Base compartment class

The base class for compartment models.

Methods

Public methods

• BaseCompartment$get_signal()

• BaseCompartment$get_parameter_names()

• BaseCompartment$get_parameters()

• BaseCompartment$clone()

---

Method get_signal()

Computes the signal attenuation predicted by the model.

Usage

BaseCompartment$get_signal(
  small_delta,
  big_delta,
  G,
  direction = c(0, 0, 1),
  echo_time = NULL,
  n_max = 20L,
  m_max = 50L
)

Arguments

small_delta

A numeric value specifying the duration of the gradient pulse in milliseconds.

big_delta

A numeric value specifying the duration between the gradient pulses in milliseconds.

G

A numeric value specifying the strength of the gradient in mT.\(\mu\)m\(^{-1}\).

direction

A numeric vector specifying the direction of the gradient. Defaults to c(0, 0, 1).

echo_time

A numeric value specifying the echo time in milliseconds.

n_max

An integer value specifying the maximum order of the Bessel function. Defaults to 20L.

m_max

An integer value specifying the maximum number of extrema for the Bessel function. Defaults to 50L.

Returns

A numeric value storing the predicted signal attenuation.

Examples

freeComp <- FreeCompartment$new()
freeComp$get_signal(small_delta = 30, big_delta = 30, G = 0.040)

sphereComp <- SphereCompartment$new()
sphereComp$get_signal(small_delta = 30, big_delta = 30, G = 0.040)

sodermanComp <- SodermanCompartment$new()
sodermanComp$get_signal(small_delta = 30, big_delta = 30, G = 0.040)

staniszComp <- StaniszCompartment$new()
staniszComp$get_signal(small_delta = 30, big_delta = 30, G = 0.040)

neumanComp <- NeumanCompartment$new()
neumanComp$get_signal(
  small_delta = 30, big_delta = 30, G = 0.040,
  echo_time = 40
)

callaghanComp <- CallaghanCompartment$new()
callaghanComp$get_signal(small_delta = 30, big_delta = 30, G = 0.040)

vanGelderenComp <- VanGelderenCompartment$new()
vanGelderenComp$get_signal(small_delta = 30, big_delta = 30, G = 0.040)

---

Method get_parameter_names()

Returns the names of the compartment parameters

Usage

BaseCompartment$get_parameter_names()

Returns

A character vector storing the names of the compartment parameters.

Examples

freeComp <- FreeCompartment$new()
freeComp$get_parameter_names()

---

Method get_parameters()

Returns the values of the compartment parameters

Usage

BaseCompartment$get_parameters()

Returns

A numeric vector storing the values of the compartment parameters.

Examples

freeComp <- FreeCompartment$new()
freeComp$get_parameters()

---

Method clone()

The objects of this class are cloneable with this method.

Usage

BaseCompartment$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

## ------------------------------------------------
## Method `BaseCompartment$get_signal`
## ------------------------------------------------

freeComp <- FreeCompartment$new()
freeComp$get_signal(small_delta = 30, big_delta = 30, G = 0.040)
#> [1] 0.002063224

sphereComp <- SphereCompartment$new()
sphereComp$get_signal(small_delta = 30, big_delta = 30, G = 0.040)
#> [1] 0.1205943

sodermanComp <- SodermanCompartment$new()
sodermanComp$get_signal(small_delta = 30, big_delta = 30, G = 0.040)
#> [1] 0.01565033

staniszComp <- StaniszCompartment$new()
staniszComp$get_signal(small_delta = 30, big_delta = 30, G = 0.040)
#> [1] 0.08850973

neumanComp <- NeumanCompartment$new()
neumanComp$get_signal(
  small_delta = 30, big_delta = 30, G = 0.040,
  echo_time = 40
)
#> [1] 1

callaghanComp <- CallaghanCompartment$new()
callaghanComp$get_signal(small_delta = 30, big_delta = 30, G = 0.040)
#> [1] 0.02624805

vanGelderenComp <- VanGelderenCompartment$new()
vanGelderenComp$get_signal(small_delta = 30, big_delta = 30, G = 0.040)
#> [1] 0.1205943

## ------------------------------------------------
## Method `BaseCompartment$get_parameter_names`
## ------------------------------------------------

freeComp <- FreeCompartment$new()
freeComp$get_parameter_names()
#> [1] "FreeDiffusivity"

## ------------------------------------------------
## Method `BaseCompartment$get_parameters`
## ------------------------------------------------

freeComp <- FreeCompartment$new()
freeComp$get_parameters()
#> $FreeDiffusivity
#> [1] 3
#>