294 update bundles to use BundleWorkflow interface (#339)

Part of #294 . ### Description This PR updates several bundles with `BundleWorkflow ` interface, and also fix a few errors. Commands in all bundles are tested with `monai==1.2.0rc3` locally with the changes except the following two: ~~1. `wholeBody_ct_segmentation`~~ (checked) ~~2. `pathology_nuclei_segmentation_classification`~~ (checked) ~~because I do not have these two datasets locally.~~ ### Status **Ready** ### Please ensure all the checkboxes:  - [x] Codeformat tests passed locally by running `./runtests.sh --codeformat`. - [ ] In-line docstrings updated. - [ ] Update `version` and `changelog` in `metadata.json` if changing an existing bundle. - [ ] Please ensure the naming rules in config files meet our requirements (please refer to: `CONTRIBUTING.md`). - [ ] Ensure versions of packages such as `monai`, `pytorch` and `numpy` are correct in `metadata.json`. - [ ] Descriptions should be consistent with the content, such as `eval_metrics` of the provided weights and TorchScript modules. - [ ] Files larger than 25MB are excluded and replaced by providing download links in `large_file.yml`. - [ ] Avoid using path that contains personal information within config files (such as use `/home/your_name/` for `"bundle_root"`). --------- Signed-off-by: Yiheng Wang <vennw@nvidia.com> Signed-off-by: tangy5 <yucheng.tang@vanderbilt.edu> Co-authored-by: tangy5 <yucheng.tang@vanderbilt.edu> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Project-MONAI · Apr 4, 2023 · dfc77f2 · dfc77f2
1 parent b75873c
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diff --git a/ci/verify_tensorrt.py b/ci/verify_tensorrt.py
@@ -28,7 +28,7 @@ def verify_tensorrt(bundle_path: str, net_id: str, config_file: str, precision:
         trt_export(
             net_id=net_id,
             filepath=trt_model_path,
-            ckpt_file=os.path.join(bundle_path, "models/models.pt"),
+            ckpt_file=os.path.join(bundle_path, "models/model.pt"),
             meta_file=os.path.join(bundle_path, "configs/metadata.json"),
             config_file=os.path.join(bundle_path, config_file),
             precision=precision,
@@ -63,6 +63,7 @@ def verify_all_tensorrt_bundles(models_path="models"):
             except BaseException:
                 print(f"verify bundle {bundle} with precision {precision} failed.")
                 raise
+    print("all TensorRT supported bundles are verified correctly.")
 
 
 if __name__ == "__main__":

diff --git a/models/brats_mri_segmentation/configs/evaluate.json b/models/brats_mri_segmentation/configs/evaluate.json
@@ -85,8 +85,10 @@
             "summary_ops": "*"
         }
     ],
-    "evaluating": [
-        "$setattr(torch.backends.cudnn, 'benchmark', True)",
+    "initialize": [
+        "$setattr(torch.backends.cudnn, 'benchmark', True)"
+    ],
+    "run": [
         "$@validate#evaluator.run()"
     ]
 }
diff --git a/models/brats_mri_segmentation/configs/inference.json b/models/brats_mri_segmentation/configs/inference.json
@@ -35,7 +35,8 @@
         "transforms": [
             {
                 "_target_": "LoadImaged",
-                "keys": "image"
+                "keys": "image",
+                "image_only": false
             },
             {
                 "_target_": "NormalizeIntensityd",
@@ -129,8 +130,10 @@
         "val_handlers": "@handlers",
         "amp": true
     },
-    "evaluating": [
-        "$setattr(torch.backends.cudnn, 'benchmark', True)",
+    "initialize": [
+        "$setattr(torch.backends.cudnn, 'benchmark', True)"
+    ],
+    "run": [
         "$@evaluator.run()"
     ]
 }
diff --git a/models/brats_mri_segmentation/configs/metadata.json b/models/brats_mri_segmentation/configs/metadata.json
@@ -1,7 +1,8 @@
 {
     "schema": "https://github.com/Project-MONAI/MONAI-extra-test-data/releases/download/0.8.1/meta_schema_20220324.json",
-    "version": "0.3.9",
+    "version": "0.4.0",
     "changelog": {
+        "0.4.0": "adapt to BundleWorkflow interface",
         "0.3.9": "black autofix format and add name tag",
         "0.3.8": "modify dataset key name",
         "0.3.7": "restructure readme to match updated template",
@@ -17,9 +18,9 @@
         "0.1.1": "update for MetaTensor",
         "0.1.0": "complete the model package"
     },
-    "monai_version": "1.0.1",
-    "pytorch_version": "1.13.0",
-    "numpy_version": "1.22.4",
+    "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",

diff --git a/models/brats_mri_segmentation/configs/multi_gpu_train.json b/models/brats_mri_segmentation/configs/multi_gpu_train.json
@@ -24,13 +24,17 @@
     },
     "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",
-        "$dist.init_process_group(backend='nccl')",
+        "$dist.is_initialized() or dist.init_process_group(backend='nccl')",
         "$torch.cuda.set_device(@device)",
         "$monai.utils.set_determinism(seed=123)",
-        "$setattr(torch.backends.cudnn, 'benchmark', True)",
-        "$@train#trainer.run()",
+        "$setattr(torch.backends.cudnn, 'benchmark', True)"
+    ],
+    "run": [
+        "$@train#trainer.run()"
+    ],
+    "finalize": [
         "$dist.destroy_process_group()"
     ]
 }
diff --git a/models/brats_mri_segmentation/configs/train.json b/models/brats_mri_segmentation/configs/train.json
@@ -60,7 +60,8 @@
                 "keys": [
                     "image",
                     "label"
-                ]
+                ],
+                "image_only": false
             },
             {
                 "_target_": "ConvertToMultiChannelBasedOnBratsClassesd",
@@ -318,9 +319,11 @@
             "amp": "@amp"
         }
     },
-    "training": [
+    "initialize": [
         "$monai.utils.set_determinism(seed=123)",
-        "$setattr(torch.backends.cudnn, 'benchmark', True)",
+        "$setattr(torch.backends.cudnn, 'benchmark', True)"
+    ],
+    "run": [
         "$@train#trainer.run()"
     ]
 }
diff --git a/models/brats_mri_segmentation/docs/README.md b/models/brats_mri_segmentation/docs/README.md
@@ -69,24 +69,24 @@ 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=8 -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=8 -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']"
 ```
 
 #### 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

diff --git a/models/endoscopic_inbody_classification/configs/evaluate.json b/models/endoscopic_inbody_classification/configs/evaluate.json
@@ -41,8 +41,10 @@
             "summary_ops": "*"
         }
     ],
-    "evaluating": [
-        "$setattr(torch.backends.cudnn, 'benchmark', True)",
+    "initialize": [
+        "$setattr(torch.backends.cudnn, 'benchmark', True)"
+    ],
+    "run": [
         "$@validate#evaluator.run()"
     ]
 }
diff --git a/models/endoscopic_inbody_classification/configs/inference.json b/models/endoscopic_inbody_classification/configs/inference.json
@@ -4,7 +4,7 @@
         "$import os",
         "$import torch"
     ],
-    "bundle_root": "/workspace/bundle/endoscopic_inbody_classification",
+    "bundle_root": ".",
     "dataset_dir": "/workspace/data/endoscopic_inbody_classification",
     "test_json": "$@bundle_root+'/label/test_samples.json'",
     "test_fp": "$open(@test_json,'r', encoding='utf8')",
@@ -105,8 +105,10 @@
         "postprocessing": "@postprocessing",
         "val_handlers": "@handlers"
     },
-    "evaluating": [
-        "$setattr(torch.backends.cudnn, 'benchmark', True)",
+    "initialize": [
+        "$setattr(torch.backends.cudnn, 'benchmark', True)"
+    ],
+    "run": [
         "$@evaluator.run()"
     ]
 }
diff --git a/models/endoscopic_inbody_classification/configs/metadata.json b/models/endoscopic_inbody_classification/configs/metadata.json
@@ -1,7 +1,8 @@
 {
     "schema": "https://github.com/Project-MONAI/MONAI-extra-test-data/releases/download/0.8.1/meta_schema_20220324.json",
-    "version": "0.3.6",
+    "version": "0.3.7",
     "changelog": {
+        "0.3.7": "adapt to BundleWorkflow interface",
         "0.3.6": "add name tag",
         "0.3.5": "fix a comment issue in the data_process script",
         "0.3.4": "add note for multi-gpu training with example dataset",
@@ -15,9 +16,9 @@
         "0.1.0": "complete the first version model package",
         "0.0.1": "initialize the model package structure"
     },
-    "monai_version": "1.0.1",
-    "pytorch_version": "1.13.0",
-    "numpy_version": "1.22.4",
+    "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"

diff --git a/models/endoscopic_inbody_classification/configs/multi_gpu_train.json b/models/endoscopic_inbody_classification/configs/multi_gpu_train.json
@@ -24,13 +24,17 @@
     },
     "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",
-        "$dist.init_process_group(backend='nccl')",
+        "$dist.is_initialized() or dist.init_process_group(backend='nccl')",
         "$torch.cuda.set_device(@device)",
         "$monai.utils.set_determinism(seed=123)",
-        "$setattr(torch.backends.cudnn, 'benchmark', True)",
-        "$@train#trainer.run()",
+        "$setattr(torch.backends.cudnn, 'benchmark', True)"
+    ],
+    "run": [
+        "$@train#trainer.run()"
+    ],
+    "finalize": [
         "$dist.destroy_process_group()"
     ]
 }
diff --git a/models/endoscopic_inbody_classification/configs/train.json b/models/endoscopic_inbody_classification/configs/train.json
@@ -4,7 +4,7 @@
         "$import json",
         "$import ignite"
     ],
-    "bundle_root": "/workspace/bundle/endoscopic_inbody_classification",
+    "bundle_root": ".",
     "ckpt_dir": "$@bundle_root + '/models'",
     "output_dir": "$@bundle_root + '/eval'",
     "dataset_dir": "/workspace/data/endoscopic_inbody_classification",
@@ -251,9 +251,11 @@
             "val_handlers": "@validate#handlers"
         }
     },
-    "training": [
-        "$monai.utils.set_determinism(seed=0)",
-        "$setattr(torch.backends.cudnn, 'benchmark', True)",
+    "initialize": [
+        "$monai.utils.set_determinism(seed=123)",
+        "$setattr(torch.backends.cudnn, 'benchmark', True)"
+    ],
+    "run": [
         "$@train#trainer.run()"
     ]
 }
diff --git a/models/endoscopic_inbody_classification/docs/README.md b/models/endoscopic_inbody_classification/docs/README.md
@@ -75,19 +75,14 @@ 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).
@@ -97,19 +92,13 @@ In addition, if using the 20 samples example dataset, the preprocessing script w
 #### 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']"
 ```
 
 #### 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
 ```
 The classification result of every images in `test.json` will be printed to the screen.
 

diff --git a/models/endoscopic_tool_segmentation/configs/evaluate.json b/models/endoscopic_tool_segmentation/configs/evaluate.json
@@ -68,8 +68,10 @@
             "summary_ops": "*"
         }
     ],
-    "evaluating": [
-        "$setattr(torch.backends.cudnn, 'benchmark', True)",
+    "initialize": [
+        "$setattr(torch.backends.cudnn, 'benchmark', True)"
+    ],
+    "run": [
         "$@validate#evaluator.run()"
     ]
 }
diff --git a/models/endoscopic_tool_segmentation/configs/inference.json b/models/endoscopic_tool_segmentation/configs/inference.json
@@ -3,7 +3,7 @@
         "$import glob",
         "$import os"
     ],
-    "bundle_root": "/workspace/bundle/endoscopic_tool_segmentation",
+    "bundle_root": ".",
     "output_dir": "$@bundle_root + '/eval'",
     "dataset_dir": "/workspace/data/endoscopic_tool_dataset",
     "datalist": "$list(sorted(glob.glob(os.path.join(@dataset_dir,'test', '*', '*[!seg].jpg'))))",
@@ -130,8 +130,10 @@
         "postprocessing": "@postprocessing",
         "val_handlers": "@handlers"
     },
-    "evaluating": [
-        "$setattr(torch.backends.cudnn, 'benchmark', True)",
+    "initialize": [
+        "$setattr(torch.backends.cudnn, 'benchmark', True)"
+    ],
+    "run": [
         "$@evaluator.run()"
     ]
 }
diff --git a/models/endoscopic_tool_segmentation/configs/metadata.json b/models/endoscopic_tool_segmentation/configs/metadata.json
@@ -1,7 +1,8 @@
 {
     "schema": "https://github.com/Project-MONAI/MONAI-extra-test-data/releases/download/0.8.1/meta_schema_20220324.json",
-    "version": "0.4.3",
+    "version": "0.4.4",
     "changelog": {
+        "0.4.4": "adapt to BundleWorkflow interface",
         "0.4.3": "update this bundle to support TensorRT convert",
         "0.4.2": "support monai 1.2 new FlexibleUNet",
         "0.4.1": "add name tag",
@@ -15,8 +16,8 @@
         "0.0.1": "initialize the model package structure"
     },
     "monai_version": "1.2.0rc3",
-    "pytorch_version": "1.13.0",
-    "numpy_version": "1.22.4",
+    "pytorch_version": "1.13.1",
+    "numpy_version": "1.22.2",
     "optional_packages_version": {
         "nibabel": "4.0.1",
         "pytorch-ignite": "0.4.9"

diff --git a/models/endoscopic_tool_segmentation/configs/multi_gpu_evaluate.json b/models/endoscopic_tool_segmentation/configs/multi_gpu_evaluate.json
@@ -15,14 +15,18 @@
     },
     "validate#dataloader#sampler": "@validate#sampler",
     "validate#handlers#1#_disabled_": "$dist.get_rank() > 0",
-    "evaluating": [
+    "initialize": [
         "$import torch.distributed as dist",
-        "$dist.init_process_group(backend='nccl')",
+        "$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()"
     ]
 }