Added argparse to support setting cwd and disabling public link sharing

README.md

@@ -10,7 +10,7 @@ license: mit
 app_file: app.py
 ---
 
-<div align="center">
+<div align="center">M
 <h1 align="center">neukit</h1>
 <h3 align="center">Automatic brain extraction and preoperative tumor segmentation from MRI</h3>
 
@@ -36,6 +36,8 @@ To access the live demo, click on the `Hugging Face` badge above. Below is a sna
 
 ## Development
 
+### Docker
+
 Alternatively, you can deploy the software locally. Note that this is only relevant for development purposes. Simply dockerize the app and run it:
 
 ```
@@ -45,6 +47,28 @@ docker run -it -p 7860:7860 neukit
 
 Then open `http://127.0.0.1:7860` in your favourite internet browser to view the demo.
 
+### Python
+
+It is also possible to run the app locally without Docker. Just setup a virtual environment and run the app.
+Note that the current working directory would need to be adjusted based on where `neukit` is located on disk.
+
+```
+git clone https://github.com/andreped/neukit.git
+cd neukit/
+
+virtualenv -ppython3 venv --clear
+source venv/bin/activate
+pip install -r requirements.txt
+
+python app.py --cwd ./
+```
+
+## Troubleshooting
+
+Note that due to `share=True` being enabled by default when launching the app,
+internet access is required for the app to be launched. This can disabled by setting
+the argument to `--share 0`.
+
 ## Citation
 
 If you found the tool useful in your research, please, cite the corresponding software paper:

app.py

@@ -1,14 +1,24 @@
 from neukit.gui import WebUI
+from argparse import ArgumentParser
+import os
 
 
 def main():
-    print("Launching demo...")
+    parser = ArgumentParser()
+    parser.add_argument("--cwd", type=str, default="/home/user/app/", help="Set current working directory (path to app.py).")
+    parser.add_argument("--share", type=int, default=1, help="Whether to enable the app to be accessible online -> setups a public link which requires internet access.")
+    args = parser.parse_args()
+
+    print("Current working directory:", args.cwd)
 
-    # cwd = "/Users/andreped/workspace/neukit/"  # local testing -> macOS
-    cwd = "/home/user/app/"  # production -> docker
+    if not os.path.exists(args.cwd):
+        raise ValueError("Chosen 'cwd' is not a valid path!")
+    if not args.share in [0, 1]:
+        raise ValueError("The 'share' argument can only be set to 0 or 1 (boolean), but was:", args.share)
 
     # initialize and run app
-    app = WebUI(cwd=cwd)
+    print("Launching demo...")
+    app = WebUI(cwd=args.cwd, share=args.share)
     app.run()
 
 

neukit/gui.py

@@ -1,4 +1,5 @@
 import gradio as gr
+import os
 
 from .inference import run_model
 from .utils import load_ct_to_numpy
@@ -7,7 +8,7 @@ from .utils import nifti_to_glb
 
 
 class WebUI:
-    def __init__(self, model_name: str = None, cwd: str = "/home/user/app/"):
+    def __init__(self, model_name: str = None, cwd: str = "/home/user/app/", share: int = 1):
         # global states
         self.images = []
         self.pred_images = []
@@ -17,6 +18,7 @@ class WebUI:
 
         self.model_name = model_name
         self.cwd = cwd
+        self.share = share
 
         self.class_name = "meningioma"  # default
         self.class_names = {
@@ -64,7 +66,7 @@ class WebUI:
         path = mesh_file_name.name
         run_model(
             path,
-            model_path=self.cwd + "resources/models/",
+            model_path=os.path.join(self.cwd, "resources/models/"),
             task=self.class_names[self.class_name],
             name=self.result_names[self.class_name],
         )
@@ -127,8 +129,8 @@ class WebUI:
             with gr.Row():
                 gr.Examples(
                     examples=[
-                        self.cwd + "RegLib_C01_1.nii",
-                        self.cwd + "RegLib_C01_2.nii",
+                        os.path.join(self.cwd, "RegLib_C01_1.nii"),
+                        os.path.join(self.cwd, "RegLib_C01_2.nii"),
                     ],
                     inputs=file_output,
                     outputs=file_output,
@@ -164,4 +166,4 @@ class WebUI:
         # https://gradio.app/sharing-your-app/
         # inference times > 60 seconds -> need queue():
         # https://github.com/tloen/alpaca-lora/issues/60#issuecomment-1510006062
-        demo.queue().launch(server_name="0.0.0.0", server_port=7860, share=True)
+        demo.queue().launch(server_name="0.0.0.0", server_port=7860, share=self.share)