def create_data_gen_pipeline(patient_data, cf, test_pids=None, do_aug=True):
"""
create mutli-threaded train/val/test batch generation and augmentation pipeline.
:param patient_data: dictionary containing one dictionary per patient in the train/test subset
:param test_pids: (optional) list of test patient ids, calls the test generator.
:param do_aug: (optional) whether to perform data augmentation (training) or not (validation/testing)
:return: multithreaded_generator
"""
if test_pids is None:
data_gen = BatchGenerator(patient_data, batch_size=cf.batch_size,
pre_crop_size=cf.pre_crop_size, dim=cf.dim)
else:
data_gen = TestGenerator(patient_data, batch_size=cf.batch_size, n_batches=None,
pre_crop_size=cf.pre_crop_size, test_pids=test_pids, dim=cf.dim)
cf.n_workers = 1
my_transforms = []
if do_aug:
mirror_transform = Mirror(axes=(2, 3))
my_transforms.append(mirror_transform)
spatial_transform = SpatialTransform(patch_size=cf.patch_size[:cf.dim],
patch_center_dist_from_border=cf.da_kwargs['rand_crop_dist'],
do_elastic_deform=cf.da_kwargs['do_elastic_deform'],
alpha=cf.da_kwargs['alpha'], sigma=cf.da_kwargs['sigma'],
do_rotation=cf.da_kwargs['do_rotation'], angle_x=cf.da_kwargs['angle_x'],
angle_y=cf.da_kwargs['angle_y'], angle_z=cf.da_kwargs['angle_z'],
do_scale=cf.da_kwargs['do_scale'], scale=cf.da_kwargs['scale'],
random_crop=cf.da_kwargs['random_crop'])
my_transforms.append(spatial_transform)
else:
my_transforms.append(CenterCropTransform(crop_size=cf.patch_size[:cf.dim]))
my_transforms.append(ConvertSegToOnehotTransform(classes=(0, 1, 2)))
my_transforms.append(TransposeChannels())
all_transforms = Compose(my_transforms)
multithreaded_generator = MultiThreadedAugmenter(data_gen, all_transforms, num_processes=cf.n_workers, seeds=range(cf.n_workers))
return multithreaded_generator
def create_data_gen_pipeline(patient_data, cf, is_training=True):
"""
create mutli-threaded train/val/test batch generation and augmentation pipeline.
:param patient_data: dictionary containing one dictionary per patient in the train/test subset.
:param is_training: (optional) whether to perform data augmentation (training) or not (validation/testing)
:return: multithreaded_generator
"""
# create instance of batch generator as first element in pipeline.
data_gen = BatchGenerator(patient_data, batch_size=cf.batch_size, cf=cf)
# add transformations to pipeline.
my_transforms = []
if is_training:
mirror_transform = Mirror(axes=np.arange(cf.dim))
my_transforms.append(mirror_transform)
spatial_transform = SpatialTransform(patch_size=cf.patch_size[:cf.dim],
patch_center_dist_from_border=cf.da_kwargs['rand_crop_dist'],
do_elastic_deform=cf.da_kwargs['do_elastic_deform'],
alpha=cf.da_kwargs['alpha'], sigma=cf.da_kwargs['sigma'],
do_rotation=cf.da_kwargs['do_rotation'], angle_x=cf.da_kwargs['angle_x'],
angle_y=cf.da_kwargs['angle_y'], angle_z=cf.da_kwargs['angle_z'],
do_scale=cf.da_kwargs['do_scale'], scale=cf.da_kwargs['scale'],
random_crop=cf.da_kwargs['random_crop'])
my_transforms.append(spatial_transform)
# print('debug spatial_transform, my_transforms')
# import IPython;IPython.embed()
else:
my_transforms.append(CenterCropTransform(crop_size=cf.patch_size[:cf.dim]))
my_transforms.append(ConvertSegToBoundingBoxCoordinates(cf.dim, get_rois_from_seg_flag=False, class_specific_seg_flag=cf.class_specific_seg_flag))
all_transforms = Compose(my_transforms)
# multithreaded_generator = SingleThreadedAugmenter(data_gen, all_transforms)
multithreaded_generator = MultiThreadedAugmenter(data_gen, all_transforms, num_processes=cf.n_workers, seeds=range(cf.n_workers))
return multithreaded_generator
def create_data_gen_pipeline(cf, patient_data, do_aug=True, **kwargs):
"""
create mutli-threaded train/val/test batch generation and augmentation pipeline.
:param patient_data: dictionary containing one dictionary per patient in the train/test subset.
:param is_training: (optional) whether to perform data augmentation (training) or not (validation/testing)
:return: multithreaded_generator
"""
# create instance of batch generator as first element in pipeline.
data_gen = BatchGenerator(cf, patient_data, **kwargs)
my_transforms = []
if do_aug:
if cf.da_kwargs["mirror"]:
mirror_transform = Mirror(axes=cf.da_kwargs['mirror_axes'])
my_transforms.append(mirror_transform)
spatial_transform = SpatialTransform(patch_size=cf.patch_size[:cf.dim],
patch_center_dist_from_border=cf.da_kwargs['rand_crop_dist'],
do_elastic_deform=cf.da_kwargs['do_elastic_deform'],
alpha=cf.da_kwargs['alpha'], sigma=cf.da_kwargs['sigma'],
do_rotation=cf.da_kwargs['do_rotation'], angle_x=cf.da_kwargs['angle_x'],
angle_y=cf.da_kwargs['angle_y'], angle_z=cf.da_kwargs['angle_z'],
do_scale=cf.da_kwargs['do_scale'], scale=cf.da_kwargs['scale'],
random_crop=cf.da_kwargs['random_crop'])
my_transforms.append(spatial_transform)
else:
my_transforms.append(CenterCropTransform(crop_size=cf.patch_size[:cf.dim]))
my_transforms.append(ConvertSegToBoundingBoxCoordinates(cf.dim, cf.roi_items, False, cf.class_specific_seg))
all_transforms = Compose(my_transforms)
# multithreaded_generator = SingleThreadedAugmenter(data_gen, all_transforms)
multithreaded_generator = MultiThreadedAugmenter(data_gen, all_transforms, num_processes=data_gen.n_filled_threads,
seeds=range(data_gen.n_filled_threads))
return multithreaded_generator
def main():
# assign global args
global args
args = parser.parse_args()
# make a folder for the experiment
general_folder_name = args.output_path
try:
os.mkdir(general_folder_name)
except OSError:
pass
# create train, test split, return the indices, patients in test_split wont be seen during whole training
train_idx, val_idx, test_idx = CreateTrainValTestSplit(
HistoFile_path=args.input_file,
num_splits=args.num_splits,
num_test_folds=args.num_test_folds,
num_val_folds=args.num_val_folds,
seed=args.seed)
IDs = train_idx + val_idx
print('size of training set {}'.format(len(train_idx)))
print('size of validation set {}'.format(len(val_idx)))
print('size of test set {}'.format(len(test_idx)))
# data loading
Data = ProstataData(args.input_file) #For details on this class see README
# train and validate
for cv in range(args.cv_start, args.cv_end):
best_epoch = 0
train_loss = []
val_loss = []
# define patients for training and validation
train_idx, val_idx = split_training(IDs,
len_val=62,
cv=cv,
cv_runs=args.cv_number)
oversampling_factor, Slices_total, Natural_probability_tu_slice, Natural_probability_PRO_slice = get_oversampling(
Data,
train_idx=sorted(train_idx),
Batch_Size=args.b,
patch_size=args.patch_size)
training_batches = Slices_total / args.b
lr = args.lr
base_lr = args.lr
args.seed += 1
print('train_idx', train_idx, len(train_idx))
print('val_idx', val_idx, len(val_idx))
# get class frequencies
print('calculating class frequencie')
Tumor_frequencie_ADC, Prostate_frequencie_ADC, Background_frequencie_ADC,\
Tumor_frequencie_T2, Prostate_frequencie_T2, Background_frequencie_T2\
, ADC_mean, ADC_std, BVAL_mean, BVAL_std, T2_mean, T2_std \
= get_class_frequencies(Data, train_idx, patch_size=args.patch_size)
print ADC_mean, ADC_std, BVAL_mean, BVAL_std, T2_mean, T2_std
print('ADC', Tumor_frequencie_ADC, Prostate_frequencie_ADC,
Background_frequencie_ADC)
print('T2', Tumor_frequencie_T2, Prostate_frequencie_T2,
Background_frequencie_T2)
all_ADC = np.float(Background_frequencie_ADC +
Prostate_frequencie_ADC + Tumor_frequencie_ADC)
all_T2 = np.float(Background_frequencie_T2 + Prostate_frequencie_T2 +
Tumor_frequencie_T2)
print all_ADC
print all_T2
W1_ADC = 1 / (Background_frequencie_ADC / all_ADC)**0.25
W2_ADC = 1 / (Prostate_frequencie_ADC / all_ADC)**0.25
W3_ADC = 1 / (Tumor_frequencie_ADC / all_ADC)**0.25
Wa_ADC = W1_ADC / (W1_ADC + W2_ADC + W3_ADC)
Wb_ADC = W2_ADC / (W1_ADC + W2_ADC + W3_ADC)
Wc_ADC = W3_ADC / (W1_ADC + W2_ADC + W3_ADC)
print 'Weights ADC', Wa_ADC, Wb_ADC, Wc_ADC
weight_ADC = (Wa_ADC, Wb_ADC, Wc_ADC)
W1_T2 = 1 / (Background_frequencie_T2 / all_T2)**0.25
W2_T2 = 1 / (Prostate_frequencie_T2 / all_T2)**0.25
W3_T2 = 1 / (Tumor_frequencie_T2 / all_T2)**0.25
Wa_T2 = W1_T2 / (W1_T2 + W2_T2 + W3_T2)
Wb_T2 = W2_T2 / (W1_T2 + W2_T2 + W3_T2)
Wc_T2 = W3_T2 / (W1_T2 + W2_T2 + W3_T2)
print 'Weights T2', Wa_T2, Wb_T2, Wc_T2
weight_T2 = (Wa_T2, Wb_T2, Wc_T2)
# define model
Net = UNetPytorch(in_shape=(3, args.patch_size[0], args.patch_size[1]))
Net_Name = 'UNetPytorch'
model = Net.cuda()
# model parameter
optimizer = torch.optim.Adam(model.parameters(),
lr,
weight_decay=args.weight_decay)
criterion_ADC = CrossEntropyLoss2d(
weight=torch.FloatTensor(weight_ADC)).cuda()
criterion_T2 = CrossEntropyLoss2d(
weight=torch.FloatTensor(weight_T2)).cuda()
# new folder name for cv
folder_name = general_folder_name + '/CV_{}'.format(cv)
try:
os.mkdir(folder_name)
except OSError:
pass
checkpoint_file = folder_name + '/checkpoint_' + '{}.pth.tar'.format(
Net_Name)
# augmentation
for epoch in range(args.epochs):
torch.manual_seed(args.seed + epoch + cv)
np.random.seed(epoch + cv)
np.random.shuffle(train_idx)
if epoch == 0:
my_transforms = []
spatial_transform = SpatialTransform(
args.patch_size,
np.array(args.patch_size) // 2,
do_elastic_deform=True,
alpha=(100., 450.),
sigma=(13., 17.),
do_rotation=True,
angle_z=(-np.pi / 2., np.pi / 2.),
do_scale=True,
scale=(0.75, 1.25),
border_mode_data='constant',
border_cval_data=0,
order_data=3,
random_crop=True)
resample_transform = ResampleTransform(zoom_range=(0.7, 1.3))
brightness_transform = BrightnessTransform(0.0, 0.1, True)
my_transforms.append(resample_transform)
my_transforms.append(
ContrastAugmentationTransform((0.75, 1.25), True))
my_transforms.append(brightness_transform)
my_transforms.append(Mirror((2, 3)))
all_transforms = Compose(my_transforms)
sometimes_spatial_transforms = RndTransform(
spatial_transform,
prob=args.p,
alternative_transform=CenterCropTransform(args.patch_size))
sometimes_other_transforms = RndTransform(all_transforms,
prob=1.0)
final_transform = Compose(
[sometimes_spatial_transforms, sometimes_other_transforms])
Center_Crop = CenterCropTransform(args.patch_size)
if epoch == 30:
my_transforms = []
spatial_transform = SpatialTransform(
args.patch_size,
np.array(args.patch_size) // 2,
do_elastic_deform=True,
alpha=(0., 250.),
sigma=(11., 14.),
do_rotation=True,
angle_z=(-np.pi / 2., np.pi / 2.),
do_scale=True,
scale=(0.85, 1.15),
border_mode_data='constant',
border_cval_data=0,
order_data=3,
random_crop=True)
resample_transform = ResampleTransform(zoom_range=(0.8, 1.2))
brightness_transform = BrightnessTransform(0.0, 0.1, True)
my_transforms.append(resample_transform)
my_transforms.append(
ContrastAugmentationTransform((0.85, 1.15), True))
my_transforms.append(brightness_transform)
all_transforms = Compose(my_transforms)
sometimes_spatial_transforms = RndTransform(
spatial_transform,
prob=args.p,
alternative_transform=CenterCropTransform(args.patch_size))
sometimes_other_transforms = RndTransform(all_transforms,
prob=1.0)
final_transform = Compose(
[sometimes_spatial_transforms, sometimes_other_transforms])
Center_Crop = CenterCropTransform(args.patch_size)
if epoch == 50:
my_transforms = []
spatial_transform = SpatialTransform(
args.patch_size,
np.array(args.patch_size) // 2,
do_elastic_deform=True,
alpha=(0., 150.),
sigma=(10., 12.),
do_rotation=True,
angle_z=(-np.pi / 2., np.pi / 2.),
do_scale=True,
scale=(0.85, 1.15),
border_mode_data='constant',
border_cval_data=0,
order_data=3,
random_crop=False)
resample_transform = ResampleTransform(zoom_range=(0.9, 1.1))
brightness_transform = BrightnessTransform(0.0, 0.1, True)
my_transforms.append(resample_transform)
my_transforms.append(
ContrastAugmentationTransform((0.95, 1.05), True))
my_transforms.append(brightness_transform)
all_transforms = Compose(my_transforms)
sometimes_spatial_transforms = RndTransform(
spatial_transform,
prob=args.p,
alternative_transform=CenterCropTransform(args.patch_size))
sometimes_other_transforms = RndTransform(all_transforms,
prob=1.0)
final_transform = Compose(
[sometimes_spatial_transforms, sometimes_other_transforms])
Center_Crop = CenterCropTransform(args.patch_size)
train_loader = BatchGenerator(
Data,
BATCH_SIZE=args.b,
split_idx=train_idx,
seed=args.seed,
ProbabilityTumorSlices=oversampling_factor,
epoch=epoch,
ADC_mean=ADC_mean,
ADC_std=ADC_std,
BVAL_mean=BVAL_mean,
BVAL_std=BVAL_std,
T2_mean=T2_mean,
T2_std=T2_std)
val_loader = BatchGenerator(Data,
BATCH_SIZE=0,
split_idx=val_idx,
seed=args.seed,
ProbabilityTumorSlices=None,
epoch=epoch,
test=True,
ADC_mean=ADC_mean,
ADC_std=ADC_std,
BVAL_mean=BVAL_mean,
BVAL_std=BVAL_std,
T2_mean=T2_mean,
T2_std=T2_std)
#train on training set
train_losses = train(train_loader=train_loader,
model=model,
optimizer=optimizer,
criterion_ADC=criterion_ADC,
criterion_T2=criterion_T2,
final_transform=final_transform,
workers=args.workers,
seed=args.seed,
training_batches=training_batches)
train_loss.append(train_losses)
# evaluate on validation set
val_losses = validate(val_loader=val_loader,
model=model,
folder_name=folder_name,
criterion_ADC=criterion_ADC,
criterion_T2=criterion_T2,
split_ixs=val_idx,
epoch=epoch,
workers=1,
Center_Crop=Center_Crop,
seed=args.seed)
val_loss.append(val_losses)
# write TrainingsCSV to folder name
TrainingsCSV = pd.DataFrame({
'train_loss': train_loss,
'val_loss': val_loss
})
TrainingsCSV.to_csv(folder_name + '/TrainingsCSV.csv')
if val_losses <= min(val_loss):
best_epoch = epoch
print 'best epoch', epoch
save_checkpoint(
{
'epoch': epoch,
'arch': args.arch,
'state_dict': model.state_dict(),
'optimizer': optimizer.state_dict()
},
filename=checkpoint_file)
optimizer, lr = adjust_learning_rate(optimizer, base_lr, epoch)
# delete all output except best epoch
clear_image_data(folder_name, best_epoch, epoch)