Config Schema

The config file controls the packing behavior. It specifies parameters such as packing algorithms, output formats, performance settings, and debugging options that don’t affect the biological content but control how the simulation is executed.

Field Path	Type	Description	Default Value	Notes
clean_grid_cache	boolean	Clear cached grid before packing	False
format	string	Output format	simularium
inner_grid_method	string	Method used to create the inner grid	trimesh	e.g., trimesh, raytrace
live_packing	boolean	Enable real-time packing visualization	False	Not implemented currently
load_from_grid_file	boolean	Load objects from a grid file	False
name	string	Name of the config	default	Used to identify this config run
number_of_packings	number (>=1)	Number of independent packing replicates	1
open_results_in_browser	boolean	Open results in browser after run	True
ordered_packing	boolean	Use deterministic packing order	False
out	string	Output directory path	"out/"
overwrite_place_method	boolean	Override object-specific place methods	False
parallel	boolean	Enable parallel packing	False
place_method	string	Default packing method	spheresSST	e.g., jitter, spheresSST
randomness_seed	number	Random seed value	None	Helps reproduce packing runs
save_analyze_result	boolean	Save packing analysis result	False	Saves additional data and figures from packing.
save_converted_recipe	boolean	Export converted recipe	False	Save recipe converted from older to newer versions.
save_gradient_data_as_image	boolean	Save gradient values as image	False
save_plot_figures	boolean	Save analysis figures
show_grid_plot	boolean	Display grid visualization	False
show_progress_bar	boolean	Show progress bar in terminal	False
show_sphere_trees	boolean	Visualize sphere trees	False
spacing	number	Override object spacing	None
upload_results	boolean	Upload results to S3	True
use_periodicity	boolean	Enable periodic boundary conditions	False
version	number	Config version number	1.0	For internal tracking
image_export_options.hollow	boolean	Export hollow images	False
image_export_options.projection_axis	string	Camera position for projection axis	z	e.g., x, y, z
image_export_options.voxel_size	array [x, y, z]	Voxel size for image export		[1, 1, 1]

Example:

{
    "name": "example",
    "out": "path/to/output/folder",
    "save_analyze_result": true,
    "show_progress_bar": true,
    "save_plot_figures": false,
    "load_from_grid_file": true,
    "spacing": 2,
    "image_export_options": {
        "hollow": false,
        "voxel_size": [
            1,
            1,
            1
        ],
        "projection_axis": "z"
    },
    "open_results_in_browser": false,
    "upload_results": false
}