From 6c7f3b34181e088ffadc9c63a38add8b523cc618 Mon Sep 17 00:00:00 2001 From: Dimitri Papadopoulos <3234522+DimitriPapadopoulos@users.noreply.github.com> Date: Tue, 20 Sep 2022 19:38:22 +0200 Subject: [PATCH] DOC: Fix typos found by copdespell --- doc/changelog/1.X.X-changelog.rst | 4 ++-- doc/devel/cmd_interface_devel.rst | 4 ++-- doc/devel/filename_generation.rst | 4 ++-- doc/devel/interface_specs.rst | 2 +- doc/devel/matlab_interface_devel.rst | 2 +- nipype/algorithms/__init__.py | 2 +- nipype/algorithms/confounds.py | 2 +- nipype/algorithms/metrics.py | 8 +++---- nipype/algorithms/misc.py | 2 +- nipype/algorithms/rapidart.py | 2 +- nipype/interfaces/ants/base.py | 4 ++-- nipype/interfaces/ants/legacy.py | 4 ++-- nipype/interfaces/ants/registration.py | 4 ++-- nipype/interfaces/ants/resampling.py | 4 ++-- nipype/interfaces/ants/segmentation.py | 2 +- nipype/interfaces/base/core.py | 2 +- .../base/tests/test_resource_monitor.py | 2 +- nipype/interfaces/brainsuite/brainsuite.py | 4 ++-- nipype/interfaces/camino/connectivity.py | 2 +- nipype/interfaces/camino/convert.py | 2 +- nipype/interfaces/camino/dti.py | 4 ++-- nipype/interfaces/camino/odf.py | 2 +- nipype/interfaces/cat12/preprocess.py | 4 ++-- nipype/interfaces/cat12/surface.py | 6 ++--- nipype/interfaces/cmtk/cmtk.py | 2 +- nipype/interfaces/diffusion_toolkit/dti.py | 2 +- nipype/interfaces/dipy/base.py | 2 +- nipype/interfaces/dtitk/base.py | 4 ++-- nipype/interfaces/freesurfer/longitudinal.py | 2 +- nipype/interfaces/freesurfer/model.py | 6 ++--- nipype/interfaces/freesurfer/preprocess.py | 12 +++++----- nipype/interfaces/freesurfer/registration.py | 2 +- .../interfaces/freesurfer/tests/test_utils.py | 2 +- nipype/interfaces/freesurfer/utils.py | 22 +++++++++---------- nipype/interfaces/fsl/aroma.py | 2 +- nipype/interfaces/fsl/base.py | 4 ++-- nipype/interfaces/fsl/dti.py | 8 +++---- nipype/interfaces/fsl/fix.py | 2 +- nipype/interfaces/fsl/maths.py | 2 +- nipype/interfaces/fsl/preprocess.py | 6 ++--- nipype/interfaces/fsl/tests/test_maths.py | 6 ++--- nipype/interfaces/fsl/utils.py | 8 +++---- nipype/interfaces/mipav/developer.py | 8 +++---- nipype/interfaces/mrtrix/tracking.py | 4 ++-- nipype/interfaces/mrtrix3/utils.py | 4 ++-- nipype/interfaces/niftyseg/maths.py | 2 +- nipype/interfaces/niftyseg/stats.py | 2 +- nipype/interfaces/nipy/model.py | 4 ++-- .../interfaces/slicer/diffusion/diffusion.py | 6 ++--- .../interfaces/slicer/filtering/denoising.py | 2 +- .../slicer/filtering/histogrammatching.py | 2 +- .../resamplescalarvectordwivolume.py | 2 +- .../slicer/legacy/diffusion/denoising.py | 2 +- .../slicer/registration/brainsresample.py | 2 +- .../slicer/registration/specialized.py | 6 ++--- nipype/interfaces/tests/test_nilearn.py | 2 +- nipype/pipeline/engine/tests/test_engine.py | 4 ++-- nipype/pipeline/engine/workflows.py | 2 +- nipype/pipeline/plugins/base.py | 2 +- nipype/pipeline/plugins/legacymultiproc.py | 2 +- nipype/pipeline/plugins/multiproc.py | 2 +- nipype/pipeline/plugins/oar.py | 2 +- nipype/pipeline/plugins/pbs.py | 2 +- nipype/pipeline/plugins/sge.py | 4 ++-- nipype/pipeline/plugins/sgegraph.py | 4 ++-- nipype/pipeline/plugins/slurmgraph.py | 4 ++-- nipype/scripts/cli.py | 2 +- nipype/testing/data/README | 2 +- 68 files changed, 126 insertions(+), 126 deletions(-) diff --git a/doc/changelog/1.X.X-changelog.rst b/doc/changelog/1.X.X-changelog.rst index 433212f4ce..776014e6c0 100644 --- a/doc/changelog/1.X.X-changelog.rst +++ b/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) diff --git a/doc/devel/cmd_interface_devel.rst b/doc/devel/cmd_interface_devel.rst index e0153cf678..3a35700fa7 100644 --- a/doc/devel/cmd_interface_devel.rst +++ b/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:: diff --git a/doc/devel/filename_generation.rst b/doc/devel/filename_generation.rst index c10b18c12f..5772ab33c1 100644 --- a/doc/devel/filename_generation.rst +++ b/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 diff --git a/doc/devel/interface_specs.rst b/doc/devel/interface_specs.rst index 13d44e1528..fa74aca753 100644 --- a/doc/devel/interface_specs.rst +++ b/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. diff --git a/doc/devel/matlab_interface_devel.rst b/doc/devel/matlab_interface_devel.rst index 516e000d43..1616f92c1c 100644 --- a/doc/devel/matlab_interface_devel.rst +++ b/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 diff --git a/nipype/algorithms/__init__.py b/nipype/algorithms/__init__.py index b28fc516d2..e34dc850ab 100644 --- a/nipype/algorithms/__init__.py +++ b/nipype/algorithms/__init__.py @@ -4,7 +4,7 @@ """ Package contains pure python neuroimaging algorithms -Exaples: artifactdetect +Examples: artifactdetect """ __docformat__ = "restructuredtext" diff --git a/nipype/algorithms/confounds.py b/nipype/algorithms/confounds.py index 63dc3def2a..f6be6c6311 100644 --- a/nipype/algorithms/confounds.py +++ b/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 diff --git a/nipype/algorithms/metrics.py b/nipype/algorithms/metrics.py index b58e7fc59b..155598bcd3 100644 --- a/nipype/algorithms/metrics.py +++ b/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, ) diff --git a/nipype/algorithms/misc.py b/nipype/algorithms/misc.py index 175d7642b8..23006aad8b 100644 --- a/nipype/algorithms/misc.py +++ b/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") diff --git a/nipype/algorithms/rapidart.py b/nipype/algorithms/rapidart.py index 0a819c466b..e764dc9243 100644 --- a/nipype/algorithms/rapidart.py +++ b/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 """ diff --git a/nipype/interfaces/ants/base.py b/nipype/interfaces/ants/base.py index 1c6cb4047f..a868e54b97 100644 --- a/nipype/interfaces/ants/base.py +++ b/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" diff --git a/nipype/interfaces/ants/legacy.py b/nipype/interfaces/ants/legacy.py index 0cc8b7e864..6be07f35a2 100644 --- a/nipype/interfaces/ants/legacy.py +++ b/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" ), ) diff --git a/nipype/interfaces/ants/registration.py b/nipype/interfaces/ants/registration.py index 478b26dc36..cd2145b8d5 100644 --- a/nipype/interfaces/ants/registration.py +++ b/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. diff --git a/nipype/interfaces/ants/resampling.py b/nipype/interfaces/ants/resampling.py index 607202c109..8738c2dada 100644 --- a/nipype/interfaces/ants/resampling.py +++ b/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"], ) diff --git a/nipype/interfaces/ants/segmentation.py b/nipype/interfaces/ants/segmentation.py index 5f8a76e302..9467c4086f 100644 --- a/nipype/interfaces/ants/segmentation.py +++ b/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" diff --git a/nipype/interfaces/base/core.py b/nipype/interfaces/base/core.py index c8099be630..8a20da3fb1 100644 --- a/nipype/interfaces/base/core.py +++ b/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") diff --git a/nipype/interfaces/base/tests/test_resource_monitor.py b/nipype/interfaces/base/tests/test_resource_monitor.py index 47a515f64c..79ca422385 100644 --- a/nipype/interfaces/base/tests/test_resource_monitor.py +++ b/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): diff --git a/nipype/interfaces/brainsuite/brainsuite.py b/nipype/interfaces/brainsuite/brainsuite.py index 84177a16ad..f353017e58 100644 --- a/nipype/interfaces/brainsuite/brainsuite.py +++ b/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). ", diff --git a/nipype/interfaces/camino/connectivity.py b/nipype/interfaces/camino/connectivity.py index 2b7d0ff337..6fdc8239f7 100644 --- a/nipype/interfaces/camino/connectivity.py +++ b/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 diff --git a/nipype/interfaces/camino/convert.py b/nipype/interfaces/camino/convert.py index a5b4b70fb3..0dd998c0c6 100644 --- a/nipype/interfaces/camino/convert.py +++ 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." diff --git a/nipype/interfaces/camino/dti.py b/nipype/interfaces/camino/dti.py index 6d210c1b0b..3e223532f6 100644 --- a/nipype/interfaces/camino/dti.py +++ b/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 ------- diff --git a/nipype/interfaces/camino/odf.py b/nipype/interfaces/camino/odf.py index 0cd8b0c49c..3825cf1bb6 100644 --- a/nipype/interfaces/camino/odf.py +++ b/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] diff --git a/nipype/interfaces/cat12/preprocess.py b/nipype/interfaces/cat12/preprocess.py index 69fe16b752..eec0ea936d 100644 --- a/nipype/interfaces/cat12/preprocess.py +++ b/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)" ) diff --git a/nipype/interfaces/cat12/surface.py b/nipype/interfaces/cat12/surface.py index 41f8a5f680..5e74f8d015 100644 --- a/nipype/interfaces/cat12/surface.py +++ b/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) ) diff --git a/nipype/interfaces/cmtk/cmtk.py b/nipype/interfaces/cmtk/cmtk.py index a2718b92b5..8775a8517e 100644 --- a/nipype/interfaces/cmtk/cmtk.py +++ b/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, ) diff --git a/nipype/interfaces/diffusion_toolkit/dti.py b/nipype/interfaces/diffusion_toolkit/dti.py index 9fc409f8f4..03488712ed 100644 --- a/nipype/interfaces/diffusion_toolkit/dti.py +++ b/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 diff --git a/nipype/interfaces/dipy/base.py b/nipype/interfaces/dipy/base.py index 6577ea6012..d8a1c0fbf5 100644 --- a/nipype/interfaces/dipy/base.py +++ b/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 -------- diff --git a/nipype/interfaces/dtitk/base.py b/nipype/interfaces/dtitk/base.py index aad1b4d521..efbd79ad98 100644 --- a/nipype/interfaces/dtitk/base.py +++ b/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. - If change_ext is True, it will use the extentions specified in - intputs.output_type. + If change_ext is True, it will use the extensions specified in + inputs.output_type. Parameters ---------- diff --git a/nipype/interfaces/freesurfer/longitudinal.py b/nipype/interfaces/freesurfer/longitudinal.py index 899a67bb50..5c3f621e87 100644 --- a/nipype/interfaces/freesurfer/longitudinal.py +++ b/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, diff --git a/nipype/interfaces/freesurfer/model.py b/nipype/interfaces/freesurfer/model.py index 9ab1ac96a3..f1b7fafe53 100644 --- a/nipype/interfaces/freesurfer/model.py +++ b/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 -------- diff --git a/nipype/interfaces/freesurfer/preprocess.py b/nipype/interfaces/freesurfer/preprocess.py index 30974490b6..a30749cf56 100644 --- a/nipype/interfaces/freesurfer/preprocess.py +++ b/nipype/interfaces/freesurfer/preprocess.py @@ -135,7 +135,7 @@ class UnpackSDICOMDirInputSpec(FSTraitedSpec): argstr="-scanonly %s", desc="only scan the directory and put result in file", ) - log_file = File(exists=True, argstr="-log %s", desc="explicilty set log file") + log_file = File(exists=True, argstr="-log %s", desc="explicitly set log file") spm_zeropad = traits.Int( argstr="-nspmzeropad %d", desc="set frame number zero padding width for SPM" ) @@ -2415,7 +2415,7 @@ class FitMSParamsOutputSpec(TraitedSpec): class FitMSParams(FSCommand): - """Estimate tissue paramaters from a set of FLASH images. + """Estimate tissue parameters from a set of FLASH images. Examples -------- @@ -2655,7 +2655,7 @@ class WatershedSkullStrip(FSCommand): """This program strips skull and other outer non-brain tissue and produces the brain volume from T1 volume or the scanned volume. - The "watershed" segmentation algorithm was used to dertermine the + The "watershed" segmentation algorithm was used to determine the intensity values for white matter, grey matter, and CSF. A force field was then used to fit a spherical surface to the brain. The shape of the surface fit was then evaluated against a previously @@ -2716,7 +2716,7 @@ class NormalizeInputSpec(FSTraitedSpec): argstr="-aseg %s", exists=True, desc="The input segmentation for Normalize" ) transform = File( - exists=True, desc="Tranform file from the header of the input file" + exists=True, desc="Transform file from the header of the input file" ) @@ -2779,7 +2779,7 @@ class CANormalizeInputSpec(FSTraitedSpec): exists=True, mandatory=True, position=-2, - desc="The tranform file in lta format", + desc="The transform file in lta format", ) # optional mask = File(argstr="-mask %s", exists=True, desc="Specifies volume to use as mask") @@ -3257,7 +3257,7 @@ def run(self, **inputs): def aggregate_outputs(self, runtime=None, needed_outputs=None): # it is necessary to find the output files and move - # them to the correct loacation + # them to the correct location predicted_outputs = self._list_outputs() for name in ["out_file", "out_rotation"]: out_file = predicted_outputs[name] diff --git a/nipype/interfaces/freesurfer/registration.py b/nipype/interfaces/freesurfer/registration.py index 5d7780f85c..8b1624c87d 100644 --- a/nipype/interfaces/freesurfer/registration.py +++ b/nipype/interfaces/freesurfer/registration.py @@ -211,7 +211,7 @@ class EMRegisterOutputSpec(TraitedSpec): class EMRegister(FSCommandOpenMP): - """This program creates a tranform in lta format + """This program creates a transform in lta format Examples ======== diff --git a/nipype/interfaces/freesurfer/tests/test_utils.py b/nipype/interfaces/freesurfer/tests/test_utils.py index 996453d654..0ee9dd3751 100644 --- a/nipype/interfaces/freesurfer/tests/test_utils.py +++ b/nipype/interfaces/freesurfer/tests/test_utils.py @@ -154,7 +154,7 @@ def test_surfshots(create_files_in_directory_plus_dummy_file): # Create testing files files, cwd = create_files_in_directory_plus_dummy_file - # Test input settins + # Test input settings fotos.inputs.subject_id = "fsaverage" fotos.inputs.hemi = "lh" fotos.inputs.surface = "pial" diff --git a/nipype/interfaces/freesurfer/utils.py b/nipype/interfaces/freesurfer/utils.py index 4a526cdca8..9ee65366d2 100644 --- a/nipype/interfaces/freesurfer/utils.py +++ b/nipype/interfaces/freesurfer/utils.py @@ -462,7 +462,7 @@ class SurfaceSmoothOutputSpec(TraitedSpec): class SurfaceSmooth(FSCommand): """Smooth a surface image with mri_surf2surf. - The surface is smoothed by an interative process of averaging the + The surface is smoothed by an iterative process of averaging the value at each vertex with those of its adjacent neighbors. You may supply either the number of iterations to run or a desired effective FWHM of the smoothing process. If the latter, the underlying program will calculate @@ -878,7 +878,7 @@ class SurfaceSnapshotsInputSpec(FSTraitedSpec): ) overlay_range_offset = traits.Float( argstr="-foffset %.3f", - desc="overlay range will be symettric around offset value", + desc="overlay range will be symmetric around offset value", ) truncate_overlay = traits.Bool( @@ -1438,13 +1438,13 @@ class MRITessellateInputSpec(FSTraitedSpec): mandatory=True, position=-3, argstr="%s", - desc="Input volume to tesselate voxels from.", + desc="Input volume to tessellate voxels from.", ) label_value = traits.Int( position=-2, argstr="%d", mandatory=True, - desc='Label value which to tesselate from the input volume. (integer, if input is "filled.mgz" volume, 127 is rh, 255 is lh)', + desc='Label value which to tessellate from the input volume. (integer, if input is "filled.mgz" volume, 127 is rh, 255 is lh)', ) out_file = File( argstr="%s", @@ -1600,13 +1600,13 @@ class MRIMarchingCubesInputSpec(FSTraitedSpec): mandatory=True, position=1, argstr="%s", - desc="Input volume to tesselate voxels from.", + desc="Input volume to tessellate voxels from.", ) label_value = traits.Int( position=2, argstr="%d", mandatory=True, - desc='Label value which to tesselate from the input volume. (integer, if input is "filled.mgz" volume, 127 is rh, 255 is lh)', + desc='Label value which to tessellate from the input volume. (integer, if input is "filled.mgz" volume, 127 is rh, 255 is lh)', ) connectivity_value = traits.Int( 1, @@ -1676,7 +1676,7 @@ class SmoothTessellationInputSpec(FSTraitedSpec): argstr="%s", position=-2, copyfile=True, - desc="Input volume to tesselate voxels from.", + desc="Input volume to tessellate voxels from.", ) curvature_averaging_iterations = traits.Int( argstr="-a %d", desc="Number of curvature averaging iterations (default=10)" @@ -1842,7 +1842,7 @@ class ExtractMainComponentOutputSpec(TraitedSpec): class ExtractMainComponent(CommandLine): - """Extract the main component of a tesselated surface + """Extract the main component of a tessellated surface Examples -------- @@ -2329,7 +2329,7 @@ class MRIFillOutputSpec(TraitedSpec): class MRIFill(FSCommand): """ This program creates hemispheric cutting planes and fills white matter - with specific values for subsequent surface tesselation. + with specific values for subsequent surface tessellation. Examples ======== @@ -2730,7 +2730,7 @@ class MakeSurfacesInputSpec(FSTraitedSpec): ) fix_mtl = traits.Bool(argstr="-fix_mtl", desc="Undocumented flag") no_white = traits.Bool(argstr="-nowhite", desc="Undocumented flag") - white_only = traits.Bool(argstr="-whiteonly", desc="Undocumented flage") + white_only = traits.Bool(argstr="-whiteonly", desc="Undocumented flag") in_aseg = File(argstr="-aseg %s", exists=True, desc="Input segmentation file") in_T1 = File(argstr="-T1 %s", exists=True, desc="Input brain or T1 file") mgz = traits.Bool( @@ -2850,7 +2850,7 @@ def _format_arg(self, name, spec, value): return spec.argstr % suffix elif name == "in_orig": if value.endswith("lh.orig") or value.endswith("rh.orig"): - # {lh,rh}.orig inputs are not sepcified on command line + # {lh,rh}.orig inputs are not specified on command line return else: # if the input orig file is different than lh.orig or rh.orig diff --git a/nipype/interfaces/fsl/aroma.py b/nipype/interfaces/fsl/aroma.py index 4a3eb32034..f4cab884a2 100644 --- a/nipype/interfaces/fsl/aroma.py +++ b/nipype/interfaces/fsl/aroma.py @@ -43,7 +43,7 @@ class ICA_AROMAInputSpec(CommandLineInputSpec): dim = traits.Int( argstr="-dim %d", desc="Dimensionality reduction when running " - "MELODIC (defualt is automatic estimation)", + "MELODIC (default is automatic estimation)", ) TR = traits.Float( argstr="-tr %.3f", diff --git a/nipype/interfaces/fsl/base.py b/nipype/interfaces/fsl/base.py index d65630dacf..dbafde7f87 100644 --- a/nipype/interfaces/fsl/base.py +++ b/nipype/interfaces/fsl/base.py @@ -206,8 +206,8 @@ 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. - If change_ext is True, it will use the extentions specified in - intputs.output_type. + If change_ext is True, it will use the extensions specified in + inputs.output_type. Parameters ---------- diff --git a/nipype/interfaces/fsl/dti.py b/nipype/interfaces/fsl/dti.py index e1e6c2af8d..a49c508c64 100644 --- a/nipype/interfaces/fsl/dti.py +++ b/nipype/interfaces/fsl/dti.py @@ -877,7 +877,7 @@ def _list_outputs(self): out_dir = self.inputs.out_dir outputs["log"] = os.path.abspath(os.path.join(out_dir, "probtrackx.log")) - # utputs['way_total'] = os.path.abspath(os.path.join(out_dir, + # outputs['way_total'] = os.path.abspath(os.path.join(out_dir, # 'waytotal')) if isdefined(self.inputs.opd is True): if isinstance(self.inputs.seed, list) and isinstance( @@ -1352,7 +1352,7 @@ class TractSkeletonInputSpec(FSLCommandInputSpec): exists=True, mandatory=True, argstr="-i %s", - desc="input image (typcially mean FA volume)", + desc="input image (typically mean FA volume)", ) _proj_inputs = ["threshold", "distance_map", "data_file"] project_data = traits.Bool( @@ -1402,7 +1402,7 @@ class TractSkeleton(FSLCommand): ``search_mask_file`` and ``use_cingulum_mask`` inputs are also used in data projection, but ``use_cingulum_mask`` is set to True by default. This mask controls where the projection algorithm searches within a circular space - around a tract, rather than in a single perpindicular direction. + around a tract, rather than in a single perpendicular direction. Example ------- @@ -1476,7 +1476,7 @@ class DistanceMapInputSpec(FSLCommandInputSpec): desc="image to calculate distance values for", ) mask_file = File( - exists=True, argstr="--mask=%s", desc="binary mask to contrain calculations" + exists=True, argstr="--mask=%s", desc="binary mask to constrain calculations" ) invert_input = traits.Bool(argstr="--invert", desc="invert input image") local_max_file = traits.Either( diff --git a/nipype/interfaces/fsl/fix.py b/nipype/interfaces/fsl/fix.py index ddfc01d19c..5c978f0a97 100644 --- a/nipype/interfaces/fsl/fix.py +++ b/nipype/interfaces/fsl/fix.py @@ -96,7 +96,7 @@ class TrainingSetCreator(BaseInterface): the ones that have a hand_labels_noise.txt file in them. This is outsourced as a separate class, so that the pipeline is - rerun everytime a handlabeled file has been changed, or a new one + rerun every time a handlabeled file has been changed, or a new one created. """ diff --git a/nipype/interfaces/fsl/maths.py b/nipype/interfaces/fsl/maths.py index f3276024b7..6e7baf74ce 100644 --- a/nipype/interfaces/fsl/maths.py +++ b/nipype/interfaces/fsl/maths.py @@ -420,7 +420,7 @@ class DilateInput(KernelInput): argstr="-dil%s", position=6, mandatory=True, - desc="filtering operation to perfoem in dilation", + desc="filtering operation to perform in dilation", ) diff --git a/nipype/interfaces/fsl/preprocess.py b/nipype/interfaces/fsl/preprocess.py index 5ab9a92010..80ef25534a 100644 --- a/nipype/interfaces/fsl/preprocess.py +++ b/nipype/interfaces/fsl/preprocess.py @@ -780,7 +780,7 @@ class ApplyXFM(FLIRT): """Currently just a light wrapper around FLIRT, with no modifications - ApplyXFM is used to apply an existing tranform to an image + ApplyXFM is used to apply an existing transform to an image Examples @@ -836,7 +836,7 @@ class MCFLIRTInputSpec(FSLCommandInputSpec): argstr="-stages %d", desc="stages (if 4, perform final search with sinc interpolation", ) - init = File(exists=True, argstr="-init %s", desc="inital transformation matrix") + init = File(exists=True, argstr="-init %s", desc="initial transformation matrix") interpolation = traits.Enum( "spline", "nn", @@ -1165,7 +1165,7 @@ class FNIRTInputSpec(FSLCommandInputSpec): argstr="--lambda=%s", desc=( "Weight of regularisation, default depending on --ssqlambda and " - "--regmod switches. See user documetation." + "--regmod switches. See user documentation." ), sep=",", ) diff --git a/nipype/interfaces/fsl/tests/test_maths.py b/nipype/interfaces/fsl/tests/test_maths.py index 9b05645997..d082910e42 100644 --- a/nipype/interfaces/fsl/tests/test_maths.py +++ b/nipype/interfaces/fsl/tests/test_maths.py @@ -132,7 +132,7 @@ def test_meanimage(create_files_in_directory_plus_output_type): # Test the underlying command assert meaner.cmd == "fslmaths" - # Test the defualt opstring + # Test the default opstring assert meaner.cmdline == "fslmaths a.nii -Tmean b.nii" # Test the other dimensions @@ -158,7 +158,7 @@ def test_stdimage(create_files_in_directory_plus_output_type): # Test the underlying command assert stder.cmd == "fslmaths" - # Test the defualt opstring + # Test the default opstring assert stder.cmdline == "fslmaths a.nii -Tstd b.nii" # Test the other dimensions @@ -184,7 +184,7 @@ def test_maximage(create_files_in_directory_plus_output_type): # Test the underlying command assert maxer.cmd == "fslmaths" - # Test the defualt opstring + # Test the default opstring assert maxer.cmdline == "fslmaths a.nii -Tmax b.nii" # Test the other dimensions diff --git a/nipype/interfaces/fsl/utils.py b/nipype/interfaces/fsl/utils.py index 51d0d7fce5..4bb44d00b3 100644 --- a/nipype/interfaces/fsl/utils.py +++ b/nipype/interfaces/fsl/utils.py @@ -764,7 +764,7 @@ class ImageStatsInputSpec(FSLCommandInputSpec): exists=True, argstr="-K %s", position=2, - desc="generate seperate n submasks from indexMask, " + desc="generate separate n submasks from indexMask, " "for indexvalues 1..n where n is the maximum index " "value in indexMask, and generate statistics for each submask", ) @@ -1282,7 +1282,7 @@ class PlotTimeSeriesInputSpec(FSLCommandInputSpec): labels = traits.Either( traits.Str, traits.List(traits.Str), argstr="%s", desc="label or list of labels" ) - y_min = traits.Float(argstr="--ymin=%.2f", desc="minumum y value", xor=("y_range",)) + y_min = traits.Float(argstr="--ymin=%.2f", desc="minimum y value", xor=("y_range",)) y_max = traits.Float(argstr="--ymax=%.2f", desc="maximum y value", xor=("y_range",)) y_range = traits.Tuple( traits.Float, @@ -1434,7 +1434,7 @@ class PlotMotionParams(FSLCommand): translations, while SPM prints them in the opposite order. This interface should be able to plot timecourses of motion parameters generated from other sources as long as they fall under one of these two patterns. For - more flexibilty, see the :class:`fsl.PlotTimeSeries` interface. + more flexibility, see the :class:`fsl.PlotTimeSeries` interface. """ @@ -1873,7 +1873,7 @@ class InvWarpInputSpec(FSLCommandInputSpec): ), ) regularise = traits.Float( - argstr="--regularise=%f", desc="Regularization strength (deafult=1.0)." + argstr="--regularise=%f", desc="Regularization strength (default=1.0)." ) noconstraint = traits.Bool( argstr="--noconstraint", desc="Do not apply Jacobian constraint" diff --git a/nipype/interfaces/mipav/developer.py b/nipype/interfaces/mipav/developer.py index 52e2b01b01..af9bf5977b 100644 --- a/nipype/interfaces/mipav/developer.py +++ b/nipype/interfaces/mipav/developer.py @@ -481,7 +481,7 @@ class MedicAlgorithmLesionToadsInputSpec(CommandLineInputSpec): desc="Atlas File - No Lesion - T1 Only", exists=True, argstr="--inAtlas4 %s" ) inMaximum = traits.Int( - desc="Maximum distance from the interventricular WM boundary to downweight the lesion membership to avoid false postives", + desc="Maximum distance from the interventricular WM boundary to downweight the lesion membership to avoid false positives", argstr="--inMaximum %d", ) inMaximum2 = traits.Int(desc="Maximum Ventircle Distance", argstr="--inMaximum2 %d") @@ -499,7 +499,7 @@ class MedicAlgorithmLesionToadsInputSpec(CommandLineInputSpec): argstr="--inAtlas5 %f", ) inSmooting = traits.Float( - desc="Controls the effect of neighberhood voxels on the membership", + desc="Controls the effect of neighborhood voxels on the membership", argstr="--inSmooting %f", ) inMaximum4 = traits.Float( @@ -603,7 +603,7 @@ class MedicAlgorithmLesionToadsOutputSpec(TraitedSpec): class MedicAlgorithmLesionToads(SEMLikeCommandLine): - """Algorithm for simulataneous brain structures and MS lesion segmentation of MS Brains. + """Algorithm for simultaneous brain structures and MS lesion segmentation of MS Brains. The brain segmentation is topologically consistent and the algorithm can use multiple MR sequences as input data. @@ -1085,7 +1085,7 @@ class MedicAlgorithmSPECTRE2010InputSpec(CommandLineInputSpec): argstr="--inAtlas %s", ) inInitial = traits.Int( - desc="Erosion of the inital mask, which is based on the probability mask and the classification., The initial mask is ouput as the d0 volume at the conclusion of SPECTRE.", + desc="Erosion of the initial mask, which is based on the probability mask and the classification., The initial mask is output as the d0 volume at the conclusion of SPECTRE.", argstr="--inInitial %d", ) inImage = traits.Enum( diff --git a/nipype/interfaces/mrtrix/tracking.py b/nipype/interfaces/mrtrix/tracking.py index b7465cdbf2..4619740fc2 100644 --- a/nipype/interfaces/mrtrix/tracking.py +++ b/nipype/interfaces/mrtrix/tracking.py @@ -119,7 +119,7 @@ class Tracks2ProbInputSpec(CommandLineInputSpec): exists=True, argstr="-template %s", position=1, - desc="an image file to be used as a template for the output (the output image wil have the same transform and field of view)", + desc="an image file to be used as a template for the output (the output image will have the same transform and field of view)", ) voxel_dims = traits.List( traits.Float, @@ -215,7 +215,7 @@ class StreamlineTrackInputSpec(CommandLineInputSpec): mandatory=True, position=-2, desc="the image containing the source data." - "The type of data required depends on the type of tracking as set in the preceeding argument. For DT methods, " + "The type of data required depends on the type of tracking as set in the preceding argument. For DT methods, " "the base DWI are needed. For SD methods, the SH harmonic coefficients of the FOD are needed.", ) diff --git a/nipype/interfaces/mrtrix3/utils.py b/nipype/interfaces/mrtrix3/utils.py index d5f8c2c5f5..89bbd2d1f1 100644 --- a/nipype/interfaces/mrtrix3/utils.py +++ b/nipype/interfaces/mrtrix3/utils.py @@ -453,7 +453,7 @@ class ComputeTDIInputSpec(CommandLineInputSpec): argstr="-upsample %d", desc="upsample the tracks by" " some ratio using Hermite interpolation before " - "mappping", + "mapping", ) precise = traits.Bool( @@ -938,7 +938,7 @@ class MRMathInputSpec(MRTrix3BaseInputSpec): desc="operation to computer along a specified axis", ) axis = traits.Int( - 0, argstr="-axis %d", desc="specfied axis to perform the operation along" + 0, argstr="-axis %d", desc="specified axis to perform the operation along" ) diff --git a/nipype/interfaces/niftyseg/maths.py b/nipype/interfaces/niftyseg/maths.py index c297940695..4f5edfe0f4 100644 --- a/nipype/interfaces/niftyseg/maths.py +++ b/nipype/interfaces/niftyseg/maths.py @@ -65,7 +65,7 @@ class MathsCommand(NiftySegCommand): The executable seg_maths enables the sequential execution of arithmetic operations, like multiplication (-mul), division (-div) or addition (-add), binarisation (-bin) or thresholding (-thr) operations and - convolution by a Gaussian kernel (-smo). It also alows mathematical + convolution by a Gaussian kernel (-smo). It also allows mathematical morphology based operations like dilation (-dil), erosion (-ero), connected components (-lconcomp) and hole filling (-fill), Euclidean (- euc) and geodesic (-geo) distance transforms, local image similarity diff --git a/nipype/interfaces/niftyseg/stats.py b/nipype/interfaces/niftyseg/stats.py index d872e180eb..88e173ac5d 100644 --- a/nipype/interfaces/niftyseg/stats.py +++ b/nipype/interfaces/niftyseg/stats.py @@ -121,7 +121,7 @@ class UnaryStatsInput(StatsInput): * B - Bounding box of all nonzero voxels [ xmin xsize ymin ysize zmin zsize ] * xvox - Output the number of voxels in the x direction. Replace x with y/z for other directions. - * xdim - Output the voxel dimention in the x direction. + * xdim - Output the voxel dimension in the x direction. Replace x with y/z for other directions. """, diff --git a/nipype/interfaces/nipy/model.py b/nipype/interfaces/nipy/model.py index b931947c19..d232fcea1b 100644 --- a/nipype/interfaces/nipy/model.py +++ b/nipype/interfaces/nipy/model.py @@ -20,7 +20,7 @@ class FitGLMInputSpec(BaseInterfaceInputSpec): desc=( "Session specific information generated by" " ``modelgen.SpecifyModel``, FitGLM does " - "not support multiple runs uless they are " + "not support multiple runs unless they are " "concatenated (see SpecifyModel options)" ), ) @@ -29,7 +29,7 @@ class FitGLMInputSpec(BaseInterfaceInputSpec): "Canonical With Derivative", "FIR", desc=( - "that specifies the hemodynamic reponse " + "that specifies the hemodynamic response " "function it can be 'Canonical', 'Canonical " "With Derivative' or 'FIR'" ), diff --git a/nipype/interfaces/slicer/diffusion/diffusion.py b/nipype/interfaces/slicer/diffusion/diffusion.py index 2668f060c4..d5ffadae17 100644 --- a/nipype/interfaces/slicer/diffusion/diffusion.py +++ b/nipype/interfaces/slicer/diffusion/diffusion.py @@ -52,7 +52,7 @@ class ResampleDTIVolumeInputSpec(CommandLineInputSpec): "nn", "ws", "bs", - desc="Sampling algorithm (linear , nn (nearest neighborhoor), ws (WindowedSinc), bs (BSpline) )", + desc="Sampling algorithm (linear , nn (nearest neighbor), ws (WindowedSinc), bs (BSpline) )", argstr="--interpolation %s", ) correction = traits.Enum( @@ -424,7 +424,7 @@ class DiffusionWeightedVolumeMaskingInputSpec(CommandLineInputSpec): argstr="%s", ) otsuomegathreshold = traits.Float( - desc="Control the sharpness of the threshold in the Otsu computation. 0: lower threshold, 1: higher threhold", + desc="Control the sharpness of the threshold in the Otsu computation. 0: lower threshold, 1: higher threshold", argstr="--otsuomegathreshold %f", ) removeislands = traits.Bool( @@ -549,7 +549,7 @@ class DWIToDTIEstimation(SEMLikeCommandLine): description: Performs a tensor model estimation from diffusion weighted images. - There are three estimation methods available: least squares, weigthed least squares and non-linear estimation. The first method is the traditional method for tensor estimation and the fastest one. Weighted least squares takes into account the noise characteristics of the MRI images to weight the DWI samples used in the estimation based on its intensity magnitude. The last method is the more complex. + There are three estimation methods available: least squares, weighted least squares and non-linear estimation. The first method is the traditional method for tensor estimation and the fastest one. Weighted least squares takes into account the noise characteristics of the MRI images to weight the DWI samples used in the estimation based on its intensity magnitude. The last method is the more complex. version: 0.1.0.$Revision: 1892 $(alpha) diff --git a/nipype/interfaces/slicer/filtering/denoising.py b/nipype/interfaces/slicer/filtering/denoising.py index c28fc0746d..6f3af80d2b 100644 --- a/nipype/interfaces/slicer/filtering/denoising.py +++ b/nipype/interfaces/slicer/filtering/denoising.py @@ -153,7 +153,7 @@ class GaussianBlurImageFilter(SEMLikeCommandLine): category: Filtering.Denoising - description: Apply a gaussian blurr to an image + description: Apply a gaussian blur to an image version: 0.1.0.$Revision: 1.1 $(alpha) diff --git a/nipype/interfaces/slicer/filtering/histogrammatching.py b/nipype/interfaces/slicer/filtering/histogrammatching.py index e6132bd987..f67e9a9e1a 100644 --- a/nipype/interfaces/slicer/filtering/histogrammatching.py +++ b/nipype/interfaces/slicer/filtering/histogrammatching.py @@ -64,7 +64,7 @@ class HistogramMatching(SEMLikeCommandLine): description: Normalizes the grayscale values of a source image based on the grayscale values of a reference image. This filter uses a histogram matching technique where the histograms of the two images are matched only at a specified number of quantile values. - The filter was orginally designed to normalize MR images of the sameMR protocol and same body part. The algorithm works best if background pixels are excluded from both the source and reference histograms. A simple background exclusion method is to exclude all pixels whose grayscale values are smaller than the mean grayscale value. ThresholdAtMeanIntensity switches on this simple background exclusion method. + The filter was originally designed to normalize MR images of the sameMR protocol and same body part. The algorithm works best if background pixels are excluded from both the source and reference histograms. A simple background exclusion method is to exclude all pixels whose grayscale values are smaller than the mean grayscale value. ThresholdAtMeanIntensity switches on this simple background exclusion method. Number of match points governs the number of quantile values to be matched. diff --git a/nipype/interfaces/slicer/filtering/resamplescalarvectordwivolume.py b/nipype/interfaces/slicer/filtering/resamplescalarvectordwivolume.py index 0d7c0777dd..98c0baa178 100644 --- a/nipype/interfaces/slicer/filtering/resamplescalarvectordwivolume.py +++ b/nipype/interfaces/slicer/filtering/resamplescalarvectordwivolume.py @@ -52,7 +52,7 @@ class ResampleScalarVectorDWIVolumeInputSpec(CommandLineInputSpec): "nn", "ws", "bs", - desc="Sampling algorithm (linear or nn (nearest neighborhoor), ws (WindowedSinc), bs (BSpline) )", + desc="Sampling algorithm (linear or nn (nearest neighbor), ws (WindowedSinc), bs (BSpline) )", argstr="--interpolation %s", ) transform_order = traits.Enum( diff --git a/nipype/interfaces/slicer/legacy/diffusion/denoising.py b/nipype/interfaces/slicer/legacy/diffusion/denoising.py index b868193511..2e5345c34c 100644 --- a/nipype/interfaces/slicer/legacy/diffusion/denoising.py +++ b/nipype/interfaces/slicer/legacy/diffusion/denoising.py @@ -32,7 +32,7 @@ class DWIUnbiasedNonLocalMeansFilterInputSpec(CommandLineInputSpec): argstr="--rc %s", ) hp = traits.Float( - desc="This parameter is related to noise; the larger the parameter, the more agressive the filtering. Should be near 1, and only values between 0.8 and 1.2 are allowed", + desc="This parameter is related to noise; the larger the parameter, the more aggressive the filtering. Should be near 1, and only values between 0.8 and 1.2 are allowed", argstr="--hp %f", ) ng = traits.Int( diff --git a/nipype/interfaces/slicer/registration/brainsresample.py b/nipype/interfaces/slicer/registration/brainsresample.py index bf7b4f5547..653be8e916 100644 --- a/nipype/interfaces/slicer/registration/brainsresample.py +++ b/nipype/interfaces/slicer/registration/brainsresample.py @@ -74,7 +74,7 @@ class BRAINSResampleInputSpec(CommandLineInputSpec): defaultValue = traits.Float(desc="Default voxel value", argstr="--defaultValue %f") gridSpacing = InputMultiPath( traits.Int, - desc="Add warped grid to output image to help show the deformation that occured with specified spacing. A spacing of 0 in a dimension indicates that grid lines should be rendered to fall exactly (i.e. do not allow displacements off that plane). This is useful for makeing a 2D image of grid lines from the 3D space ", + desc="Add warped grid to output image to help show the deformation that occurred with specified spacing. A spacing of 0 in a dimension indicates that grid lines should be rendered to fall exactly (i.e. do not allow displacements off that plane). This is useful for making a 2D image of grid lines from the 3D space ", sep=",", argstr="--gridSpacing %s", ) diff --git a/nipype/interfaces/slicer/registration/specialized.py b/nipype/interfaces/slicer/registration/specialized.py index 01cfafbc6a..1de0c117ea 100644 --- a/nipype/interfaces/slicer/registration/specialized.py +++ b/nipype/interfaces/slicer/registration/specialized.py @@ -198,7 +198,7 @@ class VBRAINSDemonWarpInputSpec(CommandLineInputSpec): argstr="--registrationFilterType %s", ) smoothDisplacementFieldSigma = traits.Float( - desc="A gaussian smoothing value to be applied to the deformation feild at each iteration.", + desc="A gaussian smoothing value to be applied to the deformation field at each iteration.", argstr="--smoothDisplacementFieldSigma %f", ) numberOfPyramidLevels = traits.Int( @@ -460,7 +460,7 @@ class BRAINSDemonWarpInputSpec(CommandLineInputSpec): argstr="--registrationFilterType %s", ) smoothDisplacementFieldSigma = traits.Float( - desc="A gaussian smoothing value to be applied to the deformation feild at each iteration.", + desc="A gaussian smoothing value to be applied to the deformation field at each iteration.", argstr="--smoothDisplacementFieldSigma %f", ) numberOfPyramidLevels = traits.Int( @@ -517,7 +517,7 @@ class BRAINSDemonWarpInputSpec(CommandLineInputSpec): "ROIAUTO", "ROI", "BOBF", - desc="What mode to use for using the masks: NOMASK|ROIAUTO|ROI|BOBF. If ROIAUTO is choosen, then the mask is implicitly defined using a otsu forground and hole filling algorithm. Where the Region Of Interest mode uses the masks to define what parts of the image should be used for computing the deformation field. Brain Only Background Fill uses the masks to pre-process the input images by clipping and filling in the background with a predefined value.", + desc="What mode to use for using the masks: NOMASK|ROIAUTO|ROI|BOBF. If ROIAUTO is chosen, then the mask is implicitly defined using a otsu foreground and hole filling algorithm. Where the Region Of Interest mode uses the masks to define what parts of the image should be used for computing the deformation field. Brain Only Background Fill uses the masks to pre-process the input images by clipping and filling in the background with a predefined value.", argstr="--maskProcessingMode %s", ) fixedBinaryVolume = File( diff --git a/nipype/interfaces/tests/test_nilearn.py b/nipype/interfaces/tests/test_nilearn.py index edf17ea058..2066c00768 100644 --- a/nipype/interfaces/tests/test_nilearn.py +++ b/nipype/interfaces/tests/test_nilearn.py @@ -169,7 +169,7 @@ def assert_expected_output(self, labels, wanted): for j, segment in enumerate(time): npt.assert_almost_equal(segment, wanted[i][j], decimal=1) - # dj: self doesnt have orig_dir at this point, not sure how to change it. + # dj: self doesn't have orig_dir at this point, not sure how to change it. # should work without it # def teardown_class(self): # self.orig_dir.chdir() diff --git a/nipype/pipeline/engine/tests/test_engine.py b/nipype/pipeline/engine/tests/test_engine.py index 0f076af380..a44922910d 100644 --- a/nipype/pipeline/engine/tests/test_engine.py +++ b/nipype/pipeline/engine/tests/test_engine.py @@ -572,7 +572,7 @@ def test_write_graph_dotfile(tmpdir, graph_type, simple): ) # graph_detailed is the same for orig, flat, exec (if no iterables) - # graph_detailed is not created for hierachical or colored + # graph_detailed is not created for hierarchical or colored if graph_type not in ["hierarchical", "colored"]: with open("graph_detailed.dot") as f: graph_str = f.read() @@ -665,7 +665,7 @@ def test_write_graph_dotfile_iterables(tmpdir, graph_type, simple): in graph_str ) - # graph_detailed is not created for hierachical or colored + # graph_detailed is not created for hierarchical or colored if graph_type not in ["hierarchical", "colored"]: with open("graph_detailed.dot") as f: graph_str = f.read() diff --git a/nipype/pipeline/engine/workflows.py b/nipype/pipeline/engine/workflows.py index 563ce6a840..5cff775284 100644 --- a/nipype/pipeline/engine/workflows.py +++ b/nipype/pipeline/engine/workflows.py @@ -120,7 +120,7 @@ def connect(self, *args, **kwargs): 'targetinput'), ...]), ...] sourceoutput1 will always be the first argument to func - and func will be evaluated and the results sent ot targetinput + and func will be evaluated and the results sent to targetinput currently func needs to define all its needed imports within the function as we use the inspect module to get at the source code diff --git a/nipype/pipeline/plugins/base.py b/nipype/pipeline/plugins/base.py index dbcf415b4e..a927b24686 100644 --- a/nipype/pipeline/plugins/base.py +++ b/nipype/pipeline/plugins/base.py @@ -81,7 +81,7 @@ class DistributedPluginBase(PluginBase): a boolean numpy array (N,) signifying whether a process is currently running. depidx : :obj:`numpy.matrix` - a boolean matrix (NxN) storing the dependency structure accross + a boolean matrix (NxN) storing the dependency structure across processes. Process dependencies are derived from each column. """ diff --git a/nipype/pipeline/plugins/legacymultiproc.py b/nipype/pipeline/plugins/legacymultiproc.py index cb48702ef6..747ff00c16 100644 --- a/nipype/pipeline/plugins/legacymultiproc.py +++ b/nipype/pipeline/plugins/legacymultiproc.py @@ -269,7 +269,7 @@ def _submit_job(self, node, updatehash=False): return self._taskid def _prerun_check(self, graph): - """Check if any node exeeds the available resources""" + """Check if any node exceeds the available resources""" tasks_mem_gb = [] tasks_num_th = [] for node in graph.nodes(): diff --git a/nipype/pipeline/plugins/multiproc.py b/nipype/pipeline/plugins/multiproc.py index ca7820939d..7df35cab9d 100644 --- a/nipype/pipeline/plugins/multiproc.py +++ b/nipype/pipeline/plugins/multiproc.py @@ -182,7 +182,7 @@ def _submit_job(self, node, updatehash=False): return self._taskid def _prerun_check(self, graph): - """Check if any node exeeds the available resources""" + """Check if any node exceeds the available resources""" tasks_mem_gb = [] tasks_num_th = [] for node in graph.nodes(): diff --git a/nipype/pipeline/plugins/oar.py b/nipype/pipeline/plugins/oar.py index 4ce64305eb..bc7d2ba09d 100644 --- a/nipype/pipeline/plugins/oar.py +++ b/nipype/pipeline/plugins/oar.py @@ -27,7 +27,7 @@ class OARPlugin(SGELikeBatchManagerBase): """ - # Addtional class variables + # Additional class variables _max_jobname_len = 15 _oarsub_args = "" diff --git a/nipype/pipeline/plugins/pbs.py b/nipype/pipeline/plugins/pbs.py index b322d88743..4ff172a067 100644 --- a/nipype/pipeline/plugins/pbs.py +++ b/nipype/pipeline/plugins/pbs.py @@ -24,7 +24,7 @@ class PBSPlugin(SGELikeBatchManagerBase): """ - # Addtional class variables + # Additional class variables _max_jobname_len = 15 def __init__(self, **kwargs): diff --git a/nipype/pipeline/plugins/sge.py b/nipype/pipeline/plugins/sge.py index 2690e78fcf..d6512b9103 100644 --- a/nipype/pipeline/plugins/sge.py +++ b/nipype/pipeline/plugins/sge.py @@ -50,7 +50,7 @@ def __init__( self._job_time = job_time # The job start time self._job_info_creation_time = ( time.time() - ) # When this job was created (for comparing against initalization) + ) # When this job was created (for comparing against initialization) self._job_queue_name = job_queue_name # Where the job is running self._job_slots = int(job_slots) # How many slots are being used self._qsub_command_line = qsub_command_line @@ -270,7 +270,7 @@ def _parse_qstat_job_list(self, xml_job_list): self._task_dictionary[dictionary_job].set_state("zombie") else: sge_debug_print( - "ERROR: Job not in still in intializing mode, " + "ERROR: Job not in still in initialization mode, " "and not in done list {0}: {1}".format( dictionary_job, self._task_dictionary[dictionary_job] ) diff --git a/nipype/pipeline/plugins/sgegraph.py b/nipype/pipeline/plugins/sgegraph.py index 489e48186c..48fc1ce132 100644 --- a/nipype/pipeline/plugins/sgegraph.py +++ b/nipype/pipeline/plugins/sgegraph.py @@ -85,7 +85,7 @@ def make_job_name(jobnumber, nodeslist): node_status_done = node_completed_status(node) # if the node itself claims done, then check to ensure all - # dependancies are also done + # dependencies are also done if node_status_done and idx in dependencies: for child_idx in dependencies[idx]: if child_idx in cache_doneness_per_node: @@ -127,7 +127,7 @@ def make_job_name(jobnumber, nodeslist): if idx in dependencies: values = " " for jobid in dependencies[idx]: - # Avoid dependancies of done jobs + # Avoid dependencies of done jobs if ( not self._dont_resubmit_completed_jobs or not cache_doneness_per_node[jobid] diff --git a/nipype/pipeline/plugins/slurmgraph.py b/nipype/pipeline/plugins/slurmgraph.py index 9468c76ba1..e54c5f4291 100644 --- a/nipype/pipeline/plugins/slurmgraph.py +++ b/nipype/pipeline/plugins/slurmgraph.py @@ -85,7 +85,7 @@ def make_job_name(jobnumber, nodeslist): node_status_done = node_completed_status(node) # if the node itself claims done, then check to ensure all - # dependancies are also done + # dependencies are also done if node_status_done and idx in dependencies: for child_idx in dependencies[idx]: if child_idx in cache_doneness_per_node: @@ -127,7 +127,7 @@ def make_job_name(jobnumber, nodeslist): if idx in dependencies: values = "" for jobid in dependencies[idx]: - # Avoid dependancies of done jobs + # Avoid dependencies of done jobs if ( not self._dont_resubmit_completed_jobs or not cache_doneness_per_node[jobid] diff --git a/nipype/scripts/cli.py b/nipype/scripts/cli.py index 73b599a978..284b9fbb96 100644 --- a/nipype/scripts/cli.py +++ b/nipype/scripts/cli.py @@ -164,7 +164,7 @@ def run(ctx, module, interface, list, help): iface_parser.print_help() except: print( - "An error ocurred when trying to print the full" + "An error occurred when trying to print the full" "command help, printing usage." ) finally: diff --git a/nipype/testing/data/README b/nipype/testing/data/README index 550854c57e..ed70b57e43 100644 --- a/nipype/testing/data/README +++ b/nipype/testing/data/README @@ -1,5 +1,5 @@ This directory contains empty, dummy files which are meant to be used -in the doctests of nipype. For verion 0.3 of nipype, we're using +in the doctests of nipype. For version 0.3 of nipype, we're using Traits and for input files, the code checks to confirm the assigned files actually exist. It doesn't matter what the files are, or even if they contain "real data", only that they exist. Again, these files