X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmOrientation.cxx;h=26f70d7abaee8d8d7dc05157b155549276ea2541;hb=ab9b96bb7b0c77c1beaee820985debe75f04b831;hp=6632d4c80b968ec2205592b9293f3c88a60d1187;hpb=69d2c65c131c9752b1d64aa9b21de29c3acfe62d;p=gdcm.git diff --git a/src/gdcmOrientation.cxx b/src/gdcmOrientation.cxx index 6632d4c8..26f70d7a 100644 --- a/src/gdcmOrientation.cxx +++ b/src/gdcmOrientation.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmOrientation.cxx,v $ Language: C++ - Date: $Date: 2005/07/24 02:34:42 $ - Version: $Revision: 1.1 $ + Date: $Date: 2005/09/21 16:39:53 $ + Version: $Revision: 1.11 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -18,6 +18,8 @@ #include "gdcmOrientation.h" #include "gdcmFile.h" +#include "gdcmDebug.h" +#include // for sqrt namespace gdcm { @@ -34,21 +36,20 @@ namespace gdcm * (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 + * # 0 : Not Applicable (neither 0020,0037 Image Orientation Patient + * # nor 0020,0032 Image 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 Orientation::TypeOrientation( File *f ) { @@ -56,23 +57,29 @@ double Orientation::TypeOrientation( File *f ) bool succ = f->GetImageOrientationPatient( iop ); if ( !succ ) { - return 0.; + gdcmErrorMacro( "No Image Orientation (0020,0037) found in the file, cannot proceed." ) + return 0; } - +/* +std::cout << " iop : "; +for(int i=0;i<6;i++) + std::cout << iop[i] << " "; +std::cout << std::endl; +*/ 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]; + ori2.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 + { { { 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; @@ -81,6 +88,10 @@ double Orientation::TypeOrientation( File *f ) Res res; // [ , ] res.first = 0; res.second = 99999; + + std::cout << "-------------- res : " << res.first << "|" << res.second + << std::endl; + for (int numDicPlane=0; numDicPlane<6; numDicPlane++) { ++i; @@ -93,32 +104,36 @@ double Orientation::TypeOrientation( File *f ) refB.y = dicPlane[numDicPlane][1][1]; refB.z = dicPlane[numDicPlane][1][2]; res=VerfCriterion( i, CalculLikelyhood2Vec(refA,refB,ori1,ori2), res ); + std::cout << "-------------- res : " << res.first << "|" << res.second + << std::endl; res=VerfCriterion( -i, CalculLikelyhood2Vec(refB,refA,ori1,ori2), res ); + std::cout << "-------------- res : " << res.first << "|" << res.second + << std::endl; } 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] +// 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 -Orientation::VerfCriterion(int typeCriterion, double criterionNew, Res const & in) +Orientation::VerfCriterion(int typeCriterion, double criterionNew, Res const &in) { Res res; +// double type = in.first; double criterion = in.second; - if (criterionNew < criterion) + if (/*criterionNew < 0.1 && */criterionNew < criterion) { - res.first = criterionNew; - res.second = typeCriterion; + res.first = typeCriterion; + res.second = criterionNew; } /* // type = res[0] @@ -132,7 +147,7 @@ Orientation::VerfCriterion(int typeCriterion, double criterionNew, Res const & i return res; } -inline double square_dist(vector3D const &v1, vector3D const & v2) +inline double square_dist(vector3D const &v1, vector3D const &v2) { double res; res = (v1.x - v2.x)*(v1.x - v2.x) + @@ -158,8 +173,8 @@ inline double square_dist(vector3D const &v1, vector3D const & v2) //------------------------- Other : ------------------------------------- // The calculus is based with vectors normalice double -Orientation::CalculLikelyhood2Vec(vector3D const & refA, vector3D const & refB, - vector3D const & ori1, vector3D const & ori2 ) +Orientation::CalculLikelyhood2Vec(vector3D const &refA, vector3D const &refB, + vector3D const &ori1, vector3D const &ori2 ) { vector3D ori3 = ProductVectorial(ori1,ori2); @@ -178,7 +193,7 @@ Orientation::CalculLikelyhood2Vec(vector3D const & refA, vector3D const & refB, // (vec) : - Vector 3D //------------------------- Other : ------------------------------------- vector3D -Orientation::ProductVectorial(vector3D const & vec1, vector3D const & vec2) +Orientation::ProductVectorial(vector3D const &vec1, vector3D const &vec2) { vector3D vec3; vec3.x = vec1.y*vec2.z - vec1.z*vec2.y; @@ -188,5 +203,279 @@ Orientation::ProductVectorial(vector3D const & vec1, vector3D const & vec2) return vec3; } -} // end namespace gdcm + +// --------------------------------------------------------------------------- +// Here is the original Python code, kindly supplied by THERALYS +// +// C++ code doesn't give good results +// --> FIXME + +/* + +def TypeOrientation(self,file0): +""" +# ------------------------- Purpose : ----------------------------------- +# - This function compare the orientation of the given image and the +# basics orientations (Axial, Cornal, Sagital) +# ------------------------- Parameters : -------------------------------- +# - : - type : string +# - The name of the first image file of the serie +# ------------------------- Return : ------------------------------------ +# 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 +# + # ------------------------- Other : ------------------------------------- +# This method finds the most similar basic orientation. +""" +try: + toRead = gdcm.File(file0) + ValDict = GetValuesDict(toRead) + try: + imageOrientation=ValDict["Image Orientation (Patient)"] + except KeyError: + imageOrientation=ValDict["Image Orientation"] + + ori1=[float(split(imageOrientation,"\\")[0]),\ + float(split(imageOrientation,"\\")[1]),\ + float(split(imageOrientation,"\\")[2])] + ori2=[float(split(imageOrientation,"\\")[3]),\ + float(split(imageOrientation,"\\")[4]),\ + float(split(imageOrientation,"\\")[5])] + +## two vectors perpendicular describe one plane + dicPlane=[ [ [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 + + 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] + + except KeyError: + return 0 + + + def VerfCriterion(self,typeCriterion,criterionNew,res): + type = res[0] + criterion = res[1] +# if criterionNew<0.1 and criterionNew : - type : vector 3D (float) + # - : - type : vector 3D (float) + # - Description of the first plane + # - : - type : vector 3D (float) + # - : - type : vector 3D (float) + # - Description of the second plane + # ------------------------- Return : ------------------------------------ + # float : 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 + """ + + ori3=self.ProductVectorial(ori1,ori2) + refC=self.ProductVectorial(refA,refB) + res=math.pow(refC[0]-ori3[0],2) + math.pow(refC[1]-ori3[1],2) + math.pow(refC[2]-ori3[2],2) + return math.sqrt(res) + + def ProductVectorial(self,vec1,vec2): + """ + # ------------------------- Purpose : ----------------------------------- + # - Calculus of the poduct vectorial between two vectors 3D + # ------------------------- Parameters : -------------------------------- + # - : - type : vector 3D (float) + # - : - type : vector 3D (float) + # ------------------------- Return : ------------------------------------ + # (vec) : - Vector 3D + # ------------------------- Other : ------------------------------------- + """ + vec3=[0,0,0] + vec3[0]=vec1[1]*vec2[2] - vec1[2]*vec2[1] + vec3[1]=-( vec1[0]*vec2[2] - vec1[2]*vec2[0]) + vec3[2]=vec1[0]*vec2[1] - vec1[1]*vec2[0] + return vec3 + + def GetValuesDict(image): + """ + Returns a dictionnary containing values associated with Field Names + dict["Dicom Field Name"]="Dicom field value" + """ + val=image.GetFirstEntry() + dic={} + while(val): + if isinstance(val,gdcm.ValEntryPtr): + dic[val.GetName()]=val.GetValue() + val=image.GetNextEntry() + return dic + +*/ + + +// ------------------------------------------------------------------------ +/* +2.2.2 Orientation of DICOM images + + +http://www.dclunie.com/medical-image-faq/html/part2.html#DICOMOrientation +says : + +A question that is frequently asked in comp.protocols.dicom is how to determine + which side of an image is which (e.g. left, right) and so on. + The short answer is that for projection radiographs this is specified + explicitly using the Patient Orientation attribute, and for cross-sectional + images it needs to be derived from the Image Orientation (Patient) direction + cosines. In the standard these are explained as follows: + + * "C.7.6.1.1.1 Patient Orientation. + The Patient Orientation (0020,0020) relative to the image + plane shall be specified by two values that designate the + anatomical direction of the positive row axis (left to right) + and the positive column axis (top to bottom). + The first entry is the direction of the rows, given by the + direction of the last pixel in the first row from the first + pixel in that row. + The second entry is the direction of the columns, given by + the direction of the last pixel in the first column from the + first pixel in that column. + Anatomical direction shall be designated by the capital + letters: A (anterior), P (posterior), R (right),L (left), + H (head), F (foot). + Each value of the orientation attribute shall contain at + least one of these characters. + If refinements in the orientation descriptions are to be + specified, then they shall be designated by one or two + additional letters in each value. + Within each value, the letters shall be ordered with the + principal orientation designated in the first character." + + * "C.7.6.2.1.1 Image Position And Image Orientation. + The Image Position (0020,0032) specifies the x, y, and z + coordinates of the upper left hand corner of the image; + it is the center of the first voxel transmitted. + Image Orientation (0020,0037) specifies the direction + cosines of the first row and the first column with respect to + the patient. These Attributes shall be provided as a pair. + Row value for the x, y, and z axes respectively followed by + the Column value for the x, y, and z axes respectively. + The direction of the axes is defined fully by the patient's + orientation. + The x-axis is increasing to the left hand sid of the patient. + The y-axis is increasing to the posterior side of the patient + The z-axis is increasing toward the head of the patient. + The patient based coordinate system is a right handed system, + i.e. the vector cross product of a unit vector along the + positive x-axis and a unit vector along the positive y-axis + is equal to a unit vector along the positive z-axis." + +Some simple code to take one of the direction cosines (vectors) from the +Image Orientation (Patient) attribute and generate strings equivalent to one +of the values of Patient Orientation looks like this (noting that if the vector +is not aligned exactly with one of the major axes, the resulting string will +have multiple letters in as described under "refinements" in C.7.6.1.1.1): + +*/ + +/** + * \brief computes the Patient Orientation relative to the image plane + * from the 'Image Orientation (Patient)' + * The first entry is the direction of the rows, given by the + * direction of the last pixel in the first row from the first + * pixel in that row. + * The second entry is the direction of the columns, given by + * the direction of the last pixel in the first column from the + * first pixel in that column. + * Anatomical direction is designated by the capital + * letters: A (anterior), P (posterior), R (right),L (left), + * H (head), F (foot). + * Refinements in the orientation descriptions are designated + * by one or two additional letters in each value. + * @return orientation string as "rawOrientation\columnsOrientation" + */ +std::string Orientation::GetOrientation ( File *f ) +{ + float iop[6]; + if ( !f->GetImageOrientationPatient( iop ) ) + return GDCM_UNFOUND; + + std::string orientation; + orientation = GetSingleOrientation ( iop ) + + "\\" + + GetSingleOrientation ( iop + 3 ); + return orientation; +} + + +std::string Orientation::GetSingleOrientation ( float *iop) +{ + std::string orientation; + + char orientationX = iop[0] < 0 ? 'R' : 'L'; + char orientationY = iop[1] < 0 ? 'A' : 'P'; + char orientationZ = iop[2] < 0 ? 'F' : 'H'; + + double absX = iop[0]; + if (absX < 0) absX = -absX; + double absY = iop[1]; + if (absY < 0) absY = -absY; + double absZ = iop[2]; + if (absZ < 0) absZ = -absZ; + + for (int i=0; i<3; ++i) + { + if (absX>.0001 && absX>absY && absX>absZ) + { + orientation = orientation + orientationX; + absX=0; + } + else if (absY>.0001 && absY>absX && absY>absZ) + { + orientation = orientation + orientationY; + absY=0; + } + else if (absZ>.0001 && absZ>absX && absZ>absY) + { + orientation = orientation + orientationZ; + absZ=0; + } + else + break; + } + return orientation; +} + + + +} // end namespace gdcm