Core

getMonadIDs(args...)

Deprecated alias for monadIDs. Use monadIDs instead.

getSimulationIDs(args...)

Deprecated alias for simulationIDs. Use simulationIDs instead.

initializeModelManager()
initializeModelManager(path_to_project_dir::AbstractString)
initializeModelManager(path_to_physicell::AbstractString, path_to_data::AbstractString)

Initialize the PhysiCellModelManager.jl project model manager, identifying the data folder, PhysiCell folder, and loading the central database.

If no arguments are provided, it assumes that the PhysiCell and data directories are in the current working directory.

Arguments

• path_to_project_dir::AbstractString: Path to the project directory as either an absolute or relative path. This folder must contain the PhysiCell and data directories.
• path_to_physicell::AbstractString: Path to the PhysiCell directory as either an absolute or relative path.
• path_to_data::AbstractString: Path to the data directory as either an absolute or relative path.

monadIDs()

Return a vector of all monad IDs in the database.

Alternate forms take a monad, sampling, or trial object (or an array of any combination of them) and return the corresponding monad IDs.

Examples

monadIDs() # all monad IDs in the database
monadIDs(monad) # just a vector with the monad ID, i.e. [monad.id]
monadIDs(sampling) # all monad IDs in a sampling
monadIDs(trial) # all monad IDs in a trial
monadIDs([trial1, trial2]) # all monad IDs between trial1 and trial2

setNumberOfParallelSims(n::Int)

Set the maximum number of parallel simulations to n.

simulationIDs()

Return a vector of all simulation IDs in the database.

Alternate forms take a simulation, monad, sampling, or trial object (or an array of any combination of them) and return the corresponding simulation IDs.

Examples

simulationIDs() # all simulation IDs in the database
simulationIDs(simulation) # just a vector with the simulation ID, i.e. [simulation.id]
simulationIDs(monad) # all simulation IDs in a monad
simulationIDs(sampling) # all simulation IDs in a sampling
simulationIDs(trial) # all simulation IDs in a trial
simulationIDs([trial1, trial2]) # all simulation IDs between trial1 and trial2

PCMMMissingProject

An exception type for when a PhysiCellModelManager.jl project cannot be found during initialization.

Fields

• msg::String: The error message.

baseToExecutable(s::String)

Convert a string to an executable name based on the operating system. If the operating system is Windows, append ".exe" to the string.

constituentIDs(T::AbstractTrial)
constituentIDs(::Type{T}, id::Int) where {T<:AbstractTrial}

Read a CSV file containing constituent IDs from T and return them as a vector of integers.

For a trial, this is the sampling IDs. For a sampling, this is the monad IDs. For a monad, this is the simulation IDs.

Examples

ids = constituentIDs(Sampling(1)) # read the IDs of the monads in sampling 1
ids = constituentIDs(Sampling, 1) # identical to above but does not need to create the Sampling object

ids = constituentIDs(Monad, 1) # read the IDs of the simulations in monad 1
ids = constituentIDs(Trial, 1) # read the IDs of the samplings in trial 1

constituentType(T::Type{<:AbstractTrial})
constituentType(T::AbstractTrial)

Return the type of the constituents of T. Used in the constituentIDs function.

constituentTypeFilename(T::Type{<:AbstractTrial})
constituentTypeFilename(T::AbstractTrial)

Return the filename of the constituents of T. Used in the constituentIDs function.

lowerClassString(T::AbstractTrial)
lowerClassString(T::Type{<:AbstractTrial})

Return the lowercase string representation of the type of T, excluding the module name. Without this, it may return, e.g., Main.PhysiCellModelManager.Sampling.

Examples

lowerClassString(Simulation) # "simulation"
lowerClassString(Simulation(1)) # "simulation"

pcmmLogo()

Return a string representation of the awesome PhysiCellModelManager.jl logo.

samplingSimulationIDs(sampling_id::Int)

Internal function to get the simulation IDs for a given sampling ID. Users should use simulationIDs instead.

setMarchFlag(flag::String)

Set the march flag to flag. Used for compiling the PhysiCell code.

trialFolder(T::Type{<:AbstractTrial})

Return the path to the folder for the AbstractTrial object, T.

Examples

simulation = Simulation(1)
trialFolder(Simulation)
# output
"abs/path/to/data/outputs/simulations/1"

trialFolder(T::Type{<:AbstractTrial}, id::Int)

Return the path to the folder for a given subtype of AbstractTrial and ID.

Examples

trialFolder(Simulation, 1)
# output
"abs/path/to/data/outputs/simulations/1"

trialMonads(trial_id::Int)

Internal function to get the monad IDs for a given trial ID. Users should use monadIDs instead.

trialSimulationIDs(trial_id::Int)

Internal function to get the simulation IDs for a given trial ID. Users should use simulationIDs instead.