update doc

README.md

@@ -47,6 +47,8 @@ size_categories:
 
 # Datasets
 
+[File structure](https://huggingface.co/datasets/YongchengYAO/MedVision/blob/main/doc/file-structure.md): raw data  will be automatically downloaded and processed, and our annotations are in each dataset folder
+
 📝 The MedVision dataset consists of public medical images and
       quantitative annotations from this study. MRI: Magnetic Resonance Imaging;
       CT: Computed Tomography; PET: positron emission tomography; US: Ultrasound;
@@ -145,7 +147,7 @@ export MedVision_FORCE_INSTALL_CODE="False"
 
 The dataset codebase `medvision_ds` can be used to scale the dataset, including adding new annotation types and datasets.
 
-🛠️ **Install** 
+## 🛠️ **Install** 
 
 ```bash
 pip install "git+https://huggingface.co/datasets/YongchengYAO/MedVision.git#subdirectory=src"
@@ -164,7 +166,7 @@ pip install huggingface_hub
 python -c "from medvision_bm.utils import install_medvision_ds; install_medvision_ds(data_dir='<local-data-folder>')"
 ```
 
-🧑🏻‍💻 Use [utility functions](https://huggingface.co/datasets/YongchengYAO/MedVision/tree/main/src/medvision_ds/utils) for image processing
+## 🧑🏻‍💻 Use [utility functions](https://huggingface.co/datasets/YongchengYAO/MedVision/tree/main/src/medvision_ds/utils) for image processing
 
 ```python
 from medvision_ds.utils.data_conversion import (
@@ -181,7 +183,7 @@ from medvision_ds.utils.preprocess_utils import (
 ) 
 ```
 
-👩🏼‍💻Examples of dataset scaling:
+## 👩🏼‍💻Examples of dataset scaling:
 
 - Setup automatic data processing pipeline 
 

doc/file-structure.md

@@ -2,14 +2,11 @@
 
 ```
 ├── Data                                          # <== MedVision_DATA_DIR
-  ├── .cache                                      # <== huggingface, vllm cache
   ├── Datasets                                    # <== preprocessed data
     ├── AbdomenAtlas1.0Mini
       ├── Images
-        ├── tmp_prepared_png                # <== PNG files (if save_processed_img_to_disk=true)
-        ├── *.nii.gz                        # <== 3D medical images
       ├── Masks
-      ├── benchmark_plan_*.json.gz            # <== Our annotations
+      ├── benchmark_plan_*.json.gz            		# <== Our annotations
     ├── AbdomenCT-1K
       ├── Images
       ├── Masks
@@ -212,7 +209,6 @@
         ├── Masks
       ├── benchmark_plan_*.json.gz
   ├── src                                         # <== source code for medvision_ds
-  ├── tmp_*                                       # <== tmp folder for combined/filtered/formatted datasets
   ├── .downloaded_datasets.json                   # <== dataset status tracker
 ```