Segment Anything Model (SAM) 在医疗图像上应用

#jupyter-notebook
import numpy as np
import torch
import matplotlib.pyplot as plt
import cv2

def show_anns(anns):
    if len(anns) == 0:
        return
    sorted_anns = sorted(anns, key=(lambda x: x['area']), reverse=True)
    ax = plt.gca()
    ax.set_autoscale_on(False)
    polygons = []
    color = []
    for ann in sorted_anns:
        m = ann['segmentation']
        img = np.ones((m.shape[0], m.shape[1], 3))
        color_mask = np.random.random((1, 3)).tolist()[0]
        for i in range(3):
            img[:,:,i] = color_mask[i]
        ax.imshow(np.dstack((img, m*0.35)))

image = cv2.imread('./test/axialAbdomen24.jpg')
image = cv2.cvtColor(image, cv2.COLOR_BGR2RGB)

plt.figure(figsize=(20,20))
plt.imshow(image)
plt.axis('off')
plt.show()

import sys
sys.path.append("..")
from segment_anything import sam_model_registry, SamAutomaticMaskGenerator, SamPredictor

sam_checkpoint = "./checkpoint/sam_vit_h_4b8939.pth" #提前下载的checkpoint(default) [https://github.com/facebookresearch/segment-anything/blob/main/README.md] 
model_type = "vit_h"

device = "cuda"

sam = sam_model_registry[model_type](checkpoint=sam_checkpoint)
# sam.to(device=device)

mask_generator = SamAutomaticMaskGenerator(sam)

masks = mask_generator.generate(image)

print(len(masks))
print(masks[0].keys())

plt.figure(figsize=(20,20))
plt.imshow(image)
show_anns(masks)
plt.axis('off')
plt.show()