adapt to BundleWorkflow interface

README.md

@@ -148,13 +148,13 @@ A graph showing the validation F1-score 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.
@@ -163,19 +163,19 @@ 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

@@ -64,12 +64,14 @@
             "summary_ops": "*"
         }
     ],
-    "evaluating": [
+    "initialize": [
         "$import sys",
         "$sys.path.append(@bundle_root)",
         "$setattr(torch.backends.cudnn, 'benchmark', True)",
         "$import scripts",
-        "$monai.data.register_writer('json', scripts.ClassificationWriter)",
+        "$monai.data.register_writer('json', scripts.ClassificationWriter)"
+    ],
+    "run": [
         "$@validate#evaluator.run()"
     ]
 }

configs/inference.json

@@ -5,7 +5,7 @@
         "$import pathlib",
         "$import os"
     ],
-    "bundle_root": "/workspace/data/pathology_nuclei_classification",
+    "bundle_root": ".",
     "output_dir": "$@bundle_root + '/eval'",
     "dataset_dir": "/workspace/data/CoNSePNuclei",
     "images": "$list(sorted(glob.glob(@dataset_dir + '/Test/Images/*.png')))[:1]",
@@ -107,10 +107,12 @@
         "val_handlers": "@handlers",
         "amp": true
     },
-    "evaluating": [
+    "initialize": [
         "$setattr(torch.backends.cudnn, 'benchmark', True)",
         "$import scripts",
-        "$monai.data.register_writer('json', scripts.ClassificationWriter)",
+        "$monai.data.register_writer('json', scripts.ClassificationWriter)"
+    ],
+    "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 nuclei classification",
     "task": "Pathology Nuclei classification",

configs/multi_gpu_evaluate.json

@@ -15,18 +15,22 @@
     },
     "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)",
         "$import scripts",
-        "$monai.data.register_writer('json', scripts.ClassificationWriter)",
-        "$@validate#evaluator.run()",
+        "$monai.data.register_writer('json', scripts.ClassificationWriter)"
+    ],
+    "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_nuclei_classification",
+    "bundle_root": ".",
     "ckpt_dir": "$@bundle_root + '/models'",
     "output_dir": "$@bundle_root + '/eval'",
     "dataset_dir": "/workspace/data/CoNSePNuclei",
@@ -340,11 +340,13 @@
             "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

@@ -141,13 +141,13 @@ A graph showing the validation F1-score 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.
@@ -156,19 +156,19 @@ 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