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竹子都/unet++医学细胞分割实战

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val.py 4.21 KB
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xiaosha 提交于 2021-01-09 15:55 . first commit
import argparse
import os
from glob import glob
import matplotlib.pyplot as plt
import numpy as np
import cv2
import torch
import torch.backends.cudnn as cudnn
import yaml
from albumentations.augmentations import transforms
from albumentations.core.composition import Compose
from sklearn.model_selection import train_test_split
from tqdm import tqdm
import archs
from dataset import Dataset
from metrics import iou_score
from utils import AverageMeter
"""
需要指定参数:--name dsb2018_96_NestedUNet_woDS
"""
def parse_args():
parser = argparse.ArgumentParser()
parser.add_argument('--name', default="dsb2018_96_NestedUNet_woDS",
help='model name')
args = parser.parse_args()
return args
def main():
args = parse_args()
with open('models/%s/config.yml' % args.name, 'r') as f:
config = yaml.load(f, Loader=yaml.FullLoader)
print('-'*20)
for key in config.keys():
print('%s: %s' % (key, str(config[key])))
print('-'*20)
cudnn.benchmark = True
# create model
print("=> creating model %s" % config['arch'])
model = archs.__dict__[config['arch']](config['num_classes'],
config['input_channels'],
config['deep_supervision'])
model = model.cuda()
# Data loading code
img_ids = glob(os.path.join('inputs', config['dataset'], 'images', '*' + config['img_ext']))
img_ids = [os.path.splitext(os.path.basename(p))[0] for p in img_ids]
_, val_img_ids = train_test_split(img_ids, test_size=0.2, random_state=41)
model.load_state_dict(torch.load('models/%s/model.pth' %
config['name']))
model.eval()
val_transform = Compose([
transforms.Resize(config['input_h'], config['input_w']),
transforms.Normalize(),
])
val_dataset = Dataset(
img_ids=val_img_ids,
img_dir=os.path.join('inputs', config['dataset'], 'images'),
mask_dir=os.path.join('inputs', config['dataset'], 'masks'),
img_ext=config['img_ext'],
mask_ext=config['mask_ext'],
num_classes=config['num_classes'],
transform=val_transform)
val_loader = torch.utils.data.DataLoader(
val_dataset,
batch_size=config['batch_size'],
shuffle=False,
num_workers=config['num_workers'],
drop_last=False)
avg_meter = AverageMeter()
for c in range(config['num_classes']):
os.makedirs(os.path.join('outputs', config['name'], str(c)), exist_ok=True)
with torch.no_grad():
for input, target, meta in tqdm(val_loader, total=len(val_loader)):
input = input.cuda()
target = target.cuda()
# compute output
if config['deep_supervision']:
output = model(input)[-1]
else:
output = model(input)
iou = iou_score(output, target)
avg_meter.update(iou, input.size(0))
output = torch.sigmoid(output).cpu().numpy()
for i in range(len(output)):
for c in range(config['num_classes']):
cv2.imwrite(os.path.join('outputs', config['name'], str(c), meta['img_id'][i] + '.jpg'),
(output[i, c] * 255).astype('uint8'))
print('IoU: %.4f' % avg_meter.avg)
plot_examples(input, target, model,num_examples=3)
torch.cuda.empty_cache()
def plot_examples(datax, datay, model,num_examples=6):
fig, ax = plt.subplots(nrows=num_examples, ncols=3, figsize=(18,4*num_examples))
m = datax.shape[0]
for row_num in range(num_examples):
image_indx = np.random.randint(m)
image_arr = model(datax[image_indx:image_indx+1]).squeeze(0).detach().cpu().numpy()
ax[row_num][0].imshow(np.transpose(datax[image_indx].cpu().numpy(), (1,2,0))[:,:,0])
ax[row_num][0].set_title("Orignal Image")
ax[row_num][1].imshow(np.squeeze((image_arr > 0.40)[0,:,:].astype(int)))
ax[row_num][1].set_title("Segmented Image localization")
ax[row_num][2].imshow(np.transpose(datay[image_indx].cpu().numpy(), (1,2,0))[:,:,0])
ax[row_num][2].set_title("Target image")
plt.show()
if __name__ == '__main__':
main()
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unet++医学细胞分割实战
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