From 223e69d1bb93731de598f37e59642c3cb4fc1428 Mon Sep 17 00:00:00 2001
From: Dimitri Papadopoulos
<3234522+DimitriPapadopoulos@users.noreply.github.com>
Date: Wed, 21 Sep 2022 18:21:47 +0200
Subject: [PATCH] DOC: Fix a few more typos
---
doc/devel/interface_specs.rst | 4 ++--
doc/devel/provenance.rst | 2 +-
nipype/interfaces/afni/utils.py | 2 +-
nipype/interfaces/diffusion_toolkit/dti.py | 2 +-
nipype/interfaces/dtitk/utils.py | 2 +-
nipype/interfaces/minc/minc.py | 2 +-
nipype/interfaces/mipav/developer.py | 4 ++--
nipype/interfaces/semtools/diffusion/gtract.py | 2 +-
nipype/interfaces/slicer/generate_classes.py | 2 +-
nipype/interfaces/slicer/registration/brainsfit.py | 2 +-
nipype/interfaces/slicer/registration/brainsresample.py | 2 +-
nipype/interfaces/spm/model.py | 2 +-
nipype/pipeline/engine/utils.py | 2 +-
nipype/utils/spm_flat_config.m | 2 +-
nipype/utils/tests/test_filemanip.py | 2 +-
15 files changed, 17 insertions(+), 17 deletions(-)
diff --git a/doc/devel/interface_specs.rst b/doc/devel/interface_specs.rst
index fa74aca753..5b4e3678f2 100644
--- a/doc/devel/interface_specs.rst
+++ b/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:
diff --git a/doc/devel/provenance.rst b/doc/devel/provenance.rst
index 5e1694a3ae..b76f57ccf1 100644
--- a/doc/devel/provenance.rst
+++ b/doc/devel/provenance.rst
@@ -5,7 +5,7 @@ W3C PROV support
Overview
--------
-We're using the the `W3C PROV data model `_ to
+We're using the `W3C PROV data model `_ to
capture and represent provenance in Nipype.
For an overview see:
diff --git a/nipype/interfaces/afni/utils.py b/nipype/interfaces/afni/utils.py
index bf6f339d1d..ef27d86b13 100644
--- a/nipype/interfaces/afni/utils.py
+++ b/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",
diff --git a/nipype/interfaces/diffusion_toolkit/dti.py b/nipype/interfaces/diffusion_toolkit/dti.py
index 03488712ed..c42db76d5b 100644
--- a/nipype/interfaces/diffusion_toolkit/dti.py
+++ b/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",
)
diff --git a/nipype/interfaces/dtitk/utils.py b/nipype/interfaces/dtitk/utils.py
index c5850450a6..da030439de 100644
--- a/nipype/interfaces/dtitk/utils.py
+++ b/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()),
diff --git a/nipype/interfaces/minc/minc.py b/nipype/interfaces/minc/minc.py
index 6948f0453a..9d28832f50 100644
--- a/nipype/interfaces/minc/minc.py
+++ b/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:
diff --git a/nipype/interfaces/mipav/developer.py b/nipype/interfaces/mipav/developer.py
index af9bf5977b..03069fcf98 100644
--- a/nipype/interfaces/mipav/developer.py
+++ b/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)
diff --git a/nipype/interfaces/semtools/diffusion/gtract.py b/nipype/interfaces/semtools/diffusion/gtract.py
index e6342c8a06..2e5a5816c5 100644
--- a/nipype/interfaces/semtools/diffusion/gtract.py
+++ b/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",
)
diff --git a/nipype/interfaces/slicer/generate_classes.py b/nipype/interfaces/slicer/generate_classes.py
index 195579aaec..89125a963f 100644
--- a/nipype/interfaces/slicer/generate_classes.py
+++ b/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
# --test
diff --git a/nipype/interfaces/slicer/registration/brainsfit.py b/nipype/interfaces/slicer/registration/brainsfit.py
index ddbb330a63..5780d29096 100644
--- a/nipype/interfaces/slicer/registration/brainsfit.py
+++ b/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(
diff --git a/nipype/interfaces/slicer/registration/brainsresample.py b/nipype/interfaces/slicer/registration/brainsresample.py
index 653be8e916..9512a05195 100644
--- a/nipype/interfaces/slicer/registration/brainsresample.py
+++ b/nipype/interfaces/slicer/registration/brainsresample.py
@@ -94,7 +94,7 @@ class BRAINSResample(SEMLikeCommandLine):
category: Registration
description:
- This program resamples an image image using a deformation field or a transform (BSpline, Affine, Rigid, etc.).
+ This program resamples an image using a deformation field or a transform (BSpline, Affine, Rigid, etc.).
version: 3.0.0
diff --git a/nipype/interfaces/spm/model.py b/nipype/interfaces/spm/model.py
index 260742f5b0..0c2eece0d5 100644
--- a/nipype/interfaces/spm/model.py
+++ b/nipype/interfaces/spm/model.py
@@ -616,7 +616,7 @@ class ThresholdInputSpec(SPMCommandInputSpec):
desc=(
"In case no clusters survive the "
"topological inference step this "
- "will pick a culster with the highes "
+ "will pick a culster with the highest "
"sum of t-values. Use with care."
),
)
diff --git a/nipype/pipeline/engine/utils.py b/nipype/pipeline/engine/utils.py
index a7a3f6f8c3..94f9852268 100644
--- a/nipype/pipeline/engine/utils.py
+++ b/nipype/pipeline/engine/utils.py
@@ -1030,7 +1030,7 @@ def generate_expanded_graph(graph_in):
iterables = {}
# the source node iterables values
src_values = [getattr(iter_src.inputs, field) for field in src_fields]
- # if there is one source field, then the key is the the source value,
+ # if there is one source field, then the key is the source value,
# otherwise the key is the tuple of source values
if len(src_values) == 1:
key = src_values[0]
diff --git a/nipype/utils/spm_flat_config.m b/nipype/utils/spm_flat_config.m
index 6e489251b2..4f5f2929dd 100644
--- a/nipype/utils/spm_flat_config.m
+++ b/nipype/utils/spm_flat_config.m
@@ -1,7 +1,7 @@
function cfgstruct = spm_flat_config(print_names)
% Get a flat spm_config structure, with option to print out names
%
-% This calls spm_config() to get the the nested configuration
+% This calls spm_config() to get the nested configuration
% structure from spm. We use this to fetch documentation, the
% flattened structure is much easier to search through. If
% print_names is true (value of 1) it will print out the configuration
diff --git a/nipype/utils/tests/test_filemanip.py b/nipype/utils/tests/test_filemanip.py
index f02ad4164e..8d4597317c 100644
--- a/nipype/utils/tests/test_filemanip.py
+++ b/nipype/utils/tests/test_filemanip.py
@@ -631,7 +631,7 @@ def test_path_strict_resolve(tmpdir):
"""Check the monkeypatch to test strict resolution of Path."""
tmpdir.chdir()
- # Default strict=False should work out out of the box
+ # Default strict=False should work out of the box
testfile = Path("somefile.txt")
resolved = "%s/somefile.txt" % tmpdir
assert str(path_resolve(testfile)) == resolved