X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmHeaderHelper.cxx;h=1f38148f95c259b7c94010d1da930901ba49b3c3;hb=aba8714645174c0c7d3c7aadf6af1832743e2971;hp=60e1fbee2e8775be786332f0cbe3dae105506916;hpb=5a6910a313a526514242a21b868c7186fca14168;p=gdcm.git diff --git a/src/gdcmHeaderHelper.cxx b/src/gdcmHeaderHelper.cxx index 60e1fbee..1f38148f 100644 --- a/src/gdcmHeaderHelper.cxx +++ b/src/gdcmHeaderHelper.cxx @@ -1,60 +1,61 @@ -// $Header: /cvs/public/gdcm/src/Attic/gdcmHeaderHelper.cxx,v 1.18 2004/01/13 11:32:30 jpr Exp $ - +// gdcmHeaderHelper.cxx +//----------------------------------------------------------------------------- #include "gdcmHeaderHelper.h" #include "gdcmUtil.h" //for debug #include #include -//#include //for bzero -//directory manipulation (os indep). -//cygwin ???? -> _WIN32 ?? #ifdef _MSC_VER -#include -int GetDir(std::string dPath, std::list &filenames) -{ - //For now dPath should have an ending "\" - WIN32_FIND_DATA FileData; - HANDLE hFile; - hFile = FindFirstFile((dPath+"*").c_str(), &FileData); - if ( hFile == INVALID_HANDLE_VALUE ) - { - //No files ! - return false; - } + #include + + int GetDir(std::string dPath, std::list &filenames) + { + //For now dPath should have an ending "\" + WIN32_FIND_DATA FileData; + HANDLE hFile; + hFile = FindFirstFile((dPath+"*").c_str(), &FileData); + if ( hFile == INVALID_HANDLE_VALUE ) + { + //No files ! + return false; + } - if( strncmp(FileData.cFileName, ".", 1) != 0 ) - filenames.push_back( dPath+FileData.cFileName ); - while( FindNextFile(hFile, &FileData ) != 0) - { - if( strncmp(FileData.cFileName, ".", 1) != 0 ) - filenames.push_back( dPath+FileData.cFileName ); - } - return true; -} + if( strncmp(FileData.cFileName, ".", 1) != 0 ) + filenames.push_back( dPath+FileData.cFileName ); + while( FindNextFile(hFile, &FileData ) != 0) + { + if( strncmp(FileData.cFileName, ".", 1) != 0 ) + filenames.push_back( dPath+FileData.cFileName ); + } + return true; + } #else -#include + #include -int GetDir(std::string dPath, std::list &filenames) -{ - DIR *dir = opendir( dPath.c_str() ); - struct dirent *entry; - while((entry = readdir(dir)) != NULL) - { -// if( strncmp(entry->d_name, ".", 1) != 0 && strncmp(entry->d_name, "..", 2) != 0) - if( strncmp(entry->d_name, ".", 1) != 0 ) + int GetDir(std::string dPath, std::list &filenames) { - filenames.push_back( dPath + "/" + entry->d_name ); + DIR *dir = opendir( dPath.c_str() ); + struct dirent *entry; + while((entry = readdir(dir)) != NULL) + { + // if( strncmp(entry->d_name, ".", 1) != 0 && strncmp(entry->d_name, "..", 2) != 0) + if( strncmp(entry->d_name, ".", 1) != 0 ) + { + filenames.push_back( dPath + "/" + entry->d_name ); + } + } + closedir(dir); + return true; } - } - closedir(dir); - return true; -} #endif -//---------------------------------------------------------------------------- +//----------------------------------------------------------------------------- +// gdcmHeaderHelper +//----------------------------------------------------------------------------- +// Constructor / Destructor /** * \ingroup gdcmHeaderHelper * \brief cstor @@ -62,7 +63,7 @@ int GetDir(std::string dPath, std::list &filenames) gdcmHeaderHelper::gdcmHeaderHelper() : gdcmHeader( ) { } -//---------------------------------------------------------------------------- + /** * \ingroup gdcmHeaderHelper * \brief cstor @@ -71,7 +72,12 @@ gdcmHeaderHelper::gdcmHeaderHelper(const char *InFilename, bool exception_on_error) : gdcmHeader( InFilename , exception_on_error) { } -//---------------------------------------------------------------------------- + +//----------------------------------------------------------------------------- +// Print + +//----------------------------------------------------------------------------- +// Public /** * \ingroup gdcmHeaderHelper * \brief Return the size (in bytes) of a single pixel of data. @@ -96,69 +102,6 @@ int gdcmHeaderHelper::GetPixelSize() { return 0; } -//---------------------------------------------------------------------------- -/** - * \ingroup gdcmHeaderHelper - * \brief This function is intended to user who doesn't whan - * \ to have to manage a LUT and expects to get an RBG Pixel image - * \ (or a monochrome one ...) - * \warning to be used with GetImagePixels() - * @return 1 if Gray level, 3 if Color (RGB, YBR or PALETTE COLOR) - */ -int gdcmHeaderHelper::GetNumberOfScalarComponents() { - - if (GetSamplesPerPixel() ==3) - return 3; - - // 0028 0100 US IMG Bits Allocated - // (in order no to be messed up by old RGB images) - if (gdcmHeader::GetPubElValByNumber(0x0028,0x0100) == "24") - return 3; - - std::string PhotometricInterpretation = - gdcmHeader::GetPubElValByNumber(0x0028,0x0004); - - if ( ( PhotometricInterpretation == "PALETTE COLOR ") ) { - if (HasLUT()) // PALETTE COLOR is NOT enough - return 3; - else - return 1; - } - - //beware of trailing space at end of string - if (PhotometricInterpretation.find(GDCM_UNFOUND) < - PhotometricInterpretation.length() || - PhotometricInterpretation.find("MONOCHROME1") < - PhotometricInterpretation.length() || - PhotometricInterpretation.find("MONOCHROME2") < - PhotometricInterpretation.length() ) - return 1; - else - // we assume that *all* kinds of YBR are dealt with - return 3; -} - -//---------------------------------------------------------------------------- -/** - * \ingroup gdcmHeaderHelper - * \brief This function is intended to user that DOESN'T want - * \to get RGB pixels image when it's stored as a PALETTE COLOR image - * \ - the (vtk) user is supposed to know how deal with LUTs - - * \warning to be used with GetImagePixelsRaw() - * @return 1 if Gray level, 3 if Color (RGB or YBR - NOT 'PALETTE COLOR' -) - */ -int gdcmHeaderHelper::GetNumberOfScalarComponentsRaw() { - - // 0028 0100 US IMG Bits Allocated - // (in order no to be messed up by old RGB images) - if (gdcmHeader::GetPubElValByNumber(0x0028,0x0100) == "24") - return 3; - - // we assume that *all* kinds of YBR are dealt with - return GetSamplesPerPixel(); -} - -//---------------------------------------------------------------------------- /** * \ingroup gdcmHeaderHelper * \brief Build the Pixel Type of the image. @@ -198,7 +141,7 @@ std::string gdcmHeaderHelper::GetPixelType() { return( BitsAlloc + Signed); } -//---------------------------------------------------------------------------- + /** * \ingroup gdcmHeaderHelper * \brief gets the info from 0028,0030 : Pixel Spacing @@ -222,7 +165,7 @@ float gdcmHeaderHelper::GetXSpacing() { } return xspacing; } -//---------------------------------------------------------------------------- + /** * \ingroup gdcmHeaderHelper * \brief gets the info from 0028,0030 : Pixel Spacing @@ -247,7 +190,6 @@ float gdcmHeaderHelper::GetYSpacing() { return yspacing; } -//---------------------------------------------------------------------------- /** *\ingroup gdcmHeaderHelper *\brief gets the info from 0018,0088 : Space Between Slices @@ -284,8 +226,112 @@ float gdcmHeaderHelper::GetZSpacing() { } } -//---------------------------------------------------------------------------- -// +float gdcmHeaderHelper::GetRescaleIntercept() +{ + float resInter = 0.; + std::string StrRescInter = GetPubElValByNumber(0x0028,0x1052); //0028 1052 DS IMG Rescale Intercept + if (StrRescInter != GDCM_UNFOUND) { + if( sscanf( StrRescInter.c_str(), "%f", &resInter) != 1) { + dbg.Verbose(0, "gdcmHeader::GetRescaleIntercept: Rescale Slope is empty"); + // bug in the element 0x0028,0x1052 + } + } + return resInter; +} + +float gdcmHeaderHelper::GetRescaleSlope() +{ + float resSlope = 1.; + std::string StrRescSlope = GetPubElValByNumber(0x0028,0x1053); //0028 1053 DS IMG Rescale Slope + if (StrRescSlope != GDCM_UNFOUND) { + if( sscanf( StrRescSlope.c_str(), "%f", &resSlope) != 1) { + dbg.Verbose(0, "gdcmHeader::GetRescaleSlope: Rescale Slope is empty"); + // bug in the element 0x0028,0x1053 + } + } + return resSlope; +} + +/** + * \ingroup gdcmHeaderHelper + * \brief This function is intended to user who doesn't whan + * \ to have to manage a LUT and expects to get an RBG Pixel image + * \ (or a monochrome one ...) + * \warning to be used with GetImagePixels() + * @return 1 if Gray level, 3 if Color (RGB, YBR or PALETTE COLOR) + */ +int gdcmHeaderHelper::GetNumberOfScalarComponents() { + + if (GetSamplesPerPixel() ==3) + return 3; + + // 0028 0100 US IMG Bits Allocated + // (in order no to be messed up by old RGB images) + if (gdcmHeader::GetPubElValByNumber(0x0028,0x0100) == "24") + return 3; + + std::string PhotometricInterpretation = + gdcmHeader::GetPubElValByNumber(0x0028,0x0004); + + if ( ( PhotometricInterpretation == "PALETTE COLOR ") ) { + if (HasLUT()) // PALETTE COLOR is NOT enough + return 3; + else + return 1; + } + + //beware of trailing space at end of string + if (PhotometricInterpretation.find(GDCM_UNFOUND) < + PhotometricInterpretation.length() || + PhotometricInterpretation.find("MONOCHROME1") < + PhotometricInterpretation.length() || + PhotometricInterpretation.find("MONOCHROME2") < + PhotometricInterpretation.length() ) + return 1; + else + // we assume that *all* kinds of YBR are dealt with + return 3; +} + +/** + * \ingroup gdcmHeaderHelper + * \brief This function is intended to user that DOESN'T want + * \to get RGB pixels image when it's stored as a PALETTE COLOR image + * \ - the (vtk) user is supposed to know how deal with LUTs - + * \warning to be used with GetImagePixelsRaw() + * @return 1 if Gray level, 3 if Color (RGB or YBR - NOT 'PALETTE COLOR' -) + */ +int gdcmHeaderHelper::GetNumberOfScalarComponentsRaw() { + + // 0028 0100 US IMG Bits Allocated + // (in order no to be messed up by old RGB images) + if (gdcmHeader::GetPubElValByNumber(0x0028,0x0100) == "24") + return 3; + + // we assume that *all* kinds of YBR are dealt with + return GetSamplesPerPixel(); +} + +std::string gdcmHeaderHelper::GetStudyUID() +{ + return GetPubElValByNumber(0x0020,0x000d); //0020 000d UI REL Study Instance UID +} + +std::string gdcmHeaderHelper::GetSeriesUID() +{ + return GetPubElValByNumber(0x0020,0x000e); //0020 000e UI REL Series Instance UID +} + +std::string gdcmHeaderHelper::GetClassUID() +{ + return GetPubElValByNumber(0x0008,0x0016); //0008 0016 UI ID SOP Class UID +} + +std::string gdcmHeaderHelper::GetInstanceUID() +{ + return GetPubElValByNumber(0x0008,0x0018); //0008 0018 UI ID SOP Instance UID +} + // Image Position Patient (0020,0032): // If not found (ACR_NEMA) we try Image Position (0020,0030) // If not found (ACR-NEMA), we consider Slice Location (0020,1041) @@ -295,7 +341,6 @@ float gdcmHeaderHelper::GetZSpacing() { // TODO : find a way to inform the caller nothing was found // TODO : How to tell the caller a wrong number of values was found? - /** * \ingroup gdcmHeaderHelper * \brief gets the info from 0020,0032 : Image Position Patient @@ -320,7 +365,7 @@ float gdcmHeaderHelper::GetXOrigin() { return 0.; return xImPos; } -//---------------------------------------------------------------------------- + /** * \ingroup gdcmHeaderHelper * \brief gets the info from 0020,0032 : Image Position Patient @@ -345,7 +390,7 @@ float gdcmHeaderHelper::GetYOrigin() { return 0.; return yImPos; } -//---------------------------------------------------------------------------- + /** * \ingroup gdcmHeaderHelper * \brief gets the info from 0020,0032 : Image Position Patient @@ -397,7 +442,7 @@ float gdcmHeaderHelper::GetZOrigin() { dbg.Verbose(0, "gdcmHeader::GetYImagePosition: unfound Location (0020,0050)"); return 0.; // Hopeless } -//---------------------------------------------------------------------------- + /** * \ingroup gdcmHeaderHelper * \brief gets the info from 0020,0013 : Image Number @@ -416,7 +461,7 @@ int gdcmHeaderHelper::GetImageNumber() { } return 0; //Hopeless } -//---------------------------------------------------------------------------- + /** * \ingroup gdcmHeaderHelper * \brief gets the info from 0008,0060 : Modality @@ -476,72 +521,6 @@ ModalityType gdcmHeaderHelper::GetModality(void) { return Unknow; } -//---------------------------------------------------------------------------- -std::string gdcmHeaderHelper::GetStudyUID() -{ - return GetPubElValByNumber(0x0020,0x000d); //0020 000d UI REL Study Instance UID -} -//---------------------------------------------------------------------------- -std::string gdcmHeaderHelper::GetSeriesUID() -{ - return GetPubElValByNumber(0x0020,0x000e); //0020 000e UI REL Series Instance UID -} -//---------------------------------------------------------------------------- -std::string gdcmHeaderHelper::GetClassUID() -{ - return GetPubElValByNumber(0x0008,0x0016); //0008 0016 UI ID SOP Class UID -} -//---------------------------------------------------------------------------- -std::string gdcmHeaderHelper::GetInstanceUID() -{ - return GetPubElValByNumber(0x0008,0x0018); //0008 0018 UI ID SOP Instance UID -} -//---------------------------------------------------------------------------- -float gdcmHeaderHelper::GetRescaleIntercept() -{ - float resInter = 0.; - std::string StrRescInter = GetPubElValByNumber(0x0028,0x1052); //0028 1052 DS IMG Rescale Intercept - if (StrRescInter != GDCM_UNFOUND) { - if( sscanf( StrRescInter.c_str(), "%f", &resInter) != 1) { - dbg.Verbose(0, "gdcmHeader::GetRescaleIntercept: Rescale Slope is empty"); - // bug in the element 0x0028,0x1052 - } - } - return resInter; -} -//---------------------------------------------------------------------------- -float gdcmHeaderHelper::GetRescaleSlope() -{ - float resSlope = 1.; - std::string StrRescSlope = GetPubElValByNumber(0x0028,0x1053); //0028 1053 DS IMG Rescale Slope - if (StrRescSlope != GDCM_UNFOUND) { - if( sscanf( StrRescSlope.c_str(), "%f", &resSlope) != 1) { - dbg.Verbose(0, "gdcmHeader::GetRescaleSlope: Rescale Slope is empty"); - // bug in the element 0x0028,0x1053 - } - } - return resSlope; -} - - - - - - - - - -gdcmSerieHeaderHelper::~gdcmSerieHeaderHelper() -{ - //! \todo - for (std::list::iterator it = CoherentGdcmFileList.begin(); - it != CoherentGdcmFileList.end(); it++) - { - delete *it; - } - CoherentGdcmFileList.clear(); -} -//---------------------------------------------------------------------------- /** * \ingroup gdcmHeaderHelper * \brief gets the info from 0020,0037 : Image Orientation Patient @@ -576,30 +555,59 @@ void gdcmHeaderHelper::GetImageOrientationPatient( float* iop ) { } } -//---------------------------------------------------------------------------- +//----------------------------------------------------------------------------- +// Protected + +//----------------------------------------------------------------------------- +// Private + +//----------------------------------------------------------------------------- + + + +//----------------------------------------------------------------------------- +// gdcmSerieHeaderHelper +//----------------------------------------------------------------------------- +// Constructor / Destructor +gdcmSerieHeaderHelper::~gdcmSerieHeaderHelper() +{ + //! \todo + for (std::list::iterator it = CoherentGdcmFileList.begin(); + it != CoherentGdcmFileList.end(); it++) + { + delete *it; + } + CoherentGdcmFileList.clear(); +} + +//----------------------------------------------------------------------------- +// Print + +//----------------------------------------------------------------------------- +// Public /** - * \ingroup gdcmHeaderHelper - * \brief add a gdcmFile to the list based on file name - */ + * \ingroup gdcmHeaderHelper + * \brief add a gdcmFile to the list based on file name + */ void gdcmSerieHeaderHelper::AddFileName(std::string filename) { gdcmHeaderHelper *GdcmFile = new gdcmHeaderHelper( filename.c_str() ); this->CoherentGdcmFileList.push_back( GdcmFile ); } -//---------------------------------------------------------------------------- + /** - * \ingroup gdcmHeaderHelper - * \brief add a gdcmFile to the list - */ + * \ingroup gdcmHeaderHelper + * \brief add a gdcmFile to the list + */ void gdcmSerieHeaderHelper::AddGdcmFile(gdcmHeaderHelper *file) { this->CoherentGdcmFileList.push_back( file ); } -//---------------------------------------------------------------------------- + /** - * \ingroup gdcmHeaderHelper - * \brief \todo - */ + * \ingroup gdcmHeaderHelper + * \brief \todo + */ void gdcmSerieHeaderHelper::SetDirectory(std::string dir) { std::list filenames_list; @@ -612,7 +620,7 @@ void gdcmSerieHeaderHelper::SetDirectory(std::string dir) this->CoherentGdcmFileList.push_back( file ); } } -//---------------------------------------------------------------------------- + //This could be implemented in a 'Strategy Pattern' approach //But as I don't know how to do it, I leave it this way //BTW, this is also a Strategy, I don't know this is the best approach :) @@ -631,17 +639,27 @@ void gdcmSerieHeaderHelper::OrderGdcmFileList() FileNameOrdering(); } } -//---------------------------------------------------------------------------- + +std::list &gdcmSerieHeaderHelper::GetGdcmFileList() +{ + return CoherentGdcmFileList; +} + +//----------------------------------------------------------------------------- +// Protected + +//----------------------------------------------------------------------------- +// Private /** - * \ingroup gdcmHeaderHelper - * \brief - We may order, considering : - -# Image Number - -# Image Position Patient - -# More to come :) -*/ -//based on Jolinda's algorithm + * \ingroup gdcmHeaderHelper + * \brief + * We may order, considering : + * -# Image Number + * -# Image Position Patient + * -# More to come :) + */ bool gdcmSerieHeaderHelper::ImagePositionPatientOrdering() +//based on Jolinda's algorithm { //iop is calculated based on the file file float *cosines = new float[6]; @@ -748,7 +766,7 @@ bool gdcmSerieHeaderHelper::ImagePositionPatientOrdering() return true; } -//---------------------------------------------------------------------------- + //Based on Image Number bool gdcmSerieHeaderHelper::ImageNumberOrdering() { @@ -798,18 +816,14 @@ bool gdcmSerieHeaderHelper::ImageNumberOrdering() CoherentGdcmFileVector.clear(); delete[] partition; - return mult; + return (mult!=0); } -//---------------------------------------------------------------------------- + bool gdcmSerieHeaderHelper::FileNameOrdering() { //using the sort //sort(CoherentGdcmFileList.begin(), CoherentGdcmFileList.end()); return true; } -//---------------------------------------------------------------------------- -std::list &gdcmSerieHeaderHelper::GetGdcmFileList() -{ - return CoherentGdcmFileList; -} -//---------------------------------------------------------------------------- + +//-----------------------------------------------------------------------------