X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmOrientation.cxx;h=91cf0fe8b3d012c06ee08d4e4ec1f102563d0bdd;hb=df832cf7f90b4ca5aca2f628c1756fb276779fac;hp=2b2773a3c88f174a12e5c8ce70b7af5e0330c596;hpb=798798c424a52ea234a92110a550f6dd4fa80ef4;p=gdcm.git diff --git a/src/gdcmOrientation.cxx b/src/gdcmOrientation.cxx index 2b2773a3..91cf0fe8 100644 --- a/src/gdcmOrientation.cxx +++ b/src/gdcmOrientation.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmOrientation.cxx,v $ Language: C++ - Date: $Date: 2005/09/22 14:41:25 $ - Version: $Revision: 1.12 $ + Date: $Date: 2007/09/17 12:20:00 $ + Version: $Revision: 1.26 $ 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 @@ -51,21 +51,46 @@ namespace gdcm * # 6 : Heart Sagital * # -6 : Heart Sagital invert */ -double Orientation::TypeOrientation( File *f ) + +static const char *OrientationTypeStrings[] = { + "Not Applicable", + "Axial", + "Coronal", + "Sagital", + "Heart Axial", + "Heart Coronal", + "Heart Sagital", + "Axial invert", + "Coronal invert", + "Sagital invert", + "Heart Axial invert", + "Heart Coronal invert", + "Heart Sagital invert", + NULL +}; + +/// \brief returns human readable interpretation of the most +/// similar basic orientation (Axial, Coronal, Sagital, ...) 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, Sagital, ...) 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; } -/* -std::cout << " iop : "; -for(int i=0;i<6;i++) - std::cout << iop[i] << " "; -std::cout << std::endl; -*/ vector3D ori1; vector3D ori2; @@ -89,9 +114,6 @@ std::cout << std::endl; res.first = 0; res.second = 99999; - std::cout << "-------------- res : " << res.first << "|" << res.second - << std::endl; - for (int numDicPlane=0; numDicPlane<6; numDicPlane++) { ++i; @@ -104,46 +126,28 @@ std::cout << std::endl; 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] -*/ + // 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 type = in.first; double criterion = in.second; if (/*criterionNew < 0.1 && */criterionNew < criterion) { - res.first = typeCriterion; - res.second = criterionNew; + type = typeCriterion; + criterion = criterionNew; } -/* -// type = res[0] -// criterion = res[1] -// # if criterionNew<0.1 and criterionNew 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 @@ -410,21 +274,22 @@ 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 + * \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 + * - or from 0020 0035Image Orientation (RET) - + * - 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 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 + * - Refinements in the orientation descriptions are designated * by one or two additional letters in each value. * Use it when "Patient Orientation" (0020,0020) is not found - * @return orientation string as "rawOrientation\columnsOrientation" + * @return orientation string as "rowsOrientation\columnsOrientation" */ std::string Orientation::GetOrientation ( File *f ) { @@ -479,5 +344,215 @@ std::string Orientation::GetSingleOrientation ( float *iop) } +/*------------------------------------------------------------------- + +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