Merge pull request #108 from Hendrik-code/development_robert

Development robert

Author: Hendrik-code

TPTBox/core/nii_poi_abstract.py

@@ -1,7 +1,6 @@
 from __future__ import annotations
 
 import sys
-import warnings
 from dataclasses import dataclass
 from typing import TYPE_CHECKING, Any
 
@@ -495,6 +494,7 @@ def local_to_global(self, x: COORDINATE) -> tuple:
         Returns:
             tuple: World-space coordinate rounded to 7 decimal places.
         """
+        # TODO ITK version
         a = self.rotation @ (np.array(x) * np.array(self.zoom)) + self.origin
         return tuple(round(float(v), 7) for v in a)
 

TPTBox/core/nii_wrapper.py

@@ -1202,8 +1202,7 @@ def resample_from_to(self, to_vox_map:Image_Reference|Has_Grid|tuple[SHAPE,AFFIN
                     pad = tuple((int(b), int(a)) for b, a in zip(pad_before, pad_after))
                     ret = s.apply_pad(pad, mode=mode,inplace=inplace,verbose=verbose)
 
-                    #TODO SET raise_error=False before committing
-                    valid = ret.assert_affine(mapping,raise_error=True,origin_tolerance=0.0001,error_tolerance=0.0001,shape_tolerance=0)
+                    valid = ret.assert_affine(mapping,raise_error=False,origin_tolerance=0.0001,error_tolerance=0.0001,shape_tolerance=0)
                     if valid:
                         log.print(f"resample_from_to only needs padding/cropping {pad}",verbose=verbose)
                         ret.affine = mapping.affine #remove floating point error
@@ -2446,7 +2445,7 @@ def to_stls(
 
     def to_stl(
         self: NII,
-        label: int,
+        label: int|Enum|Sequence[int]|Sequence[Enum],
         out_path: Path | dict[int, Path] | None = None,
         bb: tuple | None = None,
         to_world: bool = True,
@@ -2499,7 +2498,6 @@ def to_stl(
             not support per-vertex attributes such as scalar values from marching cubes.
         """
         from stl import mesh
-
         seg = self.extract_label(label)
         # Prepare binary mask
         seg_arr = np.pad(seg.clamp(0, 1).get_array(), 1)

TPTBox/core/poi_fun/poi_abstract.py

@@ -1030,12 +1030,16 @@ def join_left(self, pois: Self, inplace=False, _right_join=False) -> Self:
             Self: The combined set of centroids, either in-place or as a new set, depending on the 'inplace' parameter.
         """
         ctd_list = self.centroids
+        if "label_name" in pois.info and "label_name" not in self.info:
+            self.info["label_name"] = {}
         if not inplace:
             ctd_list = ctd_list.copy()
         for x, y, c in pois.items():
             if (x, y) in self and not _right_join:
                 continue
             ctd_list[x, y] = c
+            if "label_name" in pois.info and f"({x}, {y})" in pois.info["label_name"]:
+                self.info["label_name"][f"({x}, {y})"] = pois.info["label_name"][f"({x}, {y})"]
         if inplace:
             return self
         return self.copy(ctd_list)

TPTBox/core/poi_fun/save_load.py

@@ -135,8 +135,12 @@ def convert(o):
             return str(o.absolute())
         raise TypeError(type(o))
 
-    with open(out_path, "w") as f:
-        json.dump(json_object, f, default=convert, indent=4)
+    try:
+        with open(out_path, "w") as f:
+            json.dump(json_object, f, default=convert, indent=4)
+    except TypeError:
+        Path(out_path).unlink(missing_ok=True)
+        raise
     log.print("POIs saved:", out_path, print_add, ltype=Log_Type.SAVE, verbose=verbose)
 
 

TPTBox/core/vert_constants.py

@@ -1223,8 +1223,15 @@ def save_as_name(cls) -> bool:
     Rib_Left = 63
     Rib_Right = 64
     # 66-80 Free
+    # Sacrum Subregions
+    Sacrum_Sacral_Ala_Left = 70
+    Sacrum_Sacral_Ala_Right = 71
+    Sacrum_Posterior_Sacral_Elements = 72
+    Sacrum_Body = 73
+    Sacrum_Endplate = 74
     # Muscle inserts
     # https://www.frontiersin.org/articles/10.3389/fbioe.2022.862804/full
+    Metal = 80
     # 81-91
     Muscle_Inserts_Spinosus_Process = 81
     Muscle_Inserts_Transverse_Process_Left = 83

TPTBox/registration/_deformable/multilabel_segmentation.py

@@ -325,7 +325,7 @@ def transform_nii(self, nii_atlas: NII, allow_only_same_grid_as_moving: bool = T
         nii_reg = self.reg_deform.transform_nii(nii_atlas)
         if nii_reg.seg:
             nii_reg.set_dtype_("smallest_uint")
-        out = nii_reg.resample_from_to(self.target_grid_org)
+        out = nii_reg.resample_from_to(self.target_grid_org, mode="constant")
         if self.same_side:
             return out
         axis = out.get_axis("R")

unit_tests/test_testsamples.py

@@ -113,6 +113,12 @@ def test_POIs_CT(self):
             Location.Vertebral_Body_Endplate_Inferior,
             Location.Rib_Left,
             Location.Rib_Right,
+            Location.Sacrum_Sacral_Ala_Left,
+            Location.Sacrum_Sacral_Ala_Right,
+            Location.Sacrum_Posterior_Sacral_Elements,
+            Location.Sacrum_Body,
+            Location.Sacrum_Endplate,
+            Location.Metal,
         ]
         self.make_POIs(vert_nii, subreg_nii, label, ignore_list)
 
@@ -134,6 +140,12 @@ def test_POIs_MR(self):
             Location.Vertebral_Body_Endplate_Inferior,
             Location.Rib_Left,
             Location.Rib_Right,
+            Location.Sacrum_Sacral_Ala_Left,
+            Location.Sacrum_Sacral_Ala_Right,
+            Location.Sacrum_Posterior_Sacral_Elements,
+            Location.Sacrum_Body,
+            Location.Sacrum_Endplate,
+            Location.Metal,
         ]
         self.make_POIs(vert_nii, subreg_nii, label, ignore_list)