FIX: Reverse ordering of ITK composite h5 files for TransformChain

This PR makes the ``TransformChain`` class more consistent with the
overall coordinate system, assuming that transforms are chained with the
*points* criteria.

In other words, in the typical setup where we have estimated one
initializing affine and then perhaps two levels of nonlinear
deformations, when calculating the coordinates of a given index in the
reference image, the last nonlinear should be applied first, then the
second, and finally the affine to pull information from the moving
image.

In other words, the chaining (composition) operation works exactly as
a single transformation procedure.

Resolves #81.

Author: oesteban

nitransforms/manip.py

@@ -131,8 +131,8 @@ def map(self, x, inverse=False):
             raise TransformError("Cannot apply an empty transforms chain.")
 
         transforms = self.transforms
-        if not inverse:
-            transforms = self.transforms[::-1]
+        if inverse:
+            transforms = list(reversed(self.transforms))
 
         for xfm in transforms:
             x = xfm(x, inverse=inverse)
@@ -157,9 +157,9 @@ def from_filename(cls, filename, fmt="X5", reference=None, moving=None):
             xforms = itk.ITKCompositeH5.from_filename(filename)
             for xfmobj in xforms:
                 if isinstance(xfmobj, itk.ITKLinearTransform):
-                    retval.append(Affine(xfmobj.to_ras(), reference=reference))
+                    retval.insert(0, Affine(xfmobj.to_ras(), reference=reference))
                 else:
-                    retval.append(DisplacementsFieldTransform(xfmobj))
+                    retval.insert(0, DisplacementsFieldTransform(xfmobj))
 
             return TransformChain(retval)