X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmHeader.cxx;h=bc28cd19ea484773535b420a477dc7439d6fb4a9;hb=4beda181275414e5cba990113f8d16424b2c09e6;hp=ed7402e262d11799a96c2bd2395cd8d89fd283dc;hpb=f0ea8af1179c35ddc83da32df10813899427214d;p=gdcm.git diff --git a/src/gdcmHeader.cxx b/src/gdcmHeader.cxx index ed7402e2..bc28cd19 100644 --- a/src/gdcmHeader.cxx +++ b/src/gdcmHeader.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmHeader.cxx,v $ Language: C++ - Date: $Date: 2004/11/05 20:23:14 $ - Version: $Revision: 1.198 $ + Date: $Date: 2005/01/06 15:36:48 $ + Version: $Revision: 1.220 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -22,6 +22,7 @@ #include "gdcmDebug.h" #include "gdcmTS.h" #include "gdcmValEntry.h" +#include //sscanf #include @@ -47,7 +48,7 @@ Header::Header( std::string const & filename ): // Note: this IS the right place for the code // Image Location - std::string imgLocation = GetEntryByNumber(0x0028, 0x0200); + const std::string &imgLocation = GetEntryByNumber(0x0028, 0x0200); if ( imgLocation == GDCM_UNFOUND ) { // default value @@ -75,14 +76,38 @@ Header::Header( std::string const & filename ): { NumPixel = 0x0010; } + + // Now, we know GrPixel and NumPixel. + // Let's create a VirtualDictEntry to allow a further VR modification + // and force VR to match with BitsAllocated. + + DocEntry* entry = GetDocEntryByNumber(GrPixel, NumPixel); + if ( entry != 0 ) + { + + std::string PixelVR; + // 8 bits allocated is a 'O Bytes' , as well as 24 (old ACR-NEMA RGB) + // more than 8 (i.e 12, 16) is a 'O Words' + if ( GetBitsAllocated() == 8 || GetBitsAllocated() == 24 ) + PixelVR = "OB"; + else + PixelVR = "OW"; + + DictEntry* newEntry = NewVirtualDictEntry( + GrPixel, NumPixel, + PixelVR, "PXL", "Pixel Data"); + + entry->SetDictEntry( newEntry ); + } } /** - * \brief Constructor + * \brief Constructor used when we want to generate dicom files from scratch */ Header::Header() :Document() { + InitializeDefaultHeader(); } /** @@ -92,7 +117,6 @@ Header::~Header () { } - /** * \brief Performs some consistency checking on various 'File related' * (as opposed to 'DicomDir related') entries @@ -101,8 +125,16 @@ Header::~Header () * @param filetype Type of the File to be written * (ACR-NEMA, ExplicitVR, ImplicitVR) */ -void Header::Write(std::ofstream* fp,FileType filetype) +bool Header::Write(std::string fileName, FileType filetype) { + std::ofstream* fp = new std::ofstream(fileName.c_str(), + std::ios::out | std::ios::binary); + if (*fp == NULL) + { + dbg.Verbose(2, "Failed to open (write) File: " , fileName.c_str()); + return false; + } + // Bits Allocated if ( GetEntryByNumber(0x0028,0x0100) == "12") { @@ -162,7 +194,12 @@ void Header::Write(std::ofstream* fp,FileType filetype) RemoveEntryNoDestroy(e); } } - Document::Write(fp,filetype); + Document::WriteContent(fp,filetype); + + fp->close(); + delete fp; + + return true; } //----------------------------------------------------------------------------- @@ -187,7 +224,7 @@ bool Header::IsReadable() return false; } - std::string res = GetEntryByNumber(0x0028, 0x0005); + const std::string &res = GetEntryByNumber(0x0028, 0x0005); if ( res != GDCM_UNFOUND && atoi(res.c_str()) > 4 ) { return false; // Image Dimensions @@ -219,8 +256,7 @@ bool Header::IsReadable() */ int Header::GetXSize() { - std::string strSize; - strSize = GetEntryByNumber(0x0028,0x0011); + const std::string &strSize = GetEntryByNumber(0x0028,0x0011); if ( strSize == GDCM_UNFOUND ) { return 0; @@ -237,7 +273,7 @@ int Header::GetXSize() */ int Header::GetYSize() { - std::string strSize = GetEntryByNumber(0x0028,0x0010); + const std::string &strSize = GetEntryByNumber(0x0028,0x0010); if ( strSize != GDCM_UNFOUND ) { return atoi( strSize.c_str() ); @@ -248,7 +284,7 @@ int Header::GetYSize() } // The Rows (0028,0010) entry was optional for ACR/NEMA. It might - // hence be a signal (1d image). So we default to 1: + // hence be a signal (1D image). So we default to 1: return 1; } @@ -264,17 +300,17 @@ int Header::GetZSize() { // Both DicomV3 and ACR/Nema consider the "Number of Frames" // as the third dimension. - std::string strSize = GetEntryByNumber(0x0028,0x0008); + const 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 - strSize = GetEntryByNumber(0x0028,0x0012); - if ( strSize != GDCM_UNFOUND ) + const std::string &strSize2 = GetEntryByNumber(0x0028,0x0012); + if ( strSize2 != GDCM_UNFOUND ) { - return atoi( strSize.c_str() ); + return atoi( strSize2.c_str() ); } return 1; @@ -288,7 +324,7 @@ int Header::GetZSize() float Header::GetXSpacing() { float xspacing, yspacing; - std::string strSpacing = GetEntryByNumber(0x0028,0x0030); + const std::string &strSpacing = GetEntryByNumber(0x0028,0x0030); if ( strSpacing == GDCM_UNFOUND ) { @@ -303,14 +339,26 @@ float Header::GetXSpacing() // if single value is found, xspacing is defaulted to yspacing if ( nbValues == 1 ) { - return yspacing; + xspacing = yspacing; } + + if ( xspacing == 0.0 ) + xspacing = 1.0; + + return xspacing; + } + + // to avoid troubles with David Clunie's-like images + if ( xspacing == 0. && yspacing == 0.) + return 1.; + if ( xspacing == 0.) { - dbg.Verbose(0, "Header::GetYSpacing: gdcmData/CT-MONO2-8-abdo.dcm problem"); + dbg.Verbose(0, "Header::GetXSpacing: gdcmData/CT-MONO2-8-abdo.dcm problem"); // seems to be a bug in the header ... - sscanf( strSpacing.c_str(), "%f\\0\\%f", &yspacing, &xspacing); + nbValues = sscanf( strSpacing.c_str(), "%f\\0\\%f", &yspacing, &xspacing); + assert( nbValues == 2 ); } return xspacing; @@ -323,7 +371,7 @@ float Header::GetXSpacing() */ float Header::GetYSpacing() { - float yspacing = 0; + float yspacing = 1.; std::string strSpacing = GetEntryByNumber(0x0028,0x0030); if ( strSpacing == GDCM_UNFOUND ) @@ -335,13 +383,16 @@ float Header::GetYSpacing() // if sscanf cannot read any float value, it won't affect yspacing sscanf( strSpacing.c_str(), "%f", &yspacing); + if ( yspacing == 0.0 ) + yspacing = 1.0; + return yspacing; } /** * \brief gets the info from 0018,0088 : Space Between Slices - * else from 0018,0050 : Slice Thickness - * else 1.0 + * else from 0018,0050 : Slice Thickness + * else 1.0 * @return Z dimension of a voxel-to be */ float Header::GetZSpacing() @@ -356,12 +407,12 @@ float Header::GetZSpacing() // Si le Spacing Between Slices est absent, // on suppose que les coupes sont jointives - std::string strSpacingBSlices = GetEntryByNumber(0x0018,0x0088); + const std::string &strSpacingBSlices = GetEntryByNumber(0x0018,0x0088); if ( strSpacingBSlices == GDCM_UNFOUND ) { dbg.Verbose(0, "Header::GetZSpacing: unfound StrSpacingBSlices"); - std::string strSliceThickness = GetEntryByNumber(0x0018,0x0050); + const std::string &strSliceThickness = GetEntryByNumber(0x0018,0x0050); if ( strSliceThickness == GDCM_UNFOUND ) { return 1.; @@ -372,13 +423,11 @@ float Header::GetZSpacing() // we assume slices join together // (no overlapping, no interslice gap) // if they don't, we're fucked up - return atof( strSliceThickness.c_str() ); + return (float)atof( strSliceThickness.c_str() ); } } - else - { - return atof( strSpacingBSlices.c_str() ); - } + //else + return (float)atof( strSpacingBSlices.c_str() ); } /** @@ -389,7 +438,7 @@ float Header::GetRescaleIntercept() { float resInter = 0.; /// 0028 1052 DS IMG Rescale Intercept - std::string strRescInter = GetEntryByNumber(0x0028,0x1052); + const std::string &strRescInter = GetEntryByNumber(0x0028,0x1052); if ( strRescInter != GDCM_UNFOUND ) { if( sscanf( strRescInter.c_str(), "%f", &resInter) != 1 ) @@ -462,8 +511,8 @@ int Header::GetNumberOfScalarComponents() // beware of trailing space at end of string // DICOM tags are never of odd length if ( strPhotometricInterpretation == GDCM_UNFOUND || - strPhotometricInterpretation == "MONOCHROME1 " || - strPhotometricInterpretation == "MONOCHROME2 " ) + Util::DicomStringEqual(strPhotometricInterpretation, "MONOCHROME1") || + Util::DicomStringEqual(strPhotometricInterpretation, "MONOCHROME2") ) { return 1; } @@ -821,7 +870,7 @@ int Header::GetBitsAllocated() */ int Header::GetSamplesPerPixel() { - std::string strSize = GetEntryByNumber(0x0028,0x0002); + const std::string& strSize = GetEntryByNumber(0x0028,0x0002); if ( strSize == GDCM_UNFOUND ) { dbg.Verbose(0, "Header::GetBitsStored: this is supposed to " @@ -839,9 +888,9 @@ int Header::GetSamplesPerPixel() */ bool Header::IsMonochrome() { - std::string PhotometricInterp = GetEntryByNumber( 0x0028, 0x0004 ); - if ( PhotometricInterp == "MONOCHROME1 " - || PhotometricInterp == "MONOCHROME2 " ) + const std::string& PhotometricInterp = GetEntryByNumber( 0x0028, 0x0004 ); + if ( Util::DicomStringEqual(PhotometricInterp, "MONOCHROME1") + || Util::DicomStringEqual(PhotometricInterp, "MONOCHROME2") ) { return true; } @@ -968,7 +1017,7 @@ std::string Header::GetPixelType() { return "FD"; } - if ( bitsAlloc == "12" ) + else if ( bitsAlloc == "12" ) { // It will be unpacked bitsAlloc = "16"; @@ -986,7 +1035,7 @@ std::string Header::GetPixelType() dbg.Verbose(0, "Header::GetPixelType: unfound Pixel Representation"); bitsAlloc = "0"; } - if ( sign == "0" ) + else if ( sign == "0" ) { sign = "U"; } @@ -1150,7 +1199,7 @@ std::string Header::GetTransfertSyntaxName() return "Uncompressed ACR-NEMA"; } - while ( ! isdigit(transfertSyntax[transfertSyntax.length()-1]) ) + while ( ! isdigit((unsigned char)transfertSyntax[transfertSyntax.length()-1]) ) { transfertSyntax.erase(transfertSyntax.length()-1, 1); } @@ -1162,27 +1211,6 @@ std::string Header::GetTransfertSyntaxName() return tsName; } -/** - * \brief Sets the Pixel Area size in the Header - * --> not-for-rats function - * @param ImageDataSize new Pixel Area Size - * warning : nothing else is checked - */ -void Header::SetImageDataSize(size_t ImageDataSize) -{ - ///FIXME I don't understand this code why do we set two times 'car' ? - std::string car = Util::Format("%d", ImageDataSize); - - DocEntry *a = GetDocEntryByNumber(GrPixel, NumPixel); - a->SetLength(ImageDataSize); - - ImageDataSize += 8; - car = Util::Format("%d", ImageDataSize); - car = Util::DicomString( car.c_str() ); - - SetEntryByNumber(car, GrPixel, NumPixel); -} - //----------------------------------------------------------------------------- // Protected @@ -1301,6 +1329,82 @@ void Header::GetImageOrientationPatient( float iop[6] ) } } +/** + * \brief Initialize a default DICOM header that should contain all the + * field require by other reader. DICOM standard does not + * explicitely defines those fields, heuristic has been choosen. + * This is not perfect as we are writting a CT image... + */ +void Header::InitializeDefaultHeader() +{ + typedef struct + { + const char *value; + uint16_t group; + uint16_t elem; + } DICOM_DEFAULT_VALUE; + + std::string date = Util::GetCurrentDate(); + std::string time = Util::GetCurrentTime(); + std::string uid = Util::CreateUniqueUID(); + std::string uidMedia = uid; + std::string uidClass = uid + ".1"; + std::string uidInst = uid + ".10"; + std::string uidStudy = uid + ".100"; + std::string uidSerie = uid + ".1000"; + + static DICOM_DEFAULT_VALUE defaultvalue[] = { + { "146 ", 0x0002, 0x0000}, // Meta Element Group Length // FIXME: how to recompute ? + { "1.2.840.10008.5.1.4.1.1.2", 0x0002, 0x0002}, // Media Storage SOP Class UID (CT Image Storage) + { uidClass.c_str(), 0x0002, 0x0003}, // Media Storage SOP Instance UID + { uidClass.c_str(), 0x0002, 0x0012}, // META Implementation Class UID + { "GDCM", 0x0002, 0x0016}, // Source Application Entity Title + + { date.c_str(), 0x0008, 0x0012}, // Instance Creation Date + { time.c_str(), 0x0008, 0x0013}, // Instance Creation Time + { "1.2.840.10008.5.1.4.1.1.2", 0x0008, 0x0016}, // SOP Class UID + { uidInst.c_str(), 0x0008, 0x0018}, // SOP Instance UID + { "CT", 0x0008, 0x0060}, // Modality + { "GDCM", 0x0008, 0x0070}, // Manufacturer + { "GDCM", 0x0008, 0x0080}, // Institution Name + { "http://www-creatis.insa-lyon.fr/Public/Gdcm", 0x0008, 0x0081}, // Institution Address + + { "GDCM", 0x0010, 0x0010}, // Patient's Name + { "GDCMID", 0x0010, 0x0020}, // Patient ID + + { uidStudy.c_str(), 0x0020, 0x000d}, // Study Instance UID + { uidSerie.c_str(), 0x0020, 0x000e}, // Series Instance UID + { "1", 0x0020, 0x0010}, // StudyID + { "1", 0x0020, 0x0011}, // SeriesNumber + + { "1", 0x0028, 0x0002}, // Samples per pixel 1 or 3 + { "MONOCHROME1", 0x0028, 0x0004}, // photochromatic interpretation + { "0", 0x0028, 0x0010}, // nbRows + { "0", 0x0028, 0x0011}, // nbCols + { "8", 0x0028, 0x0100}, // BitsAllocated 8 or 12 or 16 + { "8", 0x0028, 0x0101}, // BitsStored <= BitsAllocated + { "7", 0x0028, 0x0102}, // HighBit <= BitsAllocated - 1 + { "0", 0x0028, 0x0103}, // Pixel Representation 0(unsigned) or 1(signed) + { 0, 0, 0 } + }; + + // default value + // Special case this is the image (not a string) + GrPixel = 0x7fe0; + NumPixel = 0x0010; + ReplaceOrCreateByNumber(0, 0, GrPixel, NumPixel); + + // All remaining strings: + unsigned int i = 0; + DICOM_DEFAULT_VALUE current = defaultvalue[i]; + while( current.value ) + { + ReplaceOrCreateByNumber(current.value, current.group, current.elem); + current = defaultvalue[++i]; + } +} + + //----------------------------------------------------------------------------- // Private