|
a |
|
b/src/data.py |
|
|
1 |
import torch |
|
|
2 |
from torch.utils.data import Dataset |
|
|
3 |
import json |
|
|
4 |
import os |
|
|
5 |
from PIL import Image |
|
|
6 |
import numpy as np |
|
|
7 |
from torchvision import transforms |
|
|
8 |
import yaml |
|
|
9 |
|
|
|
10 |
|
|
|
11 |
class IHDataset(Dataset): |
|
|
12 |
"""Intracranial Hemorrhage dataset.""" |
|
|
13 |
def __init__(self, root_dir, stage='train', transform=None): |
|
|
14 |
self.root_dir = root_dir |
|
|
15 |
self.stage = stage |
|
|
16 |
self.transform = transform |
|
|
17 |
self.data_dir = os.path.join(self.root_dir, self.stage) |
|
|
18 |
|
|
|
19 |
with open(os.path.join(root_dir, f'annots/{stage}.csv'), 'r') as csv: |
|
|
20 |
lines = [line.strip().split(',') for line in csv.readlines()] |
|
|
21 |
header, lines = lines[0], lines[1:] |
|
|
22 |
# k: dicom ID, v: IH/noIH (1/0) |
|
|
23 |
self.annots = {k:[] for k in header} |
|
|
24 |
for line in lines: |
|
|
25 |
for k,v in zip(header,line): |
|
|
26 |
self.annots[k].append(v) |
|
|
27 |
|
|
|
28 |
self.idx_to_slice_id = dict(enumerate(self.annots['ID'])) |
|
|
29 |
self.slice_id_to_idx = {v:k for k,v in self.idx_to_slice_id.items()} |
|
|
30 |
|
|
|
31 |
test_patients_path = os.path.join(root_dir, |
|
|
32 |
f'annots/patient_stats_test.yaml') |
|
|
33 |
self.test_patients = yaml.safe_load(open(test_patients_path, 'r')) |
|
|
34 |
|
|
|
35 |
def __len__(self): |
|
|
36 |
return len(self.annots['ID']) |
|
|
37 |
|
|
|
38 |
def __getitem__(self, idx): |
|
|
39 |
img_name = f'{self.idx_to_slice_id[idx]}.png' |
|
|
40 |
img_path = os.path.join(self.data_dir, img_name) |
|
|
41 |
sample = Image.open(img_path) |
|
|
42 |
|
|
|
43 |
if self.transform: |
|
|
44 |
sample = self.transform(sample) |
|
|
45 |
|
|
|
46 |
target = int(self.annots['IH'][idx]) |
|
|
47 |
return sample, target |
|
|
48 |
|
|
|
49 |
def getSlice(self, slice_id): |
|
|
50 |
idx = self.slice_id_to_idx[slice_id] |
|
|
51 |
return self.__getitem__(idx) |
|
|
52 |
|
|
|
53 |
|
|
|
54 |
class IHTestDataset(Dataset): |
|
|
55 |
"""Intracranial Hemorrhage dataset.""" |
|
|
56 |
def __init__(self, root_dir, stage='', transform=None): |
|
|
57 |
self.root_dir = root_dir |
|
|
58 |
self.transform = transform |
|
|
59 |
self.data_dir = root_dir if root_dir[-1] == '/' else root_dir + '/' |
|
|
60 |
import glob |
|
|
61 |
self.data = glob.glob(self.data_dir + '*') |
|
|
62 |
self.idx_to_img_path = dict(enumerate(self.data)) |
|
|
63 |
|
|
|
64 |
def __len__(self): |
|
|
65 |
return len(self.data) |
|
|
66 |
|
|
|
67 |
def __getitem__(self, idx): |
|
|
68 |
img_path = self.idx_to_img_path[idx] |
|
|
69 |
sample = Image.open(img_path) |
|
|
70 |
if self.transform: |
|
|
71 |
sample = self.transform(sample) |
|
|
72 |
return sample, img_path |
|
|
73 |
|
|
|
74 |
|
|
|
75 |
def get_datasets(conf): |
|
|
76 |
dataset = conf['data']['name'] |
|
|
77 |
root_dir = conf['data']['path'] |
|
|
78 |
train_transform = conf['train_transform'] |
|
|
79 |
valid_transform = conf['valid_transform'] |
|
|
80 |
test_transform = conf['test_transform'] |
|
|
81 |
if dataset == 'IHDataset': |
|
|
82 |
train_dataset = IHDataset(root_dir=root_dir, |
|
|
83 |
stage='train', |
|
|
84 |
transform=train_transform) |
|
|
85 |
valid_dataset = IHDataset(root_dir=root_dir, |
|
|
86 |
stage='valid', |
|
|
87 |
transform=valid_transform) |
|
|
88 |
test_dataset = IHDataset(root_dir=root_dir, |
|
|
89 |
stage='test', |
|
|
90 |
transform=test_transform) |
|
|
91 |
patients_dataset = IHDataset(root_dir=root_dir, |
|
|
92 |
stage='test_no_balanced', |
|
|
93 |
transform=test_transform) |
|
|
94 |
elif dataset == 'IHTestDataset': |
|
|
95 |
return None, None, IHTestDataset(root_dir=root_dir, |
|
|
96 |
transform=test_transform), None |
|
|
97 |
else: |
|
|
98 |
print('Dataset {dataset} not supported.') |
|
|
99 |
exit() |
|
|
100 |
return train_dataset, valid_dataset, test_dataset, patients_dataset |
|
|
101 |
|
|
|
102 |
|
|
|
103 |
def get_dataloaders(conf): |
|
|
104 |
from torch.utils.data import DataLoader |
|
|
105 |
train_dataset = conf['train_dataset'] |
|
|
106 |
valid_dataset = conf['valid_dataset'] |
|
|
107 |
test_dataset = conf['test_dataset'] |
|
|
108 |
batch_size = conf['data']['batch_size'] |
|
|
109 |
num_workers = conf['data']['num_workers'] |
|
|
110 |
train_loader = DataLoader(dataset=train_dataset, |
|
|
111 |
batch_size=batch_size, |
|
|
112 |
num_workers=num_workers, |
|
|
113 |
shuffle=True, |
|
|
114 |
pin_memory=True) |
|
|
115 |
valid_loader = DataLoader(dataset=valid_dataset, |
|
|
116 |
batch_size= batch_size, |
|
|
117 |
num_workers=num_workers, |
|
|
118 |
shuffle=False, |
|
|
119 |
pin_memory=True) |
|
|
120 |
test_loader = DataLoader(dataset=valid_dataset, |
|
|
121 |
batch_size= batch_size, |
|
|
122 |
num_workers=num_workers, |
|
|
123 |
shuffle=False, |
|
|
124 |
pin_memory=True) |
|
|
125 |
|
|
|
126 |
return train_loader, valid_loader, test_loader |
|
|
127 |
|
|
|
128 |
|
|
|
129 |
if __name__ == '__main__': |
|
|
130 |
''' |
|
|
131 |
print(os.listdir('./data/windowed')) |
|
|
132 |
ds = IHDataset(root_dir='./data/windowed/', stage='valid') |
|
|
133 |
sample, target = ds[2] |
|
|
134 |
arr = np.transpose(255 * (0.5 * sample + 0.5), (1,2,0)) |
|
|
135 |
im = Image.fromarray(np.uint8(arr)) |
|
|
136 |
im.save('example.jpg') |
|
|
137 |
print(target) |
|
|
138 |
print(len(ds)) |
|
|
139 |
''' |
|
|
140 |
ds = IHTestDataset(root_dir='../patients_windowed/001_1/') |
|
|
141 |
sample, img_path = ds[0] |
|
|
142 |
print('Img path:', img_path) |
|
|
143 |
arr = sample |
|
|
144 |
im = Image.fromarray(np.uint8(arr)) |
|
|
145 |
im.save('example.jpg') |