Minor fixes to the documentation and formatting.

Renaming api files and directory to be consistently using dots as submodule separators (instead of somethimes dots sometimes underscores).
Fix Errors due to bad escape sequences.

Author: dkuegler

CerebNet/data_loader/augmentation.py

@@ -206,7 +206,7 @@ def __init__(
             AUGMENTATION.BIAS_FIELD_COEFFICIENTS
             Magnitude :math:`n` of polynomial coefficients.
             If a tuple :math:`(a, b)` is specified, then
-            :math:`n \sim \mathcal{U}(a, b)`.
+            :math:`n \\sim \\mathcal{U}(a, b)`.
             AUGMENTATION.BIAS_FIELD_ORDER
             Order of the basis polynomial functions.
             AUGMENTATION.PROB

CerebNet/datasets/utils.py

@@ -362,10 +362,10 @@ def read_lta(file: Path | str) -> LTADict:
     from functools import partial
 
     import numpy as np
-    parameter_pattern = re.compile("^\s*([^=]+)\s*=\s*([^#]*)\s*(#.*)")
+    parameter_pattern = re.compile("^\\s*([^=]+)\\s*=\\s*([^#]*)\\s*(#.*)")
     vol_info_pattern = re.compile("^(.*) volume info$")
-    shape_pattern = re.compile("^(\s*\d+)+$")
-    matrix_pattern = re.compile("^(-?\d+\.\S+\s+)+$")
+    shape_pattern = re.compile("^(\\s*\\d+)+$")
+    matrix_pattern = re.compile("^(-?\\d+\\.\\S+\\s+)+$")
 
     _Type = TypeVar("_Type", bound=type)
 

FastSurferCNN/segstats.py

@@ -316,7 +316,7 @@ def make_arguments(helpformatter: bool = False) -> argparse.ArgumentParser:
         help="Keep ids for the table that do not exist in the segmentation "
              "(default: drop).",
     )
-    advanced = add_arguments(advanced, ["device", "sid", "sd"])
+    add_arguments(advanced, ["device", "sid", "sd"])
     advanced.add_argument(
         "--lut",
         type=Path,
@@ -538,7 +538,7 @@ def _check_arg_path(
     ------
     ValueError
         If attribute does not exist, is not a Path (or convertible to a Path), or if
-        the file does not exist, but reuire_exist is True.
+        the file does not exist, but `require_exist` is True.
     """
     if (_attr_val := getattr(__args, __attr), None) is None:
         raise ValueError(f"No {__attr} passed.")
@@ -601,8 +601,7 @@ def check_shape_affine(
     """
     if img1.shape != img2.shape or not np.allclose(img1.affine, img2.affine):
         raise RuntimeError(
-            f"The shapes or affines of the {name1} and the {name2} image are not "
-            f"similar, both must be the same!"
+            f"The shapes or affines of the {name1} and the {name2} image are not similar, both must be the same!"
         )
 
 
@@ -689,8 +688,7 @@ def infer_labels_excludeid(
     data: "npt.NDArray[int]",
 ) -> tuple["npt.NDArray[int]", list[int]]:
     """
-    Infer the labels and excluded ids from command line arguments, the lookup table, or
-    the segmentation image.
+    Infer the labels and excluded ids from command line arguments, the lookup table, or the segmentation image.
 
     Parameters
     ----------
@@ -1385,7 +1383,7 @@ def _table_body(file: IO, _dataframe: pd.DataFrame) -> None:
 
 def read_statsfile(path: Path) -> tuple[dict[str, MeasureTuple | str], pd.DataFrame]:
     """
-    Read the stats table of a stats file. The file must have columns (')
+    Read the stats table of a stats file.
 
     Parameters
     ----------

FastSurferCNN/utils/parser_defaults.py

@@ -43,6 +43,9 @@
 from FastSurferCNN.utils.dataclasses import field, get_field
 from FastSurferCNN.utils.parallel import get_num_threads, set_num_threads
 
+T_AddArgs = TypeVar("T_AddArgs", bound="CanAddArguments")
+
+
 FASTSURFER_ROOT = Path(__file__).parents[2]
 PLANE_SHORT = {"checkpoint": "ckpt", "config": "cfg"}
 PLANE_HELP = {
@@ -353,8 +356,6 @@ class SubjectDirectoryConfig:
     ),
 }
 
-T_AddArgs = TypeVar("T_AddArgs", bound=CanAddArguments)
-
 
 def add_arguments(parser: T_AddArgs, flags: Iterable[str]) -> T_AddArgs:
     """