Add AFNI command 3dNotes.

1. Add 3dNotes to preprocess. It probably belongs in a utils file.
2. Fix typos in QualityIndexOutputSpec and AutoboxOutputSpec.
3. Remove a couple of extra empty lines.

Author: tsalo

nipype/interfaces/afni/preprocess.py

@@ -2102,7 +2102,6 @@ class CalcInputSpec(AFNICommandInputSpec):
     other = File(desc='other options', argstr='')
 
 
-
 class Calc(AFNICommand):
     """This program does voxel-by-voxel arithmetic on 3D datasets
 
@@ -2326,7 +2325,7 @@ class AutoboxInputSpec(AFNICommandInputSpec):
                 cropping box, and will clip off small isolated blobs.""")
 
 
-class AutoboxOuputSpec(TraitedSpec):  # out_file not mandatory
+class AutoboxOutputSpec(TraitedSpec):  # out_file not mandatory
     x_min = traits.Int()
     x_max = traits.Int()
     y_min = traits.Int()
@@ -2357,7 +2356,7 @@ class Autobox(AFNICommand):
 
     _cmd = '3dAutobox'
     input_spec = AutoboxInputSpec
-    output_spec = AutoboxOuputSpec
+    output_spec = AutoboxOutputSpec
 
     def aggregate_outputs(self, runtime=None, needed_outputs=None):
         outputs = self._outputs()
@@ -2923,7 +2922,6 @@ class OutlierCountOutputSpec(TraitedSpec):
         keep_extension=False, position=-1, desc='capture standard output')
 
 
-
 class OutlierCount(CommandLine):
     """Create a 3D dataset from 2D image files using AFNI to3d command
 
@@ -2989,8 +2987,7 @@ class QualityIndexInputSpec(CommandLineInputSpec):
 
 
 class QualityIndexOutputSpec(TraitedSpec):
-    out_file = File(desc='file containing the caputured standard output')
-
+    out_file = File(desc='file containing the captured standard output')
 
 
 class QualityIndex(CommandLine):
@@ -3013,3 +3010,56 @@ class QualityIndex(CommandLine):
     _cmd = '3dTqual'
     input_spec = QualityIndexInputSpec
     output_spec = QualityIndexOutputSpec
+
+
+class NotesInputSpec(AFNICommandInputSpec):
+    in_file = File(desc="input file to 3dNotes",
+                   argstr="%s",
+                   position=-1,
+                   mandatory=True,
+                   exists=True,
+                   copyfile=False)
+    add = traits.Str(desc="note to add",
+                     argstr="-a '%s'")
+    add_history = traits.Str(desc="note to add to history",
+                             argstr="-h '%s'",
+                             xor=["rep_history"])
+    rep_history = traits.Str(desc="note with which to replace history",
+                             argstr="-HH '%s'",
+                             xor=["add_history"])
+    delete = traits.Int(desc="delete note number num",
+                        argstr="-d %d")
+    ses = traits.Bool(desc="print to stdout the expanded notes",
+                      argstr="-ses")
+    out_file = File(desc='output image file name',
+                    argstr='%s')
+
+
+class Notes(CommandLine):
+    """
+    A program to add, delete, and show notes for AFNI datasets.
+
+    For complete details, see the `3dNotes Documentation.
+    <http://afni.nimh.nih.gov/pub/dist/doc/program_help/3dNotes.html>
+
+    Examples
+    ========
+
+    >>> from nipype.interfaces import afni as afni
+    >>> notes = afni.Notes()
+    >>> notes.inputs.in_file = "functional.HEAD"
+    >>> notes.inputs.add = "This note is added."
+    >>> notes.inputs.add_history = "This note is added to history."
+    >>> notes.cmdline #doctest:
+    '3dNotes -a "This note is added." -h "This note is added to history." functional.HEAD'
+    >>> res = notes.run()   # doctest: +SKIP
+    """
+
+    _cmd = '3dNotes'
+    input_spec = NotesInputSpec
+    output_spec = AFNICommandOutputSpec
+    
+    def _list_outputs(self):
+        outputs = self.output_spec().get()
+        outputs["out_file"] = os.path.abspath(self.inputs.in_file)
+        return outputs