// gdcmHeader.cxx //----------------------------------------------------------------------------- #include "gdcmHeader.h" #include #include // For nthos: #ifdef _MSC_VER #include #else #include #endif #include // for isalpha #ifdef GDCM_NO_ANSI_STRING_STREAM # include # define ostringstream ostrstream # else # include #endif #include "gdcmUtil.h" #include "gdcmTS.h" //----------------------------------------------------------------------------- // Refer to gdcmHeader::CheckSwap() const unsigned int gdcmHeader::HEADER_LENGTH_TO_READ = 256; // Refer to gdcmHeader::SetMaxSizeLoadElementValue() const unsigned int gdcmHeader::MAX_SIZE_LOAD_ELEMENT_VALUE = 4096; //----------------------------------------------------------------------------- // Constructor / Destructor /** * \ingroup gdcmHeader * \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 */ gdcmHeader::gdcmHeader(const char *InFilename, bool exception_on_error, bool enable_sequences ) { if (enable_sequences) enableSequences = 1; else enableSequences = 0; SetMaxSizeLoadElementValue(MAX_SIZE_LOAD_ELEMENT_VALUE); 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(MAX_SIZE_LOAD_ELEMENT_VALUE); Initialise(); } /** * \ingroup gdcmHeader * \brief Canonical destructor. */ gdcmHeader::~gdcmHeader (void) { dicom_vr = (gdcmVR*)0; Dicts = (gdcmDictSet*)0; RefPubDict = (gdcmDict*)0; RefShaDict = (gdcmDict*)0; return; } //----------------------------------------------------------------------------- // Print /** * \ingroup gdcmHeader * \brief * @return */ void gdcmHeader::PrintPubElVal(std::ostream & os) { PubElValSet.Print(os); } /** * \ingroup gdcmHeader * \brief * @return */ void gdcmHeader::PrintPubDict(std::ostream & os) { RefPubDict->Print(os); } //----------------------------------------------------------------------------- // Public /** * \ingroup gdcmHeader * \brief This predicate, based on hopefully reasonable heuristics, * decides whether or not the current gdcmHeader was properly parsed * and contains the mandatory information for being considered as * a well formed and usable image. * @return true when gdcmHeader is the one of a reasonable Dicom file, * false otherwise. */ bool gdcmHeader::IsReadable(void) { std::string res = GetPubElValByNumber(0x0028, 0x0005); if ( res != GDCM_UNFOUND && atoi(res.c_str()) > 4 ) { return false; // Image Dimensions } if ( GetPubElValByNumber(0x0028, 0x0100) == GDCM_UNFOUND ) return false; // "Bits Allocated" if ( GetPubElValByNumber(0x0028, 0x0101) == GDCM_UNFOUND ) return false; // "Bits Stored" if ( GetPubElValByNumber(0x0028, 0x0102) == GDCM_UNFOUND ) return false; // "High Bit" if ( GetPubElValByNumber(0x0028, 0x0103) == GDCM_UNFOUND ) return false; // "Pixel Representation" return true; } /** * \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; } /** * \ingroup gdcmHeader * \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. */ bool gdcmHeader::IsJPEGBaseLineProcess1TransferSyntax(void) { gdcmElValue* Element = PubElValSet.GetElementByNumber(0x0002, 0x0010); if ( !Element ) return false; LoadElementValueSafe(Element); std::string Transfer = Element->GetValue(); if ( Transfer == "1.2.840.10008.1.2.4.50" ) return true; return false; } /** * \ingroup gdcmHeader * \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. */ bool gdcmHeader::IsJPEGExtendedProcess2_4TransferSyntax(void) { gdcmElValue* Element = PubElValSet.GetElementByNumber(0x0002, 0x0010); if ( !Element ) return false; LoadElementValueSafe(Element); std::string Transfer = Element->GetValue(); if ( Transfer == "1.2.840.10008.1.2.4.51" ) return true; return false; } /** * \ingroup gdcmHeader * \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. */ 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); if ( !Element ) return false; LoadElementValueSafe(Element); std::string Transfer = Element->GetValue(); if ( Transfer == "1.2.840.10008.1.2.5" ) return true; return false; } /** * \ingroup gdcmHeader * \brief * * @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 * 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) ) return true; return false; } /** * \ingroup gdcmHeader * \brief * @return */ FileType gdcmHeader::GetFileType(void) { return(filetype); } /** * \ingroup gdcmHeader * \brief Retrieve the number of columns of image. * @return The encountered size when found, 0 by default. */ int gdcmHeader::GetXSize(void) { // We cannot check for "Columns" because the "Columns" tag is present // both in IMG (0028,0011) and OLY (6000,0011) sections of the dictionary. std::string StrSize = GetPubElValByNumber(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. */ 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); 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 // hence be a signal (1d image). So we default to 1: return 1; } /** * \ingroup gdcmHeader * \brief Retrieve the number of planes of volume or the number * of frames of a multiframe. * \warning When present we consider the "Number of Frames" as the third * dimension. When absent we consider the third dimension as * being the "Planes" tag content. * @return The encountered size when found, 1 by default. */ int gdcmHeader::GetZSize(void) { // Both DicomV3 and ACR/Nema consider the "Number of Frames" // as the third dimension. std::string StrSize = GetPubElValByNumber(0x0028,0x0008); if (StrSize != GDCM_UNFOUND) return atoi(StrSize.c_str()); // We then consider the "Planes" entry as the third dimension [we // cannot retrieve by name since "Planes tag is present both in // IMG (0028,0012) and OLY (6000,0012) sections of the dictionary]. StrSize = GetPubElValByNumber(0x0028,0x0012); if (StrSize != GDCM_UNFOUND) return atoi(StrSize.c_str()); return 1; } /** * \ingroup gdcmHeader * \brief Retrieve the number of Bits Stored * (as opposite to number of Bits Allocated) * * @return The encountered number of Bits Stored, 0 by default. */ int gdcmHeader::GetBitsStored(void) { std::string StrSize = GetPubElValByNumber(0x0028,0x0101); if (StrSize == GDCM_UNFOUND) return 1; return atoi(StrSize.c_str()); } /** * \ingroup gdcmHeader * \brief Retrieve the number of Bits Allocated * (8, 12 -compacted ACR-NEMA files, 16, ...) * * @return The encountered number of Bits Allocated, 0 by default. */ int gdcmHeader::GetBitsAllocated(void) { std::string StrSize = GetPubElValByNumber(0x0028,0x0100); if (StrSize == GDCM_UNFOUND) return 1; return atoi(StrSize.c_str()); } /** * \ingroup gdcmHeader * \brief Retrieve the number of Samples Per Pixel * (1 : gray level, 3 : RGB -1 or 3 Planes-) * * @return The encountered number of Samples Per Pixel, 1 by default. */ int gdcmHeader::GetSamplesPerPixel(void) { std::string StrSize = GetPubElValByNumber(0x0028,0x0002); if (StrSize == GDCM_UNFOUND) return 1; // Well, it's supposed to be mandatory ... return atoi(StrSize.c_str()); } /** * \ingroup gdcmHeader * \brief Retrieve the Planar Configuration for RGB images * (0 : RGB Pixels , 1 : R Plane + G Plane + B Plane) * * @return The encountered Planar Configuration, 0 by default. */ int gdcmHeader::GetPlanarConfiguration(void) { std::string StrSize = GetPubElValByNumber(0x0028,0x0006); if (StrSize == GDCM_UNFOUND) return 0; return atoi(StrSize.c_str()); } /** * \ingroup gdcmHeader * \brief Return the size (in bytes) of a single pixel of data. * @return The size in bytes of a single pixel of data. * */ int gdcmHeader::GetPixelSize(void) { 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; dbg.Verbose(0, "gdcmHeader::GetPixelSize: Unknown pixel type"); return 0; } /** * \ingroup gdcmHeader * \brief Build the Pixel Type of the image. * Possible values are: * - 8U unsigned 8 bit, * - 8S signed 8 bit, * - 16U unsigned 16 bit, * - 16S signed 16 bit, * - 32U unsigned 32 bit, * - 32S signed 32 bit, * \warning 12 bit images appear as 16 bit. * \ 24 bit images appear as 8 bit * @return */ std::string gdcmHeader::GetPixelType(void) { std::string BitsAlloc; BitsAlloc = GetPubElValByNumber(0x0028, 0x0100); // Bits Allocated if (BitsAlloc == GDCM_UNFOUND) { dbg.Verbose(0, "gdcmHeader::GetPixelType: unfound Bits Allocated"); BitsAlloc = std::string("16"); } if (BitsAlloc == "12") // It will be unpacked BitsAlloc = std::string("16"); else if (BitsAlloc == "24") // (in order no to be messed up BitsAlloc = std::string("8"); // by old RGB images) std::string Signed; Signed = GetPubElValByNumber(0x0028, 0x0103); // "Pixel Representation" if (Signed == GDCM_UNFOUND) { dbg.Verbose(0, "gdcmHeader::GetPixelType: unfound Pixel Representation"); BitsAlloc = std::string("0"); } if (Signed == "0") Signed = std::string("U"); else Signed = std::string("S"); return( BitsAlloc + Signed); } /** * \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 = GetPubElValByNumber(0x0028, 0x0200); if ( ImageLocation == GDCM_UNFOUND ) { // Image Location 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 Recover the pixel area length (in Bytes) . */ size_t gdcmHeader::GetPixelAreaLength(void) { // If this file complies with the norm we should encounter the // "Image Location" tag (0x0028, 0x0200). This tag contains the // the group that contains the pixel data (hence the "Pixel Data" // is found by indirection through the "Image Location"). // Inside the group pointed by "Image Location" the searched element // is conventionally the element 0x0010 (when the norm is respected). // When the "Image Location" is absent we default to group 0x7fe0. guint16 grPixel; guint16 numPixel; std::string ImageLocation = GetPubElValByNumber(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; gdcmElValue* PixelElement = PubElValSet.GetElementByNumber(grPixel, numPixel); if (PixelElement) return PixelElement->GetLength(); else return 0; } /** * \ingroup gdcmHeader * \brief tells us if LUT are used * \warning Right now, Segmented xxx Palette Color Lookup Table Data * \ are NOT considered as LUT, since nobody knows *\ how to deal with them * @return int acts as a Boolean */ bool gdcmHeader::HasLUT(void) { // Check the presence of the LUT Descriptors if (GetPubElValByNumber(0x0028,0x1101) == GDCM_UNFOUND) return false; // LutDescriptorGreen if (GetPubElValByNumber(0x0028,0x1102) == GDCM_UNFOUND) return false; // LutDescriptorBlue if (GetPubElValByNumber(0x0028,0x1103) == GDCM_UNFOUND) return false; // It is not enough // we check also if (GetPubElValByNumber(0x0028,0x1201) == GDCM_UNFOUND) return false; if (GetPubElValByNumber(0x0028,0x1202) == GDCM_UNFOUND) return false; if (GetPubElValByNumber(0x0028,0x1203) == GDCM_UNFOUND) return false; return true; } /** * \ingroup gdcmHeader * \brief gets the info from 0028,1101 : Lookup Table Desc-Red * \ else 0 * @return Lookup Table nBit * \ when (0028,0004),Photometric Interpretation = [PALETTE COLOR ] */ int gdcmHeader::GetLUTNbits(void) { std::vector tokens; //int LutLength; //int LutDepth; int LutNbits; //Just hope Lookup Table Desc-Red = Lookup Table Desc-Red = Lookup Table Desc-Blue // Consistency already checked in GetLUTLength std::string LutDescription = GetPubElValByNumber(0x0028,0x1101); if (LutDescription == GDCM_UNFOUND) return 0; tokens.erase(tokens.begin(),tokens.end()); // clean any previous value Tokenize (LutDescription, tokens, "\\"); //LutLength=atoi(tokens[0].c_str()); //LutDepth=atoi(tokens[1].c_str()); LutNbits=atoi(tokens[2].c_str()); tokens.clear(); return LutNbits; } /** * \ingroup gdcmHeader * \brief builts Red/Green/Blue/Alpha LUT from Header * \ when (0028,0004),Photometric Interpretation = [PALETTE COLOR ] * \ and (0028,1101),(0028,1102),(0028,1102) * \ - xxx Palette Color Lookup Table Descriptor - are found * \ and (0028,1201),(0028,1202),(0028,1202) * \ - xxx Palette Color Lookup Table Data - are found * \warning does NOT deal with : * \ 0028 1100 Gray Lookup Table Descriptor (Retired) * \ 0028 1221 Segmented Red Palette Color Lookup Table Data * \ 0028 1222 Segmented Green Palette Color Lookup Table Data * \ 0028 1223 Segmented Blue Palette Color Lookup Table Data * \ no known Dicom reader deails with them :-( * @return Lookup Table RGBA */ unsigned char * gdcmHeader::GetLUTRGBA(void) { // Not so easy : see // http://www.barre.nom.fr/medical/dicom2/limitations.html#Color%20Lookup%20Tables // and OT-PAL-8-face.dcm // if Photometric Interpretation # PALETTE COLOR, no LUT to be done if (gdcmHeader::GetPubElValByNumber(0x0028,0x0004) != "PALETTE COLOR ") { return NULL; } int lengthR, debR, nbitsR; int lengthG, debG, nbitsG; int lengthB, debB, nbitsB; // Get info from Lut Descriptors // (the 3 LUT descriptors may be different) std::string LutDescriptionR = GetPubElValByNumber(0x0028,0x1101); if (LutDescriptionR == GDCM_UNFOUND) return NULL; std::string LutDescriptionG = GetPubElValByNumber(0x0028,0x1102); if (LutDescriptionG == GDCM_UNFOUND) return NULL; std::string LutDescriptionB = GetPubElValByNumber(0x0028,0x1103); if (LutDescriptionB == GDCM_UNFOUND) return NULL; std::vector tokens; tokens.erase(tokens.begin(),tokens.end()); // clean any previous value Tokenize (LutDescriptionR, tokens, "\\"); lengthR=atoi(tokens[0].c_str()); // Red LUT length in Bytes debR =atoi(tokens[1].c_str()); // subscript of the first Lut Value nbitsR =atoi(tokens[2].c_str()); // Lut item size (in Bits) tokens.clear(); tokens.erase(tokens.begin(),tokens.end()); // clean any previous value Tokenize (LutDescriptionG, tokens, "\\"); lengthG=atoi(tokens[0].c_str()); // Green LUT length in Bytes debG =atoi(tokens[1].c_str()); nbitsG =atoi(tokens[2].c_str()); tokens.clear(); tokens.erase(tokens.begin(),tokens.end()); // clean any previous value Tokenize (LutDescriptionB, tokens, "\\"); lengthB=atoi(tokens[0].c_str()); // Blue LUT length in Bytes debB =atoi(tokens[1].c_str()); nbitsB =atoi(tokens[2].c_str()); tokens.clear(); // Load LUTs into memory, (as they were stored on disk) unsigned char *lutR = (unsigned char *) GetPubElValVoidAreaByNumber(0x0028,0x1201); unsigned char *lutG = (unsigned char *) GetPubElValVoidAreaByNumber(0x0028,0x1202); unsigned char *lutB = (unsigned char *) GetPubElValVoidAreaByNumber(0x0028,0x1203); if (!lutR || !lutG || !lutB ) { return NULL; } // forge the 4 * 8 Bits Red/Green/Blue/Alpha LUT unsigned char *LUTRGBA = (unsigned char *)calloc(1024,1); // 256 * 4 (R, G, B, Alpha) if (!LUTRGBA) { return NULL; } memset(LUTRGBA, 0, 1024); // Bits Allocated int nb; std::string str_nb = GetPubElValByNumber(0x0028,0x0100); if (str_nb == GDCM_UNFOUND ) { nb = 16; } else { nb = atoi(str_nb.c_str() ); } int mult; if (nbitsR==16 && nb==8) // when LUT item size is different than pixel size mult=2; // high byte must be = low byte else // See PS 3.3-2003 C.11.1.1.2 p 619 mult=1; // if we get a black image, let's just remove the '+1' // from 'i*mult+1' and check again // if it works, we shall have to check the 3 Palettes // to see which byte is ==0 (first one, or second one) // and fix the code // We give up the checking to avoid some overhead unsigned char *a; int i; a = LUTRGBA+0; for(i=0;iGetValue(TransfertSyntax); //delete ts; // Seg Fault when deleted ?! return tsName; } /** * \ingroup gdcmHeader * \brief Searches within the public dictionary for element value of * a given tag. * @param tagName name of the searched element. * @return Corresponding element value when it exists, and the string * GDCM_UNFOUND ("gdcm::Unfound") otherwise. */ std::string gdcmHeader::GetPubElValByName(std::string tagName) { gdcmDictEntry *dictEntry = RefPubDict->GetTagByName(tagName); if( dictEntry == NULL) return GDCM_UNFOUND; return(PubElValSet.GetElValueByNumber(dictEntry->GetGroup(), dictEntry->GetElement())); } /** * \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 searched element. * @return Corresponding element value representation when it exists, * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise. */ std::string gdcmHeader::GetPubElValRepByName(std::string tagName) { gdcmDictEntry *dictEntry = RefPubDict->GetTagByName(tagName); if( dictEntry == NULL) return GDCM_UNFOUND; gdcmElValue* elem = PubElValSet.GetElementByNumber( dictEntry->GetGroup(), dictEntry->GetElement()); return elem->GetVR(); } /** * \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 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 */ bool gdcmHeader::SetPubElValByName(std::string content, std::string tagName) { //return ( PubElValSet.SetElValueByName (content, tagName) ); gdcmDictEntry *dictEntry = RefPubDict->GetTagByName(tagName); if( dictEntry == NULL) return false; return(PubElValSet.SetElValueByNumber(content, dictEntry->GetGroup(), dictEntry->GetElement())); } /** * \ingroup gdcmHeader * \brief Accesses an existing gdcmElValue (i.e. a Dicom Element) * 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 Dicom Element to modify * @param element element of the Dicom Element to modify */ bool 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 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. */ bool gdcmHeader::SetPubElValLengthByNumber(guint32 length, guint16 group, guint16 element) { return ( PubElValSet.SetElValueLengthByNumber (length, 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 searched 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); return pub; } /** * \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 searched 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); return pub; } /** * \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 searched tag. * @param element Element of the searched 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); return pub; } /** * \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 searched tag. * @param element Element of the searched 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); return pub; } /** * \ingroup gdcmElValSet * \brief Sets the value (string) of the target Dicom Element * @param content string value of the Dicom Element * @param tagName name of the searched Dicom Element. * @return true when found */ bool gdcmHeader::SetElValueByName(std::string content, std::string tagName) { gdcmDictEntry *dictEntry = RefPubDict->GetTagByName(tagName); if( dictEntry == NULL) return false; TagKey key = gdcmDictEntry::TranslateToKey(dictEntry->GetGroup(), dictEntry->GetElement()); if ( ! PubElValSet.GetTagHt().count(key)) return false; int l = content.length(); if(l%2) { // Odd length are padded with a space (020H). l++; content = content + '\0'; } //tagHt[key]->SetValue(content); gdcmElValue * a; IterHT p; TagElValueHT::iterator p2; // DO NOT remove the following lines : they explain the stuff //p= tagHt.equal_range(key); // get a pair of iterators first-last synonym //p2=p.first; // iterator on the first synonym //a=p2->second; // H Table target column (2-nd col) // or, easier : a = ((PubElValSet.GetTagHt().equal_range(key)).first)->second; a-> SetValue(content); //std::string vr = tagHt[key]->GetVR(); std::string vr = a->GetVR(); guint32 lgr; if( (vr == "US") || (vr == "SS") ) lgr = 2; else if( (vr == "UL") || (vr == "SL") ) lgr = 4; else lgr = l; //tagHt[key]->SetLength(lgr); a->SetLength(lgr); return true; } /** * \ingroup gdcmHeader * \brief * @param exception_on_error * @return */ FILE *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(fp); //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(fp); 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(NULL); } /** * \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; } /** * \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 * @return integer, acts as a Boolean */ bool gdcmHeader::Write(FILE * fp, FileType type) { // TODO : move the following lines (and a lot of others, to be written) // to a future function CheckAndCorrectHeader if (type == ImplicitVR) { std::string implicitVRTransfertSyntax = "1.2.840.10008.1.2"; ReplaceOrCreateByNumber(implicitVRTransfertSyntax,0x0002, 0x0010); //FIXME Refer to standards on page 21, chapter 6.2 "Value representation": // values with a VR of UI shall be padded with a single trailing null // Dans le cas suivant on doit pader manuellement avec un 0 PubElValSet.SetElValueLengthByNumber(18, 0x0002, 0x0010); } if (type == ExplicitVR) { std::string explicitVRTransfertSyntax = "1.2.840.10008.1.2.1"; ReplaceOrCreateByNumber(explicitVRTransfertSyntax,0x0002, 0x0010); //FIXME Refer to standards on page 21, chapter 6.2 "Value representation": // values with a VR of UI shall be padded with a single trailing null // Dans le cas suivant on doit pader manuellement avec un 0 PubElValSet.SetElValueLengthByNumber(20, 0x0002, 0x0010); } return PubElValSet.Write(fp, type); } /** * \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 ElValue (0x7fe0, 0x0010) exists ... sprintf(car,"%d",ImageDataSize); gdcmElValue *a = GetElValueByNumber(0x7fe0, 0x0010); a->SetLength(ImageDataSize); ImageDataSize+=8; sprintf(car,"%d",ImageDataSize); content1=car; SetPubElValByNumber(content1, 0x7fe0, 0x0000); } /** * \ingroup gdcmHeader * \brief Swaps back the bytes of 4-byte long integer accordingly to * processor order. * @return The properly swaped 32 bits 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); } //----------------------------------------------------------------------------- // Protected /** * \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 Checks if a given ElValue (group,number) * \ exists in the Public ElValSet * @param Group * @param Elem * @return integer acts as a boolean */ bool gdcmHeader::CheckIfExistByNumber(guint16 Group, guint16 Elem ) { return (PubElValSet.CheckIfExistByNumber(Group, Elem)); } /** * \ingroup gdcmHeader * \brief Gets (from Header) the offset of a 'non string' element value * \ (LoadElementValue has already be executed) * @param Group * @param Elem * @return File Offset of the Element Value */ size_t gdcmHeader::GetPubElValOffsetByNumber(guint16 Group, guint16 Elem) { gdcmElValue* elValue = PubElValSet.GetElementByNumber(Group, Elem); if (!elValue) { dbg.Verbose(1, "gdcmHeader::GetElValueByNumber", "failed to Locate gdcmElValue"); return (size_t)0; } return elValue->GetOffset(); } /** * \ingroup gdcmHeader * \brief Gets (from Header) a 'non string' element value * \ (LoadElementValue has already be executed) * @param Group * @param Elem * @return Pointer to the 'non string' area */ void * gdcmHeader::GetPubElValVoidAreaByNumber(guint16 Group, guint16 Elem) { gdcmElValue* elValue = PubElValSet.GetElementByNumber(Group, Elem); if (!elValue) { dbg.Verbose(1, "gdcmHeader::GetElValueByNumber", "failed to Locate gdcmElValue"); return (NULL); } return elValue->GetVoidArea(); } /** * \ingroup gdcmHeader * \brief Loads (from disk) the element content * when a string is not suitable */ void * gdcmHeader::LoadElementVoidArea(guint16 Group, guint16 Elem) { gdcmElValue * Element= PubElValSet.GetElementByNumber(Group, Elem); if ( !Element ) return NULL; size_t o =(size_t)Element->GetOffset(); fseek(fp, o, SEEK_SET); int l=Element->GetLength(); void * a = malloc(l); if(!a) { return NULL; } /* int res = */ PubElValSet.SetVoidAreaByNumber(a, Group, Elem); // TODO check the result size_t l2 = fread(a, 1, l ,fp); if(l != l2) { free(a); return NULL; } return a; } /** * \ingroup gdcmHeader * \brief TODO * @param Value * @param Group * @param Elem * \return integer acts as a boolean */ bool 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 false; PubElValSet.Add(a); } PubElValSet.SetElValueByNumber(Value, Group, Elem); return(true); } /** * \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 * */ bool gdcmHeader::ReplaceOrCreateByNumber(char* Value, guint16 Group, guint16 Elem ) { gdcmElValue* nvElValue=NewElValueByNumber(Group, Elem); // TODO : check if fails PubElValSet.Add(nvElValue); std::string v = Value; PubElValSet.SetElValueByNumber(v, Group, Elem); return(true); } /** * \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 */ bool gdcmHeader::ReplaceIfExistByNumber(char* Value, guint16 Group, guint16 Elem ) { //gdcmElValue* elValue = PubElValSet.GetElementByNumber(Group, Elem); std::string v = Value; PubElValSet.SetElValueByNumber(v, Group, Elem); return true; } //----------------------------------------------------------------------------- // Private /** * \ingroup gdcmHeader * \brief Loads the element values of all the elements present in the * public tag based hash table. */ void gdcmHeader::LoadElements(void) { rewind(fp); // We don't use any longer the HashTable, since a lot a stuff is missing // when SeQuences were encountered // //TagElValueHT ht = PubElValSet.GetTagHt(); //for (TagElValueHT::iterator tag = ht.begin(); tag != ht.end(); ++tag) { // LoadElementValue(tag->second); //} for (ListTag::iterator i = GetPubListElem().begin(); i != GetPubListElem().end(); ++i){ LoadElementValue(*i); } rewind(fp); // Load 'non string' values std::string PhotometricInterpretation = GetPubElValByNumber(0x0028,0x0004); if( PhotometricInterpretation == "PALETTE COLOR " ){ LoadElementVoidArea(0x0028,0x1200); // gray LUT LoadElementVoidArea(0x0028,0x1201); // R LUT LoadElementVoidArea(0x0028,0x1202); // G LUT LoadElementVoidArea(0x0028,0x1203); // B LUT LoadElementVoidArea(0x0028,0x1221); // Segmented Red Palette Color LUT Data LoadElementVoidArea(0x0028,0x1222); // Segmented Green Palette Color LUT Data LoadElementVoidArea(0x0028,0x1223); // Segmented Blue Palette Color LUT Data } // -------------------------------------------------------------- // Special Patch to allow gdcm to read ACR-LibIDO formated images // // if recognition code tells us we deal with a LibIDO image // we switch lineNumber and columnNumber // std::string RecCode; RecCode = GetPubElValByNumber(0x0008, 0x0010); if (RecCode == "ACRNEMA_LIBIDO_1.1" || RecCode == "CANRME_AILIBOD1_1." ) { filetype = ACR_LIBIDO; std::string rows = GetPubElValByNumber(0x0028, 0x0010); std::string columns = GetPubElValByNumber(0x0028, 0x0011); SetPubElValByNumber(columns, 0x0028, 0x0010); SetPubElValByNumber(rows , 0x0028, 0x0011); } // ----------------- End of Special Patch ---------------- } /** * \ingroup gdcmHeader * \brief Loads the element content if it's length is not bigger * than the value specified with * gdcmHeader::SetMaxSizeLoadElementValue() * @param ElVal string value of the Dicom Element */ 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); // the test was commented out to 'go inside' the SeQuences // we don't any longer skip them ! // if( vr == "SQ" ) // SkipLoad = true; // A SeQuence "contains" a set of Elements. // (fffe e000) tells us an Element is beginning // (fffe e00d) tells us an Element just ended // (fffe e0dd) tells us the current SeQuence just ended if( group == 0xfffe ) SkipLoad = true; 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(); s << " x(" << std::hex << ElVal->GetLength() << ")"; ElVal->SetValue(s.str()); return; } // When an integer is expected, read and convert the following two or // four bytes properly i.e. as an integer as opposed to a string. // Actually, elements with Value Multiplicity > 1 // contain a set of integers (not a single one) // Any compacter code suggested (?) 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; } } } #ifdef GDCM_NO_ANSI_STRING_STREAM s << std::ends; // to avoid oddities on Solaris #endif //GDCM_NO_ANSI_STRING_STREAM 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 */ 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(-1); 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 // encounter 1024 (0x0400) chances are the encoding changed and we // found a group with big endian encoding. // We shall use this second strategy. In order to make sure that we // can interpret the presence of an apparently big endian encoded // length of a "Group Length" without committing a big mistake, we // add an additional check: we look in the 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()); return; } /** * \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 * * @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 * @param ElVal * @return */ void gdcmHeader::SkipElementValue(gdcmElValue * ElVal) { SkipBytes(ElVal->GetLength()); } /** * \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) { ElVal->SetReadLength(FoundLength); // will be updated only if a bug is found 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) && (ElVal->GetElement() != 0x0080) ) ) { // end of remove area FoundLength =10; ElVal->SetReadLength(10); // a bug is to be fixed } } // to fix some garbage 'Leonardo' Siemens images // May be commented out to avoid overhead else if ( (ElVal->GetGroup() == 0x0009) && ( (ElVal->GetElement() == 0x1113) || (ElVal->GetElement() == 0x1114) ) ){ FoundLength =4; ElVal->SetReadLength(4); // a bug is to be fixed } // end of fix // to try to 'go inside' SeQuences (with length), and not to skip them else if ( ElVal->GetVR() == "SQ") { if (enableSequences) // only if the user does want to ! FoundLength =0; } ElVal->SetUsableLength(FoundLength); } /** * \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(); guint16 group = ElVal->GetGroup(); 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 { std::ostringstream s; s << "Erroneous Group Length element length on :" \ << std::hex << group << " , " << element; dbg.Error("gdcmHeader::IsAnInteger", s.str().c_str()); } } if ( (vr == "UL") || (vr == "US") || (vr == "SL") || (vr == "SS") ) return true; return false; } /** * \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 */ void gdcmHeader::SkipBytes(guint32 NBytes) { //FIXME don't dump the returned value (void)fseek(fp, (long)NBytes, SEEK_CUR); } /** * \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 Discover what the swap code is (among little endian, big endian, * bad little endian, bad big endian). * */ void gdcmHeader::CheckSwap() { // 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 // // 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; //cout << net2host << endl; // 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 * @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 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 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 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 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 Searches within the public dictionary for a Dicom Element of * a given tag. * @param tagName name of the searched Dicom Element. * @return Corresponding Dicom Element when it exists, and NULL * otherwise. */ gdcmElValue* gdcmHeader::GetElementByName(std::string tagName) { gdcmDictEntry *dictEntry = RefPubDict->GetTagByName(tagName); if( dictEntry == NULL) return (gdcmElValue*)NULL; return(PubElValSet.GetElementByNumber(dictEntry->GetGroup(), dictEntry->GetElement())); } /** * \ingroup gdcmHeader * \brief Small utility function that creates a new manually crafted * (as opposed as read from the file) gdcmElValue with user * specified name and adds it to the public tag hash table. * \note A fake TagKey is generated so the PubDict can keep it's coherence. * @param NewTagName The name to be given to this new tag. * @param VR The Value Representation to be given to this new tag. * @ return The newly hand crafted Element Value. */ gdcmElValue* gdcmHeader::NewManualElValToPubDict(std::string NewTagName, std::string VR) { gdcmElValue* NewElVal = (gdcmElValue*)0; guint32 StuffGroup = 0xffff; // Group to be stuffed with additional info guint32 FreeElem = 0; gdcmDictEntry* NewEntry = (gdcmDictEntry*)0; FreeElem = PubElValSet.GenerateFreeTagKeyInGroup(StuffGroup); if (FreeElem == UINT32_MAX) { dbg.Verbose(1, "gdcmHeader::NewManualElValToPubDict", "Group 0xffff in Public Dict is full"); return (gdcmElValue*)0; } NewEntry = new gdcmDictEntry(StuffGroup, FreeElem, VR, "GDCM", NewTagName); NewElVal = new gdcmElValue(NewEntry); PubElValSet.Add(NewElVal); return NewElVal; } //-----------------------------------------------------------------------------