Installation

Local Installation

Clone the UNAGI repository and open it

git clone https://github.com/Karlxy0511/IPF_Dashboard.git
cd IPF_Dashboard

Optimially, set up a virtual enviroment to avoid package version conflicts between different projects on your machine. In this case, we call it env:
1. For mac:
```
 python3 -m venv env
 source env/bin/activate
```
2. For windows:
```
 python -m venv env
 env\Scripts\activate
```
Make sure the base interpreter is set to Python3.9. Install the correct version of the necessary packages. Windows users should replace ‘pip3’ with ‘pip’:
```
pip3 install -r requirements.txt
```
Place the h5ad database on the same level with the \assets directory.
Run setup.sh
```
chmod u+x setup/setup.sh
./setup/setup.sh dataset_06_22_22.h5ad
```
If you are unable to run setup.sh on your machine, please do the following:
- Create a folder in the same directory called stage-dataset by running mkdir stage-dataset; this will be gitignored
- Run the segmentation script (replace ‘python3’ with ‘python’ if you are a windows user)
```
cd setup
python3 segmentation.py --data ../dataset_06_22_22.h5ad --seg stages
cd ..
```
Run UNAGI. UNAGI.py requires arguments for both the dataset and iDrem paths. For our current iteration it is (replace ‘python3’ with ‘python’ if you are a windows user) :
```
python3 UNAGI.py --data dataset_06_22_22.h5ad --idrem assets/idrem
```
Wait for about 3 minutes till a text message shows on your terminal. You can now visit UNAGI at localhost:8050/unagi on your web browser.

Usage

In order to successfully run the file you need the \assets directory as well as the h5ad database in the same folder as the file. Add all extrenous .css files to assets.