Merge pull request #3510 from DimitriPapadopoulos/codespell

DOC: Fix typos found by copdespell

Author: effigies

doc/changelog/1.X.X-changelog.rst

@@ -47,8 +47,8 @@ graph nodes might conflict with pydot parsing.
 Bug-fix release in the 1.8.x series.
 
 The previous release vendored ``distutils.version.LooseVersion``, and the vendored objects did not
-preserve compatiblity with the ``distutils`` objects. This release switches to the
-``looseversion`` package that ensures compatiblity.
+preserve compatibility with the ``distutils`` objects. This release switches to the
+``looseversion`` package that ensures compatibility.
 
 
 1.8.0 (May 10, 2022)

doc/devel/cmd_interface_devel.rst

@@ -65,7 +65,7 @@ extra inputs: environ (a dictionary of environmental variables), and args (a
 string defining extra flags). In addition input spec can define the relation
 between the inputs and the generated command line. To achieve this we have
 added two metadata: ``argstr`` (string defining how the argument should be
-formated) and ``position`` (number defining the order of the arguments).
+formatted) and ``position`` (number defining the order of the arguments).
 For example
 
 .. testcode::
@@ -204,7 +204,7 @@ keep_extension (optional)
 
 In addition one can add functionality to your class or base class, to allow
 changing extensions specific to package or interface. This overload function is
-trigerred only if keep_extension is not defined.
+triggered only if keep_extension is not defined.
 
 .. testcode::
 

doc/devel/filename_generation.rst

@@ -148,8 +148,8 @@ case?
     Out[115]: 'bet foo.nii /Users/cburns/tmp/junk/not_bar.nii'
 
 
-In this case we provide ``outfile`` but not as an absolue path, so the
-absolue path is generated and used for the ``cmdline`` when run, but
+In this case we provide ``outfile`` but not as an absolute path, so the
+absolute path is generated and used for the ``cmdline`` when run, but
 ``mybet.inputs.outfile`` is not updated with the absolute path.
 
 .. sourcecode:: ipython

doc/devel/interface_specs.rst

@@ -437,7 +437,7 @@ SPM
 ^^^
 
 ``field``
-	name of the structure refered by the SPM job manager
+	name of the structure referred by the SPM job manager
 
 	**Required:** This metadata is required by all SPM-mediated
 	  interface classes.

doc/devel/matlab_interface_devel.rst

@@ -9,7 +9,7 @@ Example 1
 +++++++++
 
 This is a minimal script for wrapping MATLAB code. You should replace the MATLAB
-code template, and define approriate inputs and outputs.
+code template, and define appropriate inputs and outputs.
 
 .. literalinclude:: matlab_example1.py
 

nipype/algorithms/__init__.py

@@ -4,7 +4,7 @@
 """
 Package contains pure python neuroimaging algorithms
 
-Exaples: artifactdetect
+Examples: artifactdetect
 
 """
 __docformat__ = "restructuredtext"

nipype/algorithms/confounds.py

@@ -1152,7 +1152,7 @@ def is_outlier(points, thresh=3.5):
         a modified z-score (based on the median absolute deviation) greater
         than this value will be classified as outliers.
 
-    :return: A bolean mask, of size numobservations-length array.
+    :return: A boolean mask, of size numobservations-length array.
 
     .. note:: References
 

nipype/algorithms/metrics.py

@@ -42,13 +42,13 @@ class DistanceInputSpec(BaseInterfaceInputSpec):
         "eucl_wmean",
         "eucl_max",
         desc='""eucl_min": Euclidean distance between two closest points\
-        "eucl_cog": mean Euclidian distance between the Center of Gravity\
+        "eucl_cog": mean Euclidean distance between the Center of Gravity\
         of volume1 and CoGs of volume2\
-        "eucl_mean": mean Euclidian minimum distance of all volume2 voxels\
+        "eucl_mean": mean Euclidean minimum distance of all volume2 voxels\
         to volume1\
-        "eucl_wmean": mean Euclidian minimum distance of all volume2 voxels\
+        "eucl_wmean": mean Euclidean minimum distance of all volume2 voxels\
         to volume1 weighted by their values\
-        "eucl_max": maximum over minimum Euclidian distances of all volume2\
+        "eucl_max": maximum over minimum Euclidean distances of all volume2\
         voxels to volume1 (also known as the Hausdorff distance)',
         usedefault=True,
     )

nipype/algorithms/misc.py

@@ -1178,7 +1178,7 @@ def _list_outputs(self):
 
 
 class SplitROIsInputSpec(TraitedSpec):
-    in_file = File(exists=True, mandatory=True, desc="file to be splitted")
+    in_file = File(exists=True, mandatory=True, desc="file to be split")
     in_mask = File(exists=True, desc="only process files inside mask")
     roi_size = traits.Tuple(traits.Int, traits.Int, traits.Int, desc="desired ROI size")
 

nipype/algorithms/rapidart.py

@@ -38,7 +38,7 @@
 def _get_affine_matrix(params, source):
     """Return affine matrix given a set of translation and rotation parameters
 
-    params : np.array (upto 12 long) in native package format
+    params : np.array (up to 12 long) in native package format
     source : the package that generated the parameters
              supports SPM, AFNI, FSFAST, FSL, NIPY
     """

nipype/interfaces/ants/base.py

@@ -11,7 +11,7 @@
 
 iflogger = logging.getLogger("nipype.interface")
 
-# -Using -1 gives primary responsibilty to ITKv4 to do the correct
+# -Using -1 gives primary responsibility to ITKv4 to do the correct
 #  thread limitings.
 # -Using 1 takes a very conservative approach to avoid overloading
 #  the computer (when running MultiProc) by forcing everything to
@@ -20,7 +20,7 @@
 LOCAL_DEFAULT_NUMBER_OF_THREADS = 1
 # -Using NSLOTS has the same behavior as ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS
 #  as long as ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS is not set.  Otherwise
-#  ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS takes precidence.
+#  ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS takes precedence.
 #  This behavior states that you the user explicitly specifies
 #  num_threads, then respect that no matter what SGE tries to limit.
 PREFERED_ITKv4_THREAD_LIMIT_VARIABLE = "NSLOTS"

nipype/interfaces/ants/legacy.py

@@ -58,7 +58,7 @@ class antsIntroductionInputSpec(ANTSCommandInputSpec):
             "maximum number of iterations (must be "
             "list of integers in the form [J,K,L...]: "
             "J = coarsest resolution iterations, K = "
-            "middle resolution interations, L = fine "
+            "middle resolution iterations, L = fine "
             "resolution iterations"
         ),
     )
@@ -231,7 +231,7 @@ class buildtemplateparallelInputSpec(ANTSCommandInputSpec):
             "maximum number of iterations (must be "
             "list of integers in the form [J,K,L...]: "
             "J = coarsest resolution iterations, K = "
-            "middle resolution interations, L = fine "
+            "middle resolution iterations, L = fine "
             "resolution iterations"
         ),
     )

nipype/interfaces/ants/registration.py

@@ -453,7 +453,7 @@ class RegistrationInputSpec(ANTSCommandInputSpec):
         usedefault=True,  # This should be true for explicit completeness
         desc=(
             "Initialize linear transforms from the previous stage. By enabling this option, "
-            "the current linear stage transform is directly intialized from the previous "
+            "the current linear stage transform is directly initialized from the previous "
             "stages linear transform; this allows multiple linear stages to be run where "
             "each stage directly updates the estimated linear transform from the previous "
             "stage. (e.g. Translation -> Rigid -> Affine). "
@@ -641,7 +641,7 @@ class Registration(ANTSCommand):
     *stages*. For example first an Affine, then a Rigid, and ultimately a non-linear
     (Syn)-transformation.
 
-    antsRegistration can be initialized using one ore more transforms from moving_image
+    antsRegistration can be initialized using one or more transforms from moving_image
     to fixed_image with the ``initial_moving_transform``-input. For example, when you
     already have a warpfield that corrects for geometrical distortions in an EPI (functional) image,
     that you want to apply before an Affine registration to a structural image.

nipype/interfaces/ants/resampling.py

@@ -34,7 +34,7 @@ class WarpTimeSeriesImageMultiTransformInputSpec(ANTSCommandInputSpec):
     tightest_box = traits.Bool(
         argstr="--tightest-bounding-box",
         desc=(
-            "computes tightest bounding box (overrided by " "reference_image if given)"
+            "computes tightest bounding box (overridden by " "reference_image if given)"
         ),
         xor=["reference_image"],
     )
@@ -186,7 +186,7 @@ class WarpImageMultiTransformInputSpec(ANTSCommandInputSpec):
     tightest_box = traits.Bool(
         argstr="--tightest-bounding-box",
         desc=(
-            "computes tightest bounding box (overrided by " "reference_image if given)"
+            "computes tightest bounding box (overridden by " "reference_image if given)"
         ),
         xor=["reference_image"],
     )

nipype/interfaces/ants/segmentation.py

@@ -698,7 +698,7 @@ class CorticalThicknessInputSpec(ANTSCommandInputSpec):
 class CorticalThicknessOutputSpec(TraitedSpec):
     BrainExtractionMask = File(exists=True, desc="brain extraction mask")
     ExtractedBrainN4 = File(exists=True, desc="extracted brain from N4 image")
-    BrainSegmentation = File(exists=True, desc="brain segmentaion image")
+    BrainSegmentation = File(exists=True, desc="brain segmentation image")
     BrainSegmentationN4 = File(exists=True, desc="N4 corrected image")
     BrainSegmentationPosteriors = OutputMultiPath(
         File(exists=True), desc="Posterior probability images"

nipype/interfaces/base/core.py

@@ -987,7 +987,7 @@ class MpiCommandLine(CommandLine):
 
     @property
     def cmdline(self):
-        """Adds 'mpiexec' to begining of command"""
+        """Adds 'mpiexec' to beginning of command"""
         result = []
         if self.inputs.use_mpi:
             result.append("mpiexec")

nipype/interfaces/base/tests/test_resource_monitor.py

@@ -79,7 +79,7 @@ def test_cmdline_profiling(tmpdir, mem_gb, n_procs, use_resource_monitor):
 
 
 @pytest.mark.skipif(
-    True, reason="test disabled temporarily, until funcion profiling works"
+    True, reason="test disabled temporarily, until function profiling works"
 )
 @pytest.mark.parametrize("mem_gb,n_procs", [(0.5, 3), (2.2, 8), (0.8, 4), (1.5, 1)])
 def test_function_profiling(tmpdir, mem_gb, n_procs, use_resource_monitor):

nipype/interfaces/brainsuite/brainsuite.py

@@ -1492,7 +1492,7 @@ class BDPInputSpec(CommandLineInputSpec):
     )
     ignoreFieldmapFOV = traits.Bool(
         argstr="--ignore-fieldmap-fov",
-        desc="Supresses the error generated by an insufficient field of view of the "
+        desc="Suppresses the error generated by an insufficient field of view of the "
         "input fieldmap and continues with the processing. It is useful only when "
         "used with fieldmap-based distortion correction. See "
         "fieldmap-correction for a detailed explanation. ",
@@ -1677,7 +1677,7 @@ class BDPInputSpec(CommandLineInputSpec):
         desc="Enables estimation of diffusion tensors and/or ODFs (and statistics if "
         "applicable) in the native diffusion coordinate in addition to the "
         "default T1-coordinate. All native diffusion coordinate files are saved "
-        'in a seperate folder named "diffusion_coord_outputs". In case statistics '
+        'in a separate folder named "diffusion_coord_outputs". In case statistics '
         "computation is required, it will also transform/save all label/mask "
         "files required to diffusion coordinate (see generateStats for "
         "details). ",

nipype/interfaces/camino/connectivity.py

@@ -133,7 +133,7 @@ class Conmat(CommandLine):
     Such fibers will add to the diagonal elements of the matrix. To remove
     these entries, run procstreamlines with -endpointfile before running conmat.
 
-    If the seed point is inside a labled region, it counts as one end of the
+    If the seed point is inside a labeled region, it counts as one end of the
     connection.  So ::
 
          ----[SEED inside A]---------B

nipype/interfaces/camino/convert.py

@@ -780,7 +780,7 @@ class AnalyzeHeaderInputSpec(StdOutCommandLineInputSpec):
         position=3,
         desc=(
             "Reads header information from file and "
-            "intializes a new header with the values read "
+            "initializes a new header with the values read "
             "from the file. You may replace any "
             "combination of fields in the new header by "
             "specifying subsequent options."

nipype/interfaces/camino/dti.py

@@ -621,7 +621,7 @@ class PicoPDFsInputSpec(StdOutCommandLineInputSpec):
         units="NA",
         desc="The maximum number of PDs in a voxel (default 3) for PD data."
         "This option determines the size of the input and output voxels."
-        "This means that the data file may be large enough to accomodate three or more PDs,"
+        "This means that the data file may be large enough to accommodate three or more PDs,"
         "but does not mean that any of the voxels are classified as containing three or more PDs.",
     )
 
@@ -1251,7 +1251,7 @@ class TrackBootstrapInputSpec(TrackInputSpec):
 
 class TrackBootstrap(Track):
     """
-    Performs bootstrap streamline tractography using mulitple scans of the same subject
+    Performs bootstrap streamline tractography using multiple scans of the same subject
 
     Example
     -------

nipype/interfaces/camino/odf.py

@@ -170,7 +170,7 @@ class LinRecon(StdOutCommandLine):
     Reads  a  linear  transformation from the matrix file assuming the
     imaging scheme specified in the scheme file. Performs the linear
     transformation on the data in every voxel and outputs the result to
-    the standard output. The ouput in every voxel is actually: ::
+    the standard output. The output in every voxel is actually: ::
 
         [exit code, ln(S(0)), p1, ..., pR]
 

nipype/interfaces/cat12/preprocess.py

@@ -136,7 +136,7 @@ class CAT12SegmentInputSpec(SPMCommandInputSpec):
         " method that refines the probability maps of the SPM approach by region-growing techniques of "
         "the gcut approach with a final surface-based optimization strategy. This is currently the method"
         " with the most accurate and reliable results. If you use already skull-stripped data you can "
-        "turn off skull-stripping although this is automaticaly detected in most cases. Please note that "
+        "turn off skull-stripping although this is automatically detected in most cases. Please note that "
         "the choice of the skull-stripping method will also influence the estimation of TIV, because the"
         " methods mainly differ in the handling of the outer CSF around the cortical surface. "
         "\nPossible Values:\n - none (already skull-stripped): -1;\n - SPM approach: 0; "
@@ -329,7 +329,7 @@ class CAT12SegmentInputSpec(SPMCommandInputSpec):
     # Labels
     _help_label_desc = (
         "This is the option to save a labeled version of your segmentations in the %s space for fast visual "
-        "comparision. Labels are saved as Partial Volume Estimation (PVE) values with different mix "
+        "comparison. Labels are saved as Partial Volume Estimation (PVE) values with different mix "
         "classes for GM-WM (2.5) and GM-CSF (1.5). BG=0, CSF=1, GM=2, WM=3, WMH=4 (if WMHC=3), "
         "SL=1.5 (if SLC)"
     )

nipype/interfaces/cat12/surface.py

@@ -33,7 +33,7 @@ class ExtractAdditionalSurfaceParametersInputSpec(SPMCommandInputSpec):
         False,
         field="SD",
         usedefault=True,
-        desc="Extract sulcus depth based on euclidian distance between the central "
+        desc="Extract sulcus depth based on euclidean distance between the central "
         "surface anf its convex hull.",
     )
     fractal_dimension = traits.Bool(
@@ -92,7 +92,7 @@ class ExtractAdditionalSurfaceParameters(SPMCommand):
     * Sulcus depth
     * Toro's gyrification index
     * Shaer's local gyrification index
-    * Laplacian gyrification indeces
+    * Laplacian gyrification indices
     * Addicional surfaces
     * Measure normalization
     * Lazy processing
@@ -153,7 +153,7 @@ def _list_outputs(self):
                         )
 
                         # Add all hemisphere files into one list, this is important because only the left hemisphere
-                        # files are used as input in the Surface ROI Tools, fpr instance.
+                        # files are used as input in the Surface ROI Tools, for instance.
                         outputs[all_files_hemisphere].append(
                             os.path.join(pth, generated_filename)
                         )

nipype/interfaces/cmtk/cmtk.py

@@ -282,7 +282,7 @@ def cmat(
             )
         except IndexError:
             iflogger.error(
-                "AN INDEXERROR EXCEPTION OCCURED FOR FIBER %s. "
+                "AN INDEXERROR EXCEPTION OCCURRED FOR FIBER %s. "
                 "PLEASE CHECK ENDPOINT GENERATION",
                 i,
             )

nipype/interfaces/diffusion_toolkit/dti.py

@@ -173,7 +173,7 @@ class DTITrackerInputSpec(CommandLineInputSpec):
 Input and output file type. Accepted values are:
 
 * analyze -> analyze format 7.5
-* ni1     -> nifti format saved in seperate .hdr and .img file
+* ni1     -> nifti format saved in separate .hdr and .img file
 * nii     -> nifti format with one .nii file
 * nii.gz  -> nifti format with compression
 

nipype/interfaces/dipy/base.py

@@ -265,7 +265,7 @@ def get_dipy_workflows(module):
     -------
     l_wkflw : list of tuple
         This a list of tuple containing 2 elements:
-        Worflow name, Workflow class obj
+        Workflow name, Workflow class obj
 
     Examples
     --------

nipype/interfaces/dtitk/base.py

@@ -58,8 +58,8 @@ def _gen_fname(self, basename, cwd=None, suffix=None, change_ext=True, ext=None)
         """Generate a filename based on the given parameters.
 
         The filename will take the form: cwd/basename<suffix><ext>.
-        If change_ext is True, it will use the extentions specified in
-        <instance>intputs.output_type.
+        If change_ext is True, it will use the extensions specified in
+        <instance>inputs.output_type.
 
         Parameters
         ----------

nipype/interfaces/freesurfer/longitudinal.py

@@ -78,7 +78,7 @@ class RobustTemplateInputSpec(FSTraitedSpecOpenMP):
     fixed_timepoint = traits.Bool(
         default_value=False,
         argstr="--fixtp",
-        desc="map everthing to init TP# (init TP is not resampled)",
+        desc="map everything to init TP# (init TP is not resampled)",
     )
     no_iteration = traits.Bool(
         default_value=False,

nipype/interfaces/freesurfer/model.py

@@ -425,7 +425,7 @@ class GLMFitInputSpec(FSTraitedSpec):
         argstr="--perm-force",
         desc="force perumtation test, even when design matrix is not orthog",
     )
-    diag = traits.Int(argstr="--diag %d", desc="Gdiag_no : set diagnositc level")
+    diag = traits.Int(argstr="--diag %d", desc="Gdiag_no : set diagnostic level")
     diag_cluster = traits.Bool(
         argstr="--diag-cluster", desc="save sig volume and exit from first sim loop"
     )
@@ -773,7 +773,7 @@ class ConcatenateInputSpec(FSTraitedSpec):
     mask_file = File(exists=True, argstr="--mask %s", desc="Mask input with a volume")
     vote = traits.Bool(
         argstr="--vote",
-        desc="Most frequent value at each voxel and fraction of occurances",
+        desc="Most frequent value at each voxel and fraction of occurrences",
     )
     sort = traits.Bool(argstr="--sort", desc="Sort each voxel by ascending frame value")
 
@@ -1118,7 +1118,7 @@ class SegStatsReconAll(SegStats):
     """
     This class inherits SegStats and modifies it for use in a recon-all workflow.
     This implementation mandates implicit inputs that SegStats.
-    To ensure backwards compatability of SegStats, this class was created.
+    To ensure backwards compatibility of SegStats, this class was created.
 
     Examples
     --------