-// $Header: /cvs/public/gdcm/src/Attic/gdcmHeader.cxx,v 1.73 2003/07/01 10:04:36 frog Exp $
-
-#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 "gdcmHeader.h"
-using namespace std;
-
-
-// TODO : remove DEBUG
-#define DEBUG 0
-
-// Refer to gdcmHeader::CheckSwap()
-#define HEADER_LENGTH_TO_READ 256
-// Refer to gdcmHeader::SetMaxSizeLoadElementValue()
-#define _MaxSizeLoadElementValue_ 1024
-
-/**
- * \ingroup gdcmHeader
- * \brief
- */
-void gdcmHeader::Initialise(void) {
- dicom_vr = gdcmGlobal::GetVR();
- dicom_ts = gdcmGlobal::GetTS();
- Dicts = gdcmGlobal::GetDicts();
- RefPubDict = Dicts->GetDefaultPubDict();
- RefShaDict = (gdcmDict*)0;
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief
- * @param InFilename
- * @param exception_on_error
- */
- gdcmHeader::gdcmHeader(const char *InFilename, bool exception_on_error) {
- SetMaxSizeLoadElementValue(_MaxSizeLoadElementValue_);
- filename = InFilename;
- Initialise();
- if ( !OpenFile(exception_on_error))
- return;
- ParseHeader();
- LoadElements();
- CloseFile();
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief
- * @param exception_on_error
- */
-gdcmHeader::gdcmHeader(bool exception_on_error) {
- SetMaxSizeLoadElementValue(_MaxSizeLoadElementValue_);
- Initialise();
-}
-
-/**
- * \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 )
- return true;
- dbg.Verbose(0, "gdcmHeader::gdcmHeader cannot open file", filename.c_str());
- return false;
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief
- * @return
- */
-bool gdcmHeader::CloseFile(void) {
- int closed = fclose(fp);
- fp = (FILE *)0;
- if (! closed)
- return false;
- return true;
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief Canonical destructor.
- */
-gdcmHeader::~gdcmHeader (void) {
- dicom_vr = (gdcmVR*)0;
- Dicts = (gdcmDictSet*)0;
- RefPubDict = (gdcmDict*)0;
- RefShaDict = (gdcmDict*)0;
- return;
-}
-
-// 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
- * \brief Discover what the swap code is (among little endian, big endian,
- * bad little endian, bad big endian).
- *
- */
-void gdcmHeader::CheckSwap()
-{
- // 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 : pour 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.
- */
-void gdcmHeader::FindVR( gdcmElValue *ElVal) {
- if (filetype != ExplicitVR)
- return;
-
- 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
- // 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 = 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 allready 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);
- string Transfer = Element->GetValue();
- if ( Transfer == "1.2.840.10008.1.2" )
- return true;
- return false;
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief Determines if the Transfer Syntax was allready encountered
- * 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);
- string Transfer = Element->GetValue();
- if ( Transfer == "1.2.840.10008.1.2.1" )
- return true;
- return false;
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief Determines if the Transfer Syntax was allready encountered
- * 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);
- string Transfer = Element->GetValue();
- if ( Transfer == "1.2.840.10008.1.2.1.99" )
- return true;
- return false;
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief Determines if the Transfer Syntax was allready encountered
- * 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);
- string Transfer = Element->GetValue();
- if ( Transfer == "1.2.840.10008.1.2.2" ) //1.2.2 ??? A verifier !
- return true;
- return false;
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief Determines if the Transfer Syntax was allready encountered
- * and if it corresponds to a JPEGBaseLineProcess1 one.
- *
- * @return True when JPEGBaseLineProcess1found. False in all other cases.
- */
-bool gdcmHeader::IsJPEGBaseLineProcess1TransferSyntax(void) {
- gdcmElValue* Element = PubElValSet.GetElementByNumber(0x0002, 0x0010);
- if ( !Element )
- return false;
- LoadElementValueSafe(Element);
- string Transfer = Element->GetValue();
- if ( Transfer == "1.2.840.10008.1.2.4.50" )
- 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;
- return false;
-}
-
-
-/**
- * \ingroup gdcmHeader
- * \brief Determines if the Transfer Syntax was allready encountered
- * and if it corresponds to a JPEGExtendedProcess2-4 one.
- *
- * @return True when JPEGExtendedProcess2-4 found. False in all other cases.
- */
-bool gdcmHeader::IsJPEGExtendedProcess2_4TransferSyntax(void) {
- gdcmElValue* Element = PubElValSet.GetElementByNumber(0x0002, 0x0010);
- if ( !Element )
- return false;
- LoadElementValueSafe(Element);
- string Transfer = Element->GetValue();
- if ( Transfer == "1.2.840.10008.1.2.4.51" )
- return true;
- return false;
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief Determines if the Transfer Syntax was allready encountered
- * and if it corresponds to a JPEGExtendeProcess3-5 one.
- *
- * @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);
- string Transfer = Element->GetValue();
- if ( Transfer == "1.2.840.10008.1.2.4.52" )
- return true;
- return false;
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief Determines if the Transfer Syntax was allready encountered
- * 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);
- string Transfer = Element->GetValue();
- if ( Transfer == "1.2.840.10008.1.2.4.53" )
- 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) )
- 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;
- 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 (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 && 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 || ( g==0xb00c && n==0x0eb6 ) ) /* for bogus header JPR */
- FoundSequenceDelimiter = true;
- else if ( n != 0xe000 ){
- char msg[100]; // for sprintf. Sorry
- sprintf(msg,"wrong element (%04x) for an item sequence (%04x,%04x)\n",n, g,n);
- dbg.Verbose(1, "gdcmHeader::FindLengthOB: ",msg);
- if (DEBUG) printf("wrong element (%04x) for an item sequence (%04x,%04x)\n",n, g,n);
- errno = 1;
- return 0;
- }
- 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;
-}
-
-/**
- * \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(10);
- 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);
- 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 allready 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.");
- }
- 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
- *
- * @return
- */
- void gdcmHeader::SkipElementValue(gdcmElValue * ElVal) {
- SkipBytes(ElVal->GetLength());
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief
- *
- * @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();
- 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).
- 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) {
- 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;
- 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
- *
- * @return
- */
-guint16 gdcmHeader::ReadInt16(void) {
- guint16 g;
- size_t item_read;
- item_read = fread (&g, (size_t)2,(size_t)1, fp);
- if ( item_read != 1 ) {
- dbg.Verbose(1, "gdcmHeader::ReadInt16", " Failed to read :");
- if(feof(fp))
- dbg.Verbose(1, "gdcmHeader::ReadInt16", " End of File encountered");
- if(ferror(fp))
- dbg.Verbose(1, "gdcmHeader::ReadInt16", " File Error");
- 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);
- if ( item_read != 1 ) {
-
- dbg.Verbose(1, "gdcmHeader::ReadInt32", " Failed to read :");
- if(feof(fp))
- dbg.Verbose(1, "gdcmHeader::ReadInt32", " End of File encountered");
- if(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.
- * 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
- */
-int gdcmHeader::ReplaceOrCreateByNumber(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 ???
-
- gdcmElValue* nvElValue=NewElValueByNumber(Group, Elem);
- PubElValSet.Add(nvElValue);
- PubElValSet.SetElValueByNumber(Value, Group, Elem);
- return(1);
-}
-
-
-/**
- * \ingroup gdcmHeader
- * \brief TODO
- * @param
- */
-int gdcmHeader::ReplaceOrCreateByNumber(char* Value, guint16 Group, guint16 Elem ) {
-
- gdcmElValue* nvElValue=NewElValueByNumber(Group, Elem);
- PubElValSet.Add(nvElValue);
- string v = Value;
- PubElValSet.SetElValueByNumber(v, Group, Elem);
- return(1);
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief TODO
- * @param
- */
-
- 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(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 ( (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 = NewElValueByNumber(g, n);
- FindVR(NewElVal);
- FindLength(NewElVal);
- if (errno == 1) {
- // Call it quits
- if (DEBUG) printf("in gdcmHeader::ReadNextElement : g %04x n %04x errno %d\n",g, n, errno);
- return (gdcmElValue *)0;
- }
- NewElVal->SetOffset(ftell(fp));
- if ( (g==0x7fe0) && (n==0x0010) )
- if (DEBUG)
- printf("sortie de gdcmHeader::ReadNextElement 7fe0 0010 \n");
- return NewElVal;
-}
+// gdcmHeader.cxx
+//-----------------------------------------------------------------------------
+#include "gdcmHeader.h"
-/**
- * \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 group = ElVal->GetGroup();
- guint16 element = ElVal->GetElement();
- string vr = ElVal->GetVR();
- guint32 length = ElVal->GetLength();
+#include <stdio.h>
+#include <cerrno>
+#include <cctype> // for isalpha
+
+#include "gdcmUtil.h"
+#include "gdcmTS.h"
- // 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 {
- if (DEBUG) printf("Erroneous Group Length element length (%04x , %04x) : %d\n",
- group, element,length);
-
- dbg.Error("gdcmHeader::IsAnInteger",
- "Erroneous Group Length element length.");
- }
- }
- if ( (vr == "UL") || (vr == "US") || (vr == "SL") || (vr == "SS") )
- return true;
-
- return false;
-}
+//-----------------------------------------------------------------------------
+// Constructor / Destructor
/**
* \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
+ * \brief
+ * @param InFilename
+ * @param exception_on_error
+ * @param enable_sequences = true to allow the header
+ * to be parsed *inside* the SeQuences,
+ * when they have an actual length
+ * @param ignore_shadow = true if user wants to skip shadow groups
+ * during parsing, to save memory space
+ */
+gdcmHeader::gdcmHeader(const char *InFilename,
+ bool exception_on_error,
+ bool enable_sequences,
+ bool ignore_shadow):
+ gdcmParser(InFilename,exception_on_error,enable_sequences,ignore_shadow)
+{
+
+ // for some ACR-NEMA images GrPixel, NumPixel is *not* 7fe0,0010
+ // We may encounter the 'RETired' (0x0028, 0x0200) tag
+ // (Image Location") . This Element contains the number of
// 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;
- 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(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;
+
+ // This IS the right place for the code
+
+ std::string ImageLocation = GetEntryByNumber(0x0028, 0x0200);
+ if ( ImageLocation == GDCM_UNFOUND ) { // Image Location
+ GrPixel = 0x7fe0; // default value
+ } else {
+ GrPixel = (guint16) atoi( ImageLocation.c_str() );
+ }
+ if (GrPixel == 0xe07f) // sometimes Image Location value doesn't follow
+ GrPixel = 0x7fe0; // the supposed processor endianity.
+ // see gdcmData/cr172241.dcm
+ if (GrPixel != 0x7fe0)
+ // This is a kludge for old dirty Philips imager.
+ NumPixel = 0x1010;
+ else
+ NumPixel = 0x0010;
+
+ TagKey key = gdcmDictEntry::TranslateToKey(GrPixel, NumPixel);
+ countGrPixel = GetEntry().count(key);
}
/**
* \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" otherwise.
+ * \brief Constructor
+ * @param exception_on_error
*/
-string gdcmHeader::GetPubElValByNumber(guint16 group, guint16 element) {
- return PubElValSet.GetElValueByNumber(group, element);
+gdcmHeader::gdcmHeader(bool exception_on_error) :
+ gdcmParser(exception_on_error)
+{
}
/**
* \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" otherwise.
+ * \brief Canonical destructor.
*/
-string gdcmHeader::GetPubElValRepByNumber(guint16 group, guint16 element) {
- gdcmElValue* elem = PubElValSet.GetElementByNumber(group, element);
- if ( !elem )
- return "gdcm::Unfound";
- return elem->GetVR();
+gdcmHeader::~gdcmHeader (void) {
}
-/**
- * \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" otherwise.
- */
-string gdcmHeader::GetPubElValByName(string TagName) {
- return PubElValSet.GetElValueByName(TagName);
-}
+//-----------------------------------------------------------------------------
+// Print
-/**
- * \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" otherwise.
- */
-string gdcmHeader::GetPubElValRepByName(string TagName) {
- gdcmElValue* elem = PubElValSet.GetElementByName(TagName);
- if ( !elem )
- return "gdcm::Unfound";
- return elem->GetVR();
-}
+// see gdcmParser.cxx
+//-----------------------------------------------------------------------------
+// Public
/**
* \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" otherwise.
+ * \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.
*/
-string gdcmHeader::GetShaElValByNumber(guint16 group, guint16 element) {
- return ShaElValSet.GetElValueByNumber(group, element);
+bool gdcmHeader::IsReadable(void) {
+ 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" i.e. 'Sign'
+ return true;
}
/**
* \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" otherwise.
+ * \brief Determines if the Transfer Syntax was already encountered
+ * and if it corresponds to a JPEGBaseLineProcess1 one.
+ * @return True when JPEGBaseLineProcess1found. False in all other cases.
*/
-string gdcmHeader::GetShaElValRepByNumber(guint16 group, guint16 element) {
- gdcmElValue* elem = ShaElValSet.GetElementByNumber(group, element);
- if ( !elem )
- return "gdcm::Unfound";
- return elem->GetVR();
-}
+bool gdcmHeader::IsJPEGBaseLineProcess1TransferSyntax(void) {
+ gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010);
+ if ( !Element )
+ return false;
+ LoadHeaderEntrySafe(Element);
-/**
- * \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" otherwise.
- */
-string gdcmHeader::GetShaElValByName(string TagName) {
- return ShaElValSet.GetElValueByName(TagName);
+ std::string Transfer = Element->GetValue();
+ if ( Transfer == "1.2.840.10008.1.2.4.50" )
+ return true;
+ return false;
}
/**
* \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" otherwise.
+ * \brief Determines if the Transfer Syntax was already encountered
+ * and if it corresponds to a JPEGExtendedProcess2-4 one.
+ * @return True when JPEGExtendedProcess2-4 found. False in all other cases.
*/
-string gdcmHeader::GetShaElValRepByName(string TagName) {
- gdcmElValue* elem = ShaElValSet.GetElementByName(TagName);
- if ( !elem )
- return "gdcm::Unfound";
- return elem->GetVR();
+bool gdcmHeader::IsJPEGExtendedProcess2_4TransferSyntax(void) {
+ gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010);
+ if ( !Element )
+ return false;
+ LoadHeaderEntrySafe(Element);
+ return ( Element->GetValue() == "1.2.840.10008.1.2.4.51" );
}
/**
* \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" otherwise.
+ * \brief Determines if the Transfer Syntax was already encountered
+ * and if it corresponds to a JPEGExtendeProcess3-5 one.
+ * @return True when JPEGExtendedProcess3-5 found. False in all other cases.
*/
-string gdcmHeader::GetElValByNumber(guint16 group, guint16 element) {
- string pub = GetPubElValByNumber(group, element);
- if (pub.length())
- return pub;
- return GetShaElValByNumber(group, element);
-}
+bool gdcmHeader::IsJPEGExtendedProcess3_5TransferSyntax(void) {
+ gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010);
+ if ( !Element )
+ return false;
+ LoadHeaderEntrySafe(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" otherwise.
- */
-string gdcmHeader::GetElValRepByNumber(guint16 group, guint16 element) {
- string pub = GetPubElValRepByNumber(group, element);
- if (pub.length())
- return pub;
- return GetShaElValRepByNumber(group, element);
+ std::string Transfer = Element->GetValue();
+ if ( Transfer == "1.2.840.10008.1.2.4.52" )
+ return true;
+ return false;
}
/**
* \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" otherwise.
+ * \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.
*/
-string gdcmHeader::GetElValByName(string TagName) {
- string pub = GetPubElValByName(TagName);
- if (pub.length())
- return pub;
- return GetShaElValByName(TagName);
-}
+bool gdcmHeader::IsJPEGSpectralSelectionProcess6_8TransferSyntax(void) {
+ gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010);
+ if ( !Element )
+ return false;
+ LoadHeaderEntrySafe(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 TagName name of the researched element.
- * @return Corresponding element value representation when it exists,
- * and the string "gdcm::Unfound" otherwise.
- */
-string gdcmHeader::GetElValRepByName(string TagName) {
- string pub = GetPubElValRepByName(TagName);
- if (pub.length())
- return pub;
- return GetShaElValRepByName(TagName);
+ std::string Transfer = Element->GetValue();
+ if ( Transfer == "1.2.840.10008.1.2.4.53" )
+ return true;
+ return false;
}
/**
* \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
+ * \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.
*/
-int gdcmHeader::SetPubElValByNumber(string content, guint16 group,
- guint16 element)
-
-//TODO : homogeneiser les noms : SetPubElValByNumber qui appelle PubElValSet.SetElValueByNumber
-// pourquoi pas SetPubElValueByNumber ??
-{
+bool gdcmHeader::IsRLELossLessTransferSyntax(void) {
+ gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010);
+ if ( !Element )
+ return false;
+ LoadHeaderEntrySafe(Element);
- return ( PubElValSet.SetElValueByNumber (content, group, element) );
+ std::string Transfer = Element->GetValue();
+ if ( Transfer == "1.2.840.10008.1.2.5" ) {
+ return true;
+ }
+ return false;
}
/**
* \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
+ * \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.
*/
-int gdcmHeader::SetPubElValByName(string content, string TagName) {
- return ( PubElValSet.SetElValueByName (content, TagName) );
-}
+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);
-/**
- * \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.
- */
+ 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;
-int gdcmHeader::SetPubElValLengthByNumber(guint32 length, guint16 group,
- guint16 element) {
- return ( PubElValSet.SetElValueLengthByNumber (length, group, element) );
+ return false;
}
/**
* \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.
+ * \brief Determines if the Transfer Syntax was already encountered
+ * and if it corresponds to a JPEG2000 one
+ * @return True when JPEG2000 (Lossly or LossLess) found. False in all
+ * other cases.
*/
-int gdcmHeader::SetShaElValByNumber(string content,
- guint16 group, guint16 element) {
- return ( ShaElValSet.SetElValueByNumber (content, group, element) );
-}
+bool gdcmHeader::IsJPEG2000(void) {
+ gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010);
+ if ( !Element )
+ return false;
+ LoadHeaderEntrySafe(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(string content, string ShadowTagName) {
- return ( ShaElValSet.SetElValueByName (content, ShadowTagName) );
+ 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 Parses the header of the file but WITHOUT loading element values.
+ * \brief Predicate for dicom version 3 file.
+ * @return True when the file is a dicom version 3.
*/
-void gdcmHeader::ParseHeader(bool exception_on_error) throw(gdcmFormatError) {
- gdcmElValue * newElValue = (gdcmElValue *)0;
-
- rewind(fp);
- CheckSwap();
- while ( (newElValue = ReadNextElement()) ) {
- SkipElementValue(newElValue);
- PubElValSet.Add(newElValue);
- }
+bool gdcmHeader::IsDicomV3(void) {
+ // Checking if Transfert Syntax exists is enough
+ // Anyway, it's to late check if the 'Preamble' was found ...
+ // And ... would it be a rich idea to check ?
+ // (some 'no Preamble' DICOM images exist !)
+ return (GetHeaderEntryByNumber(0x0002, 0x0010) != NULL);
}
-
-//
-// 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.
+ * 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.
- string StrSize = GetPubElValByNumber(0x0028,0x0011);
- if (StrSize == "gdcm::Unfound")
+ std::string StrSize;
+ 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 ACR-MEMA 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.
- string StrSize = GetPubElValByNumber(0x0028,0x0010);
- if (StrSize != "gdcm::Unfound")
+ 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;
}
* 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.
+ * being the ACR-NEMA "Planes" tag content.
+ * @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.
- string StrSize = GetPubElValByNumber(0x0028,0x0008);
- if (StrSize != "gdcm::Unfound")
+ 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);
- if (StrSize != "gdcm::Unfound")
+ // We then consider the "Planes" entry as the third dimension
+ 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) {
- string StrSize = GetPubElValByNumber(0x0028,0x0101);
- if (StrSize == "gdcm::Unfound")
- return 1;
+int gdcmHeader::GetBitsStored(void) {
+ std::string StrSize = GetEntryByNumber(0x0028,0x0101);
+ if (StrSize == GDCM_UNFOUND)
+ 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 Bits Allocated
+ * (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 = GetEntryByNumber(0x0028,0x0100);
+ if (StrSize == GDCM_UNFOUND)
+ 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) {
- string StrSize = GetPubElValByNumber(0x0028,0x0002);
- if (StrSize == "gdcm::Unfound")
+int gdcmHeader::GetSamplesPerPixel(void) {
+ 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());
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Retrieve the Planar Configuration for RGB images
+ * (0 : RGB Pixels , 1 : R Plane + G Plane + B Plane)
+ * @return The encountered Planar Configuration, 0 by default.
+ */
+int gdcmHeader::GetPlanarConfiguration(void) {
+ std::string StrSize = 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) {
- string PixelType = GetPixelType();
+ std::string PixelType = GetPixelType();
if (PixelType == "8U" || PixelType == "8S")
return 1;
if (PixelType == "16U" || PixelType == "16S")
return 2;
if (PixelType == "32U" || PixelType == "32S")
return 4;
+ if (PixelType == "FD")
+ return 8;
dbg.Verbose(0, "gdcmHeader::GetPixelSize: Unknown pixel type");
return 0;
}
* - 16S signed 16 bit,
* - 32U unsigned 32 bit,
* - 32S signed 32 bit,
+ * - FD floating double 64 bits (Not kosher DICOM, but so usefull!)
* \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
*/
-string gdcmHeader::GetPixelType(void) {
- string BitsAlloc;
- BitsAlloc = GetElValByName("Bits Allocated");
- if (BitsAlloc == "gdcm::Unfound") {
+std::string gdcmHeader::GetPixelType(void) {
+ std::string BitsAlloc = GetEntryByNumber(0x0028, 0x0100); // 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") {
+ BitsAlloc = std::string("16");
+ }
+ if (BitsAlloc == "64") // )
+ return ("FD");
+ if (BitsAlloc == "12") // It will be unpacked
+ BitsAlloc = std::string("16");
+ else if (BitsAlloc == "24") // (in order no to be messed up
+ BitsAlloc = std::string("8"); // by old RGB images)
+
+ std::string Signed = GetEntryByNumber(0x0028, 0x0103); // "Pixel Representation"
+ if (Signed == GDCM_UNFOUND) {
dbg.Verbose(0, "gdcmHeader::GetPixelType: unfound Pixel Representation");
- BitsAlloc = string("0");
+ BitsAlloc = std::string("0");
}
if (Signed == "0")
- Signed = string("U");
+ Signed = std::string("U");
else
- Signed = string("S");
+ Signed = std::string("S");
return( BitsAlloc + Signed);
}
/**
* \ingroup gdcmHeader
- * \brief This predicate, based on hopefully reasonnable heuristics,
- * decides whether or not the current gdcmHeader was properly parsed
- * and contains the mandatory information for being considered as
- * a well formed and usable image.
- * @return true when gdcmHeader is the one of a reasonable Dicom file,
- * false otherwise.
- */
-bool gdcmHeader::IsReadable(void) {
- if ( GetElValByName("Image Dimensions") != "gdcm::Unfound"
- && atoi(GetElValByName("Image Dimensions").c_str()) > 4 ) {
- return false;
- }
- if ( GetElValByName("Bits Allocated") == "gdcm::Unfound" )
- return false;
- if ( GetElValByName("Bits Stored") == "gdcm::Unfound" )
- return false;
- if ( GetElValByName("High Bit") == "gdcm::Unfound" )
- return false;
- if ( GetElValByName("Pixel Representation") == "gdcm::Unfound" )
- return false;
- return true;
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief Small utility function that creates a new manually crafted
- * (as opposed as read from the file) gdcmElValue with user
- * specified name and adds it to the public tag hash table.
- * \note A fake TagKey is generated so the PubDict can keep it's coherence.
- * @param NewTagName The name to be given to this new tag.
- * @param VR The Value Representation to be given to this new tag.
- * @ return The newly hand crafted Element Value.
+ * \brief Recover the offset (from the beginning of the file)
+ * \ of *image* pixels (not *icone image* pixels, if any !)
+ * @return Pixel Offset
*/
-gdcmElValue* gdcmHeader::NewManualElValToPubDict(string NewTagName, string VR) {
- gdcmElValue* NewElVal = (gdcmElValue*)0;
- guint32 StuffGroup = 0xffff; // Group to be stuffed with additional info
- guint32 FreeElem = 0;
- gdcmDictEntry* NewEntry = (gdcmDictEntry*)0;
+size_t gdcmHeader::GetPixelOffset(void) {
+ //
+ // If the element (0x0088,0x0200) 'icone image sequence' is found
+ // (grPixel,numPixel) is stored twice : the first one for the icon
+ // the second one for the image ...
+ // pb : sometimes , (0x0088,0x0200) exists, but doesn't contain *anything*
+ // see gdcmData/MxTwinLossLess.dcm ...
- 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 icone = GetEntryByNumber(0x0088,0x0200); //icone image sequence
+
+ IterHT it = GetHeaderEntrySameNumber(GrPixel,NumPixel);
+ TagKey key = gdcmDictEntry::TranslateToKey(GrPixel,NumPixel);
+ gdcmHeaderEntry* PixelElement;
+ if (countGrPixel == 1)
+ PixelElement = (it.first)->second;
+ else {
+ PixelElement = (++it.first)->second; // hope there are no more than 2 !
+ }
+ if (PixelElement) {
+ return PixelElement->GetOffset();
+ } else {
+ return 0;
+ std::cout << "Big trouble : Pixel Element ("
+ << std::hex << GrPixel<<","<< NumPixel<< ") NOT found"
+ << std::endl;
+ }
}
-
+// TODO : unify those two (previous one and next one)
/**
* \ingroup gdcmHeader
- * \brief Loads the element values of all the elements present in the
- * public tag based hash table.
+ * \brief Recover the pixel area length (in Bytes)
+ * @return Pixel Element Length, as stored in the header
+ * (NOT the memory space necessary to hold the Pixels
+ * - in case of embeded compressed image-)
+ * 0 : NOT USABLE file. The caller has to check.
*/
-void gdcmHeader::LoadElements(void) {
- rewind(fp);
- TagElValueHT ht = PubElValSet.GetTagHt();
- for (TagElValueHT::iterator tag = ht.begin(); tag != ht.end(); ++tag) {
- LoadElementValue(tag->second);
- }
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief
- * @return
- */
-void gdcmHeader::PrintPubElVal(std::ostream & os) {
- PubElValSet.Print(os);
-}
+size_t gdcmHeader::GetPixelAreaLength(void) {
+
+ IterHT it = GetHeaderEntrySameNumber(GrPixel,NumPixel);
+ TagKey key = gdcmDictEntry::TranslateToKey(GrPixel,NumPixel);
+ gdcmHeaderEntry* PixelElement;
+
+ if (countGrPixel==1)
+ PixelElement = (it.first)->second;
+ else
+ PixelElement = (++it.first)->second;
-/**
- * \ingroup gdcmHeader
- * \brief
- * @return
- */
-void gdcmHeader::PrintPubDict(std::ostream & os) {
- RefPubDict->Print(os);
+ if (PixelElement) {
+ return PixelElement->GetLength();
+ } else {
+ std::cout << "Big trouble : Pixel Element ("
+ << std::hex << GrPixel<<","<< NumPixel<< ") NOT found"
+ << std::endl;
+ return 0;
+ }
}
/**
* \ingroup gdcmHeader
- * \brief
- * @return
+ * \brief tells us if LUT are used
+ * \warning Right now, 'Segmented xxx Palette Color Lookup Table Data'
+ * \ are NOT considered as LUT, since nobody knows
+ * \ how to deal with them
+ * \ Please warn me if you know sbdy that *does* know ... jprx
+ * @return true if LUT Descriptors and LUT Tables were found
*/
-
-int gdcmHeader::Write(FILE * fp, FileType type) {
- return PubElValSet.Write(fp, type);
+bool gdcmHeader::HasLUT(void) {
+
+ // Check the presence of the LUT Descriptors, and LUT Tables
+ // LutDescriptorRed
+ if ( !GetHeaderEntryByNumber(0x0028,0x1101) )
+ return false;
+ // LutDescriptorGreen
+ if ( !GetHeaderEntryByNumber(0x0028,0x1102) )
+ return false;
+ // LutDescriptorBlue
+ if ( !GetHeaderEntryByNumber(0x0028,0x1103) )
+ return false;
+ // Red Palette Color Lookup Table Data
+ if ( !GetHeaderEntryByNumber(0x0028,0x1201) )
+ return false;
+ // Green Palette Color Lookup Table Data
+ if ( !GetHeaderEntryByNumber(0x0028,0x1202) )
+ return false;
+ // Blue Palette Color Lookup Table Data
+ if ( !GetHeaderEntryByNumber(0x0028,0x1203) )
+ return false;
+ return true;
}
/**
* \ingroup gdcmHeader
- * \brief
- * @return
+ * \brief gets the info from 0028,1101 : Lookup Table Desc-Red
+ * \ else 0
+ * @return Lookup Table number of Bits , 0 by default
+ * \ when (0028,0004),Photometric Interpretation = [PALETTE COLOR ]
+ * @ return bit number of each LUT item
*/
-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;
+int gdcmHeader::GetLUTNbits(void) {
+ std::vector<std::string> tokens;
+ //int LutLength;
+ //int LutDepth;
+ int LutNbits;
+ //Just hope Lookup Table Desc-Red = Lookup Table Desc-Red = Lookup Table Desc-Blue
+ // Consistency already checked in GetLUTLength
+ std::string LutDescription = GetEntryByNumber(0x0028,0x1101);
+ if (LutDescription == GDCM_UNFOUND)
+ return 0;
+ tokens.erase(tokens.begin(),tokens.end()); // clean any previous value
+ Tokenize (LutDescription, tokens, "\\");
+ //LutLength=atoi(tokens[0].c_str());
+ //LutDepth=atoi(tokens[1].c_str());
+ LutNbits=atoi(tokens[2].c_str());
+ tokens.clear();
+ return LutNbits;
}
/**
* \ingroup gdcmHeader
- * \brief
- * @return
- */
-float gdcmHeader::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;
+ * \brief builts Red/Green/Blue/Alpha LUT from Header
+ * \ when (0028,0004),Photometric Interpretation = [PALETTE COLOR ]
+ * \ and (0028,1101),(0028,1102),(0028,1102)
+ * \ - xxx Palette Color Lookup Table Descriptor - are found
+ * \ and (0028,1201),(0028,1202),(0028,1202)
+ * \ - xxx Palette Color Lookup Table Data - are found
+ * \warning does NOT deal with :
+ * \ 0028 1100 Gray Lookup Table Descriptor (Retired)
+ * \ 0028 1221 Segmented Red Palette Color Lookup Table Data
+ * \ 0028 1222 Segmented Green Palette Color Lookup Table Data
+ * \ 0028 1223 Segmented Blue Palette Color Lookup Table Data
+ * \ no known Dicom reader deals with them :-(
+ * @return a RGBA Lookup Table
+ */
+unsigned char * gdcmHeader::GetLUTRGBA(void) {
+// Not so easy : see
+// http://www.barre.nom.fr/medical/dicom2/limitations.html#Color%20Lookup%20Tables
+
+// if Photometric Interpretation # PALETTE COLOR, no LUT to be done
+ if (GetEntryByNumber(0x0028,0x0004) != "PALETTE COLOR ") {
+ return NULL;
+ }
+ int lengthR, debR, nbitsR;
+ int lengthG, debG, nbitsG;
+ int lengthB, debB, nbitsB;
+
+// 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();
+
+ 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()); // subscript of the first Lut Value
+ nbitsG =atoi(tokens[2].c_str()); // Lut item size (in Bits)
+ tokens.clear();
+
+ tokens.erase(tokens.begin(),tokens.end()); // clean any previous value
+ Tokenize (LutDescriptionB, tokens, "\\");
+ lengthB=atoi(tokens[0].c_str()); // Blue LUT length in Bytes
+ debB =atoi(tokens[1].c_str()); // subscript of the first Lut Value
+ nbitsB =atoi(tokens[2].c_str()); // Lut item size (in Bits)
+ 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);
+
+ 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;
+
+ 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 (useless ?)overhead
+ // (optimistic asumption)
+ unsigned char *a;
+ int i;
+
+ a = LUTRGBA+0;
+ for(i=0;i<lengthR;i++) {
+ *a = lutR[i*mult+1];
+ a+=4;
+ }
+ a = LUTRGBA+1;
+ for(i=0;i<lengthG;i++) {
+ *a = lutG[i*mult+1];
+ a+=4;
+ }
+ a = LUTRGBA+2;
+ for(i=0;i<lengthB;i++) {
+ *a = lutB[i*mult+1];
+ a+=4;
+ }
+ a = LUTRGBA+3;
+ for(i=0;i<256;i++) {
+ *a = 1; // Alpha component
+ a+=4;
+ }
+
+ //How to free the now useless LUTs?
+ //free(LutR); free(LutB); free(LutG); // Seg Fault when used
+ return(LUTRGBA);
}
-
/**
- * \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());
+ * \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;
}
-//
-// 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 (0020,0032)");
- StrImPos = GetPubElValByNumber(0x0020,0x0030); // For ACR-NEMA images
- if (StrImPos == "gdcm::Unfound") {
- dbg.Verbose(0, "gdcmHeader::GetXImagePosition: unfound Image Position (RET) (0020,0030)");
- string StrSliceLoc = GetPubElValByNumber(0x0020,0x1041); // for *very* old ACR-NEMA images
- if (StrSliceLoc == "gdcm::Unfound") {
- dbg.Verbose(0, "gdcmHeader::GetXImagePosition: unfound Slice Location (0020,1041)");
- // 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 Sets the Pixel Area size in the Header
+ * --> not-for-rats function
+ * @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 (GrPixel, NumPixel) is unique ...
+ // TODO deal with multiplicity (see gdcmData/icone.dcm)
+ sprintf(car,"%d",ImageDataSize);
+
+ gdcmHeaderEntry *a = GetHeaderEntryByNumber(GrPixel, NumPixel);
+ a->SetLength(ImageDataSize);
+
+ ImageDataSize+=8;
+ sprintf(car,"%d",ImageDataSize);
+ content1=car;
+ SetEntryByNumber(content1, GrPixel, NumPixel);
}
-/**
- * \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 (0020,0032)");
- StrImPos = GetPubElValByNumber(0x0020,0x0030); // For ACR-NEMA images
- if (StrImPos == "gdcm::Unfound") {
- dbg.Verbose(0, "gdcmHeader::GetYImagePosition: unfound Image Position (RET) (0020,0030)");
- string StrSliceLoc = GetPubElValByNumber(0x0020,0x1041); // for *very* old ACR-NEMA images
- if (StrSliceLoc == "gdcm::Unfound") {
- dbg.Verbose(0, "gdcmHeader::GetYImagePosition: unfound Slice Location (0020,1041)");
- // 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.;
- 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 (0020,0032)");
- return 0.; // bug in the element 0x0020,0x0032
- } else {
- return zImPos;
- }
- }
-
- StrImPos = GetPubElValByNumber(0x0020,0x0030); // For ACR-NEMA images
- if (StrImPos != "gdcm::Unfound") {
- if( sscanf( StrImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3) {
- dbg.Verbose(0, "gdcmHeader::GetZImagePosition: wrong Image Position (RET) (0020,0030)");
- return 0.; // bug in the element 0x0020,0x0032
- } else {
- return zImPos;
- }
- }
-
- string StrSliceLocation = GetPubElValByNumber(0x0020,0x1041);// for *very* old ACR-NEMA images
- if (StrSliceLocation != "gdcm::Unfound") {
- if( sscanf( StrSliceLocation.c_str(), "%f", &zImPos) !=1) {
- dbg.Verbose(0, "gdcmHeader::GetZImagePosition: wrong Slice Location (0020,1041)");
- return 0.; // bug in the element 0x0020,0x1041
- } else {
- return zImPos;
- }
- }
- dbg.Verbose(0, "gdcmHeader::GetZImagePosition: unfound Slice Location (0020,1041)");
-
- string StrLocation = GetPubElValByNumber(0x0020,0x0050);
- if (StrLocation != "gdcm::Unfound") {
- if( sscanf( StrLocation.c_str(), "%f", &zImPos) !=1) {
- dbg.Verbose(0, "gdcmHeader::GetZImagePosition: wrong Location (0020,0050)");
- return 0.; // bug in the element 0x0020,0x0050
- } else {
- return zImPos;
+ * \ingroup gdcmHeader
+ * \brief compares 2 Headers, according to DICOMDIR rules
+ * --> not-for-rats function
+ * \warning does NOT work with ACR-NEMA files
+ * \todo find a trick to solve the pb (use RET fields ?)
+ * @param header
+ * @return true if 'smaller'
+ */
+ bool gdcmHeader::operator<(gdcmHeader &header){
+ std::string s1,s2;
+
+ // Patient Name
+ s1=this->GetEntryByNumber(0x0010,0x0010);
+ s2=header.GetEntryByNumber(0x0010,0x0010);
+ if(s1 < s2)
+ return(true);
+ else if(s1 > s2)
+ return(false);
+ else
+ {
+ // Patient ID
+ s1=this->GetEntryByNumber(0x0010,0x0020);
+ s2=header.GetEntryByNumber(0x0010,0x0020);
+ if (s1 < s2)
+ return(true);
+ else if (s1 > s2)
+ return(1);
+ else
+ {
+ // Study Instance UID
+ s1=this->GetEntryByNumber(0x0020,0x000d);
+ s2=header.GetEntryByNumber(0x0020,0x000d);
+ if (s1 < s2)
+ return(true);
+ else if(s1 > s2)
+ return(false);
+ else
+ {
+ // Serie Instance UID
+ s1=this->GetEntryByNumber(0x0020,0x000e);
+ s2=header.GetEntryByNumber(0x0020,0x000e);
+ if (s1 < s2)
+ return(true);
+ else if(s1 > s2)
+ return(false);
+ }
}
}
- dbg.Verbose(0, "gdcmHeader::GetYImagePosition: unfound Slice Location");
-
- return 0.; // Hopeless
+ return(false);
}
+//-----------------------------------------------------------------------------
+// Protected
+//-----------------------------------------------------------------------------
+// Private
+//-----------------------------------------------------------------------------
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff