Minor tweaks to DWI metadata handling changes

core/axes.cpp

@@ -25,7 +25,7 @@ namespace MR
 
     Shuffle get_shuffle_to_make_RAS(const transform_type &T) {
       Shuffle result;
-      result.permutations = closest(T.matrix().topLeftCorner<3, 3>());
+      result.permutations = closest(T.linear());
       // Figure out whether any of the rows of the transform point in the
       //   opposite direction to the MRtrix convention
       result.flips[result.permutations[0]] = T(0, result.permutations[0]) < 0.0;
@@ -37,7 +37,7 @@ namespace MR
 
 
     permutations_type closest(const Eigen::Matrix3d &M) {
-      permutations_type result{3, 3, 3};
+      permutations_type result{-1, -1, -1};
 
       // Find which row of the transform is closest to each scanner axis
       Eigen::Matrix3d::Index index(0);
@@ -67,6 +67,7 @@ namespace MR
       if (result[1] == result[2])
         result[2] = not_any_of (result[0], result[1]);
       assert (result[0] != result[1] && result[1] != result[2] && result[2] != result[0]);
+      assert (std::min(result.begin(), result.end()) == 0);
 
       return result;
     }

core/header.cpp

@@ -21,6 +21,7 @@
 
 #include "app.h"
 #include "axes.h"
+#include "math/math.h"
 #include "mrtrix.h"
 #include "metadata/phase_encoding.h"
 #include "metadata/slice_encoding.h"
@@ -811,11 +812,4 @@ namespace MR
 
 
 
-  Header::Realignment::Realignment() {
-    applied_transform_.matrix().fill(0);
-    orig_transform_.matrix().fill(std::numeric_limits<default_type>::signaling_NaN());
-  }
-
-
-
 }

core/header.h

@@ -213,7 +213,9 @@ namespace MR
           //   therefore can store as integer
           // TODO Calculate translations; turn into affine transform; verify
           using applied_transform_type = Eigen::Matrix<int, 3, 3>;
-          Realignment();
+          Realignment() :
+              orig_transform_ (Eigen::Matrix<default_type,3,4>::Constant(std::numeric_limits<default_type>::signaling_NaN())),
+              applied_transform_ (applied_transform_type::Constant(0)) {}
           bool is_identity() const { return shuffle_.is_identity(); }
           bool valid() const { return shuffle_.valid(); }
           const Axes::permutations_type& permutations() const { return shuffle_.permutations; }

core/image.h

@@ -61,7 +61,6 @@ namespace MR
 
         FORCE_INLINE const std::string& name() const { return buffer->name(); }
         FORCE_INLINE const transform_type& transform() const { return buffer->transform(); }
-        //FORCE_INLINE const Header::Realignment& realignment() const { return buffer->realignment(); }
 
         FORCE_INLINE size_t  ndim () const { return buffer->ndim(); }
         FORCE_INLINE ssize_t size (size_t axis) const { return buffer->size (axis); }