utils.py
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import os
import time
import importlib
import collections
import pickle as cp
import glob
import numpy as np
import pandas as pd
from natsort import natsorted
from PIL import Image
import torch
import torchvision
import torch.nn.functional as F
import torchvision.models as models
import torchvision.transforms as transforms
from torch.utils.data import Subset
from torch.utils.data import Dataset, DataLoader
from sklearn.model_selection import StratifiedShuffleSplit
from sklearn.model_selection import train_test_split
from sklearn.model_selection import KFold
from networks import basenet
from networks import grayResNet, grayResNet2
DATASET_PATH = '/content/drive/My Drive/CD2 Project/data/BraTS_Training/train_frame/'
TRAIN_DATASET_PATH = '/content/drive/My Drive/CD2 Project/data/BraTS_Training/train_frame/'
VAL_DATASET_PATH = '/content/drive/My Drive/CD2 Project/data/BraTS_Training/val_frame/'
current_epoch = 0
def split_dataset(args, dataset, k):
# load dataset
X = list(range(len(dataset)))
Y = dataset.targets
#Y = [0]* len(X)
#print("X:\n", type(X), np.shape(X), '\n', X, '\n')
# split to k-fold
# assert len(X) == len(Y)
def _it_to_list(_it):
return list(zip(*list(_it)))
sss = StratifiedShuffleSplit(n_splits=k, random_state=args.seed, test_size=0.1)
Dm_indexes, Da_indexes = _it_to_list(sss.split(X, Y))
# print(type(Dm_indexes), np.shape(Dm_indexes))
# print("DM\n", len(Dm_indexes), Dm_indexes, "\nDA\n", len(Da_indexes),Da_indexes)
return Dm_indexes, Da_indexes
#(images[j], first[j]), global_step=step)
def concat_image_features(image, features, max_features=3):
_, h, w = image.shape
max_features = min(features.size(0), max_features)
image_feature = image.clone()
for i in range(max_features):
# features torch.Size([64, 16, 16])
feature = features[i:i+1]
#torch.Size([1, 16, 16])
_min, _max = torch.min(feature), torch.max(feature)
feature = (feature - _min) / (_max - _min + 1e-6)
# torch.Size([1, 16, 16])
feature = torch.cat([feature]*1, 0)
#feature = torch.cat([feature]*3, 0)
# torch.Size([3, 16, 16]) -> [1, 16, 16]
feature = feature.view(1, 1, feature.size(1), feature.size(2))
#feature = feature.view(1, 3, feature.size(1), feature.size(2))
# torch.Size([1, 3, 16, 16])-> [1, 1, 16, 16]
feature = F.upsample(feature, size=(h,w), mode="bilinear")
# torch.Size([1, 3, 32, 32])-> [1, 1, 32, 32]
feature = feature.view(1, h, w) #(3, h, w) input of size 3072
# torch.Size([3, 32, 32])->[1, 32, 32]
#print("img_feature & feature size:\n", image_feature.size(),"\n", feature.size())
# img_feature & feature size:
# torch.Size([1, 32, 32]) -> [1, 32, 64]
# torch.Size([3, 32, 32] ->[1, 32, 32]
image_feature = torch.cat((image_feature, feature), 2) ### dim = 2
#print("\nimg feature size: ", image_feature.size()) #[1, 240, 720]
return image_feature
def get_model_name(args):
from datetime import datetime, timedelta, timezone
now = datetime.now(timezone.utc)
tz = timezone(timedelta(hours=9))
now = now.astimezone(tz)
date_time = now.strftime("%B_%d_%H:%M:%S")
model_name = '__'.join([date_time, args.network, str(args.seed)])
return model_name
def dict_to_namedtuple(d):
Args = collections.namedtuple('Args', sorted(d.keys()))
for k,v in d.items():
if type(v) is dict:
d[k] = dict_to_namedtuple(v)
elif type(v) is str:
try:
d[k] = eval(v)
except:
d[k] = v
args = Args(**d)
return args
def parse_args(kwargs):
# combine with default args
kwargs['dataset'] = kwargs['dataset'] if 'dataset' in kwargs else 'BraTS'
kwargs['network'] = kwargs['network'] if 'network' in kwargs else 'resnet50'
kwargs['optimizer'] = kwargs['optimizer'] if 'optimizer' in kwargs else 'adam'
kwargs['learning_rate'] = kwargs['learning_rate'] if 'learning_rate' in kwargs else 0.0001
kwargs['seed'] = kwargs['seed'] if 'seed' in kwargs else None
kwargs['use_cuda'] = kwargs['use_cuda'] if 'use_cuda' in kwargs else True
kwargs['use_cuda'] = kwargs['use_cuda'] and torch.cuda.is_available()
kwargs['num_workers'] = kwargs['num_workers'] if 'num_workers' in kwargs else 4
kwargs['print_step'] = kwargs['print_step'] if 'print_step' in kwargs else 500
kwargs['val_step'] = kwargs['val_step'] if 'val_step' in kwargs else 500
kwargs['scheduler'] = kwargs['scheduler'] if 'scheduler' in kwargs else 'exp'
kwargs['batch_size'] = kwargs['batch_size'] if 'batch_size' in kwargs else 128
kwargs['start_step'] = kwargs['start_step'] if 'start_step' in kwargs else 0
kwargs['max_step'] = kwargs['max_step'] if 'max_step' in kwargs else 6500
kwargs['fast_auto_augment'] = kwargs['fast_auto_augment'] if 'fast_auto_augment' in kwargs else False
kwargs['augment_path'] = kwargs['augment_path'] if 'augment_path' in kwargs else None
# to named tuple
args = dict_to_namedtuple(kwargs)
return args, kwargs
def select_model(args):
# grayResNet2
resnet_dict = {'resnet18':grayResNet2.resnet18(), 'resnet34':grayResNet2.resnet34(),
'resnet50':grayResNet2.resnet50(), 'resnet101':grayResNet2.resnet101(), 'resnet152':grayResNet2.resnet152()}
if args.network in resnet_dict:
backbone = resnet_dict[args.network]
#testing
# print("\nRESNET50 LAYERS\n")
# for layer in backbone.children():
# print(layer)
# print("LAYER THE END\n")
model = basenet.BaseNet(backbone, args)
else:
Net = getattr(importlib.import_module('networks.{}'.format(args.network)), 'Net')
model = Net(args)
#print(model) # print model architecture
return model
def select_optimizer(args, model):
if args.optimizer == 'sgd':
optimizer = torch.optim.SGD(model.parameters(), lr=args.learning_rate, momentum=0.9, weight_decay=0.0001)
elif args.optimizer == 'rms':
#optimizer = torch.optim.RMSprop(model.parameters(), lr=args.learning_rate, momentum=0.9, weight_decay=1e-5)
optimizer = torch.optim.RMSprop(model.parameters(), lr=args.learning_rate)
elif args.optimizer == 'adam':
optimizer = torch.optim.Adam(model.parameters(), lr=args.learning_rate)
else:
raise Exception('Unknown Optimizer')
return optimizer
def select_scheduler(args, optimizer):
if not args.scheduler or args.scheduler == 'None':
return None
elif args.scheduler =='clr':
return torch.optim.lr_scheduler.CyclicLR(optimizer, 0.01, 0.015, mode='triangular2', step_size_up=250000, cycle_momentum=False)
elif args.scheduler =='exp':
return torch.optim.lr_scheduler.ExponentialLR(optimizer, gamma=0.9999283, last_epoch=-1)
else:
raise Exception('Unknown Scheduler')
class CustomDataset(Dataset):
def __init__(self, path, transform = None):
self.path = path
self.transform = transform
#self.imgpath = glob.glob(path + '/*.png'
self.imgs = natsorted(os.listdir(path))
self.len = len(self.imgs)
#self.len = self.img.shape[0]
self.targets = [0]* self.len
def __len__(self):
return self.len
def __getitem__(self, idx):
# print("\n\nIDX: ", idx, '\n', type(idx), '\n')
# print("\n\nimgs[idx]: ", self.imgs[idx], '\n', type(self.imgs[idx]), '\n')
#img, targets = self.img[idx], self.targets[idx]
img_loc = os.path.join(self.path, self.imgs[idx])
targets = self.targets[idx]
#img = self.img[idx]
image = Image.open(img_loc)
#print("Image:\n", image)
#print("type of img:\n", type(image)) #<class 'PIL.PngImagePlugin.PngImageFile'>
#w, h = image.size
#print(image.size) #(240, 240)
#image = image.reshape(w, h)
# image = np.array(image) * 255
# image = image.astype('uint8')
# image = Image.fromarray(image, mode = 'L')
if self.transform is not None:
#img = self.transform(img)
# print("\ngetitem image max:\n", np.amax(np.array(image)), np.array(image).shape)
#image [0, 255]
tensor_image = self.transform(image) ##
"""
range [0, 1] -> [0, 255]
RuntimeError: Input type (torch.cuda.DoubleTensor) and weight type (torch.cuda.FloatTensor) should be the same
# tensor_image = np.array(tensor_image) * 255
# tensor_image = tensor_image.astype('uint8')
# tensor_image = np.reshape(tensor_image, (32, 32))
# tensor_image = Image.fromarray(tensor_image, mode = 'L')
# tensor_image = np.reshape(tensor_image, (1, 32, 32))
# tensor_image = tensor_image.astype('float')
"""
#print("\ngetitem tensor_image max:\n", np.amax(np.array(tensor_image)), np.array(tensor_image).shape)
# tensor_image range: [0, 1], shape: (1, 32, 32)
#return img, targets
return tensor_image, targets
def get_dataset(args, transform, split='train'):
assert split in ['train', 'val', 'test', 'trainval']
if args.dataset == 'cifar10':
train = split in ['train', 'val', 'trainval']
dataset = torchvision.datasets.CIFAR10(DATASET_PATH,
train=train,
transform=transform,
download=True)
if split in ['train', 'val']:
split_path = os.path.join(DATASET_PATH,
'cifar-10-batches-py', 'train_val_index.cp')
if not os.path.exists(split_path):
[train_index], [val_index] = split_dataset(args, dataset, k=1)
split_index = {'train':train_index, 'val':val_index}
cp.dump(split_index, open(split_path, 'wb'))
split_index = cp.load(open(split_path, 'rb'))
dataset = Subset(dataset, split_index[split])
elif args.dataset == 'imagenet':
dataset = torchvision.datasets.ImageNet(DATASET_PATH,
split=split,
transform=transform,
download=(split is 'val'))
elif args.dataset == 'BraTS':
if split in ['train']:
dataset = CustomDataset(TRAIN_DATASET_PATH, transform=transform)
else: #test
dataset = CustomDataset(VAL_DATASET_PATH, transform=transform)
else:
raise Exception('Unknown dataset')
return dataset
def get_dataloader(args, dataset, shuffle=False, pin_memory=True):
data_loader = torch.utils.data.DataLoader(dataset,
batch_size=args.batch_size,
shuffle=shuffle,
num_workers=args.num_workers,
pin_memory=pin_memory)
return data_loader
def get_inf_dataloader(args, dataset):
global current_epoch
data_loader = iter(get_dataloader(args, dataset, shuffle=True))
while True:
try:
#print("batch=dataloader:\n", batch, '\n')
batch = next(data_loader)
except StopIteration:
current_epoch += 1
data_loader = iter(get_dataloader(args, dataset, shuffle=True))
batch = next(data_loader)
yield batch
def get_train_transform(args, model, log_dir=None):
if args.fast_auto_augment:
#assert args.dataset == 'BraTS' # TODO: FastAutoAugment for Imagenet
from fast_auto_augment import fast_auto_augment
if args.augment_path:
transform = cp.load(open(args.augment_path, 'rb'))
os.system('cp {} {}'.format(
args.augment_path, os.path.join(log_dir, 'augmentation.cp')))
else:
transform = fast_auto_augment(args, model, K=4, B=1, num_process=4) ##
if log_dir:
cp.dump(transform, open(os.path.join(log_dir, 'augmentation.cp'), 'wb'))
elif args.dataset == 'cifar10':
transform = transforms.Compose([
transforms.Pad(4),
transforms.RandomCrop(32),
transforms.RandomHorizontalFlip(),
transforms.ToTensor()
])
elif args.dataset == 'imagenet':
resize_h, resize_w = model.img_size[0], int(model.img_size[1]*1.875)
transform = transforms.Compose([
transforms.Resize([resize_h, resize_w]),
transforms.RandomCrop(model.img_size),
transforms.RandomHorizontalFlip(),
transforms.ToTensor()
])
# elif args.dataset == 'BraTS':
# resize_h, resize_w = 256, 256
# transform = transforms.Compose([
# transforms.Resize([resize_h, resize_w]),
# transforms.RandomCrop(model.img_size),
# transforms.RandomHorizontalFlip(),
# transforms.ToTensor()
# ])
else:
raise Exception('Unknown Dataset')
print(transform)
return transform
def get_valid_transform(args, model):
if args.dataset == 'cifar10':
val_transform = transforms.Compose([
transforms.Resize(32),
transforms.ToTensor()
])
elif args.dataset == 'imagenet':
resize_h, resize_w = model.img_size[0], int(model.img_size[1]*1.875)
val_transform = transforms.Compose([
transforms.Resize([resize_h, resize_w]),
transforms.ToTensor()
])
elif args.dataset == 'BraTS':
resize_h, resize_w = 240, 240
val_transform = transforms.Compose([
transforms.Resize([resize_h, resize_w]),
transforms.ToTensor()
])
else:
raise Exception('Unknown Dataset')
return val_transform
def train_step(args, model, optimizer, scheduler, criterion, batch, step, writer, device=None):
model.train()
images, target = batch
if device:
images = images.to(device)
target = target.to(device)
elif args.use_cuda:
images = images.cuda(non_blocking=True)
target = target.cuda(non_blocking=True)
# compute output
start_t = time.time()
output, first = model(images)
forward_t = time.time() - start_t
loss = criterion(output, target)
# measure accuracy and record loss
acc1, acc5 = accuracy(output, target, topk=(1, 5))
acc1 /= images.size(0)
acc5 /= images.size(0)
# compute gradient and do SGD step
optimizer.zero_grad()
start_t = time.time()
loss.backward()
backward_t = time.time() - start_t
optimizer.step()
if scheduler: scheduler.step()
if writer and step % args.print_step == 0:
n_imgs = min(images.size(0), 10)
tag = 'train/' + str(step)
for j in range(n_imgs):
writer.add_image(tag,
concat_image_features(images[j], first[j]), global_step=step)
return acc1, acc5, loss, forward_t, backward_t
# validate(args, model, criterion, test_loader, step=0, writer=writer)
def validate(args, model, criterion, valid_loader, step, writer, device=None):
# switch to evaluate mode
model.eval()
acc1, acc5 = 0, 0
samples = 0
infer_t = 0
img_count = 0
with torch.no_grad():
for i, (images, target) in enumerate(valid_loader): ## loop [0, 148]
#print("\n1 images size: ", images.size()) #[4, 1, 240, 240]
start_t = time.time()
if device:
images = images.to(device)
target = target.to(device)
elif args.use_cuda is not None: #
images = images.cuda(non_blocking=True)
target = target.cuda(non_blocking=True)
#print("\n2 images size: ", images.size()) #[4, 1, 240, 240]
# compute output
# first = nn.Sequential(*list(backbone.children())[:1])
output, first = model(images)
loss = criterion(output, target)
infer_t += time.time() - start_t
# measure accuracy and record loss
_acc1, _acc5 = accuracy(output, target, topk=(1, 5))
acc1 += _acc1
acc5 += _acc5
samples += images.size(0)
if writer:
# print("\n3 images.size(0): ", images.size(0))
n_imgs = min(images.size(0), 10)
for j in range(n_imgs):
tag = 'valid/' + str(img_count)
writer.add_image(tag,
concat_image_features(images[j], first[j]), global_step=step)
img_count = img_count + 1
acc1 /= samples
acc5 /= samples
return acc1, acc5, loss, infer_t
#_acc1, _acc5 = accuracy(output, target, topk=(1, 5))
def accuracy(output, target, topk=(1,)):
"""Computes the accuracy over the k top predictions for the specified values of k"""
with torch.no_grad():
maxk = max(topk)
batch_size = target.size(0)
_, pred = output.topk(maxk, 1, True, True)
pred = pred.t()
correct = pred.eq(target.view(1, -1).expand_as(pred))
res = []
for k in topk:
correct_k = correct[:k].view(-1).float().sum(0, keepdim=True)
res.append(correct_k)
return res