fix how to load pkl classifier file; fix: run correct subtasks script

wasserth · Jul 23, 2024 · 07f85d0 · 07f85d0
1 parent 47e7330
commit 07f85d0
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Showing 2 changed files with 4 additions and 2 deletions.
diff --git a/.github/workflows/run_tests_subtasks.yml b/.github/workflows/run_tests_subtasks.yml
@@ -25,5 +25,5 @@ jobs:
           pip install .
 
       - name: Run test script
-        run: ./tests/tests.sh ${{ secrets.TOTALSEGMENTATOR_LICENSE }}
+        run: ./tests/tests_subtasks.sh ${{ secrets.TOTALSEGMENTATOR_LICENSE }}
         shell: bash
diff --git a/totalsegmentator/bin/totalseg_get_phase.py b/totalsegmentator/bin/totalseg_get_phase.py
@@ -6,6 +6,7 @@
 import json
 import pickle
 from pprint import pprint
+import pkg_resources
 
 import nibabel as nib
 import numpy as np
@@ -85,7 +86,8 @@ def get_ct_contrast_phase(ct_img: nib.Nifti1Image, model_file: Path = None):
         features.append(stats_hn[organ]["intensity"])
 
     if model_file is None:
-        classifier_path = Path(__file__).parents[2] / "resources" / "contrast_phase_classifiers_2024_07_19.pkl"
+        # classifier_path = Path(__file__).parents[2] / "resources" / "contrast_phase_classifiers_2024_07_19.pkl"
+        classifier_path = pkg_resources.resource_filename('totalsegmentator', 'resources/contrast_phase_classifiers_2024_07_19.pkl')
     else: 
         # manually set model file
         classifier_path = model_file