Merge branch 'master' into enh/AddCSVRow

Conflicts:
	CHANGES

Author: oesteban

CHANGES

@@ -2,6 +2,9 @@ Next Release
 ============
 
 * ENH: New miscelaneous interface: AddCSVRow
+* ENH: FUGUE interface has been refactored to use the name_template system, 3 examples 
+       added to doctests, some bugs solved.
+* ENH: Added new interfaces (fsl.utils.WarpUtils, ConvertWarp) to fnirtfileutils and convertwarp
 * API: Interfaces to external packages are no longer available in the top-level
        ``nipype`` namespace, and must be imported directly (e.g.
        ``from nipype.interfaces import fsl``).

nipype/algorithms/misc.py

@@ -835,10 +835,10 @@ def __init__(self, infields=None, force_run=True, **kwargs):
 
         if infields:
             for key in infields:
-                self.inputs.add_trait( key, traits.Any )
+                self.inputs.add_trait(key, traits.Any)
                 self.inputs._outputs[key] = Undefined
                 undefined_traits[key] = Undefined
-        self.inputs.trait_set(trait_change_notify=False, **undefined_traits )
+        self.inputs.trait_set(trait_change_notify=False, **undefined_traits)
 
         if force_run:
             self._always_run = True
@@ -876,7 +876,7 @@ def _run_interface(self, runtime):
 
         if op.exists(self.inputs.in_file):
             formerdf = pd.read_csv(self.inputs.in_file, index_col=0)
-            df = pd.concat( [formerdf, df], ignore_index=True )
+            df = pd.concat([formerdf, df], ignore_index=True )
 
         with open(self.inputs.in_file, 'w') as f:
             df.to_csv(f)

nipype/interfaces/afni/tests/test_auto_Volreg.py

@@ -32,6 +32,11 @@ def test_Volreg_inputs():
     name_source='in_file',
     name_template='%s.1D',
     ),
+    oned_matrix_save=dict(argstr='-1Dmatrix_save %s',
+    keep_extension=True,
+    name_source='in_file',
+    name_template='%s.aff12.1D',
+    ),
     out_file=dict(argstr='-prefix %s',
     name_source='in_file',
     name_template='%s_volreg',
@@ -57,6 +62,7 @@ def test_Volreg_inputs():
 def test_Volreg_outputs():
     output_map = dict(md1d_file=dict(),
     oned_file=dict(),
+    oned_matrix_save=dict(),
     out_file=dict(),
     )
     outputs = Volreg.output_spec()

nipype/interfaces/ants/tests/test_auto_LaplacianThickness.py

@@ -0,0 +1,65 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from nipype.testing import assert_equal
+from nipype.interfaces.ants.segmentation import LaplacianThickness
+
+def test_LaplacianThickness_inputs():
+    input_map = dict(args=dict(argstr='%s',
+    ),
+    dT=dict(argstr='dT=%d',
+    position=6,
+    ),
+    environ=dict(nohash=True,
+    usedefault=True,
+    ),
+    ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    input_gm=dict(argstr='%s',
+    copyfile=True,
+    mandatory=True,
+    position=2,
+    ),
+    input_wm=dict(argstr='%s',
+    copyfile=True,
+    mandatory=True,
+    position=1,
+    ),
+    num_threads=dict(nohash=True,
+    usedefault=True,
+    ),
+    opt_tolerance=dict(argstr='optional-laplacian-tolerance=%d',
+    position=8,
+    ),
+    output_image=dict(argstr='%s',
+    genfile=True,
+    hash_files=False,
+    position=3,
+    ),
+    prior_thickness=dict(argstr='priorthickval=%d',
+    position=5,
+    ),
+    smooth_param=dict(argstr='smoothparam=%d',
+    position=4,
+    ),
+    sulcus_prior=dict(argstr='use-sulcus-prior',
+    position=7,
+    ),
+    terminal_output=dict(mandatory=True,
+    nohash=True,
+    ),
+    )
+    inputs = LaplacianThickness.input_spec()
+
+    for key, metadata in input_map.items():
+        for metakey, value in metadata.items():
+            yield assert_equal, getattr(inputs.traits()[key], metakey), value
+
+def test_LaplacianThickness_outputs():
+    output_map = dict(output_image=dict(),
+    )
+    outputs = LaplacianThickness.output_spec()
+
+    for key, metadata in output_map.items():
+        for metakey, value in metadata.items():
+            yield assert_equal, getattr(outputs.traits()[key], metakey), value
+

nipype/interfaces/fsl/__init__.py

@@ -16,7 +16,7 @@
                     ImageStats, FilterRegressor, Overlay, Slicer,
                     PlotTimeSeries, PlotMotionParams, ConvertXFM,
                     SwapDimensions, PowerSpectrum, Reorient2Std,
-                    Complex, InvWarp)
+                    Complex, InvWarp, WarpUtils, ConvertWarp)
 
 from .epi import (PrepareFieldmap, TOPUP, ApplyTOPUP, Eddy, EPIDeWarp,
                   SigLoss, EddyCorrect)