Intensity transforms

intensity_transforms

ClipIntensity dataclass

ClipIntensity(lower: float, upper: float)

Bases: imgtools.transforms.intensity_transforms.IntensityTransform

ClipIntensity operation class.

A callable class that clips image grey level intensities to specified range.

Parameters:

Name	Type	Description	Default
lower	float	The lower bound on grey level intensity. Voxels with lower intensity will be set to this value.	required
upper	float	The upper bound on grey level intensity. Voxels with higer intensity will be set to this value.	required

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	Always False for intensity transforms.

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

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

    Returns
    -------
    bool
        Always False for intensity transforms.
    """
    return False

IntensityTransform

Bases: imgtools.transforms.base_transform.BaseTransform

Base class for intensity transforms.

Intensity transforms modify the pixel/voxel intensity values of an image without changing its spatial properties.

All intensity transforms operate on individual pixel/voxel values independently, leaving the image dimensions, spacing, and orientation unchanged.

Examples:

>>> # This is an abstract base class and cannot be instantiated directly.
>>> # Use one of its subclasses like ClipIntensity or WindowIntensity.

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	Always False for intensity transforms.

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

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

    Returns
    -------
    bool
        Always False for intensity transforms.
    """
    return False

N4BiasFieldCorrection dataclass

N4BiasFieldCorrection()

Bases: imgtools.transforms.intensity_transforms.IntensityTransform

N4BiasFieldCorrection operation class.

A callable class that applies N4 bias field correction to reduce smooth intensity inhomogeneities (bias fields) commonly found in MR imaging. This transform corrects voxel intensities while preserving image geometry (spacing, orientation, and dimensions).

The correction uses SimpleITK's N4BiasFieldCorrectionImageFilter, which implements the N4 algorithm (Tustison et al., 2010).

Notes

• This transform is computationally intensive and may take several seconds to minutes depending on image size.
• Best suited for MR images; application to other modalities is typically not meaningful.
• No rotation, translation, or scaling is applied.

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	Always False for intensity transforms.

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

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

    Returns
    -------
    bool
        Always False for intensity transforms.
    """
    return False

WindowIntensity dataclass

WindowIntensity(window: float, level: float)

Bases: imgtools.transforms.intensity_transforms.IntensityTransform

WindowIntensity operation class.

A callable class that restricts image grey level intensities to a given window and level. This is commonly used in medical imaging to enhance visibility of specific tissue types (e.g., bone window, lung window in CT).

The window/level parameters define a range centered at the 'level' value with a width of 'window'. All intensities outside this range are clipped.

Parameters:

Name	Type	Description	Default
window	float	The width of the intensity window. Must be positive.	required
level	float	The mid-point of the intensity window.	required

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	Always False for intensity transforms.

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

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

    Returns
    -------
    bool
        Always False for intensity transforms.
    """
    return False