Spaces:
Sleeping
Sleeping
Upload 4 files
Browse files- Dockerfile +12 -0
- lung.py +132 -0
- lung_xray_classify.pth +3 -0
- requirements.txt +9 -0
Dockerfile
ADDED
|
@@ -0,0 +1,12 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
FROM python:3.9
|
| 2 |
+
|
| 3 |
+
WORKDIR /app
|
| 4 |
+
|
| 5 |
+
COPY . /app
|
| 6 |
+
|
| 7 |
+
RUN pip install --upgrade pip
|
| 8 |
+
RUN pip install -r requirements.txt
|
| 9 |
+
|
| 10 |
+
EXPOSE 7860
|
| 11 |
+
|
| 12 |
+
CMD ["python", "app.py"]
|
lung.py
ADDED
|
@@ -0,0 +1,132 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
|
| 2 |
+
import torch
|
| 3 |
+
import torch.nn as nn
|
| 4 |
+
from torchvision import models, transforms
|
| 5 |
+
from flask import Flask, jsonify, request, render_template
|
| 6 |
+
from PIL import Image
|
| 7 |
+
import os
|
| 8 |
+
import numpy as np
|
| 9 |
+
import matplotlib.pyplot as plt
|
| 10 |
+
from PIL import Image
|
| 11 |
+
import numpy as np
|
| 12 |
+
import cv2
|
| 13 |
+
import cv2
|
| 14 |
+
import torch
|
| 15 |
+
|
| 16 |
+
from pytorch_grad_cam import GradCAM
|
| 17 |
+
from pytorch_grad_cam.utils.image import show_cam_on_image
|
| 18 |
+
from pytorch_grad_cam.utils.model_targets import ClassifierOutputTarget
|
| 19 |
+
|
| 20 |
+
from flask_cors import CORS
|
| 21 |
+
|
| 22 |
+
|
| 23 |
+
|
| 24 |
+
def get_edge_for_visualization(pil_img):
|
| 25 |
+
|
| 26 |
+
w, h = pil_img.size
|
| 27 |
+
scale = 256 / min(w, h)
|
| 28 |
+
new_w, new_h = int(w * scale), int(h * scale)
|
| 29 |
+
resized = pil_img.resize((new_w, new_h), Image.BILINEAR)
|
| 30 |
+
|
| 31 |
+
|
| 32 |
+
left = (resized.width - 224) // 2
|
| 33 |
+
top = (resized.height - 224) // 2
|
| 34 |
+
cropped = resized.crop((left, top, left + 224, top + 224))
|
| 35 |
+
|
| 36 |
+
|
| 37 |
+
gray = cv2.cvtColor(np.array(cropped), cv2.COLOR_RGB2GRAY)
|
| 38 |
+
blurred = cv2.GaussianBlur(gray, (5, 5), 0)
|
| 39 |
+
edges = 255 - cv2.Canny(blurred, 30, 80)
|
| 40 |
+
|
| 41 |
+
|
| 42 |
+
edge_rgb = np.stack([edges]*3, axis=-1).astype(np.float32) / 255.0
|
| 43 |
+
|
| 44 |
+
return edge_rgb
|
| 45 |
+
|
| 46 |
+
app = Flask(__name__)
|
| 47 |
+
CORS(app)
|
| 48 |
+
os.makedirs("static", exist_ok=True)
|
| 49 |
+
|
| 50 |
+
# Device setup
|
| 51 |
+
device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
|
| 52 |
+
|
| 53 |
+
|
| 54 |
+
# Transform setup (same as training)
|
| 55 |
+
data_transforms = transforms.Compose([
|
| 56 |
+
transforms.Resize(256),
|
| 57 |
+
transforms.CenterCrop(224),
|
| 58 |
+
transforms.ToTensor(),
|
| 59 |
+
transforms.Normalize(
|
| 60 |
+
mean=[0.485, 0.456, 0.406],
|
| 61 |
+
std=[0.229, 0.224, 0.225]
|
| 62 |
+
)
|
| 63 |
+
])
|
| 64 |
+
|
| 65 |
+
|
| 66 |
+
model = models.resnet18(pretrained=False)
|
| 67 |
+
model.fc = nn.Linear(model.fc.in_features, 3)
|
| 68 |
+
|
| 69 |
+
model.load_state_dict(torch.load("lung_xray_classify.pth", map_location=device))
|
| 70 |
+
model.to(device)
|
| 71 |
+
model.eval()
|
| 72 |
+
|
| 73 |
+
|
| 74 |
+
class_names = ['COVID', 'HEALTHY', 'PNEUMONIA']
|
| 75 |
+
|
| 76 |
+
# @app.route("/")
|
| 77 |
+
# def home():
|
| 78 |
+
# return render_template("index.html")
|
| 79 |
+
|
| 80 |
+
@app.route("/predict_lung", methods=["POST"])
|
| 81 |
+
def predict():
|
| 82 |
+
if "file" not in request.files:
|
| 83 |
+
return jsonify({"error": "No file provided"}), 400
|
| 84 |
+
|
| 85 |
+
file = request.files["file"]
|
| 86 |
+
filepath = os.path.join("static", file.filename)
|
| 87 |
+
file.save(filepath)
|
| 88 |
+
|
| 89 |
+
try:
|
| 90 |
+
image = Image.open(filepath).convert("RGB")
|
| 91 |
+
input_tensor = data_transforms(image).unsqueeze(0).to(device)
|
| 92 |
+
|
| 93 |
+
with torch.no_grad():
|
| 94 |
+
output = model(input_tensor)
|
| 95 |
+
pred_idx = torch.argmax(output, dim=1).item()
|
| 96 |
+
pred_label = class_names[pred_idx]
|
| 97 |
+
classes = [ClassifierOutputTarget(pred_idx)];
|
| 98 |
+
target_layer = [model.layer4[-1]]
|
| 99 |
+
|
| 100 |
+
cam = GradCAM(model = model, target_layers = target_layer)
|
| 101 |
+
|
| 102 |
+
heatmap = cam(input_tensor = input_tensor, targets = classes);
|
| 103 |
+
edge_img = get_edge_for_visualization(image)
|
| 104 |
+
cam_image = show_cam_on_image(edge_img, heatmap[0], use_rgb=True)
|
| 105 |
+
input_img = np.array(image);
|
| 106 |
+
input_img = input_img.astype(np.float32)/255
|
| 107 |
+
input_img = cv2.resize(input_img, (224,224))
|
| 108 |
+
cam_image_real = show_cam_on_image(input_img, heatmap[0], use_rgb=True)
|
| 109 |
+
cam_image_path = os.path.join("static", f"cam_{file.filename}")
|
| 110 |
+
cv2.imwrite(cam_image_path, cv2.cvtColor(cam_image_real, cv2.COLOR_RGB2BGR))
|
| 111 |
+
file={
|
| 112 |
+
"prediction": pred_label,
|
| 113 |
+
"cam_image_url": f"/static/lung_cam_{file.filename}"
|
| 114 |
+
}
|
| 115 |
+
print(file)
|
| 116 |
+
return jsonify(file)
|
| 117 |
+
|
| 118 |
+
|
| 119 |
+
|
| 120 |
+
|
| 121 |
+
|
| 122 |
+
|
| 123 |
+
|
| 124 |
+
|
| 125 |
+
except Exception as e:
|
| 126 |
+
return jsonify({"error": str(e)}), 500
|
| 127 |
+
|
| 128 |
+
|
| 129 |
+
if __name__ == '__main__':
|
| 130 |
+
app.run(debug=True)
|
| 131 |
+
|
| 132 |
+
|
lung_xray_classify.pth
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:3704b0e4825e0d049f13227d73e472fed43a8cd06d89dbb109a8d63084cc104c
|
| 3 |
+
size 44792424
|
requirements.txt
ADDED
|
@@ -0,0 +1,9 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
flask
|
| 2 |
+
flask-cors
|
| 3 |
+
torch==2.2.0
|
| 4 |
+
torchvision==0.17.0
|
| 5 |
+
pillow
|
| 6 |
+
numpy
|
| 7 |
+
matplotlib
|
| 8 |
+
opencv-python-headless
|
| 9 |
+
git+https://github.com/jacobgil/pytorch-grad-cam.git
|