Fixed Deconvolve output mapping

Beefed up AFNICommand Base to include _gen_fname() method (lifted from
FSLCommand Base class). Minor bug edits in Deconvolve cmdline code.

Author: rmarkello

nipype/interfaces/afni/base.py

@@ -10,7 +10,8 @@
 from sys import platform
 
 from ... import logging
-from ...utils.filemanip import split_filename
+from ...utils.filemanip import split_filename, fname_presuffix
+
 from ..base import (
     CommandLine, traits, CommandLineInputSpec, isdefined, File, TraitedSpec)
 from ...external.due import BibTeX
@@ -70,7 +71,7 @@ def version():
         return tuple(v)
 
     @classmethod
-    def outputtype_to_ext(cls, outputtype):
+    def output_type_to_ext(cls, outputtype):
         """Get the file extension for the given output type.
 
         Parameters
@@ -217,7 +218,7 @@ def set_default_output_type(cls, outputtype):
 
     def _overload_extension(self, value, name=None):
         path, base, _ = split_filename(value)
-        return os.path.join(path, base + Info.outputtype_to_ext(self.inputs.outputtype))
+        return os.path.join(path, base + Info.output_type_to_ext(self.inputs.outputtype))
 
     def _list_outputs(self):
         outputs = super(AFNICommand, self)._list_outputs()
@@ -231,6 +232,51 @@ def _list_outputs(self):
                         outputs[name] = outputs[name] + "+orig.BRIK"
         return outputs
 
+    def _gen_fname(self, basename, cwd=None, suffix=None, change_ext=True,
+                   ext=None):
+        """Generate a filename based on the given parameters.
+
+        The filename will take the form: cwd/basename<suffix><ext>.
+        If change_ext is True, it will use the extentions specified in
+        <instance>intputs.output_type.
+
+        Parameters
+        ----------
+        basename : str
+            Filename to base the new filename on.
+        cwd : str
+            Path to prefix to the new filename. (default is os.getcwd())
+        suffix : str
+            Suffix to add to the `basename`.  (defaults is '' )
+        change_ext : bool
+            Flag to change the filename extension to the FSL output type.
+            (default True)
+
+        Returns
+        -------
+        fname : str
+            New filename based on given parameters.
+
+        """
+
+        if basename == '':
+            msg = 'Unable to generate filename for command %s. ' % self.cmd
+            msg += 'basename is not set!'
+            raise ValueError(msg)
+        if cwd is None:
+            cwd = os.getcwd()
+        if ext is None:
+            ext = Info.output_type_to_ext(self.inputs.outputtype)
+        if change_ext:
+            if suffix:
+                suffix = ''.join((suffix, ext))
+            else:
+                suffix = ext
+        if suffix is None:
+            suffix = ''
+        fname = fname_presuffix(basename, suffix=suffix,
+                                use_ext=False, newpath=cwd)
+        return fname
 
 def no_afni():
     """ Checks if AFNI is available """

nipype/interfaces/afni/model.py

@@ -121,7 +121,7 @@ class DeconvolveInputSpec(AFNICommandInputSpec):
         desc='Stop running after writing .xmat.1D file',
         argstr='-x1D_stop')
     out_file = File(
-        'bucket.nii',
+        'Decon.nii',
         desc='Output statistics file',
         argstr='-bucket %s')
     jobs = traits.Int(
@@ -157,7 +157,7 @@ class DeconvolveInputSpec(AFNICommandInputSpec):
                      Str(desc='model')),
         desc='Generate a response model from a set of stimulus times'
              ' given in file.',
-        argstr='-stim_times %d %s %s...')
+        argstr='-stim_times %d %s \'%s\'...')
     stim_label = traits.List(
         traits.Tuple(traits.Int(desc='k-th input stimulus'),
                      Str(desc='stimulus label')),
@@ -178,7 +178,7 @@ class DeconvolveInputSpec(AFNICommandInputSpec):
         Str(desc='symbolic general linear test'),
         desc='General linear tests (i.e., contrasts) using symbolic '
              'conventions (e.g., \'+Label1 -Label2\')',
-        argstr='-gltsym SYM: %s...')
+        argstr='-gltsym \'SYM: %s\'...')
     glt_label = traits.List(
         traits.Tuple(traits.Int(desc='k-th general linear test'),
                      Str(desc='GLT label')),
@@ -187,10 +187,14 @@ class DeconvolveInputSpec(AFNICommandInputSpec):
         requires=['gltsym'])
 
 
-class DeconvolveOutputSpec(AFNICommandOutputSpec):
-    out_file = File(desc='output statistics file')
-    reml_script = File(desc='Autogenerated script for 3dREML')
-    x1D = File(desc='save out X matrix')
+class DeconvolveOutputSpec(TraitedSpec):
+    out_file = File(
+        desc='output statistics file',
+        exists=True)
+    reml_script = File(
+        desc='Autogenerated script for 3dREML')
+    x1D = File(
+        desc='save out X matrix')
 
 
 class Deconvolve(AFNICommand):
@@ -234,16 +238,17 @@ def _list_outputs(self):
         outputs = self.output_spec().get()
         if isdefined(self.inputs.x1D):
             if not self.inputs.x1D.endswith('.xmat.1D'):
-                outputs['x1D'] = self.inputs.x1D + '.xmat.1D'
+                outputs['x1D'] = os.path.abspath(self.inputs.x1D + '.xmat.1D')
             else:
-                outputs['x1D'] = self.inputs.x1D
+                outputs['x1D'] = os.path.abspath(self.inputs.x1D)
 
         _gen_fname_opts = {}
         _gen_fname_opts['basename'] = self.inputs.out_file
         _gen_fname_opts['cwd'] = os.getcwd()
+        _gen_fname_opts['suffix'] = '.REML_cmd'
 
-        outputs['reml_script'] = self._gen_fname(suffix='.REML_cmd', **_gen_fname_opts)
-        outputs['out_file'] = self.inputs.out_file
+        outputs['reml_script'] = self._gen_fname(**_gen_fname_opts)
+        outputs['out_file'] = os.path.abspath(self.inputs.out_file)
         return outputs