adapt to BundleWorkflow interface

README.md

@@ -127,13 +127,13 @@ A graph showing the validation mean Dice over 50 epochs.
 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 you may need to remove `--standalone`, modify `--nnodes` or do some other necessary changes according to the machine you used.
@@ -142,19 +142,19 @@ Please refer to [pytorch's official tutorial](https://pytorch.org/tutorials/inte
 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
 ```
 
 # Disclaimer

configs/evaluate.json

@@ -49,10 +49,12 @@
  "summary_ops": "*"
  }
  ],
- "evaluating": [
+ "initialize": [
  "$import sys",
  "$sys.path.append(@bundle_root)",
- "$setattr(torch.backends.cudnn, 'benchmark', True)",
+ "$setattr(torch.backends.cudnn, 'benchmark', True)"
+ ],
+ "run": [
  "$@validate#evaluator.run()"
  ]
 }

configs/inference.json

@@ -5,7 +5,7 @@
  "$import pathlib",
  "$import os"
  ],
- "bundle_root": "/workspace/data/pathology_nuclick_annotation",
+ "bundle_root": ".",
  "output_dir": "$@bundle_root + '/eval'",
  "dataset_dir": "/workspace/data/CoNSePNuclei",
  "images": "$list(sorted(glob.glob(@dataset_dir + '/Test/Images/*.png')))[:1]",
@@ -123,8 +123,10 @@
  "val_handlers": "@handlers",
  "amp": true
  },
- "evaluating": [
- "$setattr(torch.backends.cudnn, 'benchmark', True)",
+ "initialize": [
+ "$setattr(torch.backends.cudnn, 'benchmark', True)"
+ ],
+ "run": [
  "[email protected]()"
  ]
 }

configs/metadata.json

@@ -1,19 +1,21 @@
 {
  "schema": "https://github.com/Project-MONAI/MONAI-extra-test-data/releases/download/0.8.1/meta_schema_20220324.json",
- "version": "0.0.5",
+ "version": "0.0.6",
  "changelog": {
+ "0.0.6": "adapt to BundleWorkflow interface",
  "0.0.5": "add name tag",
  "0.0.4": "Fix evaluation",
  "0.0.3": "Update to use MONAI 1.1.0",
  "0.0.2": "Update The Torch Vision Transform",
  "0.0.1": "initialize the model package structure"
  },
- "monai_version": "1.1.0",
- "pytorch_version": "1.13.0",
- "numpy_version": "1.21.2",
+ "monai_version": "1.2.0rc3",
+ "pytorch_version": "1.13.1",
+ "numpy_version": "1.22.2",
  "optional_packages_version": {
  "nibabel": "4.0.1",
- "pytorch-ignite": "0.4.9"
+ "pytorch-ignite": "0.4.9",
+ "torchvision": "0.14.1"
  },
  "name": "Pathology nuclick annotation",
  "task": "Pathology Nuclick annotation",

configs/multi_gpu_evaluate.json

@@ -15,16 +15,20 @@
  },
  "validate#dataloader#sampler": "@validate#sampler",
  "validate#handlers#1#_disabled_": "$dist.get_rank() > 0",
- "evaluating": [
+ "initialize": [
  "$import sys",
  "$sys.path.append(@bundle_root)",
  "$import torch.distributed as dist",
- "$dist.init_process_group(backend='nccl')",
+ "$dist.is_initialized() or dist.init_process_group(backend='nccl')",
  "$torch.cuda.set_device(@device)",
  "$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()"
  ]
 }

configs/multi_gpu_train.json

@@ -24,18 +24,22 @@
  },
  "validate#dataloader#sampler": "@validate#sampler",
  "validate#evaluator#val_handlers": "$None if dist.get_rank() > 0 else @validate#handlers",
- "training": [
+ "initialize": [
  "$import sys",
  "$sys.path.append(@bundle_root)",
  "$import torch.distributed as dist",
- "$dist.init_process_group(backend='nccl')",
+ "$dist.is_initialized() or 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()"
  ]
 }

configs/train.json

@@ -6,7 +6,7 @@
  "$import pathlib",
  "$import os"
  ],
- "bundle_root": "/workspace/data/pathology_nuclick_annotation",
+ "bundle_root": ".",
  "ckpt_dir": "$@bundle_root + '/models'",
  "output_dir": "$@bundle_root + '/eval'",
  "dataset_dir": "/workspace/data/CoNSePNuclei",
@@ -318,11 +318,13 @@
  "amp": true
  }
  },
- "training": [
+ "initialize": [
  "$import sys",
  "$sys.path.append(@bundle_root)",
  "$monai.utils.set_determinism(seed=123)",
- "$setattr(torch.backends.cudnn, 'benchmark', True)",
+ "$setattr(torch.backends.cudnn, 'benchmark', True)"
+ ],
+ "run": [
  "$@train#trainer.run()"
  ]
 }

docs/README.md

@@ -120,13 +120,13 @@ A graph showing the validation mean Dice over 50 epochs.
 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 you may need to remove `--standalone`, modify `--nnodes` or do some other necessary changes according to the machine you used.
@@ -135,19 +135,19 @@ Please refer to [pytorch's official tutorial](https://pytorch.org/tutorials/inte
 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
 ```
 
 # Disclaimer