update tests for v2

wasserth · Aug 29, 2023 · d2907f6 · d2907f6
1 parent 2515ad4
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diff --git a/.gitignore b/.gitignore
@@ -14,6 +14,7 @@ store/
 unittest_prediction
 unittest_prediction_fast
 unittest_prediction_roi_subset
+unittest_prediction_fast.nii.gz
 
 *.tfstate
 *.tfstate.backup

diff --git a/README.md b/README.md
@@ -60,11 +60,8 @@ runtime.
 ![Alt text](resources/imgs/overview_subclasses.png)
 
 We added some more models to TotalSegmentator beyond the default one. This allows segmentation of even 
-more classes in more detailed subparts of the image. First you have to run TotalSegmentator with the 
-normal settings to get the normal masks. These masks are required to crop the image to a subregion on 
-which the detailed model will run.
+more classes in more detailed subparts of the image.
 ```
-TotalSegmentator -i ct.nii.gz -o segmentations --fast
 TotalSegmentator -i ct.nii.gz -o segmentations -ta lung_vessels
 ```
 Overview of available subtasks and the classes which they contain.

diff --git a/tests.sh b/tests.sh
@@ -1,35 +1,41 @@
 set -e
 
-echo "License key: $1"
+# To run these tests simply do 
+# ./tests.sh <license_key>
 
-# # 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 multilabel prediction
+TotalSegmentator -i tests/reference_files/example_ct_sm.nii.gz -o tests/unittest_prediction.nii.gz -bs --ml
+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
-# 2 cpus: (w/o statistics)
+# Test organ predictions - fast - statistics
+# 2 cpus: (statistics <1s)
 #   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 -d cpu
-# pytest -v tests/test_end_to_end.py::test_end_to_end::test_lung_vessels
+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_fast
+pytest -v tests/test_end_to_end.py::test_end_to_end::test_statistics
+# pytest -v tests/test_end_to_end.py::test_end_to_end::test_preview
+
+# Test organ predictions - fast - multilabel
+TotalSegmentator -i tests/reference_files/example_ct_sm.nii.gz -o tests/unittest_prediction_fast.nii.gz --fast --ml -d cpu
+pytest -v tests/test_end_to_end.py::test_end_to_end::test_prediction_multilabel_fast
+
+# Test organ predictions - fast - multilabel - body_seg
+TotalSegmentator -i tests/reference_files/example_ct_sm.nii.gz -o tests/unittest_prediction_fast_body_seg.nii.gz --fast --ml -bs -d cpu
+pytest -v tests/test_end_to_end.py::test_end_to_end::test_prediction_multilabel_fast_body_seg
+
+# Test vessel predictions
+TotalSegmentator -i tests/reference_files/example_ct_sm.nii.gz -o tests/unittest_prediction -ta lung_vessels -d cpu  # ~1min
+pytest -v tests/test_end_to_end.py::test_end_to_end::test_lung_vessels
+
+# Test tissue types (with license) + body_seg
+TotalSegmentator -i tests/reference_files/example_ct_sm.nii.gz -o tests/unittest_prediction -ta tissue_types -d cpu -l $1
+pytest -v tests/test_end_to_end.py::test_end_to_end::test_tissue_types
diff --git a/tests/reference_files/example_seg.nii.gz b/tests/reference_files/example_seg.nii.gz
diff --git a/tests/reference_files/example_seg/adrenal_gland_left.nii.gz b/tests/reference_files/example_seg/adrenal_gland_left.nii.gz
diff --git a/tests/reference_files/example_seg/adrenal_gland_right.nii.gz b/tests/reference_files/example_seg/adrenal_gland_right.nii.gz
diff --git a/tests/reference_files/example_seg/aorta.nii.gz b/tests/reference_files/example_seg/aorta.nii.gz
diff --git a/tests/reference_files/example_seg/autochthon_left.nii.gz b/tests/reference_files/example_seg/autochthon_left.nii.gz
diff --git a/tests/reference_files/example_seg/autochthon_right.nii.gz b/tests/reference_files/example_seg/autochthon_right.nii.gz
diff --git a/tests/reference_files/example_seg/brain.nii.gz b/tests/reference_files/example_seg/brain.nii.gz
diff --git a/tests/reference_files/example_seg/clavicula_left.nii.gz b/tests/reference_files/example_seg/clavicula_left.nii.gz
diff --git a/tests/reference_files/example_seg/clavicula_right.nii.gz b/tests/reference_files/example_seg/clavicula_right.nii.gz
diff --git a/tests/reference_files/example_seg/colon.nii.gz b/tests/reference_files/example_seg/colon.nii.gz
diff --git a/tests/reference_files/example_seg/duodenum.nii.gz b/tests/reference_files/example_seg/duodenum.nii.gz
diff --git a/tests/reference_files/example_seg/esophagus.nii.gz b/tests/reference_files/example_seg/esophagus.nii.gz
diff --git a/tests/reference_files/example_seg/face.nii.gz b/tests/reference_files/example_seg/face.nii.gz
diff --git a/tests/reference_files/example_seg/femur_left.nii.gz b/tests/reference_files/example_seg/femur_left.nii.gz
diff --git a/tests/reference_files/example_seg/femur_right.nii.gz b/tests/reference_files/example_seg/femur_right.nii.gz
diff --git a/tests/reference_files/example_seg/gallbladder.nii.gz b/tests/reference_files/example_seg/gallbladder.nii.gz
diff --git a/tests/reference_files/example_seg/gluteus_maximus_left.nii.gz b/tests/reference_files/example_seg/gluteus_maximus_left.nii.gz
diff --git a/tests/reference_files/example_seg/gluteus_maximus_right.nii.gz b/tests/reference_files/example_seg/gluteus_maximus_right.nii.gz
diff --git a/tests/reference_files/example_seg/gluteus_medius_left.nii.gz b/tests/reference_files/example_seg/gluteus_medius_left.nii.gz
diff --git a/tests/reference_files/example_seg/gluteus_medius_right.nii.gz b/tests/reference_files/example_seg/gluteus_medius_right.nii.gz
diff --git a/tests/reference_files/example_seg/gluteus_minimus_left.nii.gz b/tests/reference_files/example_seg/gluteus_minimus_left.nii.gz
diff --git a/tests/reference_files/example_seg/gluteus_minimus_right.nii.gz b/tests/reference_files/example_seg/gluteus_minimus_right.nii.gz
diff --git a/tests/reference_files/example_seg/heart_atrium_left.nii.gz b/tests/reference_files/example_seg/heart_atrium_left.nii.gz
diff --git a/tests/reference_files/example_seg/heart_atrium_right.nii.gz b/tests/reference_files/example_seg/heart_atrium_right.nii.gz
diff --git a/tests/reference_files/example_seg/heart_myocardium.nii.gz b/tests/reference_files/example_seg/heart_myocardium.nii.gz
diff --git a/tests/reference_files/example_seg/heart_ventricle_left.nii.gz b/tests/reference_files/example_seg/heart_ventricle_left.nii.gz
diff --git a/tests/reference_files/example_seg/heart_ventricle_right.nii.gz b/tests/reference_files/example_seg/heart_ventricle_right.nii.gz
diff --git a/tests/reference_files/example_seg/hip_left.nii.gz b/tests/reference_files/example_seg/hip_left.nii.gz
diff --git a/tests/reference_files/example_seg/hip_right.nii.gz b/tests/reference_files/example_seg/hip_right.nii.gz
diff --git a/tests/reference_files/example_seg/humerus_left.nii.gz b/tests/reference_files/example_seg/humerus_left.nii.gz
diff --git a/tests/reference_files/example_seg/humerus_right.nii.gz b/tests/reference_files/example_seg/humerus_right.nii.gz
diff --git a/tests/reference_files/example_seg/iliac_artery_left.nii.gz b/tests/reference_files/example_seg/iliac_artery_left.nii.gz
diff --git a/tests/reference_files/example_seg/iliac_artery_right.nii.gz b/tests/reference_files/example_seg/iliac_artery_right.nii.gz
diff --git a/tests/reference_files/example_seg/iliac_vena_left.nii.gz b/tests/reference_files/example_seg/iliac_vena_left.nii.gz
diff --git a/tests/reference_files/example_seg/iliac_vena_right.nii.gz b/tests/reference_files/example_seg/iliac_vena_right.nii.gz
diff --git a/tests/reference_files/example_seg/iliopsoas_left.nii.gz b/tests/reference_files/example_seg/iliopsoas_left.nii.gz
diff --git a/tests/reference_files/example_seg/iliopsoas_right.nii.gz b/tests/reference_files/example_seg/iliopsoas_right.nii.gz
diff --git a/tests/reference_files/example_seg/inferior_vena_cava.nii.gz b/tests/reference_files/example_seg/inferior_vena_cava.nii.gz
diff --git a/tests/reference_files/example_seg/kidney_left.nii.gz b/tests/reference_files/example_seg/kidney_left.nii.gz
diff --git a/tests/reference_files/example_seg/kidney_right.nii.gz b/tests/reference_files/example_seg/kidney_right.nii.gz
diff --git a/tests/reference_files/example_seg/liver.nii.gz b/tests/reference_files/example_seg/liver.nii.gz
diff --git a/tests/reference_files/example_seg/lung.nii.gz b/tests/reference_files/example_seg/lung.nii.gz
diff --git a/tests/reference_files/example_seg/lung_lower_lobe_left.nii.gz b/tests/reference_files/example_seg/lung_lower_lobe_left.nii.gz
diff --git a/tests/reference_files/example_seg/lung_lower_lobe_right.nii.gz b/tests/reference_files/example_seg/lung_lower_lobe_right.nii.gz
diff --git a/tests/reference_files/example_seg/lung_middle_lobe_right.nii.gz b/tests/reference_files/example_seg/lung_middle_lobe_right.nii.gz
diff --git a/tests/reference_files/example_seg/lung_trachea_bronchia.nii.gz b/tests/reference_files/example_seg/lung_trachea_bronchia.nii.gz
diff --git a/tests/reference_files/example_seg/lung_upper_lobe_left.nii.gz b/tests/reference_files/example_seg/lung_upper_lobe_left.nii.gz
diff --git a/tests/reference_files/example_seg/lung_upper_lobe_right.nii.gz b/tests/reference_files/example_seg/lung_upper_lobe_right.nii.gz
diff --git a/tests/reference_files/example_seg/lung_vessels.nii.gz b/tests/reference_files/example_seg/lung_vessels.nii.gz
diff --git a/tests/reference_files/example_seg/pancreas.nii.gz b/tests/reference_files/example_seg/pancreas.nii.gz
diff --git a/tests/reference_files/example_seg/portal_vein_and_splenic_vein.nii.gz b/tests/reference_files/example_seg/portal_vein_and_splenic_vein.nii.gz
diff --git a/tests/reference_files/example_seg/pulmonary_artery.nii.gz b/tests/reference_files/example_seg/pulmonary_artery.nii.gz
diff --git a/tests/reference_files/example_seg/rib_left_1.nii.gz b/tests/reference_files/example_seg/rib_left_1.nii.gz
diff --git a/tests/reference_files/example_seg/rib_left_10.nii.gz b/tests/reference_files/example_seg/rib_left_10.nii.gz
diff --git a/tests/reference_files/example_seg/rib_left_11.nii.gz b/tests/reference_files/example_seg/rib_left_11.nii.gz
diff --git a/tests/reference_files/example_seg/rib_left_12.nii.gz b/tests/reference_files/example_seg/rib_left_12.nii.gz
diff --git a/tests/reference_files/example_seg/rib_left_2.nii.gz b/tests/reference_files/example_seg/rib_left_2.nii.gz
diff --git a/tests/reference_files/example_seg/rib_left_3.nii.gz b/tests/reference_files/example_seg/rib_left_3.nii.gz
diff --git a/tests/reference_files/example_seg/rib_left_4.nii.gz b/tests/reference_files/example_seg/rib_left_4.nii.gz
diff --git a/tests/reference_files/example_seg/rib_left_5.nii.gz b/tests/reference_files/example_seg/rib_left_5.nii.gz
diff --git a/tests/reference_files/example_seg/rib_left_6.nii.gz b/tests/reference_files/example_seg/rib_left_6.nii.gz
diff --git a/tests/reference_files/example_seg/rib_left_7.nii.gz b/tests/reference_files/example_seg/rib_left_7.nii.gz
diff --git a/tests/reference_files/example_seg/rib_left_8.nii.gz b/tests/reference_files/example_seg/rib_left_8.nii.gz
diff --git a/tests/reference_files/example_seg/rib_left_9.nii.gz b/tests/reference_files/example_seg/rib_left_9.nii.gz
diff --git a/tests/reference_files/example_seg/rib_right_1.nii.gz b/tests/reference_files/example_seg/rib_right_1.nii.gz
diff --git a/tests/reference_files/example_seg/rib_right_10.nii.gz b/tests/reference_files/example_seg/rib_right_10.nii.gz
diff --git a/tests/reference_files/example_seg/rib_right_11.nii.gz b/tests/reference_files/example_seg/rib_right_11.nii.gz
diff --git a/tests/reference_files/example_seg/rib_right_12.nii.gz b/tests/reference_files/example_seg/rib_right_12.nii.gz
diff --git a/tests/reference_files/example_seg/rib_right_2.nii.gz b/tests/reference_files/example_seg/rib_right_2.nii.gz
diff --git a/tests/reference_files/example_seg/rib_right_3.nii.gz b/tests/reference_files/example_seg/rib_right_3.nii.gz
diff --git a/tests/reference_files/example_seg/rib_right_4.nii.gz b/tests/reference_files/example_seg/rib_right_4.nii.gz
diff --git a/tests/reference_files/example_seg/rib_right_5.nii.gz b/tests/reference_files/example_seg/rib_right_5.nii.gz
diff --git a/tests/reference_files/example_seg/rib_right_6.nii.gz b/tests/reference_files/example_seg/rib_right_6.nii.gz
diff --git a/tests/reference_files/example_seg/rib_right_7.nii.gz b/tests/reference_files/example_seg/rib_right_7.nii.gz
diff --git a/tests/reference_files/example_seg/rib_right_8.nii.gz b/tests/reference_files/example_seg/rib_right_8.nii.gz
diff --git a/tests/reference_files/example_seg/rib_right_9.nii.gz b/tests/reference_files/example_seg/rib_right_9.nii.gz
diff --git a/tests/reference_files/example_seg/sacrum.nii.gz b/tests/reference_files/example_seg/sacrum.nii.gz
diff --git a/tests/reference_files/example_seg/scapula_left.nii.gz b/tests/reference_files/example_seg/scapula_left.nii.gz
diff --git a/tests/reference_files/example_seg/scapula_right.nii.gz b/tests/reference_files/example_seg/scapula_right.nii.gz
diff --git a/tests/reference_files/example_seg/small_bowel.nii.gz b/tests/reference_files/example_seg/small_bowel.nii.gz
diff --git a/tests/reference_files/example_seg/spleen.nii.gz b/tests/reference_files/example_seg/spleen.nii.gz
diff --git a/tests/reference_files/example_seg/stomach.nii.gz b/tests/reference_files/example_seg/stomach.nii.gz
diff --git a/tests/reference_files/example_seg/trachea.nii.gz b/tests/reference_files/example_seg/trachea.nii.gz
diff --git a/tests/reference_files/example_seg/urinary_bladder.nii.gz b/tests/reference_files/example_seg/urinary_bladder.nii.gz
diff --git a/tests/reference_files/example_seg/vertebrae_C1.nii.gz b/tests/reference_files/example_seg/vertebrae_C1.nii.gz
diff --git a/tests/reference_files/example_seg/vertebrae_C2.nii.gz b/tests/reference_files/example_seg/vertebrae_C2.nii.gz
diff --git a/tests/reference_files/example_seg/vertebrae_C3.nii.gz b/tests/reference_files/example_seg/vertebrae_C3.nii.gz
diff --git a/tests/reference_files/example_seg/vertebrae_C4.nii.gz b/tests/reference_files/example_seg/vertebrae_C4.nii.gz
diff --git a/tests/reference_files/example_seg/vertebrae_C5.nii.gz b/tests/reference_files/example_seg/vertebrae_C5.nii.gz
diff --git a/tests/reference_files/example_seg/vertebrae_C6.nii.gz b/tests/reference_files/example_seg/vertebrae_C6.nii.gz
diff --git a/tests/reference_files/example_seg/vertebrae_C7.nii.gz b/tests/reference_files/example_seg/vertebrae_C7.nii.gz
diff --git a/tests/reference_files/example_seg/vertebrae_L1.nii.gz b/tests/reference_files/example_seg/vertebrae_L1.nii.gz
diff --git a/tests/reference_files/example_seg/vertebrae_L2.nii.gz b/tests/reference_files/example_seg/vertebrae_L2.nii.gz
diff --git a/tests/reference_files/example_seg/vertebrae_L3.nii.gz b/tests/reference_files/example_seg/vertebrae_L3.nii.gz
diff --git a/tests/reference_files/example_seg/vertebrae_L4.nii.gz b/tests/reference_files/example_seg/vertebrae_L4.nii.gz
diff --git a/tests/reference_files/example_seg/vertebrae_L5.nii.gz b/tests/reference_files/example_seg/vertebrae_L5.nii.gz
diff --git a/tests/reference_files/example_seg/vertebrae_T1.nii.gz b/tests/reference_files/example_seg/vertebrae_T1.nii.gz
diff --git a/tests/reference_files/example_seg/vertebrae_T10.nii.gz b/tests/reference_files/example_seg/vertebrae_T10.nii.gz
diff --git a/tests/reference_files/example_seg/vertebrae_T11.nii.gz b/tests/reference_files/example_seg/vertebrae_T11.nii.gz
diff --git a/tests/reference_files/example_seg/vertebrae_T12.nii.gz b/tests/reference_files/example_seg/vertebrae_T12.nii.gz
diff --git a/tests/reference_files/example_seg/vertebrae_T2.nii.gz b/tests/reference_files/example_seg/vertebrae_T2.nii.gz
diff --git a/tests/reference_files/example_seg/vertebrae_T3.nii.gz b/tests/reference_files/example_seg/vertebrae_T3.nii.gz
diff --git a/tests/reference_files/example_seg/vertebrae_T4.nii.gz b/tests/reference_files/example_seg/vertebrae_T4.nii.gz
diff --git a/tests/reference_files/example_seg/vertebrae_T5.nii.gz b/tests/reference_files/example_seg/vertebrae_T5.nii.gz
diff --git a/tests/reference_files/example_seg/vertebrae_T6.nii.gz b/tests/reference_files/example_seg/vertebrae_T6.nii.gz
diff --git a/tests/reference_files/example_seg/vertebrae_T7.nii.gz b/tests/reference_files/example_seg/vertebrae_T7.nii.gz
diff --git a/tests/reference_files/example_seg/vertebrae_T8.nii.gz b/tests/reference_files/example_seg/vertebrae_T8.nii.gz
diff --git a/tests/reference_files/example_seg/vertebrae_T9.nii.gz b/tests/reference_files/example_seg/vertebrae_T9.nii.gz
diff --git a/tests/reference_files/example_seg_fast.nii.gz b/tests/reference_files/example_seg_fast.nii.gz
diff --git a/tests/reference_files/example_seg_fast/adrenal_gland_left.nii.gz b/tests/reference_files/example_seg_fast/adrenal_gland_left.nii.gz
diff --git a/tests/reference_files/example_seg_fast/adrenal_gland_right.nii.gz b/tests/reference_files/example_seg_fast/adrenal_gland_right.nii.gz
diff --git a/tests/reference_files/example_seg_fast/aorta.nii.gz b/tests/reference_files/example_seg_fast/aorta.nii.gz
diff --git a/tests/reference_files/example_seg_fast/atrial_appendage_left.nii.gz b/tests/reference_files/example_seg_fast/atrial_appendage_left.nii.gz
diff --git a/tests/reference_files/example_seg_fast/autochthon_left.nii.gz b/tests/reference_files/example_seg_fast/autochthon_left.nii.gz
diff --git a/tests/reference_files/example_seg_fast/autochthon_right.nii.gz b/tests/reference_files/example_seg_fast/autochthon_right.nii.gz
diff --git a/tests/reference_files/example_seg_fast/brachiocephalic_trunk.nii.gz b/tests/reference_files/example_seg_fast/brachiocephalic_trunk.nii.gz
diff --git a/tests/reference_files/example_seg_fast/brachiocephalic_vein_left.nii.gz b/tests/reference_files/example_seg_fast/brachiocephalic_vein_left.nii.gz
diff --git a/tests/reference_files/example_seg_fast/brachiocephalic_vein_right.nii.gz b/tests/reference_files/example_seg_fast/brachiocephalic_vein_right.nii.gz
diff --git a/tests/reference_files/example_seg_fast/brain.nii.gz b/tests/reference_files/example_seg_fast/brain.nii.gz
diff --git a/tests/reference_files/example_seg_fast/clavicula_left.nii.gz b/tests/reference_files/example_seg_fast/clavicula_left.nii.gz
diff --git a/tests/reference_files/example_seg_fast/clavicula_right.nii.gz b/tests/reference_files/example_seg_fast/clavicula_right.nii.gz
diff --git a/tests/reference_files/example_seg_fast/colon.nii.gz b/tests/reference_files/example_seg_fast/colon.nii.gz
diff --git a/tests/reference_files/example_seg_fast/common_carotid_artery_left.nii.gz b/tests/reference_files/example_seg_fast/common_carotid_artery_left.nii.gz
diff --git a/tests/reference_files/example_seg_fast/common_carotid_artery_right.nii.gz b/tests/reference_files/example_seg_fast/common_carotid_artery_right.nii.gz
diff --git a/tests/reference_files/example_seg_fast/costal_cartilages.nii.gz b/tests/reference_files/example_seg_fast/costal_cartilages.nii.gz
diff --git a/tests/reference_files/example_seg_fast/duodenum.nii.gz b/tests/reference_files/example_seg_fast/duodenum.nii.gz
diff --git a/tests/reference_files/example_seg_fast/esophagus.nii.gz b/tests/reference_files/example_seg_fast/esophagus.nii.gz
diff --git a/tests/reference_files/example_seg_fast/face.nii.gz b/tests/reference_files/example_seg_fast/face.nii.gz
diff --git a/tests/reference_files/example_seg_fast/femur_left.nii.gz b/tests/reference_files/example_seg_fast/femur_left.nii.gz
diff --git a/tests/reference_files/example_seg_fast/femur_right.nii.gz b/tests/reference_files/example_seg_fast/femur_right.nii.gz
diff --git a/tests/reference_files/example_seg_fast/gallbladder.nii.gz b/tests/reference_files/example_seg_fast/gallbladder.nii.gz
diff --git a/tests/reference_files/example_seg_fast/gluteus_maximus_left.nii.gz b/tests/reference_files/example_seg_fast/gluteus_maximus_left.nii.gz
diff --git a/tests/reference_files/example_seg_fast/gluteus_maximus_right.nii.gz b/tests/reference_files/example_seg_fast/gluteus_maximus_right.nii.gz
diff --git a/tests/reference_files/example_seg_fast/gluteus_medius_left.nii.gz b/tests/reference_files/example_seg_fast/gluteus_medius_left.nii.gz
diff --git a/tests/reference_files/example_seg_fast/gluteus_medius_right.nii.gz b/tests/reference_files/example_seg_fast/gluteus_medius_right.nii.gz
diff --git a/tests/reference_files/example_seg_fast/gluteus_minimus_left.nii.gz b/tests/reference_files/example_seg_fast/gluteus_minimus_left.nii.gz
diff --git a/tests/reference_files/example_seg_fast/gluteus_minimus_right.nii.gz b/tests/reference_files/example_seg_fast/gluteus_minimus_right.nii.gz
diff --git a/tests/reference_files/example_seg_fast/heart.nii.gz b/tests/reference_files/example_seg_fast/heart.nii.gz
diff --git a/tests/reference_files/example_seg_fast/heart_atrium_left.nii.gz b/tests/reference_files/example_seg_fast/heart_atrium_left.nii.gz
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diff --git a/tests/reference_files/example_seg_fast/heart_myocardium.nii.gz b/tests/reference_files/example_seg_fast/heart_myocardium.nii.gz
diff --git a/tests/reference_files/example_seg_fast/heart_ventricle_left.nii.gz b/tests/reference_files/example_seg_fast/heart_ventricle_left.nii.gz
diff --git a/tests/reference_files/example_seg_fast/heart_ventricle_right.nii.gz b/tests/reference_files/example_seg_fast/heart_ventricle_right.nii.gz
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diff --git a/tests/reference_files/example_seg_fast/iliac_artery_left.nii.gz b/tests/reference_files/example_seg_fast/iliac_artery_left.nii.gz
diff --git a/tests/reference_files/example_seg_fast/iliac_artery_right.nii.gz b/tests/reference_files/example_seg_fast/iliac_artery_right.nii.gz
diff --git a/tests/reference_files/example_seg_fast/iliac_vena_left.nii.gz b/tests/reference_files/example_seg_fast/iliac_vena_left.nii.gz
diff --git a/tests/reference_files/example_seg_fast/iliac_vena_right.nii.gz b/tests/reference_files/example_seg_fast/iliac_vena_right.nii.gz
diff --git a/tests/reference_files/example_seg_fast/iliopsoas_left.nii.gz b/tests/reference_files/example_seg_fast/iliopsoas_left.nii.gz
diff --git a/tests/reference_files/example_seg_fast/iliopsoas_right.nii.gz b/tests/reference_files/example_seg_fast/iliopsoas_right.nii.gz
diff --git a/tests/reference_files/example_seg_fast/inferior_vena_cava.nii.gz b/tests/reference_files/example_seg_fast/inferior_vena_cava.nii.gz
diff --git a/tests/reference_files/example_seg_fast/kidney_cyst_left.nii.gz b/tests/reference_files/example_seg_fast/kidney_cyst_left.nii.gz
diff --git a/tests/reference_files/example_seg_fast/kidney_cyst_right.nii.gz b/tests/reference_files/example_seg_fast/kidney_cyst_right.nii.gz
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diff --git a/tests/reference_files/example_seg_fast/liver.nii.gz b/tests/reference_files/example_seg_fast/liver.nii.gz
diff --git a/tests/reference_files/example_seg_fast/lung_lower_lobe_left.nii.gz b/tests/reference_files/example_seg_fast/lung_lower_lobe_left.nii.gz
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diff --git a/tests/reference_files/example_seg_fast/lung_middle_lobe_right.nii.gz b/tests/reference_files/example_seg_fast/lung_middle_lobe_right.nii.gz
diff --git a/tests/reference_files/example_seg_fast/lung_upper_lobe_left.nii.gz b/tests/reference_files/example_seg_fast/lung_upper_lobe_left.nii.gz
diff --git a/tests/reference_files/example_seg_fast/lung_upper_lobe_right.nii.gz b/tests/reference_files/example_seg_fast/lung_upper_lobe_right.nii.gz
diff --git a/tests/reference_files/example_seg_fast/pancreas.nii.gz b/tests/reference_files/example_seg_fast/pancreas.nii.gz
diff --git a/tests/reference_files/example_seg_fast/portal_vein_and_splenic_vein.nii.gz b/tests/reference_files/example_seg_fast/portal_vein_and_splenic_vein.nii.gz
diff --git a/tests/reference_files/example_seg_fast/prostate.nii.gz b/tests/reference_files/example_seg_fast/prostate.nii.gz
diff --git a/tests/reference_files/example_seg_fast/pulmonary_artery.nii.gz b/tests/reference_files/example_seg_fast/pulmonary_artery.nii.gz
diff --git a/tests/reference_files/example_seg_fast/pulmonary_vein.nii.gz b/tests/reference_files/example_seg_fast/pulmonary_vein.nii.gz
diff --git a/tests/reference_files/example_seg_fast/rib_left_1.nii.gz b/tests/reference_files/example_seg_fast/rib_left_1.nii.gz
diff --git a/tests/reference_files/example_seg_fast/rib_left_10.nii.gz b/tests/reference_files/example_seg_fast/rib_left_10.nii.gz
diff --git a/tests/reference_files/example_seg_fast/rib_left_11.nii.gz b/tests/reference_files/example_seg_fast/rib_left_11.nii.gz
diff --git a/tests/reference_files/example_seg_fast/rib_left_12.nii.gz b/tests/reference_files/example_seg_fast/rib_left_12.nii.gz
diff --git a/tests/reference_files/example_seg_fast/rib_left_2.nii.gz b/tests/reference_files/example_seg_fast/rib_left_2.nii.gz
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diff --git a/tests/reference_files/example_seg_fast/rib_left_5.nii.gz b/tests/reference_files/example_seg_fast/rib_left_5.nii.gz
diff --git a/tests/reference_files/example_seg_fast/rib_left_6.nii.gz b/tests/reference_files/example_seg_fast/rib_left_6.nii.gz
diff --git a/tests/reference_files/example_seg_fast/rib_left_7.nii.gz b/tests/reference_files/example_seg_fast/rib_left_7.nii.gz
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diff --git a/tests/reference_files/example_seg_fast/rib_left_9.nii.gz b/tests/reference_files/example_seg_fast/rib_left_9.nii.gz
diff --git a/tests/reference_files/example_seg_fast/rib_right_1.nii.gz b/tests/reference_files/example_seg_fast/rib_right_1.nii.gz
diff --git a/tests/reference_files/example_seg_fast/rib_right_10.nii.gz b/tests/reference_files/example_seg_fast/rib_right_10.nii.gz
diff --git a/tests/reference_files/example_seg_fast/rib_right_11.nii.gz b/tests/reference_files/example_seg_fast/rib_right_11.nii.gz
diff --git a/tests/reference_files/example_seg_fast/rib_right_12.nii.gz b/tests/reference_files/example_seg_fast/rib_right_12.nii.gz
diff --git a/tests/reference_files/example_seg_fast/rib_right_2.nii.gz b/tests/reference_files/example_seg_fast/rib_right_2.nii.gz
diff --git a/tests/reference_files/example_seg_fast/rib_right_3.nii.gz b/tests/reference_files/example_seg_fast/rib_right_3.nii.gz
diff --git a/tests/reference_files/example_seg_fast/rib_right_4.nii.gz b/tests/reference_files/example_seg_fast/rib_right_4.nii.gz
diff --git a/tests/reference_files/example_seg_fast/rib_right_5.nii.gz b/tests/reference_files/example_seg_fast/rib_right_5.nii.gz
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diff --git a/tests/reference_files/example_seg_fast/rib_right_7.nii.gz b/tests/reference_files/example_seg_fast/rib_right_7.nii.gz
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diff --git a/tests/reference_files/example_seg_fast/rib_right_9.nii.gz b/tests/reference_files/example_seg_fast/rib_right_9.nii.gz
diff --git a/tests/reference_files/example_seg_fast/sacrum.nii.gz b/tests/reference_files/example_seg_fast/sacrum.nii.gz
diff --git a/tests/reference_files/example_seg_fast/scapula_left.nii.gz b/tests/reference_files/example_seg_fast/scapula_left.nii.gz
diff --git a/tests/reference_files/example_seg_fast/scapula_right.nii.gz b/tests/reference_files/example_seg_fast/scapula_right.nii.gz
diff --git a/tests/reference_files/example_seg_fast/skull.nii.gz b/tests/reference_files/example_seg_fast/skull.nii.gz
diff --git a/tests/reference_files/example_seg_fast/small_bowel.nii.gz b/tests/reference_files/example_seg_fast/small_bowel.nii.gz
diff --git a/tests/reference_files/example_seg_fast/spinal_cord.nii.gz b/tests/reference_files/example_seg_fast/spinal_cord.nii.gz
diff --git a/tests/reference_files/example_seg_fast/spleen.nii.gz b/tests/reference_files/example_seg_fast/spleen.nii.gz