simulariumio.physicell package

Subpackages

• simulariumio.physicell.dep package
  • Submodules
  • simulariumio.physicell.dep.pyMCDS module
    • pyMCDS
      • pyMCDS.get_2D_mesh()
      • pyMCDS.get_cell_df()
      • pyMCDS.get_cell_df_at()
      • pyMCDS.get_cell_variables()
      • pyMCDS.get_concentrations()
      • pyMCDS.get_concentrations_at()
      • pyMCDS.get_containing_voxel_ijk()
      • pyMCDS.get_linear_voxels()
      • pyMCDS.get_mesh()
      • pyMCDS.get_mesh_spacing()
      • pyMCDS.get_substrate_names()
      • pyMCDS.get_time()
  • Module contents

Submodules

simulariumio.physicell.physicell_converter module

class simulariumio.physicell.physicell_converter.PhysicellConverter(input_data: PhysicellData, progress_callback: Callable[[float], None] | None = None, callback_interval: float = 10)

Bases: TrajectoryConverter

This object reads simulation trajectory outputs from PhysiCell (http://physicell.org/) and plot data and writes them in the JSON format used by the Simularium viewer

Parameters:

input_dataPhysicellData

An object containing info for reading PhysiCell simulation trajectory outputs and plot data

progress_callbackCallable[[float], None] (optional)

Callback function that accepts 1 float argument and returns None which will be called at a given progress interval, determined by callback_interval requested, providing the current percent progress Default: None

callback_intervalfloat (optional)

If a progress_callback was provided, the period between updates to be sent to the callback, in seconds Default: 10

simulariumio.physicell.physicell_data module

class simulariumio.physicell.physicell_data.PhysicellData(timestep: float, path_to_output_dir: str, meta_data: MetaData | None = None, nth_timestep_to_read: int = 1, display_data: Dict[int, DisplayData] | None = None, phase_names: Dict[int, Dict[int, str]] | None = None, max_owner_cells: int = -1, owner_cell_display_name: str = 'cell', time_units: UnitData | None = None, plots: List[Dict[str, Any]] | None = None)

Bases: object

This object holds simulation trajectory outputs from PhysiCell (http://physicell.org/) and plot data

Parameters:

timestepfloat

A float amount of time that passes each step

path_to_output_dirstring

A string path to the PhysiCell output directory containing MultiCellDS XML and MATLAB files

meta_dataMetaData (optional)

An object containing metadata for the trajectory including box size, scale factor, and camera defaults

nth_timestep_to_read: int (optional)

Visualize every Nth timestep e.g. if 10, only every 10th timestep will be visualized Default: 1

display_dataDict[int, DisplayData] (optional)

The cell type ID from PhysiCell data mapped to DisplayData, including names and display info to use for rendering that agent type in the Simularium Viewer Default: for names, “cell[cell type ID from PhysiCell data]”,

for radius, calculate from cell’s volume, for rendering, use default representations and colors

phase_namesDict[int, Dict[int, str]] (optional)

the cell type ID from PhysiCell data mapped to display names for phases of that type Default: “phase[cell phase ID from PhysiCell data]”

max_owner_cellsint (optional)

MAX_OWNER_CELLS constant from PhysiCell OwnerCell module. Every cell with ID >= this will be displayed as part of a group of subcell spheres Default: all cells will be rendered as individual spheres

owner_cell_display_namestr (optional)

Display name for cells that are rendered as groups of spheres Default: “cell”

time_units: UnitData (optional)

multiplier and unit name for time values Default: 1.0 second

plotsList[Dict[str, Any]] (optional)

An object containing plot data already in Simularium format

display_data: Dict[int, DisplayData]

max_owner_cells: int

meta_data: MetaData

nth_timestep_to_read: int

owner_cell_display_name: str

path_to_output_dir: str

phase_names: Dict[int, Dict[int, str]]

plots: List[Dict[str, Any]]

time_units: UnitData

timestep: float

Module contents