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load_model

LoadModel

Bases: Module

A class representing a loaded model.

Parameters:

Name Type Description Default
trunk Module

The trunk of the model. Defaults to None.

 None
weights_path str

The path to the weights file. Defaults to None.

 None
heads list

The list of head layers in the model. Defaults to [].

 []

Attributes:

Name Type Description
trunk Module

The trunk of the model.
heads Sequential

The concatenated head layers of the model.

Methods:

Name Description
forward

torch.Tensor) -> torch.Tensor: Forward pass through the model.
load

Load the pretrained model weights.
Source code in fmcib/models/load_model.py 
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class LoadModel(nn.Module):
    """
    A class representing a loaded model.

    Args:
        trunk (nn.Module, optional): The trunk of the model. Defaults to None.
        weights_path (str, optional): The path to the weights file. Defaults to None.
        heads (list, optional): The list of head layers in the model. Defaults to [].

    Attributes:
        trunk (nn.Module): The trunk of the model.
        heads (nn.Sequential): The concatenated head layers of the model.

    Methods:
        forward(x: torch.Tensor) -> torch.Tensor: Forward pass through the model.
        load(weights): Load the pretrained model weights.
    """

    def __init__(self, trunk=None, weights_path=None, heads=[]) -> None:
        """
        Initialize the model.

        Args:
            trunk (optional): The trunk of the model.
            weights_path (optional): The path to the weights file.
            heads (list, optional): A list of layer sizes for the heads of the model.

        Returns:
            None

        Raises:
            None
        """
        super().__init__()
        self.trunk = trunk
        self.device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
        head_layers = []
        for idx in range(len(heads) - 1):
            current_layers = []
            current_layers.append(nn.Linear(heads[idx], heads[idx + 1], bias=True))

            if idx != (len(heads) - 2):
                current_layers.append(nn.ReLU(inplace=True))

            head_layers.append(nn.Sequential(*current_layers))

        if len(head_layers):
            self.heads = nn.Sequential(*head_layers)
        else:
            self.heads = nn.Identity()

        if weights_path is not None:
            self.load(weights_path)

    def forward(self, x: torch.Tensor):
        """
        Forward pass of the neural network.

        Args:
            x (torch.Tensor): The input tensor.

        Returns:
            torch.Tensor: The output tensor.
        """
        out = self.trunk(x)
        out = self.heads(out)
        return out

    def load(self, weights):
        """
        Load pretrained model weights from a file.

        Args:
            weights (str): The path to the file containing the pretrained model weights.

        Raises:
            KeyError: If the input weights file does not contain the expected keys.
            Exception: If there is an error when loading the pretrained heads.

        Returns:
            None.

        Note:
            This function assumes that the pretrained model weights file is in the format expected by the model architecture.

        Warnings:
            - Missing keys: This warning message indicates the keys in the pretrained model weights file that are missing from the current model.
            - Unexpected keys: This warning message indicates the keys in the pretrained model weights file that are not expected by the current model.

        Raises the appropriate warnings and logs informational messages.
        """
        pretrained_model = torch.load(weights, map_location=self.device, weights_only=True)

        if "trunk_state_dict" in pretrained_model:  # Loading ViSSL pretrained model
            trained_trunk = pretrained_model["trunk_state_dict"]
            msg = self.trunk.load_state_dict(trained_trunk, strict=False)
            logger.warning(f"Missing keys: {msg[0]} and unexpected keys: {msg[1]}")

        if "state_dict" in pretrained_model:  # Loading Med3D pretrained model
            trained_model = pretrained_model["state_dict"]

            # match the keys (https://github.com/Project-MONAI/MONAI/issues/6811)
            weights = {key.replace("module.", ""): value for key, value in trained_model.items()}
            weights = {key.replace("model.trunk.", ""): value for key, value in trained_model.items()}
            msg = self.trunk.load_state_dict(weights, strict=False)
            logger.warning(f"Missing keys: {msg[0]} and unexpected keys: {msg[1]}")

            weights = {key.replace("model.heads.", ""): value for key, value in trained_model.items()}
            msg = self.heads.load_state_dict(weights, strict=False)
            logger.warning(f"Missing keys: {msg[0]} and unexpected keys: {msg[1]}")

        # Load trained heads
        if "head_state_dict" in pretrained_model:
            trained_heads = pretrained_model["head_state_dict"]

            try:
                msg = self.heads.load_state_dict(trained_heads, strict=False)
            except Exception as e:
                logger.error(f"Failed to load trained heads with error {e}. This is expected if the models do not match!")
            logger.warning(f"Missing keys: {msg[0]} and unexpected keys: {msg[1]}")

        logger.info(f"Loaded pretrained model weights \n")

__init__(trunk=None, weights_path=None, heads=[])

Initialize the model.

Parameters:

Name Type Description Default
trunk optional

The trunk of the model.

 None
weights_path optional

The path to the weights file.

 None
heads list

A list of layer sizes for the heads of the model.

 []

Returns:

Type Description
None

None
Source code in fmcib/models/load_model.py 
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def __init__(self, trunk=None, weights_path=None, heads=[]) -> None:
    """
    Initialize the model.

    Args:
        trunk (optional): The trunk of the model.
        weights_path (optional): The path to the weights file.
        heads (list, optional): A list of layer sizes for the heads of the model.

    Returns:
        None

    Raises:
        None
    """
    super().__init__()
    self.trunk = trunk
    self.device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
    head_layers = []
    for idx in range(len(heads) - 1):
        current_layers = []
        current_layers.append(nn.Linear(heads[idx], heads[idx + 1], bias=True))

        if idx != (len(heads) - 2):
            current_layers.append(nn.ReLU(inplace=True))

        head_layers.append(nn.Sequential(*current_layers))

    if len(head_layers):
        self.heads = nn.Sequential(*head_layers)
    else:
        self.heads = nn.Identity()

    if weights_path is not None:
        self.load(weights_path)

forward(x)

Forward pass of the neural network.

Parameters:

Name Type Description Default
x Tensor

The input tensor.

 required

Returns:

Type Description

torch.Tensor: The output tensor.
Source code in fmcib/models/load_model.py 
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def forward(self, x: torch.Tensor):
    """
    Forward pass of the neural network.

    Args:
        x (torch.Tensor): The input tensor.

    Returns:
        torch.Tensor: The output tensor.
    """
    out = self.trunk(x)
    out = self.heads(out)
    return out

load(weights)

Load pretrained model weights from a file.

Parameters:

Name Type Description Default
weights str

The path to the file containing the pretrained model weights.

 required

Raises:

Type Description
KeyError

If the input weights file does not contain the expected keys.
Exception

If there is an error when loading the pretrained heads.

Returns:

Type Description

None.
Note

This function assumes that the pretrained model weights file is in the format expected by the model architecture.

Warns:

Type Description
- Missing keys

This warning message indicates the keys in the pretrained model weights file that are missing from the current model.
- Unexpected keys

This warning message indicates the keys in the pretrained model weights file that are not expected by the current model.

Raises the appropriate warnings and logs informational messages.

Source code in fmcib/models/load_model.py 
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def load(self, weights):
    """
    Load pretrained model weights from a file.

    Args:
        weights (str): The path to the file containing the pretrained model weights.

    Raises:
        KeyError: If the input weights file does not contain the expected keys.
        Exception: If there is an error when loading the pretrained heads.

    Returns:
        None.

    Note:
        This function assumes that the pretrained model weights file is in the format expected by the model architecture.

    Warnings:
        - Missing keys: This warning message indicates the keys in the pretrained model weights file that are missing from the current model.
        - Unexpected keys: This warning message indicates the keys in the pretrained model weights file that are not expected by the current model.

    Raises the appropriate warnings and logs informational messages.
    """
    pretrained_model = torch.load(weights, map_location=self.device, weights_only=True)

    if "trunk_state_dict" in pretrained_model:  # Loading ViSSL pretrained model
        trained_trunk = pretrained_model["trunk_state_dict"]
        msg = self.trunk.load_state_dict(trained_trunk, strict=False)
        logger.warning(f"Missing keys: {msg[0]} and unexpected keys: {msg[1]}")

    if "state_dict" in pretrained_model:  # Loading Med3D pretrained model
        trained_model = pretrained_model["state_dict"]

        # match the keys (https://github.com/Project-MONAI/MONAI/issues/6811)
        weights = {key.replace("module.", ""): value for key, value in trained_model.items()}
        weights = {key.replace("model.trunk.", ""): value for key, value in trained_model.items()}
        msg = self.trunk.load_state_dict(weights, strict=False)
        logger.warning(f"Missing keys: {msg[0]} and unexpected keys: {msg[1]}")

        weights = {key.replace("model.heads.", ""): value for key, value in trained_model.items()}
        msg = self.heads.load_state_dict(weights, strict=False)
        logger.warning(f"Missing keys: {msg[0]} and unexpected keys: {msg[1]}")

    # Load trained heads
    if "head_state_dict" in pretrained_model:
        trained_heads = pretrained_model["head_state_dict"]

        try:
            msg = self.heads.load_state_dict(trained_heads, strict=False)
        except Exception as e:
            logger.error(f"Failed to load trained heads with error {e}. This is expected if the models do not match!")
        logger.warning(f"Missing keys: {msg[0]} and unexpected keys: {msg[1]}")

    logger.info(f"Loaded pretrained model weights \n")