requested changes

Author: robert-graf

TPTBox/core/bids_files.py

@@ -988,7 +988,7 @@ def open_nii(self):
         except KeyError as e:
             raise ValueError(f"nii.gz not present. Found only {self.file.keys()}\t{self.file}\n\n{self}") from e
 
-    def get_grid_info(self, add_gird_info_to_json=True):
+    def get_grid_info(self, add_grid_info_to_json=True):
         """returns the Grid info. It looks up if this info is in json. If not it loads the File, computes the Grid and saves it in the json"""
         from TPTBox.core.dicom.dicom_extract import _add_grid_info_to_json
         from TPTBox.core.nii_poi_abstract import Grid
@@ -998,7 +998,7 @@ def get_grid_info(self, add_gird_info_to_json=True):
             return None
         if not self.has_json():
             self.file["json"] = Path(str(nii_file).split(".")[0] + ".json")
-        return Grid(**_add_grid_info_to_json(nii_file, self.file["json"], add=add_gird_info_to_json)["grid"])
+        return Grid(**_add_grid_info_to_json(nii_file, self.file["json"], add=add_grid_info_to_json)["grid"])
 
     def get_nii_file(self) -> Path:  # type: ignore
         for key in _supported_nii_files:

TPTBox/core/poi_fun/vertebra_direction.py

@@ -197,7 +197,7 @@ def _get_sub_array_by_direction(d: DIRECTIONS, cords: np.ndarray) -> np.ndarray:
         never_called(d)
 
 
-def get_direction(d: DIRECTIONS, poi: POI, vert_id: int) -> np.ndarray:
+def get_direction(d: DIRECTIONS, poi: POI, vert_id: int, verbose=True) -> np.ndarray:
     """Get the sub-array of coordinates along a specified direction.
     cords must be in PIR direction
     Returns:
@@ -209,6 +209,7 @@ def get_direction(d: DIRECTIONS, poi: POI, vert_id: int) -> np.ndarray:
         Assumes the input `cords` array has shape (3, n), where n is the number of coordinates.
     """
     if vert_id == 1:
+        _log.on_warning("C1 has no direction computation use C2 as direction", verbose=verbose)
         vert_id = 2
     P, I, R = get_vert_direction_PIR(poi, vert_id, to_pir=False)  # noqa: N806
     if d == "P":

TPTBox/segmentation/_deface.py

@@ -3,7 +3,7 @@
 import numpy as np
 
 from TPTBox import BIDS_FILE, BIDS_Global_info, Image_Reference, to_nii
-from TPTBox.core.nii_wrapper import NII
+from TPTBox.core.nii_wrapper import DIRECTIONS, NII
 from TPTBox.segmentation.VibeSeg.inference_nnunet import run_inference_on_file, run_VibeSeg
 
 
@@ -21,7 +21,7 @@ def _compute_deface_mask_cta(ct_img: Image_Reference, outpath: str | Path | None
     return run_VibeSeg(ct_img, out_path=outpath, dataset_id=1, keep_size=False, override=override, gpu=gpu, **args)
 
 
-def _extend_mask_anterior(mask: NII, n: int) -> NII:
+def _extend_mask(mask: NII, n: int, direction: DIRECTIONS = "A") -> NII:
     """
     Extend a binary mask n voxels further in anterior (A) direction.
 
@@ -42,7 +42,7 @@ def _extend_mask_anterior(mask: NII, n: int) -> NII:
     arr = m.extract_label(1).get_array()
 
     # Axis corresponding to Anterior-Posterior
-    axis = m.get_axis("A")
+    axis = m.get_axis(direction)
 
     # Orientation: +1 index is "A" or "P"
     # Typically values are ("A","P") or ("P","A")
@@ -55,7 +55,7 @@ def _extend_mask_anterior(mask: NII, n: int) -> NII:
 
     coords = idx[axis]
 
-    if ori == "A":
+    if ori == direction:
         anterior_idx = coords.max()
         slicer = [slice(None)] * arr.ndim
         slicer[axis] = slice(0, 1)
@@ -103,7 +103,7 @@ def compute_deface_mask_cta(
     f2[ct > -600] = 0
     f2 = f2.filter_connected_components(max_count_component=1, keep_label=True)
 
-    mask = _extend_mask_anterior(f2, 4)
+    mask = _extend_mask(f2, 4)
     mask[face_org == 1] = 2
 
     m2 = mask.extract_label(1)

TPTBox/spine/spinestats/body_quadrants.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 from pathlib import Path
 
 import numpy as np