElValByNumber(guint16 group, guint16 element) {
+std::string gdcmHeader::GetShaElValByNumber(guint16 group, guint16 element) {
return ShaElValSet.GetElValueByNumber(group, element);
}
* to convert the string typed content to caller's native type
* (think of C++ vs Python). The VR is actually of a higher level
* of semantics than just the native C++ type.
- * @param group Group of the researched tag.
- * @param element Element of the researched tag.
+ * @param group Group of the searched tag.
+ * @param element Element of the searched tag.
* @return Corresponding element value representation when it exists,
- * and the string "gdcm::Unfound" otherwise.
+ * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise.
*/
-string gdcmHeader::GetShaElValRepByNumber(guint16 group, guint16 element) {
+std::string gdcmHeader::GetShaElValRepByNumber(guint16 group, guint16 element) {
gdcmElValue* elem = ShaElValSet.GetElementByNumber(group, element);
if ( !elem )
- return "gdcm::Unfound";
+ return GDCM_UNFOUND;
return elem->GetVR();
}
* \ingroup gdcmHeader
* \brief Searches within the elements parsed with the shadow dictionary
* for an element value of given tag.
- * @param TagName name of the researched element.
+ * @param TagName name of the searched element.
* @return Corresponding element value when it exists, and the string
- * "gdcm::Unfound" otherwise.
+ * GDCM_UNFOUND ("gdcm::Unfound") otherwise.
*/
-string gdcmHeader::GetShaElValByName(string TagName) {
+std::string gdcmHeader::GetShaElValByName(std::string TagName) {
return ShaElValSet.GetElValueByName(TagName);
}
* to convert the string typed content to caller's native type
* (think of C++ vs Python). The VR is actually of a higher level
* of semantics than just the native C++ type.
- * @param TagName name of the researched element.
+ * @param TagName name of the searched element.
* @return Corresponding element value representation when it exists,
- * and the string "gdcm::Unfound" otherwise.
+ * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise.
*/
-string gdcmHeader::GetShaElValRepByName(string TagName) {
+std::string gdcmHeader::GetShaElValRepByName(std::string TagName) {
gdcmElValue* elem = ShaElValSet.GetElementByName(TagName);
if ( !elem )
- return "gdcm::Unfound";
+ return GDCM_UNFOUND;
return elem->GetVR();
}
* \brief Searches within elements parsed with the public dictionary
* and then within the elements parsed with the shadow dictionary
* for the element value of a given tag.
- * @param group Group of the researched tag.
- * @param element Element of the researched tag.
+ * @param group Group of the searched tag.
+ * @param element Element of the searched tag.
* @return Corresponding element value representation when it exists,
- * and the string "gdcm::Unfound" otherwise.
+ * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise.
*/
-string gdcmHeader::GetElValByNumber(guint16 group, guint16 element) {
- string pub = GetPubElValByNumber(group, element);
+std::string gdcmHeader::GetElValByNumber(guint16 group, guint16 element) {
+ std::string pub = GetPubElValByNumber(group, element);
if (pub.length())
return pub;
return GetShaElValByNumber(group, element);
* to convert the string typed content to caller's native type
* (think of C++ vs Python). The VR is actually of a higher level
* of semantics than just the native C++ type.
- * @param group Group of the researched tag.
- * @param element Element of the researched tag.
+ * @param group Group of the searched tag.
+ * @param element Element of the searched tag.
* @return Corresponding element value representation when it exists,
- * and the string "gdcm::Unfound" otherwise.
+ * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise.
*/
-string gdcmHeader::GetElValRepByNumber(guint16 group, guint16 element) {
- string pub = GetPubElValRepByNumber(group, element);
+std::string gdcmHeader::GetElValRepByNumber(guint16 group, guint16 element) {
+ std::string pub = GetPubElValRepByNumber(group, element);
if (pub.length())
return pub;
return GetShaElValRepByNumber(group, element);
* \brief Searches within elements parsed with the public dictionary
* and then within the elements parsed with the shadow dictionary
* for the element value of a given tag.
- * @param TagName name of the researched element.
+ * @param TagName name of the searched element.
* @return Corresponding element value when it exists,
- * and the string "gdcm::Unfound" otherwise.
+ * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise.
*/
-string gdcmHeader::GetElValByName(string TagName) {
- string pub = GetPubElValByName(TagName);
+std::string gdcmHeader::GetElValByName(std::string TagName) {
+ std::string pub = GetPubElValByName(TagName);
if (pub.length())
return pub;
return GetShaElValByName(TagName);
* to convert the string typed content to caller's native type
* (think of C++ vs Python). The VR is actually of a higher level
* of semantics than just the native C++ type.
- * @param TagName name of the researched element.
+ * @param TagName name of the searched element.
* @return Corresponding element value representation when it exists,
- * and the string "gdcm::Unfound" otherwise.
+ * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise.
*/
-string gdcmHeader::GetElValRepByName(string TagName) {
- string pub = GetPubElValRepByName(TagName);
+std::string gdcmHeader::GetElValRepByName(std::string TagName) {
+ std::string pub = GetPubElValRepByName(TagName);
if (pub.length())
return pub;
return GetShaElValRepByName(TagName);
* @param group group of the ElVal to modify
* @param element element of the ElVal to modify
*/
-int gdcmHeader::SetPubElValByNumber(string content, guint16 group,
+int gdcmHeader::SetPubElValByNumber(std::string content, guint16 group,
guint16 element)
-//TODO : homogeneiser les noms : SetPubElValByNumber qui appelle PubElValSet.SetElValueByNumber
+//TODO : homogeneiser les noms : SetPubElValByNumber
+// qui appelle PubElValSet.SetElValueByNumber
// pourquoi pas SetPubElValueByNumber ??
{
* @param content new value to substitute with
* @param TagName name of the tag to be modified
*/
-int gdcmHeader::SetPubElValByName(string content, string TagName) {
+int gdcmHeader::SetPubElValByName(std::string content, std::string TagName) {
return ( PubElValSet.SetElValueByName (content, TagName) );
}
* @param element element of the ElVal to modify
* @return 1 on success, 0 otherwise.
*/
-int gdcmHeader::SetShaElValByNumber(string content,
+int gdcmHeader::SetShaElValByNumber(std::string content,
guint16 group, guint16 element) {
return ( ShaElValSet.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(std::string content, std::string ShadowTagName) {
+ return ( ShaElValSet.SetElValueByName (content, ShadowTagName) );
}
/**
rewind(fp);
CheckSwap();
- while ( (newElValue = ReadNextElement()) ) {
+ while ( (newElValue = ReadNextElement()) ) {
SkipElementValue(newElValue);
PubElValSet.Add(newElValue);
}
}
+/**
+ * \ingroup gdcmHeader
+ * \brief This predicate, based on hopefully reasonable 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(std::string NewTagName,
+ std::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);
+
+ // We don't use any longer the HashTable, since a lot a stuff is missing
+ // when SeQuences were encountered
+ //
+ //TagElValueHT ht = PubElValSet.GetTagHt();
+ //for (TagElValueHT::iterator tag = ht.begin(); tag != ht.end(); ++tag) {
+ // LoadElementValue(tag->second);
+ //}
+
+ for (ListTag::iterator i = GetListElem().begin();
+ i != GetListElem().end();
+ ++i){
+ LoadElementValue(*i);
+ }
+
+ rewind(fp);
+
+ // Load 'non string' values
+ std::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
+ }
+
+ // --------------------------------------------------------------
+ // Special Patch to allow gdcm to read ACR-LibIDO formated images
+ //
+ // if recognition code tells us we deal with a LibIDO image
+ // we switch lineNumber and columnNumber
+ //
+ std::string RecCode;
+ RecCode = GetPubElValByNumber(0x0008, 0x0010);
+ if (RecCode == "ACRNEMA_LIBIDO_1.1" ||
+ RecCode == "CANRME_AILIBOD1_1." ) {
+ filetype = ACR_LIBIDO;
+ std::string rows = GetPubElValByNumber(0x0028, 0x0010);
+ std::string columns = GetPubElValByNumber(0x0028, 0x0011);
+ SetPubElValByNumber(columns, 0x0028, 0x0010);
+ SetPubElValByNumber(rows , 0x0028, 0x0011);
+ }
+ // ----------------- End of Special Patch ----------------
+}
+
+/**
+ * \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 integer, acts as a Boolean
+ */
+int gdcmHeader::Write(FILE * fp, FileType type) {
+
+ // TODO : move the following lines (and a lot of others, to be written)
+ // to a future function CheckAndCorrectHeader
+
+ if (type == ImplicitVR) {
+ std::string implicitVRTransfertSyntax = "1.2.840.10008.1.2";
+ ReplaceOrCreateByNumber(implicitVRTransfertSyntax,0x0002, 0x0010);
+
+ //FIXME Refer to standards on page 21, chapter 6.2 "Value representation":
+ // values with a VR of UI shall be padded with a single trailing null
+ // Dans le cas suivant on doit pader manuellement avec un 0
+
+ PubElValSet.SetElValueLengthByNumber(18, 0x0002, 0x0010);
+ }
+
+ if (type == ExplicitVR) {
+ std::string explicitVRTransfertSyntax = "1.2.840.10008.1.2.1";
+ ReplaceOrCreateByNumber(explicitVRTransfertSyntax,0x0002, 0x0010);
+
+ //FIXME Refer to standards on page 21, chapter 6.2 "Value representation":
+ // values with a VR of UI shall be padded with a single trailing null
+ // Dans le cas suivant on doit pader manuellement avec un 0
+
+ PubElValSet.SetElValueLengthByNumber(20, 0x0002, 0x0010);
+ }
+
+ return PubElValSet.Write(fp, type);
+}
+
+//
+// ------------------------ 'non string' elements related functions
+//
+
+/**
+ * \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) {
+ std::cout << "Big Broblem (LoadElementVoidArea, malloc) "
+ << std::hex << Group << " " << Elem << std::endl;
+ return NULL;
+ }
+ /* int res = */ PubElValSet.SetVoidAreaByNumber(a, Group, Elem);
+ // TODO check the result
+ size_t l2 = fread(a, 1, l ,fp);
+ if(l != l2) {
+ std::cout << "Big Broblem (LoadElementVoidArea, fread) "
+ << std::hex << Group << " " << Elem << std::endl;
+ free(a);
+ return NULL;
+ }
+ return a;
+}
+
+/**
+ * \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();
+}
+
//
-// 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
+// =============================================================================
+// Heuristics based accessors
+//==============================================================================
//
-// --> 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 :-(
+
+// TODO : move to an other file.
+
/**
* \ingroup gdcmHeader
int gdcmHeader::GetXSize(void) {
// We cannot check for "Columns" because the "Columns" tag is present
// both in IMG (0028,0011) and OLY (6000,0011) sections of the dictionary.
- string StrSize = GetPubElValByNumber(0x0028,0x0011);
- if (StrSize == "gdcm::Unfound")
+ std::string StrSize = GetPubElValByNumber(0x0028,0x0011);
+ if (StrSize == GDCM_UNFOUND)
return 0;
return atoi(StrSize.c_str());
}
int gdcmHeader::GetYSize(void) {
// We cannot check for "Rows" because the "Rows" tag is present
// both in IMG (0028,0010) and OLY (6000,0010) sections of the dictionary.
- string StrSize = GetPubElValByNumber(0x0028,0x0010);
- if (StrSize != "gdcm::Unfound")
+ std::string StrSize = GetPubElValByNumber(0x0028,0x0010);
+ if (StrSize != GDCM_UNFOUND)
return atoi(StrSize.c_str());
if ( IsDicomV3() )
return 0;
int gdcmHeader::GetZSize(void) {
// Both in DicomV3 and ACR/Nema the consider the "Number of Frames"
// as the third dimension.
- string StrSize = GetPubElValByNumber(0x0028,0x0008);
- if (StrSize != "gdcm::Unfound")
+ std::string StrSize = GetPubElValByNumber(0x0028,0x0008);
+ if (StrSize != GDCM_UNFOUND)
return atoi(StrSize.c_str());
// We then consider the "Planes" entry as the third dimension [we
// cannot retrieve by name since "Planes tag is present both in
// IMG (0028,0012) and OLY (6000,0012) sections of the dictionary].
StrSize = GetPubElValByNumber(0x0028,0x0012);
- if (StrSize != "gdcm::Unfound")
+ if (StrSize != GDCM_UNFOUND)
return atoi(StrSize.c_str());
return 1;
}
-
/**
* \ingroup gdcmHeader
* \brief Retrieve the number of Bits Stored
* @return The encountered number of Bits Stored, 0 by default.
*/
int gdcmHeader::GetBitsStored(void) {
- string StrSize = GetPubElValByNumber(0x0028,0x0101);
- if (StrSize == "gdcm::Unfound")
+ std::string StrSize = GetPubElValByNumber(0x0028,0x0101);
+ if (StrSize == GDCM_UNFOUND)
return 1;
return atoi(StrSize.c_str());
}
+/**
+ * \ingroup gdcmHeader
+ * \brief Retrieve the number of Bits Allocated
+ * (8, 12 -compacted ACR-NEMA files, 16, ...)
+ *
+ * @return The encountered number of Bits Allocated, 0 by default.
+ */
+int gdcmHeader::GetBitsAllocated(void) {
+ std::string StrSize = GetPubElValByNumber(0x0028,0x0100);
+ 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)
+ * (1 : gray level, 3 : RGB -1 or 3 Planes-)
*
* @return The encountered number of Samples Per Pixel, 1 by default.
*/
int gdcmHeader::GetSamplesPerPixel(void) {
- string StrSize = GetPubElValByNumber(0x0028,0x0002);
- if (StrSize == "gdcm::Unfound")
+ std::string StrSize = GetPubElValByNumber(0x0028,0x0002);
+ if (StrSize == GDCM_UNFOUND)
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) {
+ std::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.
*
*/
int gdcmHeader::GetPixelSize(void) {
- string PixelType = GetPixelType();
+ std::string PixelType = GetPixelType();
if (PixelType == "8U" || PixelType == "8S")
return 1;
if (PixelType == "16U" || PixelType == "16S")
* - 32U unsigned 32 bit,
* - 32S signed 32 bit,
* \warning 12 bit images appear as 16 bit.
+ * \ 24 bit images appear as 8 bit
* @return
*/
-string gdcmHeader::GetPixelType(void) {
- string BitsAlloc;
+std::string gdcmHeader::GetPixelType(void) {
+ std::string BitsAlloc;
BitsAlloc = GetElValByName("Bits Allocated");
- if (BitsAlloc == "gdcm::Unfound") {
+ if (BitsAlloc == GDCM_UNFOUND) {
dbg.Verbose(0, "gdcmHeader::GetPixelType: unfound Bits Allocated");
- BitsAlloc = string("16");
+ BitsAlloc = std::string("16");
}
- if (BitsAlloc == "12")
- BitsAlloc = string("16");
-
- string Signed;
+ if (BitsAlloc == "12") // It will be unpacked
+ BitsAlloc = std::string("16");
+ else if (BitsAlloc == "24") // (in order no to be messed up
+ BitsAlloc = std::string("8"); // by old RGB images)
+
+ std::string Signed;
Signed = GetElValByName("Pixel Representation");
- if (Signed == "gdcm::Unfound") {
+ if (Signed == GDCM_UNFOUND) {
dbg.Verbose(0, "gdcmHeader::GetPixelType: unfound Pixel Representation");
- BitsAlloc = string("0");
+ BitsAlloc = std::string("0");
}
if (Signed == "0")
- Signed = string("U");
+ Signed = std::string("U");
else
- Signed = string("S");
-
- 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);
-}
+std::cout << "GetPixelType : " << BitsAlloc + Signed << std::endl;
+ Signed = std::string("S");
-/**
- * \ingroup gdcmHeader
- * \brief
- * @return
- */
-void gdcmHeader::PrintPubDict(std::ostream & os) {
- RefPubDict->Print(os);
+ return( BitsAlloc + Signed);
}
/**
* \ingroup gdcmHeader
- * \brief
- * @return
+ * \brief gets the info from 0002,0010 : Transfert Syntax
+ * \ else 1.
+ * @return Transfert Syntax Name (as oposite to Transfert Syntax UID)
*/
-
-int gdcmHeader::Write(FILE * fp, FileType type) {
- return PubElValSet.Write(fp, type);
+std::string gdcmHeader::GetTransferSyntaxName(void) {
+ std::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();
+ std::string tsName=ts->GetValue(TransfertSyntax);
+ //delete ts; // Seg Fault when deleted ?!
+ return tsName;
}
-/**
- * \ingroup gdcmHeader
- * \brief
- * @return
- */
-float gdcmHeader::GetXSpacing(void) {
- float xspacing, yspacing;
- string StrSpacing = GetPubElValByNumber(0x0028,0x0030);
-
- if (StrSpacing == "gdcm::Unfound") {
- dbg.Verbose(0, "gdcmHeader::GetXSpacing: unfound Pixel Spacing");
- return 1.;
- }
- if( sscanf( StrSpacing.c_str(), "%f\\%f", &xspacing, &yspacing) != 2)
- return 0.;
- //else
- return xspacing;
-}
+// -------------------------------- Lookup Table related functions ------------
/**
* \ingroup gdcmHeader
- * \brief
- * @return
+ * \brief tells us if LUT are used
+ * \warning Right now, Segmented xxx Palette Color Lookup Table Data
+ * \ are NOT considered as LUT, since nobody knows
+ *\ how to deal with them
+ * @return int acts as a Boolean
*/
-float gdcmHeader::GetYSpacing(void) {
- float xspacing, yspacing;
- string StrSpacing = GetPubElValByNumber(0x0028,0x0030);
- if (StrSpacing == "gdcm::Unfound") {
- dbg.Verbose(0, "gdcmHeader::GetYSpacing: unfound Pixel Spacing");
- 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;
-}
-
-
-/**
- * \ingroup gdcmHeader
- * \brief
- * @return
- */
-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
- return atof(StrSliceThickness.c_str());
- } else {
- return atof(StrSpacingBSlices.c_str());
- }
-}
+int gdcmHeader::HasLUT(void) {
-//
-// 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
-// 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
- */
-float gdcmHeader::GetXImagePosition(void) {
- float xImPos, yImPos, zImPos;
- // 0020,0032 : Image Position Patient
- // 0020,1041 : Slice Location
- 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.;
- }
- 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;
+ // Check the presence of the LUT Descriptors
+ if (GetPubElValByNumber(0x0028,0x1101) == GDCM_UNFOUND)
+ return 0;
+ // LutDescriptorGreen
+ if (GetPubElValByNumber(0x0028,0x1102) == GDCM_UNFOUND)
+ return 0;
+ // LutDescriptorBlue
+ if (GetPubElValByNumber(0x0028,0x1103) == GDCM_UNFOUND)
+ return 0;
+ // It is not enough
+ // we check also
+ if (GetPubElValByNumber(0x0028,0x1201) == GDCM_UNFOUND)
+ return 0;
+ if (GetPubElValByNumber(0x0028,0x1202) == GDCM_UNFOUND)
+ return 0;
+ if (GetPubElValByNumber(0x0028,0x1203) == GDCM_UNFOUND)
+ return 0;
+ return 1;
}
/**
* \ingroup gdcmHeader
- * \brief
- * @return
+ * \brief gets the info from 0028,1101 : Lookup Table Desc-Red
+ * \ else 0
+ * @return Lookup Table nBit
+ * \ when (0028,0004),Photometric Interpretation = [PALETTE COLOR ]
*/
-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.;
- }
- 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;
+
+int gdcmHeader::GetLUTNbits(void) {
+ std::vector<std::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
+ std::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
- * @return
- */
-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?
+ * \brief builts Red/Green/Blue/Alpha LUT from Header
+ * \ when (0028,0004),Photometric Interpretation = [PALETTE COLOR ]
+ * \ and (0028,1101),(0028,1102),(0028,1102)
+ * \ - xxx Palette Color Lookup Table Descriptor - are found
+ * \ and (0028,1201),(0028,1202),(0028,1202)
+ * \ - xxx Palette Color Lookup Table Data - are found
+ * \warning does NOT deal with :
+ * \ 0028 1100 Gray Lookup Table Descriptor (Retired)
+ * \ 0028 1221 Segmented Red Palette Color Lookup Table Data
+ * \ 0028 1222 Segmented Green Palette Color Lookup Table Data
+ * \ 0028 1223 Segmented Blue Palette Color Lookup Table Data
+ * \ no known Dicom reader deails with them :-(
+ * @return Lookup Table RGBA
+ */
- 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");
- 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);
- if (StrSliceLocation != "gdcm::Unfound") {
- if( sscanf( StrSliceLocation.c_str(), "%f", &zImPos) !=1) {
- dbg.Verbose(0, "gdcmHeader::GetZImagePosition: wrong Slice Location");
- return 0.; // bug in the element 0x0020,0x1041
- } else {
- return zImPos;
- }
- }
- dbg.Verbose(0, "gdcmHeader::GetYImagePosition: unfound Slice Location");
-
- string StrLocation = GetPubElValByNumber(0x0020,0x0050);
- if (StrLocation != "gdcm::Unfound") {
- if( sscanf( StrLocation.c_str(), "%f", &zImPos) !=1) {
- dbg.Verbose(0, "gdcmHeader::GetZImagePosition: wrong Location");
- return 0.; // bug in the element 0x0020,0x0050
- } else {
- return zImPos;
- }
- }
- dbg.Verbose(0, "gdcmHeader::GetYImagePosition: unfound Slice Location");
+unsigned char * gdcmHeader::GetLUTRGBA(void) {
+// Not so easy : see
+// http://www.barre.nom.fr/medical/dicom2/limitations.html#Color%20Lookup%20Tables
+// and OT-PAL-8-face.dcm
+
+// if Photometric Interpretation # PALETTE COLOR, no LUT to be done
+
+ if (gdcmHeader::GetPubElValByNumber(0x0028,0x0004) != "PALETTE COLOR ") {
+ return NULL;
+ }
+
+ int lengthR, debR, nbitsR;
+ int lengthG, debG, nbitsG;
+ int lengthB, debB, nbitsB;
- return 0.; // Hopeless
-}
-
-
+// Get info from Lut Descriptors
+// (the 3 LUT descriptors may be different)
+
+ std::string LutDescriptionR = GetPubElValByNumber(0x0028,0x1101);
+ if (LutDescriptionR == GDCM_UNFOUND)
+ return NULL;
+ std::string LutDescriptionG = GetPubElValByNumber(0x0028,0x1102);
+ if (LutDescriptionG == GDCM_UNFOUND)
+ return NULL;
+ std::string LutDescriptionB = GetPubElValByNumber(0x0028,0x1103);
+ if (LutDescriptionB == GDCM_UNFOUND)
+ return NULL;
+
+ std::vector<std::string> tokens;
+
+ tokens.erase(tokens.begin(),tokens.end()); // clean any previous value
+ Tokenize (LutDescriptionR, tokens, "\\");
+ lengthR=atoi(tokens[0].c_str()); // Red LUT length in Bytes
+ debR =atoi(tokens[1].c_str()); // subscript of the first Lut Value
+ nbitsR =atoi(tokens[2].c_str()); // Lut item size (in Bits)
+ tokens.clear();
+
+ tokens.erase(tokens.begin(),tokens.end()); // clean any previous value
+ Tokenize (LutDescriptionG, tokens, "\\");
+ lengthG=atoi(tokens[0].c_str()); // Green LUT length in Bytes
+ debG =atoi(tokens[1].c_str());
+ nbitsG =atoi(tokens[2].c_str());
+ tokens.clear();
+
+ tokens.erase(tokens.begin(),tokens.end()); // clean any previous value
+ Tokenize (LutDescriptionB, tokens, "\\");
+ lengthB=atoi(tokens[0].c_str()); // Blue LUT length in Bytes
+ debB =atoi(tokens[1].c_str());
+ nbitsB =atoi(tokens[2].c_str());
+ tokens.clear();
+
+// Load LUTs into memory, (as they were stored on disk)
+
+ unsigned char *lutR =(unsigned char *)
+ GetPubElValVoidAreaByNumber(0x0028,0x1201);
+ unsigned char *lutG =(unsigned char *)
+ GetPubElValVoidAreaByNumber(0x0028,0x1202);
+ unsigned char *lutB =(unsigned char *)
+ GetPubElValVoidAreaByNumber(0x0028,0x1203);
+
+ if (!lutR || !lutG || !lutB ) {
+ return NULL;
+ }
+ // forge the 4 * 8 Bits Red/Green/Blue/Alpha LUT
+
+ unsigned char *LUTRGBA = (unsigned char *)calloc(1024,1); // 256 * 4 (R, G, B, Alpha)
+ if (!LUTRGBA) {
+ return NULL;
+ }
+ memset(LUTRGBA, 0, 1024);
+ // Bits Allocated
+ int nb;
+ std::string str_nb = GetPubElValByNumber(0x0028,0x0100);
+ if (str_nb == GDCM_UNFOUND ) {
+ nb = 16;
+ } else {
+ nb = atoi(str_nb.c_str() );
+ }
+ int mult;
+
+ if (nbitsR==16 && nb==8) // when LUT item size is different than pixel size
+ mult=2; // high byte must be = low byte
+ else // See PS 3.3-2003 C.11.1.1.2 p 619
+ mult=1;
+
+
+ // if we get a black image, let's just remove the '+1'
+ // from 'i*mult+1' and check again
+ // if it works, we shall have to check the 3 Palettes
+ // to see which byte is ==0 (first one, or second one)
+ // and fix the code
+ // We give up the checking to avoid some overhead
+
+ unsigned char *a;
+ int i;
+ a= LUTRGBA+0;
+ for(i=0;i<lengthR;i++) {
+ *a = lutR[i*mult+1];
+ a+=4;
+ }
+ a= LUTRGBA+1;
+ for(i=0;i<lengthG;i++) {
+ *a = lutG[i*mult+1];
+ a+=4;
+ }
+ a= LUTRGBA+2;
+ for(i=0;i<lengthB;i++) {
+ *a = lutB[i*mult+1];
+ a+=4;
+ }
+ a= LUTRGBA+3;
+ for(i=0;i<256;i++) {
+ *a = 1; // Alpha component
+ a+=4;
+ }
+
+//How to free the now useless LUTs?
+//
+//free(LutR); free(LutB); free(LutG);
+ return(LUTRGBA);
+}
+
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff