Quantities of interest

compute_ccc(x, y, bias=True, use_pearson=False)

Compute the concordance correlation coefficient between two arrays x and y.

Parameters:

Name	Type	Description	Default
x	ndarray	First vector.	required
y	ndarray	Second vector.	required
bias	bool	Bias correction. Defaults to True.	True
use_pearson	bool	Use Pearson correlation coefficient. Defaults to False.	False

Returns:

Name	Type	Description
float	float	The concordance correlation coefficient.

compute_dice(y_true, y_pred)

Compute the Dice coefficient between y_true and y_pred.

Parameters:

Name	Type	Description	Default
y_true	ndarray	Ground truth mask.	required
y_pred	ndarray	Predicted mask.	required

Returns:

Name	Type	Description
float	float	The computed Dice coefficient.

compute_voxel_ccc(x_img, y_img, roi_img, bias=True, use_pearson=False)

Compute the voxel-wise concordance correlation coefficient between two NIfTI files.

Parameters:

Name	Type	Description	Default
x_img	Image3D	x image.	required
y_img	Image3D	y image.	required
roi_img	Image3D	ROI image.	required
bias	bool	Bias correction. Defaults to True.	True
use_pearson	bool	Use Pearson correlation coefficient. Defaults to False.	False

Returns:

Name	Type	Description
float	float	Voxel-wise concordance correlation coefficient.

compute_voxel_dice(x_img, y_img, threshold=0.5)

Compute voxel-wise Dice coefficient between two NIfTI files.

Parameters:

Name	Type	Description	Default
x_img	Image3D	x image.	required
y_img	Image3D	y image.	required
threshold	float	Value to threshold on. Defaults to 0.5.	0.5

Returns:

Name	Type	Description
float	float	Dice coefficient.

compute_voxel_ttc(x_img, carrying_capacity)

Compute voxel-wise total tumor cellularity (TTC) from a NIfTI file.

Parameters:

Name	Type	Description	Default
x_img	Image3D	Image3D object.	required
carrying_capacity	float	Carrying capacity.	required

Returns:

Name	Type	Description
float	float	Total tumor cellularity.

compute_voxel_ttv(x_img, threshold=0.5)

Compute voxel-wise total tumor volume (TTV) from a NIfTI file.

Parameters:

Name	Type	Description	Default
x_img	Image3D	Image3D object.	required
threshold	float	Threshold for tumor detection. Defaults to 0.5.	0.5

Returns:

Name	Type	Description
float	float	Total tumor volume.