[6f3ba0]: / U-Net / black_blood.py

Download this file

126 lines (73 with data), 3.1 kB

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
import argparse
import logging
import os
import numpy as np
import torch
import torch.nn.functional as F
from PIL import Image
from torchvision import transforms
from utils.data_loading import BasicDataset
from unet.unet_model import UNet
from utils.utils import plot_img_and_mask
device = torch.device('cuda:4' if torch.cuda.is_available() else 'cpu')
directory = r'/home/data/spleen_blood/data/test/imgs'
def predict_img(net,
full_img,
device,
scale_factor=1,
out_threshold=0.5):
net.eval()
img = torch.from_numpy(BasicDataset.preprocess(None, full_img, scale_factor, is_mask=False))
img = img.unsqueeze(0)
img = img.to(device=device, dtype=torch.float32)
with torch.no_grad():
output = net(img).cpu()
output = F.interpolate(output, (full_img.size[1], full_img.size[0]), mode='bilinear')
if net.n_classes > 1:
mask = output.argmax(dim=1)
else:
mask = torch.sigmoid(output) > out_threshold
return mask[0].long().squeeze().numpy()
def get_output_filenames(in_files):
return f'{os.path.splitext(in_files)[0]}_OUT.png'
def mask_to_image(mask: np.ndarray, mask_values):
if isinstance(mask_values[0], list):
out = np.zeros((mask.shape[-2], mask.shape[-1], len(mask_values[0])), dtype=np.uint8)
elif mask_values == [0, 1]:
out = np.zeros((mask.shape[-2], mask.shape[-1]), dtype=bool)
else:
out = np.zeros((mask.shape[-2], mask.shape[-1]), dtype=np.uint8)
if mask.ndim == 3:
mask = np.argmax(mask, axis=0)
for i, v in enumerate(mask_values):
out[mask == i] = v
return Image.fromarray(out)
if __name__ == '__main__':
logging.basicConfig(level=logging.INFO, format='%(levelname)s: %(message)s')
model = './epoch_26_acc_0.90_best_val_acc.pth'
for fn in os.listdir(directory):
in_files = os.path.join(directory, fn)
out_files = get_output_filenames(in_files)
#print(fn, in_files, out_files)
net = UNet(n_channels=1, n_classes=5, bilinear=True)
logging.info(f'Loading model {model}')
logging.info(f'Using device {device}')
net.to(device=device)
state_dict = torch.load(model, map_location=device)
mask_values = state_dict.pop('mask_values', [0, 1])
net.load_state_dict(state_dict)
logging.info('Model loaded!')
filename = in_files
logging.info(f'Predicting image {filename} ...')
img = Image.open(filename)
mask = predict_img(net=net,
full_img=img,
scale_factor=0.5,
out_threshold=0.5,
device=device)
out_filename = out_files
result = mask_to_image(mask, mask_values)
result.save(out_filename)
logging.info(f'Mask saved to {out_filename}')
#logging.info(f'Visualizing results for image {filename}, close to continue...')
#plot_img_and_mask(img, mask)