Merge pull request #3516 from DimitriPapadopoulos/doc

DOC: Fix a few more typos

Author: effigies

doc/devel/interface_specs.rst

@@ -148,7 +148,7 @@ base class down to subclasses).:
 
 	        ``SlicerCommandLineInputSpec``: Defines inputs common to all Slicer classes (``module``)
 
-Most developers will only need to code at the the interface-level (i.e. implementing custom class inheriting from one of the above classes).
+Most developers will only need to code at the interface-level (i.e. implementing custom class inheriting from one of the above classes).
 
 Output Specs
 ^^^^^^^^^^^^
@@ -519,7 +519,7 @@ SPM
 
 For SPM-mediated interfaces:
 
-* ``_jobtype`` and ``_jobname``: special names used used by the SPM job manager. You can find them by saving your batch job as an .m file and looking up the code.
+* ``_jobtype`` and ``_jobname``: special names used by the SPM job manager. You can find them by saving your batch job as an .m file and looking up the code.
 
 And optionally:
 

doc/devel/provenance.rst

@@ -5,7 +5,7 @@ W3C PROV support
 Overview
 --------
 
-We're using the the `W3C PROV data model <http://www.w3.org/TR/prov-dm/>`_ to
+We're using the `W3C PROV data model <http://www.w3.org/TR/prov-dm/>`_ to
 capture and represent provenance in Nipype.
 
 For an overview see:

nipype/interfaces/afni/utils.py

@@ -2151,7 +2151,7 @@ class NwarpCatInputSpec(AFNICommandInputSpec):
         usedefault=True,
     )
     expad = traits.Int(
-        desc="Pad the nonlinear warps by the given number of voxels voxels in "
+        desc="Pad the nonlinear warps by the given number of voxels in "
         "all directions. The warp displacements are extended by linear "
         "extrapolation from the faces of the input grid..",
         argstr="-expad %d",

nipype/interfaces/diffusion_toolkit/dti.py

@@ -208,7 +208,7 @@ class DTITrackerInputSpec(CommandLineInputSpec):
         desc="set angle threshold. default value is 35 degree", argstr="-at %f"
     )
     angle_threshold_weight = traits.Float(
-        desc="set angle threshold weighting factor. weighting will be be applied "
+        desc="set angle threshold weighting factor. weighting will be applied "
         "on top of the angle_threshold",
         argstr="-atw %f",
     )

nipype/interfaces/dtitk/utils.py

@@ -161,7 +161,7 @@ class TVResampleInputSpec(CommandLineInputSpec):
         desc="how to align output volume to input volume",
     )
     interpolation = traits.Enum(
-        "LEI", "EI", argstr="-interp %s", desc="Log Euclidean Euclidean Interpolation"
+        "LEI", "EI", argstr="-interp %s", desc="Log Euclidean Interpolation"
     )
     array_size = traits.Tuple(
         (traits.Int(), traits.Int(), traits.Int()),

nipype/interfaces/minc/minc.py

@@ -1285,7 +1285,7 @@ class BeastInputSpec(CommandLineInputSpec):
      -positive:         Specify mask of positive segmentation (inside mask) instead of the default mask.
      -output_selection: Specify file to output selected files.
      -count:            Specify file to output the patch count.
-     -mask:             Specify a segmentation mask instead of the the default mask.
+     -mask:             Specify a segmentation mask instead of the default mask.
      -no_mask:          Do not apply a segmentation mask. Perform the segmentation over the entire image.
      -no_positive:      Do not apply a positive mask.
     Generic options for all commands:

nipype/interfaces/mipav/developer.py

@@ -1253,7 +1253,7 @@ class MedicAlgorithmSPECTRE2010InputSpec(CommandLineInputSpec):
         traits.Bool,
         File(),
         hash_files=False,
-        desc="Tissue classification of of the whole input volume.",
+        desc="Tissue classification of the whole input volume.",
         argstr="--outFANTASM %s",
     )
     outd0 = traits.Either(
@@ -1310,7 +1310,7 @@ class MedicAlgorithmSPECTRE2010OutputSpec(TraitedSpec):
     )
     outPrior = File(desc="Probability prior from the atlas registrations", exists=True)
     outFANTASM = File(
-        desc="Tissue classification of of the whole input volume.", exists=True
+        desc="Tissue classification of the whole input volume.", exists=True
     )
     outd0 = File(desc="Initial Brainmask", exists=True)
     outMidsagittal = File(desc="Plane dividing the brain hemispheres", exists=True)

nipype/interfaces/semtools/diffusion/gtract.py

@@ -1119,7 +1119,7 @@ class gtractCoRegAnatomyInputSpec(CommandLineInputSpec):
         argstr="--inputVolume %s",
     )
     inputAnatomicalVolume = File(
-        desc="Required: input anatomical image file name. It is recommended that that the input anatomical image has been skull stripped and has the same orientation as the DWI scan.",
+        desc="Required: input anatomical image file name. It is recommended that the input anatomical image has been skull stripped and has the same orientation as the DWI scan.",
         exists=True,
         argstr="--inputAnatomicalVolume %s",
     )

nipype/interfaces/slicer/generate_classes.py

@@ -196,7 +196,7 @@ def generate_class(
             if longFlagNode:
                 # Prefer to use longFlag as name if it is given, rather than the parameter name
                 longFlagName = longFlagNode[0].firstChild.nodeValue
-                # SEM automatically strips prefixed "--" or "-" from from xml before processing
+                # SEM automatically strips prefixed "--" or "-" from xml before processing
                 # we need to replicate that behavior here The following
                 # two nodes in xml have the same behavior in the program
                 # <longflag>--test</longflag>

nipype/interfaces/slicer/registration/brainsfit.py

@@ -279,7 +279,7 @@ class BRAINSFitInputSpec(CommandLineInputSpec):
         argstr="--numberOfThreads %d",
     )
     forceMINumberOfThreads = traits.Int(
-        desc="Force the the maximum number of threads to use for non thread safe MI metric.  CAUTION: Inconsistent results my arise!",
+        desc="Force the maximum number of threads to use for non thread safe MI metric.  CAUTION: Inconsistent results my arise!",
         argstr="--forceMINumberOfThreads %d",
     )
     debugLevel = traits.Int(