inc

DuneConverter

class DuneConverter

Public Functions

explicit DuneConverter(const model::Model &model, const std::map<std::string, double, std::less<>> &substitutions = {}, bool forExternalUse = false, const QString &outputIniFile = {}, int doublePrecision = 18)

QString getIniFile() const

const mesh::Mesh2d *getMesh() const

const mesh::Mesh3d *getMesh3d() const

const std::unordered_map<std::string, std::vector<double>> &getConcentrations() const

const std::unordered_map<std::string, std::vector<std::string>> &getSpeciesNames() const

const std::vector<std::string> &getCompartmentNames() const

common::VoxelF getOrigin() const

common::VolumeF getVoxelSize() const

common::Volume getImageSize() const

Pde

class Pde

Public Functions

explicit Pde(const model::Model *doc_ptr, const std::vector<std::string> &speciesIDs, const std::vector<std::string> &reactionIDs, const std::vector<std::string> &relabelledSpeciesIDs = {}, const PdeScaleFactors &pdeScaleFactors = {}, const std::vector<std::string> &extraVariables = {}, const std::vector<std::string> &relabelledExtraVariables = {}, const std::map<std::string, double, std::less<>> &substitutions = {})

const std::vector<std::string> &getRHS() const

const std::vector<std::vector<std::string>> &getJacobian() const

Simulation

class Simulation

Public Functions

explicit Simulation(model::Model &smeModel)

~Simulation()

std::size_t doTimesteps(double time, std::size_t nSteps = 1, double timeout_ms = -1.0)

std::size_t doMultipleTimesteps(const std::vector<std::pair<std::size_t, double>> &timesteps, double timeout_ms = -1.0, const std::function<bool()> &stopRunningCallback = {})

const std::string &errorMessage() const

const common::ImageStack &errorImages() const

const std::vector<std::string> &getCompartmentIds() const

const std::vector<std::string> &getSpeciesIds(std::size_t compartmentIndex) const

const std::vector<QRgb> &getSpeciesColors(std::size_t compartmentIndex) const

const std::vector<double> &getTimePoints() const

const AvgMinMax &getAvgMinMax(std::size_t timeIndex, std::size_t compartmentIndex, std::size_t speciesIndex) const

std::vector<double> getConc(std::size_t timeIndex, std::size_t compartmentIndex, std::size_t speciesIndex) const

std::vector<double> getConcArray(std::size_t timeIndex, std::size_t compartmentIndex, std::size_t speciesIndex) const

void applyConcsToModel(model::Model &m, std::size_t timeIndex) const

std::vector<double> getDcdt(std::size_t compartmentIndex, std::size_t speciesIndex) const

std::vector<double> getDcdtArray(std::size_t compartmentIndex, std::size_t speciesIndex) const

double getLowerOrderConc(std::size_t compartmentIndex, std::size_t speciesIndex, std::size_t pixelIndex) const

common::ImageStack getConcImage(std::size_t timeIndex, const std::vector<std::vector<std::size_t>> &speciesToDraw = {}, bool normaliseOverAllTimepoints = false, bool normaliseOverAllSpecies = false) const

const std::vector<std::string> &getPyNames(std::size_t compartmentIndex) const

std::vector<std::vector<double>> getPyConcs(std::size_t timeIndex, std::size_t compartmentIndex) const

std::vector<std::vector<double>> getPyDcdts(std::size_t compartmentIndex) const

std::size_t getNCompletedTimesteps() const

const SimulationData &getSimulationData() const

bool getIsRunning() const

bool getIsStopping() const

void requestStop()

SimulationData

class SimulationData

Public Functions

void clear()

std::size_t size() const

void reserve(std::size_t n)

void pop_back()

template<class Archive> inline void serialize(Archive &ar, std::uint32_t const version)

Public Members

std::vector<double> timePoints

std::vector<std::vector<std::vector<double>>> concentration

std::vector<std::vector<std::vector<AvgMinMax>>> avgMinMax

std::vector<std::vector<std::vector<double>>> concentrationMax

std::vector<std::size_t> concPadding

std::string xmlModel

struct AvgMinMax

Public Functions

template<class Archive> inline void serialize(Archive &ar, std::uint32_t const version)

Public Members

double avg = 0

double min = std::numeric_limits<double>::max()

double max = 0

SimulationOptions

struct Options

Public Functions

template<class Archive> inline void serialize(Archive &ar, std::uint32_t const version)

Public Members

DuneOptions dune

PixelOptions pixel

enum class sme::simulate::SimulatorType

Values:

enumerator DUNE

enumerator Pixel

struct PixelOptions

Public Functions

template<class Archive> inline void serialize(Archive &ar, std::uint32_t const version)

Public Members

PixelIntegratorType integrator = {PixelIntegratorType::RK212}

PixelIntegratorError maxErr

double maxTimestep = {std::numeric_limits<double>::max()}

bool enableMultiThreading = {false}

std::size_t maxThreads = {0}

bool doCSE = {true}

unsigned optLevel = {3}

struct PixelIntegratorError

Public Functions

template<class Archive> inline void serialize(Archive &ar, std::uint32_t const version)

Public Members

double abs = {std::numeric_limits<double>::max()}

double rel = {0.005}

enum class sme::simulate::PixelIntegratorType

Values:

enumerator RK101

enumerator RK212

enumerator RK323

enumerator RK435

struct DuneOptions

Public Functions

template<class Archive> inline void serialize(Archive &ar, std::uint32_t const version)

Public Members

DuneDiscretizationType discretization = {DuneDiscretizationType::FEM1}

std::string integrator = {"Alexander2"}

double dt = {1e-1}

double minDt = {1e-10}

double maxDt = {1e4}

double increase = {1.5}

double decrease = {0.5}

bool writeVTKfiles = {false}

double newtonRelErr = {1e-8}

double newtonAbsErr = {0.0}

std::string linearSolver = {"RestartedGMRes"}

enum class sme::simulate::DuneDiscretizationType

Values:

enumerator FEM1

Optimization

class Optimization

Optimize model parameters.

Optimizes the supplied model parameters to minimize the supplied cost functions.

Public Functions

explicit Optimization(sme::model::Model &model)

Constructs an Optimization object from the supplied model.

Parameters:: model – [in] the model to optimize

std::size_t evolve(std::size_t n = 1): Do n iterations of parameter optimization.

bool applyParametersToModel(sme::model::Model *model) const: Apply the current best parameter values to the supplied model.

const std::vector<std::vector<double>> &getParams() const: The best set of parameters from each iteration.

std::vector<QString> getParamNames() const: The names of the parameters being optimized.

const std::vector<double> &getFitness() const: The best fitness from each iteration.

bool setBestResults(double fitness, std::vector<std::vector<double>> &&results)

Try to set a new set of best results for each target.

The best results are only updated if fitness is lower than the current bestResultsFitness

common::ImageStack getTargetImage(std::size_t index) const: Get an image of the a target.

std::optional<common::ImageStack> getUpdatedBestResultImage(std::size_t index): Get an image of the current best result for a target.

std::size_t getIterations() const: The number of completed evolve iterations.

bool getIsRunning() const: True if the optimization is currently running.

bool getIsStopping() const: True if requestStop() has been called.

void requestStop(): Stop the evolution as soon as possible.

const std::string &getErrorMessage() const: Returns a message if an error occurred - empty if no errors occurred.

OptimizationOptions

struct OptimizeOptions

Optimization options.

Public Functions

template<class Archive> inline void serialize(Archive &ar, std::uint32_t const version)

Public Members

OptAlgorithm optAlgorithm: The algorithm to use.

std::vector<OptParam> optParams: The parameters to optimize.

std::vector<OptCost> optCosts: The costs to minimize.

struct OptParam

Defines a parameter to be used in optimization.

Public Functions

template<class Archive> inline void serialize(Archive &ar, std::uint32_t const version)

Public Members

OptParamType optParamType: The type of parameter.

std::string name: The name of this OptParam as displayed to the user.

std::string id: The id of the parameter in the model.

std::string parentId: The id of the parent of the parameter in the model (optional)

double lowerBound: The lower bound on the allowed values of the parameter.

double upperBound: The upper bound on the allowed values of the parameter.

enum class sme::simulate::OptParamType

Types of model parameters that can be used in optimization.

Values:

enumerator ModelParameter

enumerator ReactionParameter

struct OptCost

Defines a cost function to be minimized.

Public Functions

template<class Archive> inline void serialize(Archive &ar, std::uint32_t const version)

Public Members

OptCostType optCostType: The type of cost function.

OptCostDiffType optCostDiffType: The type of difference (e.g. absolute, relative) used in the cost function.

std::string name: The name of this OptCost as displayed to the user.

std::string id: The id of the species in the model.

double simulationTime = {1.0}: The simulation time at which the cost function should be calculated.

double weight = {1.0}

The scale factor to multiply the cost by.

This assigns a relative weight to this cost when the optimization involves the sum of multiple cost functions.

std::size_t compartmentIndex: The index of the compartment containing the species.

std::size_t speciesIndex: The index of the species.

std::vector<double> targetValues

The target values to compare with the species concentration or dcdt.

Should contain a value for each pixel in the image, including those outside of the compartment the species is located in. If empty, the target values are assumed to be zero everywhere.

double epsilon = {1e-15}

A small number to avoid dividing by zero in relative differences.

A small value to be added to the denominator of relative differences to avoid numerical issues caused by dividing by zero.

enum class sme::simulate::OptCostType

Types of costs that can be used in optimization.

Values:

enumerator Concentration

enumerator ConcentrationDcdt

enum class sme::simulate::OptCostDiffType

Types of differences that can be used in costs.

Values:

enumerator Absolute

enumerator Relative

struct OptAlgorithm

Optimization algorithm options.

Public Functions

template<class Archive> inline void serialize(Archive &ar, std::uint32_t const version)

Public Members

OptAlgorithmType optAlgorithmType = {OptAlgorithmType::PSO}: The algorithm to use.

std::size_t islands = {1}: The number of islands.

std::size_t population = {2}: The population size in each island.

enum class sme::simulate::OptAlgorithmType

Types of algorithms that can be used in optimization.

Values:

enumerator PSO

enumerator GPSO

enumerator DE

enumerator iDE

enumerator jDE

enumerator pDE

enumerator ABC

enumerator gaco