-// gdcmHeader.cxx
+// $Header: /cvs/public/gdcm/src/Attic/gdcmHeader.cxx,v 1.69 2003/06/17 17:44:48 jpr Exp $
#include <stdio.h>
#include <cerrno>
#include <sstream>
#include "gdcmUtil.h"
#include "gdcmHeader.h"
+using namespace std;
-#include "iddcmjpeg.h"
+
+// TODO : remove DEBUG
+#define DEBUG 0
// Refer to gdcmHeader::CheckSwap()
#define HEADER_LENGTH_TO_READ 256
// Refer to gdcmHeader::SetMaxSizeLoadElementValue()
#define _MaxSizeLoadElementValue_ 1024
-VRHT * gdcmHeader::dicom_vr = (VRHT*)0;
-
void gdcmHeader::Initialise(void) {
- if (!gdcmHeader::dicom_vr)
- InitVRDict();
- Dicts = new gdcmDictSet();
+ dicom_vr = gdcmGlobal::GetVR();
+ dicom_ts = gdcmGlobal::GetTS();
+ Dicts = gdcmGlobal::GetDicts();
RefPubDict = Dicts->GetDefaultPubDict();
RefShaDict = (gdcmDict*)0;
}
-gdcmHeader::gdcmHeader(const char *InFilename, bool exception_on_error)
- throw(gdcmFileError) {
+gdcmHeader::gdcmHeader(const char *InFilename, bool exception_on_error) {
SetMaxSizeLoadElementValue(_MaxSizeLoadElementValue_);
filename = InFilename;
Initialise();
- fp=fopen(InFilename,"rb");
+ if ( !OpenFile(exception_on_error))
+ return;
+ ParseHeader();
+ LoadElements();
+ CloseFile();
+}
+
+gdcmHeader::gdcmHeader(bool exception_on_error) {
+ SetMaxSizeLoadElementValue(_MaxSizeLoadElementValue_);
+ Initialise();
+}
+
+bool gdcmHeader::OpenFile(bool exception_on_error)
+ throw(gdcmFileError) {
+ fp=fopen(filename.c_str(),"rb");
if(exception_on_error) {
if(!fp)
throw gdcmFileError("gdcmHeader::gdcmHeader(const char *, bool)");
}
- else
- dbg.Error(!fp, "gdcmHeader::gdcmHeader cannot open file", InFilename);
- ParseHeader();
- LoadElements();
- AddAndDefaultElements();
+ if ( fp )
+ return true;
+ dbg.Verbose(0, "gdcmHeader::gdcmHeader cannot open file", filename.c_str());
+ return false;
}
+bool gdcmHeader::CloseFile(void) {
+ int closed = fclose(fp);
+ fp = (FILE *)0;
+ if (! closed)
+ return false;
+ return true;
+}
gdcmHeader::~gdcmHeader (void) {
- //FIXME obviously there is much to be done here !
- fclose(fp);
+ dicom_vr = (gdcmVR*)0;
+ Dicts = (gdcmDictSet*)0;
+ RefPubDict = (gdcmDict*)0;
+ RefShaDict = (gdcmDict*)0;
return;
}
-void gdcmHeader::InitVRDict (void) {
- if (dicom_vr) {
- dbg.Verbose(0, "gdcmHeader::InitVRDict:", "VR dictionary allready set");
- return;
- }
- VRHT *vr = new VRHT;
- (*vr)["AE"] = "Application Entity"; // At most 16 bytes
- (*vr)["AS"] = "Age String"; // Exactly 4 bytes
- (*vr)["AT"] = "Attribute Tag"; // 2 16-bit unsigned short integers
- (*vr)["CS"] = "Code String"; // At most 16 bytes
- (*vr)["DA"] = "Date"; // Exactly 8 bytes
- (*vr)["DS"] = "Decimal String"; // At most 16 bytes
- (*vr)["DT"] = "Date Time"; // At most 26 bytes
- (*vr)["FL"] = "Floating Point Single"; // 32-bit IEEE 754:1985 float
- (*vr)["FD"] = "Floating Point Double"; // 64-bit IEEE 754:1985 double
- (*vr)["IS"] = "Integer String"; // At most 12 bytes
- (*vr)["LO"] = "Long String"; // At most 64 chars
- (*vr)["LT"] = "Long Text"; // At most 10240 chars
- (*vr)["OB"] = "Other Byte String"; // String of bytes (vr independant)
- (*vr)["OW"] = "Other Word String"; // String of 16-bit words (vr dep)
- (*vr)["PN"] = "Person Name"; // At most 64 chars
- (*vr)["SH"] = "Short String"; // At most 16 chars
- (*vr)["SL"] = "Signed Long"; // Exactly 4 bytes
- (*vr)["SQ"] = "Sequence of Items"; // Not Applicable
- (*vr)["SS"] = "Signed Short"; // Exactly 2 bytes
- (*vr)["ST"] = "Short Text"; // At most 1024 chars
- (*vr)["TM"] = "Time"; // At most 16 bytes
- (*vr)["UI"] = "Unique Identifier"; // At most 64 bytes
- (*vr)["UL"] = "Unsigned Long "; // Exactly 4 bytes
- (*vr)["UN"] = "Unknown"; // Any length of bytes
- (*vr)["US"] = "Unsigned Short "; // Exactly 2 bytes
- (*vr)["UT"] = "Unlimited Text"; // At most 2^32 -1 chars
- dicom_vr = vr;
-}
+// Fourth semantics:
+// CMD Command
+// META Meta Information
+// DIR Directory
+// ID
+// PAT Patient
+// ACQ Acquisition
+// REL Related
+// IMG Image
+// SDY Study
+// VIS Visit
+// WAV Waveform
+// PRC
+// DEV Device
+// NMI Nuclear Medicine
+// MED
+// BFS Basic Film Session
+// BFB Basic Film Box
+// BIB Basic Image Box
+// BAB
+// IOB
+// PJ
+// PRINTER
+// RT Radio Therapy
+// DVH
+// SSET
+// RES Results
+// CRV Curve
+// OLY Overlays
+// PXL Pixels
+//
/**
* \ingroup gdcmHeader
entCur = deb + 128;
if(memcmp(entCur, "DICM", (size_t)4) == 0) {
- filetype = TrueDicom;
dbg.Verbose(1, "gdcmHeader::CheckSwap:", "looks like DICOM Version3");
- } else {
- filetype = Unknown;
- dbg.Verbose(1, "gdcmHeader::CheckSwap:", "not a DICOM Version3 file");
- }
-
- if(filetype == TrueDicom) {
// Next, determine the value representation (VR). Let's skip to the
// first element (0002, 0000) and check there if we find "UL"
// - or "OB" if the 1st one is (0002,0001) -,
// * the 4 bytes of the first tag (0002, 0000),or (0002, 0001)
// i.e. a total of 136 bytes.
entCur = deb + 136;
+ // FIXME
+ // 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, "OB", (size_t)2) == 0) ||
+ (memcmp(entCur, "UI", (size_t)2) == 0) )
{
filetype = ExplicitVR;
dbg.Verbose(1, "gdcmHeader::CheckSwap:",
rewind(fp);
fseek (fp, 132L, SEEK_SET);
return;
- } // End of TrueDicom
+ } // End of DicomV3
// Alas, this is not a DicomV3 file and whatever happens there is no file
// preamble. We can reset the file position indicator to where the data
// is (i.e. the beginning of the file).
+ dbg.Verbose(1, "gdcmHeader::CheckSwap:", "not a DICOM Version3 file");
rewind(fp);
// Our next best chance would be to be considering a 'clean' ACR/NEMA file.
// It is time for despaired wild guesses. So, let's assume this file
// happens to be 'dirty' ACR/NEMA, i.e. the length of the group is
// not present. Then the only info we have is the net2host one.
+ filetype = Unknown;
if (! net2host )
sw = 0;
else
sw = 3412;
}
-void gdcmHeader::GetPixels(size_t lgrTotale, void* _Pixels) {
- size_t pixelsOffset;
- pixelsOffset = GetPixelOffset();
- fseek(fp, pixelsOffset, SEEK_SET);
- if (IsJPEGLossless()) {
- _Pixels=_IdDcmJpegRead(fp);
- } else {
- fread(_Pixels, 1, lgrTotale, fp);
- }
-}
-
-
-
/**
* \ingroup gdcmHeader
* \brief Find the value representation of the current tag.
char VR[3];
string vr;
int lgrLue;
+ char msg[100]; // for sprintf. Sorry
+
long PositionOnEntry = ftell(fp);
// Warning: we believe this is explicit VR (Value Representation) because
// we used a heuristic that found "UL" in the first tag. Alas this
// CLEANME searching the dicom_vr at each occurence is expensive.
// PostPone this test in an optional integrity check at the end
// of parsing or only in debug mode.
- if ( RealExplicit && !dicom_vr->count(vr) )
+ if ( RealExplicit && !dicom_vr->Count(vr) )
RealExplicit= false;
if ( RealExplicit ) {
}
// We thought this was explicit VR, but we end up with an
- // implicit VR tag. Let's backtrack.
- dbg.Verbose(1, "gdcmHeader::FindVR:", "Falsely explicit vr file");
+ // implicit VR tag. Let's backtrack.
+
+ sprintf(msg,"Falsely explicit vr file (%04x,%04x)\n", ElVal->GetGroup(),ElVal->GetElement());
+ dbg.Verbose(1, "gdcmHeader::FindVR: ",msg);
+
fseek(fp, PositionOnEntry, SEEK_SET);
// When this element is known in the dictionary we shall use, e.g. for
// the semantics (see the usage of IsAnInteger), the vr proposed by the
return false;
}
-// faire qq chose d'intelligent a la place de ça
-
+/**
+ * \ingroup gdcmHeader
+ * \brief
+ *
+ * @return
+ */
bool gdcmHeader::IsJPEGLossless(void) {
gdcmElValue* Element = PubElValSet.GetElementByNumber(0x0002, 0x0010);
+ // faire qq chose d'intelligent a la place de ça
if ( !Element )
return false;
LoadElementValueSafe(Element);
return false;
}
+/**
+ * \ingroup gdcmHeader
+ * \brief Predicate for dicom version 3 file.
+ * @return True when the file is a dicom version 3.
+ */
+bool gdcmHeader::IsDicomV3(void) {
+ if ( (filetype == ExplicitVR)
+ || (filetype == ImplicitVR) )
+ return true;
+ return false;
+}
+
/**
* \ingroup gdcmHeader
* \brief When the length of an element value is obviously wrong (because
ElVal->SetLength(FoundLength);
}
-guint32 gdcmHeader::FindLengthOB(void) {
+/**
+ * \ingroup gdcmHeader
+ * \brief
+ *
+ * @return
+ */
+ guint32 gdcmHeader::FindLengthOB(void) {
// See PS 3.5-2001, section A.4 p. 49 on encapsulation of encoded pixel data.
guint16 g;
guint16 n;
while ( ! FoundSequenceDelimiter) {
g = ReadInt16();
n = ReadInt16();
+
+ 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);
+
if (errno == 1)
return 0;
TotalLength += 4; // We even have to decount the group and element
- if ( g != 0xfffe ) {
- dbg.Verbose(1, "gdcmHeader::FindLengthOB: ",
- "wrong group for an item sequence.");
+
+ if ( g != 0xfffe && g!=0xb00c ) /*for bogus headerJPR */ {
+ 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 )
+
+ if ( n == 0xe0dd || ( g==0xb00c && n==0x0eb6 ) ) /* for bogus header JPR */
FoundSequenceDelimiter = true;
- else if ( n != 0xe000) {
- dbg.Verbose(1, "gdcmHeader::FindLengthOB: ",
- "wrong element for an item sequence.");
+ else if ( n != 0xe000 ){
+ char msg[100]; // for sprintf. Sorry
+ sprintf(msg,"wrong element (%04x) for an item sequence (%04x,%04x)\n",n, g,n);
+ dbg.Verbose(1, "gdcmHeader::FindLengthOB: ",msg);
+ 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);
SkipBytes(ItemLength);
}
fseek(fp, PositionOnEntry, SEEK_SET);
return TotalLength;
}
-void gdcmHeader::FindLength(gdcmElValue * ElVal) {
+/**
+ * \ingroup gdcmHeader
+ * \brief
+ *
+ * @return
+ */
+ void gdcmHeader::FindLength (gdcmElValue * ElVal) {
guint16 element = ElVal->GetElement();
+ guint16 group = ElVal->GetGroup(); // JPR a virer
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 ( (filetype == ExplicitVR) && ! ElVal->IsImplicitVr() ) {
-
if ( (vr=="OB") || (vr=="OW") || (vr=="SQ") || (vr=="UN") ) {
+
// The following reserved two bytes (see PS 3.5-2001, section
// 7.1.2 Data element structure with explicit vr p27) must be
// skipped before proceeding on reading the length on 4 bytes.
fseek(fp, 2L, SEEK_CUR);
+
guint32 length32 = ReadInt32();
if ( (vr == "OB") && (length32 == 0xffffffff) ) {
ElVal->SetLength(FindLengthOB());
return;
}
- FixFoundLength(ElVal, length32);
+ FixFoundLength(ElVal, length32);
return;
}
// endian encoding". When this is the case, chances are we have got our
// hands on a big endian encoded file: we switch the swap code to
// big endian and proceed...
- if ( (element == 0x000) && (length16 == 0x0400) ) {
+ if ( (element == 0x0000) && (length16 == 0x0400) ) {
if ( ! IsExplicitVRBigEndianTransferSyntax() ) {
dbg.Verbose(0, "gdcmHeader::FindLength", "not explicit VR");
errno = 1;
// and the dictionary entry depending on them.
guint16 CorrectGroup = SwapShort(ElVal->GetGroup());
guint16 CorrectElem = SwapShort(ElVal->GetElement());
- gdcmDictEntry * NewTag = GetDictEntryByKey(CorrectGroup, CorrectElem);
+ gdcmDictEntry * NewTag = GetDictEntryByNumber(CorrectGroup,
+ CorrectElem);
if (!NewTag) {
// This correct tag is not in the dictionary. Create a new one.
NewTag = new gdcmDictEntry(CorrectGroup, CorrectElem);
* @return The suggested integer.
*/
guint32 gdcmHeader::SwapLong(guint32 a) {
- // FIXME: il pourrait y avoir un pb pour les entiers negatifs ...
switch (sw) {
case 0 :
break;
return (a);
}
-void gdcmHeader::SkipBytes(guint32 NBytes) {
+/**
+ * \ingroup gdcmHeader
+ * \brief
+ *
+ * @return
+ */
+ void gdcmHeader::SkipBytes(guint32 NBytes) {
//FIXME don't dump the returned value
(void)fseek(fp, (long)NBytes, SEEK_CUR);
}
-void gdcmHeader::SkipElementValue(gdcmElValue * ElVal) {
+/**
+ * \ingroup gdcmHeader
+ * \brief
+ *
+ * @return
+ */
+ void gdcmHeader::SkipElementValue(gdcmElValue * ElVal) {
SkipBytes(ElVal->GetLength());
}
-void gdcmHeader::SetMaxSizeLoadElementValue(long NewSize) {
+/**
+ * \ingroup gdcmHeader
+ * \brief
+ *
+ * @return
+ */
+ void gdcmHeader::SetMaxSizeLoadElementValue(long NewSize) {
if (NewSize < 0)
return;
if ((guint32)NewSize >= (guint32)0xffffffff) {
void gdcmHeader::LoadElementValue(gdcmElValue * ElVal) {
size_t item_read;
guint16 group = ElVal->GetGroup();
- guint16 elem = ElVal->GetElement();
string vr = ElVal->GetVR();
guint32 length = ElVal->GetLength();
bool SkipLoad = false;
// on devrait pouvoir faire + compact (?)
- if ( IsAnInteger(ElVal) ) {
- guint32 NewInt;
- ostringstream s;
- int nbInt;
- if (vr == "US" || vr == "SS") {
- nbInt = length / 2;
- NewInt = ReadInt16();
- s << NewInt;
- if (nbInt > 1) {
- for (int i=1; i < nbInt; i++) {
- s << '\\';
- NewInt = ReadInt16();
- s << NewInt;
- //printf("%s\n", s.str().c_str());
- }
- }
+ if ( IsAnInteger(ElVal) ) {
+ guint32 NewInt;
+ ostringstream s;
+ int nbInt;
+ if (vr == "US" || vr == "SS") {
+ nbInt = length / 2;
+ NewInt = ReadInt16();
+ s << NewInt;
+ if (nbInt > 1) {
+ for (int i=1; i < nbInt; i++) {
+ s << '\\';
+ NewInt = ReadInt16();
+ s << NewInt;
+ }
+ }
- } else if (vr == "UL" || vr == "SL") {
- nbInt = length / 4;
- NewInt = ReadInt32();
- s << NewInt;
- if (nbInt > 1) {
- for (int i=1; i < nbInt; i++) {
- s << '\\';
- NewInt = ReadInt32();
- s << NewInt;
- }
- }
- }
- ElVal->SetValue(s.str());
- return;
- }
+ } else if (vr == "UL" || vr == "SL") {
+ nbInt = length / 4;
+ NewInt = ReadInt32();
+ s << NewInt;
+ if (nbInt > 1) {
+ for (int i=1; i < nbInt; i++) {
+ s << '\\';
+ NewInt = ReadInt32();
+ s << NewInt;
+ }
+ }
+ }
+ ElVal->SetValue(s.str());
+ return;
+ }
- // FIXME The exact size should be length if we move to strings or whatever
+ // We need an additional byte for storing \0 that is not on disk
char* NewValue = (char*)malloc(length+1);
if( !NewValue) {
dbg.Verbose(1, "LoadElementValue: Failed to allocate NewValue");
return;
}
ElVal->SetValue(NewValue);
+ free(NewValue);
}
/**
fseek(fp, PositionOnEntry, SEEK_SET);
}
-
+/**
+ * \ingroup gdcmHeader
+ * \brief
+ *
+ * @return
+ */
guint16 gdcmHeader::ReadInt16(void) {
guint16 g;
size_t item_read;
item_read = fread (&g, (size_t)2,(size_t)1, fp);
- errno = 0;
if ( item_read != 1 ) {
- dbg.Verbose(1, "gdcmHeader::ReadInt16", " File read error");
+ dbg.Verbose(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");
errno = 1;
return 0;
}
+ errno = 0;
g = SwapShort(g);
return g;
}
+/**
+ * \ingroup gdcmHeader
+ * \brief
+ *
+ * @return
+ */
guint32 gdcmHeader::ReadInt32(void) {
guint32 g;
size_t item_read;
item_read = fread (&g, (size_t)4,(size_t)1, fp);
- errno = 0;
if ( item_read != 1 ) {
- dbg.Verbose(1, "gdcmHeader::ReadInt32", " File read error");
+
+ dbg.Verbose(1, "gdcmHeader::ReadInt32", " Failed to read :");
+ if(feof(fp))
+ dbg.Verbose(1, "gdcmHeader::ReadInt32", " End of File encountered");
+ if(ferror(fp))
+ dbg.Verbose(1, "gdcmHeader::ReadInt32", " File Error");
errno = 1;
return 0;
}
+ errno = 0;
g = SwapLong(g);
return g;
}
+/**
+ * \ingroup gdcmHeader
+ * \brief
+ *
+ * @return
+ */
+ gdcmElValue* gdcmHeader::GetElValueByNumber(guint16 Group, guint16 Elem) {
+
+ gdcmElValue* elValue = PubElValSet.GetElementByNumber(Group, Elem);
+ if (!elValue) {
+ dbg.Verbose(1, "gdcmHeader::GetElValueByNumber",
+ "failed to Locate gdcmElValue");
+ return (gdcmElValue*)0;
+ }
+ return elValue;
+}
+
/**
* \ingroup gdcmHeader
* \brief Build a new Element Value from all the low level arguments.
* @param Group group of the underlying DictEntry
* @param Elem element of the underlying DictEntry
*/
-gdcmElValue* gdcmHeader::NewElValueByKey(guint16 Group, guint16 Elem) {
+gdcmElValue* gdcmHeader::NewElValueByNumber(guint16 Group, guint16 Elem) {
// Find out if the tag we encountered is in the dictionaries:
- gdcmDictEntry * NewTag = GetDictEntryByKey(Group, Elem);
+ gdcmDictEntry * NewTag = GetDictEntryByNumber(Group, Elem);
if (!NewTag)
NewTag = new gdcmDictEntry(Group, Elem);
gdcmElValue* NewElVal = new gdcmElValue(NewTag);
if (!NewElVal) {
- dbg.Verbose(1, "gdcmHeader::NewElValueByKey",
+ dbg.Verbose(1, "gdcmHeader::NewElValueByNumber",
"failed to allocate gdcmElValue");
return (gdcmElValue*)0;
}
* \brief TODO
* @param
*/
-int gdcmHeader::ReplaceOrCreateByNumber(guint16 Group, guint16 Elem, string Value) {
+int gdcmHeader::ReplaceOrCreateByNumber(string Value, guint16 Group, guint16 Elem ) {
- gdcmElValue* nvElValue=NewElValueByKey(Group, Elem);
+ gdcmElValue* nvElValue=NewElValueByNumber(Group, Elem);
PubElValSet.Add(nvElValue);
PubElValSet.SetElValueByNumber(Value, Group, Elem);
return(1);
}
-
/**
* \ingroup gdcmHeader
* \brief Build a new Element Value from all the low level arguments.
g = ReadInt16();
n = ReadInt16();
+
+ if ( (g==0x7fe0) && (n==0x0010) )
+ if (DEBUG)
+ printf("in gdcmHeader::ReadNextElement try to read 7fe0 0010 \n");
+
if (errno == 1)
// We reached the EOF (or an error occured) and header parsing
// has to be considered as finished.
return (gdcmElValue *)0;
- NewElVal = NewElValueByKey(g, n);
+ NewElVal = NewElValueByNumber(g, n);
FindVR(NewElVal);
FindLength(NewElVal);
- if (errno == 1)
+ if (errno == 1) {
// Call it quits
+ if (DEBUG) printf("in gdcmHeader::ReadNextElement : g %04x n %04x errno %d\n",g, n, errno);
return (gdcmElValue *)0;
- NewElVal->SetOffset(ftell(fp));
+ }
+ NewElVal->SetOffset(ftell(fp));
+ if ( (g==0x7fe0) && (n==0x0010) )
+ if (DEBUG)
+ printf("sortie de gdcmHeader::ReadNextElement 7fe0 0010 \n");
return NewElVal;
}
if ( element == 0 ) { // This is the group length of the group
if (length == 4)
return true;
- else
+ 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.");
+ "Erroneous Group Length element length.");
+ }
}
-
- /*
- // on le traite tt de même (VR peut donner l'info)
- // faire qq chose + ruse (pas de test si pas de VR)
- if ( group % 2 != 0 )
- // We only have some semantics on documented elements, which are
- // the even ones.
- return false;
- */
-
- /*
- if ( (length != 4) && ( length != 2) )
- // Swapping only make sense on integers which are 2 or 4 bytes long.
-
- // En fait, pour les entiers de 'Value Multiplicity' supérieur a 1
- // la longueur n'est pas forcement 2 ou 4
- // ET il faudra swapper.
- return false;
- */
-
if ( (vr == "UL") || (vr == "US") || (vr == "SL") || (vr == "SS") )
return true;
-
- // est-ce encore utile?
- // mieux vaut modifier le source du Dicom Dictionnaty
- // et remplacer pour ces 2 cas RET par US
-
- if ( (group == 0x0028) && (element == 0x0005) )
- // The "Image Dimensions" tag is retained from ACR/NEMA and contains
- // the number of dimensions of the contained object (1 for Signal,
- // 2 for Image, 3 for Volume, 4 for Sequence).
- return true;
-
- if ( (group == 0x0028) && (element == 0x0200) )
- // This tag is retained from ACR/NEMA
- return true;
-
return false;
}
// 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.
+ // When the "Image Location" is absent we default to group 0x7fe0.
guint16 grPixel;
guint16 numPixel;
string ImageLocation = GetPubElValByName("Image Location");
grPixel = (guint16) atoi( ImageLocation.c_str() );
}
if (grPixel != 0x7fe0)
- // FIXME is this still necessary ?
- // Now, this looks like an old dirty fix for Philips imager
+ // This is a kludge for old dirty Philips imager.
numPixel = 0x1010;
else
numPixel = 0x0010;
- gdcmElValue* PixelElement = PubElValSet.GetElementByNumber(grPixel, numPixel);
+
+ gdcmElValue* PixelElement = PubElValSet.GetElementByNumber(grPixel,
+ numPixel);
if (PixelElement)
return PixelElement->GetOffset();
else
* @param element element of the searched DictEntry
* @return Corresponding DictEntry when it exists, NULL otherwise.
*/
-gdcmDictEntry * gdcmHeader::GetDictEntryByKey(guint16 group, guint16 element) {
+gdcmDictEntry * gdcmHeader::GetDictEntryByNumber(guint16 group,
+ guint16 element) {
gdcmDictEntry * found = (gdcmDictEntry*)0;
if (!RefPubDict && !RefShaDict) {
- dbg.Verbose(0, "FIXME in gdcmHeader::GetDictEntry",
+ dbg.Verbose(0, "gdcmHeader::GetDictEntry",
"we SHOULD have a default dictionary");
}
if (RefPubDict) {
- found = RefPubDict->GetTagByKey(group, element);
+ found = RefPubDict->GetTagByNumber(group, element);
if (found)
return found;
}
if (RefShaDict) {
- found = RefShaDict->GetTagByKey(group, element);
+ found = RefShaDict->GetTagByNumber(group, element);
if (found)
return found;
}
gdcmDictEntry * gdcmHeader::GetDictEntryByName(string Name) {
gdcmDictEntry * found = (gdcmDictEntry*)0;
if (!RefPubDict && !RefShaDict) {
- dbg.Verbose(0, "FIXME in gdcmHeader::GetDictEntry",
+ dbg.Verbose(0, "gdcmHeader::GetDictEntry",
"we SHOULD have a default dictionary");
}
if (RefPubDict) {
*/
int gdcmHeader::SetPubElValByNumber(string content, guint16 group,
guint16 element)
+
+//TODO : homogeneiser les noms : SetPubElValByNumber qui appelle PubElValSet.SetElValueByNumber
+// pourquoi pas SetPubElValueByNumber ??
{
+
return ( PubElValSet.SetElValueByNumber (content, group, element) );
}
}
}
+
+//
+// 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
+//
+// --> 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 Retrieve the number of columns of image.
+ * @return The encountered size when found, 0 by default.
+ */
+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")
+ return 0;
+ return atoi(StrSize.c_str());
+}
+
/**
* \ingroup gdcmHeader
- * \brief Once the header is parsed add some gdcm convenience/helper elements
- * in the gdcmElValSet. For example add:
- * - gdcmImageType which is an entry containing a short for the
- * type of image and whose value ranges in
- * I8 (unsigned 8 bit image)
- * I16 (unsigned 8 bit image)
- * IS16 (signed 8 bit image)
- * - gdcmXsize, gdcmYsize, gdcmZsize whose values are respectively
- * the ones of the official DICOM fields Rows, Columns and Planes.
+ * \brief Retrieve the number of lines of image.
+ * \warning The defaulted value is 1 as opposed to gdcmHeader::GetXSize()
+ * @return The encountered size when found, 1 by default.
*/
-void gdcmHeader::AddAndDefaultElements(void) {
- gdcmElValue* NewElVal = (gdcmElValue*)0;
- string NewVal;
-
- NewElVal = NewManualElValToPubDict("gdcmXSize", "US");
- if (!NewElVal) return;
- NewVal = GetElValByName("Rows");
- if (NewVal != "gdcm::Unfound")
- NewElVal->SetValue(NewVal);
- else
- NewElVal->SetValue("0");
-
- NewElVal = NewManualElValToPubDict("gdcmYSize", "US");
- if (!NewElVal) return;
- NewVal = GetElValByName("Columns");
- if (NewVal != "gdcm::Unfound")
- NewElVal->SetValue(NewVal);
+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")
+ return atoi(StrSize.c_str());
+ if ( IsDicomV3() )
+ return 0;
else
- NewElVal->SetValue("0");
-
-
- NewElVal = NewManualElValToPubDict("gdcmZSize", "US");
- if (!NewElVal) return;
- NewVal = GetElValByNumber(0x0028,0x0008); // 0028 0008 IS IMG Number of Frames (DICOM)
- if (NewVal == "gdcm::Unfound") {
- NewVal = GetElValByNumber(0x0028,0x0012); // 028 0012 US IMG Planes (ACR-NEMA)
- if (NewVal == "gdcm::Unfound") { // Warning !!! : 6000 0012 US OLY Planes
- NewElVal->SetValue("0");
- } else {
- NewElVal->SetValue(NewVal);
- }
- } else {
- NewElVal->SetValue(NewVal);
- } // length is still wrong
-} // do we care about it?
+ // The Rows (0028,0010) entry is optional for ACR/NEMA. It might
+ // hence be a signal (1d image). So we default to 1:
+ return 1;
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Retrieve the number of planes of volume or the number
+ * of frames of a multiframe.
+ * \warning When present we consider the "Number of Frames" as the third
+ * dimension. When absent we consider the third dimension as
+ * being the "Planes" tag content.
+ * @return The encountered size when found, 1 by default.
+ */
+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")
+ 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")
+ return atoi(StrSize.c_str());
+ return 1;
+}
+
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Retrieve the number of Bits Stored
+ * (as opposite to number of Bits Allocated)
+ *
+ * @return The encountered number of Bits Stored, 0 by default.
+ */
+int gdcmHeader::GetBitsStored(void) {
+ string StrSize = GetPubElValByNumber(0x0028,0x0101);
+ if (StrSize == "gdcm::Unfound")
+ return 1;
+ return atoi(StrSize.c_str());
+}
+
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Retrieve the number of Samples Per Pixel
+ * (1 : gray level, 3 : RGB)
+ *
+ * @return The encountered number of Samples Per Pixel, 1 by default.
+ */
+int gdcmHeader::GetSamplesPerPixel(void) {
+ string StrSize = GetPubElValByNumber(0x0028,0x0002);
+ if (StrSize == "gdcm::Unfound")
+ return 1; // Well, it's supposed to be mandatory ...
+ return atoi(StrSize.c_str());
+}
+/**
+ * \ingroup gdcmHeader
+ * \brief Return the size (in bytes) of a single pixel of data.
+ * @return The size in bytes of a single pixel of data.
+ *
+ */
+int gdcmHeader::GetPixelSize(void) {
+ string PixelType = GetPixelType();
+ if (PixelType == "8U" || PixelType == "8S")
+ return 1;
+ if (PixelType == "16U" || PixelType == "16S")
+ return 2;
+ if (PixelType == "32U" || PixelType == "32S")
+ return 4;
+ dbg.Verbose(0, "gdcmHeader::GetPixelSize: Unknown pixel type");
+ return 0;
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Build the Pixel Type of the image.
+ * Possible values are:
+ * - 8U unsigned 8 bit,
+ * - 8S signed 8 bit,
+ * - 16U unsigned 16 bit,
+ * - 16S signed 16 bit,
+ * - 32U unsigned 32 bit,
+ * - 32S signed 32 bit,
+ * \warning 12 bit images appear as 16 bit.
+ * @return
+ */
+string gdcmHeader::GetPixelType(void) {
+ string BitsAlloc;
+ BitsAlloc = GetElValByName("Bits Allocated");
+ if (BitsAlloc == "gdcm::Unfound") {
+ dbg.Verbose(0, "gdcmHeader::GetPixelType: unfound Bits Allocated");
+ BitsAlloc = string("16");
+ }
+ if (BitsAlloc == "12")
+ BitsAlloc = string("16");
+
+ string Signed;
+ Signed = GetElValByName("Pixel Representation");
+ if (Signed == "gdcm::Unfound") {
+ dbg.Verbose(0, "gdcmHeader::GetPixelType: unfound Pixel Representation");
+ BitsAlloc = string("0");
+ }
+ if (Signed == "0")
+ Signed = string("U");
+ else
+ Signed = string("S");
+
+ return( BitsAlloc + Signed);
+}
/**
&& atoi(GetElValByName("Image Dimensions").c_str()) > 4 ) {
return false;
}
- if ( GetElValByName("Bits Allocated") == "gdcm::Unfound" )
+ if ( GetElValByName("Bits Allocated") == "gdcm::Unfound" )
return false;
- if ( GetElValByName("Bits Stored") == "gdcm::Unfound" )
+ if ( GetElValByName("Bits Stored") == "gdcm::Unfound" )
return false;
- if ( GetElValByName("High Bit") == "gdcm::Unfound" )
+ if ( GetElValByName("High Bit") == "gdcm::Unfound" )
return false;
- if ( GetElValByName("Pixel Representation") == "gdcm::Unfound" )
+ 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.
- * Refer to gdcmHeader::AddAndDefaultElements for a typical usage.
* \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.
NewElVal = new gdcmElValue(NewEntry);
PubElValSet.Add(NewElVal);
return NewElVal;
-
}
/**
TagElValueHT ht = PubElValSet.GetTagHt();
for (TagElValueHT::iterator tag = ht.begin(); tag != ht.end(); ++tag) {
LoadElementValue(tag->second);
- }
+ }
}
-void gdcmHeader::PrintPubElVal(ostream & os) {
+/**
+ * \ingroup gdcmHeader
+ * \brief
+ * @return
+ */
+void gdcmHeader::PrintPubElVal(std::ostream & os) {
PubElValSet.Print(os);
}
-void gdcmHeader::PrintPubDict(ostream & 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
+ */
+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;
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief
+ * @return
+ */
+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());
+ }
+}
+
+//
+// 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;
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief
+ * @return
+ */
+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;
+}
+
+/**
+ * \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?
+
+ 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");
+
+ return 0.; // Hopeless
+}
+
+
+
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff