FSL slice

nipype/interfaces/fsl/__init__.py

@@ -14,7 +14,7 @@
                     FLAMEO, ContrastMgr, MultipleRegressDesign, L2Model, SMM,
                     MELODIC, SmoothEstimate, Cluster, Randomise, GLM)
 from .utils import (
-    AvScale, Smooth, Merge, ExtractROI, Split, ImageMaths, ImageMeants,
+    AvScale, Smooth, Slice, Merge, ExtractROI, Split, ImageMaths, ImageMeants,
     ImageStats, FilterRegressor, Overlay, Slicer, PlotTimeSeries,
     PlotMotionParams, ConvertXFM, SwapDimensions, PowerSpectrum, Reorient2Std,
     Complex, InvWarp, WarpUtils, ConvertWarp, WarpPoints, WarpPointsToStd,

nipype/interfaces/fsl/tests/test_auto_Slice.py

@@ -0,0 +1,45 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from __future__ import unicode_literals
+from ..utils import Slice
+
+
+def test_Slice_inputs():
+    input_map = dict(
+        args=dict(argstr='%s', ),
+        environ=dict(
+            nohash=True,
+            usedefault=True,
+        ),
+        ignore_exception=dict(
+            deprecated='1.0.0',
+            nohash=True,
+            usedefault=True,
+        ),
+        in_file=dict(
+            argstr='%s',
+            copyfile=False,
+            mandatory=True,
+            position=0,
+        ),
+        out_base_name=dict(
+            argstr='%s',
+            position=1,
+        ),
+        output_type=dict(),
+        terminal_output=dict(
+            deprecated='1.0.0',
+            nohash=True,
+        ),
+    )
+    inputs = Slice.input_spec()
+
+    for key, metadata in list(input_map.items()):
+        for metakey, value in list(metadata.items()):
+            assert getattr(inputs.traits()[key], metakey) == value
+def test_Slice_outputs():
+    output_map = dict(out_files=dict(), )
+    outputs = Slice.output_spec()
+
+    for key, metadata in list(output_map.items()):
+        for metakey, value in list(metadata.items()):
+            assert getattr(outputs.traits()[key], metakey) == value

nipype/interfaces/fsl/utils.py

@@ -262,6 +262,68 @@ 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", copyfile=False)
+    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)
+        suffix = '_slice_*' + ext
+        if isdefined(self.inputs.out_base_name):
+            fname_template = os.path.abspath(
+                self.inputs.out_base_name + suffix)
+        else:
+            fname_template = fname_presuffix(self.inputs.in_file,
+                                             suffix=suffix, use_ext=False)
+
+        outputs['out_files'] = sorted(glob(fname_template))
+
+        return outputs
+
+
 class MergeInputSpec(FSLCommandInputSpec):
     in_files = traits.List(
         File(exists=True), argstr="%s", position=2, mandatory=True)