def forward(self, y_pred: torch.Tensor,
y_true: torch.Tensor) -> torch.Tensor:
"""
Args:
y_pred : the shape should be BNH[WD], where N is the number of classes.
It only supports binary segmentation.
The input should be the original logits since it will be transformed by
a sigmoid in the forward function.
y_true : the shape should be BNH[WD], where N is the number of classes.
It only supports binary segmentation.
Raises:
ValueError: When input and target are different shape
ValueError: When len(y_pred.shape) != 4 and len(y_pred.shape) != 5
ValueError: When num_classes
ValueError: When the number of classes entered does not match the expected number
"""
if y_pred.shape != y_true.shape:
raise ValueError(
f"ground truth has different shape ({y_true.shape}) from input ({y_pred.shape})"
)
if len(y_pred.shape) != 4 and len(y_pred.shape) != 5:
raise ValueError(
f"input shape must be 4 or 5, but got {y_pred.shape}")
if y_pred.shape[1] == 1:
y_pred = one_hot(y_pred, num_classes=self.num_classes)
y_true = one_hot(y_true, num_classes=self.num_classes)
if torch.max(y_true) != self.num_classes - 1:
raise ValueError(
f"Pelase make sure the number of classes is {self.num_classes-1}"
)
n_pred_ch = y_pred.shape[1]
if self.to_onehot_y:
if n_pred_ch == 1:
warnings.warn(
"single channel prediction, `to_onehot_y=True` ignored.")
else:
y_true = one_hot(y_true, num_classes=n_pred_ch)
asy_focal_loss = self.asy_focal_loss(y_pred, y_true)
asy_focal_tversky_loss = self.asy_focal_tversky_loss(y_pred, y_true)
loss: torch.Tensor = self.weight * asy_focal_loss + (
1 - self.weight) * asy_focal_tversky_loss
if self.reduction == LossReduction.SUM.value:
return torch.sum(loss) # sum over the batch and channel dims
if self.reduction == LossReduction.NONE.value:
return loss # returns [N, num_classes] losses
if self.reduction == LossReduction.MEAN.value:
return torch.mean(loss)
raise ValueError(
f'Unsupported reduction: {self.reduction}, available options are ["mean", "sum", "none"].'
)
def __call__(
self, img: Union[Sequence[NdarrayOrTensor],
NdarrayOrTensor]) -> NdarrayOrTensor:
img_ = self.get_stacked_torch(img)
if self.num_classes is not None:
has_ch_dim = True
if img_.ndimension() > 1 and img_.shape[1] > 1:
warnings.warn(
"no need to specify num_classes for One-Hot format data.")
else:
if img_.ndimension() == 1:
# if no channel dim, need to remove channel dim after voting
has_ch_dim = False
img_ = one_hot(img_, self.num_classes, dim=1)
img_ = torch.mean(img_.float(), dim=0)
if self.num_classes is not None:
# if not One-Hot, use "argmax" to vote the most common class
out_pt = torch.argmax(img_, dim=0, keepdim=has_ch_dim)
else:
# for One-Hot data, round the float number to 0 or 1
out_pt = torch.round(img_)
return self.post_convert(out_pt, img)
def forward(self, y_pred: torch.Tensor,
y_true: torch.Tensor) -> torch.Tensor:
n_pred_ch = y_pred.shape[1]
if self.to_onehot_y:
if n_pred_ch == 1:
warnings.warn(
"single channel prediction, `to_onehot_y=True` ignored.")
else:
y_true = one_hot(y_true, num_classes=n_pred_ch)
if y_true.shape != y_pred.shape:
raise ValueError(
f"ground truth has different shape ({y_true.shape}) from input ({y_pred.shape})"
)
y_pred = torch.clamp(y_pred, self.epsilon, 1.0 - self.epsilon)
cross_entropy = -y_true * torch.log(y_pred)
back_ce = torch.pow(1 - y_pred[:, 0], self.gamma) * cross_entropy[:, 0]
back_ce = (1 - self.delta) * back_ce
fore_ce = cross_entropy[:, 1]
fore_ce = self.delta * fore_ce
loss = torch.mean(
torch.sum(torch.stack([back_ce, fore_ce], dim=1), dim=1))
return loss
def __call__(
self, img: Union[Sequence[torch.Tensor],
torch.Tensor]) -> torch.Tensor:
img_ = torch.stack(img) if isinstance(img,
(tuple,
list)) else torch.as_tensor(img)
if self.num_classes is not None:
has_ch_dim = True
if img_.ndimension() > 2 and img_.shape[2] > 1:
warnings.warn(
"no need to specify num_classes for One-Hot format data.")
else:
if img_.ndimension() == 2:
# if no channel dim, need to remove channel dim after voting
has_ch_dim = False
img_ = one_hot(img_, self.num_classes, dim=2)
img_ = torch.mean(img_.float(), dim=0)
if self.num_classes is not None:
# if not One-Hot, use "argmax" to vote the most common class
return torch.argmax(img_, dim=1, keepdim=has_ch_dim)
else:
# for One-Hot data, round the float number to 0 or 1
return torch.round(img_)
def __call__(
self,
img,
argmax: Optional[bool] = None,
to_onehot: Optional[bool] = None,
n_classes: Optional[int] = None,
threshold_values: Optional[bool] = None,
logit_thresh: Optional[float] = None,
):
"""
Args:
argmax: whether to execute argmax function on input data before transform.
Defaults to ``self.argmax``.
to_onehot: whether to convert input data into the one-hot format.
Defaults to ``self.to_onehot``.
n_classes: the number of classes to convert to One-Hot format.
Defaults to ``self.n_classes``.
threshold_values: whether threshold the float value to int number 0 or 1.
Defaults to ``self.threshold_values``.
logit_thresh: the threshold value for thresholding operation..
Defaults to ``self.logit_thresh``.
"""
if argmax or self.argmax:
img = torch.argmax(img, dim=1, keepdim=True)
if to_onehot or self.to_onehot:
_nclasses = self.n_classes if n_classes is None else n_classes
assert isinstance(_nclasses, int), "One of self.n_classes or n_classes must be an integer"
img = one_hot(img, _nclasses)
if threshold_values or self.threshold_values:
img = img >= (self.logit_thresh if logit_thresh is None else logit_thresh)
return img.float()
def forward(self, input: torch.Tensor, target: torch.Tensor) -> torch.Tensor:
"""
Args:
input: the shape should be BNH[WD]. The input should be the original logits
due to the restriction of ``monai.losses.FocalLoss``.
target: the shape should be BNH[WD] or B1H[WD].
Raises:
ValueError: When number of dimensions for input and target are different.
ValueError: When number of channels for target is neither 1 nor the same as input.
"""
if len(input.shape) != len(target.shape):
raise ValueError("the number of dimensions for input and target should be the same.")
n_pred_ch = input.shape[1]
if self.to_onehot_y:
if n_pred_ch == 1:
warnings.warn("single channel prediction, `to_onehot_y=True` ignored.")
else:
target = one_hot(target, num_classes=n_pred_ch)
if not self.include_background:
if n_pred_ch == 1:
warnings.warn("single channel prediction, `include_background=False` ignored.")
else:
# if skipping background, removing first channel
target = target[:, 1:]
input = input[:, 1:]
dice_loss = self.dice(input, target)
focal_loss = self.focal(input, target)
total_loss: torch.Tensor = self.lambda_dice * dice_loss + self.lambda_focal * focal_loss
return total_loss
def test_shape(self, input_data, expected_shape, expected_result=None):
result = one_hot(**input_data)
self.assertEqual(result.shape, expected_shape)
if expected_result is not None:
self.assertTrue(np.allclose(expected_result, result.numpy()))
if "dtype" in input_data:
self.assertEqual(result.dtype, input_data["dtype"])
else:
# by default, expecting float type
self.assertEqual(result.dtype, torch.float)
def __call__(
self,
img: torch.Tensor,
argmax: Optional[bool] = None,
to_onehot: Optional[bool] = None,
num_classes: Optional[int] = None,
threshold_values: Optional[bool] = None,
logit_thresh: Optional[float] = None,
rounding: Optional[str] = None,
n_classes: Optional[int] = None,
) -> torch.Tensor:
"""
Args:
img: the input tensor data to convert, if no channel dimension when converting to `One-Hot`,
will automatically add it.
argmax: whether to execute argmax function on input data before transform.
Defaults to ``self.argmax``.
to_onehot: whether to convert input data into the one-hot format.
Defaults to ``self.to_onehot``.
num_classes: the number of classes to convert to One-Hot format.
Defaults to ``self.num_classes``.
threshold_values: whether threshold the float value to int number 0 or 1.
Defaults to ``self.threshold_values``.
logit_thresh: the threshold value for thresholding operation..
Defaults to ``self.logit_thresh``.
rounding: if not None, round the data according to the specified option,
available options: ["torchrounding"].
.. deprecated:: 0.6.0
``n_classes`` is deprecated, use ``num_classes`` instead.
"""
# in case the new num_classes is default but you still call deprecated n_classes
if n_classes is not None and num_classes is None:
num_classes = n_classes
if argmax or self.argmax:
img = torch.argmax(img, dim=0, keepdim=True)
if to_onehot or self.to_onehot:
_nclasses = self.num_classes if num_classes is None else num_classes
if not isinstance(_nclasses, int):
raise AssertionError("One of self.num_classes or num_classes must be an integer")
img = one_hot(img, num_classes=_nclasses, dim=0)
if threshold_values or self.threshold_values:
img = img >= (self.logit_thresh if logit_thresh is None else logit_thresh)
rounding = self.rounding if rounding is None else rounding
if rounding is not None:
look_up_option(rounding, ["torchrounding"])
img = torch.round(img)
return img.float()
def __call__(
self,
img: NdarrayOrTensor,
argmax: Optional[bool] = None,
to_onehot: Optional[int] = None,
threshold: Optional[float] = None,
rounding: Optional[str] = None
) -> NdarrayOrTensor:
"""
Args:
img: the input tensor data to convert, if no channel dimension when converting to `One-Hot`,
will automatically add it.
argmax: whether to execute argmax function on input data before transform.
Defaults to ``self.argmax``.
to_onehot: if not None, convert input data into the one-hot format with specified number of classes.
Defaults to ``self.to_onehot``.
threshold: if not None, threshold the float values to int number 0 or 1 with specified threshold value.
Defaults to ``self.threshold``.
rounding: if not None, round the data according to the specified option,
available options: ["torchrounding"].
"""
img_t: torch.Tensor
img_t, *_ = convert_data_type(img, torch.Tensor) # type: ignore
if argmax or self.argmax:
img_t = torch.argmax(img_t, dim=self.kwargs.get("dim", 0), keepdim=self.kwargs.get("keepdim", True))
to_onehot = self.to_onehot if to_onehot is None else to_onehot
if to_onehot is not None:
if not isinstance(to_onehot, int):
raise ValueError("the number of classes for One-Hot must be an integer.")
img_t = one_hot(
img_t, num_classes=to_onehot, dim=self.kwargs.get("dim", 0), dtype=self.kwargs.get("dtype", torch.float)
)
threshold = self.threshold if threshold is None else threshold
if threshold is not None:
img_t = img_t >= threshold
rounding = self.rounding if rounding is None else rounding
if rounding is not None:
look_up_option(rounding, ["torchrounding"])
img_t = torch.round(img_t)
img, *_ = convert_to_dst_type(img_t, img, dtype=self.kwargs.get("dtype", torch.float))
return img
def __call__(self, img, to_onehot: Optional[bool] = None, num_classes: Optional[int] = None):
"""
Args:
to_onehot: whether to convert the data to One-Hot format first.
Defaults to ``self.to_onehot``.
num_classes: the class number used to convert to One-Hot format if `to_onehot` is True.
Defaults to ``self.num_classes``.
"""
if to_onehot or self.to_onehot:
if num_classes is None:
num_classes = self.num_classes
assert isinstance(num_classes, int), "must specify class number for One-Hot."
img = one_hot(img, num_classes)
n_classes = img.shape[1]
outputs = list()
for i in range(n_classes):
outputs.append(img[:, i : i + 1])
return outputs
def do_binarization(
input_data: torch.Tensor,
bin_mode: str = "threshold",
bin_threshold: Union[float, Sequence[float]] = 0.5,
) -> torch.Tensor:
"""
Args:
input_data: the input that to be binarized, in the shape [B] or [BN] or [BNHW] or [BNHWD].
bin_mode: can be ``"threshold"`` or ``"mutually_exclusive"``, or a callable function.
- ``"threshold"``, a single threshold or a sequence of thresholds should be set.
- ``"mutually_exclusive"``, `input_data` will be converted by a combination of
argmax and to_onehot.
bin_threshold: the threshold to binarize the input data, can be a single value or a sequence of
values that each one of the value represents a threshold for a class.
Raises:
AssertionError: when `bin_threshold` is a sequence and the input has the shape [B].
AssertionError: when `bin_threshold` is a sequence but the length != the number of classes.
AssertionError: when `bin_mode` is ``"mutually_exclusive"`` the input has the shape [B].
AssertionError: when `bin_mode` is ``"mutually_exclusive"`` the input has the shape [B, 1].
"""
input_ndim = input_data.ndimension()
if bin_mode == "threshold":
if isinstance(bin_threshold, Sequence):
assert input_ndim > 1, "a sequence of thresholds are used for multi-class tasks."
error_hint = "the length of the sequence should be the same as the number of classes."
assert input_data.shape[1] == len(bin_threshold), "{}".format(
error_hint)
for cls_num in range(input_data.shape[1]):
input_data[:, cls_num] = (input_data[:, cls_num] >
bin_threshold[cls_num]).float()
else:
input_data = (input_data > bin_threshold).float()
elif bin_mode == "mutually_exclusive":
assert input_ndim > 1, "mutually_exclusive is used for multi-class tasks."
n_classes = input_data.shape[1]
assert n_classes > 1, "mutually_exclusive is used for multi-class tasks."
input_data = torch.argmax(input_data, dim=1, keepdim=True)
input_data = one_hot(input_data, num_classes=n_classes)
return input_data
def test_consistency_with_cross_entropy_2d_onehot_label(self):
# For gamma=0 the focal loss reduces to the cross entropy loss
focal_loss = FocalLoss(to_onehot_y=False, gamma=0.0, reduction="mean")
ce = nn.CrossEntropyLoss(reduction="mean")
max_error = 0
class_num = 10
batch_size = 128
for _ in range(100):
# Create a random tensor of shape (batch_size, class_num, 8, 4)
x = torch.rand(batch_size, class_num, 8, 4, requires_grad=True)
# Create a random batch of classes
l = torch.randint(low=0, high=class_num, size=(batch_size, 1, 8, 4))
if torch.cuda.is_available():
x = x.cuda()
l = l.cuda()
output0 = focal_loss(x, one_hot(l, num_classes=class_num))
output1 = ce(x, l[:, 0]) / class_num
a = float(output0.cpu().detach())
b = float(output1.cpu().detach())
if abs(a - b) > max_error:
max_error = abs(a - b)
self.assertAlmostEqual(max_error, 0.0, places=3)
def test_consistency_with_cross_entropy_classification_01(self):
# for gamma=0.1 the focal loss differs from the cross entropy loss
focal_loss = FocalLoss(to_onehot_y=True, gamma=0.1, reduction="mean")
ce = nn.BCEWithLogitsLoss(reduction="mean")
max_error = 0
class_num = 10
batch_size = 128
for _ in range(100):
# Create a random scores tensor of shape (batch_size, class_num)
x = torch.rand(batch_size, class_num, requires_grad=True)
# Create a random batch of classes
l = torch.randint(low=0, high=class_num, size=(batch_size, 1))
l = l.long()
if torch.cuda.is_available():
x = x.cuda()
l = l.cuda()
output0 = focal_loss(x, l)
output1 = ce(x, one_hot(l, num_classes=class_num))
a = float(output0.cpu().detach())
b = float(output1.cpu().detach())
if abs(a - b) > max_error:
max_error = abs(a - b)
self.assertNotAlmostEqual(max_error, 0.0, places=3)
def forward(self, y_pred: torch.Tensor,
y_true: torch.Tensor) -> torch.Tensor:
n_pred_ch = y_pred.shape[1]
if self.to_onehot_y:
if n_pred_ch == 1:
warnings.warn(
"single channel prediction, `to_onehot_y=True` ignored.")
else:
y_true = one_hot(y_true, num_classes=n_pred_ch)
if y_true.shape != y_pred.shape:
raise ValueError(
f"ground truth has different shape ({y_true.shape}) from input ({y_pred.shape})"
)
# clip the prediction to avoid NaN
y_pred = torch.clamp(y_pred, self.epsilon, 1.0 - self.epsilon)
axis = list(range(2, len(y_pred.shape)))
# Calculate true positives (tp), false negatives (fn) and false positives (fp)
tp = torch.sum(y_true * y_pred, dim=axis)
fn = torch.sum(y_true * (1 - y_pred), dim=axis)
fp = torch.sum((1 - y_true) * y_pred, dim=axis)
dice_class = (tp +
self.epsilon) / (tp + self.delta * fn +
(1 - self.delta) * fp + self.epsilon)
# Calculate losses separately for each class, enhancing both classes
back_dice = 1 - dice_class[:, 0]
fore_dice = (1 - dice_class[:, 1]) * torch.pow(1 - dice_class[:, 1],
-self.gamma)
# Average class scores
loss = torch.mean(torch.stack([back_dice, fore_dice], dim=-1))
return loss
def __call__(
self,
img: NdarrayOrTensor,
argmax: Optional[bool] = None,
to_onehot: Optional[int] = None,
threshold: Optional[float] = None,
rounding: Optional[str] = None,
n_classes: Optional[int] = None, # deprecated
num_classes: Optional[int] = None, # deprecated
logit_thresh: Optional[float] = None, # deprecated
threshold_values: Optional[bool] = None, # deprecated
) -> NdarrayOrTensor:
"""
Args:
img: the input tensor data to convert, if no channel dimension when converting to `One-Hot`,
will automatically add it.
argmax: whether to execute argmax function on input data before transform.
Defaults to ``self.argmax``.
to_onehot: if not None, convert input data into the one-hot format with specified number of classes.
Defaults to ``self.to_onehot``.
threshold: if not None, threshold the float values to int number 0 or 1 with specified threshold value.
Defaults to ``self.threshold``.
rounding: if not None, round the data according to the specified option,
available options: ["torchrounding"].
.. deprecated:: 0.6.0
``n_classes`` is deprecated, use ``to_onehot`` instead.
.. deprecated:: 0.7.0
``num_classes`` is deprecated, use ``to_onehot`` instead.
``logit_thresh`` is deprecated, use ``threshold`` instead.
``threshold_values`` is deprecated, use ``threshold`` instead.
"""
if isinstance(to_onehot, bool):
warnings.warn(
"`to_onehot=True/False` is deprecated, please use `to_onehot=num_classes` instead."
)
to_onehot = num_classes if to_onehot else None
if isinstance(threshold, bool):
warnings.warn(
"`threshold_values=True/False` is deprecated, please use `threshold=value` instead."
)
threshold = logit_thresh if threshold else None
img = convert_to_tensor(img, track_meta=get_track_meta())
img_t, *_ = convert_data_type(img, torch.Tensor)
if argmax or self.argmax:
img_t = torch.argmax(img_t, dim=0, keepdim=True)
to_onehot = self.to_onehot if to_onehot is None else to_onehot
if to_onehot is not None:
if not isinstance(to_onehot, int):
raise AssertionError(
"the number of classes for One-Hot must be an integer.")
img_t = one_hot(img_t, num_classes=to_onehot, dim=0)
threshold = self.threshold if threshold is None else threshold
if threshold is not None:
img_t = img_t >= threshold
rounding = self.rounding if rounding is None else rounding
if rounding is not None:
look_up_option(rounding, ["torchrounding"])
img_t = torch.round(img_t)
img, *_ = convert_to_dst_type(img_t, img, dtype=torch.float)
return img
def test_convergence(self, loss_type, loss_args, forward_args):
"""
The goal of this test is to assess if the gradient of the loss function
is correct by testing if we can train a one layer neural network
to segment one image.
We verify that the loss is decreasing in almost all SGD steps.
"""
learning_rate = 0.001
max_iter = 40
# define a simple 3d example
target_seg = torch.tensor(
[[
# raw 0
[[0, 0, 0, 0], [0, 1, 1, 0], [0, 1, 1, 0], [0, 0, 0, 0]],
# raw 1
[[0, 0, 0, 0], [0, 1, 1, 0], [0, 1, 1, 0], [0, 0, 0, 0]],
# raw 2
[[0, 0, 0, 0], [0, 1, 1, 0], [0, 1, 1, 0], [0, 0, 0, 0]],
]],
device=self.device,
)
target_seg = torch.unsqueeze(target_seg, dim=0)
image = 12 * target_seg + 27
image = image.float().to(self.device)
num_classes = 2
num_voxels = 3 * 4 * 4
target_onehot = one_hot(target_seg, num_classes=num_classes)
# define a one layer model
class OnelayerNet(nn.Module):
def __init__(self):
super(OnelayerNet, self).__init__()
self.layer_1 = nn.Linear(num_voxels, 200)
self.acti = nn.ReLU()
self.layer_2 = nn.Linear(200, num_voxels * num_classes)
def forward(self, x):
x = x.view(-1, num_voxels)
x = self.layer_1(x)
x = self.acti(x)
x = self.layer_2(x)
x = x.view(-1, num_classes, 3, 4, 4)
return x
# initialise the network
net = OnelayerNet().to(self.device)
# initialize the loss
loss = loss_type(**loss_args)
# initialize a SGD optimizer
optimizer = optim.Adam(net.parameters(), lr=learning_rate)
loss_history = []
init_output = None
# train the network
for iter_i in range(max_iter):
# set the gradient to zero
optimizer.zero_grad()
# forward pass
output = net(image)
if init_output is None:
init_output = torch.argmax(output, 1).detach().cpu().numpy()
if loss_args["to_onehot_y"] is False:
loss_val = loss(output, target_onehot, **forward_args)
else:
loss_val = loss(output, target_seg, **forward_args)
if iter_i % 10 == 0:
pred = torch.argmax(output, 1).detach().cpu().numpy()
gt = target_seg.detach().cpu().numpy()[:, 0]
print(
f"{loss_type.__name__} iter: {iter_i}, acc: {np.sum(pred == gt) / np.prod(pred.shape)}"
)
# backward pass
loss_val.backward()
optimizer.step()
# stats
loss_history.append(loss_val.item())
pred = torch.argmax(output, 1).detach().cpu().numpy()
target = target_seg.detach().cpu().numpy()[:, 0]
# initial predictions are bad
self.assertTrue(not np.allclose(init_output, target))
# final predictions are good
np.testing.assert_allclose(pred, target)
def forward(self,
input: torch.Tensor,
target: torch.Tensor,
smooth: float = 1e-5) -> torch.Tensor:
"""
Args:
input: the shape should be BNH[WD].
target: the shape should be BNH[WD].
smooth: a small constant to avoid nan.
Raises:
ValueError: When ``self.reduction`` is not one of ["mean", "sum", "none"].
"""
if self.sigmoid:
input = torch.sigmoid(input)
n_pred_ch = input.shape[1]
if self.softmax:
if n_pred_ch == 1:
warnings.warn(
"single channel prediction, `softmax=True` ignored.")
else:
input = torch.softmax(input, 1)
if self.other_act is not None:
input = self.other_act(input)
if self.to_onehot_y:
if n_pred_ch == 1:
warnings.warn(
"single channel prediction, `to_onehot_y=True` ignored.")
else:
target = one_hot(target, num_classes=n_pred_ch)
if not self.include_background:
if n_pred_ch == 1:
warnings.warn(
"single channel prediction, `include_background=False` ignored."
)
else:
# if skipping background, removing first channel
target = target[:, 1:]
input = input[:, 1:]
assert (
target.shape == input.shape
), f"ground truth has differing shape ({target.shape}) from input ({input.shape})"
# reducing only spatial dimensions (not batch nor channels)
reduce_axis = list(range(2, len(input.shape)))
intersection = torch.sum(target * input, dim=reduce_axis)
if self.squared_pred:
target = torch.pow(target, 2)
input = torch.pow(input, 2)
ground_o = torch.sum(target, dim=reduce_axis)
pred_o = torch.sum(input, dim=reduce_axis)
denominator = ground_o + pred_o
if self.jaccard:
denominator = 2.0 * (denominator - intersection)
f: torch.Tensor = 1.0 - (2.0 * intersection + smooth) / (denominator +
smooth)
if self.reduction == LossReduction.MEAN.value:
f = torch.mean(f) # the batch and channel average
elif self.reduction == LossReduction.SUM.value:
f = torch.sum(f) # sum over the batch and channel dims
elif self.reduction == LossReduction.NONE.value:
pass # returns [N, n_classes] losses
else:
raise ValueError(
f'Unsupported reduction: {self.reduction}, available options are ["mean", "sum", "none"].'
)
return f
def compute_roc_auc(
y_pred: torch.Tensor,
y: torch.Tensor,
to_onehot_y: bool = False,
softmax: bool = False,
other_act: Optional[Callable] = None,
average: Union[Average, str] = Average.MACRO,
):
"""Computes Area Under the Receiver Operating Characteristic Curve (ROC AUC). Referring to:
`sklearn.metrics.roc_auc_score <https://scikit-learn.org/stable/modules/generated/
sklearn.metrics.roc_auc_score.html#sklearn.metrics.roc_auc_score>`_.
Args:
y_pred: input data to compute, typical classification model output.
it must be One-Hot format and first dim is batch, example shape: [16] or [16, 2].
y: ground truth to compute ROC AUC metric, the first dim is batch.
example shape: [16, 1] will be converted into [16, 2] (where `2` is inferred from `y_pred`).
to_onehot_y: whether to convert `y` into the one-hot format. Defaults to False.
softmax: whether to add softmax function to `y_pred` before computation. Defaults to False.
other_act: callable function to replace `softmax` as activation layer if needed, Defaults to ``None``.
for example: `other_act = lambda x: torch.log_softmax(x)`.
average: {``"macro"``, ``"weighted"``, ``"micro"``, ``"none"``}
Type of averaging performed if not binary classification.
Defaults to ``"macro"``.
- ``"macro"``: calculate metrics for each label, and find their unweighted mean.
This does not take label imbalance into account.
- ``"weighted"``: calculate metrics for each label, and find their average,
weighted by support (the number of true instances for each label).
- ``"micro"``: calculate metrics globally by considering each element of the label
indicator matrix as a label.
- ``"none"``: the scores for each class are returned.
Raises:
ValueError: When ``y_pred`` dimension is not one of [1, 2].
ValueError: When ``y`` dimension is not one of [1, 2].
ValueError: When ``softmax=True`` and ``other_act is not None``. Incompatible values.
TypeError: When ``other_act`` is not an ``Optional[Callable]``.
ValueError: When ``average`` is not one of ["macro", "weighted", "micro", "none"].
Note:
ROCAUC expects y to be comprised of 0's and 1's. `y_pred` must be either prob. estimates or confidence values.
"""
y_pred_ndim = y_pred.ndimension()
y_ndim = y.ndimension()
if y_pred_ndim not in (1, 2):
raise ValueError(
"Predictions should be of shape (batch_size, n_classes) or (batch_size, )."
)
if y_ndim not in (1, 2):
raise ValueError(
"Targets should be of shape (batch_size, n_classes) or (batch_size, )."
)
if y_pred_ndim == 2 and y_pred.shape[1] == 1:
y_pred = y_pred.squeeze(dim=-1)
y_pred_ndim = 1
if y_ndim == 2 and y.shape[1] == 1:
y = y.squeeze(dim=-1)
if y_pred_ndim == 1:
if to_onehot_y:
warnings.warn(
"y_pred has only one channel, to_onehot_y=True ignored.")
if softmax:
warnings.warn("y_pred has only one channel, softmax=True ignored.")
return _calculate(y, y_pred)
else:
n_classes = y_pred.shape[1]
if to_onehot_y:
y = one_hot(y, n_classes)
if softmax and other_act is not None:
raise ValueError(
"Incompatible values: softmax=True and other_act is not None.")
if softmax:
y_pred = y_pred.float().softmax(dim=1)
if other_act is not None:
if not callable(other_act):
raise TypeError(
f"other_act must be None or callable but is {type(other_act).__name__}."
)
y_pred = other_act(y_pred)
assert y.shape == y_pred.shape, "data shapes of y_pred and y do not match."
average = Average(average)
if average == Average.MICRO:
return _calculate(y.flatten(), y_pred.flatten())
else:
y, y_pred = y.transpose(0, 1), y_pred.transpose(0, 1)
auc_values = [
_calculate(y_, y_pred_) for y_, y_pred_ in zip(y, y_pred)
]
if average == Average.NONE:
return auc_values
if average == Average.MACRO:
return np.mean(auc_values)
if average == Average.WEIGHTED:
weights = [sum(y_) for y_ in y]
return np.average(auc_values, weights=weights)
raise ValueError(
f'Unsupported average: {average}, available options are ["macro", "weighted", "micro", "none"].'
)
def compute_meandice(
y_pred: torch.Tensor,
y: torch.Tensor,
include_background: bool = True,
to_onehot_y: bool = False,
mutually_exclusive: bool = False,
sigmoid: bool = False,
other_act: Optional[Callable] = None,
logit_thresh: float = 0.5,
) -> torch.Tensor:
"""Computes Dice score metric from full size Tensor and collects average.
Args:
y_pred: input data to compute, typical segmentation model output.
it must be one-hot format and first dim is batch, example shape: [16, 3, 32, 32].
y: ground truth to compute mean dice metric, the first dim is batch.
example shape: [16, 1, 32, 32] will be converted into [16, 3, 32, 32].
alternative shape: [16, 3, 32, 32] and set `to_onehot_y=False` to use 3-class labels directly.
include_background: whether to skip Dice computation on the first channel of
the predicted output. Defaults to True.
to_onehot_y: whether to convert `y` into the one-hot format. Defaults to False.
mutually_exclusive: if True, `y_pred` will be converted into a binary matrix using
a combination of argmax and to_onehot. Defaults to False.
sigmoid: whether to add sigmoid function to y_pred before computation. Defaults to False.
other_act: callable function to replace `sigmoid` as activation layer if needed, Defaults to ``None``.
for example: `other_act = torch.tanh`.
logit_thresh: the threshold value used to convert (for example, after sigmoid if `sigmoid=True`)
`y_pred` into a binary matrix. Defaults to 0.5.
Raises:
ValueError: When ``sigmoid=True`` and ``other_act is not None``. Incompatible values.
TypeError: When ``other_act`` is not an ``Optional[Callable]``.
ValueError: When ``sigmoid=True`` and ``mutually_exclusive=True``. Incompatible values.
Returns:
Dice scores per batch and per class, (shape [batch_size, n_classes]).
Note:
This method provides two options to convert `y_pred` into a binary matrix
(1) when `mutually_exclusive` is True, it uses a combination of ``argmax`` and ``to_onehot``,
(2) when `mutually_exclusive` is False, it uses a threshold ``logit_thresh``
(optionally with a ``sigmoid`` function before thresholding).
"""
n_classes = y_pred.shape[1]
n_len = len(y_pred.shape)
if sigmoid and other_act is not None:
raise ValueError(
"Incompatible values: sigmoid=True and other_act is not None.")
if sigmoid:
y_pred = y_pred.float().sigmoid()
if other_act is not None:
if not callable(other_act):
raise TypeError(
f"other_act must be None or callable but is {type(other_act).__name__}."
)
y_pred = other_act(y_pred)
if n_classes == 1:
if mutually_exclusive:
warnings.warn(
"y_pred has only one class, mutually_exclusive=True ignored.")
if to_onehot_y:
warnings.warn(
"y_pred has only one channel, to_onehot_y=True ignored.")
if not include_background:
warnings.warn(
"y_pred has only one channel, include_background=False ignored."
)
# make both y and y_pred binary
y_pred = (y_pred >= logit_thresh).float()
y = (y > 0).float()
else: # multi-channel y_pred
# make both y and y_pred binary
if mutually_exclusive:
if sigmoid:
raise ValueError(
"Incompatible values: sigmoid=True and mutually_exclusive=True."
)
y_pred = torch.argmax(y_pred, dim=1, keepdim=True)
y_pred = one_hot(y_pred, num_classes=n_classes)
else:
y_pred = (y_pred >= logit_thresh).float()
if to_onehot_y:
y = one_hot(y, num_classes=n_classes)
if not include_background:
y = y[:, 1:] if y.shape[1] > 1 else y
y_pred = y_pred[:, 1:] if y_pred.shape[1] > 1 else y_pred
assert y.shape == y_pred.shape, "Ground truth one-hot has differing shape (%r) from source (%r)" % (
y.shape,
y_pred.shape,
)
y = y.float()
y_pred = y_pred.float()
# reducing only spatial dimensions (not batch nor channels)
reduce_axis = list(range(2, n_len))
intersection = torch.sum(y * y_pred, dim=reduce_axis)
y_o = torch.sum(y, reduce_axis)
y_pred_o = torch.sum(y_pred, dim=reduce_axis)
denominator = y_o + y_pred_o
f = torch.where(y_o > 0, (2.0 * intersection) / denominator,
torch.tensor(float("nan"), device=y_o.device))
return f # returns array of Dice shape: [batch, n_classes]
def forward(self, input: torch.Tensor, target: torch.Tensor, smooth: float = 1e-5):
"""
Args:
input (tensor): the shape should be BNH[WD].
target (tensor): the shape should be BNH[WD].
smooth: a small constant to avoid nan.
Raises:
ValueError: reduction={self.reduction} is invalid.
"""
if self.sigmoid:
input = torch.sigmoid(input)
n_pred_ch = input.shape[1]
if n_pred_ch == 1:
if self.softmax:
warnings.warn("single channel prediction, `softmax=True` ignored.")
if self.to_onehot_y:
warnings.warn("single channel prediction, `to_onehot_y=True` ignored.")
if not self.include_background:
warnings.warn("single channel prediction, `include_background=False` ignored.")
else:
if self.softmax:
input = torch.softmax(input, 1)
if self.to_onehot_y:
target = one_hot(target, n_pred_ch)
if not self.include_background:
# if skipping background, removing first channel
target = target[:, 1:]
input = input[:, 1:]
assert (
target.shape == input.shape
), f"ground truth has differing shape ({target.shape}) from input ({input.shape})"
# reducing only spatial dimensions (not batch nor channels)
reduce_axis = list(range(2, len(input.shape)))
intersection = torch.sum(target * input, reduce_axis)
ground_o = torch.sum(target, reduce_axis)
pred_o = torch.sum(input, reduce_axis)
denominator = ground_o + pred_o
w = self.w_func(ground_o.float())
for b in w:
infs = torch.isinf(b)
b[infs] = 0.0
b[infs] = torch.max(b)
f = 1.0 - (2.0 * (intersection * w).sum(1) + smooth) / ((denominator * w).sum(1) + smooth)
if self.reduction == LossReduction.MEAN:
f = torch.mean(f) # the batch and channel average
elif self.reduction == LossReduction.SUM:
f = torch.sum(f) # sum over the batch and channel dims
elif self.reduction == LossReduction.NONE:
pass # returns [N, n_classes] losses
else:
raise ValueError(f"reduction={self.reduction} is invalid.")
return f
def forward(self, input: torch.Tensor,
target: torch.Tensor) -> torch.Tensor:
"""
Args:
input: the shape should be BNH[WD].
target: the shape should be BNH[WD].
Raises:
ValueError: When ``self.reduction`` is not one of ["mean", "sum", "none"].
"""
if self.sigmoid:
input = torch.sigmoid(input)
n_pred_ch = input.shape[1]
if self.softmax:
if n_pred_ch == 1:
warnings.warn(
"single channel prediction, `softmax=True` ignored.")
else:
input = torch.softmax(input, 1)
if self.other_act is not None:
input = self.other_act(input)
if self.to_onehot_y:
if n_pred_ch == 1:
warnings.warn(
"single channel prediction, `to_onehot_y=True` ignored.")
else:
target = one_hot(target, num_classes=n_pred_ch)
if not self.include_background:
if n_pred_ch == 1:
warnings.warn(
"single channel prediction, `include_background=False` ignored."
)
else:
# if skipping background, removing first channel
target = target[:, 1:]
input = input[:, 1:]
if target.shape != input.shape:
raise AssertionError(
f"ground truth has differing shape ({target.shape}) from input ({input.shape})"
)
p0 = input
p1 = 1 - p0
g0 = target
g1 = 1 - g0
# reducing only spatial dimensions (not batch nor channels)
reduce_axis: List[int] = torch.arange(2, len(input.shape)).tolist()
if self.batch:
# reducing spatial dimensions and batch
reduce_axis = [0] + reduce_axis
tp = torch.sum(p0 * g0, reduce_axis)
fp = self.alpha * torch.sum(p0 * g1, reduce_axis)
fn = self.beta * torch.sum(p1 * g0, reduce_axis)
numerator = tp + self.smooth_nr
denominator = tp + fp + fn + self.smooth_dr
score: torch.Tensor = 1.0 - numerator / denominator
if self.reduction == LossReduction.SUM.value:
return torch.sum(score) # sum over the batch and channel dims
if self.reduction == LossReduction.NONE.value:
return score # returns [N, n_classes] losses
if self.reduction == LossReduction.MEAN.value:
return torch.mean(score)
raise ValueError(
f'Unsupported reduction: {self.reduction}, available options are ["mean", "sum", "none"].'
)
def forward(self,
input,
target: torch.Tensor,
smooth: float = 1e-5) -> torch.Tensor:
"""
Args:
input: the shape should be BNH[WD].
target: the shape should be BNH[WD].
smooth: a small constant to avoid nan.
Raises:
ValueError: When ``self.reduction`` is not one of ["mean", "sum", "none"].
"""
x, att_maps = input
loss_function_single_channel = Dice(to_onehot_y=False, softmax=False)
total_att_loss = 0
if self.supervised_attention:
L = len(att_maps)
att_losses = []
G_l = target
for level in range(L):
# A[level] are the attention maps as they arrive here
# G[level] are downsampled ground truth maps, they are converted to one-hot inside the loss-function
att_loss = loss_function_single_channel(
att_maps[L - level - 1], G_l)
att_losses.append(att_loss)
total_att_loss = total_att_loss + 1 / L * att_loss
if level < L - 1:
shape_curr_att_map = att_maps[L - level - 1].shape
shape_next_att_map = att_maps[L - level - 2].shape
# assert that shape of current attention map is multiple of next att map in all dimensions
assert all([
x % y == 0
for x, y in zip(shape_curr_att_map, shape_next_att_map)
])
shape_ratio = [
x // y
for x, y in zip(shape_curr_att_map, shape_next_att_map)
]
kernel_size_and_stride = shape_ratio[2:5]
G_l = torch.nn.MaxPool3d(
kernel_size=kernel_size_and_stride,
stride=kernel_size_and_stride)(G_l)
hardness_weight = None
if self.hardness_weighting:
hardness_lambda = 0.6
hardness_weight = hardness_lambda * abs(
torch.softmax(x, dim=1) -
one_hot(target, num_classes=x.shape[1])) + (1.0 -
hardness_lambda)
# img = hardness_weight.cpu().detach().numpy()
# x_ = torch.softmax(x, dim=1).cpu().detach().numpy()
# target_ = one_hot(target, num_classes=x.shape[1]).cpu().detach().numpy()
# import matplotlib.pyplot as plt
# fig, axs = plt.subplots(1, 3)
# axs[0].imshow(x_[1, 1, :, :, 20], cmap='gray')
# axs[1].imshow(target_[1, 1, :, :, 20])
# axs[2].imshow(img[1, 1, :, :, 20])
# plt.show()
# pass
loss_function_multi_channel = Dice(to_onehot_y=True,
softmax=True,
hardness_weight=hardness_weight)
pred_loss = loss_function_multi_channel(x, target)
return total_att_loss + pred_loss
def forward(self,
input: torch.Tensor,
target: torch.Tensor,
smooth: float = 1e-5):
"""
Args:
input: the shape should be BNH[WD].
target: the shape should be BNH[WD].
smooth: a small constant to avoid nan.
Raises:
ValueError: reduction={self.reduction} is invalid.
"""
if self.sigmoid:
input = torch.sigmoid(input)
n_pred_ch = input.shape[1]
if n_pred_ch == 1:
if self.softmax:
warnings.warn(
"single channel prediction, `softmax=True` ignored.")
if self.to_onehot_y:
warnings.warn(
"single channel prediction, `to_onehot_y=True` ignored.")
if not self.include_background:
warnings.warn(
"single channel prediction, `include_background=False` ignored."
)
else:
if self.softmax:
input = torch.softmax(input, 1)
if self.to_onehot_y:
target = one_hot(target, n_pred_ch)
if not self.include_background:
# if skipping background, removing first channel
target = target[:, 1:]
input = input[:, 1:]
assert (
target.shape == input.shape
), f"ground truth has differing shape ({target.shape}) from input ({input.shape})"
p0 = input
p1 = 1 - p0
g0 = target
g1 = 1 - g0
# reducing only spatial dimensions (not batch nor channels)
reduce_axis = list(range(2, len(input.shape)))
tp = torch.sum(p0 * g0, reduce_axis)
fp = self.alpha * torch.sum(p0 * g1, reduce_axis)
fn = self.beta * torch.sum(p1 * g0, reduce_axis)
numerator = tp + smooth
denominator = tp + fp + fn + smooth
score = 1.0 - numerator / denominator
if self.reduction == LossReduction.SUM:
return score.sum() # sum over the batch and channel dims
if self.reduction == LossReduction.NONE:
return score # returns [N, n_classes] losses
if self.reduction == LossReduction.MEAN:
return score.mean()
raise ValueError(f"reduction={self.reduction} is invalid.")
def forward(self, input: torch.Tensor, target: torch.Tensor) -> torch.Tensor:
"""
Args:
input: the shape should be BNH[WD].
target: the shape should be BNH[WD].
Raises:
ValueError: When ``self.reduction`` is not one of ["mean", "sum", "none"].
"""
if self.sigmoid:
input = torch.sigmoid(input)
n_pred_ch = input.shape[1]
if self.softmax:
if n_pred_ch == 1:
warnings.warn("single channel prediction, `softmax=True` ignored.")
else:
input = torch.softmax(input, 1)
if self.other_act is not None:
input = self.other_act(input)
if self.to_onehot_y:
if n_pred_ch == 1:
warnings.warn("single channel prediction, `to_onehot_y=True` ignored.")
else:
target = one_hot(target, num_classes=n_pred_ch)
if not self.include_background:
if n_pred_ch == 1:
warnings.warn("single channel prediction, `include_background=False` ignored.")
else:
# if skipping background, removing first channel
target = target[:, 1:]
input = input[:, 1:]
if target.shape != input.shape:
raise AssertionError(f"ground truth has differing shape ({target.shape}) from input ({input.shape})")
# reducing only spatial dimensions (not batch nor channels)
reduce_axis = list(range(2, len(input.shape)))
if self.batch:
# reducing spatial dimensions and batch
reduce_axis = [0] + reduce_axis
intersection = torch.sum(target * input, dim=reduce_axis)
### uncoment lines below to enable label weights
# if self.label_weights is not None: # add wights to labels
# bs=intersection.shape[0]
# w = torch.tensor(self.label_weights, dtype=torch.float32,device=torch.device('cuda:0'))
# w= w.repeat(bs, 1) ## change size to [BS, Num of classes ]
# intersection = w* intersection
if self.squared_pred:
target = torch.pow(target, 2)
input = torch.pow(input, 2)
ground_o = torch.sum(target, dim=reduce_axis)
pred_o = torch.sum(input, dim=reduce_axis)
denominator = ground_o + pred_o
if self.jaccard:
denominator = 2.0 * (denominator - intersection)
f: torch.Tensor = 1.0 - (2.0 * intersection + self.smooth_nr) / (denominator + self.smooth_dr)
if self.reduction == LossReduction.MEAN.value:
f = torch.mean(f) # the batch and channel average
elif self.reduction == LossReduction.SUM.value:
f = torch.sum(f) # sum over the batch and channel dims
elif self.reduction == LossReduction.NONE.value:
pass # returns [N, n_classes] losses
else:
raise ValueError(f'Unsupported reduction: {self.reduction}, available options are ["mean", "sum", "none"].')
return f
def forward(self, input: torch.Tensor, target: torch.Tensor) -> torch.Tensor:
"""
Args:
input: the shape should be BNH[WD].
target: the shape should be BNH[WD].
Raises:
ValueError: When ``self.reduction`` is not one of ["mean", "sum", "none"].
"""
if self.sigmoid:
input = torch.sigmoid(input)
n_pred_ch = input.shape[1]
if self.softmax:
if n_pred_ch == 1:
warnings.warn("single channel prediction, `softmax=True` ignored.")
else:
input = torch.softmax(input, 1)
if self.other_act is not None:
input = self.other_act(input)
if self.to_onehot_y:
if n_pred_ch == 1:
warnings.warn("single channel prediction, `to_onehot_y=True` ignored.")
else:
target = one_hot(target, num_classes=n_pred_ch)
if not self.include_background:
if n_pred_ch == 1:
warnings.warn("single channel prediction, `include_background=False` ignored.")
else:
# if skipping background, removing first channel
target = target[:, 1:]
input = input[:, 1:]
if target.shape != input.shape:
raise AssertionError(f"ground truth has differing shape ({target.shape}) from input ({input.shape})")
# reducing only spatial dimensions (not batch nor channels)
reduce_axis: List[int] = torch.arange(2, len(input.shape)).tolist()
if self.batch:
reduce_axis = [0] + reduce_axis
intersection = torch.sum(target * input, reduce_axis)
ground_o = torch.sum(target, reduce_axis)
pred_o = torch.sum(input, reduce_axis)
denominator = ground_o + pred_o
w = self.w_func(ground_o.float())
for b in w:
infs = torch.isinf(b)
b[infs] = 0.0
b[infs] = torch.max(b)
f: torch.Tensor = 1.0 - (2.0 * (intersection * w).sum(0 if self.batch else 1) + self.smooth_nr) / (
(denominator * w).sum(0 if self.batch else 1) + self.smooth_dr
)
if self.reduction == LossReduction.MEAN.value:
f = torch.mean(f) # the batch and channel average
elif self.reduction == LossReduction.SUM.value:
f = torch.sum(f) # sum over the batch and channel dims
elif self.reduction == LossReduction.NONE.value:
pass # returns [N, n_classes] losses
else:
raise ValueError(f'Unsupported reduction: {self.reduction}, available options are ["mean", "sum", "none"].')
return f
def forward(self, input: torch.Tensor,
target: torch.Tensor) -> torch.Tensor:
"""
Args:
input: the shape should be BNH[WD], where N is the number of classes.
target: the shape should be BNH[WD] or B1H[WD], where N is the number of classes.
Raises:
AssertionError: When input and target (after one hot transform if set)
have different shapes.
ValueError: When ``self.reduction`` is not one of ["mean", "sum", "none"].
Example:
>>> from monai.losses.dice import * # NOQA
>>> import torch
>>> from monai.losses.dice import DiceLoss
>>> B, C, H, W = 7, 5, 3, 2
>>> input = torch.rand(B, C, H, W)
>>> target_idx = torch.randint(low=0, high=C - 1, size=(B, H, W)).long()
>>> target = one_hot(target_idx[:, None, ...], num_classes=C)
>>> self = DiceLoss(reduction='none')
>>> loss = self(input, target)
>>> assert np.broadcast_shapes(loss.shape, input.shape) == input.shape
"""
if self.sigmoid:
input = torch.sigmoid(input)
n_pred_ch = input.shape[1]
if self.softmax:
if n_pred_ch == 1:
warnings.warn(
"single channel prediction, `softmax=True` ignored.")
else:
input = torch.softmax(input, 1)
if self.other_act is not None:
input = self.other_act(input)
if self.to_onehot_y:
if n_pred_ch == 1:
warnings.warn(
"single channel prediction, `to_onehot_y=True` ignored.")
else:
target = one_hot(target, num_classes=n_pred_ch)
if not self.include_background:
if n_pred_ch == 1:
warnings.warn(
"single channel prediction, `include_background=False` ignored."
)
else:
# if skipping background, removing first channel
target = target[:, 1:]
input = input[:, 1:]
if target.shape != input.shape:
raise AssertionError(
f"ground truth has different shape ({target.shape}) from input ({input.shape})"
)
# reducing only spatial dimensions (not batch nor channels)
reduce_axis: List[int] = torch.arange(2, len(input.shape)).tolist()
if self.batch:
# reducing spatial dimensions and batch
reduce_axis = [0] + reduce_axis
intersection = torch.sum(target * input, dim=reduce_axis)
if self.squared_pred:
target = torch.pow(target, 2)
input = torch.pow(input, 2)
ground_o = torch.sum(target, dim=reduce_axis)
pred_o = torch.sum(input, dim=reduce_axis)
denominator = ground_o + pred_o
if self.jaccard:
denominator = 2.0 * (denominator - intersection)
f: torch.Tensor = 1.0 - (2.0 * intersection + self.smooth_nr) / (
denominator + self.smooth_dr)
if self.reduction == LossReduction.MEAN.value:
f = torch.mean(f) # the batch and channel average
elif self.reduction == LossReduction.SUM.value:
f = torch.sum(f) # sum over the batch and channel dims
elif self.reduction == LossReduction.NONE.value:
# If we are not computing voxelwise loss components at least
# make sure a none reduction maintains a broadcastable shape
broadcast_shape = list(f.shape[0:2]) + [1] * (len(input.shape) - 2)
f = f.view(broadcast_shape)
else:
raise ValueError(
f'Unsupported reduction: {self.reduction}, available options are ["mean", "sum", "none"].'
)
return f
def forward(self, input: torch.Tensor, target: torch.Tensor) -> torch.Tensor:
"""
Args:
input: the shape should be BNH[WD].
target: the shape should be BNH[WD].
Raises:
ValueError: When ``self.reduction`` is not one of ["mean", "sum", "none"].
"""
if self.sigmoid:
input = torch.sigmoid(input)
n_pred_ch = input.shape[1]
if self.softmax:
if n_pred_ch == 1:
warnings.warn("single channel prediction, `softmax=True` ignored.")
else:
input = torch.softmax(input, 1)
if self.other_act is not None:
input = self.other_act(input)
if self.to_onehot_y:
if n_pred_ch == 1:
warnings.warn("single channel prediction, `to_onehot_y=True` ignored.")
else:
target = one_hot(target, num_classes=n_pred_ch)
if not self.include_background:
if n_pred_ch == 1:
warnings.warn("single channel prediction, `include_background=False` ignored.")
else:
# if skipping background, removing first channel
target = target[:, 1:]
input = input[:, 1:]
if target.shape != input.shape:
raise AssertionError(f"ground truth has differing shape ({target.shape}) from input ({input.shape})")
# reducing only spatial dimensions (not batch nor channels)
reduce_axis: List[int] = torch.arange(2, len(input.shape)).tolist()
if self.batch:
reduce_axis = [0] + reduce_axis
intersection = torch.sum(target * input, reduce_axis)
ground_o = torch.sum(target, reduce_axis)
pred_o = torch.sum(input, reduce_axis)
denominator = ground_o + pred_o
w = self.w_func(ground_o.float())
infs = torch.isinf(w)
if self.batch:
w[infs] = 0.0
w = w + infs * torch.max(w)
else:
w[infs] = 0.0
max_values = torch.max(w, dim=1)[0].unsqueeze(dim=1)
w = w + infs * max_values
final_reduce_dim = 0 if self.batch else 1
numer = 2.0 * (intersection * w).sum(final_reduce_dim, keepdim=True) + self.smooth_nr
denom = (denominator * w).sum(final_reduce_dim, keepdim=True) + self.smooth_dr
f: torch.Tensor = 1.0 - (numer / denom)
if self.reduction == LossReduction.MEAN.value:
f = torch.mean(f) # the batch and channel average
elif self.reduction == LossReduction.SUM.value:
f = torch.sum(f) # sum over the batch and channel dims
elif self.reduction == LossReduction.NONE.value:
# If we are not computing voxelwise loss components at least
# make sure a none reduction maintains a broadcastable shape
broadcast_shape = list(f.shape[0:2]) + [1] * (len(input.shape) - 2)
f = f.view(broadcast_shape)
else:
raise ValueError(f'Unsupported reduction: {self.reduction}, available options are ["mean", "sum", "none"].')
return f
def forward(self, input: torch.Tensor,
target: torch.Tensor) -> torch.Tensor:
"""
Args:
input: the shape should be BNH[WD], where N is the number of classes.
The input should be the original logits since it will be transferred by
`F.log_softmax` in the forward function.
target: the shape should be BNH[WD] or B1H[WD], where N is the number of classes.
Raises:
AssertionError: When input and target (after one hot transform if setted)
have different shapes.
ValueError: When ``self.reduction`` is not one of ["mean", "sum", "none"].
ValueError: When ``self.weight`` is a sequence and the length is not equal to the
number of classes.
ValueError: When ``self.weight`` is/contains a value that is less than 0.
"""
n_pred_ch = input.shape[1]
if self.to_onehot_y:
if n_pred_ch == 1:
warnings.warn(
"single channel prediction, `to_onehot_y=True` ignored.")
else:
target = one_hot(target, num_classes=n_pred_ch)
if not self.include_background:
if n_pred_ch == 1:
warnings.warn(
"single channel prediction, `include_background=False` ignored."
)
else:
# if skipping background, removing first channel
target = target[:, 1:]
input = input[:, 1:]
if target.shape != input.shape:
raise AssertionError(
f"ground truth has different shape ({target.shape}) from input ({input.shape})"
)
i = input
t = target
# Change the shape of input and target to B x N x num_voxels.
i = i.view(i.size(0), i.size(1), -1)
t = t.view(t.size(0), t.size(1), -1)
# Compute the log proba.
logpt = F.log_softmax(i, dim=1)
# Get the proba
pt = torch.exp(logpt) # B,H*W or B,N,H*W
if self.weight is not None:
class_weight: Optional[torch.Tensor] = None
if isinstance(self.weight, (float, int)):
class_weight = torch.as_tensor([self.weight] * i.size(1))
else:
class_weight = torch.as_tensor(self.weight)
if class_weight.size(0) != i.size(1):
raise ValueError(
"the length of the weight sequence should be the same as the number of classes. "
+
"If `include_background=False`, the number should not include class 0."
)
if class_weight.min() < 0:
raise ValueError(
"the value/values of weights should be no less than 0.")
class_weight = class_weight.to(i)
# Convert the weight to a map in which each voxel
# has the weight associated with the ground-truth label
# associated with this voxel in target.
at = class_weight[None, :, None] # N => 1,N,1
at = at.expand((t.size(0), -1, t.size(2))) # 1,N,1 => B,N,H*W
# Multiply the log proba by their weights.
logpt = logpt * at
# Compute the loss mini-batch.
weight = torch.pow(-pt + 1.0, self.gamma)
loss = torch.mean(-weight * t * logpt, dim=-1)
if self.reduction == LossReduction.SUM.value:
return loss.sum()
if self.reduction == LossReduction.NONE.value:
return loss
if self.reduction == LossReduction.MEAN.value:
return loss.mean()
raise ValueError(
f'Unsupported reduction: {self.reduction}, available options are ["mean", "sum", "none"].'
)
def compute_confusion_metric(
y_pred: torch.Tensor,
y: torch.Tensor,
to_onehot_y: bool = False,
activation: Optional[Union[str, Callable]] = None,
bin_mode: Optional[str] = "threshold",
bin_threshold: Union[float, Sequence[float]] = 0.5,
metric_name: str = "hit_rate",
average: Union[Average, str] = Average.MACRO,
zero_division: int = 0,
) -> Union[np.ndarray, List[float], float]:
"""
Compute confusion matrix related metrics. This function supports to calculate all metrics
mentioned in: `Confusion matrix <https://en.wikipedia.org/wiki/Confusion_matrix>`_.
Before calculating, an activation function and/or a binarization manipulation can be employed
to pre-process the original inputs. Zero division is handled by replacing the result into a
single value. Referring to:
`sklearn.metrics <https://scikit-learn.org/stable/modules/classes.html#module-sklearn.metrics>`_.
Args:
y_pred: predictions. As for classification tasks,
`y_pred` should has the shape [B] or [BN]. As for segmentation tasks,
the shape should be [BNHW] or [BNHWD].
y: ground truth, the first dim is batch.
to_onehot_y: whether to convert `y` into the one-hot format. Defaults to False.
activation: [``"sigmoid"``, ``"softmax"``]
Activation method, if specified, an activation function will be employed for `y_pred`.
Defaults to None.
The parameter can also be a callable function, for example:
``activation = lambda x: torch.log_softmax(x)``.
bin_mode: [``"threshold"``, ``"mutually_exclusive"``]
Binarization method, if specified, a binarization manipulation will be employed
for `y_pred`.
- ``"threshold"``, a single threshold or a sequence of thresholds should be set.
- ``"mutually_exclusive"``, `y_pred` will be converted by a combination of `argmax` and `to_onehot`.
bin_threshold: the threshold for binarization, can be a single value or a sequence of
values that each one of the value represents a threshold for a class.
metric_name: [``"sensitivity"``, ``"specificity"``, ``"precision"``, ``"negative predictive value"``,
``"miss rate"``, ``"fall out"``, ``"false discovery rate"``, ``"false omission rate"``,
``"prevalence threshold"``, ``"threat score"``, ``"accuracy"``, ``"balanced accuracy"``,
``"f1 score"``, ``"matthews correlation coefficient"``, ``"fowlkes mallows index"``,
``"informedness"``, ``"markedness"``]
Some of the metrics have multiple aliases (as shown in the wikipedia page aforementioned),
and you can also input those names instead.
average: [``"macro"``, ``"weighted"``, ``"micro"``, ``"none"``]
Type of averaging performed if not binary classification.
Defaults to ``"macro"``.
- ``"macro"``: calculate metrics for each label, and find their unweighted mean.
This does not take label imbalance into account.
- ``"weighted"``: calculate metrics for each label, and find their average,
weighted by support (the number of true instances for each label).
- ``"micro"``: calculate metrics globally by considering each element of the label
indicator matrix as a label.
- ``"none"``: the scores for each class are returned.
zero_division: the value to return when there is a zero division, for example, when all
predictions and labels are negative. Defaults to 0.
Raises:
AssertionError: when data shapes of `y_pred` and `y` do not match.
AssertionError: when specify activation function and ``mutually_exclusive`` mode at the same time.
"""
y_pred_ndim, y_ndim = y_pred.ndimension(), y.ndimension()
# one-hot for ground truth
if to_onehot_y:
if y_pred_ndim == 1:
warnings.warn("y_pred has only one channel, to_onehot_y=True ignored.")
else:
n_classes = y_pred.shape[1]
y = one_hot(y, num_classes=n_classes)
# check shape
assert y.shape == y_pred.shape, "data shapes of y_pred and y do not match."
# activation for predictions
if activation is not None:
assert bin_mode != "mutually_exclusive", "activation is unnecessary for mutually exclusive classes."
y_pred = do_activation(y_pred, activation=activation)
# binarization for predictions
if bin_mode is not None:
y_pred = do_binarization(y_pred, bin_mode=bin_mode, bin_threshold=bin_threshold)
# get confusion matrix elements
con_list = cal_confusion_matrix_elements(y_pred, y)
# get simplified metric name
metric_name = check_metric_name_and_unify(metric_name)
result = do_calculate_metric(con_list, metric_name, average=average, zero_division=zero_division)
return result
def dice_loss(input: tensor,
target: tensor,
include_background: bool = True,
softmax: bool = False,
to_onehot: bool = True,
squared_pred: bool = False,
reduction: Union[LossReduction, str] = LossReduction.MEAN,
smooth: float = 1e-5):
"""
loss function, from
Milletari, F. et. al. (2016) V-Net: Fully Convolutional Neural Networks forVolumetric Medical Image Segmentation, 3DV, 2016.
Args:
input: predict tensor，the shape should be BNH[WD].
target: target tensor, the shape should be BNH[WD].
include_background:
softmax: if True, apply a softmax function to the prediction.
to_onehot: whether to convert `target` into the one-hot format. Defaults to False.
squared_pred: use squared versions of targets and predictions in the denominator or not.
reduction: {``"none"``, ``"mean"``, ``"sum"``}
Specifies the reduction to apply to the output. Defaults to ``"mean"``.
- ``"none"``: no reduction will be applied.
- ``"mean"``: the sum of the output will be divided by the number of elements in the output.
- ``"sum"``: the output will be summed.
smooth: a small constant to avoid nan.
"""
n_pred_ch = input.shape[1]
if softmax:
input = torch.softmax(input, 1)
if to_onehot:
if n_pred_ch == 1:
warnings.warn("single channel prediction, `to_onehot_y=True` ignored.")
else:
# the F.one_hot can not use here, because it would return BNH[WD]C (C is the class
target = one_hot(target.to(torch.int64), num_classes=n_pred_ch)
if not include_background:
if n_pred_ch == 1:
warnings.warn("single channel prediction, `include_background=False` ignored.")
else:
# if skipping background, removing first channel
target = target[:, 1:]
input = input[:, 1:]
assert (
target.shape == input.shape
), f"ground truth has differing shape ({target.shape}) from input ({input.shape})"
# reducing only spatial dimensions (not batch nor channels)
reduce_axis = list(range(2, len(input.shape)))
intersection = torch.sum(target * input, dim=reduce_axis)
if squared_pred:
target = torch.pow(target, 2)
input = torch.pow(input, 2)
ground_o = torch.sum(target, dim=reduce_axis)
pred_o = torch.sum(input, dim=reduce_axis)
denominator = ground_o + pred_o
f = 1.0 - (2.0 * intersection + smooth) / (denominator + smooth)
reduction = LossReduction(reduction).value
if reduction == LossReduction.MEAN.value:
f = torch.mean(f) # the batch and channel average
elif reduction == LossReduction.SUM.value:
f = torch.sum(f) # sum over the batch and channel dims
elif reduction == LossReduction.NONE.value:
pass # returns [N, n_classes] losses
else:
raise ValueError(f'Unsupported reduction: {reduction}, available options are ["mean", "sum", "none"].')
return f