fixed licensing mismatch #118

TPTBox/core/dicom/nii2dicom.py

@@ -59,7 +59,7 @@ def nifti2dicom_1file(
     out_dir: str | Path,
     no_json_ok: bool = False,
     secondary: bool = False,
-    json_path: None | str | Path = None,
+    json_path: str | Path | None = None,
     out_name: str = "slice",
 ) -> None:
     r"""Convert a single NIfTI file to a DICOM series.

TPTBox/core/nii_wrapper.py

@@ -1157,7 +1157,7 @@ def rescale_(self, voxel_spacing=(1, 1, 1), c_val: float | None = None, verbose:
         return self.rescale( voxel_spacing=voxel_spacing, c_val=c_val, verbose=verbose,mode=mode, inplace=True)
 
     def resample_from_to(self, to_vox_map:Image_Reference|Has_Grid|tuple[SHAPE,AFFINE,ZOOMS], mode:MODES='nearest', order: int |None=None, c_val=None, inplace = False,verbose:logging=True,align_corners:bool=False) -> Self:
-        r"""Self will be resampled in coordinate of given other image. Adheres to global space not to local pixel space.
+        """Self will be resampled in coordinate of given other image. Adheres to global space not to local pixel space.
 
         Args:
             to_vox_map (Image_Reference|Proxy): If object, has attributes shape giving input voxel shape, and affine giving mapping of input voxels to output space. If length 2 sequence, elements are (shape, affine) with same meaning as above. The affine is a (4, 4) array-like.\n
@@ -1802,7 +1802,7 @@ def calc_convex_hull(
             return self.set_array_(convex_hull_arr)
         return self.set_array(convex_hull_arr)
 
-    def calc_convex_hull_(self, axis: None | DIRECTIONS = "S", verbose: bool = False) -> Self:
+    def calc_convex_hull_(self, axis: DIRECTIONS | None = "S", verbose: bool = False) -> Self:
         """In-place variant of `calc_convex_hull`."""
         return self.calc_convex_hull(axis=axis, inplace=True, verbose=verbose)
 

TPTBox/core/np_utils.py

@@ -508,7 +508,7 @@ def np_dilate_msk(
     connectivity: int = 3,
     use_crop: bool = True,
     mask: np.ndarray | None = None,
-    ignore_axis: None | int = None,
+    ignore_axis: int | None = None,
 ) -> np.ndarray:
     """Dilates the given array by the specified number of voxels (not including the zero label).
 
@@ -586,7 +586,7 @@ def np_erode_msk(
     use_crop: bool = True,
     connectivity: int = 3,
     border_value=0,
-    ignore_axis: None | int = None,
+    ignore_axis: int | None = None,
 ) -> np.ndarray:
     """Erodes the given array by the specified number of voxels.
 

TPTBox/core/poi_fun/vertebra_direction.py

@@ -24,7 +24,7 @@ def calc_orientation_of_vertebra_PIR(
     source_subreg_point_id=Location.Vertebra_Corpus,
     subreg_id=Location.Spinal_Canal,
     do_fill_back: bool = False,
-    spine_plot_path: None | str = None,
+    spine_plot_path: str | None = None,
     save_normals_in_info=False,
     _orientation_version=0,
 ) -> tuple[POI, NII | None]:

TPTBox/segmentation/VibeSeg/inference_nnunet.py

@@ -345,7 +345,7 @@ def run_inference_on_file(
         unknown_strings: dict[str, int] = {"max": seg_nii.max() + 1, "Intervertebral_Disc": 100}
         mapping = {}
 
-        def to_int(a: str, k: None | int = None):
+        def to_int(a: str, k: int | None = None):
             if a in unknown_strings:
                 return unknown_strings[a]
             try:

pyproject.toml

@@ -7,7 +7,7 @@ authors = [
     "Hendrik Möller <hendrik.moeller@tum.de>",
 ]
 repository = "https://github.com/Hendrik-code/TPTBox"
-license = "GNU AFFERO GENERAL PUBLIC LICENSE v3.0, 19 November 2007"
+license = "Apache License Version 2.0, January 2004"
 readme = "README.md"
 packages = [{ include = "TPTBox" }]
 
@@ -190,6 +190,8 @@ ignore = [
     "ANN202",
     # En-dashes (–) in docstrings are legitimate range notation (e.g. "C1–C7")
     "RUF002",
+    "PLR0917", # Too many positional arguments
+    "UP038", #  Use `X | Y` in `isinstance` call instead of `(X, Y)`
     ]
 
 # Allow fix for all enabled rules (when `--fix`) is provided.

unit_tests/test_testsamples.py

@@ -82,7 +82,7 @@ def test_make_snapshot_both(self, keep_images=False):
 
         self.assertFalse(Path(td).exists() and not keep_images)
 
-    def make_POIs(self, vert_nii: NII, subreg_nii: NII, vert_id: int, ignore_list: list[Location], locs: None | list[Location] = None, n=5):
+    def make_POIs(self, vert_nii: NII, subreg_nii: NII, vert_id: int, ignore_list: list[Location], locs: list[Location] | None = None, n=5):
         for i in range(n):
             locs2 = [l for l in Location if l not in ignore_list and random.random() < (i + 1) / n * 3] if locs is None else locs
             poi = calc_poi_from_subreg_vert(vert_nii, subreg_nii, subreg_id=locs2, verbose=False, _print_phases=True).extract_region(