os test edit: only run on ubuntu + windows + mac

wasserth · Sep 19, 2023 · 3dbc88b · 3dbc88b
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commit 3dbc88b
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diff --git a/.github/workflows/run_tests_os.yml b/.github/workflows/run_tests_os.yml
@@ -5,8 +5,8 @@ jobs:
   run-tests:
     strategy:
       matrix:
-        # os: [ubuntu-latest, windows-latest, macos-latest]
-        os: [ubuntu-latest, windows-latest]
+        os: [ubuntu-latest, windows-latest, macos-latest]
+        # os: [ubuntu-latest, windows-latest]
         # python-version: ["3.8", "3.10"]
         python-version: ["3.10"]  # run less in parallel to avoid download problems??
     runs-on: ${{ matrix.os }}

diff --git a/resources/train_nnunet.sh b/resources/train_nnunet.sh
@@ -1,50 +1,50 @@
 #!/bin/bash
 set -e
 
-############ Convert data ############
+# ############ Convert data ############
 
-python convert_dataset_to_nnunet.py \
-/mnt/nor/wasserthalj_data/TotalSegmentator/zenodo_upload/Totalsegmentator_dataset \
-/mnt/nor/nnunet/raw_v2/Dataset101_TotalSegmentator_public_part1 \
-class_map_part_organs
+# python convert_dataset_to_nnunet.py \
+# /mnt/nor/wasserthalj_data/TotalSegmentator/zenodo_upload/Totalsegmentator_dataset \
+# /mnt/nor/nnunet/raw_v2/Dataset101_TotalSegmentator_public_part1 \
+# class_map_part_organs
 
-python convert_dataset_to_nnunet.py \
-/mnt/nor/wasserthalj_data/TotalSegmentator/zenodo_upload/Totalsegmentator_dataset \
-/mnt/nor/nnunet/raw_v2/Dataset102_TotalSegmentator_public_part2 \
-class_map_part_vertebrae
+# python convert_dataset_to_nnunet.py \
+# /mnt/nor/wasserthalj_data/TotalSegmentator/zenodo_upload/Totalsegmentator_dataset \
+# /mnt/nor/nnunet/raw_v2/Dataset102_TotalSegmentator_public_part2 \
+# class_map_part_vertebrae
 
-python convert_dataset_to_nnunet.py \
-/mnt/nor/wasserthalj_data/TotalSegmentator/zenodo_upload/Totalsegmentator_dataset \
-/mnt/nor/nnunet/raw_v2/Dataset103_TotalSegmentator_public_part3 \
-class_map_part_cardiac
+# python convert_dataset_to_nnunet.py \
+# /mnt/nor/wasserthalj_data/TotalSegmentator/zenodo_upload/Totalsegmentator_dataset \
+# /mnt/nor/nnunet/raw_v2/Dataset103_TotalSegmentator_public_part3 \
+# class_map_part_cardiac
 
-python convert_dataset_to_nnunet.py \
-/mnt/nor/wasserthalj_data/TotalSegmentator/zenodo_upload/Totalsegmentator_dataset \
-/mnt/nor/nnunet/raw_v2/Dataset104_TotalSegmentator_public_part4 \
-class_map_part_muscles
+# python convert_dataset_to_nnunet.py \
+# /mnt/nor/wasserthalj_data/TotalSegmentator/zenodo_upload/Totalsegmentator_dataset \
+# /mnt/nor/nnunet/raw_v2/Dataset104_TotalSegmentator_public_part4 \
+# class_map_part_muscles
 
-python convert_dataset_to_nnunet.py \
-/mnt/nor/wasserthalj_data/TotalSegmentator/zenodo_upload/Totalsegmentator_dataset \
-/mnt/nor/nnunet/raw_v2/Dataset105_TotalSegmentator_public_part5 \
-class_map_part_ribs
+# python convert_dataset_to_nnunet.py \
+# /mnt/nor/wasserthalj_data/TotalSegmentator/zenodo_upload/Totalsegmentator_dataset \
+# /mnt/nor/nnunet/raw_v2/Dataset105_TotalSegmentator_public_part5 \
+# class_map_part_ribs
 
 
-############ Train model ############
+# ############ Train model ############
 
-nnUNetv2_train 101 3d_fullres 0 -tr nnUNetTrainerNoMirroring
-nnUNetv2_train 102 3d_fullres 0 -tr nnUNetTrainerNoMirroring
-nnUNetv2_train 103 3d_fullres 0 -tr nnUNetTrainerNoMirroring
-nnUNetv2_train 104 3d_fullres 0 -tr nnUNetTrainerNoMirroring
-nnUNetv2_train 105 3d_fullres 0 -tr nnUNetTrainerNoMirroring
+# nnUNetv2_train 101 3d_fullres 0 -tr nnUNetTrainerNoMirroring
+# nnUNetv2_train 102 3d_fullres 0 -tr nnUNetTrainerNoMirroring
+# nnUNetv2_train 103 3d_fullres 0 -tr nnUNetTrainerNoMirroring
+# nnUNetv2_train 104 3d_fullres 0 -tr nnUNetTrainerNoMirroring
+# nnUNetv2_train 105 3d_fullres 0 -tr nnUNetTrainerNoMirroring
 
 
-############ Predict test set ############
+# ############ Predict test set ############
 
-cd /mnt/nor/nnunet/raw_v2/Dataset101_TotalSegmentator_public_part1
-nnUNetv2_predict -i imagesTs -o labelsTs_predicted -d 101 -c 3d_fullres -tr nnUNetTrainerNoMirroring --disable_tta -f 0
+# cd /mnt/nor/nnunet/raw_v2/Dataset101_TotalSegmentator_public_part1
+# nnUNetv2_predict -i imagesTs -o labelsTs_predicted -d 101 -c 3d_fullres -tr nnUNetTrainerNoMirroring --disable_tta -f 0
 
-cd /mnt/nor/nnunet/raw_v2/Dataset102_TotalSegmentator_public_part2
-nnUNetv2_predict -i imagesTs -o labelsTs_predicted -d 102 -c 3d_fullres -tr nnUNetTrainerNoMirroring --disable_tta -f 0
+# cd /mnt/nor/nnunet/raw_v2/Dataset102_TotalSegmentator_public_part2
+# nnUNetv2_predict -i imagesTs -o labelsTs_predicted -d 102 -c 3d_fullres -tr nnUNetTrainerNoMirroring --disable_tta -f 0
 
 cd /mnt/nor/nnunet/raw_v2/Dataset103_TotalSegmentator_public_part3
 nnUNetv2_predict -i imagesTs -o labelsTs_predicted -d 103 -c 3d_fullres -tr nnUNetTrainerNoMirroring --disable_tta -f 0