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294 Update Spleen bundle with new interface #331

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Mar 24, 2023
Merged

294 Update Spleen bundle with new interface #331

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f3d01c3
modify spleen
yiheng-wang-nv Mar 23, 2023
16ec641
fix according to comments
yiheng-wang-nv Mar 24, 2023
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modify spleen
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@yiheng-wang-nv
yiheng-wang-nv committed Mar 23, 2023
commit f3d01c3e7b3868763cb29d9572d945b3e67c7005
6 changes: 4 additions & 2 deletions models/spleen_ct_segmentation/configs/evaluate.json
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Expand Up @@ -72,8 +72,10 @@
"summary_ops": "*"
}
],
"evaluating": [
"$setattr(torch.backends.cudnn, 'benchmark', True)",
"initialize": [
"$setattr(torch.backends.cudnn, 'benchmark', True)"
],
"run": [
"$@validate#evaluator.run()"
]
}
8 changes: 5 additions & 3 deletions models/spleen_ct_segmentation/configs/inference.json
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Expand Up @@ -3,7 +3,7 @@
"$import glob",
"$import os"
],
"bundle_root": "/workspace/data/spleen_ct_segmentation",
"bundle_root": ".",
"output_dir": "$@bundle_root + '/eval'",
"dataset_dir": "/workspace/data/Task09_Spleen",
"datalist": "$list(sorted(glob.glob(@dataset_dir + '/imagesTs/*.nii.gz')))",
Expand Down Expand Up @@ -146,8 +146,10 @@
"val_handlers": "@handlers",
"amp": true
},
"evaluating": [
"$setattr(torch.backends.cudnn, 'benchmark', True)",
"initialize": [
"$setattr(torch.backends.cudnn, 'benchmark', True)"
],
"run": [
"$@evaluator.run()"
]
}
5 changes: 3 additions & 2 deletions models/spleen_ct_segmentation/configs/metadata.json
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@@ -1,7 +1,8 @@
{
"schema": "https://github.com/Project-MONAI/MONAI-extra-test-data/releases/download/0.8.1/meta_schema_20220324.json",
"version": "0.3.8",
"version": "0.3.9",
"changelog": {
"0.3.9": "use new interface",
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"0.3.8": "add name tag",
"0.3.7": "restructure readme to match updated template",
"0.3.6": "enhance readme with details of model training",
Expand All @@ -16,7 +17,7 @@
"0.1.0": "complete the model package",
"0.0.1": "initialize the model package structure"
},
"monai_version": "1.0.1",
"monai_version": "1.2.0rc2",
"pytorch_version": "1.13.0",
"numpy_version": "1.21.2",
"optional_packages_version": {
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10 changes: 7 additions & 3 deletions models/spleen_ct_segmentation/configs/multi_gpu_evaluate.json
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Expand Up @@ -15,14 +15,18 @@
},
"validate#dataloader#sampler": "@validate#sampler",
"validate#handlers#1#_disabled_": "$dist.get_rank() > 0",
"evaluating": [
"initialize": [
"$import torch.distributed as dist",
"$dist.init_process_group(backend='nccl')",
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"$torch.cuda.set_device(@device)",
"$setattr(torch.backends.cudnn, 'benchmark', True)",
"$import logging",
"$@validate#evaluator.logger.setLevel(logging.WARNING if dist.get_rank() > 0 else logging.INFO)",
"$@validate#evaluator.run()",
"$@validate#evaluator.logger.setLevel(logging.WARNING if dist.get_rank() > 0 else logging.INFO)"
],
"run": [
"$@validate#evaluator.run()"
],
"finalize": [
"$dist.destroy_process_group()"
]
}
10 changes: 7 additions & 3 deletions models/spleen_ct_segmentation/configs/multi_gpu_train.json
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Expand Up @@ -24,16 +24,20 @@
},
"validate#dataloader#sampler": "@validate#sampler",
"validate#evaluator#val_handlers": "$None if dist.get_rank() > 0 else @validate#handlers",
"training": [
"initialize": [
"$import torch.distributed as dist",
"$dist.init_process_group(backend='nccl')",
"$torch.cuda.set_device(@device)",
"$monai.utils.set_determinism(seed=123)",
"$setattr(torch.backends.cudnn, 'benchmark', True)",
"$import logging",
"$@train#trainer.logger.setLevel(logging.WARNING if dist.get_rank() > 0 else logging.INFO)",
"$@validate#evaluator.logger.setLevel(logging.WARNING if dist.get_rank() > 0 else logging.INFO)",
"$@train#trainer.run()",
"$@validate#evaluator.logger.setLevel(logging.WARNING if dist.get_rank() > 0 else logging.INFO)"
],
"run": [
"$@train#trainer.run()"
],
"finalize": [
"$dist.destroy_process_group()"
]
}
8 changes: 5 additions & 3 deletions models/spleen_ct_segmentation/configs/train.json
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Expand Up @@ -4,7 +4,7 @@
"$import os",
"$import ignite"
],
"bundle_root": "/workspace/data/spleen_ct_segmentation",
"bundle_root": ".",
"ckpt_dir": "$@bundle_root + '/models'",
"output_dir": "$@bundle_root + '/eval'",
"dataset_dir": "/workspace/data/Task09_Spleen",
Expand Down Expand Up @@ -281,9 +281,11 @@
"amp": true
}
},
"training": [
"initialize": [
"$monai.utils.set_determinism(seed=123)",
"$setattr(torch.backends.cudnn, 'benchmark', True)",
"$setattr(torch.backends.cudnn, 'benchmark', True)"
],
"run": [
"$@train#trainer.run()"
]
}
10 changes: 5 additions & 5 deletions models/spleen_ct_segmentation/docs/README.md
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Expand Up @@ -52,33 +52,33 @@ For more details usage instructions, visit the [MONAI Bundle Configuration Page]
#### Execute training:

```
python -m monai.bundle run training --meta_file configs/metadata.json --config_file configs/train.json --logging_file configs/logging.conf
python -m monai.bundle run --config_file configs/train.json
```

#### Override the `train` config to execute multi-GPU training:

```
torchrun --standalone --nnodes=1 --nproc_per_node=2 -m monai.bundle run training --meta_file configs/metadata.json --config_file "['configs/train.json','configs/multi_gpu_train.json']" --logging_file configs/logging.conf
torchrun --standalone --nnodes=1 --nproc_per_node=2 -m monai.bundle run --config_file "['configs/train.json','configs/multi_gpu_train.json']"
```

Please note that the distributed training-related options depend on the actual running environment; thus, users may need to remove `--standalone`, modify `--nnodes`, or do some other necessary changes according to the machine used. For more details, please refer to [pytorch's official tutorial](https://pytorch.org/tutorials/intermediate/ddp_tutorial.html).

#### Override the `train` config to execute evaluation with the trained model:

```
python -m monai.bundle run evaluating --meta_file configs/metadata.json --config_file "['configs/train.json','configs/evaluate.json']" --logging_file configs/logging.conf
python -m monai.bundle run --config_file "['configs/train.json','configs/evaluate.json']"
```

#### Override the `train` config and `evaluate` config to execute multi-GPU evaluation:

```
torchrun --standalone --nnodes=1 --nproc_per_node=2 -m monai.bundle run evaluating --meta_file configs/metadata.json --config_file "['configs/train.json','configs/evaluate.json','configs/multi_gpu_evaluate.json']" --logging_file configs/logging.conf
torchrun --standalone --nnodes=1 --nproc_per_node=2 -m monai.bundle run --config_file "['configs/train.json','configs/evaluate.json','configs/multi_gpu_evaluate.json']"
```

#### Execute inference:

```
python -m monai.bundle run evaluating --meta_file configs/metadata.json --config_file configs/inference.json --logging_file configs/logging.conf
python -m monai.bundle run --config_file configs/inference.json
```

# References
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