// 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::SetMaxSizeLoadEntry() //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 *\TODO : may be we need one more bool, * to allow skipping the private elements while parsing the header * in order to save space */ gdcmHeader::gdcmHeader(const char *InFilename, bool exception_on_error, bool enable_sequences ): gdcmParser(InFilename,exception_on_error,enable_sequences) { } /** * \ingroup gdcmHeader * \brief * @param exception_on_error */ gdcmHeader::gdcmHeader(bool exception_on_error) : gdcmParser(exception_on_error) { } /** * \ingroup gdcmHeader * \brief Canonical destructor. */ gdcmHeader::~gdcmHeader (void) { } //----------------------------------------------------------------------------- // Print //----------------------------------------------------------------------------- // Public /** * \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) { gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010); if ( !Element ) return false; LoadHeaderEntrySafe(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) { gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010); if ( !Element ) return false; LoadHeaderEntrySafe(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) { gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010); if ( !Element ) return false; LoadHeaderEntrySafe(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) { gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010); if ( !Element ) return false; LoadHeaderEntrySafe(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) { gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010); if ( !Element ) return false; LoadHeaderEntrySafe(Element); std::string Transfer = Element->GetValue(); if ( Transfer == "1.2.840.10008.1.2.5" ) return true; return false; } /** * \ingroup gdcmHeader * \brief Determines if Transfer Syntax was already encountered * and if it corresponds to a JPEG Lossless one. * * @return True when RLE Lossless found. False in all * other cases. */ bool gdcmHeader::IsJPEGLossless(void) { gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010); // faire qq chose d'intelligent a la place de ça if ( !Element ) return false; LoadHeaderEntrySafe(Element); 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) { gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010); if ( !Element ) return false; LoadHeaderEntrySafe(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) { // Checking if Transfert Syntax exists is enough return (GetHeaderEntryByNumber(0x0002, 0x0010) != NULL); } /** * \ingroup gdcmHeader * \brief Retrieve the number of columns of image. * @return The encountered size when found, 0 by default. * 0 means the file is NOT USABLE. The caller will have to check */ int gdcmHeader::GetXSize(void) { // We cannot check for "Columns" because the "Columns" tag is present // both in IMG (0028,0011) and OLY (6000,0011) sections of the dictionary. std::string StrSize = 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 * (The file contains a Signal, not an Image). */ int gdcmHeader::GetYSize(void) { // We cannot check for "Rows" because the "Rows" tag is present // both in IMG (0028,0010) and OLY (6000,0010) sections of the dictionary. std::string StrSize = GetEntryByNumber(0x0028,0x0010); if (StrSize != GDCM_UNFOUND) return atoi(StrSize.c_str()); if ( IsDicomV3() ) return 0; else // 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; } /** * \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 (single image). */ int gdcmHeader::GetZSize(void) { // Both DicomV3 and ACR/Nema consider the "Number of Frames" // as the third dimension. 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 = GetEntryByNumber(0x0028,0x0012); if (StrSize != GDCM_UNFOUND) return atoi(StrSize.c_str()); return 1; } /** * \ingroup gdcmHeader * \brief Retrieve the number of Bits Stored (actually used) * (as opposite to number of Bits Allocated) * * @return The encountered number of Bits Stored, 0 by default. * 0 means the file is NOT USABLE. The caller has to check it ! */ int gdcmHeader::GetBitsStored(void) { std::string StrSize = 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 or 3 Planes-) * * @return The encountered number of Samples Per Pixel, 1 by default. * (Gray level Pixels) */ 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; 0 by default * 0 means the file is NOT USABLE; the caller will have to check */ 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 0S if nothing found. NOT USABLE file. The caller has to check */ 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 = 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 = GetEntryByNumber(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 = GetEntryByNumber(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; gdcmHeaderEntry* PixelElement = GetHeaderEntryByNumber(grPixel,numPixel); if (PixelElement) return PixelElement->GetOffset(); else return 0; } /** * \ingroup gdcmHeader * \brief Recover the pixel area length (in Bytes) * @return 0 by default. NOT USABLE file. The caller has to check. */ size_t gdcmHeader::GetPixelAreaLength(void) { // If this file complies with the norm we should encounter the // "Image Location" tag (0x0028, 0x0200). This tag contains the // the group that contains the pixel data (hence the "Pixel Data" // is found by indirection through the "Image Location"). // Inside the group pointed by "Image Location" the searched element // is conventionally the element 0x0010 (when the norm is respected). // When the "Image Location" is absent we default to group 0x7fe0. guint16 grPixel; guint16 numPixel; std::string ImageLocation = GetEntryByNumber(0x0028, 0x0200); if ( ImageLocation == GDCM_UNFOUND ) { grPixel = 0x7fe0; } else { grPixel = (guint16) atoi( ImageLocation.c_str() ); } if (grPixel != 0x7fe0) // This is a kludge for old dirty Philips imager. numPixel = 0x1010; else numPixel = 0x0010; gdcmHeaderEntry* PixelElement = GetHeaderEntryByNumber(grPixel,numPixel); if (PixelElement) return PixelElement->GetLength(); else return 0; } /** * \ingroup gdcmHeader * \brief tells us if LUT are used * \warning Right now, 'Segmented xxx Palette Color Lookup Table Data' * \ are NOT considered as LUT, since nobody knows * \ how to deal with them * @return a Boolean */ bool gdcmHeader::HasLUT(void) { // Check the presence of the LUT Descriptors if ( !GetHeaderEntryByNumber(0x0028,0x1101) ) return false; // LutDescriptorGreen if ( !GetHeaderEntryByNumber(0x0028,0x1102) ) return false; // LutDescriptorBlue if ( !GetHeaderEntryByNumber(0x0028,0x1103) ) return false; // It is not enough // we check also if ( !GetHeaderEntryByNumber(0x0028,0x1201) ) return false; if ( !GetHeaderEntryByNumber(0x0028,0x1202) ) return false; if ( !GetHeaderEntryByNumber(0x0028,0x1203) ) return false; return true; } /** * \ingroup gdcmHeader * \brief gets the info from 0028,1101 : Lookup Table Desc-Red * \ else 0 * @return Lookup Table number of Bits , 0 by default * \ 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 = 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 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 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 *) 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 overhead unsigned char *a; int i; a = LUTRGBA+0; for(i=0;iGetValue(TransfertSyntax); //delete ts; // Seg Fault when deleted ?! return tsName; } /** * \ingroup gdcmFile * \brief Sets the Pixel Area size in the Header * --> not-for-rats function * * \warning WARNING doit-etre etre publique ? * TODO : y aurait il un inconvenient à fusionner ces 2 fonctions * * @param ImageDataSize new Pixel Area Size * warning : nothing else is checked */ void gdcmHeader::SetImageDataSize(size_t ImageDataSize) { std::string content1; char car[20]; // Assumes HeaderEntry (0x7fe0, 0x0010) exists ... sprintf(car,"%d",ImageDataSize); gdcmHeaderEntry *a = GetHeaderEntryByNumber(0x7fe0, 0x0010); a->SetLength(ImageDataSize); ImageDataSize+=8; sprintf(car,"%d",ImageDataSize); content1=car; SetEntryByNumber(content1, 0x7fe0, 0x0000); } //----------------------------------------------------------------------------- // Protected //----------------------------------------------------------------------------- // Private //-----------------------------------------------------------------------------