DOC: Fix typos in several subfolders

Found via `codespell -q 3 -L ba,dependees,nd,nin,pinter,pullrequest,serie`

Applications/SlicerApp/Testing/Python/SlicerOptionDisableSettingsTest.py

@@ -38,7 +38,7 @@ def checkUserSettings(slicer_executable, common_args, keep_temporary_settings=Fa
     print("=> ok\n")
 
     # User settings previously added should:
-    #  * NOT be set by detault
+    #  * NOT be set by default
     #  * be set if '--keep-temporary-settings' is provided
     args = list(common_args)
     condition = 'is not None'
@@ -62,7 +62,7 @@ def checkRevisionUserSettings(slicer_executable, common_args, keep_temporary_set
     print("=> ok\n")
 
     # User revision settings previously added should:
-    #  * NOT be set by detault
+    #  * NOT be set by default
     #  * be set if '--keep-temporary-settings' is provided
     args = list(common_args)
     condition = 'is not None'

Base/Logic/vtkImageRectangularSource.cxx

@@ -209,11 +209,11 @@ void vtkImageRectangularSourceExecute(vtkImageRectangularSource *self,
     }
 }
 
-// Beginining
+// Beginning
 namespace RectSource
 {
 
-// Define in a tirangle the min and max
+// Define in a triangle the min and max
 int Min(int x1, int x2) {return (x1 < x2 ? x1 : x2);}
 int Min(int x1, int x2, int x3) {return Min(Min(x1,x2),x3);}
 int Min(int x1, int x2, int x3, int x4) {return Min(Min(x1,x2,x3),x4);}
@@ -365,7 +365,7 @@ void DefineSlice(int **Corners, int RowLength, int LineLength, T inVal, T outVal
 
   // Area of interest
   for (int y = MinInY; y <= MaxInY; y ++) {
-    // Split Rectangual in two triangles
+    // Split rectangle into two triangles
     DefineXMinMaxInTriangle(Corners[0], Corners[1], Corners[3], y, inMinX1, inMaxX1);
     DefineXMinMaxInTriangle(Corners[1], Corners[2], Corners[3], y, inMinX2, inMaxX2);
     if (inMaxX1 < 0) DefineLine(inMinX2, inMaxX2,LineLength, inVal, outVal, InsideGraySlopeFlag,Result);

Base/QTCLI/qSlicerCLIModuleUIHelper.cxx

@@ -638,7 +638,7 @@ QWidget* qSlicerCLIModuleUIHelperPrivate::createRegionTagWidget(const ModulePara
   //TODO - title + " RegionList"
   widget->setNoneEnabled(this->isNoneEnabled(moduleParameter));
   widget->setBaseName(_label);
-  // Reegion can be added without switching to another module
+  // Region can be added without switching to another module
   // therefore it makes sense to enable adding nodes.
   widget->setAddEnabled(true);
   widget->setRenameEnabled(true);

Base/QTCore/qSlicerFileWriter.h

@@ -38,7 +38,7 @@ class Q_SLICER_BASE_QTCORE_EXPORT qSlicerFileWriter
   /// Return true if the object is handled by the writer.
   virtual bool canWriteObject(vtkObject* object)const;
 
-  /// Return  a list of the supported extensions for a particuliar object.
+  /// Return a list of the supported extensions for a particular object.
   /// Please read QFileDialog::nameFilters for the allowed formats
   /// Example: "Image (*.jpg *.png *.tiff)", "Model (*.vtk)"
   virtual QStringList extensions(vtkObject* object)const = 0;

Base/QTGUI/qSlicerNodeWriter.h

@@ -53,7 +53,7 @@ class Q_SLICER_BASE_QTGUI_EXPORT qSlicerNodeWriter
   /// Return true if the object is handled by the writer.
   bool canWriteObject(vtkObject* object)const override;
 
-  /// Return  a list of the supported extensions for a particuliar object.
+  /// Return a list of the supported extensions for a particular object.
   /// Please read QFileDialog::nameFilters for the allowed formats
   /// Example: "Image (*.jpg *.png *.tiff)", "Model (*.vtk)"
   QStringList extensions(vtkObject* object)const override;

CMake/ExternalProjectDependencyForPython.cmake

@@ -62,7 +62,7 @@
 #
 #  ``OUTPUT_VAR_PREFIX <output-var-prefix>``
 #    Specify the prefix of output variables ``<output-var-prefix>_PATH`` and ``<output-var-prefix>_VERSION``.
-#    It defaults to upercase value of ``<python-module-name>``.
+#    It defaults to uppercase value of ``<python-module-name>``.
 #
 
 function(ExternalProject_FindPythonPackage)

CMake/SlicerMacroBuildApplication.cmake

@@ -647,7 +647,7 @@ macro(slicerMacroBuildApplication)
         # Slicer arguments triggering display of launcher help
         HELP_SHORT_ARG "-h"
         HELP_LONG_ARG "--help"
-        # Slicer arguments that should NOT be associated with the spash screeb
+        # Slicer arguments that should NOT be associated with the splash screen
         NOSPLASH_ARGS "--no-splash,--help,--version,--home,--program-path,--no-main-window,--settings-path,--temporary-path"
         # Extra application associated with the launcher
         EXTRA_APPLICATION_TO_LAUNCH_BUILD ${extraApplicationToLaunchListForBuildTree}

Docs/_extracli/DWIConvert.xml

@@ -131,7 +131,7 @@
       <name>useBMatrixGradientDirections</name>
       <longflag>--useBMatrixGradientDirections</longflag>
       <label>Use BMatrix Gradient Directions</label>
-      <description><![CDATA[Fill the nhdr header with the gradient directions and bvalues computed out of the BMatrix. Only changes behavior for Siemens data.  In some cases the standard public gradients are not properly computed.  The gradients can emperically computed from the private BMatrix fields.  In some cases the private BMatrix is consistent with the public grandients, but not in all cases, when it exists BMatrix is usually most robust.]]></description>
+      <description><![CDATA[Fill the nhdr header with the gradient directions and bvalues computed out of the BMatrix. Only changes behavior for Siemens data.  In some cases the standard public gradients are not properly computed.  The gradients can be empirically computed from the private BMatrix fields.  In some cases the private BMatrix is consistent with the public grandients, but not in all cases, when it exists BMatrix is usually most robust.]]></description>
       <default>false</default>
     </boolean>
     <directory>

Docs/_extracli/PerformMetricTest.xml

@@ -62,8 +62,8 @@
     <integer>
       <name>numberOfHistogramBins</name>
       <longflag>numberOfHistogramBins</longflag>
-      <label>Number Of Historgram Bins</label>
-      <description>The number of historgram bins when MMI (Mattes) is metric type.</description>
+      <label>Number Of Histogram Bins</label>
+      <description>The number of histogram bins when MMI (Mattes) is metric type.</description>
       <default>50</default>
     </integer>
 

Docs/developer_guide/build_instructions/macos.md

@@ -59,7 +59,7 @@ cmake \
 - Remarks:
   - Instead of `cmake`, you can use `ccmake` or `cmake-gui` to visually inspect and edit configure options.
   - Using top-level directory name like `/opt/sr` for Release or `/opt/s` for Debug is recommended. If `/opt` does not exist on your machine you need to use sudo for `mkdir` and `chown` in `/opt`.
-  - [Step-by-step debug instuctions](https://www.slicer.org/wiki/Documentation/Nightly/Developers/Tutorials/Debug_Instructions)
+  - [Step-by-step debug instructions](https://www.slicer.org/wiki/Documentation/Nightly/Developers/Tutorials/Debug_Instructions)
   - Additional configuration options to customize the application are described [here](overview.md#custom-builds).
 
 ### General information

Docs/developer_guide/build_instructions/windows.md

@@ -69,7 +69,7 @@ cd /d C:\D\S4D
 - Add `Qt5_DIR` variable pointing to Qt5 folder: click Add entry button, set `Name` to `Qt5_DIR`, set `Type` to `PATH`, and set `Value` to the Qt5 folder, such as `C:\Qt\5.15.2\msvc2019_64\lib\cmake\Qt5`.
 - Click `Configure`
 - Select your compiler: `Visual Studio 17 2022`, and click `Finish`
-- Click `Generate` and wait for project generation to finish (may take a few minues)
+- Click `Generate` and wait for project generation to finish (may take a few minutes)
 - Click `Open Project`
 - If building in release mode:
   - Open the top-level Slicer.sln file in the build directory in Visual Studio

Docs/developer_guide/extensions.md

@@ -300,7 +300,7 @@ The ExtensionsIndex is a repository containing a list of [extension description
 
 The ExtensionsIndex is hosted on GitHub: <https://github.com/Slicer/ExtensionsIndex>
 
-Each branch of the repository contains extension descrtiption files that corresponds to the same branch in the Slicer repository. For example, `main` branch contains descriptions for Slicer `main` branch, and `4.11` branch contains extension descripions for Slicer's `4.11` branch.
+Each branch of the repository contains extension description files that corresponds to the same branch in the Slicer repository. For example, `main` branch contains descriptions for Slicer `main` branch, and `4.11` branch contains extension descripions for Slicer's `4.11` branch.
 
 Extension developers have to make sure that the extension description in each branch of the Extensions index is compatible with the corresponding Slicer version. Extension developers often create the same branches (`main`, `4.11`, `4.13`, ...) in their repository and they specify this branch name in the extensions descriptor file.
 

Docs/developer_guide/modules/dicom.md

@@ -20,7 +20,7 @@ The existing two rules can be used as examples: the [default](https://github.com
 
 ## Plugin architecture
 
-There are many different kind of DICOM information objects and import/export of all of them would not be feasible to implement in the Slicer core (see more information in the [DICOM module user manual](../../user_guide/modules/dicom.md#dicom-plugins)). Therefore, extensions can implement custom importer/exporter clases based on DICOMLib.DICOMPlugin class and add them to slicer.modules.dicomPlugins dictionary object. The DICOM module uses these plugins to determine list of loadable and exportable items.
+There are many different kind of DICOM information objects and import/export of all of them would not be feasible to implement in the Slicer core (see more information in the [DICOM module user manual](../../user_guide/modules/dicom.md#dicom-plugins)). Therefore, extensions can implement custom importer/exporter classes based on DICOMLib.DICOMPlugin class and add them to slicer.modules.dicomPlugins dictionary object. The DICOM module uses these plugins to determine list of loadable and exportable items.
 
 ## References
 

Docs/developer_guide/mrml_overview.md

@@ -503,7 +503,7 @@ Management of slice views is distributed between several objects:
 - Slice node ([vtkMRMLSliceNode](https://apidocs.slicer.org/main/classvtkMRMLSliceNode.html)): Stores the position, orientation, and size of the slice. This is a [view node](https://apidocs.slicer.org/main/classvtkMRMLAbstractViewNode.html) and as such it stores common view properties, such as the view name, layout color, background color.
 - Slice display node ([vtkMRMLSliceDisplayNode](https://apidocs.slicer.org/main/classvtkMRMLSliceDisplayNode.html)): Specifies how the slice should be displayed, such as visibility and style of display of intersecting slices. The class is based on [classvtkMRMLModelDisplayNode](https://apidocs.slicer.org/main/classvtkMRMLModelDisplayNode.html), therefore it also specifies which 3D views the slice is displayed in.
 - Slice composite node ([vtkMRMLSliceCompositeNode](https://apidocs.slicer.org/main/classvtkMRMLSliceCompositeNode.html)): Specifies what volumes are displayed in the slice and how to blend them. It is ended up being a separate node probably because it is somewhat a mix between a data node (that tells what data to display) and a display node (that specifies how the data is displayed).
-- Slice model node ([vtkMRMLModelNode](https://apidocs.slicer.org/main/classvtkMRMLModelNode.html)): It is a model node that displays the slice in 3D views. It stores a simple rectangle mesh on that the image cross-section is renderd as a texture.
+- Slice model node ([vtkMRMLModelNode](https://apidocs.slicer.org/main/classvtkMRMLModelNode.html)): It is a model node that displays the slice in 3D views. It stores a simple rectangle mesh on that the image cross-section is rendered as a texture.
 - Slice model transform node ([vtkMRMLTransformNode](https://apidocs.slicer.org/main/classvtkMRMLTransformNode.html)). The transform node is used for positioning the slice model node in 3D views. It is faster to use a transform node to position the plane than modifying the plane points each time the slice is moved.
 - Slice logic ([vtkMRMLSliceLogic](https://apidocs.slicer.org/main/classvtkMRMLSliceLogic.html)): This is not a MRML node but a logic class, which implements operationson MRML nodes. There is one logic for each slice view. The object keeps reference to all MRML nodes, so it is a good starting point for accessing any data related to slices and performing operations on slices. Slice logics are stored in the application logic object and can be retrieved like this: `sliceLogic = slicer.app.applicationLogic().GetSliceLogicByLayoutName('Red')`. There are a few other `GetSlicerLogic...` methods to get slice logic based on slice node, slice model display node, and to get all the slice logics.
 - Slice layer logic([vtkMRMLSliceLayerLogic](https://apidocs.slicer.org/main/classvtkMRMLSliceLayerLogic.html)): Implements reslicing and interpolation for a volume. There is one slice layer logic for each volume layer (foreground, background, label) for each slice view.

Docs/developer_guide/python_faq.md

@@ -129,7 +129,7 @@ Module logic methods can be explored by using the `help` Python function (`help(
 
 ### Adding reusable widgets provided by modules
 
-Most Slicer core modules provide a set of resuable, conigurable GUI widgets that can help developers in building their module's user interface.
+Most Slicer core modules provide a set of reusable, configurable GUI widgets that can help developers in building their module's user interface.
 
 For example, Volumes module offers a widget that can display and edit basic properties of volume nodes:
 

Docs/user_guide/modules/annotations.md

@@ -60,8 +60,8 @@ Create and edit annotations, supplementary information associated with a scene.
 
 - **Modify Annotation Properties: Advanced**:
   - **Text**: Set the descriptive text, text color, scale, opacity on this panel
-  - **Points**: Set the coordinate location of the point(s), glyph color, scale, glyph type, opacity, ambient, diffuse, specular material properites on this panel
-  - **Lines**: This panel is only enabled for rulers. Set the line color, label visibility, label position along the line (from 0-1), tick spacing, maximum number of ticks, opacity, ambient, diffuse, specular material properites on this panel
+  - **Points**: Set the coordinate location of the point(s), glyph color, scale, glyph type, opacity, ambient, diffuse, specular material properties on this panel
+  - **Lines**: This panel is only enabled for rulers. Set the line color, label visibility, label position along the line (from 0-1), tick spacing, maximum number of ticks, opacity, ambient, diffuse, specular material properties on this panel
   - **ROI**: This panel is only enabled for regions of interest. Set the ranges for the ROI along it's axes, LR, PA, IS. Toggle the ROI visibility and if it's updated interactively on this panel
 
 - **Toolbar**:

Docs/user_guide/modules/volumerendering.md

@@ -68,7 +68,7 @@ See [video demo/tutorial of these steps](https://youtu.be/xZwyW6SaoM4?t=12) for
   - Crop: Simple controls for the cropping box (ROI). More controls are available in the "Advanced..." section. Enable/Disable cropping of the volume. Show/Hide the cropping box. Reset the box ROI to the volume's bounds.
   - Rendering: Select a volume rendering method. A default method can be set in the application settings Volume Rendering panel.
     - VTK CPU Ray Casting: Available on all computers, regardless of capabilities of graphics hardware. The volume rendering is entirely realized on the CPU, therefore it is slower than other options.
-    - VTK GPU Ray Casting (default): Uses graphics hardware for rendering, typically much faster than CPU volume rendering. This is the recommended method for computers that have sufficiant graphics capabilities. It supports surface smoothing to remove staircase artifacts.
+    - VTK GPU Ray Casting (default): Uses graphics hardware for rendering, typically much faster than CPU volume rendering. This is the recommended method for computers that have sufficient graphics capabilities. It supports surface smoothing to remove staircase artifacts.
     - VTK Multi-Volume: Uses graphics hardware for rendering. Can render multiple overlapping volumes but it has several limitations (see details in [limitations](#limitations) section at the bottom of this page.
 - Advanced: More controls to control the volume rendering. Contains 3 tabs: "Techniques", "Volume Properties" and "ROI"
   - Techniques: Advanced properties of the current volume rendering method.

Docs/user_guide/modules/volumes.md

@@ -88,7 +88,7 @@ Note: Consumer file formats, such as jpg, png, and tiff are not well suited for
   - Image Dimensions: The number of pixels in "IJK" space - this is the way the data is arranged in memory. The IJK indices (displayed in the DataProbe) go from 0 to dimension-1 in each direction.
   - Image Spacing: The physical distance between pixel centers when mapped to patient space expressed in millimeters.
   - Image Origin: The location of the center of the 0,0,0 (IJK) pixel expressed with respect to patient space. Patient space is organized with respect to the subject's Right, Anterior, and Superior anatomical directions. See [coordinate systems page](https://www.slicer.org/w/index.php/Coordinate_systems) for more information.
-  - IJK to RAS Direction Matrix: The trasnform matrix from the IJK to RAS coordinate systems
+  - IJK to RAS Direction Matrix: The transform matrix from the IJK to RAS coordinate systems
   - Center Volume: This button will apply a transform to the volume that shifts its center to the origin in patient space. Harden the transform on the volume to permanently change the image origin.
   - Scan Order: Describes the image orientation (how the IJK space is oriented with respect to patient RAS.
   - Number of Scalars: Most CT or MR scans have one scalar component (grayscale). Color images have three components (red, green, blue).

Docs/user_guide/user_interface.md

@@ -171,7 +171,7 @@ View Controllers module provides an alternate way of displaying these controller
 - **Rotate to volume plane** changes the orientation of the slice to match the closest acquisition orientation of the displayed volume.
 - **Orientation Marker** controls display of human, cube, etc in lower right corner.
 - **Ruler** controls display of ruler in slice view.
-- **View link** button synchronizes properties of views in the same view group, such as foreground/backgroudn/label volume selection, foreground/label volume opacity, zoom factor.
+- **View link** button synchronizes properties of views in the same view group, such as foreground/background/label volume selection, foreground/label volume opacity, zoom factor.
   - For parallel views (i.e., that are set to the same orientation,OD such as `axial`), the view center position is synchronized as well.
   - Long-click on the button exposes **hot-linked** option, which controls when properties are synchronized (immediately or when the mouse button is released).
   - A view group typically consists of 3 orthogonal views (e.g., in `Four-Up` view, `R`, `G`, `Y, views are in the same group). In layouts that contain multiple triplets of slice views, each triplet forms a separate group (e.g., in `Three over three` layout there are two view groups, one group is `R`, `G`, `Y`, the other groups is `R+`, `G+`, `Y+`).

Libs/MRML/Core/Testing/CMakeLists.txt

@@ -231,7 +231,7 @@ simple_test( vtkThinPlateSplineTransformTest1 )
 function(SIMPLE_TEST_WITH_SCENE TESTNAME SCENEFILENAME)
   # Extract list of external files to download. Note that the ${_externalfiles} variable
   # is only specified to trigger download of data files used in the scene, the arguments
-  # are NOT explcitly used in ${KIT}CxxTests test executable.
+  # are NOT explicitly used in ${KIT}CxxTests test executable.
   string(REPLACE "|" ";" scenefilename_and_externalfiles ${SCENEFILENAME})
   list(GET scenefilename_and_externalfiles 0 SCENEFILENAME)
   list(LENGTH scenefilename_and_externalfiles _length)

Libs/MRML/Core/Testing/vtkMRMLNonlinearTransformNodeTest1.cxx

@@ -242,7 +242,7 @@ int TestCompositeTransformHardenSplit(const char *filename)
   CHECK_EXIT_SUCCESS(testTransformAccuracy(transformFromWorldAfterHardening.GetPointer(), transformToWorldAfterHardening.GetPointer(),
     testPoints, transformedPoints.GetPointer(), transformedPointsBackToTest.GetPointer()));
 
-  // Split trasnform
+  // Split transform
   CHECK_BOOL(bsplineTransformNode->Split(), true);
 
   // Test if transform to world is the same after splitting

Libs/MRML/Core/vtkEventBroker.cxx

@@ -864,7 +864,7 @@ void vtkEventBroker::ProcessEventQueue ()
   // - register your pointer to the observation in case it
   //   gets deleted during handling of the event
   // - if the observation is no longer in the queue, stop processing events
-  // - unregister before after dequeing in case the observation should go away
+  // - unregister before after dequeuing in case the observation should go away
   //
   while ( this->GetNumberOfQueuedObservations() > 0 )
     {