adding interface fsl.Slice

Author: salma1601

nipype/interfaces/fsl/__init__.py

@@ -13,12 +13,13 @@
 from .model import (Level1Design, FEAT, FEATModel, FILMGLS, FEATRegister,
                     FLAMEO, ContrastMgr, MultipleRegressDesign, L2Model, SMM,
                     MELODIC, SmoothEstimate, Cluster, Randomise, GLM)
-from .utils import (
-    AvScale, Smooth, Merge, ExtractROI, Split, ImageMaths, ImageMeants,
-    ImageStats, FilterRegressor, Overlay, Slicer, PlotTimeSeries,
-    PlotMotionParams, ConvertXFM, SwapDimensions, PowerSpectrum, Reorient2Std,
-    Complex, InvWarp, WarpUtils, ConvertWarp, WarpPoints, WarpPointsToStd,
-    WarpPointsFromStd, RobustFOV, CopyGeom, MotionOutliers)
+from .utils import (AvScale, Smooth, Merge, ExtractROI, Split, ImageMaths, ImageMeants,
+                    ImageStats, FilterRegressor, Overlay, Slicer, Slice,
+                    PlotTimeSeries, PlotMotionParams, ConvertXFM,
+                    SwapDimensions, PowerSpectrum, Reorient2Std,
+                    Complex, InvWarp, WarpUtils, ConvertWarp, WarpPoints,
+                    WarpPointsToStd, WarpPointsFromStd, RobustFOV,
+                    CopyGeom, MotionOutliers)
 
 from .epi import (PrepareFieldmap, TOPUP, ApplyTOPUP, Eddy, EPIDeWarp, SigLoss,
                   EddyCorrect, EpiReg)

nipype/interfaces/fsl/utils.py

@@ -262,6 +262,70 @@ def _format_arg(self, name, trait_spec, value):
         return super(Smooth, self)._format_arg(name, trait_spec, value)
 
 
+class SliceInputSpec(FSLCommandInputSpec):
+    in_file = File(exists=True, argstr="%s", position=0, mandatory=True,
+                   desc="input filename")
+    out_base_name = traits.Str(argstr="%s", position=1, desc="outputs prefix")
+
+
+class SliceOutputSpec(TraitedSpec):
+    out_files = OutputMultiPath(File(exists=True))
+
+
+class Slice(FSLCommand):
+    """Use fslslice to split a 3D file into lots of 2D files (along z-axis).
+
+
+    Examples
+    --------
+
+    >>> from nipype.interfaces.fsl import Slice
+    >>> slice = Slice()
+    >>> slice.inputs.in_file = 'functional.nii'
+    >>> slice.inputs.out_base_name = 'sl'
+    >>> slice.cmdline
+    'fslslice functional.nii sl'
+
+
+    """
+
+    _cmd = 'fslslice'
+    input_spec = SliceInputSpec
+    output_spec = SliceOutputSpec
+
+    def _list_outputs(self):
+        """Create a Bunch which contains all possible files generated
+        by running the interface.  Some files are always generated, others
+        depending on which ``inputs`` options are set.
+
+        Returns
+        -------
+
+        outputs : Bunch object
+            Bunch object containing all possible files generated by
+            interface object.
+
+            If None, file was not generated
+            Else, contains path, filename of generated outputfile
+
+        """
+        outputs = self._outputs().get()
+        ext = Info.output_type_to_ext(self.inputs.output_type)
+        if isdefined(self.inputs.out_base_name):
+            outbase = self.inputs.out_base_name + '_slice_*'
+            out_dir = os.getcwd()
+        else:
+            out_dir = os.path.dirname(self.inputs.in_file)
+            in_base, _ = os.path.splitext(self.inputs.in_file)
+            if '.gz' in self.inputs.in_file:
+                in_base, _ = os.path.splitext(in_base)
+
+            outbase = in_base + '_slice*'
+        outputs['out_files'] = sorted(glob(os.path.join(out_dir,
+                                                        outbase + ext)))
+        return outputs
+
+
 class MergeInputSpec(FSLCommandInputSpec):
     in_files = traits.List(
         File(exists=True), argstr="%s", position=2, mandatory=True)