Moved orientation function

miscmaths.cc

@@ -1030,98 +1030,28 @@ float rms_deviation(const Matrix& affmat1, const Matrix& affmat2,
 }
 
 
-Matrix mat44_to_newmat(mat44 inmat)
+  // helper function - calls nifti, but with FSL default case
+void get_axis_orientations(const Matrix& sform_mat, int sform_code,
+			   const Matrix& qform_mat, int qform_code,
+			   int& icode, int& jcode, int& kcode)
 {
-  Matrix retmat(4,4);
-  for (int ii=0; ii<4; ii++) {
-    for (int jj=0; jj<4; jj++) {
-      retmat(ii+1,jj+1) = inmat.m[ii][jj];
-    }
-  }
-  return retmat;
-}
-
-
-mat44 newmat_to_mat44(const Matrix& inmat)
-{
-  mat44 retmat;
-  for (int ii=0; ii<4; ii++) {
-    for (int jj=0; jj<4; jj++) {
-      retmat.m[ii][jj] = inmat(ii+1,jj+1);
-    }
-  }
-  return retmat;
+  Matrix vox2mm(4,4);
+  if (sform_code!=NIFTI_XFORM_UNKNOWN) {
+    vox2mm = sform_mat;
+  } else if (qform_code!=NIFTI_XFORM_UNKNOWN) {
+    vox2mm = qform_mat;
+  } else {
+    // ideally should be sampling_mat(), but for orientation it doesn't matter
+    vox2mm = Identity(4);
+    vox2mm(1,1) = -vox2mm(1,1);
+  }
+  mat44 v2mm;
+  for (int ii=0; ii<4; ii++) { for (int jj=0; jj<4; jj++) {
+      v2mm.m[ii][jj] = vox2mm(ii+1,jj+1);
+    } }
+  mat44_to_orientation(v2mm,&icode,&jcode,&kcode);
 }
-
-
-int FslGetLeftRightOrder(int sform_code, const Matrix& sform_mat, 
-			 int qform_code, const Matrix& qform_mat)
-{
-  int retval;
-  // call the function within fslio
-  retval = FslGetLeftRightOrder2(sform_code,newmat_to_mat44(sform_mat),
-				 qform_code,newmat_to_mat44(qform_mat));
-  return retval;
-}
-
-short FslGetVox2mmMatrix(Matrix& vox2mm, 
-			 int sform_code, const Matrix& sform_mat, 
-			 int qform_code, const Matrix& qform_mat, 
-			 float dx, float dy, float dz)
-{
-  int retval;
-  mat44 vox2mm44;
-  // call the function within fslio
-  retval = FslGetVox2mmMatrix2(&vox2mm44,sform_code,newmat_to_mat44(sform_mat),
-			       qform_code,newmat_to_mat44(qform_mat),
-			       dx,dy,dz);
-  vox2mm = mat44_to_newmat(vox2mm44);
-  return retval;
-}
-
-
-
-Matrix Vox2FlirtCoord(int sform_code, const Matrix& sform_mat, 
-		      int qform_code, const Matrix& qform_mat, 
-		      float dx, float dy, float dz,
-		      int nx, int ny, int nz) 
-{
-  Matrix v2f(4,4);
-  Identity(v2f);
-  v2f(1,1)=dx;  v2f(2,2)=dy;  v2f(3,3)=dz;
-  if (FslGetLeftRightOrder(sform_code,sform_mat,qform_code,qform_mat)
-      == FSL_NEUROLOGICAL) {
-    Matrix swapx(4,4);
-    Identity(swapx);
-    swapx(1,1)=-1;
-    swapx(1,4)=nx-1;
-    v2f = v2f * swapx;
-  }
-  return v2f;
-}
-
-
-Matrix FslGetVox2VoxMatrix(const Matrix& flirt_in2ref,
-			   int sform_code_in, const Matrix& sform_mat_in, 
-			   int qform_code_in, const Matrix& qform_mat_in, 
-			   float dx_in, float dy_in, float dz_in,
-			   int nx_in, int ny_in, int nz_in,
-			   int sform_code_ref, const Matrix& sform_mat_ref, 
-			   int qform_code_ref, const Matrix& qform_mat_ref, 
-			   float dx_ref, float dy_ref, float dz_ref,
-			   int nx_ref, int ny_ref, int nz_ref)
-{
-  Matrix vox2flirt_in, vox2flirt_ref, vox2vox;
-  vox2flirt_in = Vox2FlirtCoord(sform_code_in,sform_mat_in,qform_code_in,
-				  qform_mat_in,dx_in,dy_in,dz_in,
-				  nx_in,ny_in,nz_in);
-  vox2flirt_ref = Vox2FlirtCoord(sform_code_ref,sform_mat_ref,qform_code_ref,
-				  qform_mat_ref,dx_ref,dy_ref,dz_ref,
-				  nx_ref,ny_ref,nz_ref);
-  vox2vox = vox2flirt_ref.i() * flirt_in2ref * vox2flirt_in;
-  return vox2vox;
-}
-
+  
 
 // Added by MWW
 

miscmaths.h

@@ -24,10 +24,11 @@
 #include <string>
 #include <iterator>
 
+#include "fslio/fslio.h"
+
 #include "config.h"
 #include "newmatap.h"
 #include "kernel.h"
-#include "fslio/fslio.h"
 
 //#pragma interface
 
@@ -157,27 +158,11 @@ namespace MISCMATHS {
 		      const ColumnVector& centre, const float rmax); 
   float rms_deviation(const Matrix& affmat1, const Matrix& affmat2, 
 		      const float rmax=80.0); 
-  // the following give left-right order and voxel2mm coordinate conversions
-  //  consistent with FSLView behaviour (NB: you cannot tell left-right from
-  //  the vox2mm matrix!)
-  int FslGetLeftRightOrder(int sform_code, const Matrix& sform_mat, 
-			   int qform_code, const Matrix& qform_mat);
-  short FslGetVox2mmMatrix(Matrix& vox2mm,
-			   int sform_code, const Matrix& sform_mat, 
-			   int qform_code, const Matrix& qform_mat, 
-			   float dx, float dy, float dz);
-  Matrix FslGetVox2VoxMatrix(const Matrix& flirt_in2ref,
-			     int sform_code_in, const Matrix& sform_mat_in, 
-			     int qform_code_in, const Matrix& qform_mat_in, 
-			     float dx_in, float dy_in, float dz_in,
-			     int nx_in, int ny_in, int nz_in,
-			     int sform_code_ref, const Matrix& sform_mat_ref, 
-			     int qform_code_ref, const Matrix& qform_mat_ref, 
-			     float dx_ref, float dy_ref, float dz_ref,
-			     int nx_ref, int ny_ref, int nz_ref);
-  mat44 newmat_to_mat44(const Matrix& inmat);
-  Matrix mat44_to_newmat(mat44 inmat);
 
+  void get_axis_orientations(const Matrix& sform_mat, int sform_code,
+			     const Matrix& qform_mat, int qform_code,
+			     int& icode, int& jcode, int& kcode);
+    
   float median(const ColumnVector& x);
   
   void cart2sph(const ColumnVector& dir, float& th, float& ph);// cartesian to sperical polar coordinates