REF: AnalyzeWarp

Author: mgxd

nipype/interfaces/elastix/registration.py

@@ -178,21 +178,36 @@ def _list_outputs(self):
         return outputs
 
 
-class AnalyzeWarpInputSpec(ElastixBaseInputSpec):
-    transform_file = File(
+class AnalyzeWarpInputSpec(ApplyWarpInputSpec):
+    points = traits.Enum(
+        'all',
+        usedefault=True,
+        position=0,
+        argstr='-def %s',
+        desc='transform all points from the input-image, which effectively'
+             ' generates a deformation field.')
+    jac = traits.Enum(
+        'all',
+        usedefault=True,
+        argstr='-jac %s',
+        desc='generate an image with the determinant of the spatial Jacobian')
+    jacmat = traits.Enum(
+        'all',
+        usedefault=True,
+        argstr='-jacmat %s',
+        desc='generate an image with the spatial Jacobian matrix at each voxel')
+    moving_image = File(
         exists=True,
-        mandatory=True,
-        argstr='-tp %s',
-        desc='transform-parameter file, only 1')
-
+        argstr='-in %s',
+        desc='input image to deform (not used)')
 
 class AnalyzeWarpOutputSpec(TraitedSpec):
     disp_field = File(desc='displacements field')
     jacdet_map = File(desc='det(Jacobian) map')
     jacmat_map = File(desc='Jacobian matrix map')
 
 
-class AnalyzeWarp(CommandLine):
+class AnalyzeWarp(ApplyWarp):
     """
     Use transformix to get details from the input transform (generate
     the corresponding deformation field, generate the determinant of the
@@ -210,7 +225,6 @@ class AnalyzeWarp(CommandLine):
 
     """
 
-    _cmd = 'transformix -def all -jac all -jacmat all'
     input_spec = AnalyzeWarpInputSpec
     output_spec = AnalyzeWarpOutputSpec