Update bundle and acceleration tutorials (#921)

* [DLMED] update bundle path

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] update download command

Signed-off-by: Nic Ma <nma@nvidia.com>

Signed-off-by: Nic Ma <nma@nvidia.com>

Author: Nic-Ma

bundle/get_started.ipynb

@@ -27,7 +27,7 @@
     "- Override config content at runtime.\n",
     "- Hybrid programming with config and python code.\n",
     "\n",
-    "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Project-MONAI/tutorials/blob/main/modules/bundle/get_started.ipynb)"
+    "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Project-MONAI/tutorials/blob/main/bundle/get_started.ipynb)"
    ]
   },
   {
@@ -468,7 +468,7 @@
     "Usually we need to execute validation for every N epochs during training to verify the model and save the best model.\n",
     "\n",
     "Here we don't define the `validate` section step by step as it's similar to the `train` section. The full config is available:  \n",
-    "https://github.com/Project-MONAI/tutorials/blob/main/modules/bundle/spleen_segmentation/configs/train.json\n",
+    "https://github.com/Project-MONAI/tutorials/blob/main/bundle/spleen_segmentation/configs/train.json\n",
     "\n",
     "Just show an example of `macro text replacement` to simplify the config content and avoid duplicated text. Please note that it's just token text replacement of the config content, not refer to the instantiated python objects."
    ]
@@ -503,7 +503,7 @@
     "We can define a `metadata` file in the bundle, which contains the metadata information relating to the model, including what the shape and format of inputs and outputs are, what the meaning of the outputs are, what type of model is present, and other information. The structure is a dictionary containing a defined set of keys with additional user-specified keys.\n",
     "\n",
     "A typical `metadata` example is available:  \n",
-    "https://github.com/Project-MONAI/tutorials/blob/main/modules/bundle/spleen_segmentation/configs/metadata.json"
+    "https://github.com/Project-MONAI/tutorials/blob/main/bundle/spleen_segmentation/configs/metadata.json"
    ]
   },
   {
@@ -591,7 +591,7 @@
     "\n",
     "5. Download a bundle from Github release or URL.\n",
     "```shell\n",
-    "python -m monai.bundle download --name <bundle_name>\n",
+    "python -m monai.bundle download --name <bundle_name> --version \"0.1.0\" --bundle_dir \"./\"\n",
     "```"
    ]
   },

bundle/hybrid_programming/scripts/inference.py

@@ -23,7 +23,7 @@ def run(config_file: Union[str, Sequence[str]], ckpt_path: str):
     # edit the config content at runtime for input / output information and lazy instantiation
     datalist = list(sorted(glob.glob("/workspace/data/Task09_Spleen/imagesTs/*.nii.gz")))
     input_data = [{f"{parser['image_key']}": i} for i in datalist]
-    output_dir = "/workspace/data/tutorials/modules/bundle/hybrid_programming/eval"
+    output_dir = "/workspace/data/tutorials/bundle/hybrid_programming/eval"
     parser["input_data"] = input_data
     parser["output_dir"] = output_dir
     parser["inferer"]["roi_size"] = [160, 160, 160]

bundle/spleen_segmentation/configs/inference.json

@@ -3,7 +3,7 @@
         "$import glob",
         "$import os"
     ],
-    "bundle_root": "/workspace/data/tutorials/modules/bundle/spleen_segmentation",
+    "bundle_root": "/workspace/data/tutorials/bundle/spleen_segmentation",
     "output_dir": "$@bundle_root + '/eval'",
     "dataset_dir": "/workspace/data/Task09_Spleen",
     "datalist": "$list(sorted(glob.glob(@dataset_dir + '/imagesTs/*.nii.gz')))",

bundle/spleen_segmentation/configs/train.json

@@ -4,7 +4,7 @@
         "$import os",
         "$import ignite"
     ],
-    "bundle_root": "/workspace/data/tutorials/modules/bundle/spleen_segmentation",
+    "bundle_root": "/workspace/data/tutorials/bundle/spleen_segmentation",
     "ckpt_dir": "$@bundle_root + '/models'",
     "output_dir": "$@bundle_root + '/eval'",
     "dataset_dir": "/workspace/data/Task09_Spleen",

model_zoo/adapt_bundle_to_another_dataset/README.md

@@ -33,7 +33,7 @@ Actual Model Input: 96 x 96 x 96
 ## Modify ./spleen_ct_segmentation/configs/train.json from the downloaded example
 | Old json config | Updated json config |
 | --- | --- |
-| "bundle_root": "/workspace/data/tutorials/modules/bundle/spleen_segmentation", | "bundle_root": "./spleen_ct_segmentation", |
+| "bundle_root": "/workspace/data/tutorials/bundle/spleen_segmentation", | "bundle_root": "./spleen_ct_segmentation", |
 | "dataset_dir": "/workspace/data/Task09_Spleen",| "data_file_base_dir": "./data/btcv_spleen", |
 | "images": "$list(sorted(glob.glob(@dataset_dir + '/imagesTr/*.nii.gz')))",| "data_list_file_path": "./data/dataset_0.json", |
 | "labels": "$list(sorted(glob.glob(@dataset_dir + '/labelsTr/*.nii.gz')))",| "train_datalist": "$monai.data.load_decathlon_datalist(@data_list_file_path, is_segmentation=True, data_list_key='training', base_dir=@data_file_base_dir)", |