def __init__(self, tranforms):
self.tranform_list = []
for tranform in tranforms:
if 'LoadImaged' == tranform:
self.tranform_list.append(LoadImaged(keys=["image", "label"]))
elif 'AsChannelFirstd' == tranform:
self.tranform_list.append(AsChannelFirstd(keys="image"))
elif 'ConvertToMultiChannelBasedOnBratsClassesd' == tranform:
self.tranform_list.append(ConvertToMultiChannelBasedOnBratsClassesd(keys="label"))
elif 'Spacingd' == tranform:
self.tranform_list.append(Spacingd(keys=["image", "label"], pixdim=(1.5, 1.5, 2.0), mode=("bilinear", "nearest")))
elif 'Orientationd' == tranform:
self.tranform_list.append(Orientationd(keys=["image", "label"], axcodes="RAS"))
elif 'CenterSpatialCropd' == tranform:
self.tranform_list.append(CenterSpatialCropd(keys=["image", "label"], roi_size=[128, 128, 64]))
elif 'NormalizeIntensityd' == tranform:
self.tranform_list.append(NormalizeIntensityd(keys="image", nonzero=True, channel_wise=True))
elif 'ToTensord' == tranform:
self.tranform_list.append(ToTensord(keys=["image", "label"]))
elif 'Activations' == tranform:
self.tranform_list.append(Activations(sigmoid=True))
elif 'AsDiscrete' == tranform:
self.tranform_list.append(AsDiscrete(threshold_values=True))
else:
raise ValueError(
f"Unsupported tranform: {tranform}. Please add it to support it."
)
super().__init__(self.tranform_list)
def prepare_data(self):
data_dir = self.hparams.data_dir
# Train imgs/masks
train_imgs = []
train_masks = []
with open(data_dir + 'train_imgs.txt', 'r') as f:
train_imgs = [data_dir + image.rstrip() for image in f.readlines()]
with open(data_dir + 'train_masks.txt', 'r') as f:
train_masks = [data_dir + mask.rstrip() for mask in f.readlines()]
train_dicts = [{'image': image, 'mask': mask} for (image, mask) in zip(train_imgs, train_masks)]
train_dicts, val_dicts = train_test_split(train_dicts, test_size=0.2)
# Basic transforms
data_keys = ["image", "mask"]
data_transforms = Compose(
[
LoadNiftid(keys=data_keys),
AddChanneld(keys=data_keys),
ScaleIntensityRangePercentilesd(
keys='image',
lower=25,
upper=75,
b_min=-0.5,
b_max=0.5
)
]
)
self.train_dataset = monai.data.CacheDataset(
data=train_dicts,
transform=Compose(
[
data_transforms,
RandCropByPosNegLabeld(
keys=data_keys,
label_key="mask",
spatial_size=self.hparams.patch_size,
num_samples=4,
image_key="image",
pos=0.8,
neg=0.2
),
ToTensord(keys=data_keys)
]
),
cache_rate=1.0
)
self.val_dataset = monai.data.CacheDataset(
data=val_dicts,
transform=Compose(
[
data_transforms,
CenterSpatialCropd(keys=data_keys, roi_size=self.hparams.patch_size),
ToTensord(keys=data_keys)
]
),
cache_rate=1.0
)
def test_inverse_inferred_seg(self):
test_data = []
for _ in range(20):
image, label = create_test_image_2d(100, 101)
test_data.append({
"image": image,
"label": label.astype(np.float32)
})
batch_size = 10
# num workers = 0 for mac
num_workers = 2 if sys.platform != "darwin" else 0
transforms = Compose([
AddChanneld(KEYS),
SpatialPadd(KEYS, (150, 153)),
CenterSpatialCropd(KEYS, (110, 99))
])
num_invertible_transforms = sum(1 for i in transforms.transforms
if isinstance(i, InvertibleTransform))
dataset = CacheDataset(test_data, transform=transforms, progress=False)
loader = DataLoader(dataset,
batch_size=batch_size,
shuffle=False,
num_workers=num_workers)
device = "cuda" if torch.cuda.is_available() else "cpu"
model = UNet(
dimensions=2,
in_channels=1,
out_channels=1,
channels=(2, 4),
strides=(2, ),
).to(device)
data = first(loader)
labels = data["label"].to(device)
segs = model(labels).detach().cpu()
label_transform_key = "label" + InverseKeys.KEY_SUFFIX.value
segs_dict = {
"label": segs,
label_transform_key: data[label_transform_key]
}
segs_dict_decollated = decollate_batch(segs_dict)
# inverse of individual segmentation
seg_dict = first(segs_dict_decollated)
with allow_missing_keys_mode(transforms):
inv_seg = transforms.inverse(seg_dict)["label"]
self.assertEqual(len(data["label_transforms"]),
num_invertible_transforms)
self.assertEqual(len(seg_dict["label_transforms"]),
num_invertible_transforms)
self.assertEqual(inv_seg.shape[1:], test_data[0]["label"].shape)
def prepare_data(self):
data_df = pd.read_csv(
'/data/shared/prostate/yale_prostate/input_lists/MR_yale.csv')
train_imgs = data_df['IMAGE'][0:295].tolist()
train_masks = data_df['SEGM'][0:295].tolist()
train_dicts = [{
'image': image,
'mask': mask
} for (image, mask) in zip(train_imgs, train_masks)]
train_dicts, val_dicts = train_test_split(train_dicts, test_size=0.2)
# Basic transforms
data_keys = ["image", "mask"]
data_transforms = Compose([
LoadNiftid(keys=data_keys),
AddChanneld(keys=data_keys),
ScaleIntensityRangePercentilesd(keys='image',
lower=25,
upper=75,
b_min=-0.5,
b_max=0.5)
])
self.train_dataset = monai.data.CacheDataset(
data=train_dicts,
transform=Compose([
data_transforms,
RandCropByPosNegLabeld(keys=data_keys,
label_key="mask",
spatial_size=self.hparams.patch_size,
num_samples=4,
image_key="image",
pos=0.8,
neg=0.2),
ToTensord(keys=data_keys)
]),
cache_rate=1.0)
self.val_dataset = monai.data.CacheDataset(
data=val_dicts,
transform=Compose([
data_transforms,
CenterSpatialCropd(keys=data_keys,
roi_size=self.hparams.patch_size),
ToTensord(keys=data_keys)
]),
cache_rate=1.0)
0,
DivisiblePadd(KEYS, k=4),
))
TESTS.append((
"DivisiblePadd 3d",
"3D",
0,
DivisiblePadd(KEYS, k=[4, 8, 11]),
))
TESTS.append((
"CenterSpatialCropd 2d",
"2D",
0,
CenterSpatialCropd(KEYS, roi_size=95),
))
TESTS.append((
"CenterSpatialCropd 3d",
"3D",
0,
CenterSpatialCropd(KEYS, roi_size=[95, 97, 98]),
))
TESTS.append(("CropForegroundd 2d", "2D", 0,
CropForegroundd(KEYS, source_key="label", margin=2)))
TESTS.append(
("CropForegroundd 3d", "3D", 0, CropForegroundd(KEYS, source_key="label")))
def main_worker(args):
# disable logging for processes except 0 on every node
if args.local_rank != 0:
f = open(os.devnull, "w")
sys.stdout = sys.stderr = f
if not os.path.exists(args.dir):
raise FileNotFoundError(f"Missing directory {args.dir}")
# initialize the distributed training process, every GPU runs in a process
dist.init_process_group(backend="nccl", init_method="env://")
total_start = time.time()
train_transforms = Compose([
# load 4 Nifti images and stack them together
LoadNiftid(keys=["image", "label"]),
AsChannelFirstd(keys="image"),
ConvertToMultiChannelBasedOnBratsClassesd(keys="label"),
Spacingd(keys=["image", "label"],
pixdim=(1.5, 1.5, 2.0),
mode=("bilinear", "nearest")),
Orientationd(keys=["image", "label"], axcodes="RAS"),
RandSpatialCropd(keys=["image", "label"],
roi_size=[128, 128, 64],
random_size=False),
NormalizeIntensityd(keys="image", nonzero=True, channel_wise=True),
RandFlipd(keys=["image", "label"], prob=0.5, spatial_axis=0),
RandScaleIntensityd(keys="image", factors=0.1, prob=0.5),
RandShiftIntensityd(keys="image", offsets=0.1, prob=0.5),
ToTensord(keys=["image", "label"]),
])
# create a training data loader
train_ds = BratsCacheDataset(
root_dir=args.dir,
transform=train_transforms,
section="training",
num_workers=4,
cache_rate=args.cache_rate,
shuffle=True,
)
train_loader = DataLoader(train_ds,
batch_size=args.batch_size,
shuffle=True,
num_workers=args.workers,
pin_memory=True)
# validation transforms and dataset
val_transforms = Compose([
LoadNiftid(keys=["image", "label"]),
AsChannelFirstd(keys="image"),
ConvertToMultiChannelBasedOnBratsClassesd(keys="label"),
Spacingd(keys=["image", "label"],
pixdim=(1.5, 1.5, 2.0),
mode=("bilinear", "nearest")),
Orientationd(keys=["image", "label"], axcodes="RAS"),
CenterSpatialCropd(keys=["image", "label"], roi_size=[128, 128, 64]),
NormalizeIntensityd(keys="image", nonzero=True, channel_wise=True),
ToTensord(keys=["image", "label"]),
])
val_ds = BratsCacheDataset(
root_dir=args.dir,
transform=val_transforms,
section="validation",
num_workers=4,
cache_rate=args.cache_rate,
shuffle=False,
)
val_loader = DataLoader(val_ds,
batch_size=args.batch_size,
shuffle=False,
num_workers=args.workers,
pin_memory=True)
if dist.get_rank() == 0:
# Logging for TensorBoard
writer = SummaryWriter(log_dir=args.log_dir)
# create UNet, DiceLoss and Adam optimizer
device = torch.device(f"cuda:{args.local_rank}")
if args.network == "UNet":
model = UNet(
dimensions=3,
in_channels=4,
out_channels=3,
channels=(16, 32, 64, 128, 256),
strides=(2, 2, 2, 2),
num_res_units=2,
).to(device)
else:
model = SegResNet(in_channels=4,
out_channels=3,
init_filters=16,
dropout_prob=0.2).to(device)
loss_function = DiceLoss(to_onehot_y=False,
sigmoid=True,
squared_pred=True)
optimizer = torch.optim.Adam(model.parameters(),
lr=args.lr,
weight_decay=1e-5,
amsgrad=True)
# wrap the model with DistributedDataParallel module
model = DistributedDataParallel(model, device_ids=[args.local_rank])
# start a typical PyTorch training
total_epoch = args.epochs
best_metric = -1000000
best_metric_epoch = -1
epoch_time = AverageMeter("Time", ":6.3f")
progress = ProgressMeter(total_epoch, [epoch_time], prefix="Epoch: ")
end = time.time()
print(f"Time elapsed before training: {end-total_start}")
for epoch in range(total_epoch):
train_loss = train(train_loader, model, loss_function, optimizer,
epoch, args, device)
epoch_time.update(time.time() - end)
if epoch % args.print_freq == 0:
progress.display(epoch)
if dist.get_rank() == 0:
writer.add_scalar("Loss/train", train_loss, epoch)
if (epoch + 1) % args.val_interval == 0:
metric, metric_tc, metric_wt, metric_et = evaluate(
model, val_loader, device)
if dist.get_rank() == 0:
writer.add_scalar("Mean Dice/val", metric, epoch)
writer.add_scalar("Mean Dice TC/val", metric_tc, epoch)
writer.add_scalar("Mean Dice WT/val", metric_wt, epoch)
writer.add_scalar("Mean Dice ET/val", metric_et, epoch)
if metric > best_metric:
best_metric = metric
best_metric_epoch = epoch + 1
print(
f"current epoch: {epoch + 1} current mean dice: {metric:.4f}"
f" tc: {metric_tc:.4f} wt: {metric_wt:.4f} et: {metric_et:.4f}"
f"\nbest mean dice: {best_metric:.4f} at epoch: {best_metric_epoch}"
)
end = time.time()
print(f"Time elapsed after epoch {epoch + 1} is {end - total_start}")
if dist.get_rank() == 0:
print(
f"train completed, best_metric: {best_metric:.4f} at epoch: {best_metric_epoch}"
)
# all processes should see same parameters as they all start from same
# random parameters and gradients are synchronized in backward passes,
# therefore, saving it in one process is sufficient
torch.save(model.state_dict(), "final_model.pth")
writer.flush()
dist.destroy_process_group()
def __init__(self,
data_dir: Path,
cache_dir: Path,
splits: Sequence[Sequence[Dict]],
batch_size: int,
spacing: Sequence[float] = (1.5, 1.5, 2.0),
crop_size: Sequence[int] = [48, 48, 36],
roi_size: Sequence[int] = [192, 192, 144],
seed: int = 47, **kwargs):
"""Module that deals with preparation of the LIDC dataset for training segmentation models.
Args:
data_dir (Path): Folder where preprocessed data is stored. See `LIDCReader` docs for expected structure.
cache_dir (Path): Folder where deterministic data transformations should be cached.
splits (Sequence[Sequence[Dict]]): Data dictionaries for training
and validation split.
batch_size (int): Number of training examples in each batch.
spacing (Sequence[float]): Pixel and slice spacing. Defaults to 1.5x1.5x2mm.
crop_size (Sequence[int]): Size of crop that is used for training. Defaults to 48x48x36px.
roi_size (Sequence[int]): Size of crop that is used for validation. Defaults to 192x192x144px.
seed (int, optional): Random seed used for deterministic sampling and transformations. Defaults to 47.
"""
super().__init__()
self.data_dir = data_dir
self.cache_dir = cache_dir
self.splits = splits
self.batch_size = batch_size
self.val_split = val_split
self.spacing = spacing
self.crop_size = crop_size
self.roi_size = roi_size
self.seed = seed
reader = LIDCReader(data_dir)
self.train_transforms = Compose([
LoadImaged(keys=["image", "label"], reader=reader),
AddChanneld(keys=["image", "label"]),
Spacingd(keys=["image", "label"], pixdim=self.spacing,
mode=("bilinear", "nearest")),
ScaleIntensityd(keys=["image"]),
RandCropByPosNegLabeld(
keys=["image", "label"],
label_key="label",
spatial_size=self.crop_size,
pos=1,
neg=1,
num_samples=2,
image_key="image",
image_threshold=0,
),
ToTensord(keys=["image", "label"]),
SelectItemsd(keys=["image", "label"]),
])
self.val_transforms = Compose([
LoadImaged(keys=["image", "label"], reader=reader),
AddChanneld(keys=["image", "label"]),
Spacingd(keys=["image", "label"], pixdim=self.spacing,
mode=("bilinear", "nearest")),
ScaleIntensityd(keys=["image"]),
SpatialPadd(keys=["image", "label"], spatial_size=self.roi_size,
mode="constant"),
CenterSpatialCropd(keys=["image", "label"], roi_size=self.roi_size),
ToTensord(keys=["image", "label"]),
SelectItemsd(keys=["image", "label"]),
])
self.hparams = {
"batch_size": self.batch_size,
"val_split": self.val_split,
"spacing": self.spacing,
"crop_size": self.crop_size,
"roi_size": self.roi_size,
}
return
TESTS.append(("RandSpatialCropd 2d", "2D", 0, RandSpatialCropd(KEYS, [96, 93], None, True, False)))
TESTS.append(("RandSpatialCropd 3d", "3D", 0, RandSpatialCropd(KEYS, [96, 93, 92], None, False, False)))
TESTS.append(("BorderPadd 2d", "2D", 0, BorderPadd(KEYS, [3, 7, 2, 5])))
TESTS.append(("BorderPadd 2d", "2D", 0, BorderPadd(KEYS, [3, 7])))
TESTS.append(("BorderPadd 3d", "3D", 0, BorderPadd(KEYS, [4])))
TESTS.append(("DivisiblePadd 2d", "2D", 0, DivisiblePadd(KEYS, k=4)))
TESTS.append(("DivisiblePadd 3d", "3D", 0, DivisiblePadd(KEYS, k=[4, 8, 11])))
TESTS.append(("CenterSpatialCropd 2d", "2D", 0, CenterSpatialCropd(KEYS, roi_size=95)))
TESTS.append(("CenterSpatialCropd 3d", "3D", 0, CenterSpatialCropd(KEYS, roi_size=[95, 97, 98])))
TESTS.append(("CropForegroundd 2d", "2D", 0, CropForegroundd(KEYS, source_key="label", margin=2)))
TESTS.append(("CropForegroundd 3d", "3D", 0, CropForegroundd(KEYS, source_key="label", k_divisible=[5, 101, 2])))
TESTS.append(("ResizeWithPadOrCropd 3d", "3D", 0, ResizeWithPadOrCropd(KEYS, [201, 150, 105])))
TESTS.append(("Flipd 3d", "3D", 0, Flipd(KEYS, [1, 2])))
TESTS.append(("RandFlipd 3d", "3D", 0, RandFlipd(KEYS, 1, [1, 2])))
TESTS.append(("RandAxisFlipd 3d", "3D", 0, RandAxisFlipd(KEYS, 1)))
def test_value(self, input_param, input_data, expected_value):
result = CenterSpatialCropd(**input_param)(input_data)
assert_allclose(result["img"], expected_value, type_test=False)
def test_shape(self, input_param, input_data, expected_shape):
result = CenterSpatialCropd(**input_param)(input_data)
self.assertTupleEqual(result["img"].shape, expected_shape)
def __init__(self,
data_dir: Path,
cache_dir: Path,
splits: Sequence[Sequence[Dict]],
target: str = "malignancy",
min_anns: int = 3,
exclude_labels: Sequence[int] = [3],
label_mapping: Tuple[Sequence[int]] = ([1, 2, 4,
5], [0, 0, 1, 1]),
batch_size: int = 16,
spacing: Sequence[float] = (1.5, 1.5, 2.0),
roi_size: Sequence[int] = [40, 40, 30],
aug_prob: float = 0.0,
seed: int = 47):
"""Handles all things data related for classifying lung nodules from the LIDC-IDRI dataset. Adheres to the PyTorch Lightning DataModule interface.
Args:
data_dir (Path): Directory with preprocessed LIDC dataset, as outputted by `preprocess_data` script.
cache_dir (Path): Directory where deterministic transformations of input samples will be cached.
splits (Sequence[Dict]): Dictionaries containing metadata of training and validation sets. See `split_data` script for more information.
target (str): Target variable, as denoted in splits dictionary. Defaults to malignancy.
min_anns (int): Minimum number of annotations required for including nodule. Defaults to 0.
exclude_labels (Sequence[int]): Label values to exclude in dataset.
label_mapping (Tuple[Sequence[int]]): Label mapping for discretization.
batch_size (int, optional): Batch size for training and validation. Defaults to 16.
spacing (Sequence[float], optional): Pixel spacing (in mm) that inputs will be transformed into. Defaults to (1.5, 1.5, 2.0).
roi_size (Sequence[int], optional): Shape that inputs will be transformed into. Defaults to [40, 40, 30].
aug_prob (float): Probability of applying random data augmentation. Defaults to 0.0.
seed (int, optional): Random seed for transformations etc. Defaults to 47.
"""
super().__init__()
self.data_dir = data_dir
self.cache_dir = cache_dir
self.splits = splits
self.batch_size = batch_size
self.spacing = spacing
self.roi_size = roi_size
self.seed = seed
self.target = target
self.min_anns = min_anns
self.exclude_labels = exclude_labels
self.label_mapping = label_mapping
self.aug_prob = aug_prob
self.hparams = {
"batch_size": self.batch_size,
"spacing": self.spacing,
"roi_size": self.roi_size,
"seed": self.seed,
"target": self.target,
"min_anns": self.min_anns,
"exclude_labels": self.exclude_labels,
"label_mapping": self.label_mapping,
}
reader = LIDCReader(self.data_dir, nodule_mode=True)
self.train_transforms = Compose([
LoadImaged(keys=["image"], reader=reader),
AddChanneld(keys=["image"]),
Spacingd(keys=["image"], pixdim=self.spacing, mode="bilinear"),
ScaleIntensityd(keys=["image"]),
SpatialPadd(keys=["image"],
spatial_size=self.roi_size,
mode="constant"),
CenterSpatialCropd(keys=["image"], roi_size=self.roi_size),
MapLabelValued(keys=["label"],
orig_labels=self.label_mapping[0],
target_labels=self.label_mapping[1]),
RandAffined(
keys=["image"],
spatial_size=self.roi_size,
prob=self.aug_prob,
mode="bilinear",
rotate_range=(np.pi / 18, np.pi / 18, np.pi / 4),
scale_range=(0.1, 0.1, 0.1),
padding_mode="border",
),
ToTensord(keys=["image", "label"]),
SelectItemsd(keys=["image", "label"]),
])
self.val_transforms = Compose([
LoadImaged(keys=["image"], reader=reader),
AddChanneld(keys=["image"]),
Spacingd(keys=["image"], pixdim=self.spacing, mode="bilinear"),
ScaleIntensityd(keys=["image"]),
SpatialPadd(keys=["image"],
spatial_size=self.roi_size,
mode="constant"),
CenterSpatialCropd(keys=["image"], roi_size=self.roi_size),
MapLabelValued(keys=["label"],
orig_labels=self.label_mapping[0],
target_labels=self.label_mapping[1]),
ToTensord(keys=["image", "label"]),
SelectItemsd(keys=["image", "label"]),
])
return
CastToTyped(keys="input", dtype=np.float32),
NormalizeIntensityd(keys="input", nonzero=False),
Lambdad(keys="input", func=lambda x: x.clip(-20, 20)),
EnsureTyped(keys=("input", "mask")),
])
cfg.val_aug = Compose([
Resized(
keys=("input", "mask"),
spatial_size=1120,
size_mode="longest",
mode="bilinear",
align_corners=False,
),
SpatialPadd(keys=("input", "mask"), spatial_size=(1120, 1120)),
CenterSpatialCropd(keys=("input", "mask"),
roi_size=(cfg.img_size[0], cfg.img_size[1])),
CastToTyped(keys="input", dtype=np.float32),
NormalizeIntensityd(keys="input", nonzero=False),
Lambdad(keys="input", func=lambda x: x.clip(-20, 20)),
EnsureTyped(keys=("input", "mask")),
])
cfg.test_aug = Compose([
Resized(
keys=("input", "mask"),
spatial_size=1120,
size_mode="longest",
mode="bilinear",
align_corners=False,
),
SpatialPadd(keys=("input", "mask"), spatial_size=(1120, 1120)),
def test_value(self, input_param, input_data, expected_value):
result = CenterSpatialCropd(**input_param)(input_data)
np.testing.assert_allclose(result["img"], expected_value)
NormalizeIntensityd(keys="image", nonzero=True, channel_wise=True),
RandScaleIntensityd(keys="image", factors=0.1, prob=0.5),
RandShiftIntensityd(keys="image", offsets=0.1, prob=0.5),
ToTensord(keys=["image", "label"]),
])
val_transform = Compose([
LoadImaged(keys=["image", "label"]),
AsChannelFirstd(keys="image"),
ConvertToMultiChannelBasedOnBratsClassesd(keys="label"),
Spacingd(
keys=["image", "label"],
pixdim=(1.5, 1.5, 2.0),
mode=("bilinear", "nearest"),
),
Orientationd(keys=["image", "label"], axcodes="RAS"),
CenterSpatialCropd(keys=["image", "label"], roi_size=[128, 128, 64]),
NormalizeIntensityd(keys="image", nonzero=True, channel_wise=True),
ToTensord(keys=["image", "label"]),
])
"""## Quickly load data with DecathlonDataset
Here we use `DecathlonDataset` to automatically download and extract the dataset.
It inherits MONAI `CacheDataset`, so we set `cache_num=100` to cache 100 items for training and use the defaut args to cache all the items for validation.
"""
train_ds = DecathlonDataset(
root_dir=root_dir,
task="Task01_BrainTumour",
transform=train_transform,
section="training",
download=True,