X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmFile.cxx;h=e21f6e0a81c76b5da44d9acf5c78db0776194fe4;hb=f88cd7e3127179d20920d54df75bff206be94a09;hp=a166a0e75ecf691f92c5c9213ea0bccd6ccfaab9;hpb=0aae6ba79c12b82eee08dd7f2e22397e1eca6acf;p=gdcm.git diff --git a/src/gdcmFile.cxx b/src/gdcmFile.cxx index a166a0e7..e21f6e0a 100644 --- a/src/gdcmFile.cxx +++ b/src/gdcmFile.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmFile.cxx,v $ Language: C++ - Date: $Date: 2005/07/07 10:12:32 $ - Version: $Revision: 1.248 $ + Date: $Date: 2005/07/24 02:10:48 $ + Version: $Revision: 1.262 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -26,6 +26,42 @@ // as the Z coordinate, // 0. for all the coordinates if nothing is found // +// Image Position (Patient) (0020,0032) VM=3 What is it used for? +// --> +// The attribute Patient Orientation (0020,0020) from the General Image Module +// is of type 2C and has the condition Required if image does not require +// Image Orientation (0020,0037) and Image Position (0020,0032). +// However, if the image does require the attributes +// - Image Orientation (Patient) (0020,0037), VM=6 +// - Image Position Patient (0020,0032), VM=3 +// then attribute Patient Orientation (0020,0020) should not be present +// in the images. +// +// Remember also : +// Patient Position (0018,5100) values : HFP = Head First-Prone +// HFS = Head First-Supine +// HFDR = Head First-Decubitus Right +// HFDL = Head First-Decubitus Left +// FFDR = Feet First-Decubitus Right +// FFDL = Feet First-Decubitus Left +// FFP = Feet First-Prone +// FFS = Feet First-Supine +// can also find SEMIERECT +// SUPINE +// CS 2 Patient Orientation (0020 0020) +// When the coordinates of the image +// are always present, this field is almost never used. +// Better we don't tust it too much ... +// Found Values are : L\P +// L\FP +// P\F +// L\F +// P\FR +// R\F +// +// (0020|0037) [Image Orientation (Patient)] [1\0\0\0\1\0 ] + + // --------------------------------------------------------------- // #include "gdcmFile.h" @@ -42,9 +78,11 @@ #include #include //sscanf #include // for atoi +#include // for pow namespace gdcm { + //----------------------------------------------------------------------------- // Constructor / Destructor @@ -60,18 +98,6 @@ File::File(): NumPixel = 0x0010; } -/** - * \brief Constructor - * @param filename name of the file whose header we want to analyze - */ -File::File( std::string const &filename ) - :Document( ) -{ - RLEInfo = new RLEFramesInfo; - JPEGInfo = new JPEGFragmentsInfo; - - Load( filename ); // gdcm::Document is first Loaded, then the 'File part' -} /** * \brief Canonical destructor. @@ -86,18 +112,27 @@ File::~File () //----------------------------------------------------------------------------- // Public - /** * \brief Loader - * @param fileName file to be open for parsing * @return false if file cannot be open or no swap info was found, * or no tag was found. */ -bool File::Load( std::string const &fileName ) +bool File::Load( ) { - if ( ! this->Document::Load( fileName ) ) + if ( ! this->Document::Load( ) ) return false; + return DoTheLoadingJob( ); +} + +/** + * \brief Does the Loading Job (internal use only) + * @return false if file cannot be open or no swap info was found, + * or no tag was found. + */ +bool File::DoTheLoadingJob( ) +{ + // for some ACR-NEMA images GrPixel, NumPixel is *not* 7fe0,0010 // We may encounter the 'RETired' (0x0028, 0x0200) tag // (Image Location") . This entry contains the number of @@ -701,7 +736,7 @@ float File::GetZOrigin() * @param iop adress of the (6)float array to receive values * @return cosines of image orientation patient */ -void File::GetImageOrientationPatient( float iop[6] ) +bool File::GetImageOrientationPatient( float iop[6] ) { std::string strImOriPat; //iop is supposed to be float[6] @@ -714,6 +749,7 @@ void File::GetImageOrientationPatient( float iop[6] ) &iop[0], &iop[1], &iop[2], &iop[3], &iop[4], &iop[5]) != 6 ) { gdcmWarningMacro( "Wrong Image Orientation Patient (0020,0037). Less than 6 values were found." ); + return false; } } //For ACR-NEMA @@ -724,8 +760,10 @@ void File::GetImageOrientationPatient( float iop[6] ) &iop[0], &iop[1], &iop[2], &iop[3], &iop[4], &iop[5]) != 6 ) { gdcmWarningMacro( "wrong Image Orientation Patient (0020,0035). Less than 6 values were found." ); + return false; } } + return true; } /** @@ -1277,9 +1315,11 @@ void File::AnonymizeNoLoad() if ( d == NULL) continue; - if ( dynamic_cast(d) - || dynamic_cast(d) ) - continue; + if ( dynamic_cast(d) ) + { + gdcmWarningMacro( "You cannot 'Anonymize a SeqEntry "); + continue; + } offset = d->GetOffset(); lgth = d->GetLength(); @@ -1300,6 +1340,7 @@ void File::AnonymizeNoLoad() /** * \brief anonymize a File (remove Patient's personal info passed with * AddAnonymizeElement() + * \note You cannot Anonymize a BinEntry (to be fixed) */ bool File::AnonymizeFile() { @@ -1338,11 +1379,19 @@ bool File::AnonymizeFile() if ( d == NULL) continue; - if ( dynamic_cast(d) - || dynamic_cast(d) ) + if ( dynamic_cast(d) ) + { + gdcmWarningMacro( "You cannot 'Anonymize' a SeqEntry "); continue; + } - SetValEntry ((*it).Value, (*it).Group, (*it).Elem); + if ( dynamic_cast(d) ) + { + gdcmWarningMacro( "To 'Anonymize' a BinEntry, better use AnonymizeNoLoad (FIXME) "); + continue; + } + else + SetValEntry ((*it).Value, (*it).Group, (*it).Elem); } } @@ -1702,6 +1751,210 @@ void File::ReadAndSkipEncapsulatedBasicOffsetTable() } } +// These are the deprecated method that one day should be removed (after the next release) + +#ifndef GDCM_LEGACY_REMOVE +/** + * \brief Constructor (DEPRECATED : temporaryly kept not to break the API) + * @param filename name of the file whose header we want to analyze + * @deprecated do not use any longer + */ +File::File( std::string const &filename ) + :Document( ) +{ + RLEInfo = new RLEFramesInfo; + JPEGInfo = new JPEGFragmentsInfo; + + SetFileName( filename ); + Load( ); // gdcm::Document is first Loaded, then the 'File part' +} + +/** + * \brief Loader. (DEPRECATED : temporaryly kept not to break the API) + * @param fileName file to be open for parsing + * @return false if file cannot be open or no swap info was found, + * or no tag was found. + * @deprecated Use the Load() [ + SetLoadMode() ] + SetFileName() functions instead + */ +bool File::Load( std::string const &fileName ) +{ + GDCM_LEGACY_REPLACED_BODY(File::Load(std::string), "1.2", + File::Load()); + SetFileName( fileName ); + if ( ! this->Document::Load( ) ) + return false; + + return DoTheLoadingJob( ); +} +#endif + +// ----------------------------------------------------------------------------------------- +// THERALYS Algorithm to determine the most similar basic orientation +// +// Transliterated from original Python code. +// Kept as close as possible to the original code +// in order to speed up any further modif of Python code :-( +// ------------------------------------------------------------------------------------------ + +/** + * \brief THERALYS' Algorithm to determine the most similar basic orientation + * (Axial, Coronal, Sagital) of the image + * \note Should be run on the first gdcm::File of a 'coherent' Serie + * @return orientation code + * @return orientation code + * # 0 : Not Applicable (neither 0020,0037 Image Orientation Patient + * # nor 0020,0032Image Position found ) + * # 1 : Axial + * # -1 : Axial invert + * # 2 : Coronal + * # -2 : Coronal invert + * # 3 : Sagital + * # -3 : Sagital invert + * # 4 : Heart Axial + * # -4 : Heart Axial invert + * # 5 : Heart Coronal + * # -5 : Heart Coronal invert + * # 6 : Heart Sagital + * # -6 : Heart Sagital invert + */ +double File::TypeOrientation( ) +{ + float iop[6]; + bool succ = GetImageOrientationPatient( iop ); + if ( !succ ) + { + return 0.; + } + + vector3D ori1; + vector3D ori2; + + ori1.x = iop[0]; ori1.y = iop[1]; ori1.z = iop[2]; + ori1.x = iop[3]; ori2.y = iop[4]; ori2.z = iop[5]; + + // two perpendicular vectors describe one plane + double dicPlane[6][2][3] = + { { {1, 0, 0 },{0, 1, 0 } }, // Axial + { {1, 0, 0 },{0, 0, -1 } }, // Coronal + { {0, 1, 0 },{0, 0, -1 } }, // Sagittal + { { 0.8, 0.5, 0.0 },{-0.1, 0.1 , -0.95 } }, // Axial - HEART + { { 0.8, 0.5, 0.0 },{-0.6674, 0.687, 0.1794} }, // Coronal - HEART + { {-0.1, 0.1, -0.95},{-0.6674, 0.687, 0.1794} } // Sagittal - HEART + }; + + vector3D refA; + vector3D refB; + int i = 0; + Res res; // [ , ] + res.first = 0; + res.second = 99999; + for (int numDicPlane=0; numDicPlane<6; numDicPlane++) + { + ++i; + // refA=plane[0] + refA.x = dicPlane[numDicPlane][0][0]; + refA.y = dicPlane[numDicPlane][0][1]; + refA.z = dicPlane[numDicPlane][0][2]; + // refB=plane[1] + refB.x = dicPlane[numDicPlane][1][0]; + refB.y = dicPlane[numDicPlane][1][1]; + refB.z = dicPlane[numDicPlane][1][2]; + res=VerfCriterion( i, CalculLikelyhood2Vec(refA,refB,ori1,ori2), res ); + res=VerfCriterion( -i, CalculLikelyhood2Vec(refB,refA,ori1,ori2), res ); + } + return res.first; +/* +// i=0 +// res=[0,99999] ## [ , ] +// for plane in dicPlane: +// i=i+1 +// refA=plane[0] +// refB=plane[1] +// res=self.VerfCriterion( i , self.CalculLikelyhood2Vec(refA,refB,ori1,ori2) , res ) +// res=self.VerfCriterion( -i , self.CalculLikelyhood2Vec(refB,refA,ori1,ori2) , res ) +// return res[0] +*/ + +} + +Res +File::VerfCriterion(int typeCriterion, double criterionNew, Res const & in) +{ + Res res; + double criterion = in.second; + if (criterionNew < criterion) + { + res.first = criterionNew; + res.second = typeCriterion; + } +/* +// type = res[0] +// criterion = res[1] +// # if criterionNew<0.1 and criterionNew : - type : vector 3D (double) +//- : - type : vector 3D (double) +// - Description of the first plane +//- : - type : vector 3D (double) +//- : - type : vector 3D (double) +// - Description of the second plane +//------------------------- Return : ------------------------------------ +// double : 0 if the planes are perpendicular. While the difference of +// the orientation between the planes are big more enlarge is +// the criterion. +//------------------------- Other : ------------------------------------- +// The calculus is based with vectors normalice +double +File::CalculLikelyhood2Vec(vector3D const & refA, vector3D const & refB, + vector3D const & ori1, vector3D const & ori2 ) +{ + + vector3D ori3 = ProductVectorial(ori1,ori2); + vector3D refC = ProductVectorial(refA,refB); + double res = square_dist(refC, ori3); + + return sqrt(res); +} + +//------------------------- Purpose : ----------------------------------- +//- Calculus of the poduct vectorial between two vectors 3D +//------------------------- Parameters : -------------------------------- +//- : - type : vector 3D (double) +//- : - type : vector 3D (double) +//------------------------- Return : ------------------------------------ +// (vec) : - Vector 3D +//------------------------- Other : ------------------------------------- +vector3D +File::ProductVectorial(vector3D const & vec1, vector3D const & vec2) +{ + vector3D vec3; + vec3.x = vec1.y*vec2.z - vec1.z*vec2.y; + vec3.y = -( vec1.x*vec2.z - vec1.z*vec2.x); + vec3.z = vec1.x*vec2.y - vec1.y*vec2.x; + + return vec3; +} + //----------------------------------------------------------------------------- // Print