Cylinder bundle compartment class

A class to model restricted diffusion in a bundle of cylinders.

Super class

midi::BaseCompartment -> CylinderBundleCompartment

Methods

Public methods

• CylinderBundleCompartment$new()

• CylinderBundleCompartment$clone()

Inherited methods

• midi::BaseCompartment$get_parameter_names()
• midi::BaseCompartment$get_parameters()
• midi::BaseCompartment$get_signal()

---

Method new()

Instantiates a new cylinder bundle compartment.

Usage

CylinderBundleCompartment$new(
  cylinder_density,
  cylinder_compartments,
  axial_diffusivity = NULL,
  radial_diffusivity = NULL
)

Arguments

cylinder_density

A numeric value specifying the density of the cylinders in the voxel. Must be between 0 and 1.

cylinder_compartments

A list of instances of the CylinderCompartment class specifying the compartments within the bundle.

axial_diffusivity

A numeric value specifying the axial diffusivity in the space outside the cylinders in m\(^2\).s\(^{-1}\). If not provided, defaults to a tortuosity model reducing the intrinsic diffusivity depending on orientation dispersion. Defaults to NULL in which case the extracellular axial diffusivity is set via a tortuosity model based on the dispersion in orientation.

radial_diffusivity

A numeric value specifying the radial diffusivity in the space outside the cylinders in m\(^2\).s\(^{-1}\). Defaults to NULL in which case the extracellular radial diffusivity is set via a tortuosity model based on the intracellular density.

Returns

An instance of the CylinderBundleCompartment class.

---

Method clone()

The objects of this class are cloneable with this method.

Usage

CylinderBundleCompartment$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

withr::with_seed(1234, {
  cyls <- rcylinders(
    n = 100,
    axis_mean = c(0, 0, 1),
    radius_mean = 5,
    diffusivity_mean = 3,
    axis_concentration = 10,
    radius_sd = 1,
    diffusivity_sd = 0
  )
})

comp <- CylinderBundleCompartment$new(
  cylinder_density = 0.5,
  cylinder_compartments = cyls
)

comp$get_signal(
  small_delta = 30,
  big_delta = 30,
  G = 0.040,
  direction = c(0, 0, 1)
)
#> [1] 0.005344176

comp$get_parameters()
#> $CylinderAxisMean
#> [1] -0.028925430 -0.006517909 -0.999560322
#> 
#> $CylinderAxisConcentration
#> [1] 10.6864
#> 
#> $CylinderRadiusMean
#> [1] 5.082161
#> 
#> $CylinderRadiusStd
#> [1] 0.9930441
#> 
#> $CylinderDiffusivityMean
#> [1] 3
#> 
#> $CylinderDiffusivityStd
#> [1] 0
#> 
#> $CylinderDensity
#> [1] 0.5
#> 
#> $CylinderAxialDiffusivity
#> [1] 2.431526
#> 
#> $CylinderRadialDiffusivity
#> [1] 1.458915
#>