Add files for gradio space

README.md

@@ -1,8 +1,8 @@
 ---
 title: Spleen Segmentation
-emoji: 💻
-colorFrom: gray
-colorTo: gray
+emoji: 👀
+colorFrom: indigo
+colorTo: red
 sdk: gradio
 sdk_version: 3.1.1
 app_file: app.py

app.py

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+import os
+import gradio as gr
+import torch
+from monai import bundle
+
+BUNDLE_NAME = 'spleen_ct_segmentation_v0.1.0'
+BUNDLE_PATH = os.path.join(torch.hub.get_dir(), 'bundle', BUNDLE_NAME)
+
+examples = ['examples/spleen_46.nii.gz']
+
+model, _, _ = bundle.load(
+    name = BUNDLE_NAME,
+    source = 'hf_hub',
+    repo = 'katielink/spleen_ct_segmentation_v0.1.0',
+    load_ts_module=True,
+)
+
+device = "cuda:0" if torch.cuda.is_available() else "cpu"
+
+parser = bundle.load_bundle_config(BUNDLE_PATH, 'inference.json')
+preproc_transforms = parser.get_parsed_content('preprocessing', lazy=True, eval_expr=True, instantiate=True)
+inferer = parser.get_parsed_content('inferer', lazy=True, eval_expr=True, instantiate=True)
+
+def predict(input_file, z_axis, model=model, device=device):
+    data = {'image': [input_file.name]}
+    data = preproc_transforms(data)
+    
+    model.to(device)
+    model.eval()
+    with torch.no_grad():
+        inputs = data['image'].to(device)[None,...]
+        data['pred'] = inferer(inputs=inputs, network=model)
+    
+    input_image = data['image'].numpy()
+    pred_image = torch.argmax(data['pred'], dim=1).cpu().detach().numpy()
+    
+    return input_image[0, :, :, z_axis], pred_image[0, :, :, z_axis]*255
+
+iface = gr.Interface(
+    fn=predict,
+    inputs=[
+        gr.File(label='Nifti file'),
+        gr.Slider(0, 200, label='z-axis', value=50)
+    ], 
+    outputs=['image', 'image'],
+    title='Segment the Spleen from a CT Scan using MONAI',
+    examples=examples,
+)
+
+iface.launch()

examples/spleen_46.nii.gz

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:1dc87026596e782c25de81ab171cd2b456a8e2c76e304949e9318451406c8edf
+size 28610147

requirements.txt

@@ -0,0 +1,2 @@
+git+https://github.com/katielink/MONAI.git@4042-download-hf-hub-bundle
+huggingface_hub