X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmHeader.cxx;h=31263819c3b7ea2cace0232fb4eee99965e04bc1;hb=327dfe7647e3720b0f3125f9b19397cb9afc0ed3;hp=84aea4d314918aebaf370a2fe606bf8298b94302;hpb=d01d35846e6b6918f2e11b2f15e13555e78a39b6;p=gdcm.git diff --git a/src/gdcmHeader.cxx b/src/gdcmHeader.cxx index 84aea4d3..31263819 100644 --- a/src/gdcmHeader.cxx +++ b/src/gdcmHeader.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmHeader.cxx,v $ Language: C++ - Date: $Date: 2004/11/23 17:12:25 $ - Version: $Revision: 1.205 $ + Date: $Date: 2005/01/06 20:03:28 $ + Version: $Revision: 1.222 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -22,7 +22,7 @@ #include "gdcmDebug.h" #include "gdcmTS.h" #include "gdcmValEntry.h" -#include +#include //sscanf #include @@ -34,7 +34,7 @@ namespace gdcm * \brief Constructor * @param filename name of the file whose header we want to analyze */ -Header::Header( std::string const & filename ): +Header::Header( std::string const &filename ): Document( filename ) { // for some ACR-NEMA images GrPixel, NumPixel is *not* 7fe0,0010 @@ -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 ); + } } /** @@ -98,12 +121,20 @@ Header::~Header () * \brief Performs some consistency checking on various 'File related' * (as opposed to 'DicomDir related') entries * then writes in a file all the (Dicom Elements) included the Pixels - * @param fp file pointer on an already open file + * @param fileName file name to write to * @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") { @@ -132,7 +163,7 @@ void Header::Write(std::ofstream* fp,FileType filetype) // Drop 0028|1101, 0028|1102, 0028|1103 // Drop 0028|1201, 0028|1202, 0028|1203 - DocEntry* e = GetDocEntryByNumber(0x0028,0x01101); + DocEntry *e = GetDocEntryByNumber(0x0028,0x01101); if (e) { RemoveEntryNoDestroy(e); @@ -163,7 +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; } //----------------------------------------------------------------------------- @@ -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; } @@ -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.; @@ -375,11 +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() ); } /** @@ -390,7 +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 ) @@ -969,7 +1017,7 @@ std::string Header::GetPixelType() { return "FD"; } - if ( bitsAlloc == "12" ) + else if ( bitsAlloc == "12" ) { // It will be unpacked bitsAlloc = "16"; @@ -987,7 +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"; } @@ -1163,28 +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); - - // Change the value of the BinEntry, not the BinArea !!! - ImageDataSize += 8; - car = Util::Format("%d", ImageDataSize); - car = Util::DicomString( car.c_str() ); - - SetEntryByNumber(car, GrPixel, NumPixel); -} - //----------------------------------------------------------------------------- // Protected @@ -1305,8 +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() @@ -1318,58 +1344,48 @@ void Header::InitializeDefaultHeader() uint16_t elem; } DICOM_DEFAULT_VALUE; - const char *date = Util::GetCurrentDate().c_str(); - const char *time = Util::GetCurrentTime().c_str(); - const char *uid = Util::CreateUniqueUID().c_str(); + 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[] = { - "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, 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, 0x0020, 0x000d, // StudyInstanceUID - uid, 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 time - - date, 0x0008, 0x0012, // Instance Creation Date - time, 0x0008, 0x0013, // Instance Creation Time - date, 0x0008, 0x0020, // Study Date - date, 0x0008, 0x0022, // Acquisition Date - date, 0x0008, 0x0023, // Content Date - time, 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 @@ -1383,12 +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