Merge pull request #1117 from chrisfilo/enh/robustfov

Enh/robustfov

Author: satra

nipype/interfaces/fsl/__init__.py

@@ -16,7 +16,8 @@
                     ImageStats, FilterRegressor, Overlay, Slicer,
                     PlotTimeSeries, PlotMotionParams, ConvertXFM,
                     SwapDimensions, PowerSpectrum, Reorient2Std,
-                    Complex, InvWarp, WarpUtils, ConvertWarp, WarpPoints, WarpPointsToStd)
+                    Complex, InvWarp, WarpUtils, ConvertWarp, WarpPoints, 
+                    WarpPointsToStd, RobustFOV)
 
 from .epi import (PrepareFieldmap, TOPUP, ApplyTOPUP, Eddy, EPIDeWarp,
                   SigLoss, EddyCorrect, EpiReg)

nipype/interfaces/fsl/tests/test_auto_RobustFOV.py

@@ -0,0 +1,41 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from nipype.testing import assert_equal
+from nipype.interfaces.fsl.utils import RobustFOV
+
+def test_RobustFOV_inputs():
+    input_map = dict(args=dict(argstr='%s',
+    ),
+    environ=dict(nohash=True,
+    usedefault=True,
+    ),
+    ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    in_file=dict(argstr='-i %s',
+    mandatory=True,
+    position=0,
+    ),
+    out_roi=dict(argstr='-r %s',
+    hash_files=False,
+    name_source=['in_file'],
+    name_template='%s_ROI',
+    ),
+    output_type=dict(),
+    terminal_output=dict(nohash=True,
+    ),
+    )
+    inputs = RobustFOV.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_RobustFOV_outputs():
+    output_map = dict(out_roi=dict(),
+    )
+    outputs = RobustFOV.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/utils.py

@@ -31,6 +31,24 @@
 warn = warnings.warn
 warnings.filterwarnings('always', category=UserWarning)
 
+class RobustFOVInputSpec(FSLCommandInputSpec):
+    in_file = File(exists=True,
+                   desc='input filename',
+                   argstr='-i %s', position=0, mandatory=True)
+    out_roi = File(desc="ROI volume output name", argstr="-r %s",
+                   name_source=['in_file'], hash_files=False, 
+                   name_template='%s_ROI')
+    
+    
+class RobustFOVOutputSpec(TraitedSpec):
+    out_roi = File(exists=True, desc="ROI volume output name")
+
+
+class RobustFOV(FSLCommand):
+    _cmd = 'robustfov'
+    input_spec = RobustFOVInputSpec
+    output_spec = RobustFOVOutputSpec
+    
 
 class ImageMeantsInputSpec(FSLCommandInputSpec):
     in_file = File(exists=True,