resolved conflict

satra · satra · commit 264af7cfa3ca · 2011-01-17T17:34:06.000-05:00
diff --git a/CHANGES b/CHANGES
@@ -2,6 +2,7 @@ Release 0.4 (FUTURE)
 ======================
 
 * ENH: New interface: freesurfer.ApplyMask (mri_mask)
+* ENH: New FSL interface -- SwapDimensions (fslswapdim)
 
 Release 0.3.4 (Jan 12, 2011)
 ======================
diff --git a/nipype/interfaces/fsl/__init__.py b/nipype/interfaces/fsl/__init__.py
@@ -22,7 +22,7 @@
                                          ImageMaths, ImageMeants, ImageStats,
                                          FilterRegressor, Overlay, Slicer,
                                          PlotTimeSeries, PlotMotionParams,
-                                         ConvertXFM)
+                                         ConvertXFM, SwapDimensions)
 from nipype.interfaces.fsl.dti import (EddyCorrect, BEDPOSTX, DTIFit, 
                                        ProbTrackX, VecReg, ProjThresh,
                                        FindTheBiggest)
diff --git a/nipype/interfaces/fsl/tests/test_utils.py b/nipype/interfaces/fsl/tests/test_utils.py
@@ -355,3 +355,29 @@ def test_convertxfm():
         "convert_xfm -omat bar.mat -concat %s %s"%(filelist[1], filelist[0])
 
     clean_directory(outdir, cwd)
+
+@skipif(no_fsl)
+def test_swapdims():
+    files, testdir, origdir = create_files_in_directory()
+    swap = fsl.SwapDimensions()
+
+    # Test the underlying command
+    yield assert_equal, swap.cmd, "fslswapdim"
+
+    # Test mandatory args
+    args = [dict(in_file=files[0]), dict(new_dims=("x","y","z"))]
+    for arg in args:
+        wontrun = fsl.SwapDimensions(**arg)
+        yield assert_raises, ValueError, wontrun.run
+
+    # Now test a basic command line
+    swap.inputs.in_file = files[0]
+    swap.inputs.new_dims = ("x", "y", "z")
+    yield assert_equal, swap.cmdline, "fslswapdim a.nii x y z %s"%os.path.join(testdir, "a_newdims.nii")
+
+    # Test that we can set an output name
+    swap.inputs.out_file = "b.nii"
+    yield assert_equal, swap.cmdline, "fslswapdim a.nii x y z b.nii"
+
+    # Clean up
+    clean_directory(testdir, origdir)
diff --git a/nipype/interfaces/fsl/utils.py b/nipype/interfaces/fsl/utils.py
@@ -832,3 +832,45 @@ def _gen_filename(self, name):
         if name == "out_file":
             return self._list_outputs()["out_file"]
         return None
+
+
+class SwapDimensionsInputSpec(FSLCommandInputSpec):
+
+    in_file = File(exists=True, mandatory=True, argstr="%s", position="1",
+                   desc="input image")
+    _dims = ["x","-x","y","-y","z","-z","RL","LR","AP","PA","IS","SI"]
+    new_dims = traits.Tuple(traits.Enum(_dims), traits.Enum(_dims), traits.Enum(_dims),
+                            argstr="%s %s %s", mandatory=True,
+                            desc="3-tuple of new dimension order")
+    out_file = File(genfile=True, argstr="%s", desc="image to write")
+
+class SwapDimensionsOutputSpec(TraitedSpec):
+
+    out_file = File(exists=True, desc="image with new dimensions")
+
+class SwapDimensions(FSLCommand):
+    """Use fslswapdim to alter the orientation of an image.
+
+    This interface accepts a three-tuple corresponding to the new
+    orientation.  You may either provide dimension ids in the form of
+    (-)x, (-)y, or (-z), or nifti-syle dimension codes (RL, LR, AP, PA, IS, SI).
+
+    """
+    _cmd = "fslswapdim"
+    input_spec = SwapDimensionsInputSpec
+    output_spec = SwapDimensionsOutputSpec
+
+    def _list_outputs(self):
+        outputs = self._outputs().get()
+        outputs["out_file"] = self.inputs.out_file
+        if not isdefined(self.inputs.out_file):
+            outputs["out_file"] = fname_presuffix(self.inputs.in_file,
+                                                  suffix="_newdims",
+                                                  use_ext=True,
+                                                  newpath=os.getcwd())
+        return outputs
+
+    def _gen_filename(self, name):
+        if name == "out_file":
+            return self._list_outputs()["out_file"]
+        return None
