FIX: Resolving absolute to relative paths in output

nipype/algorithms/tests/test_auto_AddCSVRow.py

@@ -6,7 +6,10 @@
 def test_AddCSVRow_inputs():
     input_map = dict(
         _outputs=dict(usedefault=True, ),
-        in_file=dict(mandatory=True, ),
+        in_file=dict(
+            extensions=None,
+            mandatory=True,
+        ),
     )
     inputs = AddCSVRow.input_spec()
 

nipype/interfaces/afni/preprocess.py

@@ -1000,7 +1000,7 @@ class ClipLevel(AFNICommandBase):
     input_spec = ClipLevelInputSpec
     output_spec = ClipLevelOutputSpec
 
-    def aggregate_outputs(self, runtime=None, needed_outputs=None):
+    def aggregate_outputs(self, runtime=None, needed_outputs=None, rebase_cwd=None):
 
         outputs = self._outputs()
 
@@ -2115,21 +2115,15 @@ class Seg(AFNICommandBase):
     input_spec = SegInputSpec
     output_spec = AFNICommandOutputSpec
 
-    def aggregate_outputs(self, runtime=None, needed_outputs=None):
-
-        import glob
-
-        outputs = self._outputs()
+    def _list_outputs(self):
+        from nipype.utils.filemanip import Path
 
+        prefix = 'Segsy'
         if isdefined(self.inputs.prefix):
-            outfile = os.path.join(os.getcwd(), self.inputs.prefix,
-                                   'Classes+*.BRIK')
-        else:
-            outfile = os.path.join(os.getcwd(), 'Segsy', 'Classes+*.BRIK')
-
-        outputs.out_file = glob.glob(outfile)[0]
+            prefix = self.inputs.prefix
 
-        return outputs
+        return {'out_file': str(
+            sorted(Path() / prefix).glob('Classes+*.BRIK')[0])}
 
 
 class SkullStripInputSpec(AFNICommandInputSpec):

nipype/interfaces/afni/tests/test_auto_Allineate.py

@@ -86,6 +86,7 @@ def test_Allineate_inputs():
         ),
         out_weight_file=dict(
             argstr='-wtprefix %s',
+            extensions=None,
             xor=['allcostx'],
         ),
         outputtype=dict(),

nipype/interfaces/afni/tests/test_auto_ClipLevel.py

@@ -17,6 +17,7 @@ def test_ClipLevel_inputs():
         ),
         grad=dict(
             argstr='-grad %s',
+            extensions=None,
             position=3,
             xor='doall',
         ),

nipype/interfaces/afni/tests/test_auto_LocalBistat.py

@@ -26,7 +26,10 @@ def test_LocalBistat_inputs():
             mandatory=True,
             position=-1,
         ),
-        mask_file=dict(argstr='-mask %s', ),
+        mask_file=dict(
+            argstr='-mask %s',
+            extensions=None,
+        ),
         neighborhood=dict(
             argstr="-nbhd '%s(%s)'",
             mandatory=True,
@@ -37,6 +40,7 @@ def test_LocalBistat_inputs():
         ),
         out_file=dict(
             argstr='-prefix %s',
+            extensions=None,
             keep_extension=True,
             name_source='in_file1',
             name_template='%s_bistat',
@@ -49,6 +53,7 @@ def test_LocalBistat_inputs():
         ),
         weight_file=dict(
             argstr='-weight %s',
+            extensions=None,
             xor=['automask'],
         ),
     )

nipype/interfaces/afni/tests/test_auto_Localstat.py

@@ -21,7 +21,10 @@ def test_Localstat_inputs():
             mandatory=True,
             position=-1,
         ),
-        mask_file=dict(argstr='-mask %s', ),
+        mask_file=dict(
+            argstr='-mask %s',
+            extensions=None,
+        ),
         neighborhood=dict(
             argstr="-nbhd '%s(%s)'",
             mandatory=True,
@@ -33,6 +36,7 @@ def test_Localstat_inputs():
         ),
         out_file=dict(
             argstr='-prefix %s',
+            extensions=None,
             keep_extension=True,
             name_source='in_file',
             name_template='%s_localstat',

nipype/interfaces/afni/tests/test_auto_NwarpApply.py

@@ -20,7 +20,10 @@ def test_NwarpApply_inputs():
             usedefault=True,
         ),
         inv_warp=dict(argstr='-iwarp', ),
-        master=dict(argstr='-master %s', ),
+        master=dict(
+            argstr='-master %s',
+            extensions=None,
+        ),
         out_file=dict(
             argstr='-prefix %s',
             extensions=None,

nipype/interfaces/afni/tests/test_auto_OneDToolPy.py

@@ -30,6 +30,7 @@ def test_OneDToolPy_inputs():
         show_censor_count=dict(argstr='-show_censor_count', ),
         show_cormat_warnings=dict(
             argstr='-show_cormat_warnings |& tee %s',
+            extensions=None,
             position=-1,
             xor=['out_file'],
         ),

nipype/interfaces/afni/tests/test_auto_Qwarp.py

@@ -125,7 +125,10 @@ def test_Qwarp_inputs():
             name_source=['in_file'],
             name_template='ppp_%s',
         ),
-        out_weight_file=dict(argstr='-wtprefix %s', ),
+        out_weight_file=dict(
+            argstr='-wtprefix %s',
+            extensions=None,
+        ),
         outputtype=dict(),
         overwrite=dict(argstr='-overwrite', ),
         pblur=dict(argstr='-pblur %s', ),

nipype/interfaces/afni/tests/test_auto_QwarpPlusMinus.py

@@ -125,7 +125,10 @@ def test_QwarpPlusMinus_inputs():
             position=0,
             usedefault=True,
         ),
-        out_weight_file=dict(argstr='-wtprefix %s', ),
+        out_weight_file=dict(
+            argstr='-wtprefix %s',
+            extensions=None,
+        ),
         outputtype=dict(),
         overwrite=dict(argstr='-overwrite', ),
         pblur=dict(argstr='-pblur %s', ),

nipype/interfaces/afni/tests/test_auto_ROIStats.py

@@ -49,7 +49,10 @@ def test_ROIStats_inputs():
             position=-1,
         ),
         quiet=dict(argstr='-quiet', ),
-        roisel=dict(argstr='-roisel %s', ),
+        roisel=dict(
+            argstr='-roisel %s',
+            extensions=None,
+        ),
         stat=dict(argstr='%s...', ),
         zerofill=dict(
             argstr='-zerofill %s',

nipype/interfaces/afni/tests/test_auto_ReHo.py

@@ -25,13 +25,17 @@ def test_ReHo_inputs():
             argstr='-in_rois %s',
             extensions=None,
         ),
-        mask_file=dict(argstr='-mask %s', ),
+        mask_file=dict(
+            argstr='-mask %s',
+            extensions=None,
+        ),
         neighborhood=dict(
             argstr='-nneigh %s',
             xor=['sphere', 'ellipsoid'],
         ),
         out_file=dict(
             argstr='-prefix %s',
+            extensions=None,
             keep_extension=True,
             name_source='in_file',
             name_template='%s_reho',

nipype/interfaces/afni/tests/test_auto_Remlfit.py

@@ -58,6 +58,7 @@ def test_Remlfit_inputs():
         ),
         matim=dict(
             argstr='-matim %s',
+            extensions=None,
             xor=['matrix'],
         ),
         matrix=dict(

nipype/interfaces/afni/tests/test_auto_Resample.py

@@ -17,7 +17,10 @@ def test_Resample_inputs():
             mandatory=True,
             position=-1,
         ),
-        master=dict(argstr='-master %s', ),
+        master=dict(
+            argstr='-master %s',
+            extensions=None,
+        ),
         num_threads=dict(
             nohash=True,
             usedefault=True,

nipype/interfaces/afni/tests/test_auto_TCorrMap.py

@@ -93,7 +93,10 @@ def test_TCorrMap_inputs():
             name_source='in_file',
             suffix='_qmean',
         ),
-        regress_out_timeseries=dict(argstr='-ort %s', ),
+        regress_out_timeseries=dict(
+            argstr='-ort %s',
+            extensions=None,
+        ),
         seeds=dict(
             argstr='-seed %s',
             extensions=None,

nipype/interfaces/afni/tests/test_auto_Zeropad.py

@@ -55,6 +55,7 @@ def test_Zeropad_inputs():
         ),
         master=dict(
             argstr='-master %s',
+            extensions=None,
             xor=['I', 'S', 'A', 'P', 'L', 'R', 'z', 'RL', 'AP', 'IS', 'mm'],
         ),
         mm=dict(

nipype/interfaces/afni/utils.py

@@ -210,9 +210,9 @@ class Autobox(AFNICommand):
     input_spec = AutoboxInputSpec
     output_spec = AutoboxOutputSpec
 
-    def aggregate_outputs(self, runtime=None, needed_outputs=None):
-        outputs = super(Autobox, self).aggregate_outputs(
-            runtime, needed_outputs)
+    def aggregate_outputs(self, runtime=None, needed_outputs=None, rebase_cwd=None):
+        outputs = super(Autobox, self).aggregate_outputs(runtime, needed_outputs,
+                                                         rebase_cwd=rebase_cwd)
         pattern = 'x=(?P<x_min>-?\d+)\.\.(?P<x_max>-?\d+)  '\
                   'y=(?P<y_min>-?\d+)\.\.(?P<y_max>-?\d+)  '\
                   'z=(?P<z_min>-?\d+)\.\.(?P<z_max>-?\d+)'
@@ -286,7 +286,7 @@ class BrickStat(AFNICommandBase):
     input_spec = BrickStatInputSpec
     output_spec = BrickStatOutputSpec
 
-    def aggregate_outputs(self, runtime=None, needed_outputs=None):
+    def aggregate_outputs(self, runtime=None, needed_outputs=None, rebase_cwd=None):
 
         outputs = self._outputs()
 

nipype/interfaces/ants/registration.py

@@ -1487,7 +1487,7 @@ def _format_arg(self, opt, spec, val):
             return self._mask_constructor()
         return super(MeasureImageSimilarity, self)._format_arg(opt, spec, val)
 
-    def aggregate_outputs(self, runtime=None, needed_outputs=None):
+    def aggregate_outputs(self, runtime=None, needed_outputs=None, rebase_cwd=None):
         outputs = self._outputs()
         stdout = runtime.stdout.split('\n')
         outputs.similarity = float(stdout[0])

nipype/interfaces/base/core.py

@@ -32,13 +32,13 @@
 from ... import config, logging, LooseVersion
 from ...utils.provenance import write_provenance
 from ...utils.misc import str2bool, rgetcwd
-from ...utils.filemanip import (FileNotFoundError, split_filename,
-                                which, get_dependencies)
+from ...utils.filemanip import (split_filename, which, get_dependencies,
+                                FileNotFoundError)
 from ...utils.subprocess import run_command
 
 from ...external.due import due
 
-from .traits_extension import traits, isdefined
+from .traits_extension import traits, isdefined, rebase_path_traits
 from .specs import (BaseInterfaceInputSpec, CommandLineInputSpec,
                     StdOutCommandLineInputSpec, MpiCommandLineInputSpec,
                     get_filecopy_info)
@@ -110,7 +110,7 @@ def run(self):
         """Execute the command."""
         raise NotImplementedError
 
-    def aggregate_outputs(self, runtime=None, needed_outputs=None):
+    def aggregate_outputs(self, runtime=None, needed_outputs=None, rebase_cwd=None):
         """Called to populate outputs"""
         raise NotImplementedError
 
@@ -204,10 +204,10 @@ def _check_requires(self, spec, name, value):
             ]
             if any(values) and isdefined(value):
                 if len(values) > 1:
-                    fmt = ("%s requires values for inputs %s because '%s' is set. " 
+                    fmt = ("%s requires values for inputs %s because '%s' is set. "
                            "For a list of required inputs, see %s.help()")
                 else:
-                    fmt = ("%s requires a value for input %s because '%s' is set. " 
+                    fmt = ("%s requires a value for input %s because '%s' is set. "
                            "For a list of required inputs, see %s.help()")
                 msg = fmt % (self.__class__.__name__,
                              ', '.join("'%s'" % req for req in spec.requires),
@@ -299,7 +299,7 @@ def _duecredit_cite(self):
             r['path'] = self.__module__
             due.cite(**r)
 
-    def run(self, cwd=None, ignore_exception=None, **inputs):
+    def run(self, cwd=None, ignore_exception=None, rebase_cwd=None, **inputs):
         """Execute this interface.
 
         This interface will not raise an exception if runtime.returncode is
@@ -327,6 +327,9 @@ def run(self, cwd=None, ignore_exception=None, **inputs):
         if cwd is None:
             cwd = syscwd
 
+        if rebase_cwd:
+            rebase_cwd = cwd
+
         os.chdir(cwd)  # Change to the interface wd
 
         enable_rm = config.resource_monitor and self.resource_monitor
@@ -442,42 +445,46 @@ def run(self, cwd=None, ignore_exception=None, **inputs):
         return results
 
     def _list_outputs(self):
-        """ List the expected outputs
-        """
+        """List the expected outputs."""
         if self.output_spec:
             raise NotImplementedError
         else:
             return None
 
     def aggregate_outputs(self, runtime=None, needed_outputs=None):
-        """ Collate expected outputs and check for existence
-        """
+        """Collate expected outputs and check for existence."""
+        outputs = self._outputs()  # Generate an output spec object
+        if needed_outputs is not None and not needed_outputs:
+            return outputs
 
-        predicted_outputs = self._list_outputs()
-        outputs = self._outputs()
-        if predicted_outputs:
-            _unavailable_outputs = []
-            if outputs:
-                _unavailable_outputs = \
-                    self._check_version_requirements(self._outputs())
-            for key, val in list(predicted_outputs.items()):
-                if needed_outputs and key not in needed_outputs:
-                    continue
-                if key in _unavailable_outputs:
-                    raise KeyError(('Output trait %s not available in version '
-                                    '%s of interface %s. Please inform '
-                                    'developers.') % (key, self.version,
-                                                      self.__class__.__name__))
-                try:
-                    setattr(outputs, key, val)
-                except TraitError as error:
-                    if getattr(error, 'info',
-                               'default').startswith('an existing'):
-                        msg = ("File/Directory '%s' not found for %s output "
-                               "'%s'." % (val, self.__class__.__name__, key))
-                        raise FileNotFoundError(msg)
-                    raise error
+        predicted_outputs = self._list_outputs()  # Predictions from _list_outputs
+        if not predicted_outputs:
+            return outputs
 
+        # Precalculate the list of output trait names that should be
+        # aggregated
+        aggregate_names = set(predicted_outputs.keys())
+        if needed_outputs:
+            aggregate_names = set(needed_outputs).intersection(aggregate_names)
+
+        if outputs and aggregate_names:
+            _na_outputs = self._check_version_requirements(outputs)
+            na_names = aggregate_names.intersection(set(_na_outputs))
+            if na_names:
+                raise TypeError("""\
+Output trait(s) %s not available in version %s of interface %s.\
+""" % (', '.join(na_names), self.version, self.__class__.__name__))
+
+        for key in aggregate_names:
+            val = predicted_outputs[key]
+            try:
+                setattr(outputs, key, val)
+            except TraitError as error:
+                if 'an existing' in getattr(error, 'info', 'default'):
+                    msg = "No such file or directory for output '%s' of a %s interface" % \
+                        (key, self.__class__.__name__)
+                    raise FileNotFoundError(val, message=msg)
+                raise error
         return outputs
 
     @property