Program: gdcm
Module: $RCSfile: gdcmOrientation.cxx,v $
Language: C++
- Date: $Date: 2005/09/21 16:39:53 $
- Version: $Revision: 1.11 $
+ 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
#include "gdcmDebug.h"
#include <math.h> // for sqrt
-namespace gdcm
+namespace GDCM_NAME_SPACE
{
//--------------------------------------------------------------------
// THERALYS Algorithm to determine the most similar basic orientation
/**
* \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
* # -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;
}
-/*
-std::cout << " iop : ";
-for(int i=0;i<6;i++)
- std::cout << iop[i] << " ";
-std::cout << std::endl;
-*/
vector3D ori1;
vector3D ori2;
res.first = 0;
res.second = 99999;
- std::cout << "-------------- res : " << res.first << "|" << res.second
- << std::endl;
-
for (int numDicPlane=0; numDicPlane<6; numDicPlane++)
{
++i;
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] ## [ <result> , <memory of the last succes calculus> ]
-// 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<criterion:
-// if criterionNew<criterion:
-// criterion=criterionNew
-// type=typeCriterion
-// return [ type , criterion ]
-*/
+ res.first = type;
+ res.second = criterion;
return res;
}
}
-
-// ---------------------------------------------------------------------------
-// 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 : --------------------------------
-# - <file0> : - 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] ## [ <result> , <memory of the last succes calcule> ]
- 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<criterion:
- if criterionNew<criterion:
- criterion=criterionNew
- type=typeCriterion
- return [ type , criterion ]
-
-
- def CalculLikelyhood2Vec(self,refA,refB,ori1,ori2):
-"""
- # ------------------------- Purpose : -----------------------------------
- # - This function determine the orientation similarity of two planes.
- # Each plane is described by two vector.
- # ------------------------- Parameters : --------------------------------
- # - <refA> : - type : vector 3D (float)
- # - <refB> : - type : vector 3D (float)
- # - Description of the first plane
- # - <ori1> : - type : vector 3D (float)
- # - <ori2> : - 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 : --------------------------------
- # - <vec1> : - type : vector 3D (float)
- # - <vec2> : - 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
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
+ 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
+ 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).
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;
+ The "Image Position (Patient)" (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.
+ The "Image Orientation (Patient)" (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 x-axis is increasing to the left hand side 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
*/
/**
- * \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
- * by one or two additional letters in each value.
- * @return orientation string as "rawOrientation\columnsOrientation"
+ * - 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 "rowsOrientation\columnsOrientation"
*/
std::string Orientation::GetOrientation ( File *f )
{
}
+/*-------------------------------------------------------------------
+
+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
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff