add test for roi subset

.gitignore

@@ -13,6 +13,7 @@ tmp_weights_DELETE/
 store/
 unittest_prediction
 unittest_prediction_fast
+unittest_prediction_roi_subset
 
 *.tfstate
 *.tfstate.backup

bin/TotalSegmentator

@@ -60,6 +60,9 @@ def main():
     parser.add_argument("-rs", "--roi_subset", type=str, nargs="+",
                         help="Define a subset of classes to save (space separated list of class names). If running 1.5mm model, will only run the appropriate models for these rois.")
 
+    # When this is used together with --roi_subset and --ml, then statistics will be calculated for all classes
+    # in the class_map_part_X with is calculated. Some of the rois will be cropped and therefore the volume will
+    # only be of the cropped region, making it an incorrect volume.
     parser.add_argument("-s", "--statistics", action="store_true", 
                         help="Calc volume (in mm3) and mean intensity. Results will be in statistics.json",
                         default=False)

tests.sh

@@ -1,20 +1,35 @@
 set -e
 
-# Test organ predictions
-TotalSegmentator -i tests/reference_files/example_ct.nii.gz -o tests/unittest_prediction --test 1
-pytest -v tests/test_end_to_end.py::test_end_to_end::test_prediction_liver
-pytest -v tests/test_end_to_end.py::test_end_to_end::test_prediction_vertebrae
+echo "License key: $1"
 
-# Test multilabel prediction
-TotalSegmentator -i tests/reference_files/example_ct.nii.gz -o tests/unittest_prediction.nii.gz --ml --test 1
-pytest -v tests/test_end_to_end.py::test_end_to_end::test_prediction_multilabel
+# # Test organ predictions
+# TotalSegmentator -i tests/reference_files/example_ct.nii.gz -o tests/unittest_prediction --test 1
+# pytest -v tests/test_end_to_end.py::test_end_to_end::test_prediction_liver
+# pytest -v tests/test_end_to_end.py::test_end_to_end::test_prediction_vertebrae
+
+# # Test multilabel prediction
+# TotalSegmentator -i tests/reference_files/example_ct.nii.gz -o tests/unittest_prediction.nii.gz --ml --test 1
+# pytest -v tests/test_end_to_end.py::test_end_to_end::test_prediction_multilabel
+
+# Test organ prediction - roi subset
+# 20 cpu
+#   example_ct_sm.nii.gz: 20s, 3.1GB
+#   example_ct.nii.gz: 22s, 3.1GB
+# 2 cpus:
+#   example_ct_sm.nii.gz: 34s, 3.0GB
+#   example_ct.nii.gz: 36s, 3.0GB
+TotalSegmentator -i tests/reference_files/example_ct_sm.nii.gz -o tests/unittest_prediction_roi_subset -rs liver brain -d cpu
+pytest -v tests/test_end_to_end.py::test_end_to_end::test_prediction_liver_roi_subset
 
 # Test organ predictions - fast
-TotalSegmentator -i tests/reference_files/example_ct.nii.gz -o tests/unittest_prediction_fast --fast --statistics
-pytest -v tests/test_end_to_end.py::test_end_to_end::test_prediction_liver_fast
-pytest -v tests/test_end_to_end.py::test_end_to_end::test_prediction_vertebrae_fast
-pytest -v tests/test_end_to_end.py::test_end_to_end::test_statistics
+# 2 cpus: (w/o statistics)
+#   example_ct_sm.nii.gz: 13s, 4.1GB
+#   example_ct.nii.gz: 16s, 4.1GB
+# TotalSegmentator -i tests/reference_files/example_ct_sm.nii.gz -o tests/unittest_prediction_fast --fast --statistics -d cpu
+# pytest -v tests/test_end_to_end.py::test_end_to_end::test_prediction_liver_fast
+# pytest -v tests/test_end_to_end.py::test_end_to_end::test_prediction_vertebrae_fast
+# pytest -v tests/test_end_to_end.py::test_end_to_end::test_statistics
 
-# Test vessel predictions
-TotalSegmentator -i tests/reference_files/example_ct.nii.gz -o tests/unittest_prediction -ta lung_vessels --test 3
-pytest -v tests/test_end_to_end.py::test_end_to_end::test_lung_vessels
+# # Test vessel predictions
+# TotalSegmentator -i tests/reference_files/example_ct.nii.gz -o tests/unittest_prediction -ta lung_vessels --test 3 -d cpu
+# pytest -v tests/test_end_to_end.py::test_end_to_end::test_lung_vessels