-
Notifications
You must be signed in to change notification settings - Fork 5
/
load_data.py
58 lines (50 loc) · 2.12 KB
/
load_data.py
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
import torch
from torch.utils.data import Dataset
import numpy as np
import os
from mrc import parse_mrc
from PIL import Image
class ParticleImages(Dataset):
def __init__(self, vol_path, image_path):
self.particle_images = np.load(os.path.join(image_path, "particle_stack.npy"), 'r')
self.rotations = np.load(os.path.join(image_path, "poses.npy"), 'r')
self.apply_ctf = False
ctf_path = os.path.join(image_path, "ctf.npy")
if os.path.exists(ctf_path):
self.ctf = np.load(os.path.join(image_path, "ctf.npy"), 'r')
self.apply_ctf = True
self.n_projections = self.rotations.shape[0]
self.vol, hdr = parse_mrc(os.path.join(vol_path, 'volume.mrc'))
self.apix = hdr.get_apix()
self.sidelen = self.vol.shape[0]
freqs = np.fft.fftshift(np.fft.fftfreq(self.sidelen))
self.freqs = np.stack(np.meshgrid(freqs, freqs), axis=-1).reshape(-1, 2) / self.apix
def __len__(self):
return self.n_projections
def __getitem__(self, idx):
projected_image = torch.tensor(self.particle_images[idx]).float()
if self.apply_ctf:
ctf_params = torch.tensor(self.ctf[idx]).float()
else:
ctf_params = torch.zeros((7,)) # dummy ctf
return projected_image, ctf_params, idx
class ImageDataset(Dataset):
def __init__(self, path, just_one=True):
imgs = np.load(path)
imgs = np.concatenate([imgs['train_data'], imgs['test_data']], axis=0)
self.n_imgs = imgs.shape[0]
self.train_res = imgs.shape[1] // 2
self.test_res = imgs.shape[1]
self.just_one = just_one
train_imgs = []
for i in range(self.n_imgs):
img = Image.fromarray(imgs[i]).resize((self.train_res, self.train_res), Image.ANTIALIAS)
train_imgs.append(np.array(img) / 255.)
self.train_imgs = np.stack(train_imgs, axis=0)
self.test_imgs = imgs / 255.
def __len__(self):
if self.just_one:
return 1
return self.n_imgs
def __getitem__(self, idx):
return self.train_imgs[idx], self.test_imgs[idx]