Skip to content

Navigation Menu

Sign in
Appearance settings

Search code, repositories, users, issues, pull requests...

Provide feedback

We read every piece of feedback, and take your input very seriously.

Saved searches

Use saved searches to filter your results more quickly
Sign up
Appearance settings

Commit 4f315a9

Browse files
DOC: Fix typos found by codespell
1 parent e5be008 commit 4f315a9

File tree

38 files changed

+128
-128
lines changed

38 files changed

+128
-128
lines changed

‎nipype/caching/memory.py‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -287,7 +287,7 @@ def clear_runs_since(self, day=None, month=None, year=None, warn=True):
287287
os.remove(log_name)
288288

289289
def _clear_all_but(self, runs, warn=True):
290-
"""Remove all the runs appart from those given to the function
290+
"""Remove all the runs apart from those given to the function
291291
input.
292292
"""
293293
rm_all_but(self.base_dir, set(runs.keys()), warn=warn)

‎nipype/interfaces/afni/base.py‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -262,8 +262,8 @@ def _gen_fname(self, basename, cwd=None, suffix=None, change_ext=True, ext=None)
262262
Generate a filename based on the given parameters.
263263
264264
The filename will take the form: cwd/basename<suffix><ext>.
265-
If change_ext is True, it will use the extentions specified in
266-
<instance>intputs.output_type.
265+
If change_ext is True, it will use the extensions specified in
266+
<instance>inputs.output_type.
267267
268268
Parameters
269269
----------

‎nipype/interfaces/afni/model.py‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -265,7 +265,7 @@ class DeconvolveInputSpec(AFNICommandInputSpec):
265265
class DeconvolveOutputSpec(TraitedSpec):
266266
out_file = File(desc="output statistics file", exists=True)
267267
reml_script = File(
268-
desc="automatical generated script to run 3dREMLfit", exists=True
268+
desc="automatically generated script to run 3dREMLfit", exists=True
269269
)
270270
x1D = File(desc="save out X matrix", exists=True)
271271
cbucket = File(desc="output regression coefficients file (if generated)")
@@ -528,7 +528,7 @@ class RemlfitInputSpec(AFNICommandInputSpec):
528528
"be included.",
529529
argstr="-Rglt %s",
530530
)
531-
fitts_file = File(desc="ouput dataset for REML fitted model", argstr="-Rfitts %s")
531+
fitts_file = File(desc="output dataset for REML fitted model", argstr="-Rfitts %s")
532532
errts_file = File(
533533
desc="output dataset for REML residuals = data - fitted model",
534534
argstr="-Rerrts %s",
@@ -584,7 +584,7 @@ class RemlfitOutputSpec(AFNICommandOutputSpec):
584584
"but ONLY for the GLTs added on the REMLfit command "
585585
"line itself via 'gltsym' (if generated)"
586586
)
587-
fitts_file = File(desc="ouput dataset for REML fitted model (if generated)")
587+
fitts_file = File(desc="output dataset for REML fitted model (if generated)")
588588
errts_file = File(
589589
desc="output dataset for REML residuals = data - fitted model (if " "generated"
590590
)

‎nipype/interfaces/afni/preprocess.py‎

Lines changed: 10 additions & 10 deletions
Original file line numberDiff line numberDiff line change
@@ -821,7 +821,7 @@ class AutoTLRCInputSpec(CommandLineInputSpec):
821821

822822

823823
class AutoTLRC(AFNICommand):
824-
"""A minmal wrapper for the AutoTLRC script
824+
"""A minimal wrapper for the AutoTLRC script
825825
The only option currently supported is no_ss.
826826
For complete details, see the `3dQwarp Documentation.
827827
<https://afni.nimh.nih.gov/pub/dist/doc/program_help/@auto_tlrc.html>`_
@@ -1327,7 +1327,7 @@ class ECMInputSpec(CentralityInputSpec):
13271327
)
13281328
fecm = traits.Bool(
13291329
desc="Fast centrality method; substantial speed increase but cannot "
1330-
"accomodate thresholding; automatically selected if -thresh or "
1330+
"accommodate thresholding; automatically selected if -thresh or "
13311331
"-sparsity are not set",
13321332
argstr="-fecm",
13331333
)
@@ -2933,7 +2933,7 @@ class TProjectInputSpec(AFNICommandInputSpec):
29332933
the output dataset:
29342934
29352935
* mode = ZERO -- put zero values in their place;
2936-
output datset is same length as input
2936+
output dataset is same length as input
29372937
* mode = KILL -- remove those time points;
29382938
output dataset is shorter than input
29392939
* mode = NTRP -- censored values are replaced by interpolated
@@ -3073,7 +3073,7 @@ class TProject(AFNICommand):
30733073
as ``-passband``. In this way, you can bandpass time-censored data, and at
30743074
the same time, remove other time series of no interest
30753075
(e.g., physiological estimates, motion parameters).
3076-
Shifts voxel time series from input so that seperate slices are aligned to
3076+
Shifts voxel time series from input so that separate slices are aligned to
30773077
the same temporal origin.
30783078
30793079
Examples
@@ -3188,7 +3188,7 @@ class TShiftOutputSpec(AFNICommandOutputSpec):
31883188

31893189

31903190
class TShift(AFNICommand):
3191-
"""Shifts voxel time series from input so that seperate slices are aligned
3191+
"""Shifts voxel time series from input so that separate slices are aligned
31923192
to the same temporal origin.
31933193
31943194
For complete details, see the `3dTshift Documentation.
@@ -3658,7 +3658,7 @@ class QwarpInputSpec(AFNICommandInputSpec):
36583658
with 3dNwarpApply and 3dNwarpCat, for example.
36593659
* To be clear, this is the warp from source dataset
36603660
coordinates to base dataset coordinates, where the
3661-
values at each base grid point are the xyz displacments
3661+
values at each base grid point are the xyz displacements
36623662
needed to move that grid point's xyz values to the
36633663
corresponding xyz values in the source dataset:
36643664
base( (x,y,z) + WARP(x,y,z) ) matches source(x,y,z)
@@ -4034,7 +4034,7 @@ class QwarpInputSpec(AFNICommandInputSpec):
40344034
The goal is greater speed, and it seems to help this"
40354035
positively piggish program to be more expeditious."
40364036
* However, accuracy is somewhat lower with '-duplo',"
4037-
for reasons that currenly elude Zhark; for this reason,"
4037+
for reasons that currently elude Zhark; for this reason,"
40384038
the Emperor does not usually use '-duplo'.
40394039
40404040
""",
@@ -4225,21 +4225,21 @@ class QwarpInputSpec(AFNICommandInputSpec):
42254225
)
42264226
hel = traits.Bool(
42274227
desc="Hellinger distance: a matching function for the adventurous"
4228-
"This option has NOT be extensively tested for usefullness"
4228+
"This option has NOT be extensively tested for usefulness"
42294229
"and should be considered experimental at this infundibulum.",
42304230
argstr="-hel",
42314231
xor=["nmi", "mi", "lpc", "lpa", "pear"],
42324232
)
42334233
mi = traits.Bool(
42344234
desc="Mutual Information: a matching function for the adventurous"
4235-
"This option has NOT be extensively tested for usefullness"
4235+
"This option has NOT be extensively tested for usefulness"
42364236
"and should be considered experimental at this infundibulum.",
42374237
argstr="-mi",
42384238
xor=["mi", "hel", "lpc", "lpa", "pear"],
42394239
)
42404240
nmi = traits.Bool(
42414241
desc="Normalized Mutual Information: a matching function for the adventurous"
4242-
"This option has NOT been extensively tested for usefullness"
4242+
"This option has NOT been extensively tested for usefulness"
42434243
"and should be considered experimental at this infundibulum.",
42444244
argstr="-nmi",
42454245
xor=["nmi", "hel", "lpc", "lpa", "pear"],

‎nipype/interfaces/afni/utils.py‎

Lines changed: 9 additions & 9 deletions
Original file line numberDiff line numberDiff line change
@@ -539,27 +539,27 @@ class CatInputSpec(AFNICommandInputSpec):
539539
argstr="-sel %s",
540540
)
541541
out_int = traits.Bool(
542-
desc="specifiy int data type for output",
542+
desc="specify int data type for output",
543543
argstr="-i",
544544
xor=["out_format", "out_nice", "out_double", "out_fint", "out_cint"],
545545
)
546546
out_nice = traits.Bool(
547-
desc="specifiy nice data type for output",
547+
desc="specify nice data type for output",
548548
argstr="-n",
549549
xor=["out_format", "out_int", "out_double", "out_fint", "out_cint"],
550550
)
551551
out_double = traits.Bool(
552-
desc="specifiy double data type for output",
552+
desc="specify double data type for output",
553553
argstr="-d",
554554
xor=["out_format", "out_nice", "out_int", "out_fint", "out_cint"],
555555
)
556556
out_fint = traits.Bool(
557-
desc="specifiy int, rounded down, data type for output",
557+
desc="specify int, rounded down, data type for output",
558558
argstr="-f",
559559
xor=["out_format", "out_nice", "out_double", "out_int", "out_cint"],
560560
)
561561
out_cint = traits.Bool(
562-
desc="specifiy int, rounded up, data type for output",
562+
desc="specify int, rounded up, data type for output",
563563
xor=["out_format", "out_nice", "out_double", "out_fint", "out_int"],
564564
)
565565

@@ -693,7 +693,7 @@ class CenterMassInputSpec(CommandLineInputSpec):
693693
argstr="-set %f %f %f",
694694
)
695695
local_ijk = traits.Bool(
696-
desc="Output values as (i,j,k) in local orienation", argstr="-local_ijk"
696+
desc="Output values as (i,j,k) in local orientation", argstr="-local_ijk"
697697
)
698698
roi_vals = traits.List(
699699
traits.Int,
@@ -2554,11 +2554,11 @@ class ReHoInputSpec(CommandLineInputSpec):
25542554

25552555
class ReHoOutputSpec(TraitedSpec):
25562556
out_file = File(exists=True, desc="Voxelwise regional homogeneity map")
2557-
out_vals = File(desc="Table of labelwise regional homogenity values")
2557+
out_vals = File(desc="Table of labelwise regional homogeneity values")
25582558

25592559

25602560
class ReHo(AFNICommandBase):
2561-
"""Compute regional homogenity for a given neighbourhood.l,
2561+
"""Compute regional homogeneity for a given neighbourhood.l,
25622562
based on a local neighborhood of that voxel.
25632563
25642564
For complete details, see the `3dReHo Documentation.
@@ -2740,7 +2740,7 @@ class TCatSBInputSpec(AFNICommandInputSpec):
27402740

27412741
class TCatSubBrick(AFNICommand):
27422742
"""Hopefully a temporary function to allow sub-brick selection until
2743-
afni file managment is improved.
2743+
afni file management is improved.
27442744
27452745
For complete details, see the `3dTcat Documentation.
27462746
<https://afni.nimh.nih.gov/pub/dist/doc/program_help/3dTcat.html>`_

‎nipype/interfaces/c3.py‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -84,7 +84,7 @@ class C3dInputSpec(CommandLineInputSpec):
8484
desc=(
8585
"Write all images on the convert3d stack as multiple files."
8686
" Supports both list of output files or a pattern for the output"
87-
" filenames (using %d substituion)."
87+
" filenames (using %d substitution)."
8888
),
8989
)
9090
pix_type = traits.Enum(

‎nipype/interfaces/dcmstack.py‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -55,7 +55,7 @@ class NiftiGeneratorBase(BaseInterface):
5555
embedded meta data."""
5656

5757
def _get_out_path(self, meta, idx=None):
58-
"""Return the output path for the gernerated Nifti."""
58+
"""Return the output path for the generated Nifti."""
5959
if self.inputs.out_format:
6060
out_fmt = self.inputs.out_format
6161
else:
@@ -262,7 +262,7 @@ def _outputs(self):
262262
return outputs
263263

264264
def _run_interface(self, runtime):
265-
# If the 'meta_keys' input is a list, covert it to a dict
265+
# If the 'meta_keys' input is a list, convert it to a dict
266266
self._make_name_map()
267267
nw = NiftiWrapper.from_filename(self.inputs.in_file)
268268
self.result = {}
@@ -342,7 +342,7 @@ class MergeNiftiInputSpec(NiftiGeneratorBaseInputSpec):
342342
merge_dim = traits.Int(
343343
desc="Dimension to merge along. If not "
344344
"specified, the last singular or "
345-
"non-existant dimension is used."
345+
"non-existent dimension is used."
346346
)
347347

348348

‎nipype/interfaces/freesurfer/preprocess.py‎

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -2361,8 +2361,8 @@ def _format_arg(self, name, spec, value):
23612361
def _list_outputs(self):
23622362
outputs = self.output_spec().get()
23632363
cwd = os.getcwd()
2364-
prefices = dict(src=self.inputs.source_file, trg=self.inputs.target_file)
2365-
suffices = dict(
2364+
prefixes = dict(src=self.inputs.source_file, trg=self.inputs.target_file)
2365+
suffixes = dict(
23662366
out_reg_file=("src", "_robustreg.lta", False),
23672367
registered_file=("src", "_robustreg", True),
23682368
weights_file=("src", "_robustweights", True),
@@ -2372,12 +2372,12 @@ def _list_outputs(self):
23722372
half_source_xfm=("src", "_robustxfm.lta", False),
23732373
half_targ_xfm=("trg", "_robustxfm.lta", False),
23742374
)
2375-
for name, sufftup in list(suffices.items()):
2375+
for name, sufftup in list(suffixes.items()):
23762376
value = getattr(self.inputs, name)
23772377
if value:
23782378
if value is True:
23792379
outputs[name] = fname_presuffix(
2380-
prefices[sufftup[0]],
2380+
prefixes[sufftup[0]],
23812381
suffix=sufftup[1],
23822382
newpath=cwd,
23832383
use_ext=sufftup[2],

‎nipype/interfaces/io.py‎

Lines changed: 8 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -764,7 +764,7 @@ def _list_outputs(self):
764764
out_files.append(s3dst)
765765
# Otherwise, copy locally src -> dst
766766
if not s3_flag or isdefined(self.inputs.local_copy):
767-
# Create output directory if it doesnt exist
767+
# Create output directory if it doesn't exist
768768
if not os.path.exists(path):
769769
try:
770770
os.makedirs(path)
@@ -1318,7 +1318,7 @@ class SelectFilesInputSpec(DynamicTraitedSpec, BaseInterfaceInputSpec):
13181318
sort_filelist = traits.Bool(
13191319
True,
13201320
usedefault=True,
1321-
desc="When matching mutliple files, return them" " in sorted order.",
1321+
desc="When matching multiple files, return them" " in sorted order.",
13221322
)
13231323
raise_on_empty = traits.Bool(
13241324
True,
@@ -1346,7 +1346,7 @@ class SelectFiles(IOBase):
13461346
13471347
This interface uses Python's {}-based string formatting syntax to plug
13481348
values (possibly known only at workflow execution time) into string
1349-
templates and collect files from persistant storage. These templates can
1349+
templates and collect files from persistent storage. These templates can
13501350
also be combined with glob wildcards (``*``, ``?``) and character ranges (``[...]``).
13511351
The field names in the formatting template (i.e. the terms in braces) will
13521352
become inputs fields on the interface, and the keys in the templates
@@ -1513,7 +1513,7 @@ class DataFinder(IOBase):
15131513
Will recursively search any subdirectories by default. This can be limited
15141514
with the min/max depth options.
15151515
Matched paths are available in the output 'out_paths'. Any named groups of
1516-
captured text from the regular expression are also available as ouputs of
1516+
captured text from the regular expression are also available as outputs of
15171517
the same name.
15181518
15191519
Examples
@@ -1583,7 +1583,7 @@ def _run_interface(self, runtime):
15831583
]
15841584
self.result = None
15851585
for root_path in self.inputs.root_paths:
1586-
# Handle tilda/env variables and remove extra seperators
1586+
# Handle tilda/env variables and remove extra separators
15871587
root_path = os.path.normpath(
15881588
os.path.expandvars(os.path.expanduser(root_path))
15891589
)
@@ -1612,7 +1612,7 @@ def _run_interface(self, runtime):
16121612
for key, vals in list(self.result.items()):
16131613
self.result[key] = vals[0]
16141614
else:
1615-
# sort all keys acording to out_paths
1615+
# sort all keys according to out_paths
16161616
for key in list(self.result.keys()):
16171617
if key == "out_paths":
16181618
continue
@@ -2083,15 +2083,15 @@ class XNATSinkInputSpec(DynamicTraitedSpec, BaseInterfaceInputSpec):
20832083

20842084
assessor_id = Str(
20852085
desc=(
2086-
"Option to customize ouputs representation in XNAT - "
2086+
"Option to customize outputs representation in XNAT - "
20872087
"assessor level will be used with specified id"
20882088
),
20892089
xor=["reconstruction_id"],
20902090
)
20912091

20922092
reconstruction_id = Str(
20932093
desc=(
2094-
"Option to customize ouputs representation in XNAT - "
2094+
"Option to customize outputs representation in XNAT - "
20952095
"reconstruction level will be used with specified id"
20962096
),
20972097
xor=["assessor_id"],

‎nipype/interfaces/matlab.py‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -191,7 +191,7 @@ def _gen_matlab_command(self, argstr, script_lines):
191191
else:
192192
prescript.insert(0, "fprintf(1,'Executing code at %s:\\n',datestr(now));")
193193
for path in paths:
194-
# addpath() is not available after compliation
194+
# addpath() is not available after compilation
195195
# https://www.mathworks.com/help/compiler/ismcc.html
196196
# https://www.mathworks.com/help/compiler/isdeployed.html
197197
prescript.append("if ~(ismcc || isdeployed), addpath('%s'); end;\n" % path)

0 commit comments

Comments
(0)

AltStyle によって変換されたページ (->オリジナル) /