several fixups

- [x] Add `num_threads` as a property synchronized with `inputs.num_threads` in
  afni interfaces
- [x] Add syncrhonization between `Node.n_procs` and `Interface.inputs.num_threads`
- [x] Minor documentation fixes of the old profiler callback-log.

Author: oesteban

nipype/interfaces/afni/base.py

@@ -130,6 +130,8 @@ def _run_interface(self, runtime):
 
 
 class AFNICommandInputSpec(CommandLineInputSpec):
+    num_threads = traits.Int(1, usedefault=True, nohash=True,
+                             desc='set number of threads')
     outputtype = traits.Enum('AFNI', list(Info.ftypes.keys()),
                              desc='AFNI output filetype')
     out_file = File(name_template="%s_afni", desc='output image file name',
@@ -141,6 +143,7 @@ class AFNICommandOutputSpec(TraitedSpec):
     out_file = File(desc='output file',
                     exists=True)
 
+
 class AFNICommand(AFNICommandBase):
     """Shared options for several AFNI commands """
     input_spec = AFNICommandInputSpec
@@ -172,9 +175,33 @@ class AFNICommand(AFNICommandBase):
                     'tags': ['implementation'],
                     }]
 
+    @property
+    def num_threads(self):
+        return self.inputs.num_threads
+
+    @num_threads.setter
+    def num_threads(self, value):
+        self.inputs.num_threads = value
+
+    @classmethod
+    def set_default_output_type(cls, outputtype):
+        """Set the default output type for AFNI classes.
+
+        This method is used to set the default output type for all afni
+        subclasses.  However, setting this will not update the output
+        type for any existing instances.  For these, assign the
+        <instance>.inputs.outputtype.
+        """
+
+        if outputtype in Info.ftypes:
+            cls._outputtype = outputtype
+        else:
+            raise AttributeError('Invalid AFNI outputtype: %s' % outputtype)
+
     def __init__(self, **inputs):
         super(AFNICommand, self).__init__(**inputs)
         self.inputs.on_trait_change(self._output_update, 'outputtype')
+        self.inputs.on_trait_change(self._nthreads_update, 'num_threads')
 
         if self._outputtype is None:
             self._outputtype = Info.outputtype()
@@ -184,11 +211,9 @@ def __init__(self, **inputs):
         else:
             self._output_update()
 
-    def _run_interface(self, runtime):
-        # Update num threads estimate from OMP_NUM_THREADS env var
-        # Default to 1 if not set
-        self.inputs.environ['OMP_NUM_THREADS'] = str(self.num_threads)
-        return super(AFNICommand, self)._run_interface(runtime)
+    def _nthreads_update(self):
+        """Update environment with new number of threads"""
+        self.inputs.environ['OMP_NUM_THREADS'] = '%d' % self.inputs.num_threads
 
     def _output_update(self):
         """ i think? updates class private attribute based on instance input
@@ -197,21 +222,6 @@ def _output_update(self):
         """
         self._outputtype = self.inputs.outputtype
 
-    @classmethod
-    def set_default_output_type(cls, outputtype):
-        """Set the default output type for AFNI classes.
-
-        This method is used to set the default output type for all afni
-        subclasses.  However, setting this will not update the output
-        type for any existing instances.  For these, assign the
-        <instance>.inputs.outputtype.
-        """
-
-        if outputtype in Info.ftypes:
-            cls._outputtype = outputtype
-        else:
-            raise AttributeError('Invalid AFNI outputtype: %s' % outputtype)
-
     def _overload_extension(self, value, name=None):
         path, base, _ = split_filename(value)
         return os.path.join(path, base + Info.output_type_to_ext(self.inputs.outputtype))
@@ -274,6 +284,7 @@ def _gen_fname(self, basename, cwd=None, suffix=None, change_ext=True,
                                 use_ext=False, newpath=cwd)
         return fname
 
+
 def no_afni():
     """ Checks if AFNI is available """
     if Info.version() is None:
@@ -285,8 +296,9 @@ class AFNIPythonCommandInputSpec(CommandLineInputSpec):
     outputtype = traits.Enum('AFNI', list(Info.ftypes.keys()),
                              desc='AFNI output filetype')
     py27_path = traits.Either('python2', File(exists=True),
-        usedefault=True,
-        default='python2')
+                              usedefault=True,
+                              default='python2')
+
 
 class AFNIPythonCommand(AFNICommand):
     @property

nipype/pipeline/engine/nodes.py

@@ -79,7 +79,7 @@ class Node(EngineBase):
 
     def __init__(self, interface, name, iterables=None, itersource=None,
                  synchronize=False, overwrite=None, needed_outputs=None,
-                 run_without_submitting=False, n_procs=1, mem_gb=0.20,
+                 run_without_submitting=False, n_procs=None, mem_gb=0.20,
                  **kwargs):
         """
         Parameters
@@ -153,12 +153,15 @@ def __init__(self, interface, name, iterables=None, itersource=None,
         if 'base_dir' in kwargs:
             base_dir = kwargs['base_dir']
         super(Node, self).__init__(name, base_dir)
+
+        # Make sure an interface is set, and that it is an Interface
         if interface is None:
             raise IOError('Interface must be provided')
         if not isinstance(interface, Interface):
             raise IOError('interface must be an instance of an Interface')
         self._interface = interface
         self.name = name
+
         self._result = None
         self.iterables = iterables
         self.synchronize = synchronize
@@ -170,8 +173,10 @@ def __init__(self, interface, name, iterables=None, itersource=None,
         self.needed_outputs = []
         self.plugin_args = {}
 
-        self._n_procs = n_procs
         self._mem_gb = mem_gb
+        self._n_procs = n_procs
+        if hasattr(self.inputs, 'num_threads') and self._n_procs is not None:
+            self.inputs.num_threads = self._n_procs
 
         if needed_outputs:
             self.needed_outputs = sorted(needed_outputs)
@@ -213,16 +218,22 @@ def mem_gb(self):
 
     @property
     def n_procs(self):
-        """Get estimated number of processes"""
-        if hasattr(self._interface, 'num_threads'):
-            self._n_procs = self._interface.num_threads
-            logger.warning('Setting "num_threads" on Interfaces has been '
-                           'deprecated as of nipype 1.0, please use Node.n_procs')
-
-        if hasattr(self._interface.inputs, 'num_threads') and isdefined(
-            self._interface.inputs.num_threads):
-            self._n_procs = self._interface.inputs.num_threads
-        return self._n_procs
+        """Get the estimated number of processes/threads"""
+        if self._n_procs is not None:
+            return self._n_procs
+        elif hasattr(self.inputs, 'num_threads') and isdefined(self.inputs.num_threads):
+            return self.inputs.num_threads
+        else:
+            return 1
+
+    @n_procs.setter
+    def n_procs(self, value):
+        """Set an estimated number of processes/threads"""
+        self._n_procs = value
+
+        # Overwrite interface's dynamic input of num_threads
+        if hasattr(self._interface.inputs, 'num_threads'):
+            self._interface.inputs.num_threads = self._n_procs
 
     def output_dir(self):
         """Return the location of the output directory for the node"""

nipype/utils/draw_gantt_chart.py

@@ -1,8 +1,9 @@
 # -*- coding: utf-8 -*-
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
-"""Module to draw an html gantt chart from logfile produced by
-callback_log.log_nodes_cb()
+"""
+Module to draw an html gantt chart from logfile produced by
+``nipype.utils.profiler.log_nodes_cb()``
 """
 from __future__ import print_function, division, unicode_literals, absolute_import