Merge pull request #913 from juhuntenburg/fix/applywarp

Fix/applywarp

Author: chrisgorgo

nipype/interfaces/fsl/preprocess.py

@@ -941,18 +941,18 @@ def write_config(self, configfile):
 
 class ApplyWarpInputSpec(FSLCommandInputSpec):
     in_file = File(exists=True, argstr='--in=%s',
-                   mandatory=True,
+                   mandatory=True, position=0,
                    desc='image to be warped')
-    out_file = File(argstr='--out=%s', genfile=True,
+    out_file = File(argstr='--out=%s', genfile=True, position=2,
                     desc='output filename', hash_files=False)
     ref_file = File(exists=True, argstr='--ref=%s',
-                    mandatory=True,
+                    mandatory=True, position=1,
                     desc='reference image')
     field_file = File(exists=True, argstr='--warp=%s',
                       desc='file containing warp field')
     abswarp = traits.Bool(argstr='--abs', xor=['relwarp'],
                           desc="treat warp field as absolute: x' = w(x)")
-    relwarp = traits.Bool(argstr='--rel', xor=['abswarp'],
+    relwarp = traits.Bool(argstr='--rel', xor=['abswarp'], position=-1,
                           desc="treat warp field as relative: x' = x + w(x)")
     datatype = traits.Enum('char', 'short', 'int', 'float', 'double',
                            argstr='--datatype=%s',
@@ -969,7 +969,7 @@ class ApplyWarpInputSpec(FSLCommandInputSpec):
     mask_file = File(exists=True, argstr='--mask=%s',
                      desc='filename for mask image (in reference space)')
     interp = traits.Enum(
-        'nn', 'trilinear', 'sinc', 'spline', argstr='--interp=%s',
+        'nn', 'trilinear', 'sinc', 'spline', argstr='--interp=%s', position=-2,
         desc='interpolation method')
 
 

nipype/interfaces/fsl/tests/test_auto_ApplyWarp.py

@@ -20,14 +20,17 @@ def test_ApplyWarp_inputs():
     ),
     in_file=dict(argstr='--in=%s',
     mandatory=True,
+    position=0,
     ),
     interp=dict(argstr='--interp=%s',
+    position=-2,
     ),
     mask_file=dict(argstr='--mask=%s',
     ),
     out_file=dict(argstr='--out=%s',
     genfile=True,
     hash_files=False,
+    position=2,
     ),
     output_type=dict(),
     postmat=dict(argstr='--postmat=%s',
@@ -36,8 +39,10 @@ def test_ApplyWarp_inputs():
     ),
     ref_file=dict(argstr='--ref=%s',
     mandatory=True,
+    position=1,
     ),
     relwarp=dict(argstr='--rel',
+    position=-1,
     xor=['abswarp'],
     ),
     superlevel=dict(argstr='--superlevel=%s',

nipype/interfaces/fsl/tests/test_preprocess.py

@@ -455,17 +455,17 @@ def test_applywarp():
                               field_file = reffile,
                               **{name : settings[1]})
         if name == 'out_file':
-            realcmd = 'applywarp --warp=%s '\
-                      '--in=%s --out=%s '\
-                      '--ref=%s'%(reffile, infile,
+            realcmd = 'applywarp --in=%s '\
+                      '--ref=%s --out=%s '\
+                      '--warp=%s'%(infile, reffile,
                                   settings[1],reffile)
         else:
             outfile = awarp._gen_fname(infile, suffix='_warp')
-            realcmd = 'applywarp --warp=%s '\
-                      '--in=%s --out=%s '\
-                      '%s --ref=%s'%(reffile, infile,
-                                     outfile, settings[0],
-                                     reffile)
+            realcmd = 'applywarp --in=%s '\
+                      '--ref=%s --out=%s '\
+                      '--warp=%s %s'%(infile, reffile,
+                                     outfile, reffile,
+                                     settings[0])
         yield assert_equal, awarp.cmdline, realcmd
 
     awarp = fsl.ApplyWarp(in_file = infile,