Merge pull request #1518 from satra/fix/stdimage

Fix/stdimage

Author: satra

nipype/interfaces/fsl/maths.py

@@ -111,6 +111,17 @@ def _format_arg(self, name, spec, value):
             return arg
         return super(Threshold, self)._format_arg(name, spec, value)
 
+class StdImageInput(MathsInput):
+
+    dimension = traits.Enum("T", "X", "Y", "Z", usedefault=True, argstr="-%sstd", position=4,
+                            desc="dimension to standard deviate across")
+
+
+class StdImage(MathsCommand):
+    """Use fslmaths to generate a standard deviation in an image across a given dimension.
+    """
+    input_spec = StdImageInput
+    _suffix = "_std"
 
 class MeanImageInput(MathsInput):
 

nipype/interfaces/fsl/tests/test_auto_StdImage.py

@@ -0,0 +1,55 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from ....testing import assert_equal
+from ..maths import StdImage
+
+
+def test_StdImage_inputs():
+    input_map = dict(args=dict(argstr='%s',
+    ),
+    dimension=dict(argstr='-%sstd',
+    position=4,
+    usedefault=True,
+    ),
+    environ=dict(nohash=True,
+    usedefault=True,
+    ),
+    ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    in_file=dict(argstr='%s',
+    mandatory=True,
+    position=2,
+    ),
+    internal_datatype=dict(argstr='-dt %s',
+    position=1,
+    ),
+    nan2zeros=dict(argstr='-nan',
+    position=3,
+    ),
+    out_file=dict(argstr='%s',
+    genfile=True,
+    hash_files=False,
+    position=-2,
+    ),
+    output_datatype=dict(argstr='-odt %s',
+    position=-1,
+    ),
+    output_type=dict(),
+    terminal_output=dict(nohash=True,
+    ),
+    )
+    inputs = StdImage.input_spec()
+
+    for key, metadata in list(input_map.items()):
+        for metakey, value in list(metadata.items()):
+            yield assert_equal, getattr(inputs.traits()[key], metakey), value
+
+
+def test_StdImage_outputs():
+    output_map = dict(out_file=dict(),
+    )
+    outputs = StdImage.output_spec()
+
+    for key, metadata in list(output_map.items()):
+        for metakey, value in list(metadata.items()):
+            yield assert_equal, getattr(outputs.traits()[key], metakey), value

nipype/interfaces/fsl/tests/test_maths.py

@@ -194,6 +194,33 @@ def test_meanimage(fsl_output_type=None):
     clean_directory(testdir, origdir)
     set_output_type(prev_type)
 
+@skipif(no_fsl)
+def test_stdimage(fsl_output_type=None):
+    prev_type = set_output_type(fsl_output_type)
+    files, testdir, origdir, out_ext = create_files_in_directory()
+
+    # Get the command
+    stder = fsl.StdImage(in_file="a.nii",out_file="b.nii")
+
+    # Test the underlying command
+    yield assert_equal, stder.cmd, "fslmaths"
+
+    # Test the defualt opstring
+    yield assert_equal, stder.cmdline, "fslmaths a.nii -Tstd b.nii"
+
+    # Test the other dimensions
+    cmdline = "fslmaths a.nii -%sstd b.nii"
+    for dim in ["X","Y","Z","T"]:
+        stder.inputs.dimension=dim
+        yield assert_equal, stder.cmdline, cmdline%dim
+
+    # Test the auto naming
+    stder = fsl.StdImage(in_file="a.nii")
+    yield assert_equal, stder.cmdline, "fslmaths a.nii -Tstd %s"%os.path.join(testdir, "a_std.nii")
+
+    # Clean up our mess
+    clean_directory(testdir, origdir)
+    set_output_type(prev_type)
 
 @skipif(no_fsl)
 def test_maximage(fsl_output_type=None):