PhysiCell Studio

runStudio(simulation_id::Int; python_path::Union{Missing,String}=pcvct_globals.path_to_python, studio_path::Union{Missing,String}=pcvct_globals.path_to_studio)

Launch PhysiCell Studio for a given simulation.

Creates temporary config and rules files to avoid overwriting the original files in the output folder. The intent of this function is to allow users to visualize the results of a simulation with Studio, rather than to modify the simulation itself.

The path to the python executable and the Studio folder must be set. When calling using pcvct, shell environment variables PCVCT_PYTHON_PATH and PCVCT_STUDIO_PATH will be used to set the path to the python executable and the Studio folder, respectively. Note: these should match how you would run PhysiCell Studio from the command line, e.g.: export PCVCT_PYTHON_PATH=python.

If the paths are not set in the environment, they can be passed as the keyword arguments python_path and studio_path to this function. In this case, the paths will be set as global variables for the duration of the Julia session and do not need to be passed again.

cleanUpStudioInputs(path_to_temp_xml::String, path_to_input_rules::Union{Nothing,String})

Clean up the temporary files created for PhysiCell Studio.

executeStudio(path_to_temp_xml::String)

Run PhysiCell Studio with the given temporary XML file.

resolveStudioGlobals(python_path::Union{Missing,String}, studio_path::Union{Missing,String})

Set the global variables path_to_python and path_to_studio to the given paths.

They are required to not be missing so that the function runStudio works.

setUpStudioInputs(simulation_id::Int)

Set up the inputs for PhysiCell Studio. Creates a temporary XML file and a temporary rules file (if applicable) in the output folder of the simulation.