convert_physicell_format#

Workflow for converting PhysiCell simulations to other formats.

Working location structure:

(name)
├── converted
│   └── converted.SIMULARIUM
│       └── (name)_(key)_(seed).simularium
└── data
    └── (name)_(key)_(seed).tar.xz

Formatted data are saved to converted.

Flows

run_flow

Main convert PhysiCell format flow.

run_flow_convert_to_simularium

Convert PhysiCell format subflow for Simularium.
run_flow(context: ContextConfig, series: SeriesConfig, parameters: ParametersConfig) → None[source]#

Main convert PhysiCell format flow.

run_flow_convert_to_simularium(context: ContextConfig, series: SeriesConfig, parameters: ParametersConfig) → None[source]#

Convert PhysiCell format subflow for Simularium.

Configs

ContextConfig

Context configuration for convert PhysiCell format flow.

ParametersConfig

Parameter configuration for convert PhysiCell format flow.

SeriesConfig

Series configuration for convert PhysiCell format flow.
class ContextConfig[source]#

Context configuration for convert PhysiCell format flow.

working_location: str#

Location for input and output files (local path or S3 bucket).

class ParametersConfig[source]#

Parameter configuration for convert PhysiCell format flow.

box_size: tuple[float, float, float] = (1.0, 1.0, 1.0)#

Size of bounding box.

timestep: float = 1.0#

Simulation timestep.

formats: list[str]#

List of convert formats.

substrate_color: str = '#d0c5c8'#

Color for substrate.

cell_colors: list[str]#

Colors for individual cells.

frame_spec: tuple[int, int, int] = (0, 1, 1)#

Specification for simulation ticks to use for converting to simularium.

class SeriesConfig[source]#

Series configuration for convert PhysiCell format flow.

name: str#

Name of the simulation series.

seeds: list[int]#

List of series random seeds.

conditions: list[dict]#

List of series condition dictionaries (must include unique condition “key”).