diff --git a/.gitignore b/.gitignore
index b6e4761..34a7449 100644
--- a/.gitignore
+++ b/.gitignore
@@ -117,6 +117,9 @@ venv.bak/
# Rope project settings
.ropeproject
+# VS Code project settings
+.vscode
+
# mkdocs documentation
/site
@@ -127,3 +130,5 @@ dmypy.json
# Pyre type checker
.pyre/
+
+IDRiD_data
diff --git a/README.md b/README.md
index 606dfe1..d558a19 100644
--- a/README.md
+++ b/README.md
@@ -19,21 +19,17 @@ Keras version implemented by Yuka Kihara can be found [here](https://github.com/
- A [visualisation demo](https://github.com/rmaphoh/RETFound_MAE/blob/main/RETFound_visualize.ipynb) is added
-### Install enviroment
+### Install environment
-Create enviroment with conda:
+1. Create environment with conda:
```
conda create -n retfound python=3.7.5 -y
conda activate retfound
```
-Install Pytorch 1.81 (cuda 11.1)
-```
-pip install torch==1.8.1+cu111 torchvision==0.9.1+cu111 torchaudio==0.8.1 -f https://download.pytorch.org/whl/torch_stable.html
-```
+2. Install dependencies
-Install others
```
git clone https://github.com/rmaphoh/RETFound_MAE/
cd RETFound_MAE
@@ -43,7 +39,9 @@ pip install -r requirement.txt
### Fine-tuning with RETFound weights
-- RETFound pre-trained weights
+To fine tune RETFound on your own data, follow these steps:
+
+1. Download the RETFound pre-trained weights
@@ -59,14 +57,14 @@ pip install -r requirement.txt
-- Organise data (using IDRiD as an [example](Example.ipynb))
+2. Organise your data into this directory structure (using IDRiD as an [example](Example.ipynb))
-- Start fine-tuning (use IDRiD as example). A fine-tuned checkpoint will be saved during training. Evaluation will be run after training.
+3. Start fine-tuning (use IDRiD as example). A fine-tuned checkpoint will be saved during training. Evaluation will be run after training.
```
@@ -85,7 +83,7 @@ python -m torch.distributed.launch --nproc_per_node=1 --master_port=48798 main_f
```
-- For evaluation only
+4. For evaluation only
```
@@ -106,7 +104,7 @@ python -m torch.distributed.launch --nproc_per_node=1 --master_port=48798 main_f
### Load the model and weights (if you want to call the model in your code)
-```
+```python
import torch
import models_vit
from util.pos_embed import interpolate_pos_embed
diff --git a/requirement.txt b/requirement.txt
index ab1ceed..375d3c6 100644
--- a/requirement.txt
+++ b/requirement.txt
@@ -1,3 +1,7 @@
+--find-links https://download.pytorch.org/whl/torch_stable.html
+torch==1.8.1+cu111
+torchvision==0.9.1+cu111
+torchaudio==0.8.1
opencv-python==4.5.3.56
pandas==0.25.3
Pillow==8.3.1
@@ -12,4 +16,3 @@ tensorboard-data-server==0.6.1
tensorboard-plugin-wit==1.8.0
timm==0.3.2
tqdm==4.62.1
-