Module qute.models.swinunetr

SwinUNETR.

Classes

class SwinUNETR (campaign_transforms: qute.campaigns._campaigns.CampaignTransforms, spatial_dims: int = 2, in_channels: int = 1, out_channels: int = 3, class_names: Optional[tuple] = None, depths: tuple[int, ...] = (2, 2, 2, 2), num_heads: tuple[int, ...] = (3, 6, 12, 24), feature_size: int = 24, criterion=DiceCELoss( (dice): DiceLoss() (cross_entropy): CrossEntropyLoss() (binary_cross_entropy): BCEWithLogitsLoss() ), metrics=<monai.metrics.meandice.DiceMetric object>, learning_rate: float = 0.01, optimizer_class=torch.optim.adamw.AdamW, lr_scheduler_class=torch.optim.lr_scheduler.PolynomialLR, lr_scheduler_parameters: dict = {'total_iters': 100, 'power': 0.95}, dropout: float = 0.0)

Wrap MONAI's SwinUNETR architecture into a PyTorch Lightning module.

The default settings are compatible with a classification task, where a single-channel input image is transformed into a three-class label image.

Constructor.

Parameters

campaign_transforms : CampaignTransforms
Define all transforms necessary for training, validation, testing and (full) prediction. @see qute.transforms.CampaignTransforms for documentation.
spatial_dims : int = 2
Whether 2D or 3D data.
in_channels : int = 1
Number of input channels.
out_channels : int = 3
Number of output channels (or labels, or classes)
class_names : Optional[tuple] = None
Names of the output classes (for logging purposes). If omitted, they will default to ("class_1", "class_2", …)
criterion : DiceCELoss(include_background=False, to_onehot_y=False, softmax=True)
Loss function. Please NOTE: for classification, the loss function must convert y to OneHot. The default loss function applies to a multi-label target where the background class is omitted.
metrics : DiceMetric(include_background=False, reduction="mean", get_not_nans=False)

Metrics used for validation and test. Set to None to omit.

The default metrics applies to a three-label target where the background (index = 0) class is omitted from calculation.

learning_rate : float = 1e-2
Learning rate for optimization.

optimizer_class=AdamW Optimizer.

lr_scheduler_class=PolynomialLR Learning rate scheduler.

lr_scheduler_parameters={"total_iters": 100, "power": 0.99} Dictionary of scheduler parameters.

dropout : float = 0.0
Dropout ratio.
Expand source code 
class SwinUNETR(UNet):
    """Wrap MONAI's SwinUNETR architecture into a PyTorch Lightning module.

    The default settings are compatible with a classification task, where
    a single-channel input image is transformed into a three-class label image.
    """

    def __init__(
        self,
        campaign_transforms: CampaignTransforms,
        spatial_dims: int = 2,
        in_channels: int = 1,
        out_channels: int = 3,
        class_names: Optional[tuple] = None,
        depths: tuple[int, ...] = (2, 2, 2, 2),
        num_heads: tuple[int, ...] = (3, 6, 12, 24),
        feature_size: int = 24,
        criterion=DiceCELoss(include_background=True, to_onehot_y=False, softmax=True),
        metrics=DiceMetric(
            include_background=True, reduction="mean", get_not_nans=False
        ),
        learning_rate: float = 1e-2,
        optimizer_class=AdamW,
        lr_scheduler_class=PolynomialLR,
        lr_scheduler_parameters: dict = {"total_iters": 100, "power": 0.95},
        dropout: float = 0.0,
    ):
        """
        Constructor.

        Parameters
        ----------

        campaign_transforms: CampaignTransforms
            Define all transforms necessary for training, validation, testing and (full) prediction.
            @see `qute.transforms.CampaignTransforms` for documentation.

        spatial_dims: int = 2
            Whether 2D or 3D data.

        in_channels: int = 1
            Number of input channels.

        out_channels: int = 3
            Number of output channels (or labels, or classes)

        class_names: Optional[tuple] = None
            Names of the output classes (for logging purposes). If omitted, they will default
            to ("class_1", "class_2", ...)

        criterion: DiceCELoss(include_background=False, to_onehot_y=False, softmax=True)
            Loss function. Please NOTE: for classification, the loss function must convert `y` to OneHot.
            The default loss function applies to a multi-label target where the background class is omitted.

        metrics: DiceMetric(include_background=False, reduction="mean", get_not_nans=False)
            Metrics used for validation and test. Set to None to omit.

            The default metrics applies to a three-label target where the background (index = 0) class
            is omitted from calculation.

        learning_rate: float = 1e-2
            Learning rate for optimization.

        optimizer_class=AdamW
            Optimizer.

        lr_scheduler_class=PolynomialLR
            Learning rate scheduler.

        lr_scheduler_parameters={"total_iters": 100, "power": 0.99}
            Dictionary of scheduler parameters.

        dropout: float = 0.0
            Dropout ratio.
        """

        super().__init__(
            campaign_transforms=campaign_transforms,
            spatial_dims=spatial_dims,
            in_channels=in_channels,
            out_channels=out_channels,
            class_names=class_names,
            channels=(16, 32),  # Not used
            strides=(2,),  # Not used
            criterion=criterion,
            metrics=metrics,
            learning_rate=learning_rate,
            optimizer_class=optimizer_class,
            lr_scheduler_class=lr_scheduler_class,
            lr_scheduler_parameters=lr_scheduler_parameters,
            dropout=dropout,
        )

        self.campaign_transforms = campaign_transforms
        self.criterion = criterion
        self.metrics = metrics
        self.learning_rate = learning_rate
        self.optimizer_class = optimizer_class
        self.scheduler_class = lr_scheduler_class
        self.scheduler_parameters = lr_scheduler_parameters
        if class_names is None:
            class_names = list((f"class_{i}" for i in range(out_channels)))
        self.class_names = class_names
        self.net = MONAISwinUNETR(
            img_size=(
                640,
                640,
            ),  # Deprecated and ignored in MONAI >= 1.3 - but must be passed
            in_channels=in_channels,
            out_channels=out_channels,
            depths=depths,
            num_heads=num_heads,
            feature_size=feature_size,
            use_checkpoint=True,
            spatial_dims=spatial_dims,
            use_v2=True,
        )

        # Log the hyperparameters
        self.save_hyperparameters(ignore=["criterion", "metrics"])

Ancestors

  • UNet
  • pytorch_lightning.core.module.LightningModule
  • lightning_fabric.utilities.device_dtype_mixin._DeviceDtypeModuleMixin
  • pytorch_lightning.core.mixins.hparams_mixin.HyperparametersMixin
  • pytorch_lightning.core.hooks.ModelHooks
  • pytorch_lightning.core.hooks.DataHooks
  • pytorch_lightning.core.hooks.CheckpointHooks
  • torch.nn.modules.module.Module

Inherited members