Merge branch 'master' into bug/afni

* master:
  added maths.MaxImage examples
  test maths.MaxImage for fslmaths -Tmax option
  add maths.MaxImage for fslmaths -Tmax option
  fix: change type of loops,speedup and between loops so its compatible with changes in the nipy code

Author: bpinsard

nipype/interfaces/fsl/maths.py

@@ -117,6 +117,28 @@ class MeanImage(MathsCommand):
     input_spec = MeanImageInput
     _suffix = "_mean"
 
+class MaxImageInput(MathsInput):
+
+    dimension = traits.Enum("T", "X", "Y", "Z", usedefault=True, argstr="-%smax", position=4,
+        desc="dimension to max across")
+
+
+class MaxImage(MathsCommand):
+    """Use fslmaths to generate a max image across a given dimension.
+
+    Examples
+    --------
+    from nipype.interfaces.fsl.maths import MaxImage
+    maxer = MaxImage() 
+    maxer.inputs.in_file = "functional.nii"
+    maxer.dimension = "T"
+    maths.cmdline
+    fslmaths functional.nii -Tmax functional_max.nii
+    
+    """
+    input_spec = MaxImageInput
+    _suffix = "_max"
+
 
 class IsotropicSmoothInput(MathsInput):
 

nipype/interfaces/fsl/tests/test_maths.py

@@ -169,6 +169,32 @@ def test_meanimage():
     # Clean up our mess
     clean_directory(testdir, origdir, ftype)
 
+@skipif(no_fsl)
+def test_maximage():
+    files, testdir, origdir, ftype = create_files_in_directory()
+
+    # Get the command
+    maxer = fsl.MaxImage(in_file="a.nii",out_file="b.nii")
+
+    # Test the underlying command
+    yield assert_equal, maxer.cmd, "fslmaths"
+
+    # Test the defualt opstring
+    yield assert_equal, maxer.cmdline, "fslmaths a.nii -Tmax b.nii"
+
+    # Test the other dimensions
+    cmdline = "fslmaths a.nii -%smax b.nii"
+    for dim in ["X","Y","Z","T"]:
+        maxer.inputs.dimension=dim
+        yield assert_equal, maxer.cmdline, cmdline%dim
+
+    # Test the auto naming
+    maxer = fsl.MaxImage(in_file="a.nii")
+    yield assert_equal, maxer.cmdline, "fslmaths a.nii -Tmax %s"%os.path.join(testdir, "a_max.nii")
+
+    # Clean up our mess
+    clean_directory(testdir, origdir, ftype)
+
 @skipif(no_fsl)
 def test_smooth():
     files, testdir, origdir, ftype = create_files_in_directory()

nipype/interfaces/nipy/preprocess.py

@@ -156,9 +156,9 @@ def _run_interface(self, runtime):
                  time_interp=self.inputs.time_interp,
                  start=self.inputs.start)
 
-        R.estimate(loops=self.inputs.loops,
-                   between_loops=self.inputs.between_loops,
-                   speedup=self.inputs.speedup)
+        R.estimate(loops=list(self.inputs.loops),
+                   between_loops=list(self.inputs.between_loops),
+                   speedup=list(self.inputs.speedup))
 
         corr_run = R.resample()
         self._out_file_path = []