amici.amici.ExpData

class amici.amici.ExpData(*args)[source]

ExpData carries all information about experimental or condition-specific data

__init__(*args)[source]

Overload 1:

default constructor


Overload 2:

Copy constructor, needs to be declared to be generated in swig


Overload 3:

constructor that only initializes dimensions

Parameters

  • nytrue (int) –

  • nztrue (int) –

  • nmaxevent (int) –


Overload 4:

constructor that initializes timepoints from vectors

Parameters

  • nytrue (int) – (dimension: scalar)

  • nztrue (int) – (dimension: scalar)

  • nmaxevent (int) – (dimension: scalar)

  • ts (DoubleVector) – (dimension: nt)


Overload 5:

constructor that initializes timepoints and fixed parameters from vectors

Parameters

  • nytrue (int) – (dimension: scalar)

  • nztrue (int) – (dimension: scalar)

  • nmaxevent (int) – (dimension: scalar)

  • ts (DoubleVector) – (dimension: nt)

  • fixedParameters (DoubleVector) – (dimension: nk)


Overload 6:

constructor that initializes timepoints and data from vectors

Parameters

  • nytrue (int) – (dimension: scalar)

  • nztrue (int) – (dimension: scalar)

  • nmaxevent (int) – (dimension: scalar)

  • ts (DoubleVector) – (dimension: nt)

  • observedData (DoubleVector) – (dimension: nt x nytrue, row-major)

  • observedDataStdDev (DoubleVector) – (dimension: nt x nytrue, row-major)

  • observedEvents (DoubleVector) – (dimension: nmaxevent x nztrue, row-major)

  • observedEventsStdDev (DoubleVector) – (dimension: nmaxevent x nztrue, row-major)


Overload 7:

constructor that initializes with Model

Parameters

model (Model) – pointer to model specification object


Overload 8:

constructor that initializes with returnData, adds noise according to specified sigmas

Parameters

  • rdata (ReturnData) – return data pointer with stored simulation results

  • sigma_y (float) – scalar standard deviations for all observables

  • sigma_z (float) – scalar standard deviations for all event observables


Overload 9:

constructor that initializes with returnData, adds noise according to specified sigmas

Parameters

  • rdata (ReturnData) – return data pointer with stored simulation results

  • sigma_y (DoubleVector) – vector of standard deviations for observables (dimension: nytrue or nt x nytrue, row-major)

  • sigma_z (DoubleVector) – vector of standard deviations for event observables (dimension: nztrue or nmaxevent x nztrue, row-major)

Methods Summary

__init__(*args)

Overload 1:

getObservedData()

get function that copies data from ExpData::observedData to output

getObservedDataPtr(it)

get function that returns a pointer to observed data at index

getObservedDataStdDev()

get function that copies data from ExpData::observedDataStdDev to output

getObservedDataStdDevPtr(it)

get function that returns a pointer to standard deviation of observed data at index

getObservedEvents()

get function that copies data from ExpData::mz to output

getObservedEventsPtr(ie)

get function that returns a pointer to observed data at ieth occurrence

getObservedEventsStdDev()

get function that copies data from ExpData::observedEventsStdDev to output

getObservedEventsStdDevPtr(ie)

get function that returns a pointer to standard deviation of observed event data at ieth occurrence

getTimepoint(it)

get function that returns timepoint at index

getTimepoints()

get function that copies data from ExpData::ts to output

isSetObservedData(it, iy)

get function that checks whether data at specified indices has been set

isSetObservedDataStdDev(it, iy)

get function that checks whether standard deviation of data at specified indices has been set

isSetObservedEvents(ie, iz)

get function that checks whether event data at specified indices has been set

isSetObservedEventsStdDev(ie, iz)

get function that checks whether standard deviation of even data at specified indices has been set

nmaxevent()

maximal number of events to track

nt()

number of timepoints

nytrue()

number of observables of the non-augmented model

nztrue()

number of event observables of the non-augmented model

setObservedData(*args)

Overload 1:

setObservedDataStdDev(*args)

Overload 1:

setObservedEvents(*args)

Overload 1:

setObservedEventsStdDev(*args)

Overload 1:

setTimepoints(ts)

set function that copies data from input to ExpData::ts

Attributes

fixedParameters

condition-specific fixed parameters of size Model::nk() or empty

fixedParametersPreequilibration

condition-specific fixed parameters for pre-equilibration of size Model::nk() or empty.

fixedParametersPresimulation

condition-specific fixed parameters for pre-simulation of size Model::nk() or empty.

parameters

condition-specific parameters of size Model::np() or empty

plist

condition-specific parameter list

pscale

condition-specific parameter scales of size Model::np()

reinitializeFixedParameterInitialStates

flag indicating whether reinitialization of states depending on fixed parameters is activated

sx0

condition-specific initial condition sensitivities of size Model::nx() * Model::nplist(), Model::nx() * ExpData::plist.size(), if ExpData::plist is not empty, or empty

t_presim

duration of pre-simulation if this is > 0, presimulation will be performed from (model->t0 - t_presim) to model->t0 using the fixedParameters in fixedParametersPresimulation

x0

condition-specific initial conditions of size Model::nx() or empty

Methods

__init__(*args)[source]

Overload 1:

default constructor


Overload 2:

Copy constructor, needs to be declared to be generated in swig


Overload 3:

constructor that only initializes dimensions

Parameters

  • nytrue (int) –

  • nztrue (int) –

  • nmaxevent (int) –


Overload 4:

constructor that initializes timepoints from vectors

Parameters

  • nytrue (int) – (dimension: scalar)

  • nztrue (int) – (dimension: scalar)

  • nmaxevent (int) – (dimension: scalar)

  • ts (DoubleVector) – (dimension: nt)


Overload 5:

constructor that initializes timepoints and fixed parameters from vectors

Parameters

  • nytrue (int) – (dimension: scalar)

  • nztrue (int) – (dimension: scalar)

  • nmaxevent (int) – (dimension: scalar)

  • ts (DoubleVector) – (dimension: nt)

  • fixedParameters (DoubleVector) – (dimension: nk)


Overload 6:

constructor that initializes timepoints and data from vectors

Parameters

  • nytrue (int) – (dimension: scalar)

  • nztrue (int) – (dimension: scalar)

  • nmaxevent (int) – (dimension: scalar)

  • ts (DoubleVector) – (dimension: nt)

  • observedData (DoubleVector) – (dimension: nt x nytrue, row-major)

  • observedDataStdDev (DoubleVector) – (dimension: nt x nytrue, row-major)

  • observedEvents (DoubleVector) – (dimension: nmaxevent x nztrue, row-major)

  • observedEventsStdDev (DoubleVector) – (dimension: nmaxevent x nztrue, row-major)


Overload 7:

constructor that initializes with Model

Parameters

model (Model) – pointer to model specification object


Overload 8:

constructor that initializes with returnData, adds noise according to specified sigmas

Parameters

  • rdata (ReturnData) – return data pointer with stored simulation results

  • sigma_y (float) – scalar standard deviations for all observables

  • sigma_z (float) – scalar standard deviations for all event observables


Overload 9:

constructor that initializes with returnData, adds noise according to specified sigmas

Parameters

  • rdata (ReturnData) – return data pointer with stored simulation results

  • sigma_y (DoubleVector) – vector of standard deviations for observables (dimension: nytrue or nt x nytrue, row-major)

  • sigma_z (DoubleVector) – vector of standard deviations for event observables (dimension: nztrue or nmaxevent x nztrue, row-major)

getObservedData() → amici.amici.DoubleVector[source]

get function that copies data from ExpData::observedData to output

Return type

DoubleVector

Returns

observed data (dimension: nt x nytrue, row-major)

getObservedDataPtr(it: int) → Iterable[float][source]

get function that returns a pointer to observed data at index

Parameters

it (int) – timepoint index

Return type

float

Returns

pointer to observed data at index (dimension: nytrue)

getObservedDataStdDev() → amici.amici.DoubleVector[source]

get function that copies data from ExpData::observedDataStdDev to output

Return type

DoubleVector

Returns

standard deviation of observed data

getObservedDataStdDevPtr(it: int) → Iterable[float][source]

get function that returns a pointer to standard deviation of observed data at index

Parameters

it (int) – timepoint index

Return type

float

Returns

pointer to standard deviation of observed data at index

getObservedEvents() → amici.amici.DoubleVector[source]

get function that copies data from ExpData::mz to output

Return type

DoubleVector

Returns

observed event data

getObservedEventsPtr(ie: int) → Iterable[float][source]

get function that returns a pointer to observed data at ieth occurrence

Parameters

ie (int) – event occurrence

Return type

float

Returns

pointer to observed event data at ieth occurrence

getObservedEventsStdDev() → amici.amici.DoubleVector[source]

get function that copies data from ExpData::observedEventsStdDev to output

Return type

DoubleVector

Returns

standard deviation of observed event data

getObservedEventsStdDevPtr(ie: int) → Iterable[float][source]

get function that returns a pointer to standard deviation of observed event data at ieth occurrence

Parameters

ie (int) – event occurrence

Return type

float

Returns

pointer to standard deviation of observed event data at ieth occurrence

getTimepoint(it: int) → float[source]

get function that returns timepoint at index

Parameters

it (int) – timepoint index

Return type

float

Returns

timepoint timepoint at index

getTimepoints() → amici.amici.DoubleVector[source]

get function that copies data from ExpData::ts to output

Return type

DoubleVector

Returns

ExpData::ts

isSetObservedData(it: int, iy: int) → bool[source]

get function that checks whether data at specified indices has been set

Parameters

  • it (int) – time index

  • iy (int) – observable index

Return type

boolean

Returns

boolean specifying if data was set

isSetObservedDataStdDev(it: int, iy: int) → bool[source]

get function that checks whether standard deviation of data at specified indices has been set

Parameters

  • it (int) – time index

  • iy (int) – observable index

Return type

boolean

Returns

boolean specifying if standard deviation of data was set

isSetObservedEvents(ie: int, iz: int) → bool[source]

get function that checks whether event data at specified indices has been set

Parameters

  • ie (int) – event index

  • iz (int) – event observable index

Return type

boolean

Returns

boolean specifying if data was set

isSetObservedEventsStdDev(ie: int, iz: int) → bool[source]

get function that checks whether standard deviation of even data at specified indices has been set

Parameters

  • ie (int) – event index

  • iz (int) – event observable index

Return type

boolean

Returns

boolean specifying if standard deviation of event data was set

nmaxevent() → int[source]

maximal number of events to track

Return type

int

Returns

maximal number of events to track

nt() → int[source]

number of timepoints

Return type

int

Returns

number of timepoints

nytrue() → int[source]

number of observables of the non-augmented model

Return type

int

Returns

number of observables of the non-augmented model

nztrue() → int[source]

number of event observables of the non-augmented model

Return type

int

Returns

number of event observables of the non-augmented model

setObservedData(*args) → None[source]

Overload 1:

set function that copies data from input to ExpData::my

Parameters

observedData (DoubleVector) – observed data (dimension: nt x nytrue, row-major)


Overload 2:

set function that copies observed data for specific observable

Parameters

  • observedData (DoubleVector) – observed data (dimension: nt)

  • iy (int) – oberved data index

Return type

None

setObservedDataStdDev(*args) → None[source]

Overload 1:

set function that copies data from input to ExpData::observedDataStdDev

Parameters

observedDataStdDev (DoubleVector) – standard deviation of observed data (dimension: nt x nytrue, row-major)


Overload 2:

set function that sets all ExpData::observedDataStdDev to the input value

Parameters

stdDev (float) – standard deviation (dimension: scalar)


Overload 3:

set function that copies standard deviation of observed data for specific observable

Parameters

  • observedDataStdDev (DoubleVector) – standard deviation of observed data (dimension: nt)

  • iy (int) – observed data index


Overload 4:

set function that sets all standard deviation of a specific observable to the input value

Parameters

  • stdDev (float) – standard deviation (dimension: scalar)

  • iy (int) – observed data index

Return type

None

setObservedEvents(*args) → None[source]

Overload 1:

set function that copies observed event data from input to ExpData::observedEvents

Parameters

observedEvents (DoubleVector) – observed data (dimension: nmaxevent x nztrue, row-major)


Overload 2:

set function that copies observed event data for specific event observable

Parameters

  • observedEvents (DoubleVector) – observed data (dimension: nmaxevent)

  • iz (int) – observed event data index

Return type

None

setObservedEventsStdDev(*args) → None[source]

Overload 1:

set function that copies data from input to ExpData::observedEventsStdDev

Parameters

observedEventsStdDev (DoubleVector) – standard deviation of observed event data


Overload 2:

set function that sets all ExpData::observedDataStdDev to the input value

Parameters

stdDev (float) – standard deviation (dimension: scalar)


Overload 3:

set function that copies standard deviation of observed data for specific observable

Parameters

  • observedEventsStdDev (DoubleVector) – standard deviation of observed data (dimension: nmaxevent)

  • iz (int) – observed data index


Overload 4:

set function that sets all standard deviation of a specific observable to the input value

Parameters

  • stdDev (float) – standard deviation (dimension: scalar)

  • iz (int) – observed data index

Return type

None

setTimepoints(ts: amici.amici.DoubleVector) → None[source]

set function that copies data from input to ExpData::ts

Parameters

ts (amici.amici.DoubleVector) – timepoints

Return type

None