Merge remote-tracking branch 'upstream/master' into rel/0.13.0-rc1

* upstream/master:
  reverting exception back to TypeError.
  changes based on feedback from review
  fix: doctest
  use properly converted path as basedir
  Adding testcase for parameterize_dirs==False
  trying to fix problems with traits4.6 (traits.HasTraits.traits has been modified)
  enh: test
  enh: removed old command
  encode() dir path has prior to computing sha1
  made melodic output paths absolute
  enh: additional eddy inputs

Author: satra

nipype/interfaces/base.py

@@ -643,7 +643,8 @@ def __deepcopy__(self, memo):
         dup_dict = deepcopy(self.get(), memo)
         # access all keys
         for key in self.copyable_trait_names():
-            _ = getattr(self, key)
+            if key in self.__dict__.keys():
+                _ = getattr(self, key)
         # clone once
         dup = self.clone_traits(memo=memo)
         for key in self.copyable_trait_names():

nipype/interfaces/fsl/epi.py

@@ -432,6 +432,19 @@ class EddyInputSpec(FSLCommandInputSpec):
                         desc='Detect and replace outlier slices')
     num_threads = traits.Int(1, usedefault=True, nohash=True,
                              desc="Number of openmp threads to use")
+    is_shelled = traits.Bool(False, argstr='--data_is_shelled',
+                             desc="Override internal check to ensure that "
+                                  "date are acquired on a set of b-value "
+                                  "shells")
+    field = traits.Str(argstr='--field=%s',
+                       desc="NonTOPUP fieldmap scaled in Hz - filename has "
+                            "to be provided without an extension. TOPUP is "
+                            "strongly recommended")
+    field_mat = File(exists=True, argstr='--field_mat=%s',
+                     desc="Matrix that specifies the relative locations of "
+                          "the field specified by --field and first volume "
+                          "in file --imain")
+    use_cuda = traits.Bool(False, desc="Run eddy using cuda gpu")
 
 
 class EddyOutputSpec(TraitedSpec):
@@ -463,13 +476,13 @@ class Eddy(FSLCommand):
     >>> eddy.inputs.in_bvec  = 'bvecs.scheme'
     >>> eddy.inputs.in_bval  = 'bvals.scheme'
     >>> eddy.cmdline # doctest: +ELLIPSIS +ALLOW_UNICODE
-    'eddy --acqp=epi_acqp.txt --bvals=bvals.scheme --bvecs=bvecs.scheme \
+    'eddy_openmp --acqp=epi_acqp.txt --bvals=bvals.scheme --bvecs=bvecs.scheme \
 --imain=epi.nii --index=epi_index.txt --mask=epi_mask.nii \
 --out=.../eddy_corrected'
     >>> res = eddy.run() # doctest: +SKIP
 
     """
-    _cmd = 'eddy'
+    _cmd = 'eddy_openmp'
     input_spec = EddyInputSpec
     output_spec = EddyOutputSpec
 
@@ -478,7 +491,8 @@ class Eddy(FSLCommand):
     def __init__(self, **inputs):
         super(Eddy, self).__init__(**inputs)
         self.inputs.on_trait_change(self._num_threads_update, 'num_threads')
-
+        if isdefined(self.inputs.use_cuda):
+            self._use_cuda()
         if not isdefined(self.inputs.num_threads):
             self.inputs.num_threads = self._num_threads
         else:
@@ -493,6 +507,12 @@ def _num_threads_update(self):
             self.inputs.environ['OMP_NUM_THREADS'] = str(
                 self.inputs.num_threads)
 
+    def _use_cuda(self):
+        if self.inputs.use_cuda:
+            _cmd = 'eddy_cuda'
+        else:
+            _cmd = 'eddy_openmp'
+
     def _format_arg(self, name, spec, value):
         if name == 'in_topup_fieldcoef':
             return spec.argstr % value.split('_fieldcoef')[0]

nipype/interfaces/fsl/model.py

@@ -1555,12 +1555,13 @@ class MELODIC(FSLCommand):
 
     def _list_outputs(self):
         outputs = self.output_spec().get()
-        outputs['out_dir'] = self.inputs.out_dir
-        if not isdefined(outputs['out_dir']):
+        if isdefined(self.inputs.out_dir):
+            outputs['out_dir'] = os.path.abspath(self.inputs.out_dir)
+        else:
             outputs['out_dir'] = self._gen_filename("out_dir")
         if isdefined(self.inputs.report) and self.inputs.report:
             outputs['report_dir'] = os.path.join(
-                self._gen_filename("out_dir"), "report")
+                outputs['out_dir'], "report")
         return outputs
 
     def _gen_filename(self, name):

nipype/interfaces/fsl/tests/test_auto_Eddy.py

@@ -8,6 +8,10 @@ def test_Eddy_inputs():
     environ=dict(nohash=True,
     usedefault=True,
     ),
+    field=dict(argstr='--field=%s',
+    ),
+    field_mat=dict(argstr='--field_mat=%s',
+    ),
     flm=dict(argstr='--flm=%s',
     ),
     fwhm=dict(argstr='--fwhm=%s',
@@ -34,9 +38,11 @@ def test_Eddy_inputs():
     mandatory=True,
     ),
     in_topup_fieldcoef=dict(argstr='--topup=%s',
-    requires=[u'in_topup_movpar'],
+    requires=['in_topup_movpar'],
+    ),
+    in_topup_movpar=dict(requires=['in_topup_fieldcoef'],
     ),
-    in_topup_movpar=dict(requires=[u'in_topup_fieldcoef'],
+    is_shelled=dict(argstr='--data_is_shelled',
     ),
     method=dict(argstr='--resamp=%s',
     ),
@@ -55,6 +61,7 @@ def test_Eddy_inputs():
     ),
     terminal_output=dict(nohash=True,
     ),
+    use_cuda=dict(),
     )
     inputs = Eddy.input_spec()
 

nipype/pipeline/engine/nodes.py

@@ -391,7 +391,7 @@ def _parameterization_dir(self, param):
             - Otherwise, return the parameterization unchanged.
         """
         if len(param) > 32:
-            return sha1(param).hexdigest()
+            return sha1(param.encode()).hexdigest()
         else:
             return param
 

nipype/pipeline/engine/tests/test_engine.py

@@ -22,7 +22,7 @@
 class InputSpec(nib.TraitedSpec):
     input1 = nib.traits.Int(desc='a random int')
     input2 = nib.traits.Int(desc='a random int')
-
+    input_file = nib.traits.File(desc='Random File')
 
 class OutputSpec(nib.TraitedSpec):
     output1 = nib.traits.List(nib.traits.Int, desc='outputs')
@@ -626,6 +626,33 @@ def func1(in1):
     assert not error_raised
 
 
+def test_parameterize_dirs_false(tmpdir):
+    from ....interfaces.utility import IdentityInterface
+    from ....testing import example_data
+
+    input_file = example_data('fsl_motion_outliers_fd.txt')
+
+    n1 = pe.Node(EngineTestInterface(), name='Node1')
+    n1.iterables = ('input_file', (input_file, input_file))
+    n1.interface.inputs.input1 = 1
+
+    n2 = pe.Node(IdentityInterface(fields='in1'), name='Node2')
+
+    wf = pe.Workflow(name='Test')
+    wf.base_dir = str(tmpdir)
+    wf.config['execution']['parameterize_dirs'] = False
+    wf.connect([(n1, n2, [('output1', 'in1')])])
+
+    error_raised = False
+    try:
+        wf.run()
+    except TypeError as typerr:
+        from nipype.pipeline.engine.base import logger
+        logger.info('Exception: %s' % str(typerr))
+        error_raised = True
+    assert not error_raised
+
+
 def test_serial_input(tmpdir):
     wd = str(tmpdir)
     os.chdir(wd)