def main():
args = get_arguments()
utils.make_dirs(args.save)
name_model = args.model + "_" + args.dataset_name + "_" + utils.datestr()
# TODO visual3D_temp.Basewriter package
writer = SummaryWriter(log_dir='../runs/' + name_model, comment=name_model)
training_generator, val_generator, full_volume, affine = medical_loaders.generate_datasets(
args, path='.././datasets')
model, optimizer = medzoo.create_model(args)
criterion = DiceLoss(classes=11, skip_index_after=args.classes)
if args.cuda:
torch.cuda.manual_seed(seed)
model = model.cuda()
print("Model transferred in GPU.....")
print("START TRAINING...")
for epoch in range(1, args.nEpochs + 1):
train_stats = train.train_dice(args, epoch, model, training_generator,
optimizer, criterion)
val_stats = train.test_dice(args, epoch, model, val_generator,
criterion)
#old
utils.write_train_val_score(writer, epoch, train_stats, val_stats)
model.save_checkpoint(args.save,
epoch,
val_stats[0],
optimizer=optimizer)
def main():
args = get_arguments()
utils.reproducibility(args, seed)
utils.make_dirs(args.save)
training_generator, val_generator, full_volume, affine = medical_loaders.generate_datasets(
args, path='/home/mulns/My_project/VV/MedicalZooPytorch/datasets')
model, optimizer = medzoo.create_model(args)
criterion = DiceLoss(classes=args.classes)
if args.cuda:
# model=torch.nn.DataParallel(model)
model = model.cuda()
print("Model transferred in GPU.....")
trainer = train.Trainer(args,
model,
criterion,
optimizer,
train_data_loader=training_generator,
valid_data_loader=val_generator,
lr_scheduler=None)
print("START TRAINING...")
trainer.training()
def get_viz_set(self, test_subject=0):
"""
Returns total 3d input volumes (t1 and t2 or more) and segmentation maps
3d total vol shape : torch.Size([1, 144, 192, 256])
"""
TEST_SUBJECT = test_subject
path_T1 = self.list_IDsT1[TEST_SUBJECT]
path_T1ce = self.list_IDsT1ce[TEST_SUBJECT]
path_T2 = self.list_IDsT2[TEST_SUBJECT]
path_flair = self.list_IDsFlair[TEST_SUBJECT]
label_path = self.labels[TEST_SUBJECT]
segmentation_map = img_loader.load_medical_image(label_path,
viz3d=True)
img_t1_tensor = img_loader.load_medical_image(path_T1,
type="T1",
viz3d=True)
img_t1ce_tensor = img_loader.load_medical_image(path_T1ce,
type="T1ce",
viz3d=True)
img_t2_tensor = img_loader.load_medical_image(path_T2,
type="T2",
viz3d=True)
img_flair_tensor = img_loader.load_medical_image(path_flair,
type="FLAIR",
viz3d=True)
### TO DO SAVE FULL VOLUME AS numpy
if self.save:
self.full_volume = []
segmentation_map = segmentation_map
img_t1_tensor = self.find_reshaped_vol(img_t1_tensor)
img_t1ce_tensor = self.find_reshaped_vol(img_t1ce_tensor)
img_t2_tensor = self.find_reshaped_vol(img_t2_tensor)
img_flair_tensor = self.find_reshaped_vol(img_flair_tensor)
self.sub_vol_path = self.root + '/MICCAI_BraTS_2018_Data_Training/generated/visualize/'
utils.make_dirs(self.sub_vol_path)
for i in range(len(img_t1_tensor)):
filename = self.sub_vol_path + 'id_' + str(
TEST_SUBJECT) + '_VIZ_' + str(i) + '_'
f_t1 = filename + 'T1.npy'
f_t1ce = filename + 'T1CE.npy'
f_t2 = filename + 'T2.npy'
f_flair = filename + 'FLAIR.npy'
f_seg = filename + 'seg.npy'
np.save(f_t1, img_t1_tensor[i])
np.save(f_t1ce, img_t1ce_tensor[i])
np.save(f_t2, img_t2_tensor[i])
np.save(f_flair, img_flair_tensor[i])
np.save(f_seg, segmentation_map[i])
self.full_volume.append(tuple((f_t1, f_t2, f_seg)))
print("Full validation volume has been generated")
else:
self.full_volume = tuple(
(img_t1_tensor, img_t2_tensor, segmentation_map))
def main():
args = get_arguments()
os.environ["CUDA_VISIBLE_DEVICES"] = "0"
## FOR REPRODUCIBILITY OF RESULTS
seed = 1777777
utils.reproducibility(args, seed)
utils.make_dirs(args.save)
utils.save_arguments(args, args.save)
training_generator, val_generator, full_volume, affine = medical_loaders.generate_datasets(
args, path='.././datasets')
model, optimizer = medzoo.create_model(args)
criterion = create_loss('CrossEntropyLoss')
criterion = DiceLoss(classes=args.classes,
weight=torch.tensor([0.1, 1, 1, 1]).cuda())
if args.cuda:
model = model.cuda()
print("Model transferred in GPU.....")
trainer = Trainer(args,
model,
criterion,
optimizer,
train_data_loader=training_generator,
valid_data_loader=val_generator,
lr_scheduler=None)
print("START TRAINING...")
trainer.training()
def main():
args = get_arguments()
utils.reproducibility(args, seed)
utils.make_dirs(args.save)
training_generator, val_generator, full_volume, affine = medical_loaders.generate_datasets(args,
path='.././datasets')
def main():
args = get_arguments()
os.environ["CUDA_VISIBLE_DEVICES"] = "1"
## FOR REPRODUCIBILITY OF RESULTS
seed = 1777777
torch.manual_seed(seed)
if args.cuda:
torch.cuda.manual_seed(seed)
np.random.seed(seed)
cudnn.deterministic = True
# FOR FASTER GPU TRAINING WHEN INPUT SIZE DOESN'T VARY
# cudnn.benchmark = True
utils.make_dirs(args.save)
training_generator, val_generator, full_volume, affine = medical_loaders.generate_datasets(args,
path='.././datasets')
model, optimizer = medzoo.create_model(args)
criterion = DiceLoss(classes=args.classes)
if args.cuda:
model = model.cuda()
print("Model transferred in GPU.....")
trainer = Trainer(args, model, criterion, optimizer, train_data_loader=training_generator,
valid_data_loader=val_generator, lr_scheduler=None)
print("START TRAINING...")
trainer.training()
def __init__(self,
mode,
sub_task='lung',
split=0.2,
fold=0,
n_classes=2,
samples=10,
dataset_path='../datasets',
crop_dim=(32, 32, 32)):
print("MANDIBLE SEGMENTATION DATASET")
self.CLASSES = n_classes
self.fold = int(fold)
self.crop_size = crop_dim
self.full_vol_dim = (256, 256, 192) # width, height,slice
self.mode = mode
self.full_volume = None
self.affine = None
self.list = []
self.samples = samples
subvol = '_vol_' + str(crop_dim[0]) + 'x' + str(
crop_dim[1]) + 'x' + str(crop_dim[2])
self.sub_vol_path = dataset_path + '/MRBrainS18/subvol_generated/' + mode + subvol + '/'
utils.make_dirs(self.sub_vol_path)
self.train_images, self.train_labels, self.val_labels, self.val_images = [], [], [], []
list_images = sorted(
glob.glob(os.path.join(dataset_path, 'MRBrainS18/images/*')))
list_labels = sorted(
glob.glob(os.path.join(dataset_path, 'MRBrainS18/labels/*')))
len_of_data = len(list_images)
for i in range(len_of_data):
if i >= (self.fold * int(split * len_of_data)) and i < (
(self.fold * int(split * len_of_data)) +
int(split * len_of_data)):
self.train_images.append(list_images[i])
self.train_labels.append(list_labels[i])
else:
self.val_images.append(list_images[i])
self.val_labels.append(list_labels[i])
if (mode == 'train'):
self.list_IDs = self.train_images
self.list_labels = self.train_labels
elif (mode == 'val'):
self.list_IDs = self.val_images
self.list_labels = self.val_labels
self.list = create_sub_volumes(self.list_IDs,
self.list_labels,
dataset_name='covid19seg',
mode=mode,
samples=samples,
full_vol_dim=self.full_vol_dim,
crop_size=self.crop_size,
sub_vol_path=self.sub_vol_path)
print("{} SAMPLES = {}".format(mode, len(self.list)))
def main():
args = get_arguments()
utils.reproducibility(args, seed)
utils.make_dirs(args.save)
training_generator, val_generator, full_volume, affine = medical_loaders.generate_datasets(
args, path='.././datasets')
model, optimizer = medzoo.create_model(args)
criterion = DiceLoss(classes=args.classes)
if args.cuda:
model = model.cuda()
print("Model transferred in GPU.....")
trainer = train.Trainer(args,
model,
criterion,
optimizer,
train_data_loader=training_generator,
valid_data_loader=val_generator,
lr_scheduler=None)
print("START TRAINING...")
trainer.training()
visualize_3D_no_overlap_new(args, full_volume, affine, model, 10, args.dim)
def main():
args = get_arguments()
seed = 1777777
torch.manual_seed(seed)
if args.cuda:
torch.cuda.manual_seed(seed)
np.random.seed(seed)
cudnn.deterministic = True
cudnn.benchmark = True
utils.make_dirs(args.save)
name_model = args.model + "_" + args.dataset_name + "_" + utils.datestr()
# TODO visual3D_temp.Basewriter package
writer = SummaryWriter(log_dir='../runs/' + name_model, comment=name_model)
training_generator, val_generator, full_volume, affine = medical_loaders.generate_datasets(
args, path='.././datasets')
model, optimizer = medzoo.create_model(args)
if args.cuda:
model = model.cuda()
print("Model transferred in GPU.....")
print("START TRAINING...")
for epoch in range(1, args.nEpochs + 1):
train(args, model, training_generator, optimizer, epoch, writer)
val_metrics, confusion_matrix = validation(args, model, val_generator,
epoch, writer)
def main():
args = get_arguments()
os.environ["CUDA_VISIBLE_DEVICES"] = "0,2"
## FOR REPRODUCIBILITY OF RESULTS
seed = 1777777
utils.reproducibility(args, seed)
utils.make_dirs(args.save)
name_model = args.model + "_" + args.dataset_name + "_" + utils.datestr()
# TODO visual3D_temp.Basewriter package
writer = SummaryWriter(log_dir='../runs/' + name_model, comment=name_model)
training_generator, val_generator, full_volume, affine = medical_loaders.generate_datasets(
args, path='.././datasets')
model, optimizer = medzoo.create_model(args)
if args.cuda:
model = model.cuda()
print("Model transferred in GPU.....")
print("START TRAINING...")
for epoch in range(1, args.nEpochs + 1):
train(args, model, training_generator, optimizer, epoch, writer)
val_metrics, confusion_matrix = validation(args, model, val_generator,
epoch, writer)
def __init__(self, dataset_path='./data', voxels_space=(2, 2, 2), modalities=2, to_canonical=False, save=True):
"""
:param dataset_path: the extracted path that contains the desired images
:param voxels_space: for reshampling the voxel space
:param modalities: 1 for T1 only, 2 for T1 and T2
:param to_canonical: If you want to convert the coordinates to RAS
for more info on this advice here https://www.slicer.org/wiki/Coordinate_systems
:param save: to save the generated data offline for faster reading
and not load RAM
"""
self.root = str(dataset_path)
self.modalities = modalities
self.pathT1 = self.root + '/ixi/T1/'
self.pathT2 = self.root + '/ixi/T2/'
self.save = save
self.CLASSES = 4
self.full_vol_dim = (150, 256, 256) # slice, width, height
self.voxels_space = voxels_space
self.modalities = str(modalities)
self.list = []
self.full_volume = None
self.to_canonical = to_canonical
self.affine = None
subvol = '_vol_' + str(self.voxels_space[0]) + 'x' + str(self.voxels_space[1]) + 'x' + str(
self.voxels_space[2])
if self.save:
self.sub_vol_path = self.root + '/ixi/generated/' + subvol + '/'
utils.make_dirs(self.sub_vol_path)
print(self.pathT1)
self.list_IDsT1 = sorted(glob.glob(os.path.join(self.pathT1, '*T1.nii.gz')))
self.list_IDsT2 = sorted(glob.glob(os.path.join(self.pathT2, '*T2.nii.gz')))
self.affine = img_loader.load_affine_matrix(self.list_IDsT1[0])
self.create_input_data()
def __init__(self, args, mode, dataset_path='../datasets', classes=4, dim=(32, 32, 32), split_id=0, samples=1000,
load=False):
self.mode = mode
self.root = dataset_path
self.classes = classes
dataset_name = "mrbrains" + str(classes)
self.training_path = self.root + '/mrbrains_2018/training'
self.dirs = os.listdir(self.training_path)
self.samples = samples
self.list = []
self.full_vol_size = (240, 240, 48)
self.threshold = 0.1
self.crop_dim = dim
self.list_flair = []
self.list_ir = []
self.list_reg_ir = []
self.list_reg_t1 = []
self.labels = []
self.full_volume = None
self.save_name = self.root + '/mrbrains_2018/training/mrbrains_2018-classes-' + str(
classes) + '-list-' + mode + '-samples-' + str(
samples) + '.txt'
if load:
## load pre-generated data
self.list = utils.load_list(self.save_name)
return
subvol = '_vol_' + str(dim[0]) + 'x' + str(dim[1]) + 'x' + str(dim[2])
self.sub_vol_path = self.root + '/mrbrains_2018/generated/' + mode + subvol + '/'
utils.make_dirs(self.sub_vol_path)
list_reg_t1 = sorted(glob.glob(os.path.join(self.training_path, '*/pr*/*g_T1.nii.gz')))
list_reg_ir = sorted(glob.glob(os.path.join(self.training_path, '*/pr*/*g_IR.nii.gz')))
list_flair = sorted(glob.glob(os.path.join(self.training_path, '*/pr*/*AIR.nii.gz')))
labels = sorted(glob.glob(os.path.join(self.training_path, '*/*egm.nii.gz')))
self.affine = img_loader.load_affine_matrix(list_reg_t1[0])
split_id = int(split_id)
if mode == 'val':
labels = [labels[split_id]]
list_reg_t1 = [list_reg_t1[split_id]]
list_reg_ir = [list_reg_ir[split_id]]
list_flair = [list_flair[split_id]]
self.full_volume = get_viz_set(list_reg_t1, list_reg_ir, list_flair, labels, dataset_name=dataset_name)
else:
labels.pop(split_id)
list_reg_t1.pop(split_id)
list_reg_ir.pop(split_id)
list_flair.pop(split_id)
self.list = create_sub_volumes(list_reg_t1, list_reg_ir, list_flair, labels,
dataset_name=dataset_name, mode=mode,
samples=samples, full_vol_dim=self.full_vol_size,
crop_size=self.crop_dim, sub_vol_path=self.sub_vol_path,
th_percent=self.threshold)
utils.save_list(self.save_name, self.list)
def __init__(self,
mode,
dataset_path='.././datasets',
split_idx=150,
crop_dim=(512, 512),
samples=100,
classes=7,
save=True):
"""
:param mode: 'train','val'
:param image_paths: image dataset paths
:param label_paths: label dataset paths
:param crop_dim: 2 element tuple to decide crop values
:param samples: number of sub-grids to create(patches of the input img)
"""
image_paths = sorted(
glob.glob(
dataset_path +
"/MICCAI_2019_pathology_challenge/Train Imgs/Train Imgs/*.jpg")
)
label_paths = sorted(
glob.glob(dataset_path +
"/MICCAI_2019_pathology_challenge/Labels/*.png"))
# TODO problem with random shuffle in val and train
# TODo cope with 3d affine and full volume for better generalization
image_paths, label_paths = utils.shuffle_lists(image_paths,
label_paths)
self.full_volume = None
self.affine = None
self.slices = 244 # dataset instances
self.mode = mode
self.crop_dim = crop_dim
self.sample_list = []
self.samples = samples
self.save = save
self.root = dataset_path
self.per_image_sample = int(self.samples / self.slices)
if self.per_image_sample < 1:
self.per_image_sample = 1
print("per image sampleeeeee", self.per_image_sample)
sub_grid = '_2dgrid_' + str(crop_dim[0]) + 'x' + str(crop_dim[1])
if self.save:
self.sub_vol_path = self.root + '/MICCAI_2019_pathology_challenge/generated/' + mode + sub_grid + '/'
utils.make_dirs(self.sub_vol_path)
if self.mode == 'train':
self.list_imgs = image_paths[0:split_idx]
self.list_labels = label_paths[0:split_idx]
elif self.mode == 'val':
self.list_imgs = image_paths[split_idx:]
self.list_labels = label_paths[split_idx:]
self.generate_samples()
def __init__(self,
mode,
dataset_path='../datasets',
classes=4,
dim=(32, 32, 32),
fold_id=0,
samples=1000,
save=True):
self.mode = mode
self.root = dataset_path
self.classes = classes
self.training_path = self.root + '/mrbrains_2018/training'
self.dirs = os.listdir(self.training_path)
self.samples = samples
self.save = save
self.list = []
self.full_vol_size = (240, 240, 48)
self.crop_dim = dim
self.fold = str(fold_id)
self.list_flair = []
self.list_ir = []
self.list_reg_ir = []
self.list_reg_t1 = []
self.labels = []
self.full_volume = None
if self.save:
subvol = '_vol_' + str(dim[0]) + 'x' + str(dim[1]) + 'x' + str(
dim[2])
self.sub_vol_path = self.root + '/mrbrains_2018/generated/' + mode + subvol + '/'
utils.make_dirs(self.sub_vol_path)
self.list_reg_t1 = sorted(
glob.glob(os.path.join(self.training_path, '*/pr*/*g_T1.nii.gz')))
self.list_reg_ir = sorted(
glob.glob(os.path.join(self.training_path, '*/pr*/*g_IR.nii.gz')))
self.list_flair = sorted(
glob.glob(os.path.join(self.training_path, '*/pr*/*AIR.nii.gz')))
self.labels = sorted(
glob.glob(os.path.join(self.training_path, '*/*egm.nii.gz')))
self.affine = img_loader.load_affine_matrix(self.list_reg_t1[0])
fold_id = int(fold_id)
if mode == 'val':
self.labels = [self.labels[fold_id]]
self.list_reg_t1 = [self.list_reg_t1[fold_id]]
self.list_reg_ir = [self.list_reg_ir[fold_id]]
self.list_flair = [self.list_flair[fold_id]]
self.get_viz_set()
else:
self.labels.pop(fold_id)
self.list_reg_t1.pop(fold_id)
self.list_reg_ir.pop(fold_id)
self.list_flair.pop(fold_id)
self.get_samples()
def get_viz_set(self, test_subject=0):
"""
Returns total 3d input volumes (t1 and t2 or more) and segmentation maps
3d total vol shape : torch.Size([1, 144, 192, 256])
"""
TEST_SUBJECT = test_subject
path_T1 = self.list_IDsT1[TEST_SUBJECT]
path_T2 = self.list_IDsT2[TEST_SUBJECT]
label_path = self.labels[TEST_SUBJECT]
segmentation_map = img_loader.load_medical_image(label_path,
viz3d=True)
img_t1_tensor = img_loader.load_medical_image(path_T1,
type="T1",
viz3d=True)
img_t2_tensor = img_loader.load_medical_image(path_T2,
type="T2",
viz3d=True)
segmentation_map = self.fix_seg_map(segmentation_map)
### TO DO SAVE FULL VOLUME AS numpy
if self.save:
self.full_volume = []
segmentation_map = segmentation_map.reshape(
-1, self.crop_size[0], self.crop_size[1], self.crop_size[2])
img_t1_tensor = img_t1_tensor.reshape(-1, self.crop_size[0],
self.crop_size[1],
self.crop_size[2])
img_t2_tensor = img_t1_tensor.reshape(-1, self.crop_size[0],
self.crop_size[1],
self.crop_size[2])
self.sub_vol_path = self.root + '/iseg_2017/generated/visualize/'
utils.make_dirs(self.sub_vol_path)
for i in range(len(img_t1_tensor)):
filename = self.sub_vol_path + 'id_' + str(
TEST_SUBJECT) + '_VIZ_' + str(i) + '_'
f_t1 = filename + 'T1.npy'
f_t2 = filename + 'T2.npy'
f_seg = filename + 'seg.npy'
np.save(f_t1, img_t1_tensor[i])
np.save(f_t2, img_t2_tensor[i])
np.save(f_seg, segmentation_map[i])
self.full_volume.append(tuple((f_t1, f_t2, f_seg)))
print("Full validation volume has been generated")
else:
self.full_volume = tuple(
(img_t1_tensor, img_t2_tensor, segmentation_map))
def __init__(self, args):
name_model = args.log_dir + args.model + "_" + args.dataset_name + "_" + utils.datestr(
)
self.writer = SummaryWriter(log_dir=args.log_dir + name_model,
comment=name_model)
utils.make_dirs(args.save)
self.csv_train, self.csv_val = self.create_stats_files(args.save)
self.dataset_name = args.dataset_name
self.classes = args.classes
self.label_names = dict_class_names[args.dataset_name]
self.data = self.create_data_structure()
def main():
args = get_arguments()
utils.reproducibility(args, seed)
utils.make_dirs(args.save)
training_generator, val_generator, full_volume, affine = medical_loaders.generate_datasets(args,
path='.././datasets')
model, optimizer = medzoo.create_model(args)
criterion = DiceLoss(classes=args.classes)
if args.cuda:
model = model.cuda()
trainer = train.Trainer(args, model, criterion, optimizer, train_data_loader=training_generator,
valid_data_loader=val_generator)
trainer.training()
def main():
args = get_arguments()
utils.reproducibility(args, seed)
utils.make_dirs(args.save)
training_generator, val_generator, full_volume, affine = medical_loaders.generate_datasets(args,
path='.././datasets')
model, optimizer = medzoo.create_model(args)
criterion = DiceLoss(classes=args.classes) # ,skip_index_after=2,weight=torch.tensor([0.00001,1,1,1]).cuda())
if args.cuda:
model = model.cuda()
print("Model transferred in GPU.....")
trainer = train.Trainer(args, model, criterion, optimizer, train_data_loader=training_generator,
valid_data_loader=val_generator)
print("START TRAINING...")
trainer.training()
def main():
args = get_arguments()
utils.reproducibility(args, seed)
utils.make_dirs(args.save)
training_generator, val_generator, full_volume, affine = medical_loaders.generate_datasets(args,
path='./datasets')
model, optimizer = medzoo.create_model(args)
criterion = DiceLoss(classes=args.classes)
# print("training_generator shape:", training_generator.dim())
# print("val_generator shape:", val_generator.dim())
if args.cuda:
model = model.cuda()
print("start training...")
# torch.save(training_generator, "training_generator.tch")
# torch.save(val_generator, "val_generator.tch")
trainer = train.Trainer(args, model, criterion, optimizer, train_data_loader=training_generator,
valid_data_loader=val_generator)
trainer.training()
def main():
args = get_arguments()
utils.make_dirs(args.save)
train_f, val_f = utils.create_stats_files(args.save)
name_model = args.model + "_" + args.dataset_name + "_" + utils.datestr()
writer = SummaryWriter(log_dir='../runs/' + name_model, comment=name_model)
best_prec1 = 100.
training_generator, val_generator, full_volume, affine = medical_loaders.generate_datasets(
args, path='.././datasets')
model, optimizer = medzoo.create_model(args)
criterion = DiceLoss(classes=args.classes)
if args.cuda:
torch.cuda.manual_seed(seed)
model = model.cuda()
print("Model transferred in GPU.....")
print("START TRAINING...")
for epoch in range(1, args.nEpochs + 1):
train_stats = train.train_dice(args, epoch, model, training_generator,
optimizer, criterion, train_f, writer)
val_stats = train.test_dice(args, epoch, model, val_generator,
criterion, val_f, writer)
utils.write_train_val_score(writer, epoch, train_stats, val_stats)
model.save_checkpoint(args.save,
epoch,
val_stats[0],
optimizer=optimizer)
# if epoch % 5 == 0:
# utils.visualize_no_overlap(args, full_volume, affine, model, epoch, DIM, writer)
#utils.save_model(model, args, val_stats[0], epoch, best_prec1)
train_f.close()
val_f.close()
def main():
args = get_arguments()
utils.make_dirs(args.save)
train_f, val_f = utils.create_stats_files(args.save)
name_model = args.model + "_" + args.dataset_name + "_" + utils.datestr()
writer = SummaryWriter(log_dir='../runs/' + name_model, comment=name_model)
best_pred = 1.01
samples_train = 200
samples_val = 200
training_generator, val_generator, full_volume, affine = medical_loaders.generate_datasets(
args,
path='.././datasets',
samples_train=samples_train,
samples_val=samples_val)
model, optimizer = medzoo.create_model(args)
criterion = medzoo.DiceLoss2D(args.classes)
if args.cuda:
torch.cuda.manual_seed(seed)
model = model.cuda()
for epoch in range(1, args.nEpochs + 1):
train_stats = train.train_dice(args, epoch, model, training_generator,
optimizer, criterion, train_f, writer)
val_stats = train.test_dice(args, epoch, model, val_generator,
criterion, val_f, writer)
utils.write_train_val_score(writer, epoch, train_stats, val_stats)
best_pred = utils.save_model(model=model,
args=args,
dice_loss=val_stats[0],
epoch=epoch,
best_pred_loss=best_pred)
train_f.close()
val_f.close()
def main():
args = get_arguments()
if args.distributed:
torch.distributed.init_process_group(backend='nccl',
init_method='env://')
args.world_size = torch.distributed.get_world_size()
assert torch.backends.cudnn.enabled, "Amp requires cudnn backend to be enabled." #1
torch.backends.cudnn.benchmark = True
utils.reproducibility(args, seed)
utils.make_dirs(args.save)
training_generator, val_generator, full_volume, affine = medical_loaders.generate_datasets(
args, path='.././datasets')
model, optimizer = medzoo.create_model(args)
criterion = DiceLoss(classes=11, skip_index_after=args.classes)
if args.sync_bn:
model = apex.parallel.convert_syncbn_model(model)
if args.cuda:
model = model.cuda()
print("Model transferred in GPU.....")
if args.distributed:
model = DDP(model, delay_allreduce=True)
trainer = train.Trainer(args,
model,
criterion,
optimizer,
train_data_loader=training_generator,
valid_data_loader=val_generator,
lr_scheduler=None)
print("START TRAINING...")
trainer.training()
train_loader,
test_loader,
logs,
trial=trial,
**kwargs)
acc = 100 - logs[0]["epoch_log"][config.trainer.epochs]["test_accuracy"]
return acc
# ## Cteate study object
# In[ ]:
utils.make_dirs(args.optuna_dir)
sampler = optuna.samplers.RandomSampler()
pruner = optuna.pruners.SuccessiveHalvingPruner(min_resource=1,
reduction_factor=2,
min_early_stopping_rate=0)
db_path = os.path.join(args.optuna_dir, "optuna.db")
study = optuna.create_study(storage=f"sqlite:///{db_path}",
study_name='experiment01',
sampler=sampler,
pruner=pruner,
direction="minimize",
load_if_exists=True)
# ## Start optimization
def __init__(self,
mode,
dataset_path='./datasets',
crop_dim=(32, 32, 32),
split_id=1,
samples=1000,
load=False):
"""
:param mode: 'train','val','test'
:param dataset_path: root dataset folder
:param crop_dim: subvolume tuple
:param fold_id: 1 to 10 values
:param samples: number of sub-volumes that you want to create
"""
self.mode = mode
self.root = str(dataset_path)
self.training_path = self.root + '/iseg_2017/iSeg-2017-Training/'
self.testing_path = self.root + '/iseg_2017/iSeg-2017-Testing/'
self.CLASSES = 4
self.full_vol_dim = (144, 192, 256) # slice, width, height
self.crop_size = crop_dim
self.list = []
self.samples = samples
self.full_volume = None
self.save_name = self.root + '/iseg_2017/iSeg-2017-Training/iseg2017-list-' + mode + '-samples-' + str(
samples) + '.txt'
if load:
self.list = utils.load_list(self.save_name)
list_IDsT1 = sorted(
glob.glob(os.path.join(self.training_path, '*T1.img')))
self.affine = img_loader.load_affine_matrix(list_IDsT1[0])
return
subvol = '_vol_' + str(crop_dim[0]) + 'x' + str(
crop_dim[1]) + 'x' + str(crop_dim[2])
self.sub_vol_path = self.root + '/iseg_2017/generated/' + mode + subvol + '/'
utils.make_dirs(self.sub_vol_path)
list_IDsT1 = sorted(
glob.glob(os.path.join(self.training_path, '*T1.img')))
list_IDsT2 = sorted(
glob.glob(os.path.join(self.training_path, '*T2.img')))
labels = sorted(
glob.glob(os.path.join(self.training_path, '*label.img')))
self.affine = img_loader.load_affine_matrix(list_IDsT1[0])
if self.mode == 'train':
list_IDsT1 = list_IDsT1[:split_id]
list_IDsT2 = list_IDsT2[:split_id]
labels = labels[:split_id]
self.list = create_sub_volumes(list_IDsT1,
list_IDsT2,
labels,
dataset_name="iseg2017",
mode=mode,
samples=samples,
full_vol_dim=self.full_vol_dim,
crop_size=self.crop_size,
sub_vol_path=self.sub_vol_path,
threshold=10)
elif self.mode == 'val':
list_IDsT1 = list_IDsT1[split_id:]
list_IDsT2 = list_IDsT2[:split_id:]
labels = labels[split_id:]
self.list = create_sub_volumes(list_IDsT1,
list_IDsT2,
labels,
dataset_name="iseg2017",
mode=mode,
samples=samples,
full_vol_dim=self.full_vol_dim,
crop_size=self.crop_size,
sub_vol_path=self.sub_vol_path,
threshold=10)
self.full_volume = get_viz_set(list_IDsT1, list_IDsT2, labels)
elif self.mode == 'test':
self.list_IDsT1 = sorted(
glob.glob(os.path.join(self.testing_path, '*T1.img')))
self.list_IDsT2 = sorted(
glob.glob(os.path.join(self.testing_path, '*T2.img')))
self.labels = None
utils.save_list(self.save_name, self.list)
def __init__(self,
args,
mode,
dataset_path='./datasets',
classes=5,
crop_dim=(32, 32, 32),
split_idx=10,
samples=10,
load=False):
"""
:param mode: 'train','val','test'
:param dataset_path: root dataset folder
:param crop_dim: subvolume tuple
:param split_idx: 1 to 10 values
:param samples: number of sub-volumes that you want to create
"""
self.mode = mode
self.root = str(dataset_path)
self.training_path = self.root + '/MICCAI_BraTS_2018_Data_Training/'
self.testing_path = self.root + ' '
self.CLASSES = 4
self.full_vol_dim = (240, 240, 155) # slice, width, height
self.crop_size = crop_dim
self.threshold = args.threshold
self.normalization = args.normalization
self.augmentation = args.augmentation
self.list = []
self.samples = samples
self.full_volume = None
self.classes = classes
self.save_name = self.root + '/MICCAI_BraTS_2018_Data_Training/brats2018-list-' + mode + '-samples-' + str(
samples) + '.txt'
if self.augmentation:
self.transform = augment3D.RandomChoice(transforms=[
augment3D.GaussianNoise(mean=0, std=0.01),
augment3D.RandomFlip(),
augment3D.ElasticTransform()
],
p=0.5)
if load:
## load pre-generated data
list_IDsT1 = sorted(
glob.glob(os.path.join(self.training_path,
'*GG/*/*t1.nii.gz')))
self.affine = img_loader.load_affine_matrix(list_IDsT1[0])
self.list = utils.load_list(self.save_name)
return
subvol = '_vol_' + str(crop_dim[0]) + 'x' + str(
crop_dim[1]) + 'x' + str(crop_dim[2])
self.sub_vol_path = self.root + '/MICCAI_BraTS_2018_Data_Training/generated/' + mode + subvol + '/'
utils.make_dirs(self.sub_vol_path)
list_IDsT1 = sorted(
glob.glob(os.path.join(self.training_path, '*GG/*/*t1.nii.gz')))
list_IDsT1ce = sorted(
glob.glob(os.path.join(self.training_path, '*GG/*/*t1ce.nii.gz')))
list_IDsT2 = sorted(
glob.glob(os.path.join(self.training_path, '*GG/*/*t2.nii.gz')))
list_IDsFlair = sorted(
glob.glob(os.path.join(self.training_path,
'*GG/*/*_flair.nii.gz')))
labels = sorted(
glob.glob(os.path.join(self.training_path, '*GG/*/*_seg.nii.gz')))
# print(len(list_IDsT1),len(list_IDsT2),len(list_IDsFlair),len(labels))
self.affine = img_loader.load_affine_matrix(list_IDsT1[0])
if self.mode == 'train':
list_IDsT1 = list_IDsT1[:split_idx]
list_IDsT1ce = list_IDsT1ce[:split_idx]
list_IDsT2 = list_IDsT2[:split_idx]
list_IDsFlair = list_IDsFlair[:split_idx]
labels = labels[:split_idx]
self.list = create_sub_volumes(list_IDsT1,
list_IDsT1ce,
list_IDsT2,
list_IDsFlair,
labels,
dataset_name="brats2018",
mode=mode,
samples=samples,
full_vol_dim=self.full_vol_dim,
crop_size=self.crop_size,
sub_vol_path=self.sub_vol_path,
normalization=self.normalization,
th_percent=self.threshold)
elif self.mode == 'val':
list_IDsT1 = list_IDsT1[split_idx:]
list_IDsT1ce = list_IDsT1ce[split_idx:]
list_IDsT2 = list_IDsT2[split_idx:]
list_IDsFlair = list_IDsFlair[split_idx:]
labels = labels[split_idx:]
self.list = create_sub_volumes(list_IDsT1,
list_IDsT1ce,
list_IDsT2,
list_IDsFlair,
labels,
dataset_name="brats2018",
mode=mode,
samples=samples,
full_vol_dim=self.full_vol_dim,
crop_size=self.crop_size,
sub_vol_path=self.sub_vol_path,
normalization=self.normalization,
th_percent=self.threshold)
elif self.mode == 'test':
self.list_IDsT1 = sorted(
glob.glob(os.path.join(self.testing_path, '*GG/*/*t1.nii.gz')))
self.list_IDsT1ce = sorted(
glob.glob(os.path.join(self.testing_path,
'*GG/*/*t1ce.nii.gz')))
self.list_IDsT2 = sorted(
glob.glob(os.path.join(self.testing_path, '*GG/*/*t2.nii.gz')))
self.list_IDsFlair = sorted(
glob.glob(
os.path.join(self.testing_path, '*GG/*/*_flair.nii.gz')))
self.labels = None
utils.save_list(self.save_name, self.list)
def test_net(args, dataset, model, kernel_dim=(32, 32, 32)):
# import ipdb;ipdb.set_trace()
num_imgs = len(dataset)
public_id_list_all = []
label_id_list_all = []
confidence_list_all = []
label_code_list_all = []
utils.make_dirs(args.nii_save_path)
for i in range(num_imgs):
print('%d/%d is tested'%(i,num_imgs))
x, target, img_path, img_affine, img_hdr = dataset.__getitem__(i)
if args.cuda:
x = x.unsqueeze(0).cuda()
# target = target.cuda()
# import ipdb;ipdb.set_trace()
# x = full_volume[:-1,...].detach()
# # target = full_volume[-1,...].unsqueeze(0).detach()
# target = full_volume[-1,...].detach()
# # import ipdb;ipdb.set_trace()
h,w,d = target.shape
# target_new = torch.zeros(6,h,w,d)
# target_new[0][target==0] = 1
# target_new[1][target==1] = 1
# target_new[2][target==2] = 1
# target_new[3][target==3] = 1
# target_new[4][target==4] = 1
# target_new[5][target==5] = 1
# target = target_new
modalities, D, H, W = x.shape
kernel_dim=(512,512,48)
kc, kh, kw = kernel_dim
dc, dh, dw = kernel_dim # stride
# Pad to multiples of kernel_dim
a = ((roundup(W, kw) - W) // 2 + W % 2, (roundup(W, kw) - W) // 2,
(roundup(H, kh) - H) // 2 + H % 2, (roundup(H, kh) - H) // 2,
(roundup(D, kc) - D) // 2 + D % 2, (roundup(D, kc) - D) // 2)
x = F.pad(x, a)
assert x.size(3) % kw == 0
assert x.size(2) % kh == 0
assert x.size(1) % kc == 0
patches = x.unfold(1, kc, dc).unfold(2, kh, dh).unfold(3, kw, dw)
unfold_shape = list(patches.size())
patches = patches.contiguous().view(-1, modalities, kc, kh, kw)
## TODO torch stack
# with torch.no_grad():
# output = model.inference(patches)
number_of_volumes = patches.shape[0]
predictions = []
for i in range(number_of_volumes):
input_tensor = patches[i, ...].unsqueeze(0)
predictions.append(model.inference(input_tensor))
output = torch.stack(predictions, dim=0).squeeze(1).detach()
N, Classes, _, _, _ = output.shape
output_unfold_shape = unfold_shape[1:]
output_unfold_shape.insert(0, Classes)
output = output.view(output_unfold_shape)
output_c = output_unfold_shape[1] * output_unfold_shape[4]
output_h = output_unfold_shape[2] * output_unfold_shape[5]
output_w = output_unfold_shape[3] * output_unfold_shape[6]
output = output.permute(0, 1, 4, 2, 5, 3, 6).contiguous()
output = output.view(-1, output_c, output_h, output_w)
y = output[:, a[4]:output_c - a[5], a[2]:output_h - a[3], a[0]:output_w - a[1]]
# x = x.unsqueeze(0)
# y = model(x).squeeze(0).cpu().detach()
# _, h,w,d = y.shape
y = torch.nn.Softmax(dim=0)(y)
y[y<0.5] = 0
# y = torch.nn.Sigmoid()(y)
index_ = np.where(y!=0)
# import ipdb;ipdb.set_trace()
# confidence_list = y[index_]
# y_new = torch.zeros(h,w,d)
# y[index_] = torch.from_numpy(index_[0]).float()
pred = torch.zeros(h,w,d)
pred_out = torch.zeros(h,w,d)
# import ipdb;ipdb.set_trace()
# pred_out = morphology.erosion(pred_out)
conf = torch.zeros(h,w,d)
# import ipdb;ipdb.set_trace()
pred[(index_[1], index_[2], index_[3])] = torch.from_numpy(index_[0]).float()
conf[(index_[1], index_[2], index_[3])] = y[index_]
# pred= segmentation.clear_border(pred)
# import ipdb;ipdb.set_trace()
# pred = morphology.erosion(pred)
# for i in range(1, 6):
# index_i= np.where(pred==i)
# if index_i[0].size == 0:
# continue
# fea_1 = np.vstack((index_i[0], index_i[1], index_i[2])).T
# label_pred = DBSCAN(eps=5).fit_predict(fea_1)
# label_counter = Counter(label_pred)
# labelId_toRm = []
# # labelId_left = []
# num_thresh = 10
# for label_id, num in label_counter.items():
# if num < num_thresh:
# labelId_toRm.append(label_id)
# # else:
# # labelId_left.append(label_id)
# if -1 not in labelId_toRm:
# labelId_toRm.append(-1)
# index_toRm_list = []
# for label_id in labelId_toRm:
# index_toRm_list.extend(np.where(label_pred == label_id)[0].tolist())
# try:
# xyz_toRm = fea_1[np.array(index_toRm_list)].T
# except:
# import ipdb;ipdb.set_trace()
# xyz_toRm_org = (xyz_toRm[0], xyz_toRm[1], xyz_toRm[2])
# pred[xyz_toRm_org] = 0.
# pred = morphology.dilation(morphology.erosion(pred))
# fig = plt.figure()
# ax = fig.gca(projection='3d')
label_id_cnt = 0
label_code_list = []
confidence_list = []
public_id_list = []
label_id_list = []
for i in range(1, 6):
pred_i = torch.zeros(h,w,d)
# index_i = np.where(pred == i)
pred_i[np.where(pred == i)] = 1
pred_i = morphology.erosion(pred_i)
pred_i = morphology.erosion(pred_i)
# pred_i = morphology.dilation(morphology.erosion(pred_i))
labels = measure.label(pred_i, connectivity=3)
# import ipdb;ipdb.set_trace()
areas = [_.area for _ in measure.regionprops(labels)]
areas.sort()
if len(areas) > 2:
for region in measure.regionprops(labels):
if region.area < areas[-2]:
# if region.area > areas[0]:
coords_ = region.coords.T
coords_org = (coords_[0], coords_[1], coords_[2])
pred_i[coords_org] = 0
labels = measure.label(pred_i, connectivity=3)
# import ipdb;ipdb.set_trace()
for i, region in enumerate(measure.regionprops(labels)):
if len(region.coords) < 10000:
continue
label_code = int(pred[tuple(region.coords[0].tolist())])
label_code = -1 if label_code == 5 else label_code
label_code_list.append(label_code)
label_id_cnt += 1
label_id_list.append(label_id_cnt)
coords_ = region.coords.T
# import ipdb;ipdb.set_trace()
# ax.scatter(coords_[0], coords_[1], coords_[2], c = np.tile(np.array([label_id_cnt*10]), len(coords_[2])))
# plt.savefig('scatter.png')
# import ipdb;ipdb.set_trace()
coords_org = (coords_[0], coords_[1], coords_[2])
confidence = float(torch.sum(conf[coords_org]) / len(coords_org[0]))
pred_out[coords_org] = label_id_cnt #float(label_id_cnt)
confidence_list.append(confidence)
# import ipdb;ipdb.set_trace()
# plt.savefig('scatter.png')
# import ipdb;ipdb.set_trace()
label_code_list.insert(0,0)
label_id_list.insert(0,0)
confidence_list.insert(0,1)
pred_cls_num = len(label_code_list)
public_id = os.path.basename(img_path).split('-')[0]
public_id_list = [public_id] * pred_cls_num
public_id_list_all.extend(public_id_list)
label_id_list_all.extend(label_id_list)
confidence_list_all.extend(confidence_list)
label_code_list_all.extend(label_code_list)
test_nii_save_path = os.path.join(args.nii_save_path,public_id+'.nii.gz')
# nib.Nifti1Image(pred, img_affine).to_filename(test_nii_save_path)
newLabelImg = nib.Nifti1Image(pred_out.numpy(), img_affine)
newLabelImg.set_data_dtype(np.dtype(np.float32))
dimsImgToSave = len(pred_out.shape)
newZooms = list(img_hdr.get_zooms()[:dimsImgToSave])
if len(newZooms) < dimsImgToSave : #Eg if original image was 3D, but I need to save a multi-channel image.
newZooms = newZooms + [1.0]*(dimsImgToSave - len(newZooms))
newLabelImg.header.set_zooms(newZooms)
nib.save(newLabelImg, test_nii_save_path)
dataframe = pd.DataFrame({'public_id':public_id_list_all, 'label_id':label_id_list_all,'confidence':confidence_list_all, 'label_code':label_code_list_all})
dataframe.to_csv(args.nii_save_path+"/ribfrac-val-pred.csv",index=False,sep=',')
def __init__(self,
mode,
dataset_path='./datasets',
crop_dim=(32, 32, 32),
fold_id=1,
samples=1000,
save=True):
"""
:param mode: 'train','val','test'
:param dataset_path: root dataset folder
:param crop_dim: subvolume tuple
:param fold_id: 1 to 10 values
:param samples: number of sub-volumes that you want to create
"""
self.mode = mode
self.root = str(dataset_path)
self.training_path = self.root + '/iseg_2017/iSeg-2017-Training/'
self.testing_path = self.root + '/iseg_2017/iSeg-2017-Testing/'
self.save = save
self.CLASSES = 4
self.full_vol_dim = (144, 192, 256) # slice, width, height
self.crop_size = crop_dim
self.fold = str(fold_id)
self.list = []
self.samples = samples
self.full_volume = None
subvol = '_vol_' + str(crop_dim[0]) + 'x' + str(
crop_dim[1]) + 'x' + str(crop_dim[2])
if self.save:
self.sub_vol_path = self.root + '/iseg_2017/generated/' + mode + subvol + '/'
utils.make_dirs(self.sub_vol_path)
list_IDsT1 = sorted(
glob.glob(os.path.join(self.training_path, '*T1.img')))
list_IDsT2 = sorted(
glob.glob(os.path.join(self.training_path, '*T2.img')))
labels = sorted(
glob.glob(os.path.join(self.training_path, '*label.img')))
self.affine = img_loader.load_affine_matrix(list_IDsT1[0])
training_labels, training_list_IDsT1, training_list_IDsT2, val_list_IDsT1, val_list_IDsT2, val_labels = [], [], [], [], [], []
print("SELECT subject with ID {} for Validation".format(self.fold))
for i in range(len(labels)):
subject_id = (labels[i].split('/')[-1]).split('-')[1]
if subject_id == self.fold:
val_list_IDsT1.append(list_IDsT1[i])
val_list_IDsT2.append(list_IDsT2[i])
val_labels.append(labels[i])
else:
training_list_IDsT1.append(list_IDsT1[i])
training_list_IDsT2.append(list_IDsT2[i])
training_labels.append(labels[i])
if self.mode == 'train':
self.list_IDsT1 = training_list_IDsT1
self.list_IDsT2 = training_list_IDsT2
self.labels = training_labels
# Generates datasets with non-empty sub-volumes!
self.create_sub_volumes()
elif self.mode == 'val':
self.list_IDsT1 = val_list_IDsT1
self.list_IDsT2 = val_list_IDsT2
self.labels = val_labels
self.create_sub_volumes()
self.get_viz_set()
elif self.mode == 'test':
self.list_IDsT1 = sorted(
glob.glob(os.path.join(self.testing_path, '*T1.img')))
self.list_IDsT2 = sorted(
glob.glob(os.path.join(self.testing_path, '*T2.img')))
self.labels = None
def __init__(self,
mode,
dataset_path='./datasets',
classes=5,
crop_dim=(200, 200, 150),
split_idx=260,
samples=10,
load=False):
"""
:param mode: 'train','val','test'
:param dataset_path: root dataset folder
:param crop_dim: subvolume tuple
:param split_idx: 1 to 10 values
:param samples: number of sub-volumes that you want to create
"""
self.mode = mode
self.root = str(dataset_path)
self.training_path = self.root + '/brats2019/MICCAI_BraTS_2019_Data_Training/'
self.testing_path = self.root + '/brats2019/MICCAI_BraTS_2019_Data_Validation/'
self.full_vol_dim = (240, 240, 155) # slice, width, height
self.crop_size = crop_dim
self.list = []
self.samples = samples
self.full_volume = None
self.classes = classes
self.save_name = self.root + '/brats2019/brats2019-list-' + mode + '-samples-' + str(
samples) + '.txt'
if load:
self.list = utils.load_list(self.save_name)
list_IDsT1 = sorted(
glob.glob(os.path.join(self.training_path,
'*GG/*/*t1.nii.gz')))
self.affine = img_loader.load_affine_matrix(list_IDsT1[0])
return
subvol = '_vol_' + str(crop_dim[0]) + 'x' + str(
crop_dim[1]) + 'x' + str(crop_dim[2])
self.sub_vol_path = self.root + '/brats2019/MICCAI_BraTS_2019_Data_Training/generated/' + mode + subvol + '/'
utils.make_dirs(self.sub_vol_path)
list_IDsT1 = sorted(
glob.glob(os.path.join(self.training_path, '*GG/*/*t1.nii.gz')))
list_IDsT1ce = sorted(
glob.glob(os.path.join(self.training_path, '*GG/*/*t1ce.nii.gz')))
list_IDsT2 = sorted(
glob.glob(os.path.join(self.training_path, '*GG/*/*t2.nii.gz')))
list_IDsFlair = sorted(
glob.glob(os.path.join(self.training_path,
'*GG/*/*_flair.nii.gz')))
labels = sorted(
glob.glob(os.path.join(self.training_path, '*GG/*/*_seg.nii.gz')))
list_IDsT1, list_IDsT1ce, list_IDsT2, list_IDsFlair, labels = utils.shuffle_lists(
list_IDsT1,
list_IDsT1ce,
list_IDsT2,
list_IDsFlair,
labels,
seed=17)
self.affine = img_loader.load_affine_matrix(list_IDsT1[0])
if self.mode == 'train':
print('Brats2019, Total data:', len(list_IDsT1))
list_IDsT1 = list_IDsT1[:split_idx]
list_IDsT1ce = list_IDsT1ce[:split_idx]
list_IDsT2 = list_IDsT2[:split_idx]
list_IDsFlair = list_IDsFlair[:split_idx]
labels = labels[:split_idx]
self.list = create_sub_volumes(list_IDsT1,
list_IDsT1ce,
list_IDsT2,
list_IDsFlair,
labels,
dataset_name="brats2019",
mode=mode,
samples=samples,
full_vol_dim=self.full_vol_dim,
crop_size=self.crop_size,
sub_vol_path=self.sub_vol_path)
elif self.mode == 'val':
list_IDsT1 = list_IDsT1[split_idx:]
list_IDsT1ce = list_IDsT1ce[split_idx:]
list_IDsT2 = list_IDsT2[split_idx:]
list_IDsFlair = list_IDsFlair[split_idx:]
labels = labels[split_idx:]
self.list = create_sub_volumes(list_IDsT1,
list_IDsT1ce,
list_IDsT2,
list_IDsFlair,
labels,
dataset_name="brats2019",
mode=mode,
samples=samples,
full_vol_dim=self.full_vol_dim,
crop_size=self.crop_size,
sub_vol_path=self.sub_vol_path)
elif self.mode == 'test':
self.list_IDsT1 = sorted(
glob.glob(os.path.join(self.testing_path, '*GG/*/*t1.nii.gz')))
self.list_IDsT1ce = sorted(
glob.glob(os.path.join(self.testing_path,
'*GG/*/*t1ce.nii.gz')))
self.list_IDsT2 = sorted(
glob.glob(os.path.join(self.testing_path, '*GG/*/*t2.nii.gz')))
self.list_IDsFlair = sorted(
glob.glob(
os.path.join(self.testing_path, '*GG/*/*_flair.nii.gz')))
self.labels = None
# Todo inference code here
utils.save_list(self.save_name, self.list)
def __init__(self,
args,
mode,
dataset_path='./datasets',
crop_dim=(32, 32, 32),
split_id=1,
samples=1000,
load=False):
"""
:param mode: 'train','val','test'
:param dataset_path: root dataset folder
:param crop_dim: subvolume tuple
:param fold_id: 1 to 10 values
:param samples: number of sub-volumes that you want to create
"""
self.mode = mode
self.root = str(dataset_path)
self.training_path = self.root + '/iseg_2019/iSeg-2019-Training/'
self.testing_path = self.root + '/iseg_2019/iSeg-2019-Validation/'
self.CLASSES = 4
self.full_vol_dim = (144, 192, 256) # slice, width, height
self.crop_size = crop_dim
self.threshold = args.threshold
self.normalization = args.normalization
self.augmentation = args.augmentation
self.list = []
self.samples = samples
self.full_volume = None
self.save_name = self.root + '/iseg_2019/iseg2019-list-' + mode + '-samples-' + str(
samples) + '.txt'
if self.augmentation:
self.transform = augment3D.RandomChoice(transforms=[
augment3D.GaussianNoise(mean=0, std=0.01),
augment3D.RandomFlip(),
augment3D.ElasticTransform()
],
p=0.5)
if load:
## load pre-generated data
self.list = utils.load_list(self.save_name)
list_IDsT1 = sorted(
glob.glob(os.path.join(self.training_path, '*T1.img')))
self.affine = img_loader.load_affine_matrix(list_IDsT1[0])
return
subvol = '_vol_' + str(crop_dim[0]) + 'x' + str(
crop_dim[1]) + 'x' + str(crop_dim[2])
self.sub_vol_path = self.root + '/iseg_2019/generated/' + mode + subvol + '/'
utils.make_dirs(self.sub_vol_path)
list_IDsT1 = sorted(
glob.glob(os.path.join(self.training_path, '*T1.img')))
list_IDsT2 = sorted(
glob.glob(os.path.join(self.training_path, '*T2.img')))
labels = sorted(
glob.glob(os.path.join(self.training_path, '*label.img')))
self.affine = img_loader.load_affine_matrix(list_IDsT1[0])
if self.mode == 'train':
list_IDsT1 = list_IDsT1[:split_id]
list_IDsT2 = list_IDsT2[:split_id]
labels = labels[:split_id]
self.list = create_sub_volumes(list_IDsT1,
list_IDsT2,
labels,
dataset_name="iseg2019",
mode=mode,
samples=samples,
full_vol_dim=self.full_vol_dim,
crop_size=self.crop_size,
sub_vol_path=self.sub_vol_path,
th_percent=self.threshold)
elif self.mode == 'val':
list_IDsT1 = list_IDsT1[split_id:]
list_IDsT2 = list_IDsT2[:split_id:]
labels = labels[split_id:]
self.list = create_sub_volumes(list_IDsT1,
list_IDsT2,
labels,
dataset_name="iseg2019",
mode=mode,
samples=samples,
full_vol_dim=self.full_vol_dim,
crop_size=self.crop_size,
sub_vol_path=self.sub_vol_path,
th_percent=self.threshold)
self.full_volume = get_viz_set(list_IDsT1,
list_IDsT2,
labels,
dataset_name="iseg2019")
elif self.mode == 'test':
self.list_IDsT1 = sorted(
glob.glob(os.path.join(self.testing_path, '*T1.img')))
self.list_IDsT2 = sorted(
glob.glob(os.path.join(self.testing_path, '*T2.img')))
self.labels = None
# todo inference here
utils.save_list(self.save_name, self.list)
def objective_func(trial):
global config
if type(args.num_trial) is int:
if trial.number > args.num_trial:
import sys
sys.exit()
# make dirs
config.trainer.base_dir = os.path.join(args.optuna_dir,
f"{trial.number:04}/")
utils.make_dirs(config.trainer.base_dir + "log")
utils.make_dirs(config.trainer.base_dir + "checkpoint")
# change config
# set loss funcs & gates
for source_id, model_losses in enumerate(config.losses):
for target_id, _ in enumerate(model_losses):
loss_name = trial.suggest_categorical(
f'{source_id:02}_{target_id:02}_loss',
LOSS_LISTS[source_id][target_id])
loss_args = copy.deepcopy(args_factory.losses[loss_name])
if "gate" in loss_args.args:
gate_name = trial.suggest_categorical(
f'{source_id:02}_{target_id:02}_gate',
GATE_LIST[source_id][target_id])
loss_args.args.gate = copy.deepcopy(
args_factory.gates[gate_name])
config.losses[source_id][target_id] = loss_args
for model_id in range(len(config.models)):
# set model
model_name = trial.suggest_categorical(f"model_{model_id}_name",
MODEL_LISTS[model_id])
model = copy.deepcopy(args_factory.models[model_name])
config.models[model_id].name = model.name
config.models[model_id].args = model.args
# set model weight
is_cutoff = all([
loss.args.gate.name == "CutoffGate"
for loss in config.losses[model_id]
])
is_ensemble = config.models[model_id].name == "Ensemble"
if is_cutoff & (not is_ensemble):
config.models[model_id].load_weight.path = model.load_weight.path
else:
config.models[model_id].load_weight.path = None
config = copy.deepcopy(config)
# save config
utils.save_json(config, config.trainer.base_dir + r"log/config.json")
# create object
trainer, nets, criterions, optimizers, train_loader, test_loader, logs = create_object(
config)
# make kwargs
kwargs = {"_trial": trial, "_callback": inform_optuna}
# set seed
trial.set_user_attr("seed", config.manualSeed)
# raise exception if target model is pretrained.
if config.models[0].load_weight.path is not None:
class BlacklistError(optuna.structs.OptunaError):
pass
raise BlacklistError()
# start trial
trainer.train(nets,
criterions,
optimizers,
train_loader,
test_loader,
logs,
trial=trial,
**kwargs)
acc = 100 - logs[0]["epoch_log"][config.trainer.epochs]["test_accuracy"]
return acc
