Merge pull request #4 from Hendrik-code/tptbox_v0.0.6

updated to tptbox v0.0.6

pyproject.toml

@@ -29,7 +29,7 @@ torchmetrics = "^1.1.2"
 tqdm = "^4.66.1"
 einops= "^0.6.1"
 nnunetv2 = "2.2"
-tptbox = "*"
+tptbox = "^0.0.6"
 antspyx = "*"
 rich = "^13.6.0"
 

spineps/seg_pipeline.py

@@ -56,7 +56,7 @@ def predict_centroids_from_both(
         labelmap[i] = 0
     vert_nii_4_centroids.map_labels_(labelmap, verbose=False)
 
-    ctd = poi.calc_centroids_from_subreg_vert(vert_nii_4_centroids, seg_nii, verbose=logger)
+    ctd = poi.calc_poi_from_subreg_vert(vert_nii_4_centroids, seg_nii, verbose=logger)
 
     if v_name2idx["S1"] in vert_nii_cleaned.unique():
         s1_nii = vert_nii_cleaned.extract_label(26, inplace=False)

spineps/utils/filepaths.py

@@ -6,7 +6,7 @@
 from pathlib import Path
 
 spineps_environment_path_override = None  # Path(
-# "/DATA/NAS/ongoing_projects/hendrik/mri_usage/models/"
+#    "/DATA/NAS/ongoing_projects/hendrik/mri_usage/models/"
 # )  # None  # You can put an absolute path to the model weights here instead of using environment variable
 spineps_environment_path_backup = Path(__file__).parent.parent.joinpath("models")  # EDIT this to use this instead of environment variable
 

unit_tests/test_filepaths.py

@@ -0,0 +1,35 @@
+# Call 'python -m unittest' on this folder  # noqa: INP001
+# coverage run -m unittest
+# coverage report
+# coverage html
+import os
+import unittest
+
+from spineps.models import Segmentation_Model, get_segmentation_model
+from spineps.utils.filepaths import (
+    filepath_model,
+    get_mri_segmentor_models_dir,
+    spineps_environment_path_backup,
+    spineps_environment_path_override,
+)
+
+
+class Test_filepaths(unittest.TestCase):
+    # def test_load_model_from_path(self):
+    #    ms_p = "/DATA/NAS/ongoing_projects/hendrik/nako-segmentation/nnUNet/nnUNet_results/Dataset122_nako_wotest_spiderarcus/nnUNetTrainerNoMirroring__nnUNetPlans__3d_fullres_custom"
+    #    mv_p = "/DATA/NAS/ongoing_projects/hendrik/nako-segmentation/nnUNet/unet3d_result/nakospider_highres_shiftposi"
+    #    model_dir = "/DATA/NAS/ongoing_projects/hendrik/nako-segmentation/nnUNet/"
+    #    ms = get_segmentation_model(in_config=filepath_model(ms_p, model_dir=model_dir))
+    #    self.assertTrue(isinstance(ms, Segmentation_Model))
+    #    mv = get_segmentation_model(in_config=filepath_model(mv_p, model_dir=model_dir))
+    #    self.assertTrue(isinstance(mv, Segmentation_Model))
+    #    self.assertTrue(True)
+
+    # def test_env_path(self):
+    #    # no override
+    #    p = get_mri_segmentor_models_dir()
+    #    if spineps_environment_path_override is not None:
+    #        self.assertEqual(p, spineps_environment_path_override)
+    #    else:
+    #        self.assertEqual(str(p) + "/", os.environ.get("SPINEPS_SEGMENTOR_MODELS"))
+    pass