adapt to BundleWorkflow interface

README.md

@@ -74,17 +74,17 @@ 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 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 on resampled LUNA16 images by setting `"whether_raw_luna16": false` in `inference.json`:
 ```
-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
 ```
 With the same command, we can execute inference on original LUNA16 images by setting `"whether_raw_luna16": true` in `inference.json`. Remember to also set `"data_list_file_path": "$@bundle_root + '/LUNA16_datasplit/mhd_original/dataset_fold0.json'"` and change `"dataset_dir"`.
 

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()"
     ]
 }

configs/inference.json

@@ -5,7 +5,7 @@
         "$import glob",
         "$import os"
     ],
-    "bundle_root": "./",
+    "bundle_root": ".",
     "ckpt_dir": "$@bundle_root + '/models'",
     "output_dir": "$@bundle_root + '/eval'",
     "data_list_file_path": "$@bundle_root + '/LUNA16_datasplit/dataset_fold0.json'",
@@ -202,8 +202,10 @@
         "val_handlers": "@handlers",
         "amp": "@amp"
     },
-    "evaluating": [
-        "$setattr(torch.backends.cudnn, 'benchmark', True)",
+    "initialize": [
+        "$setattr(torch.backends.cudnn, 'benchmark', True)"
+    ],
+    "run": [
         "[email protected]()"
     ]
 }

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": "0.5.2",
+    "version": "0.5.3",
     "changelog": {
+        "0.5.3": "adapt to BundleWorkflow interface",
         "0.5.2": "black autofix format and add name tag",
         "0.5.1": "modify dataset key name",
         "0.5.0": "use detection inferer",
@@ -16,13 +17,13 @@
         "0.1.1": "add reference for LIDC dataset",
         "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",
-        "torchvision": "0.14.0"
+        "torchvision": "0.14.1"
     },
     "name": "Lung nodule CT detection",
     "task": "CT lung nodule detection",

configs/train.json

@@ -3,7 +3,7 @@
         "$import glob",
         "$import os"
     ],
-    "bundle_root": "./",
+    "bundle_root": ".",
     "ckpt_dir": "$@bundle_root + '/models'",
     "output_dir": "$@bundle_root + '/eval'",
     "data_list_file_path": "$@bundle_root + '/LUNA16_datasplit/dataset_fold0.json'",
@@ -446,10 +446,12 @@
             "amp": "@amp"
         }
     },
-    "training": [
+    "initialize": [
         "os.environ['CUDA_LAUNCH_BLOCKING']=1",
         "$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

@@ -67,17 +67,17 @@ 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 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 on resampled LUNA16 images by setting `"whether_raw_luna16": false` in `inference.json`:
 ```
-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
 ```
 With the same command, we can execute inference on original LUNA16 images by setting `"whether_raw_luna16": true` in `inference.json`. Remember to also set `"data_list_file_path": "$@bundle_root + '/LUNA16_datasplit/mhd_original/dataset_fold0.json'"` and change `"dataset_dir"`.