New features robert (#75)

* add remove_to_label_for_cc_filter

* add remove_to

* add itk global_cord support

* add referecne for loading POI (POI.load)

* enable loading via Path

* add set_above_3_point_plane

* make an internal function to make vert-seg

* do not corp when empty instead of failing

* fix issue with empty images and cropout

* bug fixes

* ruff

* remove deprecated function

* x

* move assert_affine ot has_grid to avoid duplicat code in NII and POI

* add is_segmentation_in_border

* add support for itk_cords in Global poi

* add new POI definition

* add saving, refactor point reg

* prepare save and load global coords with POI

* enable selection of cuda,mps and cpu for reg

* refactor move save load poi in its separate  file

* add save / load for global POI

* bug fix saving

* change default Enum for POI

* ruff

* fix py 3.9; remove error in test

---------

Co-authored-by: ga84mun <robert.graf@tum.de>

Author: robert-graf

TPTBox/core/poi.py

@@ -1169,19 +1169,13 @@ def calc_centroids(
     assert first_stage == -1 or second_stage == -1, "first or second dimension must be fixed."
     msk_nii = to_nii(msk, seg=True)
     msk_data = msk_nii.get_seg_array()
-    axc: AX_CODES = nio.aff2axcodes(msk_nii.affine)  # type: ignore
     if extend_to is None:
         ctd_list = POI_Descriptor()
     else:
         if not inplace:
             extend_to = extend_to.copy()
         ctd_list = extend_to.centroids
-        extend_to.assert_affine(
-            msk_nii,
-            shape_tolerance=0.5,
-            origin_tolerance=0.5,
-        )
-        # assert extend_to.orientation == axc, (extend_to.orientation, axc)
+        extend_to.assert_affine(msk_nii, shape_tolerance=0.5, origin_tolerance=0.5)
     for i in msk_nii.unique():
         msk_temp = np.zeros(msk_data.shape, dtype=bool)
         msk_temp[msk_data == i] = True
@@ -1190,7 +1184,7 @@ def calc_centroids(
             ctd_list[first_stage, int(i)] = tuple(round(x, decimals) for x in ctr_mass)
         else:
             ctd_list[int(i), second_stage] = tuple(round(x, decimals) for x in ctr_mass)
-    return POI(ctd_list, orientation=axc, **msk_nii._extract_affine(rm_key=["orientation"]), **args)
+    return POI(ctd_list, **msk_nii._extract_affine(), **args)
 
 
 ######## Utility #######

TPTBox/registration/deformable/_deepali/deform_reg_pair.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 import json
 from pathlib import Path
 from timeit import default_timer as timer

TPTBox/registration/deformable/_deepali/registration_losses.py

@@ -1,4 +1,4 @@
-r"""Registration loss for pairwise image registration."""
+from __future__ import annotations
 
 import re
 from collections import defaultdict
@@ -24,6 +24,8 @@
 from torch import Tensor
 from torch.nn import Module
 
+r"""Registration loss for pairwise image registration."""
+
 RE_WEIGHT = re.compile(r"^((?P<mul>[0-9]+(\.[0-9]+)?)\s*[\* ])?\s*(?P<chn>[a-zA-Z0-9_-]+)\s*(\+\s*(?P<add>[0-9]+(\.[0-9]+)?))?$")
 RE_TERM_VAR = re.compile(r"^[a-zA-Z0-9_-]+\((?P<var>[a-zA-Z0-9_]+)\)$")
 

pyproject.toml

@@ -29,6 +29,7 @@ tqdm = "*"
 joblib = "*"
 scikit-learn = "*"
 antspyx = "0.4.2"
+hf-deepali = "*"
 
 [tool.poetry.dev-dependencies]
 pytest = ">=8.1.1"

unit_tests/test_testsamples.py

@@ -16,7 +16,7 @@
 
 import unittest  # noqa: E402
 
-from TPTBox import NII, Location, calc_poi_from_subreg_vert  # noqa: E402
+from TPTBox import NII, Location, Print_Logger, calc_poi_from_subreg_vert  # noqa: E402
 from TPTBox.tests.test_utils import get_test_ct, get_test_mri, get_tests_dir  # noqa: E402
 
 
@@ -84,15 +84,13 @@ def test_make_snapshot_both(self, keep_images=False):
 
     def make_POIs(self, vert_nii: NII, subreg_nii: NII, vert_id: int, ignore_list: list[Location], locs: None | list[Location] = None, n=5):
         for i in range(n):
-            if locs is None:
-                locs = [l for l in Location if l not in ignore_list and random.random() < (i + 1) / n * 3]
-            poi = calc_poi_from_subreg_vert(vert_nii, subreg_nii, subreg_id=locs, verbose=False, _print_phases=True).extract_region(vert_id)
-            for l in locs:
-                self.assertIn((vert_id, l.value), poi)
-            poi.assert_affine(
-                vert_nii,
-                shape_tolerance=0.5,
+            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(
+                vert_id
             )
+            for l in locs2:
+                self.assertIn((vert_id, l.value), poi)
+            poi.assert_affine(vert_nii, shape_tolerance=0.5)
 
     def test_POIs_CT(self):
         _, subreg_nii, vert_nii, label = get_test_ct()
@@ -107,6 +105,7 @@ def test_POIs_CT(self):
             Location.Dens_axis,
             Location.Unknown,
             Location.Endplate,
+            Location.Vertebra_Disc,  # CT example has no disc...
             Location.Spinal_Cord,
             Location.Spinal_Canal,
             Location.Spinal_Canal_ivd_lvl,