Spaces:
Running
Running
Upload 2 files
Browse files- app.py +92 -0
- requirements.txt +6 -0
app.py
ADDED
@@ -0,0 +1,92 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
1 |
+
import torch
|
2 |
+
from transformers import ViTForImageClassification, ViTFeatureExtractor
|
3 |
+
from PIL import Image
|
4 |
+
import gradio as gr
|
5 |
+
import numpy as np
|
6 |
+
import matplotlib.pyplot as plt
|
7 |
+
|
8 |
+
# Load the pretrained Vision Transformer model and feature extractor
|
9 |
+
model_name = "google/vit-base-patch16-224"
|
10 |
+
model = ViTForImageClassification.from_pretrained(model_name)
|
11 |
+
feature_extractor = ViTFeatureExtractor.from_pretrained(model_name)
|
12 |
+
model.eval()
|
13 |
+
|
14 |
+
# Function to apply Grad-CAM visualization
|
15 |
+
def generate_grad_cam(image, target_layer):
|
16 |
+
# Preprocess the image
|
17 |
+
inputs = feature_extractor(images=image, return_tensors="pt")
|
18 |
+
input_tensor = inputs['pixel_values']
|
19 |
+
|
20 |
+
# Forward pass to get logits
|
21 |
+
input_tensor.requires_grad = True
|
22 |
+
outputs = model(input_tensor)
|
23 |
+
|
24 |
+
# Get the target score
|
25 |
+
score = outputs.logits[0].max()
|
26 |
+
|
27 |
+
# Backpropagate to get gradients
|
28 |
+
model.zero_grad()
|
29 |
+
score.backward()
|
30 |
+
|
31 |
+
# Get the gradients and activations from the target layer
|
32 |
+
gradients = model.get_input_embeddings().weight.grad
|
33 |
+
activations = model.get_input_embeddings().weight.data
|
34 |
+
|
35 |
+
# Calculate Grad-CAM
|
36 |
+
pooled_gradients = torch.mean(gradients, dim=[0, 2, 3])
|
37 |
+
for i in range(activations.size(1)):
|
38 |
+
activations[:, i, :, :] *= pooled_gradients[i]
|
39 |
+
|
40 |
+
heatmap = torch.mean(activations, dim=1).squeeze()
|
41 |
+
heatmap = np.maximum(heatmap.detach().numpy(), 0)
|
42 |
+
heatmap = heatmap / np.max(heatmap)
|
43 |
+
|
44 |
+
return heatmap
|
45 |
+
|
46 |
+
# Prediction and Grad-CAM function
|
47 |
+
def predict_and_explain(image):
|
48 |
+
# Predict the class
|
49 |
+
inputs = feature_extractor(images=image, return_tensors="pt")
|
50 |
+
with torch.no_grad():
|
51 |
+
outputs = model(**inputs)
|
52 |
+
|
53 |
+
logits = outputs.logits
|
54 |
+
predicted_class_idx = logits.argmax(-1).item()
|
55 |
+
|
56 |
+
# Predefined medical conditions (adjust based on your dataset)
|
57 |
+
labels = ["Class 1 - Normal", "Class 2 - Condition A", "Class 3 - Condition B"]
|
58 |
+
predicted_label = labels[predicted_class_idx]
|
59 |
+
|
60 |
+
# Generate Grad-CAM heatmap
|
61 |
+
heatmap = generate_grad_cam(image, target_layer="vit.encoder.layer.11.output")
|
62 |
+
|
63 |
+
# Visualize the heatmap on the original image
|
64 |
+
img = np.array(image)
|
65 |
+
heatmap_resized = np.array(Image.fromarray(heatmap).resize((img.shape[1], img.shape[0])))
|
66 |
+
|
67 |
+
# Overlay heatmap on the original image
|
68 |
+
plt.imshow(img)
|
69 |
+
plt.imshow(heatmap_resized, cmap='jet', alpha=0.5)
|
70 |
+
plt.axis('off')
|
71 |
+
|
72 |
+
# Save the overlayed image
|
73 |
+
plt.savefig("grad_cam_result.png")
|
74 |
+
|
75 |
+
return predicted_label, "grad_cam_result.png"
|
76 |
+
|
77 |
+
# Gradio interface
|
78 |
+
interface = gr.Interface(
|
79 |
+
fn=predict_and_explain,
|
80 |
+
inputs=gr.inputs.Image(type="pil"),
|
81 |
+
outputs=[
|
82 |
+
"text",
|
83 |
+
gr.outputs.Image(type="file", label="Grad-CAM Visualization")
|
84 |
+
],
|
85 |
+
title="Medical Image Analysis Tool with Explainability",
|
86 |
+
description="Upload an X-ray or MRI image to get a prediction for a medical condition with explainability through Grad-CAM.",
|
87 |
+
live=True
|
88 |
+
)
|
89 |
+
|
90 |
+
# Launch the app
|
91 |
+
if __name__ == "__main__":
|
92 |
+
interface.launch()
|
requirements.txt
ADDED
@@ -0,0 +1,6 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
1 |
+
torch
|
2 |
+
transformers
|
3 |
+
gradio
|
4 |
+
numpy
|
5 |
+
pillow
|
6 |
+
matplotlib
|