Merge pull request #574 from satra/fix/name_source

Fix/name source fix for #573

Author: satra

nipype/interfaces/afni/base.py

@@ -194,50 +194,17 @@ def _gen_fname(self, basename, cwd=None, suffix='_afni', change_ext=True, prefix
 
 class AFNICommandInputSpec(AFNIBaseCommandInputSpec):
     out_file = File("%s_afni", desc='output image file name',
-                    argstr='-prefix %s', xor=['out_file', 'prefix', 'suffix'], name_source="in_file", usedefault=True)
-    prefix = traits.Str(
-        desc='output image prefix', deprecated='0.8', new_name="out_file")
-    suffix = traits.Str(
-        desc='output image suffix', deprecated='0.8', new_name="out_file")
+                    argstr='-prefix %s', xor=['out_file', 'prefix', 'suffix'],
+                    name_source="in_file", usedefault=True)
 
 
 class AFNICommand(AFNIBaseCommand):
     input_spec = AFNICommandInputSpec
 
-    def _gen_filename(self, name):
-        trait_spec = self.inputs.trait(name)
-        if name == "out_file" and (isdefined(self.inputs.prefix) or isdefined(self.inputs.suffix)):
-            suffix = ''
-            prefix = ''
-            if isdefined(self.inputs.prefix):
-                prefix = self.inputs.prefix
-            if isdefined(self.inputs.suffix):
-                suffix = self.inputs.suffix
-
-            _, base, _ = split_filename(
-                getattr(self.inputs, trait_spec.name_source))
-            return self._gen_fname(basename=base, prefix=prefix, suffix=suffix, cwd=os.getcwd())
-
-        else:
-            if getattr(self.inputs, name):
-                return os.path.join(
-                    os.getcwd(),super(AFNICommand, self)._gen_filename(name))
-
     def _overload_extension(self, value):
         path, base, _ = split_filename(value)
         return os.path.join(path, base + Info.outputtype_to_ext(self.inputs.outputtype))
 
-    def _list_outputs(self):
-        metadata = dict(name_source=lambda t: t is not None)
-        out_names = self.inputs.traits(**metadata).keys()
-        if out_names:
-            outputs = self.output_spec().get()
-            for name in out_names:
-                out = self._gen_filename(name)
-                if out and isdefined(out):
-                    outputs[name] = os.path.abspath(out)
-            return outputs
-
 
 class AFNICommandOutputSpec(TraitedSpec):
     out_file = File(desc='output file',

nipype/interfaces/afni/preprocess.py

@@ -81,7 +81,7 @@ class To3D(AFNICommand):
     >>> To3D.inputs.filetype = "anat"
     >>> To3D.inputs.outputtype = "NIFTI"
     >>> To3D.cmdline #doctest: +ELLIPSIS
-    'to3d -datum float -anat -prefix .../dicomdir.nii ./*.dcm'
+    'to3d -datum float -anat -prefix dicomdir.nii ./*.dcm'
     >>> res = To3D.run() #doctest: +SKIP
 
    """
@@ -361,7 +361,7 @@ class AutoTcorrelate(AFNICommand):
     >>> corr.inputs.mask = 'mask.nii'
     >>> corr.inputs.mask_only_targets = True
     >>> corr.cmdline # doctest: +ELLIPSIS, +NORMALIZE_WHITESPACE
-    '3dAutoTcorrelate -eta2 -mask mask.nii -mask_only_targets -prefix ...my_similarity_matrix.1D -polort -1 functional.nii'
+    '3dAutoTcorrelate -eta2 -mask mask.nii -mask_only_targets -prefix my_similarity_matrix.1D -polort -1 functional.nii'
     >>> res = corr.run() # doctest: +SKIP
     """
     input_spec = AutoTcorrelateInputSpec
@@ -374,9 +374,6 @@ def _overload_extension(self, value):
             ext = ext + ".1D"
         return os.path.join(path, base + ext)
 
-    def _gen_filename(self, name):
-        return os.path.abspath(super(AutoTcorrelate, self)._gen_filename(name))
-
 
 class TStatInputSpec(AFNICommandInputSpec):
     in_file = File(desc='input file to 3dTstat',
@@ -1163,6 +1160,7 @@ class MaskaveInputSpec(AFNICommandInputSpec):
                    mandatory=True,
                    exists=True)
     out_file = File("%s_maskave.1D", desc='output image file name',
+                    keep_extension=True,
                     argstr="> %s", name_source="in_file", usedefault=True, position=-1)
     mask = File(desc='matrix to align input file',
                 argstr='-mask %s',
@@ -1558,7 +1556,7 @@ class Calc(AFNICommand):
     >>> calc.inputs.out_file =  'functional_calc.nii.gz'
     >>> calc.inputs.outputtype = "NIFTI"
     >>> calc.cmdline #doctest: +ELLIPSIS
-    '3dcalc -a functional.nii  -b functional2.nii -expr "a*b" -prefix .../functional_calc.nii'
+    '3dcalc -a functional.nii  -b functional2.nii -expr "a*b" -prefix functional_calc.nii'
 
     """
 
@@ -1591,13 +1589,9 @@ class BlurInMaskInputSpec(AFNICommandInputSpec):
         position=1,
         mandatory=True,
         exists=True)
-    out_file = File(
-        '%s_blur',
-        desc='output to the file',
-        argstr='-prefix %s',
-        name_source='in_file',
-        position=-1,
-        genfile=True)
+    out_file = File('%s_blur', desc='output to the file', argstr='-prefix %s',
+                    name_source='in_file', position=-1, genfile=True,
+                    usedefault=True)
     mask = File(
         desc='Mask dataset, if desired.  Blurring will occur only within the mask.  Voxels NOT in the mask will be set to zero in the output.',
         argstr='-mask %s')
@@ -1635,6 +1629,8 @@ class BlurInMask(AFNICommand):
     >>> bim.inputs.in_file = 'functional.nii'
     >>> bim.inputs.mask = 'mask.nii'
     >>> bim.inputs.fwhm = 5.0
+    >>> bim.cmdline #doctest: +ELLIPSIS
+    '3dBlurInMask -input functional.nii -FWHM 5.000000 -mask mask.nii -prefix .../functional_blur+orig.BRIK'
     >>> res = bim.run()   # doctest: +SKIP
 
     """
@@ -1643,19 +1639,6 @@ class BlurInMask(AFNICommand):
     input_spec = BlurInMaskInputSpec
     output_spec = AFNICommandOutputSpec
 
-    def _list_outputs(self):
-        outputs = self.output_spec().get()
-        if not isdefined(self.inputs.out_file):
-            outputs['out_file'] = self._gen_fname(self.inputs.in_file,
-                                                  suffix=self.inputs.suffix)
-        else:
-            outputs['out_file'] = os.path.abspath(self.inputs.out_file)
-        return outputs
-
-    def _gen_filename(self, name):
-        if name == 'out_file':
-            return self._list_outputs()[name]
-
 
 class TCorrMapInputSpec(AFNIBaseCommandInputSpec):
     in_file = File(exists=True, argstr='-input %s', mandatory=True)

nipype/interfaces/base.py

@@ -694,7 +694,7 @@ def help(cls, returnhelp=False):
         if returnhelp:
             return allhelp
         else:
-            print allhelp
+            print(allhelp)
 
     @classmethod
     def _get_trait_desc(self, inputs, name, spec):
@@ -1218,7 +1218,7 @@ def help(cls, returnhelp=False):
         if returnhelp:
             return allhelp
         else:
-            print allhelp
+            print(allhelp)
 
     def _get_environ(self):
         out_environ = {}
@@ -1326,49 +1326,45 @@ def _format_arg(self, name, trait_spec, value):
                 return sep.join([argstr % elt for elt in value])
             else:
                 return argstr % sep.join(str(elt) for elt in value)
-        elif trait_spec.name_source:
-            return  argstr % self._gen_filename(name)
         else:
             # Append options using format string.
             return argstr % value
-    
-    def _gen_filename(self, name):
-            trait_spec = self.inputs.trait(name)
-            value = getattr(self.inputs, name)
-            if isdefined(value):
-                if "%s" in value:
-                    if isinstance(trait_spec.name_source, list):
-                        for ns in trait_spec.name_source:
-                            if isdefined(getattr(self.inputs, ns)):
-                                name_source = ns
-                                break
-                    else:
-                        name_source = trait_spec.name_source
-                    if name_source.endswith(os.path.sep):
-                        name_source = name_source[:-len(os.path.sep)]
-                    _, base, _ = split_filename(getattr(self.inputs, name_source))
-                    
-                    retval = value%base
+
+    def _filename_from_source(self, name):
+        trait_spec = self.inputs.trait(name)
+        retval = getattr(self.inputs, name)
+        if isdefined(retval):
+            if "%s" in retval:
+                if isinstance(trait_spec.name_source, list):
+                    for ns in trait_spec.name_source:
+                        if isdefined(getattr(self.inputs, ns)):
+                            name_source = ns
+                            break
                 else:
-                    retval = value
-            else:
-                raise NotImplementedError
-            _,_,ext = split_filename(retval)
-            if trait_spec.overload_extension or not ext:
-                return self._overload_extension(retval)
-            else:
+                    name_source = trait_spec.name_source
+                if name_source.endswith(os.path.sep):
+                    name_source = name_source[:-len(os.path.sep)]
+                _, base, _ = split_filename(getattr(self.inputs, name_source))
+                retval = os.path.abspath(retval % base)
+            _, _, ext = split_filename(retval)
+            if trait_spec.keep_extension and ext:
                 return retval
-            
+            return self._overload_extension(retval)
+        return retval
+
+    def _gen_filename(self, name):
+        raise NotImplementedError
+
     def _overload_extension(self, value):
         return value
-    
+
     def _list_outputs(self):
         metadata = dict(name_source=lambda t: t is not None)
         out_names = self.inputs.traits(**metadata).keys()
         if out_names:
             outputs = self.output_spec().get()
             for name in out_names:
-                outputs[name] = os.path.abspath(self._gen_filename(name))
+                outputs[name] = os.path.abspath(self._filename_from_source(name))
             return outputs
 
     def _parse_inputs(self, skip=None):
@@ -1391,11 +1387,12 @@ def _parse_inputs(self, skip=None):
             if skip and name in skip:
                 continue
             value = getattr(self.inputs, name)
-            if not isdefined(value):
-                if spec.genfile or spec.name_source:
+            if spec.genfile or spec.name_source:
+                value = self._filename_from_source(name)
+                if not isdefined(value):
                     value = self._gen_filename(name)
-                else:
-                    continue
+            if not isdefined(value):
+                continue
             arg = self._format_arg(name, spec, value)
             if arg is None:
                 continue

nipype/interfaces/freesurfer/model.py

@@ -100,6 +100,7 @@ class MRISPreproc(FSCommand):
     def _list_outputs(self):
         outputs = self.output_spec().get()
         outfile = self.inputs.out_file
+        outputs['out_file'] = outfile
         if not isdefined(outfile):
             outputs['out_file'] = os.path.join(os.getcwd(),
                                    'concat_%s_%s.mgz' % (self.inputs.hemi,