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train_mmgan_brats2018_single.py
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import os
import argparse
from modules.advanced_gans.models import *
from torch.autograd import Variable
from modules.models import cPix2PixDiscriminator
import time
import itertools
import pickle, gc
from modules.helpers import (ToTensor,
torch,
show_intermediate_results,
Resize,
create_dataloaders,
impute_reals_into_fake,
save_checkpoint,
load_checkpoint,
generate_training_strategy,
calculate_metrics,
printTable)
import logging
import numpy as np
import copy, sys
try:
logger = logging.getLogger(__file__.split('/')[-1])
except:
logger = logging.getLogger(__name__)
# Ignore warnings
import warnings
warnings.filterwarnings("ignore")
parser = argparse.ArgumentParser()
parser.add_argument('--epoch', type=int, default=0, help='epoch to start training from')
parser.add_argument('--n_epochs', type=int, default=2, help='number of epochs of training')
parser.add_argument('--dataset', type=str, default="BRATS2018", help='name of the dataset')
parser.add_argument('--grade', type=str, default="LGG", help='grade of tumor to train on')
parser.add_argument('--path_prefix', type=str, default="", help='path prefix to choose')
parser.add_argument('--batch_size', type=int, default=4, help='size of the batches')
parser.add_argument('--lr', type=float, default=0.0002, help='adam: learning rate')
parser.add_argument('--b1', type=float, default=0.5, help='adam: decay of first order momentum of gradient')
parser.add_argument('--b2', type=float, default=0.999, help='adam: decay of first order momentum of gradient')
parser.add_argument('--decay_epoch', type=int, default=100, help='epoch from which to start lr decay')
parser.add_argument('--n_cpu', type=int, default=0, help='number of cpu threads to use during batch generation')
parser.add_argument('--img_height', type=int, default=256, help='size of image height')
parser.add_argument('--img_width', type=int, default=256, help='size of image width')
parser.add_argument('--channels', type=int, default=4, help='number of image channels')
parser.add_argument('--out_channels', type=int, default=1, help='number of output channels')
parser.add_argument('--sample_interval', type=int, default=500, help='interval between sampling of images from generators')
parser.add_argument('--train_patient_idx', type=int, default=5, help='number of patients to train with')
parser.add_argument('--checkpoint_interval', type=int, default=-1, help='interval between model checkpoints')
parser.add_argument('--discrim_type', type=int, default=1, help='discriminator type to use, 0 for normal, 1 for PatchGAN')
parser.add_argument('--test_pats', type=int, default=2, help='number of test patients')
parser.add_argument('--model_name', type=str, default='pycharm_test', help='name of mode')
parser.add_argument('--log_level', type=str, default='info', help='logging level to choose')
parser.add_argument('--c_learning', type=int, default=2, help='whether or not use curriculum learning framework')
parser.add_argument('--type', type=str, default='T1', help='what sequence to synthesize')
parser.add_argument('--use_tanh', action='store_true', help='use tanh normalization throughout')
opt = parser.parse_args()
print(opt)
if 'info' in opt.log_level:
logging.basicConfig(level=logging.INFO)
elif 'debug' in opt.log_level:
logging.basicConfig(level=logging.DEBUG)
# =============================================================================
# Create Training and Validation data loaders
# =============================================================================
if opt.path_prefix == "":
# parent_path = '/scratch/asa224/asa224/Datasets/BRATS2018/HDF5_Datasets/'
parent_path = '/local-scratch/anmol/data/{}/HDF5_Datasets/'.format(opt.dataset)
else:
# notice there's one less asa224 here
parent_path = os.path.join(opt.path_prefix, 'scratch/asa224/Datasets/{}/HDF5_Datasets/'.format(opt.dataset))
if opt.dataset == 'BRATS2018':
if opt.grade == 'HGG':
logger.info('Running on HGG Dataset')
parent_name = 'preprocessed'
dataset_name = 'training_data_hgg'
dataset_type = 'cropped'
ALL_PATS = 210
TRAINING_PATS = 190
VALIDATION_PATS = 10
TESTING_PATS = 10
resize_slices = 148
elif opt.grade == 'LGG':
logger.info('Running on LGG Dataset')
parent_name = 'preprocessed'
dataset_name = 'training_data_lgg'
dataset_type = 'cropped'
ALL_PATS = 75
TRAINING_PATS = 70
resize_slices = 148
elif opt.dataset == 'BRATS2015':
logger.info("BRATS2015")
if opt.grade == 'HGG':
logger.info('Running on HGG Dataset')
parent_name = 'preprocessed'
dataset_name = 'training_data_hgg'
dataset_type = 'cropped'
ALL_PATS = 220
TRAINING_PATS = 200
VALIDATION_PATS = 10
TESTING_PATS = 10
resize_slices = 148
elif opt.grade == 'LGG':
logger.info('Running on LGG Dataset')
parent_name = 'preprocessed'
dataset_name = 'training_data_lgg'
dataset_type = 'cropped'
ALL_PATS = 54
TRAINING_PATS = 45
resize_slices = 148
else:
logger.critical("Invalid dataset name: {}".format(opt.dataset))
sys.exit(-1)
logger.debug('\tparent_path: \t\t{}'.format(parent_path))
logger.debug('\tparent_name: \t\t{}'.format(parent_name))
logger.debug('\tdataset_name: \t\t{}'.format(dataset_name))
logger.debug('\tdataset_type: \t\t{}'.format(dataset_type))
if resize_slices % opt.batch_size != 0:
logger.critical("Batch size is not compatible, please change it to be a multiple of {}".format(resize_slices))
sys.exit(-1)
#DEBUG ONLY
# opt.use_tanh = True
if opt.use_tanh:
which_normalization = 'tanh'
else:
which_normalization = None
train_range = list(range(0, opt.train_patient_idx))
n_dataloader, dataloader_for_viz = create_dataloaders(parent_path=parent_path,
parent_name=parent_name,
dataset_name=dataset_name,
dataset_type=dataset_type,
load_pat_names=True,
load_seg=False,
transform_fn=[Resize(size=(opt.img_height, opt.img_width)), ToTensor()],
apply_normalization=True,
which_normalization=which_normalization,
train_range=train_range,
resize_slices=resize_slices,
get_viz_dataloader=True,
num_workers=opt.n_cpu,
load_indices=None,
dataset=opt.dataset,
shuffle=False)
test_patient = []
for k in range(0, opt.test_pats):
test_patient.append(dataloader_for_viz.getitem_via_index(opt.train_patient_idx + k)) # tehre should be no +1
# if train_pat = 200
# The testing loop will evaluate at train_idx = 199 since the condition is train_idx + 1 == opt.train_patient_idx
# testing patient should start from 200 until 209.
# =============================================================================
# =============================================================================
# Initialize Networks
# =============================================================================
#
# os.makedirs('images/%s' % opt.dataset_name, exist_ok=True)
# os.makedirs('saved_models/%s' % opt.dataset_name, exist_ok=True)
cuda = True if torch.cuda.is_available() else False
# =============================================================================
# Loss functions
# =============================================================================
criterion_GAN = torch.nn.BCELoss() if opt.discrim_type == 0 else torch.nn.MSELoss()
criterion_pixelwise = torch.nn.L1Loss()
mse_fake_vs_real = torch.nn.MSELoss()
# =============================================================================
# Loss weight of L1 pixel-wise loss between translated image and real image
lambda_pixel = 100
# Calculate output of image discriminator (PatchGAN)
patch = (opt.out_channels, opt.img_height//2**4, opt.img_width//2**4)
# Initialize generator and discriminator
if which_normalization == 'tanh':
generator = GeneratorUNet(in_channels=opt.channels, out_channels=opt.out_channels, with_relu=False, with_tanh=True)
else:
generator = GeneratorUNet(in_channels=opt.channels, out_channels=opt.out_channels, with_relu=True, with_tanh=False)
discriminator = Discriminator(in_channels=opt.out_channels, out_channels=opt.out_channels, dataset='BRATS2018')
# =============================================================================
# =============================================================================
# Where to save results
# =============================================================================
if opt.path_prefix == "":
root = '/local-scratch/anmol/results_new/project_880/'
else: # NOT USED
root = os.path.join(opt.path_prefix, 'rrg_proj_dir/Results/project_880_new/mm_synthesis_gan_results/')
logger.warning("root: {}".format(root))
logger.warning('Possible bad value for opt.path_prefix')
model = opt.model_name
if not os.path.isdir(root):
os.mkdir(root)
if not os.path.isdir(os.path.join(root, model)):
os.mkdir(os.path.join(root, model))
if not os.path.isdir(os.path.join(root, model, "{}".format(opt.dataset), 'scenario_results')):
os.makedirs(os.path.join(root, model, "{}".format(opt.dataset), 'scenario_results'))
# =============================================================================
# Optimizers
optimizer_G = torch.optim.Adam(generator.parameters(), lr=opt.lr, betas=(opt.b1, opt.b2))
optimizer_D = torch.optim.Adam(discriminator.parameters(), lr=opt.lr, betas=(opt.b1, opt.b2))
# Send everything to GPU
if cuda:
generator = nn.DataParallel(generator.cuda())
discriminator = nn.DataParallel(discriminator.cuda())
criterion_GAN.cuda()
criterion_pixelwise.cuda()
mse_fake_vs_real.cuda()
# =============================================================================
# Init networks and optimizers
# =============================================================================
if opt.epoch != 0:
# Load pretrained models
logger.info('Loading previous checkpoint!')
generator, optimizer_G = load_checkpoint(generator, optimizer_G, os.path.join(root, opt.model_name,
"{}_param_{}_{}.pkl".format(
'generator', opt.model_name,
1)), pickle_module=pickle)
discriminator, optimizer_D = load_checkpoint(discriminator, optimizer_D, os.path.join(root, opt.model_name,
"{}_param_{}_{}.pkl".format(
'discriminator',
opt.model_name,
1)), pickle_module=pickle)
else:
# Initialize weights
generator.apply(weights_init_normal)
discriminator.apply(weights_init_normal)
# =============================================================================
# Tensor type
Tensor = torch.cuda.FloatTensor if cuda else torch.FloatTensor
# =============================================================================
# Training
# =============================================================================
# Book keeping
train_hist = {}
train_hist['D_losses'] = []
train_hist['G_losses'] = []
train_hist['per_epoch_ptimes'] = []
train_hist['total_ptime'] = []
train_hist['test_loss'] = {
'mse': [],
'psnr': [],
'ssim': []
}
# Get the device we're working on.
device = torch.device("cuda:0" if torch.cuda.is_available() else "cpu")
# Create all scenrios: Total will 15, but remove 0000 and 1111
scenarios = list(map(list, itertools.product([0, 1], repeat=4)))
# Generate new label placeholders for this particular batch
# This is for the G (Changed below)
# label_map = torch.ones((opt.batch_size, 4, opt.img_height, opt.img_width), requires_grad=False).cuda().type(
# torch.cuda.FloatTensor)
# This is for D (Changed below)
if opt.type == 'T1':
scenarios = [x for x in scenarios if x[0] == 0]
else:
scenarios = [x for x in scenarios if x[1] == 0]
label_list = torch.from_numpy(np.ones((opt.batch_size,
patch[0],
patch[1],
patch[2]))).cuda().type(torch.cuda.FloatTensor)
# remove the empty scenario and all available scenario
scenarios.remove([0,0,0,0])
# scenarios.remove([1,1,1,1]) # this is no longer invalid in this case.
# sort the scenarios according to decreasing difficulty. Easy scenarios last, and difficult ones first.
scenarios.sort(key=lambda x: x.count(1))
logger.info("Starting Training")
start_time = time.time()
for epoch in range(opt.epoch, opt.n_epochs, 1):
D_losses = []
D_real_losses = []
D_fake_losses = []
G_train_l1_losses = []
G_train_losses = []
G_losses = []
synth_losses = []
# patient: Whole patient dictionary containing image, seg, name etc.
# x_patient: Just the images of a single patient
# x_r: Batch of images taken from x_patient according to the batch size specified.
# x_z: Batch from x_r where some sequences are imputed with noise for input to G
epoch_start_time = time.time()
for idx_pat, patient in enumerate(n_dataloader):
logger.info("Current idx_pat: {}".format(idx_pat))
# if idx_pat > opt.train_patient_idx:
# logger.info("Now testing on patient {}".format(opt.train_patient_idx + 1))
# main_path = os.path.join(root, model, 'scenario_results')
#
# fixed_p = os.path.join(root, model, 'scenario_results', 'viz' + "_" + str(epoch + 1))
#
# logger.info("Saving result as {}".format(fixed_p))
# status = show_intermediate_results(generator, test_patient, save_path=main_path,
# all_scenarios=copy.deepcopy(scenarios), epoch=epoch,
# curr_scenario_range=None,
# batch_size_to_test=opt.batch_size)
# break
# Put the whole patient in GPU to aid quicker training
x_patient = patient['image']
batch_indices = list(range(0, resize_slices, opt.batch_size))
# this shuffles the 2D axial slice batches for efficient training
# tag1
random.shuffle(batch_indices)
# create batches out of this patient
for _num, batch_idx in enumerate(batch_indices):
logger.debug("Patient #{}\nBatch #{}".format(idx_pat, _num))
logger.debug("\tSplicing batch from x_real")
x_r = x_patient[batch_idx:batch_idx + opt.batch_size, ...]
# x_r = x_r.cuda().type(Tensor) # Tensor will be either a cuda dtype or cpu dtype
# Curriculum Learning: Train with easier cases in the first epochs, then start training on harder ones
if opt.c_learning == 1:
# Curriculum Learning: Train with easier cases in the first epochs, then start training on harder ones
if epoch <= 10:
rand_val = torch.Tensor([6]) # last one is the easier, train with that.
if epoch > 10 and epoch <= 20:
rand_val = torch.randint(low=3, high=len(scenarios), size=(1,))
if epoch > 20:
rand_val = torch.randint(low=0, high=len(scenarios), size=(1,))
elif opt.c_learning == 0:
rand_val = torch.randint(low=0, high=14, size=(1,))
elif opt.c_learning == 2:
# always train with the last scenario, means everything present.
rand_val = torch.Tensor([6]) # last one is the easier, train with that.
label_scenario = scenarios[int(rand_val.numpy()[0])]
logger.debug('\tTraining this batch with Scenario: {}'.format(label_scenario))
# create a new x_imputed and x_real with this label scenario
x_z = x_r.clone().cuda()
if opt.discrim_type == 1:
label_list_r = torch.from_numpy(
np.ones((opt.batch_size, patch[0], patch[1], patch[2]))).cuda().type(
torch.cuda.FloatTensor)
else:
# This is for D when training on real images (Unchanged)
label_list_r = torch.from_numpy(np.ones((opt.batch_size, 4))).cuda().type(Tensor)
# impute noise to the input of G
for idx, k in enumerate(label_scenario):
if k == 0:
x_z[:, idx, ...] = torch.ones((opt.img_height, opt.img_width), device=device) * -1.0
# label_map[:, idx, ...] = 0
#
# # this works with both discriminator types.
# if opt.dataset != 'ISLES2015' and opt.dataset != 'BRATS2015':
# label_list[:, idx] = 0
#
# elif k == 1:
# # label_map[:, idx, ...] = 1
#
# # this works with both discriminator types.
# if opt.dataset != 'ISLES2015' and opt.dataset != 'BRATS2015':
# label_list[:, idx] = 1
# The output is ALWAYS synthesized, so its zero always. ISLES2015 outputs just FLAIR
label_list[:, 0] = 0
# TRAIN GENERATOR G
logger.debug('\tTraining Generator')
generator.zero_grad()
optimizer_G.zero_grad()
# ADDING A RELU AT THE END OF GENERATOR FOR ISLES2015, to make sure values are positive
fake_x = generator(x_z)
if opt.type == "T1":
SEQ_IDX = 0
elif opt.type == "T2":
SEQ_IDX = 1
# if opt.dataset != 'ISLES2015' and opt.dataset != "BRATS2015":
# fake_x = impute_reals_into_fake(x_z, fake_x, label_scenario)
#
# if opt.dataset != 'ISLES2015' and opt.dataset != "BRATS2015":
# pred_fake = discriminator(fake_x, x_r)
# else:
# I may have to unsqueeze
pred_fake = discriminator(fake_x, x_r[:, SEQ_IDX, ...].unsqueeze(1))
# G_train_loss = BCE_loss(D_result, label_list)
# The discriminator should think that the pred_fake is real, so we minimize the loss between pred_fake
# and label_list_r, ie. make the pred_fake look real, and reducing the error that the discriminator makes
# when predicting it.
if pred_fake.size() != label_list_r.size():
logger.warning('Error!')
import sys
sys.exit(-1)
# fooling the discriminator. We REDUCE this loss value so that it does WELL in predicting pred_fake, and label_list_r
# not backpropagating into discriminator
# TODO
loss_GAN = criterion_GAN(pred_fake.detach(), label_list_r)
# pixel-wise loss
loss_pixel = 0
synth_loss = 0
# if opt.dataset != 'ISLES2015' and opt.dataset != "BRATS2015":
# for idx_curr_label, i in enumerate(label_scenario):
# if i == 0:
# loss_pixel += criterion_pixelwise(fake_x[:, idx_curr_label, ...], x_r[:, idx_curr_label, ...])
#
# synth_loss += mse_fake_vs_real(fake_x[:, idx_curr_label, ...], x_r[:, idx_curr_label, ...])
# else:
# fake_x is already (B, 1, 256, 256)
loss_pixel += criterion_pixelwise(fake_x, x_r[:, SEQ_IDX, ...].unsqueeze(1).type(Tensor))
synth_loss += mse_fake_vs_real(fake_x, x_r[:, SEQ_IDX, ...].unsqueeze(1).type(Tensor))
# logger.debug("Min: {}".format(x_r[:, SEQ_IDX, ...].min()))
# logger.debug("Max: {}".format(x_r[:, SEQ_IDX, ...].max()))
# logger.debug("Mean: {}".format(x_r[:, SEQ_IDX, ...].mean()))
# variable that sets the relative importance to loss_GAN and loss_pixel
lam = 0.9
G_train_total_loss = (1 - lam) * loss_GAN + lam * loss_pixel
G_train_total_loss.backward()
optimizer_G.step()
# save the losses
G_train_l1_losses.append(loss_pixel.data[0])
G_train_losses.append(loss_GAN.data[0])
G_losses.append(G_train_total_loss.data[0])
synth_losses.append(synth_loss.data[0])
# TRAIN DISCRIMINATOR D
# this takes in the real x as X-INPUT and real x as Y-INPUT
logger.debug('\tTraining Discriminator')
discriminator.zero_grad()
optimizer_D.zero_grad()
# real loss
# if opt.dataset == 'ISLES2015' or opt.dataset == "BRATS2015":
pred_real = discriminator(
x_r[:, SEQ_IDX, ...].unsqueeze(1),
x_r[:, SEQ_IDX, ...].unsqueeze(1))
# else:
# pred_real = discriminator(x_r, x_r)
loss_real = criterion_GAN(pred_real, label_list_r)
# fake loss
# fake_x = generator(x_z, label_map)s
fake_x = generator(x_z)
# if opt.dataset != 'ISLES2015' and opt.dataset != "BRATS2015":
# fake_x = impute_reals_into_fake(x_z, fake_x.detach(), label_scenario)
#
# if opt.dataset != 'ISLES2015' and opt.dataset != "BRATS2015":
# pred_fake = discriminator(fake_x.detach(), x_r)
# else:
sh = fake_x.shape
pred_fake = discriminator(fake_x.detach(),
x_r[:, SEQ_IDX, ...].unsqueeze(1))
loss_fake = criterion_GAN(pred_fake, label_list)
D_train_loss = 0.5 * (loss_real + loss_fake)
# for printing purposes
D_real_losses.append(loss_real.data[0])
D_fake_losses.append(loss_fake.data[0])
D_losses.append(D_train_loss.data[0])
D_train_loss.backward()
optimizer_D.step()
logger.info(" E [{}/{}] P #{} ".format(epoch, opt.n_epochs,
idx_pat) + 'B [%d/%d] - loss_d: [real: %.5f, fake: %.5f, comb: %.5f], loss_g: [gan: %.5f, l1: %.5f, comb: %.5f], synth_loss_mse(ut): %.5f' % (
(_num + 1), resize_slices // opt.batch_size, torch.mean(torch.FloatTensor(D_real_losses)),
torch.mean(torch.FloatTensor(D_fake_losses)),
torch.mean(torch.FloatTensor(D_losses)), torch.mean(torch.FloatTensor(G_train_losses)),
torch.mean(torch.FloatTensor(G_train_l1_losses)), torch.mean(torch.FloatTensor(G_losses)),
torch.mean(torch.FloatTensor(synth_losses))))
# Check if we have trained with exactly opt.train_patient_idx patients (if opt.train_patient_idx is 10, then idx_pat will be 9, so this condition will evaluate to true
if idx_pat + 1 == opt.train_patient_idx:
logger.info('Testing on test set for this fold')
main_path = os.path.join(root, model, "{}".format(opt.dataset), 'scenario_results')
logger.info("Saving results at {}".format(main_path))
generator.eval()
logger.info("Calculating metric on test set")
result_dict_test = calculate_metrics(generator, test_patient, save_path=main_path,
all_scenarios=copy.deepcopy(scenarios), epoch=epoch,
curr_scenario_range=[6, 7],
batch_size_to_test=1, dataset="BRATS2015", # keep this to B15 to maintain compatibility
seq_type=opt.type)
logger.info("\t\tTesting Performance Numbers")
printTable(result_dict_test)
gc.collect()
logger.info("Writing detailed visualizations for each scenario")
status = show_intermediate_results(generator, test_patient, save_path=main_path,
all_scenarios=copy.deepcopy(scenarios), epoch=epoch,
curr_scenario_range=[6, 7],
batch_size_to_test=opt.batch_size, seq_type=opt.type,
dataset="BRATS2015") # keep this to B15 to maintain
generator.train()
gc.collect()
break
epoch_end_time = time.time()
per_epoch_ptime = epoch_end_time - epoch_start_time
print(
'[%d/%d] - ptime: %.2f, loss_d: [real: %.5f, fake: %.5f, comb: %.5f], loss_g: [gan: %.5f, l1: %.5f, comb: %.5f], '
'synth_loss_mse(ut): %.5f' % (
(epoch + 1), opt.n_epochs, per_epoch_ptime, torch.mean(torch.FloatTensor(D_real_losses)),
torch.mean(torch.FloatTensor(D_fake_losses)),
torch.mean(torch.FloatTensor(D_losses)), torch.mean(torch.FloatTensor(G_train_losses)),
torch.mean(torch.FloatTensor(G_train_l1_losses)), torch.mean(torch.FloatTensor(G_losses)),
torch.mean(torch.FloatTensor(synth_losses))))
# Checkpoint the models
gen_state_checkpoint = {
'epoch': epoch + 1,
'arch': opt.model_name,
'state_dict': generator.state_dict(),
'optimizer' : optimizer_G.state_dict(),
}
des_state_checkpoint = {
'epoch': epoch + 1,
'arch': opt.model_name,
'state_dict': discriminator.state_dict(),
'optimizer': optimizer_D.state_dict(),
}
save_checkpoint(gen_state_checkpoint, os.path.join(root, model, 'generator_param_{}_{}.pkl'.format(model, epoch + 1)),
pickle_module=pickle)
save_checkpoint(des_state_checkpoint,
os.path.join(root, model, 'discriminator_param_{}_{}.pkl'.format(model, epoch + 1)),
pickle_module=pickle)
with open(os.path.join(root, model, "{}".format(opt.dataset),
'result_dict_test_epoch_{}.pkl'.format(epoch)), 'wb') as f:
pickle.dump(result_dict_test, f)
logger.info('[Testing] num_pats: {}, mse: {:.5f}, psnr: {:.5f}, ssim: {:.5f}'.format(
opt.test_pats,
result_dict_test['mean']['mse'],
result_dict_test['mean']['psnr'],
result_dict_test['mean']['ssim']
))
train_hist['D_losses'].append(torch.mean(torch.FloatTensor(D_losses)))
train_hist['G_losses'].append(torch.mean(torch.FloatTensor(G_losses)))
train_hist['test_loss']['mse'].append(result_dict_test['mean']['mse'])
train_hist['test_loss']['psnr'].append(result_dict_test['mean']['psnr'])
train_hist['test_loss']['ssim'].append(result_dict_test['mean']['ssim'])
train_hist['per_epoch_ptimes'].append(per_epoch_ptime)
end_time = time.time()
total_ptime = end_time - start_time
train_hist['total_ptime'].append(total_ptime)
print("Avg one epoch ptime: %.2f, total %d epochs ptime: %.2f" % (
torch.mean(torch.FloatTensor(train_hist['per_epoch_ptimes'])), opt.n_epochs, total_ptime))
with open(os.path.join(root, model, 'train_hist.pkl'), 'wb') as f:
pickle.dump(train_hist, f)