[cbdc43]: / src / utils.py

Download this file

105 lines (77 with data), 2.7 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
 99
100
101
102
103
104
import numpy as np
import torch
import os
import sys
def set_seed(seed=0xD153A53):
np.random.seed(seed)
torch.manual_seed(seed)
torch.cuda.manual_seed(seed)
os.environ['PYTHONHASHSEED'] = str(seed)
def get_metric(cfg):
return getattr(sys.modules['custom.metrics'], cfg.metric)
def get_criterion(cfg):
return getattr(sys.modules['custom.losses'], cfg.criterion)
def get_model(cfg):
return getattr(sys.modules['custom.models'], cfg.model)
def get_optimizer(cfg):
return getattr(sys.modules['torch.optim'], cfg.optimizer)
def get_scheduler(cfg):
if cfg.scheduler:
return getattr(sys.modules['torch.optim.lr_scheduler'], cfg.scheduler)
return FakeScheduler
def get_paths_1_dataset(data_folder, dataset_name):
paths_folder = os.path.join(data_folder, dataset_name)
last_number = 0
paths, _paths = [], []
# MedSeg has only one NIftI for many patients
if 'MedSeg' in dataset_name:
for i, name in enumerate(sorted(os.listdir(paths_folder))):
path = os.path.join(paths_folder, name)
if i % 5 == 0:
paths.append(_paths)
_paths = []
_paths.append(path)
paths.append(_paths)
return paths
# adding paths by patients
for name in sorted(os.listdir(paths_folder)):
path = os.path.join(paths_folder, name)
number_of_patient = int(name.split('_')[0])
if last_number != number_of_patient:
paths.append(_paths)
_paths = []
last_number = number_of_patient
_paths.append(path)
paths.append(_paths)
return paths
def get_paths(cfg):
# if list for adding paths from every dataset
if isinstance(cfg.dataset_name, list):
paths = []
for name in cfg.dataset_name:
paths.extend(get_paths_1_dataset(cfg.data_folder, name))
return paths
# if solo dataset
paths = get_paths_1_dataset(cfg.data_folder, cfg.dataset_name)
return paths
class OneHotEncoder:
def __init__(self, cfg):
self.zeros = [0] * cfg.num_classes
def encode_num(self, x):
zeros = self.zeros.copy()
zeros[int(x)] = 1
return zeros
def __call__(self, y):
y = np.array(y)
y = np.expand_dims(y, -1)
y = np.apply_along_axis(self.encode_num, -1, y)
y = np.swapaxes(y, -1, 1)
y = np.ascontiguousarray(y)
return torch.Tensor(y)
class FakeScheduler:
def __init__(self, *args, **kwargs):
self.lr = kwargs['lr']
def step(self, *args, **kwargs):
pass
def get_last_lr(self, *args, **kwargs):
return [self.lr]