-// $Header: /cvs/public/gdcm/src/Attic/gdcmHeader.cxx,v 1.103 2003/10/23 12:08:32 jpr Exp $
-
+// gdcmHeader.cxx
+//-----------------------------------------------------------------------------
#include "gdcmHeader.h"
#include <stdio.h>
#include <cerrno>
-// For nthos:
-#ifdef _MSC_VER
-#include <winsock.h>
-#else
-#include <netinet/in.h>
-#endif
#include <cctype> // for isalpha
-#include <sstream>
+
#include "gdcmUtil.h"
#include "gdcmTS.h"
+//-----------------------------------------------------------------------------
// Refer to gdcmHeader::CheckSwap()
-#define HEADER_LENGTH_TO_READ 256
-// Refer to gdcmHeader::SetMaxSizeLoadElementValue()
-//#define _MaxSizeLoadElementValue_ 1024
-#define _MaxSizeLoadElementValue_ 4096
-/**
- * \ingroup gdcmHeader
- * \brief
- */
-void gdcmHeader::Initialise(void) {
- dicom_vr = gdcmGlobal::GetVR();
- dicom_ts = gdcmGlobal::GetTS();
- Dicts = gdcmGlobal::GetDicts();
- RefPubDict = Dicts->GetDefaultPubDict();
- RefShaDict = (gdcmDict*)0;
-}
+//const unsigned int gdcmHeader::HEADER_LENGTH_TO_READ = 256;
-/**
- * \ingroup gdcmHeader
- * \brief
- * @param InFilename
- * @param exception_on_error
- */
-gdcmHeader::gdcmHeader(const char *InFilename, bool exception_on_error) {
- SetMaxSizeLoadElementValue(_MaxSizeLoadElementValue_);
- filename = InFilename;
- Initialise();
- if ( !OpenFile(exception_on_error))
- return;
- ParseHeader();
- LoadElements();
- CloseFile();
-}
+// Refer to gdcmHeader::SetMaxSizeLoadEntry()
+//const unsigned int gdcmHeader::MAX_SIZE_LOAD_ELEMENT_VALUE = 4096;
+//-----------------------------------------------------------------------------
+// Constructor / Destructor
/**
* \ingroup gdcmHeader
* \brief
+ * @param InFilename
* @param exception_on_error
- */
-gdcmHeader::gdcmHeader(bool exception_on_error) {
- SetMaxSizeLoadElementValue(_MaxSizeLoadElementValue_);
- Initialise();
+ * @param enable_sequences = true to allow the header
+ * to be parsed *inside* the SeQuences,
+ * when they have an actual length
+ *\TODO : may be we need one more bool,
+ * to allow skipping the private elements while parsing the header
+ * in order to save space
+ */
+gdcmHeader::gdcmHeader(const char *InFilename,
+ bool exception_on_error,
+ bool enable_sequences ):
+ gdcmParser(InFilename,exception_on_error,enable_sequences)
+{
}
/**
* \ingroup gdcmHeader
* \brief
* @param exception_on_error
- * @return
- */
- bool gdcmHeader::OpenFile(bool exception_on_error)
- throw(gdcmFileError) {
- fp=fopen(filename.c_str(),"rb");
- if(exception_on_error) {
- if(!fp)
- throw gdcmFileError("gdcmHeader::gdcmHeader(const char *, bool)");
- }
-
- 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
- * @return TRUE if the close was successfull
*/
-bool gdcmHeader::CloseFile(void) {
- int closed = fclose(fp);
- fp = (FILE *)0;
- if (! closed)
- return false;
- return true;
+gdcmHeader::gdcmHeader(bool exception_on_error) :
+ gdcmParser(exception_on_error)
+{
}
/**
* \brief Canonical destructor.
*/
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
-// 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
-// DL Delimiters
-//
+//-----------------------------------------------------------------------------
+// Print
+//-----------------------------------------------------------------------------
+// Public
/**
* \ingroup gdcmHeader
- * \brief Discover what the swap code is (among little endian, big endian,
- * bad little endian, bad big endian).
- *
+ * \brief This predicate, based on hopefully reasonable heuristics,
+ * decides whether or not the current gdcmParser was properly parsed
+ * and contains the mandatory information for being considered as
+ * a well formed and usable Dicom/Acr File.
+ * @return true when gdcmParser is the one of a reasonable Dicom/Acr file,
+ * false otherwise.
*/
-void gdcmHeader::CheckSwap()
+bool gdcmHeader::IsReadable(void)
{
- // The only guaranted way of finding the swap code is to find a
- // group tag since we know it's length has to be of four bytes i.e.
- // 0x00000004. Finding the swap code in then straigthforward. Trouble
- // occurs when we can't find such group...
- guint32 s;
- guint32 x=4; // x : for ntohs
- bool net2host; // true when HostByteOrder is the same as NetworkByteOrder
-
- int lgrLue;
- char * entCur;
- char deb[HEADER_LENGTH_TO_READ];
-
- // First, compare HostByteOrder and NetworkByteOrder in order to
- // determine if we shall need to swap bytes (i.e. the Endian type).
- if (x==ntohs(x))
- net2host = true;
- else
- net2host = false;
-
- // The easiest case is the one of a DICOM header, since it possesses a
- // file preamble where it suffice to look for the string "DICM".
- lgrLue = fread(deb, 1, HEADER_LENGTH_TO_READ, fp);
-
- entCur = deb + 128;
- if(memcmp(entCur, "DICM", (size_t)4) == 0) {
- dbg.Verbose(1, "gdcmHeader::CheckSwap:", "looks like DICOM Version3");
- // 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) -,
- // in which case we (almost) know it is explicit VR.
- // WARNING: if it happens to be implicit VR then what we will read
- // is the length of the group. If this ascii representation of this
- // length happens to be "UL" then we shall believe it is explicit VR.
- // FIXME: in order to fix the above warning, we could read the next
- // element value (or a couple of elements values) in order to make
- // sure we are not commiting a big mistake.
- // We need to skip :
- // * the 128 bytes of File Preamble (often padded with zeroes),
- // * the 4 bytes of "DICM" string,
- // * 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, "UI", (size_t)2) == 0) )
- {
- filetype = ExplicitVR;
- dbg.Verbose(1, "gdcmHeader::CheckSwap:",
- "explicit Value Representation");
- } else {
- filetype = ImplicitVR;
- dbg.Verbose(1, "gdcmHeader::CheckSwap:",
- "not an explicit Value Representation");
- }
- if (net2host) {
- sw = 4321;
- dbg.Verbose(1, "gdcmHeader::CheckSwap:",
- "HostByteOrder != NetworkByteOrder");
- } else {
- sw = 0;
- dbg.Verbose(1, "gdcmHeader::CheckSwap:",
- "HostByteOrder = NetworkByteOrder");
- }
-
- // Position the file position indicator at first tag (i.e.
- // after the file preamble and the "DICM" string).
- rewind(fp);
- fseek (fp, 132L, SEEK_SET);
- return;
- } // 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.
- // By clean we mean that the length of the first tag is written down.
- // If this is the case and since the length of the first group HAS to be
- // four (bytes), then determining the proper swap code is straightforward.
-
- entCur = deb + 4;
- // We assume the array of char we are considering contains the binary
- // representation of a 32 bits integer. Hence the following dirty
- // trick :
- s = *((guint32 *)(entCur));
-
- switch (s) {
- case 0x00040000 :
- sw = 3412;
- filetype = ACR;
- return;
- case 0x04000000 :
- sw = 4321;
- filetype = ACR;
- return;
- case 0x00000400 :
- sw = 2143;
- filetype = ACR;
- return;
- case 0x00000004 :
- sw = 0;
- filetype = ACR;
- return;
- default :
- dbg.Verbose(0, "gdcmHeader::CheckSwap:",
- "ACR/NEMA unfound swap info (time to raise bets)");
- }
-
- // We are out of luck. It is not a DicomV3 nor a 'clean' ACR/NEMA file.
- // It is time for despaired wild guesses. So, let's assume this file
- // happens to be 'dirty' ACR/NEMA, i.e. the length of the group is
- // not present. Then the only info we have is the net2host one.
- filetype = Unknown;
- if (! net2host )
- sw = 0;
- else
- sw = 4321;
- return;
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief
- */
-void gdcmHeader::SwitchSwapToBigEndian(void) {
- dbg.Verbose(1, "gdcmHeader::SwitchSwapToBigEndian",
- "Switching to BigEndian mode.");
- if ( sw == 0 ) {
- sw = 4321;
- return;
- }
- if ( sw == 4321 ) {
- sw = 0;
- return;
- }
- if ( sw == 3412 ) {
- sw = 2143;
- return;
- }
- if ( sw == 2143 )
- sw = 3412;
-}
-
-/**
- * \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];
- std::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
- // doesn't guarantee that all the tags will be in explicit VR. In some
- // cases (see e-film filtered files) one finds implicit VR tags mixed
- // within an explicit VR file. Hence we make sure the present tag
- // is in explicit VR and try to fix things if it happens not to be
- // the case.
- bool RealExplicit = true;
-
- lgrLue=fread (&VR, (size_t)2,(size_t)1, fp);
- VR[2]=0;
- 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
- // first to bytes of the length. Then we will interogate (through find)
- // the dicom_vr dictionary with oddities like "\004\0" which crashes
- // both GCC and VC++ implementations of the STL map. Hence when the
- // expected VR read happens to be non-ascii characters we consider
- // we hit falsely explicit VR tag.
-
- if ( (!isalpha(VR[0])) && (!isalpha(VR[1])) )
- RealExplicit = false;
-
- // 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) )
- RealExplicit= false;
-
- if ( RealExplicit ) {
- if ( ElVal->IsVrUnknown() ) {
- // When not a dictionary entry, we can safely overwrite the vr.
- ElVal->SetVR(vr);
- return;
- }
- if ( ElVal->GetVR() == vr ) {
- // The vr we just read and the dictionary agree. Nothing to do.
- return;
- }
- // The vr present in the file and the dictionary disagree. We assume
- // the file writer knew best and use the vr of the file. Since it would
- // be unwise to overwrite the vr of a dictionary (since it would
- // compromise it's next user), we need to clone the actual DictEntry
- // and change the vr for the read one.
- gdcmDictEntry* NewTag = new gdcmDictEntry(ElVal->GetGroup(),
- ElVal->GetElement(),
- vr,
- "FIXME",
- ElVal->GetName());
- ElVal->SetDictEntry(NewTag);
- return;
- }
-
- // 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());
- 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
- // dictionary entry. Still we have to flag the element as implicit since
- // we know now our assumption on expliciteness is not furfilled.
- // avoid .
- if ( ElVal->IsVrUnknown() )
- ElVal->SetVR("Implicit");
- ElVal->SetImplicitVr();
-}
-
-/**
- * \ingroup gdcmHeader
- * \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.
- */
-bool gdcmHeader::IsImplicitVRLittleEndianTransferSyntax(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" )
- return true;
- return false;
-}
-
-/**
- * \ingroup gdcmHeader
- * \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.
- */
-bool gdcmHeader::IsExplicitVRLittleEndianTransferSyntax(void) {
- gdcmElValue* Element = PubElValSet.GetElementByNumber(0x0002, 0x0010);
- if ( !Element )
- return false;
- LoadElementValueSafe(Element);
- std::string Transfer = Element->GetValue();
- if ( Transfer == "1.2.840.10008.1.2.1" )
- return true;
- return false;
-}
-
-/**
- * \ingroup gdcmHeader
- * \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.
- */
-bool gdcmHeader::IsDeflatedExplicitVRLittleEndianTransferSyntax(void) {
- gdcmElValue* Element = PubElValSet.GetElementByNumber(0x0002, 0x0010);
- if ( !Element )
- return false;
- LoadElementValueSafe(Element);
- std::string Transfer = Element->GetValue();
- if ( Transfer == "1.2.840.10008.1.2.1.99" )
- return true;
- return false;
-}
-
-/**
- * \ingroup gdcmHeader
- * \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.
- */
-bool gdcmHeader::IsExplicitVRBigEndianTransferSyntax(void) {
- gdcmElValue* Element = PubElValSet.GetElementByNumber(0x0002, 0x0010);
- if ( !Element )
- return false;
- LoadElementValueSafe(Element);
- std::string Transfer = Element->GetValue();
- if ( Transfer == "1.2.840.10008.1.2.2" ) //1.2.2 ??? A verifier !
- return true;
- return false;
+ if(!gdcmParser::IsReadable())
+ return(false);
+
+ std::string res = GetEntryByNumber(0x0028, 0x0005);
+ if ( res != GDCM_UNFOUND && atoi(res.c_str()) > 4 )
+ return false; // Image Dimensions
+
+ if ( !GetHeaderEntryByNumber(0x0028, 0x0100) )
+ return false; // "Bits Allocated"
+ if ( !GetHeaderEntryByNumber(0x0028, 0x0101) )
+ return false; // "Bits Stored"
+ if ( !GetHeaderEntryByNumber(0x0028, 0x0102) )
+ return false; // "High Bit"
+ if ( !GetHeaderEntryByNumber(0x0028, 0x0103) )
+ return false; // "Pixel Representation"
+ return true;
}
/**
* @return True when JPEGBaseLineProcess1found. False in all other cases.
*/
bool gdcmHeader::IsJPEGBaseLineProcess1TransferSyntax(void) {
- gdcmElValue* Element = PubElValSet.GetElementByNumber(0x0002, 0x0010);
+ gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010);
if ( !Element )
return false;
- LoadElementValueSafe(Element);
+ LoadHeaderEntrySafe(Element);
+
std::string Transfer = Element->GetValue();
if ( Transfer == "1.2.840.10008.1.2.4.50" )
return true;
return false;
}
-/**
- * \ingroup gdcmHeader
- * \brief
- *
- * @return
- */
-bool gdcmHeader::IsJPEGLossless(void) {
- gdcmElValue* Element = PubElValSet.GetElementByNumber(0x0002, 0x0010);
- // faire qq chose d'intelligent a la place de ça
- if ( !Element )
- return false;
- LoadElementValueSafe(Element);
- const char * Transfert = Element->GetValue().c_str();
- 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 already encountered
* @return True when JPEGExtendedProcess2-4 found. False in all other cases.
*/
bool gdcmHeader::IsJPEGExtendedProcess2_4TransferSyntax(void) {
- gdcmElValue* Element = PubElValSet.GetElementByNumber(0x0002, 0x0010);
+ gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010);
if ( !Element )
return false;
- LoadElementValueSafe(Element);
+ LoadHeaderEntrySafe(Element);
+
std::string Transfer = Element->GetValue();
if ( Transfer == "1.2.840.10008.1.2.4.51" )
return true;
* @return True when JPEGExtendedProcess3-5 found. False in all other cases.
*/
bool gdcmHeader::IsJPEGExtendedProcess3_5TransferSyntax(void) {
- gdcmElValue* Element = PubElValSet.GetElementByNumber(0x0002, 0x0010);
- if ( !Element )
- return false;
- LoadElementValueSafe(Element);
- std::string Transfer = Element->GetValue();
- if ( Transfer == "1.2.840.10008.1.2.4.52" )
- return true;
- return false;
-}
-
-/**
- * \ingroup gdcmHeader
- * \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
- * other cases.
- */
-bool gdcmHeader::IsJPEGSpectralSelectionProcess6_8TransferSyntax(void) {
- gdcmElValue* Element = PubElValSet.GetElementByNumber(0x0002, 0x0010);
- if ( !Element )
- return false;
- LoadElementValueSafe(Element);
- std::string Transfer = Element->GetValue();
- if ( Transfer == "1.2.840.10008.1.2.4.53" )
- 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);
+ gdcmHeaderEntry* Element = GetHeaderEntryByNumber(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;
-}
+ LoadHeaderEntrySafe(Element);
-/**
- * \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.
- * @return True when the file is a dicom version 3.
- */
-bool gdcmHeader::IsDicomV3(void) {
- if ( (filetype == ExplicitVR)
- || (filetype == ImplicitVR) )
+ if ( Transfer == "1.2.840.10008.1.2.4.52" )
return true;
return false;
}
/**
* \ingroup gdcmHeader
- * \brief When the length of an element value is obviously wrong (because
- * the parser went Jabberwocky) one can hope improving things by
- * applying this heuristic.
- */
-void gdcmHeader::FixFoundLength(gdcmElValue * ElVal, guint32 FoundLength) {
- if ( FoundLength == 0xffffffff)
- FoundLength = 0;
-
- // 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)) {
- // end of remove area
- FoundLength =10;
- }
- }
- // 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->SetLength(FoundLength);
-}
-
-/**
- * \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;
- long PositionOnEntry = ftell(fp);
- bool FoundSequenceDelimiter = false;
- guint32 TotalLength = 0;
- guint32 ItemLength;
-
- while ( ! FoundSequenceDelimiter) {
- g = ReadInt16();
- 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 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);
- errno = 1;
- return 0;
- }
- if ( n == 0xe0dd || ( g==0xb00c && n==0x0eb6 ) ) /* for bogus header */
- FoundSequenceDelimiter = true;
- else if ( n != 0xe000 ){
- char msg[100]; // for sprintf. Sorry
- sprintf(msg,"wrong element (%04x) for an item sequence (%04x,%04x)\n",
- n, g,n);
- dbg.Verbose(1, "gdcmHeader::FindLengthOB: ",msg);
- errno = 1;
- return 0;
- }
- ItemLength = ReadInt32();
- TotalLength += ItemLength + 4; // We add 4 bytes since we just read
- // the ItemLength with ReadInt32
- SkipBytes(ItemLength);
- }
- fseek(fp, PositionOnEntry, SEEK_SET);
- return TotalLength;
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief
- *
- * @return
- */
- void gdcmHeader::FindLength (gdcmElValue * ElVal) {
- guint16 element = ElVal->GetElement();
- guint16 group = ElVal->GetGroup();
- std::string vr = ElVal->GetVR();
- guint16 length16;
- if( (element == 0x0010) && (group == 0x7fe0) ) {
- dbg.SetDebug(0);
- dbg.Verbose(2, "gdcmHeader::FindLength: ",
- "we reached 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);
- return;
- }
-
- // Length is encoded on 2 bytes.
- length16 = ReadInt16();
-
- // We can tell the current file is encoded in big endian (like
- // Data/US-RGB-8-epicard) when we find the "Transfer Syntax" tag
- // and it's value is the one of the encoding of a big endian file.
- // In order to deal with such big endian encoded files, we have
- // (at least) two strategies:
- // * when we load the "Transfer Syntax" tag with value of big endian
- // encoding, we raise the proper flags. Then we wait for the end
- // of the META group (0x0002) among which is "Transfer Syntax",
- // before switching the swap code to big endian. We have to postpone
- // the switching of the swap code since the META group is fully encoded
- // in little endian, and big endian coding only starts at the next
- // group. The corresponding code can be hard to analyse and adds
- // many additional unnecessary tests for regular tags.
- // * the second strategy consists in waiting for trouble, that shall
- // 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
- // 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 already parsed elements
- // for the presence of a "Transfer Syntax" whose value has to be "big
- // endian encoding". When this is the case, chances are we have got our
- // hands on a big endian encoded file: we switch the swap code to
- // big endian and proceed...
- if ( (element == 0x0000) && (length16 == 0x0400) ) {
- if ( ! IsExplicitVRBigEndianTransferSyntax() ) {
- dbg.Verbose(0, "gdcmHeader::FindLength", "not explicit VR");
- errno = 1;
- return;
- }
- length16 = 4;
- SwitchSwapToBigEndian();
- // Restore the unproperly loaded values i.e. the group, the element
- // and the dictionary entry depending on them.
- guint16 CorrectGroup = SwapShort(ElVal->GetGroup());
- guint16 CorrectElem = SwapShort(ElVal->GetElement());
- gdcmDictEntry * NewTag = GetDictEntryByNumber(CorrectGroup,
- CorrectElem);
- if (!NewTag) {
- // This correct tag is not in the dictionary. Create a new one.
- NewTag = new gdcmDictEntry(CorrectGroup, CorrectElem);
- }
- // FIXME this can create a memory leaks on the old entry that be
- // left unreferenced.
- ElVal->SetDictEntry(NewTag);
- }
-
- // Heuristic: well some files are really ill-formed.
- if ( length16 == 0xffff) {
- length16 = 0;
- //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;
- }
-
- // Either implicit VR or a non DICOM conformal (see not below) explicit
- // VR that ommited the VR of (at least) this element. Farts happen.
- // [Note: according to the part 5, PS 3.5-2001, section 7.1 p25
- // on Data elements "Implicit and Explicit VR Data Elements shall
- // not coexist in a Data Set and Data Sets nested within it".]
- // Length is on 4 bytes.
- FixFoundLength(ElVal, ReadInt32());
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief Swaps back the bytes of 4-byte long integer accordingly to
- * processor order.
- *
- * @return The suggested integer.
- */
-guint32 gdcmHeader::SwapLong(guint32 a) {
- switch (sw) {
- case 0 :
- break;
- case 4321 :
- a=( ((a<<24) & 0xff000000) | ((a<<8) & 0x00ff0000) |
- ((a>>8) & 0x0000ff00) | ((a>>24) & 0x000000ff) );
- break;
-
- case 3412 :
- a=( ((a<<16) & 0xffff0000) | ((a>>16) & 0x0000ffff) );
- break;
-
- case 2143 :
- a=( ((a<<8) & 0xff00ff00) | ((a>>8) & 0x00ff00ff) );
- break;
- default :
- dbg.Error(" gdcmHeader::SwapLong : unset swap code");
- a=0;
- }
- return(a);
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief Swaps the bytes so they agree with the processor order
- * @return The properly swaped 16 bits integer.
- */
-guint16 gdcmHeader::SwapShort(guint16 a) {
- if ( (sw==4321) || (sw==2143) )
- a =(((a<<8) & 0x0ff00) | ((a>>8)&0x00ff));
- return (a);
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief
- *
- * @return
- */
- void gdcmHeader::SkipBytes(guint32 NBytes) {
- //FIXME don't dump the returned value
- (void)fseek(fp, (long)NBytes, SEEK_CUR);
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief
- * @param ElVal
- * @return
- */
- void gdcmHeader::SkipElementValue(gdcmElValue * ElVal) {
- SkipBytes(ElVal->GetLength());
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief
- * @param NewSize
- * @return
- */
- void gdcmHeader::SetMaxSizeLoadElementValue(long NewSize) {
- if (NewSize < 0)
- return;
- if ((guint32)NewSize >= (guint32)0xffffffff) {
- MaxSizeLoadElementValue = 0xffffffff;
- return;
- }
- MaxSizeLoadElementValue = NewSize;
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief Loads the element content if it's length is not bigger
- * than the value specified with
- * gdcmHeader::SetMaxSizeLoadElementValue()
- */
-void gdcmHeader::LoadElementValue(gdcmElValue * ElVal) {
- size_t item_read;
- guint16 group = ElVal->GetGroup();
- std::string vr= ElVal->GetVR();
- guint32 length = ElVal->GetLength();
- bool SkipLoad = false;
-
- fseek(fp, (long)ElVal->GetOffset(), SEEK_SET);
-
- // FIXME Sequences not treated yet !
- //
- // Ne faudrait-il pas au contraire trouver immediatement
- // une maniere 'propre' de traiter les sequences (vr = SQ)
- // car commencer par les ignorer risque de conduire a qq chose
- // qui pourrait ne pas etre generalisable
- // Well, I'm expecting your code !!!
-
- 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).
- // Well ...
- // Actually (fffe e000) tells us an Element is beginning
- // (fffe e00d) tells us an Element just ended
- // (fffe e0dd) tells us the current SEQuence just ended
-
- if( group == 0xfffe )
- SkipLoad = true;
-
- if ( SkipLoad ) {
- ElVal->SetLength(0);
- ElVal->SetValue("gdcm::Skipped");
- return;
- }
-
- // When the length is zero things are easy:
- if ( length == 0 ) {
- ElVal->SetValue("");
- return;
- }
-
- // The elements whose length is bigger than the specified upper bound
- // are not loaded. Instead we leave a short notice of the offset of
- // the element content and it's length.
- if (length > MaxSizeLoadElementValue) {
- std::ostringstream s;
- s << "gdcm::NotLoaded.";
- s << " Address:" << (long)ElVal->GetOffset();
- s << " Length:" << 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 (?)
-
- if ( IsAnInteger(ElVal) ) {
- guint32 NewInt;
- std::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;
- }
-
- // 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;
- }
- NewValue[length]= 0;
-
- item_read = fread(NewValue, (size_t)length, (size_t)1, fp);
- if ( item_read != 1 ) {
- free(NewValue);
- dbg.Verbose(1, "gdcmHeader::LoadElementValue","unread element value");
- ElVal->SetValue("gdcm::UnRead");
- return;
- }
- ElVal->SetValue(NewValue);
- free(NewValue);
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief Loads the element while preserving the current
- * underlying file position indicator as opposed to
- * to LoadElementValue that modifies it.
- * @param ElVal Element whose value shall be loaded.
- * @return
- */
-void gdcmHeader::LoadElementValueSafe(gdcmElValue * ElVal) {
- long PositionOnEntry = ftell(fp);
- LoadElementValue(ElVal);
- fseek(fp, PositionOnEntry, SEEK_SET);
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief Reads a supposed to be 16 Bits integer
- * \ (swaps it depending on processor endianity)
- *
- * @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(0, "gdcmHeader::ReadInt16", " Failed to read :");
- // if(feof(fp))
- // dbg.Verbose(0, "gdcmHeader::ReadInt16", " End of File encountered");
- if(ferror(fp))
- dbg.Verbose(0, "gdcmHeader::ReadInt16", " File Error");
- errno = 1;
- return 0;
- }
- errno = 0;
- g = SwapShort(g);
- return g;
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief Reads a supposed to be 32 Bits integer
- * \ (swaps it depending on processor endianity)
- *
- * @return
- */
-guint32 gdcmHeader::ReadInt32(void) {
- guint32 g;
- size_t item_read;
- item_read = fread (&g, (size_t)4,(size_t)1, fp);
- if ( item_read != 1 ) {
- //dbg.Verbose(0, "gdcmHeader::ReadInt32", " Failed to read :");
- //if(feof(fp))
- // dbg.Verbose(0, "gdcmHeader::ReadInt32", " End of File encountered");
- if(ferror(fp))
- dbg.Verbose(0, "gdcmHeader::ReadInt32", " File Error");
- errno = 1;
- return 0;
- }
- errno = 0;
- g = SwapLong(g);
- return g;
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief
- *
- * @return
- */
- gdcmElValue* gdcmHeader::GetElValueByNumber(guint16 Group, guint16 Elem) {
-
- gdcmElValue* elValue = PubElValSet.GetElementByNumber(Group, Elem);
- if (!elValue) {
- dbg.Verbose(1, "gdcmHeader::GetElValueByNumber",
- "failed to Locate gdcmElValue");
- return (gdcmElValue*)0;
- }
- return elValue;
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief Build a new Element Value from all the low level arguments.
- * Check for existence of dictionary entry, and build
- * a default one when absent.
- * @param Group group of the underlying DictEntry
- * @param Elem element of the underlying DictEntry
- */
-gdcmElValue* gdcmHeader::NewElValueByNumber(guint16 Group, guint16 Elem) {
- // Find out if the tag we encountered is in the dictionaries:
- gdcmDictEntry * NewTag = GetDictEntryByNumber(Group, Elem);
- if (!NewTag)
- NewTag = new gdcmDictEntry(Group, Elem);
-
- gdcmElValue* NewElVal = new gdcmElValue(NewTag);
- if (!NewElVal) {
- dbg.Verbose(1, "gdcmHeader::NewElValueByNumber",
- "failed to allocate gdcmElValue");
- return (gdcmElValue*)0;
- }
- return NewElVal;
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief TODO
- * @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 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);
- 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.
- * Check for existence of dictionary entry, and build
- * a default one when absent.
- * @param Name Name of the underlying DictEntry
- */
-gdcmElValue* gdcmHeader::NewElValueByName(std::string Name) {
-
- gdcmDictEntry * NewTag = GetDictEntryByName(Name);
- if (!NewTag)
- NewTag = new gdcmDictEntry(0xffff, 0xffff, "LO", "Unknown", Name);
-
- gdcmElValue* NewElVal = new gdcmElValue(NewTag);
- if (!NewElVal) {
- dbg.Verbose(1, "gdcmHeader::ObtainElValueByName",
- "failed to allocate gdcmElValue");
- return (gdcmElValue*)0;
- }
- return NewElVal;
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief Read the next tag but WITHOUT loading it's value
- * @return On succes the newly created ElValue, NULL on failure.
- */
-gdcmElValue * gdcmHeader::ReadNextElement(void) {
-
- guint16 g,n;
- gdcmElValue * NewElVal;
-
- g = ReadInt16();
- n = ReadInt16();
-
- if (errno == 1)
- // We reached the EOF (or an error occured) and header parsing
- // has to be considered as finished.
- return (gdcmElValue *)0;
-
- NewElVal = NewElValueByNumber(g, n);
- FindVR(NewElVal);
- FindLength(NewElVal);
- if (errno == 1) {
- // Call it quits
- return (gdcmElValue *)0;
- }
- NewElVal->SetOffset(ftell(fp));
- //if ( (g==0x7fe0) && (n==0x0010) )
- return NewElVal;
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief Apply some heuristics to predict wether the considered
- * element value contains/represents an integer or not.
- * @param ElVal The element value on which to apply the predicate.
- * @return The result of the heuristical predicate.
- */
-bool gdcmHeader::IsAnInteger(gdcmElValue * ElVal) {
- guint16 element = ElVal->GetElement();
- std::string vr = ElVal->GetVR();
- guint32 length = ElVal->GetLength();
-
- // When we have some semantics on the element we just read, and if we
- // a priori know we are dealing with an integer, then we shall be
- // able to swap it's element value properly.
- if ( element == 0 ) { // This is the group length of the group
- if (length == 4)
- return true;
- else {
- dbg.Error("gdcmHeader::IsAnInteger",
- "Erroneous Group Length element length.");
- }
- }
- if ( (vr == "UL") || (vr == "US") || (vr == "SL") || (vr == "SS") )
- return true;
-
- return false;
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief Recover the offset (from the beginning of the file) of the pixels.
- */
-size_t gdcmHeader::GetPixelOffset(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->GetOffset();
- else
- return 0;
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief Searches both the public and the shadow dictionary (when they
- * exist) for the presence of the DictEntry with given
- * group and element. The public dictionary has precedence on the
- * shadow one.
- * @param group group of the searched DictEntry
- * @param element element of the searched DictEntry
- * @return Corresponding DictEntry when it exists, NULL otherwise.
- */
-gdcmDictEntry * gdcmHeader::GetDictEntryByNumber(guint16 group,
- guint16 element) {
- gdcmDictEntry * found = (gdcmDictEntry*)0;
- if (!RefPubDict && !RefShaDict) {
- dbg.Verbose(0, "gdcmHeader::GetDictEntry",
- "we SHOULD have a default dictionary");
- }
- if (RefPubDict) {
- found = RefPubDict->GetTagByNumber(group, element);
- if (found)
- return found;
- }
- if (RefShaDict) {
- found = RefShaDict->GetTagByNumber(group, element);
- if (found)
- return found;
- }
- return found;
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief Searches both the public and the shadow dictionary (when they
- * exist) for the presence of the DictEntry with given name.
- * The public dictionary has precedence on the shadow one.
- * @param Name name of the searched DictEntry
- * @return Corresponding DictEntry when it exists, NULL otherwise.
- */
-gdcmDictEntry * gdcmHeader::GetDictEntryByName(std::string Name) {
- gdcmDictEntry * found = (gdcmDictEntry*)0;
- if (!RefPubDict && !RefShaDict) {
- dbg.Verbose(0, "gdcmHeader::GetDictEntry",
- "we SHOULD have a default dictionary");
- }
- if (RefPubDict) {
- found = RefPubDict->GetTagByName(Name);
- if (found)
- return found;
- }
- if (RefShaDict) {
- found = RefShaDict->GetTagByName(Name);
- if (found)
- return found;
- }
- return found;
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief Searches within the public dictionary for element value of
- * a given tag.
- * @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 ("gdcm::Unfound") otherwise.
- */
-std::string gdcmHeader::GetPubElValByNumber(guint16 group, guint16 element) {
- return PubElValSet.GetElValueByNumber(group, element);
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief Searches within the public dictionary for element value
- * representation of a given tag.
- *
- * Obtaining the VR (Value Representation) might be needed by caller
- * 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.
- * @return Corresponding element value representation when it exists,
- * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise.
- */
-std::string gdcmHeader::GetPubElValRepByNumber(guint16 group, guint16 element) {
- gdcmElValue* elem = PubElValSet.GetElementByNumber(group, element);
- if ( !elem )
- 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.
- * @return Corresponding element value when it exists, and the string
- * GDCM_UNFOUND ("gdcm::Unfound") otherwise.
- */
-std::string gdcmHeader::GetPubElValByName(std::string TagName) {
- return PubElValSet.GetElValueByName(TagName);
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief Searches within the elements parsed with the public dictionary for
- * the element value representation of a given tag.
- *
- * Obtaining the VR (Value Representation) might be needed by caller
- * 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.
- * @return Corresponding element value representation when it exists,
- * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise.
- */
-std::string gdcmHeader::GetPubElValRepByName(std::string TagName) {
- gdcmElValue* elem = PubElValSet.GetElementByName(TagName);
- if ( !elem )
- 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.
- * @return Corresponding element value representation when it exists,
- * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise.
- */
-std::string gdcmHeader::GetShaElValByNumber(guint16 group, guint16 element) {
- return ShaElValSet.GetElValueByNumber(group, element);
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief Searches within the elements parsed with the SHADOW dictionary
- * for the element value representation of a given tag.
- *
- * Obtaining the VR (Value Representation) might be needed by caller
- * 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.
- * @return Corresponding element value representation when it exists,
- * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise.
- */
-std::string gdcmHeader::GetShaElValRepByNumber(guint16 group, guint16 element) {
- gdcmElValue* elem = ShaElValSet.GetElementByNumber(group, element);
- if ( !elem )
- 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.
- * @return Corresponding element value when it exists, and the string
- * GDCM_UNFOUND ("gdcm::Unfound") otherwise.
- */
-std::string gdcmHeader::GetShaElValByName(std::string TagName) {
- return ShaElValSet.GetElValueByName(TagName);
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief Searches within the elements parsed with the shadow dictionary for
- * the element value representation of a given tag.
- *
- * Obtaining the VR (Value Representation) might be needed by caller
- * 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.
- * @return Corresponding element value representation when it exists,
- * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise.
- */
-std::string gdcmHeader::GetShaElValRepByName(std::string TagName) {
- gdcmElValue* elem = ShaElValSet.GetElementByName(TagName);
- if ( !elem )
- return GDCM_UNFOUND;
- return elem->GetVR();
-}
-
-/**
- * \ingroup gdcmHeader
- * \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.
- * @return Corresponding element value representation when it exists,
- * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise.
- */
-std::string gdcmHeader::GetElValByNumber(guint16 group, guint16 element) {
- std::string pub = GetPubElValByNumber(group, element);
- if (pub.length())
- return pub;
- return GetShaElValByNumber(group, element);
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief Searches within elements parsed with the public dictionary
- * and then within the elements parsed with the shadow dictionary
- * for the element value representation of a given tag.
- *
- * Obtaining the VR (Value Representation) might be needed by caller
- * 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.
- * @return Corresponding element value representation when it exists,
- * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise.
- */
-std::string gdcmHeader::GetElValRepByNumber(guint16 group, guint16 element) {
- std::string pub = GetPubElValRepByNumber(group, element);
- if (pub.length())
- return pub;
- return GetShaElValRepByNumber(group, element);
-}
-
-/**
- * \ingroup gdcmHeader
- * \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.
- * @return Corresponding element value when it exists,
- * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise.
- */
-std::string gdcmHeader::GetElValByName(std::string TagName) {
- std::string pub = GetPubElValByName(TagName);
- if (pub.length())
- return pub;
- return GetShaElValByName(TagName);
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief Searches within elements parsed with the public dictionary
- * and then within the elements parsed with the shadow dictionary
- * for the element value representation of a given tag.
- *
- * Obtaining the VR (Value Representation) might be needed by caller
- * 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.
- * @return Corresponding element value representation when it exists,
- * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise.
- */
-std::string gdcmHeader::GetElValRepByName(std::string TagName) {
- std::string pub = GetPubElValRepByName(TagName);
- if (pub.length())
- return pub;
- return GetShaElValRepByName(TagName);
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief Accesses an existing gdcmElValue in the PubElValSet of this instance
- * through it's (group, element) and modifies it's content with
- * the given value.
- * @param content new value to substitute with
- * @param group group of the ElVal to modify
- * @param element element of the ElVal to modify
- */
-int gdcmHeader::SetPubElValByNumber(std::string content, guint16 group,
- guint16 element)
-
-//TODO : homogeneiser les noms : SetPubElValByNumber
-// qui appelle PubElValSet.SetElValueByNumber
-// pourquoi pas SetPubElValueByNumber ??
-{
-
- return ( PubElValSet.SetElValueByNumber (content, group, element) );
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief Accesses an existing gdcmElValue in the PubElValSet 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
- */
-int gdcmHeader::SetPubElValByName(std::string content, std::string TagName) {
- return ( PubElValSet.SetElValueByName (content, TagName) );
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief Accesses an existing gdcmElValue in the PubElValSet of this instance
- * through it's (group, element) and modifies it's length with
- * the given value.
- * \warning Use with extreme caution.
- * @param length new length to substitute with
- * @param group group of the ElVal to modify
- * @param element element of the ElVal to modify
- * @return 1 on success, 0 otherwise.
- */
-
-int gdcmHeader::SetPubElValLengthByNumber(guint32 length, guint16 group,
- guint16 element) {
- return ( PubElValSet.SetElValueLengthByNumber (length, group, element) );
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief Accesses an existing gdcmElValue in the ShaElValSet of this instance
- * through it's (group, element) and modifies it's content with
- * the given value.
- * @param content new value to substitute with
- * @param group group of the ElVal to modify
- * @param element element of the ElVal to modify
- * @return 1 on success, 0 otherwise.
- */
-int gdcmHeader::SetShaElValByNumber(std::string content,
- guint16 group, guint16 element) {
- return ( ShaElValSet.SetElValueByNumber (content, group, element) );
-}
-
-/**
- * \ingroup gdcmHeader
- * \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 ShadowTagName name of the tag to be modified
- */
-int gdcmHeader::SetShaElValByName(std::string content, std::string ShadowTagName) {
- return ( ShaElValSet.SetElValueByName (content, ShadowTagName) );
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief Parses the header of the file but WITHOUT loading element values.
- */
-void gdcmHeader::ParseHeader(bool exception_on_error) throw(gdcmFormatError) {
- gdcmElValue * newElValue = (gdcmElValue *)0;
-
- rewind(fp);
- CheckSwap();
- while ( (newElValue = ReadNextElement()) ) {
- SkipElementValue(newElValue);
- PubElValSet.Add(newElValue);
- }
-}
-
-/**
- * \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.
+ * \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
+ * other cases.
*/
-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;
+bool gdcmHeader::IsJPEGSpectralSelectionProcess6_8TransferSyntax(void) {
+ gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010);
+ if ( !Element )
+ return false;
+ LoadHeaderEntrySafe(Element);
- 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;
+ std::string Transfer = Element->GetValue();
+ if ( Transfer == "1.2.840.10008.1.2.4.53" )
+ return true;
+ return false;
}
/**
* \ingroup gdcmHeader
- * \brief Loads the element values of all the elements present in the
- * public tag based hash table.
+ * \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.
*/
-void gdcmHeader::LoadElements(void) {
- rewind(fp);
- TagElValueHT ht = PubElValSet.GetTagHt();
- for (TagElValueHT::iterator tag = ht.begin(); tag != ht.end(); ++tag) {
- LoadElementValue(tag->second);
- }
- 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);
-}
+bool gdcmHeader::IsRLELossLessTransferSyntax(void) {
+ gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010);
+ if ( !Element )
+ return false;
+ LoadHeaderEntrySafe(Element);
-/**
- * \ingroup gdcmHeader
- * \brief
- * @return
- */
-void gdcmHeader::PrintPubDict(std::ostream & os) {
- RefPubDict->Print(os);
+ std::string Transfer = Element->GetValue();
+ if ( Transfer == "1.2.840.10008.1.2.5" )
+ return true;
+ return false;
}
/**
- * \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 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);
- }
+ * \ingroup gdcmHeader
+ * \brief Determines if Transfer Syntax was already encountered
+ * and if it corresponds to a JPEG Lossless one.
+ *
+ * @return True when RLE Lossless found. False in all
+ * other cases.
+ */
+bool gdcmHeader::IsJPEGLossless(void) {
+ gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010);
+ // faire qq chose d'intelligent a la place de ça
+ if ( !Element )
+ return false;
+ LoadHeaderEntrySafe(Element);
- 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);
- }
+ 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 PubElValSet.Write(fp, type);
+ return false;
}
-//
-// ------------------------ 'non string' elements related functions
-//
-
/**
- * \ingroup gdcmHeader
- * \brief Loads (from disk) the element content
- * when a string is not suitable
+ * \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.
*/
-void * gdcmHeader::LoadElementVoidArea(guint16 Group, guint16 Elem) {
- gdcmElValue * Element= PubElValSet.GetElementByNumber(Group, Elem);
+bool gdcmHeader::IsJPEG2000(void) {
+ gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010);
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;
-}
+ return false;
+ LoadHeaderEntrySafe(Element);
-/**
- * \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();
+ 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 Gets (from Header) a 'non string' element value
- * \ (LoadElementValue has already be executed)
- * @param Group
- * @param Elem
- * @return Pointer to the 'non string' area
-
+ * \brief Predicate for dicom version 3 file.
+ * @return True when the file is a dicom version 3.
*/
- 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();
+bool gdcmHeader::IsDicomV3(void) {
+ // Checking if Transfert Syntax exists is enough
+ return (GetHeaderEntryByNumber(0x0002, 0x0010) != NULL);
}
-
-//
-// =============================================================================
-// Heuristics based accessors
-//==============================================================================
-//
-
-// TODO : move to an other file.
-
-
/**
* \ingroup gdcmHeader
* \brief Retrieve the number of columns of image.
* @return The encountered size when found, 0 by default.
+ * 0 means the file is NOT USABLE. The caller will have to check
*/
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.
- std::string StrSize = GetPubElValByNumber(0x0028,0x0011);
+ std::string StrSize = GetEntryByNumber(0x0028,0x0011);
if (StrSize == GDCM_UNFOUND)
return 0;
return atoi(StrSize.c_str());
* \ingroup gdcmHeader
* \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.
+ * @return The encountered size when found, 1 by default
+ * (The file contains a Signal, not an Image).
*/
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.
- std::string StrSize = GetPubElValByNumber(0x0028,0x0010);
+ std::string StrSize = GetEntryByNumber(0x0028,0x0010);
if (StrSize != GDCM_UNFOUND)
return atoi(StrSize.c_str());
if ( IsDicomV3() )
return 0;
else
- // The Rows (0028,0010) entry is optional for ACR/NEMA. It might
+ // The Rows (0028,0010) entry was optional for ACR/NEMA. It might
// hence be a signal (1d image). So we default to 1:
return 1;
}
* \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.
+ * @return The encountered size when found, 1 by default (single image).
*/
int gdcmHeader::GetZSize(void) {
- // Both in DicomV3 and ACR/Nema the consider the "Number of Frames"
+ // Both DicomV3 and ACR/Nema consider the "Number of Frames"
// as the third dimension.
- std::string StrSize = GetPubElValByNumber(0x0028,0x0008);
+ std::string StrSize = GetEntryByNumber(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);
+ StrSize = GetEntryByNumber(0x0028,0x0012);
if (StrSize != GDCM_UNFOUND)
return atoi(StrSize.c_str());
return 1;
/**
* \ingroup gdcmHeader
- * \brief Retrieve the number of Bits Stored
+ * \brief Retrieve the number of Bits Stored (actually used)
* (as opposite to number of Bits Allocated)
*
* @return The encountered number of Bits Stored, 0 by default.
+ * 0 means the file is NOT USABLE. The caller has to check it !
*/
int gdcmHeader::GetBitsStored(void) {
- std::string StrSize = GetPubElValByNumber(0x0028,0x0101);
+ std::string StrSize = GetEntryByNumber(0x0028,0x0101);
if (StrSize == GDCM_UNFOUND)
- return 1;
+ return 0; // It's supposed to be mandatory
+ // the caller will have to check
return atoi(StrSize.c_str());
}
* (8, 12 -compacted ACR-NEMA files, 16, ...)
*
* @return The encountered number of Bits Allocated, 0 by default.
+ * 0 means the file is NOT USABLE. The caller has to check it !
*/
int gdcmHeader::GetBitsAllocated(void) {
- std::string StrSize = GetPubElValByNumber(0x0028,0x0100);
+ std::string StrSize = GetEntryByNumber(0x0028,0x0100);
if (StrSize == GDCM_UNFOUND)
- return 1;
+ return 0; // It's supposed to be mandatory
+ // the caller will have to check
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.
+ * (Gray level Pixels)
*/
int gdcmHeader::GetSamplesPerPixel(void) {
- std::string StrSize = GetPubElValByNumber(0x0028,0x0002);
+ std::string StrSize = GetEntryByNumber(0x0028,0x0002);
if (StrSize == GDCM_UNFOUND)
return 1; // Well, it's supposed to be mandatory ...
+ // but sometimes it's missing : we assume Gray pixels
return atoi(StrSize.c_str());
}
* @return The encountered Planar Configuration, 0 by default.
*/
int gdcmHeader::GetPlanarConfiguration(void) {
- std::string StrSize = GetPubElValByNumber(0x0028,0x0006);
+ std::string StrSize = GetEntryByNumber(0x0028,0x0006);
if (StrSize == GDCM_UNFOUND)
return 0;
return atoi(StrSize.c_str());
/**
* \ingroup gdcmHeader
* \brief Return the size (in bytes) of a single pixel of data.
- * @return The size in bytes of a single pixel of data.
- *
+ * @return The size in bytes of a single pixel of data; 0 by default
+ * 0 means the file is NOT USABLE; the caller will have to check
*/
int gdcmHeader::GetPixelSize(void) {
std::string PixelType = GetPixelType();
* - 32U unsigned 32 bit,
* - 32S signed 32 bit,
* \warning 12 bit images appear as 16 bit.
- * @return
+ * \ 24 bit images appear as 8 bit
+ * @return 0S if nothing found. NOT USABLE file. The caller has to check
*/
std::string gdcmHeader::GetPixelType(void) {
- std::string BitsAlloc;
- BitsAlloc = GetElValByName("Bits Allocated");
+ std::string BitsAlloc = GetEntryByNumber(0x0028, 0x0100); // Bits Allocated
if (BitsAlloc == GDCM_UNFOUND) {
dbg.Verbose(0, "gdcmHeader::GetPixelType: unfound Bits Allocated");
BitsAlloc = std::string("16");
}
- if (BitsAlloc == "12")
+ if (BitsAlloc == "12") // It will be unpacked
BitsAlloc = std::string("16");
-
- std::string Signed;
- Signed = GetElValByName("Pixel Representation");
+ else if (BitsAlloc == "24") // (in order no to be messed up
+ BitsAlloc = std::string("8"); // by old RGB images)
+
+ std::string Signed = GetEntryByNumber(0x0028, 0x0103); // "Pixel Representation"
if (Signed == GDCM_UNFOUND) {
dbg.Verbose(0, "gdcmHeader::GetPixelType: unfound Pixel Representation");
BitsAlloc = std::string("0");
}
/**
- * \ingroup gdcmHeader
- * \brief gets the info from 0002,0010 : Transfert Syntax
- * \ else 1.
- * @return Transfert Syntax Name (as oposite to Transfert Syntax UID)
- */
-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";
+ * \ingroup gdcmHeader
+ * \brief Recover the offset (from the beginning of the file) of the pixels.
+ */
+size_t gdcmHeader::GetPixelOffset(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 = GetEntryByNumber(0x0028, 0x0200);
+
+ if ( ImageLocation == GDCM_UNFOUND ) { // Image Location
+ grPixel = 0x7fe0;
+ } else {
+ grPixel = (guint16) atoi( ImageLocation.c_str() );
}
- // 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;
+ if (grPixel != 0x7fe0)
+ // This is a kludge for old dirty Philips imager.
+ numPixel = 0x1010;
+ else
+ numPixel = 0x0010;
+
+ gdcmHeaderEntry* PixelElement = GetHeaderEntryByNumber(grPixel,numPixel);
+ if (PixelElement)
+ return PixelElement->GetOffset();
+ else
+ return 0;
}
-// -------------------------------- Lookup Table related functions ------------
+/**
+ * \ingroup gdcmHeader
+ * \brief Recover the pixel area length (in Bytes)
+ * @return 0 by default. NOT USABLE file. The caller has to check.
+ */
+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 = GetEntryByNumber(0x0028, 0x0200);
+ 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;
+
+ gdcmHeaderEntry* PixelElement = GetHeaderEntryByNumber(grPixel,numPixel);
+ if (PixelElement)
+ return PixelElement->GetLength();
+ else
+ return 0;
+}
/**
* \ingroup gdcmHeader
- * \brief gets the info from 0028,1101 : Lookup Table Desc-Red
- * \ else 0
- * @return Lookup Table Length
- * \ when (0028,0004),Photometric Interpretation = [PALETTE COLOR ]
+ * \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 a Boolean
*/
-
-int gdcmHeader::GetLUTLength(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
- std::string LutDescriptionR = GetPubElValByNumber(0x0028,0x1101);
- if (LutDescriptionR == GDCM_UNFOUND)
- return 0;
- std::string LutDescriptionG = GetPubElValByNumber(0x0028,0x1102);
- if (LutDescriptionG == GDCM_UNFOUND)
- return 0;
- std::string LutDescriptionB = GetPubElValByNumber(0x0028,0x1103);
- if (LutDescriptionB == GDCM_UNFOUND)
- return 0;
- if( (LutDescriptionR != LutDescriptionG) || (LutDescriptionR != LutDescriptionB) ) {
- dbg.Verbose(0, "gdcmHeader::GetLUTLength: The CLUT R,G,B are not equal");
- return 0;
- }
- std::cout << "Lut Description " << LutDescriptionR <<std::endl;
- tokens.erase(tokens.begin(),tokens.end()); // clean any previous value
- Tokenize (LutDescriptionR, tokens, "\\");
- LutLength=atoi(tokens[0].c_str());
- //LutDepth=atoi(tokens[1].c_str());
- //LutNbits=atoi(tokens[2].c_str());
- tokens.clear();
- return LutLength;
+bool gdcmHeader::HasLUT(void) {
+
+ // Check the presence of the LUT Descriptors
+ if ( !GetHeaderEntryByNumber(0x0028,0x1101) )
+ return false;
+ // LutDescriptorGreen
+ if ( !GetHeaderEntryByNumber(0x0028,0x1102) )
+ return false;
+ // LutDescriptorBlue
+ if ( !GetHeaderEntryByNumber(0x0028,0x1103) )
+ return false;
+ // It is not enough
+ // we check also
+ if ( !GetHeaderEntryByNumber(0x0028,0x1201) )
+ return false;
+ if ( !GetHeaderEntryByNumber(0x0028,0x1202) )
+ return false;
+ if ( !GetHeaderEntryByNumber(0x0028,0x1203) )
+ return false;
+ return true;
}
/**
* \ingroup gdcmHeader
* \brief gets the info from 0028,1101 : Lookup Table Desc-Red
* \ else 0
- * @return Lookup Table nBit
+ * @return Lookup Table number of Bits , 0 by default
* \ when (0028,0004),Photometric Interpretation = [PALETTE COLOR ]
*/
-
int gdcmHeader::GetLUTNbits(void) {
std::vector<std::string> tokens;
//int LutLength;
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);
+ std::string LutDescription = GetEntryByNumber(0x0028,0x1101);
if (LutDescription == GDCM_UNFOUND)
return 0;
tokens.erase(tokens.begin(),tokens.end()); // clean any previous value
tokens.clear();
return LutNbits;
}
-
-
-/**
- * \ingroup gdcmHeader
- * \brief gets the info from 0028,1201 : Lookup Table Red
- * \ else 0
- * @return Lookup Table Red
- * \ when (0028,0004),Photometric Interpretation = [PALETTE COLOR ]
- */
-void * gdcmHeader::GetLUTRed(void) {
- return GetPubElValVoidAreaByNumber(0x0028,0x1201);
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief gets the info from 0028,1202 : Lookup Table Green
- * \ else 0
- * @return Lookup Table Red
- * \ when (0028,0004),Photometric Interpretation = [PALETTE COLOR ]
- */
- void * gdcmHeader::GetLUTGreen(void) {
- return GetPubElValVoidAreaByNumber(0x0028,0x1202);
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief gets the info from 0028,1202 : Lookup Table Blue
- * \ else 0
- * @return Lookup Table Blue
- * \ when (0028,0004),Photometric Interpretation = [PALETTE COLOR ]
- */
-void * gdcmHeader::GetLUTBlue(void) {
- return GetPubElValVoidAreaByNumber(0x0028,0x1203);
-}
/**
* \ingroup gdcmHeader
- * \brief
- * @return Lookup Table RGB
+ * \brief builts Red/Green/Blue/Alpha LUT from Header
* \ when (0028,0004),Photometric Interpretation = [PALETTE COLOR ]
- * \ and (0028,1201),(0028,1202),(0028,1202) are found
- * \warning : hazardous ! Use better GetPubElValVoidAreaByNumber
+ * \ 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 deals with them :-(
+ * @return a RGBA Lookup Table
*/
-void * gdcmHeader::GetLUTRGB(void) {
+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 (GetPubElValByNumber(0x0028,0x0004) == GDCM_UNFOUND) {
- dbg.Verbose(0, "gdcmHeader::GetLUTRGB: unfound Photometric Interpretation");
+// if Photometric Interpretation # PALETTE COLOR, no LUT to be done
+ if (GetEntryByNumber(0x0028,0x0004) != "PALETTE COLOR ") {
return NULL;
}
- void * LutR,*LutG,*LutB;
- int l;
-
- // Maybe, some day we get an image
- // that respects the definition ...
- // Let's consider no ones does.
-
- l= GetLUTLength();
- if(l==0)
- return (NULL);
- int nBits=GetLUTNbits();
-
- // a virer quand on aura trouve UNE image
- // qui correspond VRAIMENT à la definition !
- std::cout << "l " << l << " nBits " << nBits;
+ int lengthR, debR, nbitsR;
+ int lengthG, debG, nbitsG;
+ int lengthB, debB, nbitsB;
- l= l/(nBits/8);
-
- LutR =GetPubElValVoidAreaByNumber(0x0028,0x1201);
- LutG =GetPubElValVoidAreaByNumber(0x0028,0x1202);
- LutB =GetPubElValVoidAreaByNumber(0x0028,0x1203);
+// Get info from Lut Descriptors
+// (the 3 LUT descriptors may be different)
+ std::string LutDescriptionR = GetEntryByNumber(0x0028,0x1101);
+ if (LutDescriptionR == GDCM_UNFOUND)
+ return NULL;
+ std::string LutDescriptionG = GetEntryByNumber(0x0028,0x1102);
+ if (LutDescriptionG == GDCM_UNFOUND)
+ return NULL;
+ std::string LutDescriptionB = GetEntryByNumber(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();
- // Warning : Any value for nBits as to be considered as 8
- // Any value for Length as to be considered as 256
- // That's DICOM ...
+ 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();
- // Just wait before removing the following code
- /*
- if (nBits == 16) {
- guint16 * LUTRGB, *rgb;
- LUTRGB = rgb = (guint16 *) malloc(3*l*sizeof( guint16));
- guint16 * r = (guint16 *)LutR;
- guint16 * g = (guint16 *)LutG;
- guint16 * b = (guint16 *)LutB;
- for(int i=0;i<l;i++) {
- *rgb++ = *r++;
- *rgb++ = *g++;
- *rgb++ = *b++;
- }
- return(LUTRGB);
- } else
+ 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 *)
+ GetEntryVoidAreaByNumber(0x0028,0x1201);
+ unsigned char *lutG = (unsigned char *)
+ GetEntryVoidAreaByNumber(0x0028,0x1202);
+ unsigned char *lutB = (unsigned char *)
+ GetEntryVoidAreaByNumber(0x0028,0x1203);
- */ { // we assume it's always 8 Bits
- l=256; // we assume ...
- unsigned char * LUTRGB, *rgb;
- LUTRGB = rgb = (unsigned char *) malloc(3*l*sizeof( char));
- unsigned char * r = (unsigned char *)LutR;
- unsigned char * g = (unsigned char *)LutG;
- unsigned char * b = (unsigned char *)LutB;
- for(int i=0;i<l;i++) {
- //std::cout << "lut16 " << i << " : " << *r << " " << *g << " " << *b
- // << std::endl;
- printf("lut 8 %d : %d %d %d \n",i,*r,*g,*b);
- *rgb++ = *r++;
- *rgb++ = *g++;
- *rgb++ = *b++;
- }
- free(LutR); free(LutB); free(LutG);
- return(LUTRGB);
+ 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 = GetEntryByNumber(0x0028,0x0100);
+ if (str_nb == GDCM_UNFOUND ) {
+ nb = 16;
+ } else {
+ nb = atoi(str_nb.c_str() );
+ }
+ int mult;
-/* Sorry for the comments. The code will be moved in a fonction
-
- std::string x=GetPubElValByNumber(0x0028,0x1201);
- unsigned short int * lutR = (unsigned short int *)malloc((size_t)200*sizeof(short int));
- unsigned short int * lutG = (unsigned short int *)malloc((size_t)200*sizeof(short int));
- unsigned short int * lutB = (unsigned short int *)malloc((size_t)200*sizeof(short int));
-
- std::vector<std::string> tokens;
- tokens.erase(tokens.begin(),tokens.end()); // clean any previous value
- Tokenize ((const std::string)x, tokens, "\\");
- for (unsigned int i=0; i<tokens.size();i++) {
- lutR[i] = atoi(tokens[i].c_str());
- printf("%d (%x)\n",lutR[i],lutR[i]);
- }
-
- std::string y=GetPubElValByNumber(0x0028,0x1202);
- tokens.erase(tokens.begin(),tokens.end()); // clean any previous value
- Tokenize ((const std::string)y, tokens, "\\");
- for (unsigned int i=0; i<tokens.size();i++) {
- lutG[i] = atoi(tokens[i].c_str());
- }
+ 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?
- std::string z=GetPubElValByNumber(0x0028,0x1203);
- tokens.erase(tokens.begin(),tokens.end()); // clean any previous value
- Tokenize ((const std::string)z, tokens, "\\");
- for (unsigned int i=0; i<tokens.size();i++) {
- lutB[i] = atoi(tokens[i].c_str());
- }
- tokens.erase(tokens.begin(),tokens.end()); // clean any previous value
- Tokenize ((const std::string)x, tokens, "\\");
- for (unsigned int i=0; i<tokens.size();i++) {
- lutB[i] = atoi(tokens[i].c_str());
- }
+ //free(LutR); free(LutB); free(LutG); // Seg Fault when used
+ return(LUTRGBA);
+}
+/**
+ * \ingroup gdcmHeader
+ * \brief gets the info from 0002,0010 : Transfert Syntax
+ * \ else 1.
+ * @return Transfert Syntax Name (as oposite to Transfert Syntax UID)
*/
+std::string gdcmHeader::GetTransfertSyntaxName(void) {
+ // use the gdcmTS (TS : Transfert Syntax)
+ std::string TransfertSyntax = GetEntryByNumber(0x0002,0x0010);
+ if (TransfertSyntax == GDCM_UNFOUND) {
+ dbg.Verbose(0, "gdcmHeader::GetTransfertSyntaxName: 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;
+}
-//int lgth=GetLUTLength();
-//cout << "lgth " << lgth << std::endl;;
-//for (int j=0;j<lgth;j++){
-//printf ("%d : %d (%x) %d (%x) %d (%x)\n",j,lutR[j],lutR[j],lutG[j],lutG[j],lutB[j],lutB[j]);
-//}
+/**
+ * \ingroup gdcmFile
+ * \brief Sets the Pixel Area size in the Header
+ * --> not-for-rats function
+ *
+ * \warning WARNING doit-etre etre publique ?
+ * TODO : y aurait il un inconvenient à fusionner ces 2 fonctions
+ *
+ * @param ImageDataSize new Pixel Area Size
+ * warning : nothing else is checked
+ */
+void gdcmHeader::SetImageDataSize(size_t ImageDataSize) {
+ std::string content1;
+ char car[20];
+ // Assumes HeaderEntry (0x7fe0, 0x0010) exists ...
+ sprintf(car,"%d",ImageDataSize);
+
+ gdcmHeaderEntry *a = GetHeaderEntryByNumber(0x7fe0, 0x0010);
+ a->SetLength(ImageDataSize);
+
+ ImageDataSize+=8;
+ sprintf(car,"%d",ImageDataSize);
+ content1=car;
+ SetEntryByNumber(content1, 0x7fe0, 0x0000);
+}
+//-----------------------------------------------------------------------------
+// Protected
-}
-
+//-----------------------------------------------------------------------------
+// Private
+
+//-----------------------------------------------------------------------------