amici.amici.ExpData¶
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class
amici.amici.
ExpData
(*args)[source]¶ ExpData carries all information about experimental or condition-specific data
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__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
Overload 4:
constructor that initializes timepoints from vectors
- Parameters
nytrue (int) – Number of observables
nztrue (int) – Number of event outputs
nmaxevent (int) – Maximal number of events to track
ts (DoubleVector) – Timepoints (dimension: nt)
Overload 5:
constructor that initializes timepoints and fixed parameters from vectors
- Parameters
nytrue (int) – Number of observables
nztrue (int) – Number of event outputs
nmaxevent (int) – Maximal number of events to track
ts (DoubleVector) – Timepoints (dimension: nt)
fixedParameters (DoubleVector) – Model constants (dimension: nk)
Overload 6:
constructor that initializes timepoints and data from vectors
- Parameters
nytrue (int) – Number of observables
nztrue (int) – Number of event outputs
nmaxevent (int) – Maximal number of events to track
ts (DoubleVector) – Timepoints (dimension: nt)
observedData (DoubleVector) – observed data (dimension: nt x nytrue, row-major)
observedDataStdDev (DoubleVector) – standard deviation of observed data (dimension: nt x nytrue, row-major)
observedEvents (DoubleVector) – observed events (dimension: nmaxevents x nztrue, row-major)
observedEventsStdDev (DoubleVector) – standard deviation of observed events/roots (dimension: nmaxevents 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 resultssigma_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 resultssigma_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:
get function that copies data from ExpData::observedData to output
get function that returns a pointer to observed data at index
get function that copies data from ExpData::observedDataStdDev to output
get function that returns a pointer to standard deviation of observed data at index
get function that copies data from ExpData::mz to output
get function that returns a pointer to observed data at ieth occurrence
get function that copies data from ExpData::observedEventsStdDev to output
get function that returns a pointer to standard deviation of observed event data at ie-th occurrence
getTimepoint
(it)get function that returns timepoint at index
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
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
Set reinitialization of all states based on model constants for all simulation phases.
reinitializeAllFixedParameterDependentInitialStatesForPresimulation
(…)Set reinitialization of all states based on model constants for presimulation (only meaningful if preequilibration is performed).
reinitializeAllFixedParameterDependentInitialStatesForSimulation
(…)Set reinitialization of all states based on model constants for the ‘main’ simulation (only meaningful if presimulation or preequilibration is performed).
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
Model constants
fixedParametersPreequilibration
Model constants for pre-equilibration
fixedParametersPresimulation
Model constants for pre-simulation
parameters
Model parameters
plist
Parameter indices w.r.t.
pscale
Parameter scales
reinitialization_state_idxs_presim
Indices of states to be reinitialized based on provided presimulation constants / fixed parameters.
reinitialization_state_idxs_sim
Indices of states to be reinitialized based on provided constants / fixed parameters.
reinitializeFixedParameterInitialStates
Flag indicating whether reinitialization of states depending on fixed parameters is activated
sx0
Initial state sensitivities
t_presim
Duration of pre-simulation.
ts_
Timepoints for which model state/outputs/.
tstart_
starting time
x0
Initial state
Methods
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__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
Overload 4:
constructor that initializes timepoints from vectors
- Parameters
nytrue (int) – Number of observables
nztrue (int) – Number of event outputs
nmaxevent (int) – Maximal number of events to track
ts (DoubleVector) – Timepoints (dimension: nt)
Overload 5:
constructor that initializes timepoints and fixed parameters from vectors
- Parameters
nytrue (int) – Number of observables
nztrue (int) – Number of event outputs
nmaxevent (int) – Maximal number of events to track
ts (DoubleVector) – Timepoints (dimension: nt)
fixedParameters (DoubleVector) – Model constants (dimension: nk)
Overload 6:
constructor that initializes timepoints and data from vectors
- Parameters
nytrue (int) – Number of observables
nztrue (int) – Number of event outputs
nmaxevent (int) – Maximal number of events to track
ts (DoubleVector) – Timepoints (dimension: nt)
observedData (DoubleVector) – observed data (dimension: nt x nytrue, row-major)
observedDataStdDev (DoubleVector) – standard deviation of observed data (dimension: nt x nytrue, row-major)
observedEvents (DoubleVector) – observed events (dimension: nmaxevents x nztrue, row-major)
observedEventsStdDev (DoubleVector) – standard deviation of observed events/roots (dimension: nmaxevents 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 resultssigma_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 resultssigma_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)
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getObservedData
() → amici.amici.DoubleVector[source]¶ get function that copies data from ExpData::observedData to output
- Return type
- Returns
observed data (dimension: nt x nytrue, row-major)
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getObservedDataPtr
(it: int) → Iterable[float][source]¶ get function that returns a pointer to observed data at index
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getObservedDataStdDev
() → amici.amici.DoubleVector[source]¶ get function that copies data from ExpData::observedDataStdDev to output
- Return type
- Returns
standard deviation of observed data
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getObservedDataStdDevPtr
(it: int) → Iterable[float][source]¶ get function that returns a pointer to standard deviation of observed data at index
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getObservedEvents
() → amici.amici.DoubleVector[source]¶ get function that copies data from ExpData::mz to output
- Return type
- Returns
observed event data
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getObservedEventsPtr
(ie: int) → Iterable[float][source]¶ get function that returns a pointer to observed data at ieth occurrence
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getObservedEventsStdDev
() → amici.amici.DoubleVector[source]¶ get function that copies data from ExpData::observedEventsStdDev to output
- Return type
- Returns
standard deviation of observed event data
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getObservedEventsStdDevPtr
(ie: int) → Iterable[float][source]¶ get function that returns a pointer to standard deviation of observed event data at ie-th occurrence
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getTimepoints
() → amici.amici.DoubleVector[source]¶ get function that copies data from ExpData::ts to output
- Return type
- Returns
ExpData::ts
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isSetObservedData
(it: int, iy: int) → bool[source]¶ get function that checks whether data at specified indices has been set
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isSetObservedDataStdDev
(it: int, iy: int) → bool[source]¶ get function that checks whether standard deviation of data at specified indices has been set
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isSetObservedEvents
(ie: int, iz: int) → bool[source]¶ get function that checks whether event data at specified indices has been set
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isSetObservedEventsStdDev
(ie: int, iz: int) → bool[source]¶ get function that checks whether standard deviation of even data at specified indices has been set
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nmaxevent
() → int[source]¶ maximal number of events to track
- Return type
- Returns
maximal number of events to track
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nytrue
() → int[source]¶ number of observables of the non-augmented model
- Return type
- Returns
number of observables of the non-augmented model
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nztrue
() → int[source]¶ number of event observables of the non-augmented model
- Return type
- Returns
number of event observables of the non-augmented model
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reinitializeAllFixedParameterDependentInitialStates
(nx_rdata: int) → None¶ Set reinitialization of all states based on model constants for all simulation phases.
Convenience function to populate reinitialization_state_idxs_presim and reinitialization_state_idxs_sim
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reinitializeAllFixedParameterDependentInitialStatesForPresimulation
(nx_rdata: int) → None¶ Set reinitialization of all states based on model constants for presimulation (only meaningful if preequilibration is performed).
Convenience function to populate reinitialization_state_idxs_presim and reinitialization_state_idxs_sim
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reinitializeAllFixedParameterDependentInitialStatesForSimulation
(nx_rdata: int) → None¶ Set reinitialization of all states based on model constants for the ‘main’ simulation (only meaningful if presimulation or preequilibration is performed).
Convenience function to populate reinitialization_state_idxs_presim and reinitialization_state_idxs_sim
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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) – observed data index
- Return type
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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
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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
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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
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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
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