modify dataset key name

README.md

@@ -86,7 +86,7 @@ python -m monai.bundle run evaluating --meta_file configs/metadata.json --config
 ```
 python -m monai.bundle run evaluating --meta_file configs/metadata.json --config_file configs/inference.json --logging_file configs/logging.conf
 ```
-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": "$@bundle_root + '/LUNA16_datasplit/mhd_original/dataset_fold0.json'"` and change `"data_file_base_dir"`.
+With the same command, we can execute inference on original LUNA16 images by setting `"whether_raw_luna16": true` in `inference.json`. Remember to also set `"data_list_file_path": "$@bundle_root + '/LUNA16_datasplit/mhd_original/dataset_fold0.json'"` and change `"dataset_dir"`.
 
 Note that in inference.json, the transform "LoadImaged" in "preprocessing" and "AffineBoxToWorldCoordinated" in "postprocessing" has `"affine_lps_to_ras": true`.
 This depends on the input images. LUNA16 needs `"affine_lps_to_ras": true`.

configs/evaluate.json

@@ -1,5 +1,5 @@
 {
-    "test_datalist": "$monai.data.load_decathlon_datalist(@data_list_file_path, is_segmentation=True, data_list_key='validation', base_dir=@data_file_base_dir)",
+    "test_datalist": "$monai.data.load_decathlon_datalist(@data_list_file_path, is_segmentation=True, data_list_key='validation', base_dir=@dataset_dir)",
     "validate#dataset": {
         "_target_": "Dataset",
         "data": "$@test_datalist",

configs/inference.json

@@ -9,8 +9,8 @@
     "ckpt_dir": "$@bundle_root + '/models'",
     "output_dir": "$@bundle_root + '/eval'",
     "data_list_file_path": "$@bundle_root + '/LUNA16_datasplit/dataset_fold0.json'",
-    "data_file_base_dir": "/datasets/LUNA16_Images_resample",
-    "test_datalist": "$monai.data.load_decathlon_datalist(@data_list_file_path, is_segmentation=True, data_list_key='validation', base_dir=@data_file_base_dir)",
+    "dataset_dir": "/datasets/LUNA16_Images_resample",
+    "test_datalist": "$monai.data.load_decathlon_datalist(@data_list_file_path, is_segmentation=True, data_list_key='validation', base_dir=@dataset_dir)",
     "device": "$torch.device('cuda:0' if torch.cuda.is_available() else 'cpu')",
     "amp": true,
     "infer_patch_size": [

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": "0.5.0",
+    "version": "0.5.1",
     "changelog": {
+        "0.5.1": "modify dataset key name",
         "0.5.0": "use detection inferer",
         "0.4.5": "fixed some small changes with formatting in readme",
         "0.4.4": "add data resource to readme",

configs/train.json

@@ -7,8 +7,8 @@
     "ckpt_dir": "$@bundle_root + '/models'",
     "output_dir": "$@bundle_root + '/eval'",
     "data_list_file_path": "$@bundle_root + '/LUNA16_datasplit/dataset_fold0.json'",
-    "data_file_base_dir": "/datasets/LUNA16_Images_resample",
-    "train_datalist": "$monai.data.load_decathlon_datalist(@data_list_file_path, is_segmentation=True, data_list_key='training', base_dir=@data_file_base_dir)",
+    "dataset_dir": "/datasets/LUNA16_Images_resample",
+    "train_datalist": "$monai.data.load_decathlon_datalist(@data_list_file_path, is_segmentation=True, data_list_key='training', base_dir=@dataset_dir)",
     "device": "$torch.device('cuda:0' if torch.cuda.is_available() else 'cpu')",
     "epochs": 300,
     "val_interval": 10,

docs/README.md

@@ -79,7 +79,7 @@ python -m monai.bundle run evaluating --meta_file configs/metadata.json --config
 ```
 python -m monai.bundle run evaluating --meta_file configs/metadata.json --config_file configs/inference.json --logging_file configs/logging.conf
 ```
-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": "$@bundle_root + '/LUNA16_datasplit/mhd_original/dataset_fold0.json'"` and change `"data_file_base_dir"`.
+With the same command, we can execute inference on original LUNA16 images by setting `"whether_raw_luna16": true` in `inference.json`. Remember to also set `"data_list_file_path": "$@bundle_root + '/LUNA16_datasplit/mhd_original/dataset_fold0.json'"` and change `"dataset_dir"`.
 
 Note that in inference.json, the transform "LoadImaged" in "preprocessing" and "AffineBoxToWorldCoordinated" in "postprocessing" has `"affine_lps_to_ras": true`.
 This depends on the input images. LUNA16 needs `"affine_lps_to_ras": true`.