Merged

DOC: Fix typos found by copdespell #3510

Show file tree
Hide file tree
Changes from all commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Jump to
Failed to load files.
Original file line numberDiff line numberDiff line change
Expand Up@@ -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)
Expand Down
Original file line numberDiff line numberDiff line change
Expand Up@@ -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::
Expand DownExpand Up@@ -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::

Expand Down
Original file line numberDiff line numberDiff line change
Expand Up@@ -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
Expand Down
Original file line numberDiff line numberDiff line change
Expand Up@@ -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

Expand Down
Original file line numberDiff line numberDiff line change
Expand Up@@ -4,7 +4,7 @@
"""
Package contains pure python neuroimaging algorithms

Exaples: artifactdetect
Examples: artifactdetect

"""
__docformat__ = "restructuredtext"
Original file line numberDiff line numberDiff line change
Expand Up@@ -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

Expand Down
Original file line numberDiff line numberDiff line change
Expand Up@@ -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")

Expand Down
Original file line numberDiff line numberDiff line change
Expand Up@@ -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
Expand All@@ -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"
Expand Down
Original file line numberDiff line numberDiff line change
Expand Up@@ -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"
),
)
Expand DownExpand Up@@ -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"
),
)
Expand Down
Original file line numberDiff line numberDiff line change
Expand Up@@ -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"],
)
Expand DownExpand Up@@ -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"],
)
Expand Down
Original file line numberDiff line numberDiff line change
Expand Up@@ -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"
Expand Down
Original file line numberDiff line numberDiff line change
Expand Up@@ -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")
Expand Down
Original file line numberDiff line numberDiff line change
Expand Up@@ -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):
Expand Down
Original file line numberDiff line numberDiff line change
Expand Up@@ -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
Expand Down
Original file line numberDiff line numberDiff line change
Expand Up@@ -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."
Expand Down
Original file line numberDiff line numberDiff line change
Expand Up@@ -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.",
)

Expand DownExpand Up@@ -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
-------
Expand Down
Original file line numberDiff line numberDiff line change
Expand Up@@ -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]

Expand Down
Original file line numberDiff line numberDiff line change
Expand Up@@ -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(
Expand DownExpand Up@@ -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
Expand DownExpand Up@@ -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)
)
Expand Down
Original file line numberDiff line numberDiff line change
Expand Up@@ -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,
)
Expand Down
Original file line numberDiff line numberDiff line change
Expand Up@@ -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

Expand Down
Original file line numberDiff line numberDiff line change
Expand Up@@ -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
--------
Expand Down
Original file line numberDiff line numberDiff line change
Expand Up@@ -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
----------
Expand Down
Original file line numberDiff line numberDiff line change
Expand Up@@ -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,
Expand Down
Original file line numberDiff line numberDiff line change
Expand Up@@ -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"
)
Expand DownExpand Up@@ -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")

Expand DownExpand Up@@ -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
--------
Expand Down
Loading