Merge pull request #1168 from oesteban/bug/FixXFibresForUndefinedFibres

[FIX] XFibres5 fails in _list_outputs if n_fibres is undefined

Author: satra

CHANGES

@@ -1,6 +1,7 @@
 Next release
 ============
 
+* FIX: Bug in XFibres5 (https://github.com/nipy/nipype/pull/1168)
 * ENH: Attempt to use hard links for data sink.
     (https://github.com/nipy/nipype/pull/1161)
 * FIX: Updates to SGE Plugins

nipype/interfaces/fsl/dti.py

@@ -111,8 +111,9 @@ class FSLXCommandInputSpec(FSLCommandInputSpec):
                  desc='b values file')
 
     logdir = Directory('.', argstr='--logdir=%s', usedefault=True)
-    n_fibres = traits.Range(low=1, argstr='--nfibres=%d', desc=('Maximum '
-                            'number of fibres to fit in each voxel'))
+    n_fibres = traits.Range(
+        usedefault=True, low=1, default=2, argstr='--nfibres=%d',
+        desc=('Maximum number of fibres to fit in each voxel'))
     model = traits.Enum(1, 2, argstr='--model=%d',
                         desc=('use monoexponential (1, default, required for '
                               'single-shell) or multiexponential (2, multi-'
@@ -200,7 +201,9 @@ def _run_interface(self, runtime):
 
     def _list_outputs(self):
         outputs = self.output_spec().get()
-        out_dir = self._out_dir
+        n_fibres = 2
+        if isdefined(self.inputs.n_fibres):
+            n_fibres = self.inputs.n_fibres
 
         if isdefined(self.inputs.logdir):
             out_dir = os.path.abspath(self.inputs.logdir)
@@ -222,13 +225,13 @@ def _list_outputs(self):
         for k in multi_out:
             outputs[k] = []
 
-        for i in xrange(1, self.inputs.n_fibres + 1):
+        for i in xrange(1, n_fibres + 1):
             outputs['fsamples'].append(self._gen_fname('f%dsamples' % i,
                                        cwd=out_dir))
             outputs['mean_fsamples'].append(self._gen_fname(('mean_f%d'
                                             'samples') % i, cwd=out_dir))
 
-        for i in xrange(1, self.inputs.n_fibres + 1):
+        for i in xrange(1, n_fibres + 1):
             outputs['dyads'].append(self._gen_fname('dyads%d' % i,
                                     cwd=out_dir))
             outputs['phsamples'].append(self._gen_fname('ph%dsamples' % i,

nipype/interfaces/fsl/tests/test_auto_BEDPOSTX5.py

@@ -52,6 +52,7 @@ def test_BEDPOSTX5_inputs():
     model=dict(argstr='--model=%d',
     ),
     n_fibres=dict(argstr='--nfibres=%d',
+    usedefault=True,
     ),
     n_jumps=dict(argstr='--njumps=%d',
     ),

nipype/interfaces/fsl/tests/test_auto_FSLXCommand.py

@@ -50,6 +50,7 @@ def test_FSLXCommand_inputs():
     model=dict(argstr='--model=%d',
     ),
     n_fibres=dict(argstr='--nfibres=%d',
+    usedefault=True,
     ),
     n_jumps=dict(argstr='--njumps=%d',
     ),

nipype/interfaces/fsl/tests/test_auto_XFibres5.py

@@ -52,6 +52,7 @@ def test_XFibres5_inputs():
     model=dict(argstr='--model=%d',
     ),
     n_fibres=dict(argstr='--nfibres=%d',
+    usedefault=True,
     ),
     n_jumps=dict(argstr='--njumps=%d',
     ),