X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmHeader.cxx;h=6aa3cadbb240b4c22d096c4e563561b30ac4aed7;hb=8402492c91eb411888fb7e220e0f02b3d94c59db;hp=024862ddd77b5e9eec4d304630d8900f5b872216;hpb=bafdfafe6c1b30607035fc4018c0405169b348e8;p=gdcm.git diff --git a/src/gdcmHeader.cxx b/src/gdcmHeader.cxx index 024862dd..6aa3cadb 100644 --- a/src/gdcmHeader.cxx +++ b/src/gdcmHeader.cxx @@ -4,30 +4,11 @@ #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 @@ -39,15 +20,47 @@ * @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 *\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) -{ + 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. + + // 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); } /** @@ -70,8 +83,36 @@ gdcmHeader::~gdcmHeader (void) { //----------------------------------------------------------------------------- // Print +// see gdcmParser.cxx //----------------------------------------------------------------------------- // Public +/** + * \ingroup gdcmHeader + * \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. + */ +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" + return true; +} + /** * \ingroup gdcmHeader * \brief Determines if the Transfer Syntax was already encountered @@ -103,11 +144,7 @@ bool gdcmHeader::IsJPEGExtendedProcess2_4TransferSyntax(void) { 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; + return ( Element->GetValue() == "1.2.840.10008.1.2.4.51" ); } /** @@ -164,8 +201,9 @@ bool gdcmHeader::IsRLELossLessTransferSyntax(void) { LoadHeaderEntrySafe(Element); std::string Transfer = Element->GetValue(); - if ( Transfer == "1.2.840.10008.1.2.5" ) + if ( Transfer == "1.2.840.10008.1.2.5" ) { return true; + } return false; } @@ -230,9 +268,8 @@ bool gdcmHeader::IsDicomV3(void) { * 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); + std::string StrSize; + StrSize = GetEntryByNumber(0x0028,0x0011); if (StrSize == GDCM_UNFOUND) return 0; return atoi(StrSize.c_str()); @@ -246,8 +283,6 @@ int gdcmHeader::GetXSize(void) { * (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()); @@ -292,7 +327,7 @@ int gdcmHeader::GetZSize(void) { * @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) { +int gdcmHeader::GetBitsStored(void) { std::string StrSize = GetEntryByNumber(0x0028,0x0101); if (StrSize == GDCM_UNFOUND) return 0; // It's supposed to be mandatory @@ -308,7 +343,7 @@ int gdcmHeader::GetBitsStored(void) { * @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) { +int gdcmHeader::GetBitsAllocated(void) { // TODO : move to gdcmFile std::string StrSize = GetEntryByNumber(0x0028,0x0100); if (StrSize == GDCM_UNFOUND) return 0; // It's supposed to be mandatory @@ -324,7 +359,7 @@ int gdcmHeader::GetBitsAllocated(void) { * @return The encountered number of Samples Per Pixel, 1 by default. * (Gray level Pixels) */ -int gdcmHeader::GetSamplesPerPixel(void) { +int gdcmHeader::GetSamplesPerPixel(void) { // TODO : move to gdcmFile std::string StrSize = GetEntryByNumber(0x0028,0x0002); if (StrSize == GDCM_UNFOUND) return 1; // Well, it's supposed to be mandatory ... @@ -339,7 +374,7 @@ int gdcmHeader::GetSamplesPerPixel(void) { * * @return The encountered Planar Configuration, 0 by default. */ -int gdcmHeader::GetPlanarConfiguration(void) { +int gdcmHeader::GetPlanarConfiguration(void) { std::string StrSize = GetEntryByNumber(0x0028,0x0006); if (StrSize == GDCM_UNFOUND) return 0; @@ -378,7 +413,7 @@ int gdcmHeader::GetPixelSize(void) { * \ 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 gdcmHeader::GetPixelType(void) { std::string BitsAlloc = GetEntryByNumber(0x0028, 0x0100); // Bits Allocated if (BitsAlloc == GDCM_UNFOUND) { dbg.Verbose(0, "gdcmHeader::GetPixelType: unfound Bits Allocated"); @@ -402,72 +437,67 @@ std::string gdcmHeader::GetPixelType(void) { return( BitsAlloc + Signed); } + /** * \ingroup gdcmHeader - * \brief Recover the offset (from the beginning of the file) of the pixels. + * \brief Recover the offset (from the beginning of the file) + * \ of *image* pixels (not *icone image* pixels, if any !) */ -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) +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 ... + + //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 + } 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 Recover the pixel area length (in Bytes) - * @return 0 by default. NOT USABLE file. The caller has to check. + * @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. */ -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; +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 - numPixel = 0x0010; - - gdcmHeaderEntry* PixelElement = GetHeaderEntryByNumber(grPixel,numPixel); - if (PixelElement) + PixelElement = (++it.first)->second; + + if (PixelElement) { return PixelElement->GetLength(); - else + } else { + std::cout << "Big trouble : Pixel Element (" + << std::hex << GrPixel<<","<< NumPixel<< ") NOT found" + << std::endl; return 0; + } } /** @@ -481,6 +511,8 @@ size_t gdcmHeader::GetPixelAreaLength(void) { bool gdcmHeader::HasLUT(void) { // Check the presence of the LUT Descriptors + + // LutDescriptorRed if ( !GetHeaderEntryByNumber(0x0028,0x1101) ) return false; // LutDescriptorGreen @@ -489,12 +521,17 @@ bool gdcmHeader::HasLUT(void) { // LutDescriptorBlue if ( !GetHeaderEntryByNumber(0x0028,0x1103) ) return false; - // It is not enough - // we check also + + // It is not enough : + // we check also + + // Red Palette Color Lookup Table Data if ( !GetHeaderEntryByNumber(0x0028,0x1201) ) - return false; + 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; @@ -578,15 +615,15 @@ unsigned char * gdcmHeader::GetLUTRGBA(void) { 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()); + 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()); - nbitsB =atoi(tokens[2].c_str()); + 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) @@ -627,7 +664,8 @@ unsigned char * gdcmHeader::GetLUTRGBA(void) { // 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 + // We give up the checking to avoid some (useless ?)overhead + // (optimistic asumption) unsigned char *a; int i; @@ -653,7 +691,6 @@ unsigned char * gdcmHeader::GetLUTRGBA(void) { } //How to free the now useless LUTs? - //free(LutR); free(LutB); free(LutG); // Seg Fault when used return(LUTRGBA); } @@ -691,17 +728,63 @@ std::string gdcmHeader::GetTransfertSyntaxName(void) { */ void gdcmHeader::SetImageDataSize(size_t ImageDataSize) { std::string content1; - char car[20]; - // Assumes HeaderEntry (0x7fe0, 0x0010) exists ... + char car[20]; + + // Assumes HeaderEntry (GrPixel, NumPixel) is unique ... + // TODO deal with multiplicity (see gdcmData/icone.dcm) sprintf(car,"%d",ImageDataSize); - gdcmHeaderEntry *a = GetHeaderEntryByNumber(0x7fe0, 0x0010); + gdcmHeaderEntry *a = GetHeaderEntryByNumber(GrPixel, NumPixel); a->SetLength(ImageDataSize); ImageDataSize+=8; sprintf(car,"%d",ImageDataSize); content1=car; - SetEntryByNumber(content1, 0x7fe0, 0x0000); + SetEntryByNumber(content1, GrPixel, NumPixel); +} + +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); + } + } + } + return(false); } //-----------------------------------------------------------------------------