Merge pull request #54 from yarikoptic/enh-codespell

Add codespell: config, workflow (to detect new) + have it fixed a few of present typos

.codespellrc

@@ -0,0 +1,5 @@
+[codespell]
+skip = .git,*.pdf,*.svg,.codespellrc
+check-hidden = true
+# ignore-regex = 
+# ignore-words-list =

.github/workflows/codespell.yml

@@ -0,0 +1,22 @@
+---
+name: Codespell
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+permissions:
+  contents: read
+
+jobs:
+  codespell:
+    name: Check for spelling errors
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Codespell
+        uses: codespell-project/actions-codespell@v2

README.md

@@ -1,5 +1,5 @@
 # _fsub-extractor_
-This is an application for extracing **F**unctional **Su**bcomponents of **B**undles. This software can take gray matter regions, project them into white matter, and find streamlines that connect to them. It can also produce a visualization of the streamlines and sample scalar values along these streamlines (tract profile and average across all streamlines).
+This is an application for extracting **F**unctional **Su**bcomponents of **B**undles. This software can take gray matter regions, project them into white matter, and find streamlines that connect to them. It can also produce a visualization of the streamlines and sample scalar values along these streamlines (tract profile and average across all streamlines).
 
 This software was conceived of during NeuroHackademy 2022.
 

fsub_extractor/cli_starters/extractor_start.py

@@ -190,7 +190,7 @@ def get_parser():
         "--reg-type",
         "--reg_type",
         choices=["mrtrix", "itk"],
-        help="Registration software compatability for .txt files. Only set if the program does not figure this out automatically.",
+        help="Registration software compatibility for .txt files. Only set if the program does not figure this out automatically.",
     )
 
     # Extractor-specific arguments
@@ -326,7 +326,7 @@ def get_parser():
     viz_args.add_argument(
         "--saggital-offset",
         "--saggital_offset",
-        help="Float (-1,1) describing where to display saggital slice. -1.0 is left, 1.0 is right. Default is 0.0.",
+        help="Float (-1,1) describing where to display sagittal slice. -1.0 is left, 1.0 is right. Default is 0.0.",
         type=float,
         default=0.0,
         metavar=("OFFSET"),
@@ -335,9 +335,9 @@ def get_parser():
     viz_args.add_argument(
         "--camera-angle",
         "--camera_angle",
-        choices=["saggital", "axial"],
+        choices=["sagittal", "axial"],
         help="Camera angle for visualization. Default is 'saggital.'",
-        default="saggital",
+        default="sagittal",
     )
 
     return parser

fsub_extractor/functions/extractor.py

@@ -118,15 +118,15 @@ def extractor(
             )
         if float(projfrac_params_list[0]) >= 0:
             raise Exception(
-                "The 'start' paramater of projfrac-params must be negative to project into white matter."
+                "The 'start' parameter of projfrac-params must be negative to project into white matter."
             )
         if float(projfrac_params_list[1]) <= float(projfrac_params_list[0]):
             raise Exception(
-                "The 'stop' paramater of projfrac-params must be greater than the 'start' parameter."
+                "The 'stop' parameter of projfrac-params must be greater than the 'start' parameter."
             )
         if float(projfrac_params_list[-1]) <= 0:
             raise Exception(
-                "The 'delta' paramater of projfrac-params must be positive to iterate correctly."
+                "The 'delta' parameter of projfrac-params must be positive to iterate correctly."
             )
 
     # Define and prepare registration
@@ -341,7 +341,7 @@ def extractor(
             tck_file = tract
 
         ### Run MRtrix Tract Extraction ###
-        print("\n Extracing the sub-bundle \n")
+        print("\n Extracting the sub-bundle \n")
         fsub_bundle = extract_tck_mrtrix(
             tck_file,
             rois_atlas_in,
@@ -468,7 +468,7 @@ def extractor(
             ref_anat = img_viz
             show_anat = True
 
-        # Make a picture for each hemisphere passed in, if saggital view
+        # Make a picture for each hemisphere passed in, if sagittal view
         if hemi == None:
             hemi_list = ["lh"]
         else:

fsub_extractor/functions/streamline_scalar.py

@@ -38,7 +38,7 @@ def streamline_scalar(
     scalar_paths: str
         Comma-delimited paths of scalars (.nii.gz) to analyze
     scalar_names: str
-        Comma-delimited paths of scalar namess
+        Comma-delimited paths of scalar names
     n_points: int
         Number of points to use in tract profiles
     out_dir: str

fsub_extractor/utils/anat_utils.py

@@ -221,9 +221,9 @@ def convert_to_mrtrix_reg(reg_in, mrtrix_reg_out, reg_in_type="itk", overwrite=T
     Parameters
     ==========
     reg_in: str
-            Path to input registation
+            Path to input registration
     mrtrix_reg_out: str
-            Where to save output registation
+            Where to save output registration
     reg_type: str
             Format of input registration. Currently only ANTs/ITK is supported.
     overwrite: bool

fsub_extractor/utils/fury_viz.py

@@ -23,7 +23,7 @@ def visualize_sub_bundles(
     show_anat=False,
     axial_offset=0,
     saggital_offset=0,
-    camera_angle="saggital",
+    camera_angle="sagittal",
     hemi="lh",
 ):
     """Takes in tck and nifti files and makes a fury visualization
@@ -45,10 +45,10 @@ def visualize_sub_bundles(
     show_anat (Optional): Whether to overlay anatomy on the figure (default = False)
     axial_offset (Optional): Where to display axial slice (-1,1) where -1 is bottom of image and 1 is top.
         (default = 0, which is the middle of the image)
-    saggital_offset (Optional): Where to display saggital slice (-1,1) where -1 is left of image and 1 is right.
+    saggital_offset (Optional): Where to display sagittal slice (-1,1) where -1 is left of image and 1 is right.
         (default = 0, which is the middle of the image)
     camera_angle (Optional): Angle for screenshot ('saggital' (default) or 'axial')
-    hemi (Optional): For saggital picture, what hemisphere to view from. Accepts either 'lh' or 'rh'.
+    hemi (Optional): For sagittal picture, what hemisphere to view from. Accepts either 'lh' or 'rh'.
 
     Outputs
     =======
@@ -123,7 +123,7 @@ def visualize_sub_bundles(
         # add to figure
         figure.add(slice_actor)
 
-        # make a copy to make a saggital slice
+        # make a copy to make a sagittal slice
         saggital_actor = slice_actor.copy()
 
         # calculate where to display the image based on the offset
@@ -137,7 +137,7 @@ def visualize_sub_bundles(
 
     cam = figure.GetActiveCamera()
     cam.SetViewUp(0, 0, 0)
-    if camera_angle == "saggital":
+    if camera_angle == "sagittal":
         if hemi == "lh":
             cam.Yaw(270)
             cam.Roll(90)
@@ -238,7 +238,7 @@ def define_slice_actor(reference_anatomy, view="axial", offset=0):
     if view == "axial":
         offset = (slice_actor.shape[1] - (slice_actor.shape[1] // 2)) * offset
         slice_actor.display(None, None, slice_actor.shape[1] // 2 + int(offset))
-    if view == "saggital":
+    if view == "sagittal":
         offset = (slice_actor.shape[0] - (slice_actor.shape[0] // 2)) * offset
         slice_actor.display(slice_actor.shape[0] // 2 + int(offset), None, None)
 
@@ -250,13 +250,13 @@ def visualize_bundles(
     interactive,
     slice_actor=None,
     roi_actor=None,
-    camera_angle="saggital",
+    camera_angle="sagittal",
     hemi="lh",
     filename=None,
 ):
 
     """Takes in streamline actor, optional roi actor and slice actors
-    and ouputs a fury scene.
+    and outputs a fury scene.
 
     Parameters
     ==========
@@ -293,7 +293,7 @@ def visualize_bundles(
     cam = figure.GetActiveCamera()
     cam.SetViewUp(0, 0, 0)
 
-    if camera_angle == "saggital":
+    if camera_angle == "sagittal":
         if hemi == "lh":
             cam.Yaw(270)
             cam.Roll(90)