X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmHeader.cxx;h=553997c556bc7df9f2d16554f76d9bef3e8958d7;hb=d789bdcdf2fbfc1180cedcb50eea788c9bafa6ea;hp=024862ddd77b5e9eec4d304630d8900f5b872216;hpb=bafdfafe6c1b30607035fc4018c0405169b348e8;p=gdcm.git diff --git a/src/gdcmHeader.cxx b/src/gdcmHeader.cxx index 024862dd..553997c5 100644 --- a/src/gdcmHeader.cxx +++ b/src/gdcmHeader.cxx @@ -1,62 +1,72 @@ // 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 "gdcmGlobal.h" #include "gdcmUtil.h" +#include "gdcmDebug.h" #include "gdcmTS.h" +#include "gdcmValEntry.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; +#include //----------------------------------------------------------------------------- // 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 + * \brief Constructor + * @param InFilename name of the file whose header we want to analyze + * @param exception_on_error whether we want to throw an exception or not + * @param enable_sequences = true to allow the header + * to be parsed *inside* the SeQuences, when they have an actual length + * @param ignore_shadow = true if user wants to skip shadow groups + * during parsing, to save memory space */ gdcmHeader::gdcmHeader(const char *InFilename, bool exception_on_error, - bool enable_sequences ): - gdcmParser(InFilename,exception_on_error,enable_sequences) -{ + bool enable_sequences, + bool ignore_shadow): + gdcmDocument(InFilename,exception_on_error,enable_sequences,ignore_shadow) +{ +/* + typedef struct { + guint32 totalSQlength; + guint32 alreadyParsedlength; + } pileElem; +*/ + + // 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; + } /** - * \ingroup gdcmHeader - * \brief - * @param exception_on_error + * \brief Constructor + * @param exception_on_error whether we want to throw an exception or not */ gdcmHeader::gdcmHeader(bool exception_on_error) : - gdcmParser(exception_on_error) + gdcmDocument(exception_on_error) { } @@ -70,22 +80,50 @@ gdcmHeader::~gdcmHeader (void) { //----------------------------------------------------------------------------- // Print + //----------------------------------------------------------------------------- // 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(!gdcmDocument::IsReadable()) { + return(false); + } + std::string res = GetEntryByNumber(0x0028, 0x0005); + if ( res != GDCM_UNFOUND && atoi(res.c_str()) > 4 ) + return false; // Image Dimensions + if ( !GetDocEntryByNumber(0x0028, 0x0100) ) + return false; // "Bits Allocated" + if ( !GetDocEntryByNumber(0x0028, 0x0101) ) + return false; // "Bits Stored" + if ( !GetDocEntryByNumber(0x0028, 0x0102) ) + return false; // "High Bit" + if ( !GetDocEntryByNumber(0x0028, 0x0103) ) + return false; // "Pixel Representation" i.e. 'Sign' + return true; +} + /** * \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); + gdcmDocEntry* Element = GetDocEntryByNumber(0x0002, 0x0010); if ( !Element ) return false; - LoadHeaderEntrySafe(Element); + LoadDocEntrySafe(Element); - std::string Transfer = Element->GetValue(); + std::string Transfer = ((gdcmValEntry *)Element)->GetValue(); if ( Transfer == "1.2.840.10008.1.2.4.50" ) return true; return false; @@ -95,35 +133,29 @@ bool gdcmHeader::IsJPEGBaseLineProcess1TransferSyntax(void) { * \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); + gdcmDocEntry* Element = GetDocEntryByNumber(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; + LoadDocEntrySafe(Element); + return ( ((gdcmValEntry *)Element)->GetValue() == "1.2.840.10008.1.2.4.51" ); } /** * \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); + gdcmDocEntry* Element = GetDocEntryByNumber(0x0002, 0x0010); if ( !Element ) return false; - LoadHeaderEntrySafe(Element); + LoadDocEntrySafe(Element); - std::string Transfer = Element->GetValue(); + std::string Transfer = ((gdcmValEntry *)Element)->GetValue(); if ( Transfer == "1.2.840.10008.1.2.4.52" ) return true; return false; @@ -133,17 +165,16 @@ bool gdcmHeader::IsJPEGExtendedProcess3_5TransferSyntax(void) { * \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); + gdcmDocEntry* Element = GetDocEntryByNumber(0x0002, 0x0010); if ( !Element ) return false; - LoadHeaderEntrySafe(Element); + LoadDocEntrySafe(Element); - std::string Transfer = Element->GetValue(); + std::string Transfer = ((gdcmValEntry *)Element)->GetValue(); if ( Transfer == "1.2.840.10008.1.2.4.53" ) return true; return false; @@ -153,19 +184,19 @@ bool gdcmHeader::IsJPEGSpectralSelectionProcess6_8TransferSyntax(void) { * \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); + gdcmDocEntry* Element = GetDocEntryByNumber(0x0002, 0x0010); if ( !Element ) return false; - LoadHeaderEntrySafe(Element); + LoadDocEntrySafe(Element); - std::string Transfer = Element->GetValue(); - if ( Transfer == "1.2.840.10008.1.2.5" ) + std::string Transfer = ((gdcmValEntry *)Element)->GetValue(); + if ( Transfer == "1.2.840.10008.1.2.5" ) { return true; + } return false; } @@ -173,21 +204,22 @@ bool gdcmHeader::IsRLELossLessTransferSyntax(void) { * \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); + gdcmDocEntry* Element = GetDocEntryByNumber(0x0002, 0x0010); // faire qq chose d'intelligent a la place de ça if ( !Element ) return false; - LoadHeaderEntrySafe(Element); + LoadDocEntrySafe(Element); - const char * Transfert = Element->GetValue().c_str(); + const char * Transfert = ((gdcmValEntry *)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; + + if (((gdcmValEntry *)Element)->GetValue() == "1.2.840.10008.1.2.4.57") return true; return false; } @@ -195,18 +227,17 @@ bool gdcmHeader::IsJPEGLossless(void) { /** * \ingroup gdcmHeader * \brief Determines if the Transfer Syntax was already encountered - * and if it corresponds to a JPEG200 one.0 - * + * and if it corresponds to a JPEG2000 one * @return True when JPEG2000 (Lossly or LossLess) found. False in all * other cases. */ bool gdcmHeader::IsJPEG2000(void) { - gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010); + gdcmDocEntry* Element = GetDocEntryByNumber(0x0002, 0x0010); if ( !Element ) return false; - LoadHeaderEntrySafe(Element); + LoadDocEntrySafe(Element); - std::string Transfer = Element->GetValue(); + std::string Transfer = ((gdcmValEntry *)Element)->GetValue(); if ( (Transfer == "1.2.840.10008.1.2.4.90") || (Transfer == "1.2.840.10008.1.2.4.91") ) return true; @@ -220,7 +251,10 @@ bool gdcmHeader::IsJPEG2000(void) { */ bool gdcmHeader::IsDicomV3(void) { // Checking if Transfert Syntax exists is enough - return (GetHeaderEntryByNumber(0x0002, 0x0010) != NULL); + // Anyway, it's to late check if the 'Preamble' was found ... + // And ... would it be a rich idea to check ? + // (some 'no Preamble' DICOM images exist !) + return (GetDocEntryByNumber(0x0002, 0x0010) != NULL); } /** @@ -230,9 +264,8 @@ 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()); @@ -243,11 +276,9 @@ int gdcmHeader::GetXSize(void) { * \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). + * (The ACR-MEMA file contains a Signal, not an Image). */ int gdcmHeader::GetYSize(void) { - // We cannot check for "Rows" because the "Rows" tag is present - // both in IMG (0028,0010) and OLY (6000,0010) sections of the dictionary. std::string StrSize = GetEntryByNumber(0x0028,0x0010); if (StrSize != GDCM_UNFOUND) return atoi(StrSize.c_str()); @@ -265,7 +296,7 @@ int gdcmHeader::GetYSize(void) { * 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. + * being the ACR-NEMA "Planes" tag content. * @return The encountered size when found, 1 by default (single image). */ int gdcmHeader::GetZSize(void) { @@ -275,9 +306,7 @@ int gdcmHeader::GetZSize(void) { 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]. + // We then consider the "Planes" entry as the third dimension StrSize = GetEntryByNumber(0x0028,0x0012); if (StrSize != GDCM_UNFOUND) return atoi(StrSize.c_str()); @@ -288,11 +317,10 @@ int gdcmHeader::GetZSize(void) { * \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) { +int gdcmHeader::GetBitsStored(void) { std::string StrSize = GetEntryByNumber(0x0028,0x0101); if (StrSize == GDCM_UNFOUND) return 0; // It's supposed to be mandatory @@ -304,11 +332,10 @@ int gdcmHeader::GetBitsStored(void) { * \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) { +int gdcmHeader::GetBitsAllocated(void) { std::string StrSize = GetEntryByNumber(0x0028,0x0100); if (StrSize == GDCM_UNFOUND) return 0; // It's supposed to be mandatory @@ -320,15 +347,14 @@ int gdcmHeader::GetBitsAllocated(void) { * \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) { +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 + // but sometimes it's missing : *we* assume Gray pixels return atoi(StrSize.c_str()); } @@ -336,10 +362,9 @@ int gdcmHeader::GetSamplesPerPixel(void) { * \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) { +int gdcmHeader::GetPlanarConfiguration(void) { std::string StrSize = GetEntryByNumber(0x0028,0x0006); if (StrSize == GDCM_UNFOUND) return 0; @@ -360,6 +385,8 @@ int gdcmHeader::GetPixelSize(void) { return 2; if (PixelType == "32U" || PixelType == "32S") return 4; + if (PixelType == "FD") + return 8; dbg.Verbose(0, "gdcmHeader::GetPixelSize: Unknown pixel type"); return 0; } @@ -374,16 +401,19 @@ int gdcmHeader::GetPixelSize(void) { * - 16S signed 16 bit, * - 32U unsigned 32 bit, * - 32S signed 32 bit, + * - FD floating double 64 bits (Not kosher DICOM, but so usefull!) * \warning 12 bit images appear as 16 bit. - * \ 24 bit images appear as 8 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 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 == "64") // ) + return ("FD"); if (BitsAlloc == "12") // It will be unpacked BitsAlloc = std::string("16"); else if (BitsAlloc == "24") // (in order no to be messed up @@ -402,110 +432,95 @@ 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 !) + * @return Pixel Offset */ -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) { + + gdcmDocEntry* PixelElement = GetDocEntryByNumber(GrPixel,NumPixel); + + if (PixelElement) { return PixelElement->GetOffset(); - else + } else { +#ifdef GDCM_DEBUG + std::cout << "Big trouble : Pixel Element (" + << std::hex << GrPixel<<","<< NumPixel<< ") NOT found" + << std::endl; +#endif //GDCM_DEBUG return 0; + } } - +// 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; - else - numPixel = 0x0010; - - gdcmHeaderEntry* PixelElement = GetHeaderEntryByNumber(grPixel,numPixel); - if (PixelElement) +size_t gdcmHeader::GetPixelAreaLength(void) { + + gdcmDocEntry* PixelElement = GetDocEntryByNumber(GrPixel,NumPixel); + + if (PixelElement) { return PixelElement->GetLength(); - else + } else { +#ifdef GDCM_DEBUG + std::cout << "Big trouble : Pixel Element (" + << std::hex << GrPixel<<","<< NumPixel<< ") NOT found" + << std::endl; +#endif //GDCM_DEBUG 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 + * are NOT considered as LUT, since nobody knows + * how to deal with them + * Please warn me if you know sbdy that *does* know ... jprx + * @return true if LUT Descriptors and LUT Tables were found */ bool gdcmHeader::HasLUT(void) { - // Check the presence of the LUT Descriptors - if ( !GetHeaderEntryByNumber(0x0028,0x1101) ) + // Check the presence of the LUT Descriptors, and LUT Tables + // LutDescriptorRed + if ( !GetDocEntryByNumber(0x0028,0x1101) ) return false; // LutDescriptorGreen - if ( !GetHeaderEntryByNumber(0x0028,0x1102) ) + if ( !GetDocEntryByNumber(0x0028,0x1102) ) return false; // LutDescriptorBlue - if ( !GetHeaderEntryByNumber(0x0028,0x1103) ) + if ( !GetDocEntryByNumber(0x0028,0x1103) ) + return false; + // Red Palette Color Lookup Table Data + if ( !GetDocEntryByNumber(0x0028,0x1201) ) + return false; + // Green Palette Color Lookup Table Data + if ( !GetDocEntryByNumber(0x0028,0x1202) ) return false; - // It is not enough - // we check also - if ( !GetHeaderEntryByNumber(0x0028,0x1201) ) - return false; - if ( !GetHeaderEntryByNumber(0x0028,0x1202) ) + // Blue Palette Color Lookup Table Data + if ( !GetDocEntryByNumber(0x0028,0x1203) ) return false; - if ( !GetHeaderEntryByNumber(0x0028,0x1203) ) - return false; + // FIXME : (0x0028,0x3006) : LUT Data (CTX dependent) + // NOT taken into account, but we don't know how to use it ... return true; } /** * \ingroup gdcmHeader * \brief gets the info from 0028,1101 : Lookup Table Desc-Red - * \ else 0 + * else 0 * @return Lookup Table number of Bits , 0 by default - * \ when (0028,0004),Photometric Interpretation = [PALETTE COLOR ] + * when (0028,0004),Photometric Interpretation = [PALETTE COLOR ] + * @ return bit number of each LUT item */ int gdcmHeader::GetLUTNbits(void) { std::vector tokens; @@ -529,17 +544,17 @@ int gdcmHeader::GetLUTNbits(void) { /** * \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 + * 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 :-( + * 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) { @@ -548,7 +563,7 @@ unsigned char * gdcmHeader::GetLUTRGBA(void) { // if Photometric Interpretation # PALETTE COLOR, no LUT to be done if (GetEntryByNumber(0x0028,0x0004) != "PALETTE COLOR ") { - return NULL; + return NULL; } int lengthR, debR, nbitsR; int lengthG, debG, nbitsG; @@ -578,15 +593,15 @@ 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) @@ -598,16 +613,16 @@ unsigned char * gdcmHeader::GetLUTRGBA(void) { GetEntryVoidAreaByNumber(0x0028,0x1203); if (!lutR || !lutG || !lutB ) { - return NULL; + 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) + unsigned char *LUTRGBA = new unsigned char[1024]; // 256 * 4 (R, G, B, Alpha) if (!LUTRGBA) { return NULL; } memset(LUTRGBA, 0, 1024); - // Bits Allocated + // Bits Allocated int nb; std::string str_nb = GetEntryByNumber(0x0028,0x0100); if (str_nb == GDCM_UNFOUND ) { @@ -627,7 +642,8 @@ 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; @@ -653,16 +669,15 @@ unsigned char * gdcmHeader::GetLUTRGBA(void) { } //How to free the now useless LUTs? - //free(LutR); free(LutB); free(LutG); // Seg Fault when used return(LUTRGBA); } /** * \ingroup gdcmHeader - * \brief gets the info from 0002,0010 : Transfert Syntax - * \ else 1. - * @return Transfert Syntax Name (as oposite to Transfert Syntax UID) + * \brief gets the info from 0002,0010 : Transfert Syntax and gdcmTS + * else 1. + * @return the full Transfert Syntax Name (as oposite to Transfert Syntax UID) */ std::string gdcmHeader::GetTransfertSyntaxName(void) { // use the gdcmTS (TS : Transfert Syntax) @@ -679,34 +694,185 @@ std::string gdcmHeader::GetTransfertSyntaxName(void) { } /** - * \ingroup gdcmFile + * \ingroup gdcmHeader * \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 ... + char car[20]; + + // Assumes DocEntry (GrPixel, NumPixel) is unique ... + //\todo deal with multiplicity (see gdcmData/icone.dcm) sprintf(car,"%d",ImageDataSize); - gdcmHeaderEntry *a = GetHeaderEntryByNumber(0x7fe0, 0x0010); + gdcmDocEntry *a = GetDocEntryByNumber(GrPixel, NumPixel); a->SetLength(ImageDataSize); - + ImageDataSize+=8; sprintf(car,"%d",ImageDataSize); - content1=car; - SetEntryByNumber(content1, 0x7fe0, 0x0000); + content1=car; + SetEntryByNumber(content1, GrPixel, NumPixel); } + +/** + * \ingroup gdcmHeader + * \brief compares 2 Headers, according to DICOMDIR rules + * --> not-for-rats function + * \warning does NOT work with ACR-NEMA files + * \todo find a trick to solve the pb (use RET fields ?) + * @param header + * @return true if 'smaller' + */ + bool gdcmHeader::operator<(gdcmHeader &header){ + std::string s1,s2; + + // Patient Name + s1=this->GetEntryByNumber(0x0010,0x0010); + s2=header.GetEntryByNumber(0x0010,0x0010); + if(s1 < s2) + return(true); + else if(s1 > s2) + return(false); + else + { + // Patient ID + s1=this->GetEntryByNumber(0x0010,0x0020); + s2=header.GetEntryByNumber(0x0010,0x0020); + if (s1 < s2) + return(true); + else if (s1 > s2) + return(1); + else + { + // Study Instance UID + s1=this->GetEntryByNumber(0x0020,0x000d); + s2=header.GetEntryByNumber(0x0020,0x000d); + if (s1 < s2) + return(true); + else if(s1 > s2) + return(false); + else + { + // Serie Instance UID + s1=this->GetEntryByNumber(0x0020,0x000e); + s2=header.GetEntryByNumber(0x0020,0x000e); + if (s1 < s2) + return(true); + else if(s1 > s2) + return(false); + } + } + } + return(false); +} +// Replaced by gdcmDocument::WriteEntry +/* +bool gdcmHeader::WriteEntry(gdcmDocEntry *tag, FILE *_fp,FileType type) +{ +cout << " gdcmHeader::WriteEntry : entree " << endl; + guint32 length = tag->GetLength(); + + // The value of a tag MUST (see the DICOM norm) be an odd number of + // bytes. When this is not the case, pad with an additional byte: + if(length%2==1) + { + // tag->SetValue(tag->GetValue()+"\0"); // to go on compiling + tag->SetLength(tag->GetReadLength()+1); + } + + WriteEntryTagVRLength(tag, _fp, type); + + // Pixels are never loaded in the element ! + // we stop writting when Pixel are processed + // FIX : we loose trailing elements (RAB, right now) + guint16 el = tag->GetElement(); + guint16 group = tag->GetGroup(); + WriteEntryValue(tag, _fp, type); + return true; +} +*/ //----------------------------------------------------------------------------- // Protected +/** + * \ingroup gdcmHeader + * \brief anonymize a Header (removes Patient's personal info) + * (read the code to see which ones ...) + */ +bool gdcmHeader::anonymizeHeader() { + + gdcmDocEntry *patientNameHE = GetDocEntryByNumber (0x0010, 0x0010); + // gdcmDocEntry *patientIDHE = GetDocEntryByNumber (0x0010, 0x0020); + + ReplaceIfExistByNumber (" ",0x0010, 0x2154); // Telephone + ReplaceIfExistByNumber (" ",0x0010, 0x1040); // Adress + ReplaceIfExistByNumber (" ",0x0010, 0x0020); // Patient ID + + if (patientNameHE) { + std::string StudyInstanceUID = GetEntryByNumber (0x0020, 0x000d); + if (StudyInstanceUID !=GDCM_UNFOUND) + ReplaceOrCreateByNumber(StudyInstanceUID, 0x0010, 0x0010); + else + ReplaceOrCreateByNumber(std::string("anonymised"), 0x0010, 0x0010); + } + + // Just for fun :-( + // (if any) remove or replace all the stuff that contains a Date + +//0008 0012 DA ID Instance Creation Date +//0008 0020 DA ID Study Date +//0008 0021 DA ID Series Date +//0008 0022 DA ID Acquisition Date +//0008 0023 DA ID Content Date +//0008 0024 DA ID Overlay Date +//0008 0025 DA ID Curve Date +//0008 002a DT ID Acquisition Datetime +//0018 9074 DT ACQ Frame Acquisition Datetime +//0018 9151 DT ACQ Frame Reference Datetime +//0018 a002 DT ACQ Contribution Date Time +//0020 3403 SH REL Modified Image Date (RET) +//0032 0032 DA SDY Study Verified Date +//0032 0034 DA SDY Study Read Date +//0032 1000 DA SDY Scheduled Study Start Date +//0032 1010 DA SDY Scheduled Study Stop Date +//0032 1040 DA SDY Study Arrival Date +//0032 1050 DA SDY Study Completion Date +//0038 001a DA VIS Scheduled Admission Date +//0038 001c DA VIS Scheduled Discharge Date +//0038 0020 DA VIS Admitting Date +//0038 0030 DA VIS Discharge Date +//0040 0002 DA PRC Scheduled Procedure Step Start Date +//0040 0004 DA PRC Scheduled Procedure Step End Date +//0040 0244 DA PRC Performed Procedure Step Start Date +//0040 0250 DA PRC Performed Procedure Step End Date +//0040 2004 DA PRC Issue Date of Imaging Service Request +//0040 4005 DT PRC Scheduled Procedure Step Start Date and Time +//0040 4011 DT PRC Expected Completion Date and Time +//0040 a030 DT PRC Verification Date Time +//0040 a032 DT PRC Observation Date Time +//0040 a120 DT PRC DateTime +//0040 a121 DA PRC Date +//0040 a13a DT PRC Referenced Datetime +//0070 0082 DA ??? Presentation Creation Date +//0100 0420 DT ??? SOP Autorization Date and Time +//0400 0105 DT ??? Digital Signature DateTime +//2100 0040 DA PJ Creation Date +//3006 0008 DA SSET Structure Set Date +//3008 0024 DA ??? Treatment Control Point Date +//3008 0054 DA ??? First Treatment Date +//3008 0056 DA ??? Most Recent Treatment Date +//3008 0162 DA ??? Safe Position Exit Date +//3008 0166 DA ??? Safe Position Return Date +//3008 0250 DA ??? Treatment Date +//300a 0006 DA RT RT Plan Date +//300a 022c DA RT Air Kerma Rate Reference Date +//300e 0004 DA RT Review Date + return true; +} //----------------------------------------------------------------------------- // Private