All MJ changes for LR

miscmaths.cc

@@ -7,7 +7,9 @@
 /*  CCOPYRIGHT  */
 
 // Miscellaneous maths functions
-
+#define NOMINMAX
+#include <cstdlib>
+#include <cmath>
 #include "miscmaths.h"
 #include "miscprob.h"
 #include "stdlib.h"
@@ -1083,6 +1085,95 @@ void get_axis_orientations(const Matrix& sform_mat, int sform_code,
     } }
   nifti_mat44_to_orientation(v2mm,&icode,&jcode,&kcode);
 }
+
+ 
+Matrix mat44_to_newmat(mat44 inmat)
+{
+  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;
+}
+ 	 
+ 	 
+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
@@ -1647,7 +1738,6 @@ ReturnMatrix geqt(const Matrix& mat,const float a)
   return res;
 }
 
-
 ReturnMatrix leqt(const Matrix& mat1,const Matrix& mat2) 
 {
   int ctrcol = std::min(mat1.Ncols(),mat2.Ncols());

miscmaths.h

@@ -15,6 +15,7 @@
 #define __miscmaths_h
 
 #include <cmath>
+#include <cstdlib>
 #include <vector>
 #include <iostream>
 #include <assert.h>
@@ -23,7 +24,7 @@
 #include <string>
 #include <iterator>
 #include "fslio/fslio.h"
-
+#include "config.h"
 #include "newmatap.h"
 #include "kernel.h"
 
@@ -43,6 +44,10 @@ namespace MISCMATHS {
   // IO/string stuff
   template <class T> string num2str(T n, int width=-1);
 
+#if defined(_MSC_VER) && (_MSC_VER < 1300)
+  template <class T> string num2str(T n) { return num2str(n -1); }
+#endif
+
   string size(const Matrix& mat);
   bool isnum(const string& str);
   ReturnMatrix read_ascii_matrix(const string& filename, int nrows, int ncols);