diff --git a/.github/workflows/run_tests_os.yml b/.github/workflows/run_tests_os.yml index 5613f791b..9cca0c0fc 100644 --- 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 index 13a3f1b35..8ee3a8234 100755 --- 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