X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmOrientation.cxx;h=be0aa685aecd79771d2ed351de32d0a691abea9e;hb=fc4f7706c78baf3f60474c06d871b82db221f37b;hp=0516519d885638868f80357e8bf83a5bb05bc557;hpb=725f1d9140fdf297e70125c094601963f635d40a;p=gdcm.git diff --git a/src/gdcmOrientation.cxx b/src/gdcmOrientation.cxx index 0516519d..be0aa685 100644 --- a/src/gdcmOrientation.cxx +++ b/src/gdcmOrientation.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmOrientation.cxx,v $ Language: C++ - Date: $Date: 2005/09/16 16:47:56 $ - Version: $Revision: 1.7 $ + Date: $Date: 2008/08/18 12:27:10 $ + Version: $Revision: 1.27 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -21,7 +21,7 @@ #include "gdcmDebug.h" #include // for sqrt -namespace gdcm +namespace GDCM_NAME_SPACE { //-------------------------------------------------------------------- // THERALYS Algorithm to determine the most similar basic orientation @@ -33,7 +33,7 @@ namespace gdcm /** * \brief THERALYS' Algorithm to determine the most similar basic orientation - * (Axial, Coronal, Sagital) of the image + * (Axial, Coronal, Sagittal) of the image * \note Should be run on the first gdcm::File of a 'coherent' Serie * @return orientation code * # 0 : Not Applicable (neither 0020,0037 Image Orientation Patient @@ -42,25 +42,55 @@ namespace gdcm * # -1 : Axial invert * # 2 : Coronal * # -2 : Coronal invert - * # 3 : Sagital - * # -3 : Sagital invert + * # 3 : Sagittal + * # -3 : Sagittal invert * # 4 : Heart Axial * # -4 : Heart Axial invert * # 5 : Heart Coronal * # -5 : Heart Coronal invert - * # 6 : Heart Sagital - * # -6 : Heart Sagital invert + * # 6 : Heart Sagittal + * # -6 : Heart Sagittal invert */ -double Orientation::TypeOrientation( File *f ) + +static const char *OrientationTypeStrings[] = { + "Not Applicable", + "Axial", + "Coronal", + "Sagittal", + "Heart Axial", + "Heart Coronal", + "Heart Sagittal", + "Axial invert", + "Coronal invert", + "Sagittal invert", + "Heart Axial invert", + "Heart Coronal invert", + "Heart Sagittal invert", + NULL +}; + +/// \brief returns human readable interpretation of the most +/// similar basic orientation (Axial, Coronal, Sagittal, ...) of the image +const char* Orientation::GetOrientationTypeString(OrientationType const o) +{ + int k = (int)o; + if (k < 0) + k = -k + 6; + + return OrientationTypeStrings[k]; +} + +/// \brief returns of the most similar basic orientation +/// (Axial, Coronal, Sagittal, ...) of the image +OrientationType Orientation::GetOrientationType( File *f ) { float iop[6]; bool succ = f->GetImageOrientationPatient( iop ); if ( !succ ) { - gdcmErrorMacro( "No Image Orientation (0020,0037) found in the file, cannot proceed." ) - return 0; + gdcmWarningMacro( "No Image Orientation (0020,0037)/(0020,0032) found in the file, cannot proceed." ) + return NotApplicable; } - vector3D ori1; vector3D ori2; @@ -69,9 +99,9 @@ double Orientation::TypeOrientation( File *f ) // 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 + { { { 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 @@ -83,6 +113,7 @@ double Orientation::TypeOrientation( File *f ) Res res; // [ , ] res.first = 0; res.second = 99999; + for (int numDicPlane=0; numDicPlane<6; numDicPlane++) { ++i; @@ -97,39 +128,26 @@ double Orientation::TypeOrientation( File *f ) 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 thought looks like is a float value, but is indeed an int + // try casting it to int first then enum value to please VS7: + int int_res = (int)res.first; + gdcmAssertMacro( int_res <= 6 && int_res >= -6); + return (OrientationType)int_res; } Res 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; + type = typeCriterion; + criterion = criterionNew; } -/* -// type = res[0] -// criterion = res[1] -// # if criterionNew<0.1 and criterionNewGetImageOrientationPatient( iop ) ) + return GDCM_UNFOUND; + + std::string orientation; + orientation = GetSingleOrientation ( iop ) + + "\\" + + GetSingleOrientation ( iop + 3 ); + return orientation; +} -// --------------------------------------------------------------------------- -// Here is the original code, in Python, kindly supllied by THERALYS -// -// C++ code doesn't give good results -// --> FIXME -/* +std::string Orientation::GetSingleOrientation ( float *iop) +{ + std::string orientation; -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 + 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; +} + + +/*------------------------------------------------------------------- + +Some more stuff, from XMedcon + +---> Personal remark from JPRx : +--> patient_position (0x0018,0x5100) can be "HFS ", "FFS ", "HFP ", "FFP " +--> or, not so common, +// HFDR = Head First-Decubitus Right +// HFDL = Head First-Decubitus Left +// FFDR = Feet First-Decubitus Right +// FFDL = Feet First-Decubitus Left +--> the cosines may have any value -1.< <+1., for MR images ! + +enum patient_slice_orientation_type + { + patient_slice_orientation_unknown = 0, + supine_headfirst_transaxial, + supine_headfirst_sagittal, + supine_headfirst_coronal, + supine_feetfirst_transaxial, + supine_feetfirst_sagittal, + supine_feetfirst_coronal, + prone_headfirst_transaxial, + prone_headfirst_sagittal, + prone_headfirst_coronal, + prone_feetfirst_transaxial, + prone_feetfirst_sagittal, + prone_feetfirst_coronal + }; + +void GetImageOrientationPatient(gdcm::File &h,F32 image_orientation_patient[6]) +{ + h.GetImageOrientationPatient(image_orientation_patient); +} + +#if 0 +// +// this is all completely cribbed from the xmedcon library, since +// we're trying to do what it does, mostly. +patient_slice_orientation_type +GetPatSliceOrient(gdcm::File &h) +{ + F32 image_orientation_patient[6]; + + // protected, do it the hard way + // h.GetImageOrientationPatient(image_orientation_patient); + GetImageOrientationPatient(h,image_orientation_patient); + + enum { headfirst, feetfirst } patient_orientation; + enum { supine, prone } patient_rotation; + enum { transaxial, sagittal, coronal } slice_orientation; + + std::string patient_position = h.GetEntryByNumber(0x0018,0x5100); + if(patient_position == GDCM_UNFOUND) + { + patient_position = "HF"; + } + if(patient_position.find("HF") != std::string::npos) + { + patient_orientation = headfirst; + } + else if(patient_position.find("FF") != std::string::npos) + { + patient_orientation = feetfirst; + } + + if(patient_position.find("S") != std::string::npos) + { + patient_rotation = supine; + } + else if(patient_position.find("P") != std::string::npos) + { + patient_rotation = prone; + } + + if((image_orientation_patient[0] == 1 || image_orientation_patient[0] == -1) && + (image_orientation_patient[4] == +1 || image_orientation_patient[4] == -1)) + { + slice_orientation = transaxial; + } + else if((image_orientation_patient[1] == 1 || image_orientation_patient[1] == -1) && + (image_orientation_patient[5] == +1 || image_orientation_patient[5] == -1)) + { + slice_orientation = sagittal; + } + else if((image_orientation_patient[0] == 1 || image_orientation_patient[0] == -1) && + (image_orientation_patient[5] == +1 || image_orientation_patient[5] == -1)) + { + slice_orientation = coronal; + } + // + // combine results + patient_slice_orientation_type patient_slice_orientation = + patient_slice_orientation_unknown; + switch (patient_rotation) + { + case supine: + switch (patient_orientation) + { + case headfirst: + switch (slice_orientation) + { + case transaxial: + patient_slice_orientation = supine_headfirst_transaxial; + break; + case sagittal: + patient_slice_orientation = supine_headfirst_sagittal; + break; + case coronal: + patient_slice_orientation = supine_headfirst_coronal; + break; + } + break; + case feetfirst: + switch (slice_orientation) + { + case transaxial: + patient_slice_orientation = supine_feetfirst_transaxial; + break; + case sagittal: + patient_slice_orientation = supine_feetfirst_sagittal; + break; + case coronal: + patient_slice_orientation = supine_feetfirst_coronal; + break; + } + break; + } + break; + case prone: + switch (patient_orientation) + { + case headfirst: + switch (slice_orientation) + { + case transaxial: + patient_slice_orientation = prone_headfirst_transaxial; + break; + case sagittal: + patient_slice_orientation = prone_headfirst_sagittal; + break; + case coronal: + patient_slice_orientation = prone_headfirst_coronal; + break; + } + break; + case feetfirst: + switch (slice_orientation) + { + case transaxial: + patient_slice_orientation = prone_feetfirst_transaxial; + break; + case sagittal: + patient_slice_orientation = prone_feetfirst_sagittal; + break; + case coronal: + patient_slice_orientation = prone_feetfirst_coronal; + break; + } + break; + } + break; + } + if(patient_slice_orientation != patient_slice_orientation_unknown) + return patient_slice_orientation; + // + // this is what xmedcon does + if ((image_orientation_patient[0] == +1) && + (image_orientation_patient[4] == +1)) + patient_slice_orientation = supine_headfirst_transaxial; + else if ((image_orientation_patient[0] == -1) && + (image_orientation_patient[4] == +1)) + patient_slice_orientation = supine_feetfirst_transaxial; + else if ((image_orientation_patient[0] == -1) && + (image_orientation_patient[4] == -1)) + patient_slice_orientation = prone_headfirst_transaxial; + else if ((image_orientation_patient[0] == +1) && + (image_orientation_patient[4] == -1)) + patient_slice_orientation = prone_feetfirst_transaxial; + + else if ((image_orientation_patient[1] == +1) && + (image_orientation_patient[5] == -1)) + patient_slice_orientation = supine_headfirst_sagittal; + else if ((image_orientation_patient[1] == +1) && + (image_orientation_patient[5] == +1)) + patient_slice_orientation = supine_feetfirst_sagittal; + else if ((image_orientation_patient[1] == -1) && + (image_orientation_patient[5] == -1)) + patient_slice_orientation = prone_headfirst_sagittal; + else if ((image_orientation_patient[1] == -1) && + (image_orientation_patient[5] == +1)) + patient_slice_orientation = prone_feetfirst_sagittal; + + else if ((image_orientation_patient[0] == +1) && + (image_orientation_patient[5] == -1)) + patient_slice_orientation = supine_headfirst_coronal; + else if ((image_orientation_patient[0] == -1) && + (image_orientation_patient[5] == +1)) + patient_slice_orientation = supine_feetfirst_coronal; + else if ((image_orientation_patient[0] == -1) && + (image_orientation_patient[5] == -1)) + patient_slice_orientation = prone_headfirst_coronal; + else if ((image_orientation_patient[0] == +1) && + (image_orientation_patient[5] == +1)) + patient_slice_orientation = prone_feetfirst_coronal; + return patient_slice_orientation; +} +#else + +-------------------------------------------------------------------------*/ + +} // end namespace gdcm