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cornucopia.contrast

This module contains transforms that operate on image contrasts.

ContrastMixtureFinalTransform 

ContrastMixtureFinalTransform(z, mu0, sigma0, mu, sigma, **kwargs)

Bases: FinalTransform

Classwise shift and rescaling.

Parameters:

Name Type Description Default
z (K, *spatial) tensor

Probability that each voxel belongs to a given class.

 required
mu0 (K, C) tensor

Original means for each class.

 required
sigma0 (K, C, C) tensor

Original covariances for each class.

 required
mu (K, C) tensor

New means for each class.

 required
sigma (K, C, C) tensor

New covariances for each class.

 required

Other Parameters:

Name Type Description
returns

See Transform for details.
append

See Transform for details.
prefix

See Transform for details.
include

See Transform for details.
exclude

See Transform for details.
consume

See Transform for details.

ContrastMixtureTransform 

ContrastMixtureTransform(nk=16, keep_background=True, *, shared=False, **kwargs)

Bases: NonFinalTransform

Find intensity modes using a GMM and change their means and covariances.

Reference

Meyer, M.I., de la Rosa, E., Pedrosa de Barros, N., Paolella, R., Van Leemput, K. and Sima, D.M., 2021. A contrast augmentation approach to improve multi-scanner generalization in MRI. Frontiers in Neuroscience, 15, p.708196.

@article{meyer2021,
    title     = {A contrast augmentation approach to improve multi-scanner generalization in MRI},
    author    = {Meyer, Maria Ines and de la Rosa, Ezequiel and Pedrosa de Barros, Nuno and Paolella, Roberto and Van Leemput, Koen and Sima, Diana M},
    journal   = {Frontiers in Neuroscience},
    volume    = {15},
    pages     = {708196},
    year      = {2021},
    publisher = {Frontiers Media SA},
    url       = {https://www.frontiersin.org/articles/10.3389/fnins.2021.708196}
}

Parameters:

Name Type Description Default
nk int

Number of classes

 16
keep_background bool

Do not change background mean/cov. The background class is the class with minimum mean value.

 True

Other Parameters:

Name Type Description
shared bool

See NonFinalTransform for details.
returns

See Transform for details.
append

See Transform for details.
prefix

See Transform for details.
include

See Transform for details.
exclude

See Transform for details.
consume

See Transform for details.

Final class-attribute instance-attribute 

Final = ContrastMixtureFinalTransform

The transform type returned by unroll, next and final.

Next class-attribute instance-attribute 

Next = ContrastMixtureFinalTransform

The transform type returned by unroll, next and final.

ContrastLookupFinalTransform 

ContrastLookupFinalTransform(edges, mu, **kwargs)

Bases: FinalTransform

Binwise intensity shift.

Parameters:

Name Type Description Default
edges (K+1,) tensor

The limits of each input bin.

 required
mu (K,) tensor

The new mean value for each bin.

 required

Other Parameters:

Name Type Description
returns

See Transform for details.
append

See Transform for details.
prefix

See Transform for details.
include

See Transform for details.
exclude

See Transform for details.
consume

See Transform for details.

ContrastLookupTransform 

ContrastLookupTransform(nk=16, keep_background=True, *, shared=False, **kwargs)

Bases: NonFinalTransform

Segment intensities into equidistant bins and change their mean value.

Parameters:

Name Type Description Default
nk int

Number of classes

 16
keep_background bool

Do not change background mean/cov. The background class is the class with minimum mean value.

 True

Other Parameters:

Name Type Description
shared

See NonFinalTransform for details.
returns

See Transform for details.
append

See Transform for details.
prefix

See Transform for details.
include

See Transform for details.
exclude

See Transform for details.
consume

See Transform for details.

Final class-attribute instance-attribute 

Final = ContrastLookupFinalTransform

The transform type returned by unroll, next and final.

Next class-attribute instance-attribute 

Next = ContrastLookupFinalTransform

The transform type returned by unroll, next and final.