RF: Include identity transforms in image affines. Basic flirt matrix

read/write routines

fsl/data/image.py

@@ -376,6 +376,9 @@ class Nifti(notifier.Notifier, meta.Meta):
                                                            [ x, 0, 0])
             voxToScaledVoxMat = transform.concat(flip, voxToScaledVoxMat)
 
+        affines['fsl',   'fsl']   = np.eye(4)
+        affines['voxel', 'voxel'] = np.eye(4)
+        affines['world', 'world'] = np.eye(4)
         affines['voxel', 'world'] = voxToWorldMat
         affines['world', 'voxel'] = transform.invert(voxToWorldMat)
         affines['voxel', 'fsl']   = voxToScaledVoxMat

fsl/utils/transform/flirt.py

@@ -17,9 +17,21 @@ matrices. The following functions are available:
 """
 
 
+import numpy as np
+
 from .affine import concat
 
 
+def readFlirt(fname):
+    """Reads a FLIRT matrix from a file. """
+    return np.loadtxt(fname)
+
+
+def writeFlirt(xform, fname):
+    """Writes the given FLIRT matrix to a file. """
+    np.savetxt(fname, xform, fmt='%1.15g')
+
+
 def fromFlirt(xform, src, ref, from_='voxel', to='world'):
     """Convert a FLIRT affine matrix into another affine.