Merge pull request #957 from satra/enh/misc

Enh/misc -  a few cleanup and enhancement changes

Author: satra

nipype/interfaces/ants/base.py

@@ -15,7 +15,7 @@
 #  the computer (when running MultiProc) by forcing everything to
 #  single threaded.  This can be a severe penalty for registration
 #  performance.
-LOCAL_DEFAULT_NUMBER_OF_THREADS=-1
+LOCAL_DEFAULT_NUMBER_OF_THREADS=1
 # -Using NSLOTS has the same behavior as ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS
 #  as long as ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS is not set.  Otherwise
 #  ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS takes precidence.
@@ -28,8 +28,8 @@ class ANTSCommandInputSpec(CommandLineInputSpec):
     """Base Input Specification for all ANTS Commands
     """
 
-    num_threads = traits.Int(LOCAL_DEFAULT_NUMBER_OF_THREADS, usedefault=True, nohash=True,
-                             desc="Number of ITK threads to use")
+    num_threads = traits.Int(LOCAL_DEFAULT_NUMBER_OF_THREADS, usedefault=True,
+                             nohash=True, desc="Number of ITK threads to use")
 
 
 class ANTSCommand(CommandLine):

nipype/interfaces/fsl/epi.py

@@ -398,9 +398,9 @@ class EddyInputSpec(FSLCommandInputSpec):
     in_bval = File(exists=True, mandatory=True, argstr='--bvals=%s',
                    desc=('File containing the b-values for all volumes in '
                          '--imain'))
-    out_base = File(argstr='--out=%s',
-                    desc=('basename for output (warped) image'))
-
+    out_base = traits.Unicode('eddy_corrected', argstr='--out=%s',
+                              usedefault=True,
+                              desc=('basename for output (warped) image'))
     session = File(exists=True, argstr='--session=%s',
                    desc=('File containing session indices for all volumes in '
                          '--imain'))
@@ -424,6 +424,8 @@ class EddyInputSpec(FSLCommandInputSpec):
                                'squares)'))
     repol = traits.Bool(False, argstr='--repol',
                         desc='Detect and replace outlier slices')
+    num_threads = traits.Int(1, usedefault=True, nohash=True,
+                             desc="Number of openmp threads to use")
 
 
 class EddyOutputSpec(TraitedSpec):
@@ -457,27 +459,38 @@ class Eddy(FSLCommand):
     >>> eddy.cmdline #doctest: +ELLIPSIS
     'eddy --acqp=epi_acqp.txt --bvals=bvals.scheme --bvecs=bvecs.scheme \
 --imain=epi.nii --index=epi_index.txt --mask=epi_mask.nii \
---out=.../eddy_corrected'
+--out=eddy_corrected'
     >>> res = eddy.run() # doctest: +SKIP
 
     """
     _cmd = 'eddy'
     input_spec = EddyInputSpec
     output_spec = EddyOutputSpec
 
+    _num_threads = 1
+
+    def __init__(self, **inputs):
+        super(Eddy, self).__init__(**inputs)
+        self.inputs.on_trait_change(self._num_threads_update, 'num_threads')
+
+        if not isdefined(self.inputs.num_threads):
+            self.inputs.num_threads = self._num_threads
+        else:
+            self._num_threads_update()
+
+    def _num_threads_update(self):
+        self._num_threads = self.inputs.num_threads
+        if not isdefined(self.inputs.num_threads):
+            if 'OMP_NUM_THREADS' in self.inputs.environ:
+                del self.inputs.environ['OMP_NUM_THREADS']
+        else:
+            self.inputs.environ['OMP_NUM_THREADS'] = str(self.inputs.num_threads)
+
     def _format_arg(self, name, spec, value):
         if name == 'in_topup_fieldcoef':
             return spec.argstr % value.split('_fieldcoef')[0]
         return super(Eddy, self)._format_arg(name, spec, value)
 
-    def _parse_inputs(self, skip=None):
-        if skip is None:
-            skip = []
-
-        if not isdefined(self.inputs.out_base):
-            self.inputs.out_base = os.path.abspath('eddy_corrected')
-        return super(Eddy, self)._parse_inputs(skip=skip)
-
     def _list_outputs(self):
         outputs = self.output_spec().get()
         outputs['out_corrected'] = '%s.nii.gz' % self.inputs.out_base

nipype/interfaces/fsl/tests/test_auto_Eddy.py

@@ -42,7 +42,11 @@ def test_Eddy_inputs():
     ),
     niter=dict(argstr='--niter=%s',
     ),
+    num_threads=dict(nohash=True,
+    usedefault=True,
+    ),
     out_base=dict(argstr='--out=%s',
+    usedefault=True,
     ),
     output_type=dict(),
     repol=dict(argstr='--repol',

nipype/interfaces/spm/model.py

@@ -70,15 +70,19 @@ class Level1DesignInputSpec(SPMCommandInputSpec):
                         Number of basis functions
 """, mandatory=True)
     volterra_expansion_order = traits.Enum(1, 2, field='volt',
-                     desc='Model interactions - yes:1, no:2 (opt)')
+                     desc='Model interactions - yes:1, no:2')
     global_intensity_normalization = traits.Enum('none', 'scaling', field='global',
-                      desc='Global intensity normalization - scaling or none (opt)')
+                      desc='Global intensity normalization - scaling or none')
     mask_image = File(exists=True, field='mask',
-                      desc='Image  for  explicitly  masking the analysis (opt)')
+                      desc='Image  for  explicitly  masking the analysis')
     mask_threshold = traits.Either(traits.Enum('-Inf'), traits.Float(),
-                      desc="Thresholding for the mask (opt, '-Inf')", default='-Inf', usedefault=True)
-    model_serial_correlations = traits.Enum('AR(1)', 'none', field='cvi',
-                      desc='Model serial correlations AR(1) or none (opt)')
+                      desc="Thresholding for the mask",
+                      default='-Inf', usedefault=True)
+    model_serial_correlations = traits.Enum('AR(1)', 'FAST', 'none',
+                                            field='cvi',
+                                            desc=('Model serial correlations '
+                                                  'AR(1), FAST or none. FAST '
+                                                  'is available in SPM12'))
 
 
 class Level1DesignOutputSpec(TraitedSpec):

nipype/interfaces/spm/preprocess.py

@@ -599,7 +599,7 @@ class Segment(SPMCommand):
     >>> seg.run() # doctest: +SKIP
 
     """
-    
+
     if Info.version() and Info.version()['name'] == "SPM12":
         _jobtype = 'tools'
         _jobname = 'oldseg'

nipype/interfaces/spm/tests/test_preprocess.py

@@ -89,13 +89,24 @@ def test_normalize_list_outputs():
     yield assert_true, norm._list_outputs()['normalized_files'][0].startswith('w')
     clean_directory(outdir, cwd)
 
+@skipif(no_spm)
 def test_segment():
-    yield assert_equal, spm.Segment._jobtype, 'spatial'
-    yield assert_equal, spm.Segment._jobname, 'preproc'
-
+    if spm.Info.version()['name'] == "SPM12":
+        yield assert_equal, spm.Segment._jobtype, 'tools'
+        yield assert_equal, spm.Segment._jobname, 'oldseg'
+    else:
+        yield assert_equal, spm.Segment._jobtype, 'spatial'
+        yield assert_equal, spm.Segment._jobname, 'preproc'
+
+@skipif(no_spm)
 def test_newsegment():
-    yield assert_equal, spm.NewSegment._jobtype, 'tools'
-    yield assert_equal, spm.NewSegment._jobname, 'preproc8'
+    if spm.Info.version()['name'] == "SPM12":
+        yield assert_equal, spm.NewSegment._jobtype, 'spatial'
+        yield assert_equal, spm.NewSegment._jobname, 'preproc'
+    else:
+        yield assert_equal, spm.NewSegment._jobtype, 'tools'
+        yield assert_equal, spm.NewSegment._jobname, 'preproc8'
+
 
 def test_smooth():
     yield assert_equal, spm.Smooth._jobtype, 'spatial'

nipype/pipeline/engine.py

@@ -2045,8 +2045,8 @@ def __init__(self, interface, iterfield, name, serial=False, nested=False, **kwa
         serial : boolean
             flag to enforce executing the jobs of the mapnode in a serial manner rather than parallel
         nested : boolea
-            support for nested lists, if set the input list will be flattened before running, and the 
-            nested list structure of the outputs will be resored 
+            support for nested lists, if set the input list will be flattened before running, and the
+            nested list structure of the outputs will be resored
         See Node docstring for additional keyword arguments.
         """
 
@@ -2150,7 +2150,7 @@ def _make_nodes(self, cwd=None):
             cwd = self.output_dir()
         if self.nested:
             nitems = len(flatten(filename_to_list(getattr(self.inputs, self.iterfield[0]))))
-        else:    
+        else:
             nitems = len(filename_to_list(getattr(self.inputs, self.iterfield[0])))
         for i in range(nitems):
             nodename = '_' + self.name + str(i)
@@ -2216,14 +2216,14 @@ def _collate_results(self, nodes):
                     defined_vals = [isdefined(val) for val in values]
                     if any(defined_vals) and self._result.outputs:
                         setattr(self._result.outputs, key, values)
-        
+
         if self.nested:
             for key, _ in self.outputs.items():
                 values = getattr(self._result.outputs, key)
                 if isdefined(values):
                     values = unflatten(values, filename_to_list(getattr(self.inputs, self.iterfield[0])))
                 setattr(self._result.outputs, key, values)
-                        
+
         if returncode and any([code is not None for code in returncode]):
             msg = []
             for i, code in enumerate(returncode):

nipype/pipeline/tests/test_engine.py

@@ -487,7 +487,7 @@ def func1(in1):
     n1.run()
     print n1.get_output('out')
     yield assert_equal, n1.get_output('out'), [[2,[3]],4,[5,6]]
-    
+
     n2 = MapNode(Function(input_names=['in1'],
                           output_names=['out'],
                           function=func1),

nipype/utils/misc.py

@@ -206,7 +206,7 @@ def str2bool(v):
         return False
     else:
         raise ValueError("%s cannot be converted to bool"%v)
-    
+
 def flatten(S):
     if S == []:
         return S
@@ -217,14 +217,14 @@ def flatten(S):
 def unflatten(in_list, prev_structure):
     if not isinstance(in_list, Iterator):
         in_list = iter(in_list)
-        
+
     if not isinstance(prev_structure, list):
         return in_list.next()
     else:
         out = []
         for item in prev_structure:
             out.append(unflatten(in_list, item))
         return out
-    
-    
+
+
 

nipype/utils/tests/test_misc.py

@@ -54,19 +54,19 @@ def test_str2bool():
 
 def test_flatten():
     in_list = [[1,2,3],[4],[[5,6],7],8]
-    
+
     flat = flatten(in_list)
     yield assert_equal, flat, [1,2,3,4,5,6,7,8]
-    
+
     back = unflatten(flat, in_list)
     yield assert_equal, in_list, back
-    
+
     new_list = [2,3,4,5,6,7,8,9]
     back = unflatten(new_list, in_list)
     yield assert_equal, back, [[2,3,4],[5],[[6,7],8],9]
-    
+
     flat = flatten([])
     yield assert_equal, flat, []
-    
+
     back = unflatten([], [])
     yield assert_equal, back, []