X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmHeader.cxx;h=bc28cd19ea484773535b420a477dc7439d6fb4a9;hb=4beda181275414e5cba990113f8d16424b2c09e6;hp=62b38d4934bb007d0a275870b7d12129251d6c16;hpb=38d772b8588bc4e7106dbafcb24f6bff91b8c4c1;p=gdcm.git diff --git a/src/gdcmHeader.cxx b/src/gdcmHeader.cxx index 62b38d49..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: 2004/12/03 16:57:49 $ - Version: $Revision: 1.211 $ + 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 @@ -76,6 +76,29 @@ 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 ); + } } /** @@ -102,11 +125,11 @@ Header::~Header () * @param filetype Type of the File to be written * (ACR-NEMA, ExplicitVR, ImplicitVR) */ -bool Header::Write(std::string fileName,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) + if (*fp == NULL) { dbg.Verbose(2, "Failed to open (write) File: " , fileName.c_str()); return false; @@ -261,7 +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; } @@ -316,14 +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; @@ -336,7 +371,7 @@ float Header::GetXSpacing() */ float Header::GetYSpacing() { - float yspacing = 0; + float yspacing = 1.; std::string strSpacing = GetEntryByNumber(0x0028,0x0030); if ( strSpacing == GDCM_UNFOUND ) @@ -348,13 +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() @@ -369,12 +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.; @@ -388,11 +426,8 @@ float Header::GetZSpacing() return (float)atof( strSliceThickness.c_str() ); } } - else - { - return (float)atof( strSpacingBSlices.c_str() ); - } - return 1.; + //else + return (float)atof( strSpacingBSlices.c_str() ); } /** @@ -403,7 +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 ) @@ -982,7 +1017,7 @@ std::string Header::GetPixelType() { return "FD"; } - if ( bitsAlloc == "12" ) + else if ( bitsAlloc == "12" ) { // It will be unpacked bitsAlloc = "16"; @@ -1000,7 +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"; } @@ -1296,8 +1331,8 @@ void Header::GetImageOrientationPatient( float iop[6] ) /** * \brief Initialize a default DICOM header that should contain all the - * field require by other reader. DICOM standart does not - * explicitely defines thoses fields, heuristic has been choosen. + * 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() @@ -1311,56 +1346,46 @@ void Header::InitializeDefaultHeader() std::string date = Util::GetCurrentDate(); std::string time = Util::GetCurrentTime(); - std::string uid = Util::CreateUniqueUID(); + 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[] = { - { "76", 0x0002, 0x0000}, // MetaElementGroup Length // FIXME: how to recompute ? - { "1.2.840.10008.5.1.4.1.1.2", 0x0002, 0x0002}, // MediaStorageSOPInstanceUID (CT Image Storage) - { uid.c_str(), 0x0002, 0x0012}, // META Implementation Class UID - { "ISO_IR 100",0x0008, 0x0005}, // Specific Character Set - { "DERIVED\\SECONDARY\\OTHER\\GDCM", 0x0008, 0x0008}, // Image Type - { "1.2.840.10008.5.1.4.1.1.2", 0x0008, 0x0016}, // SOP Class UID - { "", 0x0008, 0x0050}, // Accession Number - { "GDCM", 0x0008, 0x0070}, // Manufacturer - { "GDCM", 0x0008, 0x0080}, // Institution Name - { "http://www-creatis.insa-lyon.fr/Public/Gdcm/", 0x0008, 0x0081}, // Institution Address - { "", 0x0008, 0x0090}, // Refering Physician Name - { "", 0x0008, 0x1030}, // Study Description - { "", 0x0008, 0x1050}, // Performing Physician's Name - { "", 0x0008, 0x1060}, // Name of Physician(s) Reading Study - { "", 0x0010, 0x0040}, // Patient's Sex - { uid.c_str(), 0x0020, 0x000d}, // StudyInstanceUID - { uid.c_str(), 0x0020, 0x000e}, // SeriesInstanceUID - { "", 0x0020, 0x0011}, // AcquisitionNumber - { "1\\0\\0\\0\\1\\0", 0x0020, 0x0037}, // Image Orientation Patient - { "1", 0x0028, 0x0002}, // Samples per pixel 1 or 3 - { "MONOCHROME2",0x0028, 0x0004}, // photochromatic interpretation - -// Date and timeG - - { date.c_str(), 0x0008, 0x0012 } , // Instance Creation Date - { time.c_str(), 0x0008, 0x0013 } , // Instance Creation Time - { date.c_str(), 0x0008, 0x0020 } , // Study Date - { date.c_str(), 0x0008, 0x0022 } , // Acquisition Date - { date.c_str(), 0x0008, 0x0023 } , // Content Date - { time.c_str(), 0x0008, 0x0030 } , // Study Time - { "CT", 0x0008, 0x0060 } , // Modality - { "GDCM", 0x0010, 0x0010 } , // Patient's Name - { "GDCMID", 0x0010, 0x0020 } , // Patient ID - { "1", 0x0020, 0x0010 } , // StudyID - { "1", 0x0020, 0x0011 } , // SeriesNumber - { "1.0", 0x0018, 0x0050 } , // slice Thickness - { "1.0", 0x0018, 0x0088 } , // space between slices - { "1.0\\1.0", 0x0028, 0x0030 } , // pixelSpacing - { "64", 0x0028, 0x0010 } , // nbRows - { "64", 0x0028, 0x0011 } , // nbCols - { "16", 0x0028, 0x0100 } , // BitsAllocated 8 or 16 - { "12", 0x0028, 0x0101 } , // BitsStored 8 or 12 - { "11", 0x0028, 0x0102 } , // HighBit 7 or 11 - { "0", 0x0028, 0x0103 } , // Pixel Representation 0(unsigned) or 1(signed) - { "1000.0", 0x0028, 0x1051 } , // Window Width - { "500.0", 0x0028, 0x1050 } , // Window Center - { 0, 0, 0 } + { "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 @@ -1374,12 +1399,12 @@ void Header::InitializeDefaultHeader() DICOM_DEFAULT_VALUE current = defaultvalue[i]; while( current.value ) { - std::string value = Util::DicomString( current.value ); //pad the string properly - ReplaceOrCreateByNumber(value, current.group, current.elem); + ReplaceOrCreateByNumber(current.value, current.group, current.elem); current = defaultvalue[++i]; } } + //----------------------------------------------------------------------------- // Private