Spatial transforms

spatial_transforms

InPlaneRotate dataclass

InPlaneRotate(angle: float, interpolation: str = 'linear')

Bases: imgtools.transforms.spatial_transforms.SpatialTransform

InPlaneRotate operation class.

A callable class that rotates an image on a plane.

Parameters:

Name	Type	Description	Default
angle	float	The angle of rotation.	required
interpolation	str	The interpolation method to use. Valid options are: - "linear" for bi/trilinear interpolation (default) - "nearest" for nearest neighbour interpolation - "bspline" for order-3 b-spline interpolation	'linear'

Methods:

Name	Description
supports_reference	Return whether this transform supports reference images.

name property

name: str

Return the name of the transform class for logging and debugging.

Returns:

Type	Description
str	The name of the transform class.

supports_reference

supports_reference() -> bool

Return whether this transform supports reference images.

Returns:

Type	Description
bool	False by default. Subclasses should override this method

Source code in src/imgtools/transforms/spatial_transforms.py

def supports_reference(self) -> bool:
    """Return whether this transform supports reference images.

    Returns
    -------
    bool
        False by default. Subclasses should override this method
    """
    return False

Resample dataclass

Resample(
    spacing: float | typing.Sequence[float] | numpy.ndarray,
    interpolation: str = "linear",
    anti_alias: bool = True,
    anti_alias_sigma: float | None = None,
    transform: SimpleITK.Transform | None = None,
    output_size: list[float] | None = None,
)

Bases: imgtools.transforms.spatial_transforms.SpatialTransform

Resample operation class.

A callable class that resamples image to a given spacing, optionally applying a transformation.

Parameters:

Name	Type	Description	Default
spacing	float | typing.Sequence[float] | numpy.ndarray	The new image spacing. If float, assumes the same spacing in all directions. Alternatively, a sequence of floats can be passed to specify spacing along each dimension. Passing 0 at any position will keep the original spacing along that dimension (useful for in-plane resampling).	required
interpolation	str	The interpolation method to use. Valid options are: - "linear" for bi/trilinear interpolation (default) - "nearest" for nearest neighbour interpolation - "bspline" for order-3 b-spline interpolation	'linear'
anti_alias	bool	Whether to smooth the image with a Gaussian kernel before resampling. Only used when downsampling, i.e. when spacing < image.GetSpacing(). This should be used to avoid aliasing artifacts.	True
anti_alias_sigma	float | None	The standard deviation of the Gaussian kernel used for anti-aliasing.	None
transform	SimpleITK.Transform | None	Transform to apply to input coordinates when resampling. If None, defaults to identity transformation.	None
output_size	list[float] | None	Size of the output image. If None, it is computed to preserve the whole extent of the input image.	None

Methods:

Name	Description
supports_reference	Return whether this transform supports reference images.

name property

name: str

Return the name of the transform class for logging and debugging.

Returns:

Type	Description
str	The name of the transform class.

supports_reference

supports_reference() -> bool

Return whether this transform supports reference images.

Returns:

Type	Description
bool	False by default. Subclasses should override this method
Return whether this transform supports reference images.

Returns:

Type	Description
bool	Always True for spatial transforms.

Source code in src/imgtools/transforms/spatial_transforms.py

def supports_reference(self) -> bool:
    """Return whether this transform supports reference images.

    Returns
    -------
    bool
        Always True for spatial transforms.
    """
    return True

Resize dataclass

Resize(
    size: int | list[int] | numpy.ndarray,
    interpolation: str = "linear",
    anti_alias: bool = True,
    anti_alias_sigma: float | None = None,
)

Bases: imgtools.transforms.spatial_transforms.SpatialTransform

Resize operation class.

A callable class that resizes image to a given size by resampling coordinates.

Parameters:

Name	Type	Description	Default
size	int | list[int] | numpy.ndarray	The new image size. If float, assumes the same size in all directions. Alternatively, a sequence of floats can be passed to specify size along each dimension. Passing 0 at any position will keep the original size along that dimension.	required
interpolation	str	The interpolation method to use. Valid options are: - "linear" for bi/trilinear interpolation (default) - "nearest" for nearest neighbour interpolation - "bspline" for order-3 b-spline interpolation	'linear'
anti_alias	bool	Whether to smooth the image with a Gaussian kernel before resampling. Only used when downsampling, i.e. when size < image.GetSize(). This should be used to avoid aliasing artifacts.	True
anti_alias_sigma	float | None	The standard deviation of the Gaussian kernel used for anti-aliasing.	None

Methods:

Name	Description
supports_reference	Return whether this transform supports reference images.

name property

name: str

Return the name of the transform class for logging and debugging.

Returns:

Type	Description
str	The name of the transform class.

supports_reference

supports_reference() -> bool

Return whether this transform supports reference images.

Returns:

Type	Description
bool	False by default. Subclasses should override this method

Source code in src/imgtools/transforms/spatial_transforms.py

def supports_reference(self) -> bool:
    """Return whether this transform supports reference images.

    Returns
    -------
    bool
        False by default. Subclasses should override this method
    """
    return False

Rotate dataclass

Rotate(
    rotation_centre: list[int],
    angles: float | list[float],
    interpolation: str = "linear",
)

Bases: imgtools.transforms.spatial_transforms.SpatialTransform

Rotate operation class.

A callable class that rotates an image around a given centre.

Parameters:

Name	Type	Description	Default
rotation_centre	list[int]	The centre of rotation in image coordinates.	required
angles	float | list[float]	The angles of rotation around x, y and z axes.	required
interpolation	str	The interpolation method to use. Valid options are: - "linear" for bi/trilinear interpolation (default) - "nearest" for nearest neighbour interpolation - "bspline" for order-3 b-spline interpolation	'linear'

Methods:

Name	Description
supports_reference	Return whether this transform supports reference images.

name property

name: str

Return the name of the transform class for logging and debugging.

Returns:

Type	Description
str	The name of the transform class.

supports_reference

supports_reference() -> bool

Return whether this transform supports reference images.

Returns:

Type	Description
bool	False by default. Subclasses should override this method

Source code in src/imgtools/transforms/spatial_transforms.py

def supports_reference(self) -> bool:
    """Return whether this transform supports reference images.

    Returns
    -------
    bool
        False by default. Subclasses should override this method
    """
    return False

SpatialTransform

Bases: imgtools.transforms.base_transform.BaseTransform

Base class for spatial transforms.

Spatial transforms modify the spatial properties of an image, such as spacing, size, or orientation.

All spatial transforms support an optional reference image parameter in their call method.

Examples:

>>> # This is an abstract base class and cannot be instantiated directly.
>>> # Use one of its subclasses like Resample, Resize, etc.

Methods:

Name	Description
supports_reference	Return whether this transform supports reference images.

name property

name: str

Return the name of the transform class for logging and debugging.

Returns:

Type	Description
str	The name of the transform class.

supports_reference

supports_reference() -> bool

Return whether this transform supports reference images.

Returns:

Type	Description
bool	False by default. Subclasses should override this method

Source code in src/imgtools/transforms/spatial_transforms.py

def supports_reference(self) -> bool:
    """Return whether this transform supports reference images.

    Returns
    -------
    bool
        False by default. Subclasses should override this method
    """
    return False

Zoom dataclass

Zoom(
    scale_factor: float | list[float],
    interpolation: str = "linear",
    anti_alias: bool = True,
    anti_alias_sigma: float | None = None,
)

Bases: imgtools.transforms.spatial_transforms.SpatialTransform

Zoom operation class.

A callable class that rescales image, preserving its spatial extent.

The rescaled image will have the same spatial extent (size) but will be rescaled by scale_factor in each dimension. Alternatively, a separate scale factor for each dimension can be specified by passing a sequence of floats.

Parameters:

Name	Type	Description	Default
scale_factor	float | list[float]	If float, each dimension will be scaled by that factor. If tuple, each dimension will be scaled by the corresponding element.	required
interpolation	str	The interpolation method to use. Valid options are: - "linear" for bi/trilinear interpolation (default) - "nearest" for nearest neighbour interpolation - "bspline" for order-3 b-spline interpolation	'linear'
anti_alias	bool	Whether to smooth the image with a Gaussian kernel before resampling. Only used when downsampling, i.e. when size < image.GetSize(). This should be used to avoid aliasing artifacts.	True
anti_alias_sigma	float | None	The standard deviation of the Gaussian kernel used for anti-aliasing.	None

Methods:

Name	Description
supports_reference	Return whether this transform supports reference images.

name property

name: str

Return the name of the transform class for logging and debugging.

Returns:

Type	Description
str	The name of the transform class.

supports_reference

supports_reference() -> bool

Return whether this transform supports reference images.

Returns:

Type	Description
bool	False by default. Subclasses should override this method

Source code in src/imgtools/transforms/spatial_transforms.py

def supports_reference(self) -> bool:
    """Return whether this transform supports reference images.

    Returns
    -------
    bool
        False by default. Subclasses should override this method
    """
    return False