Merge pull request #13 from satra/enh/denoise

Enh/denoise

Author: jessicaforbes

bin/nipype2boutiques

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!python
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 import sys

bin/nipype_cmd

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!python
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 import sys

bin/nipype_display_crash

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!python
 """Displays crash information from Nipype crash files. For certain crash files,
 one can rerun a failed node in a temp directory.
 

doc/devel/cmd_interface_devel.rst

@@ -198,11 +198,13 @@ output_name (optional)
      name of the output (if this is not set same name as the input will be
      assumed)
 
-keep_extension (optional - not used)
-     if you want the extension from the input to be kept
+keep_extension (optional)
+     if you want the extension from the input or name_template to be kept. The
+     name_template extension always overrides the input extension.
 
 In addition one can add functionality to your class or base class, to allow
-changing extensions specific to package or interface
+changing extensions specific to package or interface. This overload function is
+trigerred only if keep_extension is not defined.
 
 .. testcode::
 

nipype/algorithms/tests/test_auto_TVTKBaseInterface.py

@@ -0,0 +1,16 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from ...testing import assert_equal
+from ..mesh import TVTKBaseInterface
+
+
+def test_TVTKBaseInterface_inputs():
+    input_map = dict(ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    )
+    inputs = TVTKBaseInterface.input_spec()
+
+    for key, metadata in list(input_map.items()):
+        for metakey, value in list(metadata.items()):
+            yield assert_equal, getattr(inputs.traits()[key], metakey), value
+

nipype/interfaces/ants/tests/test_auto_Registration.py

@@ -44,6 +44,7 @@ def test_Registration_inputs():
     ),
     interpolation_parameters=dict(),
     invert_initial_moving_transform=dict(requires=['initial_moving_transform'],
+    usedefault=True,
     xor=['initial_moving_transform_com'],
     ),
     metric=dict(mandatory=True,

nipype/interfaces/base.py

@@ -1270,6 +1270,10 @@ def _process(drain=0):
         result['merged'] = [r[1] for r in temp]
     if output == 'allatonce':
         stdout, stderr = proc.communicate()
+        if stdout and isinstance(stdout, bytes):
+            stdout = stdout.decode()
+        if stderr and isinstance(stderr, bytes):
+            stderr = stderr.decode()
         result['stdout'] = str(stdout).split('\n')
         result['stderr'] = str(stderr).split('\n')
         result['merged'] = ''
@@ -1556,7 +1560,7 @@ def _filename_from_source(self, name, chain=None):
 
         trait_spec = self.inputs.trait(name)
         retval = getattr(self.inputs, name)
-
+        source_ext = None
         if not isdefined(retval) or "%s" in retval:
             if not trait_spec.name_source:
                 return retval
@@ -1585,7 +1589,7 @@ def _filename_from_source(self, name, chain=None):
 
                 # special treatment for files
                 try:
-                    _, base, _ = split_filename(source)
+                    _, base, source_ext = split_filename(source)
                 except AttributeError:
                     base = source
             else:
@@ -1594,14 +1598,17 @@ def _filename_from_source(self, name, chain=None):
 
                 chain.append(name)
                 base = self._filename_from_source(ns, chain)
+                if isdefined(base):
+                    _, _, source_ext = split_filename(base)
 
             chain = None
             retval = name_template % base
             _, _, ext = split_filename(retval)
-            if trait_spec.keep_extension and ext:
-                return retval
-            return self._overload_extension(retval, name)
-
+            if trait_spec.keep_extension and (ext or source_ext):
+                if (ext is None or not ext) and source_ext:
+                    retval = retval + source_ext
+            else:
+                retval = self._overload_extension(retval, name)
         return retval
 
     def _gen_filename(self, name):

nipype/interfaces/fsl/model.py

@@ -252,7 +252,7 @@ def _create_ev_files(
                                                               element=count,
                                                               ctype=ctype, val=val)
                         ev_txt += "\n"
-                        
+
                     for fconidx in ftest_idx:
                         fval=0
                         if con[0] in con_map.keys() and fconidx in con_map[con[0]]: