|
a |
|
b/sybil/utils/visualization.py |
|
|
1 |
import numpy as np |
|
|
2 |
import torch |
|
|
3 |
import torch.nn.functional as F |
|
|
4 |
from sybil.serie import Serie |
|
|
5 |
from typing import Dict, List, Union |
|
|
6 |
import os |
|
|
7 |
|
|
|
8 |
def collate_attentions(attention_dict: Dict[str, np.ndarray], N: int, eps=1e-6) -> np.ndarray: |
|
|
9 |
a1 = attention_dict["image_attention_1"] |
|
|
10 |
v1 = attention_dict["volume_attention_1"] |
|
|
11 |
|
|
|
12 |
a1 = torch.Tensor(a1) |
|
|
13 |
v1 = torch.Tensor(v1) |
|
|
14 |
|
|
|
15 |
# take mean attention over ensemble |
|
|
16 |
a1 = torch.exp(a1).mean(0) |
|
|
17 |
v1 = torch.exp(v1).mean(0) |
|
|
18 |
|
|
|
19 |
attention = a1 * v1.unsqueeze(-1) |
|
|
20 |
attention = attention.view(1, 25, 16, 16) |
|
|
21 |
|
|
|
22 |
attention_up = F.interpolate( |
|
|
23 |
attention.unsqueeze(0), (N, 512, 512), mode="trilinear" |
|
|
24 |
) |
|
|
25 |
attention_up = attention_up.cpu().numpy() |
|
|
26 |
attention_up = attention_up.squeeze() |
|
|
27 |
if eps: |
|
|
28 |
attention_up[attention_up <= eps] = 0.0 |
|
|
29 |
|
|
|
30 |
return attention_up |
|
|
31 |
|
|
|
32 |
def build_overlayed_images(images: List[np.ndarray], attention: np.ndarray, gain: int = 3): |
|
|
33 |
overlayed_images = [] |
|
|
34 |
N = len(images) |
|
|
35 |
for i in range(N): |
|
|
36 |
overlayed = np.zeros((512, 512, 3)) |
|
|
37 |
overlayed[..., 2] = images[i] |
|
|
38 |
overlayed[..., 1] = images[i] |
|
|
39 |
overlayed[..., 0] = np.clip( |
|
|
40 |
(attention[i, ...] * gain * 256) + images[i], |
|
|
41 |
a_min=0, |
|
|
42 |
a_max=255, |
|
|
43 |
) |
|
|
44 |
|
|
|
45 |
overlayed_images.append(np.uint8(overlayed)) |
|
|
46 |
|
|
|
47 |
return overlayed_images |
|
|
48 |
|
|
|
49 |
|
|
|
50 |
def visualize_attentions( |
|
|
51 |
series: Union[Serie, List[Serie]], |
|
|
52 |
attentions: List[Dict[str, np.ndarray]], |
|
|
53 |
save_directory: str = None, |
|
|
54 |
gain: int = 3, |
|
|
55 |
) -> List[List[np.ndarray]]: |
|
|
56 |
""" |
|
|
57 |
Args: |
|
|
58 |
series (Serie): series object |
|
|
59 |
attentions (Dict[str, np.ndarray]): attention dictionary output from model |
|
|
60 |
save_directory (str, optional): where to save the images. Defaults to None. |
|
|
61 |
gain (int, optional): how much to scale attention values by for visualization. Defaults to 3. |
|
|
62 |
|
|
|
63 |
Returns: |
|
|
64 |
List[List[np.ndarray]]: list of list of overlayed images |
|
|
65 |
""" |
|
|
66 |
|
|
|
67 |
if isinstance(series, Serie): |
|
|
68 |
series = [series] |
|
|
69 |
|
|
|
70 |
series_overlays = [] |
|
|
71 |
for serie_idx, serie in enumerate(series): |
|
|
72 |
images = serie.get_raw_images() |
|
|
73 |
N = len(images) |
|
|
74 |
cur_attention = collate_attentions(attentions[serie_idx], N) |
|
|
75 |
|
|
|
76 |
overlayed_images = build_overlayed_images(images, cur_attention, gain) |
|
|
77 |
|
|
|
78 |
if save_directory is not None: |
|
|
79 |
save_path = os.path.join(save_directory, f"serie_{serie_idx}") |
|
|
80 |
save_images(overlayed_images, save_path, f"serie_{serie_idx}") |
|
|
81 |
|
|
|
82 |
series_overlays.append(overlayed_images) |
|
|
83 |
return series_overlays |
|
|
84 |
|
|
|
85 |
|
|
|
86 |
def save_images(img_list: List[np.ndarray], directory: str, name: str): |
|
|
87 |
""" |
|
|
88 |
Saves a list of images as a GIF in the specified directory with the given name. |
|
|
89 |
|
|
|
90 |
Args: |
|
|
91 |
``img_list`` (List[np.ndarray]): A list of numpy arrays representing the images to be saved. |
|
|
92 |
``directory`` (str): The directory where the GIF should be saved. |
|
|
93 |
``name`` (str): The name of the GIF file. |
|
|
94 |
|
|
|
95 |
Returns: |
|
|
96 |
None |
|
|
97 |
""" |
|
|
98 |
import imageio |
|
|
99 |
os.makedirs(directory, exist_ok=True) |
|
|
100 |
path = os.path.join(directory, f"{name}.gif") |
|
|
101 |
imageio.mimsave(path, img_list) |