Merge pull request #785 from JensNRAD/eddy_fix

Fix for Eddy-Wrapper does not work properly #769

Author: satra

nipype/interfaces/fsl/epi.py

@@ -305,32 +305,60 @@ def _list_outputs(self):
 
 
 class EddyInputSpec( FSLCommandInputSpec ):
-    in_file =  File(exists=True, mandatory=True, desc='File containing all the images to estimate distortions for', argstr='--imain=%s' )
-    in_mask =  File(exists=True, mandatory=True, desc='Mask to indicate brain', argstr='--mask=%s' )
-    in_index = File(exists=True, mandatory=True, desc='File containing indices for all volumes in --imain into --acqp and --topup', argstr='--index=%s' )
-    in_acqp =  File(exists=True, mandatory=True, desc='File containing acquisition parameters', argstr='--acqp=%s' )
-    in_bvec =  File(exists=True, mandatory=True, desc='File containing the b-vectors for all volumes in --imain', argstr='--bvecs=%s' )
-    in_bval =  File(exists=True, mandatory=True, desc='File containing the b-values for all volumes in --imain', argstr='--bvals=%s' )
+    in_file =  File(exists=True, mandatory=True,
+                    desc=('File containing all the images to estimate '
+                          'distortions for'), argstr='--imain=%s')
+    in_mask =  File(exists=True, mandatory=True,
+                    desc='Mask to indicate brain', argstr='--mask=%s')
+    in_index = File(exists=True, mandatory=True,
+                    desc=('File containing indices for all volumes in --imain '
+                          'into --acqp and --topup'), argstr='--index=%s')
+    in_acqp =  File(exists=True, mandatory=True,
+                    desc='File containing acquisition parameters',
+                    argstr='--acqp=%s' )
+    in_bvec =  File(exists=True, mandatory=True,
+                    desc=('File containing the b-vectors for all volumes in '
+                          '--imain'), argstr='--bvecs=%s')
+    in_bval =  File(exists=True, mandatory=True,
+                    desc=('File containing the b-values for all volumes in '
+                          '--imain'), argstr='--bvals=%s')
+    out_base = File( desc='basename for output (warped) image',
+                     argstr='--out=%s' )
+    session =  File(exists=True,
+                    desc=('File containing session indices for all volumes in '
+                          '--imain'), argstr='--session=%s')
+    in_topup_fieldcoef = File(exists=True, argstr="--topup=%s", copyfile=False,
+                              requires=['in_topup_movpar'],
+                              desc=('topup file containing the field '
+                                    'coefficients'))
+    in_topup_movpar = File(exists=True, requires=['in_topup_fieldcoef'],
+                           copyfile=False, desc='topup movpar.txt file')
+    flm =  traits.Enum(('linear','quadratic','cubic'),
+                        desc='First level EC model', argstr='--flm=%s' )
+    fwhm = traits.Float(desc=('FWHM for conditioning filter when estimating '
+                              'the parameters'), argstr='--fwhm=%s')
+    niter = traits.Int( 5, desc='Number of iterations', argstr='--niter=%s')
+    method = traits.Enum(('jac','lsr'), argstr='--resamp=%s',
+                         desc=('Final resampling method (jacobian/least '
+                               'squeares)'))
+    repol = traits.Bool( False, desc='Detect and replace outlier slices',
+                         argstr='--repol' )
 
-    out_base = File( desc='basename for output (warped) image', argstr='--out=%s' )
-
-
-    session =  File(exists=True, desc='File containing session indices for all volumes in --imain', argstr='--session=%s' )
-    in_topup =  File(exists=True, desc='Base name for output files from topup', argstr='--topup=%s' )
-    flm =  traits.Enum( ('linear','quadratic','cubic'), desc='First level EC model', argstr='--flm=%s' )
-    fwhm = traits.Float( desc='FWHM for conditioning filter when estimating the parameters', argstr='--fwhm=%s' )
-    niter = traits.Int( 5, desc='Number of iterations', argstr='--niter=%s' )
-    method = traits.Enum( ('jac','lsr'), argstr='--resamp=%s', desc='Final resampling method (jacobian/least squeares)' )
-    repol = traits.Bool( False, desc='Detect and replace outlier slices', argstr='--repol' )
 
 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_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'))
 
 class Eddy( FSLCommand ):
-    """ Interface for FSL eddy, a tool for estimating and correcting eddy currents induced distortions.
-        `User guide <http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Eddy/UsersGuide>`_ and
-        `more info regarding acqp file <http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/eddy/Faq#How_do_I_know_what_to_put_into_my_--acqp_file>`_.
+    """ Interface for FSL eddy, a tool for estimating and correcting eddy
+        currents induced distortions. `User guide
+        <http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Eddy/UsersGuide>`_ and
+        `more info regarding acqp file
+        <http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/eddy/Faq#How_do_I_know_what_to_put_into_my_--acqp_file>`_.
 
         Examples
         --------
@@ -353,10 +381,15 @@ class Eddy( FSLCommand ):
     input_spec = EddyInputSpec
     output_spec = EddyOutputSpec
 
+    def _format_arg(self, name, spec, value):
+        if name == 'in_topup_fieldcoef':
+            return spec.argstr % value.split('_fieldcoef')[0]
+        return super(Eddy, self)._format_arg(name, spec, value)
+    
     def _parse_inputs( self, skip=None ):
         if skip is None:
             skip = []
-
+        
         if not isdefined(self.inputs.out_base ):
             self.inputs.out_base = os.path.abspath( './eddy_corrected' )
         return super(Eddy, self)._parse_inputs(skip=skip)
@@ -365,7 +398,7 @@ def _parse_inputs( self, skip=None ):
     def _list_outputs(self):
         outputs = self.output_spec().get()
         outputs['out_corrected'] = '%s.nii.gz' % self.inputs.out_base
-        outputs['out_parameter'] = '%s..eddy_parameters' % self.inputs.out_base
+        outputs['out_parameter'] = '%s.eddy_parameters' % self.inputs.out_base
         return outputs
 
 

nipype/interfaces/fsl/tests/test_auto_Eddy.py

@@ -33,7 +33,12 @@ def test_Eddy_inputs():
     in_mask=dict(argstr='--mask=%s',
     mandatory=True,
     ),
-    in_topup=dict(argstr='--topup=%s',
+    in_topup_fieldcoef=dict(argstr='--topup=%s',
+    copyfile=False,
+    requires=['in_topup_movpar'],
+    ),
+    in_topup_movpar=dict(copyfile=False,
+    requires=['in_topup_fieldcoef'],
     ),
     method=dict(argstr='--resamp=%s',
     ),

nipype/interfaces/vista/tests/test_auto_Vnifti2Image.py

@@ -1,39 +1,41 @@
 # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
 from nipype.testing import assert_equal
 from nipype.interfaces.vista.vista import Vnifti2Image
+
 def test_Vnifti2Image_inputs():
-    input_map = dict(ignore_exception=dict(nohash=True,
-    usedefault=True,
-    ),
-    out_file=dict(hash_files=False,
-    name_template='%s.v',
-    name_source=['in_file'],
-    keep_extension=False,
-    position=-1,
-    argstr='-out %s',
-    ),
-    args=dict(argstr='%s',
+    input_map = dict(args=dict(argstr='%s',
     ),
-    terminal_output=dict(nohash=True,
-    mandatory=True,
+    attributes=dict(argstr='-attr %s',
+    mandatory=False,
+    position=2,
     ),
     environ=dict(nohash=True,
     usedefault=True,
     ),
-    in_file=dict(position=1,
+    ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    in_file=dict(argstr='-in %s',
     mandatory=True,
-    argstr='-in %s',
+    position=1,
     ),
-    attributes=dict(position=2,
-    mandatory=False,
-    argstr='-attr %s',
+    out_file=dict(argstr='-out %s',
+    hash_files=False,
+    keep_extension=False,
+    name_source=['in_file'],
+    name_template='%s.v',
+    position=-1,
+    ),
+    terminal_output=dict(mandatory=True,
+    nohash=True,
     ),
     )
     inputs = Vnifti2Image.input_spec()
 
     for key, metadata in input_map.items():
         for metakey, value in metadata.items():
             yield assert_equal, getattr(inputs.traits()[key], metakey), value
+
 def test_Vnifti2Image_outputs():
     output_map = dict(out_file=dict(),
     )
@@ -42,3 +44,4 @@ def test_Vnifti2Image_outputs():
     for key, metadata in output_map.items():
         for metakey, value in metadata.items():
             yield assert_equal, getattr(outputs.traits()[key], metakey), value
+

nipype/interfaces/vista/tests/test_auto_VtoMat.py

@@ -1,35 +1,37 @@
 # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
 from nipype.testing import assert_equal
 from nipype.interfaces.vista.vista import VtoMat
+
 def test_VtoMat_inputs():
-    input_map = dict(ignore_exception=dict(nohash=True,
-    usedefault=True,
+    input_map = dict(args=dict(argstr='%s',
     ),
-    out_file=dict(hash_files=False,
-    name_template='%s.mat',
-    name_source=['in_file'],
-    keep_extension=False,
-    position=-1,
-    argstr='-out %s',
+    environ=dict(nohash=True,
+    usedefault=True,
     ),
-    args=dict(argstr='%s',
+    ignore_exception=dict(nohash=True,
+    usedefault=True,
     ),
-    terminal_output=dict(nohash=True,
+    in_file=dict(argstr='-in %s',
     mandatory=True,
+    position=1,
     ),
-    environ=dict(nohash=True,
-    usedefault=True,
+    out_file=dict(argstr='-out %s',
+    hash_files=False,
+    keep_extension=False,
+    name_source=['in_file'],
+    name_template='%s.mat',
+    position=-1,
     ),
-    in_file=dict(position=1,
-    mandatory=True,
-    argstr='-in %s',
+    terminal_output=dict(mandatory=True,
+    nohash=True,
     ),
     )
     inputs = VtoMat.input_spec()
 
     for key, metadata in input_map.items():
         for metakey, value in metadata.items():
             yield assert_equal, getattr(inputs.traits()[key], metakey), value
+
 def test_VtoMat_outputs():
     output_map = dict(out_file=dict(),
     )
@@ -38,3 +40,4 @@ def test_VtoMat_outputs():
     for key, metadata in output_map.items():
         for metakey, value in metadata.items():
             yield assert_equal, getattr(outputs.traits()[key], metakey), value
+