Merge pull request #1871 from effigies/patch-1

FIX: Select Eddy command at runtime

Author: satra

nipype/interfaces/fsl/epi.py

@@ -12,7 +12,8 @@
     ...                            '../../testing/data'))
     >>> os.chdir(datadir)
 """
-from __future__ import print_function, division, unicode_literals, absolute_import
+from __future__ import print_function, division, unicode_literals, \
+    absolute_import
 from builtins import str
 
 import os
@@ -106,7 +107,7 @@ def _run_interface(self, runtime):
             out_file = self.inputs.out_fieldmap
             im = nb.load(out_file, mmap=NUMPY_MMAP)
             dumb_img = nb.Nifti1Image(np.zeros(im.shape), im.affine,
-                                       im.header)
+                                      im.header)
             out_nii = nb.funcs.concat_images((im, dumb_img))
             nb.save(out_nii, out_file)
 
@@ -450,26 +451,25 @@ class EddyInputSpec(FSLCommandInputSpec):
 
 
 class EddyOutputSpec(TraitedSpec):
-    out_corrected = File(exists=True,
-                         desc=('4D image file containing all the corrected '
-                               'volumes'))
-    out_parameter = File(exists=True,
-                         desc=('text file with parameters definining the '
-                               'field and movement for each scan'))
-    out_rotated_bvecs = File(exists=True,
-                             desc=('File containing rotated b-values for all volumes'))
-    out_movement_rms = File(exists=True,
-                            desc=('Summary of the "total movement" in each volume'))
-    out_restricted_movement_rms = File(exists=True,
-                                       desc=('Summary of the "total movement" in each volume '
-                                             'disregarding translation in the PE direction'))
-    out_shell_alignment_parameters = File(exists=True,
-                                          desc=('File containing rigid body movement parameters '
-                                                'between the different shells as estimated by a '
-                                                'post-hoc mutual information based registration'))
-    out_outlier_report = File(exists=True,
-                              desc=('Text-file with a plain language report '
-                                    'on what outlier slices eddy has found'))
+    out_corrected = File(
+        exists=True, desc='4D image file containing all the corrected volumes')
+    out_parameter = File(
+        exists=True, desc=('text file with parameters definining the field and'
+                           'movement for each scan'))
+    out_rotated_bvecs = File(
+        exists=True, desc='File containing rotated b-values for all volumes')
+    out_movement_rms = File(
+        exists=True, desc='Summary of the "total movement" in each volume')
+    out_restricted_movement_rms = File(
+        exists=True, desc=('Summary of the "total movement" in each volume '
+                           'disregarding translation in the PE direction'))
+    out_shell_alignment_parameters = File(
+        exists=True, desc=('File containing rigid body movement parameters '
+                           'between the different shells as estimated by a '
+                           'post-hoc mutual information based registration'))
+    out_outlier_report = File(
+        exists=True, desc=('Text-file with a plain language report on what '
+                           'outlier slices eddy has found'))
 
 
 class Eddy(FSLCommand):
@@ -491,10 +491,16 @@ class Eddy(FSLCommand):
     >>> eddy.inputs.in_acqp  = 'epi_acqp.txt'
     >>> eddy.inputs.in_bvec  = 'bvecs.scheme'
     >>> eddy.inputs.in_bval  = 'bvals.scheme'
+    >>> eddy.inputs.use_cuda = True
     >>> eddy.cmdline # doctest: +ELLIPSIS +ALLOW_UNICODE
-    'eddy_openmp --acqp=epi_acqp.txt --bvals=bvals.scheme --bvecs=bvecs.scheme \
+    'eddy_cuda --acqp=epi_acqp.txt --bvals=bvals.scheme --bvecs=bvecs.scheme \
 --imain=epi.nii --index=epi_index.txt --mask=epi_mask.nii \
 --out=.../eddy_corrected'
+    >>> eddy.inputs.use_cuda = False
+    >>> eddy.cmdline # doctest: +ELLIPSIS +ALLOW_UNICODE
+    'eddy_openmp --acqp=epi_acqp.txt --bvals=bvals.scheme \
+--bvecs=bvecs.scheme --imain=epi.nii --index=epi_index.txt \
+--mask=epi_mask.nii --out=.../eddy_corrected'
     >>> res = eddy.run() # doctest: +SKIP
 
     """
@@ -507,12 +513,13 @@ class Eddy(FSLCommand):
     def __init__(self, **inputs):
         super(Eddy, self).__init__(**inputs)
         self.inputs.on_trait_change(self._num_threads_update, 'num_threads')
-        if isdefined(self.inputs.use_cuda):
-            self._use_cuda()
         if not isdefined(self.inputs.num_threads):
             self.inputs.num_threads = self._num_threads
         else:
             self._num_threads_update()
+        self.inputs.on_trait_change(self._use_cuda, 'use_cuda')
+        if isdefined(self.inputs.use_cuda):
+            self._use_cuda()
 
     def _num_threads_update(self):
         self._num_threads = self.inputs.num_threads
@@ -524,10 +531,21 @@ def _num_threads_update(self):
                 self.inputs.num_threads)
 
     def _use_cuda(self):
-        if self.inputs.use_cuda:
-            _cmd = 'eddy_cuda'
-        else:
-            _cmd = 'eddy_openmp'
+        self._cmd = 'eddy_cuda' if self.inputs.use_cuda else 'eddy_openmp'
+
+    def _run_interface(self, runtime):
+        # If 'eddy_openmp' is missing, use 'eddy'
+        FSLDIR = os.getenv('FSLDIR', '')
+        cmd = self._cmd
+        if all((FSLDIR != '',
+                cmd == 'eddy_openmp',
+                not os.path.exists(os.path.join(FSLDIR, cmd)))):
+            self._cmd = 'eddy'
+        runtime = super(Eddy, self)._run_interface(runtime)
+
+        # Restore command to avoid side-effects
+        self._cmd = cmd
+        return runtime
 
     def _format_arg(self, name, spec, value):
         if name == 'in_topup_fieldcoef':
@@ -551,7 +569,8 @@ def _list_outputs(self):
         out_restricted_movement_rms = os.path.abspath(
             '%s.eddy_restricted_movement_rms' % self.inputs.out_base)
         out_shell_alignment_parameters = os.path.abspath(
-            '%s.eddy_post_eddy_shell_alignment_parameters' % self.inputs.out_base)
+            '%s.eddy_post_eddy_shell_alignment_parameters'
+            % self.inputs.out_base)
         out_outlier_report = os.path.abspath(
             '%s.eddy_outlier_report' % self.inputs.out_base)
 
@@ -560,9 +579,11 @@ def _list_outputs(self):
         if os.path.exists(out_movement_rms):
             outputs['out_movement_rms'] = out_movement_rms
         if os.path.exists(out_restricted_movement_rms):
-            outputs['out_restricted_movement_rms'] = out_restricted_movement_rms
+            outputs['out_restricted_movement_rms'] = \
+                out_restricted_movement_rms
         if os.path.exists(out_shell_alignment_parameters):
-            outputs['out_shell_alignment_parameters'] = out_shell_alignment_parameters
+            outputs['out_shell_alignment_parameters'] = \
+                out_shell_alignment_parameters
         if os.path.exists(out_outlier_report):
             outputs['out_outlier_report'] = out_outlier_report