convert_arcade_format#

Workflow for converting ARCADE simulations to other formats.

Working location structure:

(name)
├── converted
│   ├── converted.COLORIZER
│   │   └── (name)_(key)_(seed)
│   │       ├── feature_(index).json
│   │       ├── frame_(index).png
│   │       ├── manifest.json
│   │       ├── outliers.json
│   │       ├── times.json
│   │       └── tracks.json
│   ├── converted.IMAGE
│   │   └── (name)_(key)_(seed)_(chunk)_(chunk).IMAGE.ome.tiff
│   ├── converted.MESH
│   │   └── (name)_(key)_(seed)_(tick)_(id)_(region).MESH.obj
│   ├── converted.PROJECTION
│   │   └── (name)_(key)_(seed)_(tick)_(regions).PROJECTION.png
│   └── converted.SIMULARIUM
│       └── (name)_(key)_(seed).simularium
├── data
│   ├── data.CELLS
│   │   └── (name)_(key)_(seed).CELLS.tar.xz
│   └── data.LOCATIONS
│       └── (name)_(key)_(seed).LOCATIONS.tar.xz
└── results
    └── (name)_(key)_(seed).csv

Different formats use inputs from results, data.CELLS, and data.LOCATIONS. Formatted data are saved to converted.

Flows

`run_flow`	Main convert ARCADE format flow.
`run_flow_convert_to_colorizer`	Convert ARCADE format subflow for colorizer.
`run_flow_convert_to_images`	Convert ARCADE format subflow for images.
`run_flow_convert_to_meshes`	Convert ARCADE format subflow for meshes.
`run_flow_convert_to_projections`	Convert ARCADE format subflow for projections.
`run_flow_convert_to_simularium_objects`	Convert ARCADE format subflow for Simularium with objects.
`run_flow_convert_to_simularium_shapes`	Convert ARCADE format subflow for Simularium with shapes.

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

Main convert ARCADE format flow.

Calls the following subflows, if the format is specified:

run_flow_convert_to_colorizer()
run_flow_convert_to_images()
run_flow_convert_to_meshes()
run_flow_convert_to_projections()
run_flow_convert_to_simularium_shapes()
run_flow_convert_to_simularium_objects()

run_flow_convert_to_colorizer(context: ContextConfig, series: SeriesConfig, parameters: ParametersConfigColorizer) → None[source]#: Convert ARCADE format subflow for colorizer.

run_flow_convert_to_images(context: ContextConfig, series: SeriesConfig, parameters: ParametersConfigImages) → None[source]#: Convert ARCADE format subflow for images.

run_flow_convert_to_meshes(context: ContextConfig, series: SeriesConfig, parameters: ParametersConfigMeshes) → None[source]#: Convert ARCADE format subflow for meshes.

run_flow_convert_to_projections(context: ContextConfig, series: SeriesConfig, parameters: ParametersConfigProjections) → None[source]#: Convert ARCADE format subflow for projections.

run_flow_convert_to_simularium_objects(context: ContextConfig, series: SeriesConfig, parameters: ParametersConfigSimulariumObjects) → None[source]#: Convert ARCADE format subflow for Simularium with objects.

run_flow_convert_to_simularium_shapes(context: ContextConfig, series: SeriesConfig, parameters: ParametersConfigSimulariumShapes) → None[source]#: Convert ARCADE format subflow for Simularium with shapes.

Configs

`ContextConfig`	Context configuration for convert ARCADE format flow.
`ParametersConfig`	Parameter configuration for convert ARCADE format flow.
`ParametersConfigColorizer`	Parameter configuration for convert ARCADE format flow - colorizer.
`ParametersConfigImages`	Parameter configuration for convert ARCADE format flow - images.
`ParametersConfigMeshes`	Parameter configuration for convert ARCADE format flow - meshes.
`ParametersConfigProjections`	Parameter configuration for convert ARCADE format flow - projections.
`ParametersConfigSimulariumObjects`	Parameter configuration for convert ARCADE format flow - simularium objects.
`ParametersConfigSimulariumShapes`	Parameter configuration for convert ARCADE format flow - simularium shapes.
`SeriesConfig`	Series configuration for convert ARCADE format flow.

class ContextConfig[source]#

Context configuration for convert ARCADE format flow.

working_location: str#: Location for input and output files (local path or S3 bucket).

class ParametersConfig[source]#

Parameter configuration for convert ARCADE format flow.

formats: list[str]#: List of convert formats.

colorizer: ParametersConfigColorizer = ParametersConfigColorizer(seeds=[0], frame_spec=(0, 1153, 1152), regions=['DEFAULT'], box=(1, 1, 1), ds=1.0, dt=1.0, chunk_size=500, features=['volume', 'height'])#: Parameters for colorizer subflow.

images: ParametersConfigImages = ParametersConfigImages(seeds=[0], frame_spec=(0, 1153, 1152), regions=['DEFAULT'], box=(1, 1, 1), chunk_size=500, binary=False, separate=False)#: Parameters for images subflow.

meshes: ParametersConfigMeshes = ParametersConfigMeshes(seeds=[0], frame_spec=(0, 1153, 1152), regions=['DEFAULT'], box=(1, 1, 1), invert=False)#: Parameters for meshes subflow.

projections: ParametersConfigProjections = ParametersConfigProjections(seeds=[0], frame_spec=(0, 1153, 1152), regions=['DEFAULT'], box=(1, 1, 1), ds=1.0, dt=1.0, scale=100, region_colors={'DEFAULT': '#FF00FF', 'NUCLEUS': '#00FFFF'})#: Parameters for projections subflow.

simularium_shapes: ParametersConfigSimulariumShapes = ParametersConfigSimulariumShapes(seeds=[0], frame_spec=(0, 1153, 1152), box=(1, 1, 1), ds=1.0, dt=1.0, phase_colors={'PROLIFERATIVE_G1': '#7F3C8D', 'PROLIFERATIVE_S': '#11A579', 'PROLIFERATIVE_G2': '#3969AC', 'PROLIFERATIVE_M': '#F2B701', 'APOPTOTIC_EARLY': '#E73F74', 'APOPTOTIC_LATE': '#80BA5A'}, resolution=0)#: Parameters for simularium shapes subflow.

simularium_objects: ParametersConfigSimulariumObjects = ParametersConfigSimulariumObjects(seeds=[0], frame_spec=(0, 1153, 1152), box=(1, 1, 1), ds=1.0, dt=1.0, phase_colors={'PROLIFERATIVE_G1': '#7F3C8D', 'PROLIFERATIVE_S': '#11A579', 'PROLIFERATIVE_G2': '#3969AC', 'PROLIFERATIVE_M': '#F2B701', 'APOPTOTIC_EARLY': '#E73F74', 'APOPTOTIC_LATE': '#80BA5A'}, url='', group_size=1)#: Parameters for simularium objects subflow.

class ParametersConfigColorizer[source]#

Parameter configuration for convert ARCADE format flow - colorizer.

seeds: list[int]#: Simulation seeds to use for converting to colorizer.

frame_spec: tuple[int, int, int] = (0, 1153, 1152)#: Specification for simulation ticks to use for converting to colorizer.

regions: list[str]#: List of subcellular regions.

box: tuple[int, int, int]#: Size of bounding box.

ds: float = 1.0#: Spatial scaling in units/um.

dt: float = 1.0#: Temporal scaling in hours/tick.

chunk_size: int = 500#: Image chunk size.

features: list[str]#: List of colorizer features.

class ParametersConfigImages[source]#

Parameter configuration for convert ARCADE format flow - images.

seeds: list[int]#: Simulation seeds to use for converting to images.

frame_spec: tuple[int, int, int] = (0, 1153, 1152)#: Specification for simulation ticks to use for converting to images.

regions: list[str]#: List of subcellular regions.

box: tuple[int, int, int]#: Size of bounding box.

chunk_size: int = 500#: Image chunk size.

binary: bool = False#: True to generate binary images, False otherwise.

separate: bool = False#: True to generate separate images for each tick, False otherwise.

class ParametersConfigMeshes[source]#

Parameter configuration for convert ARCADE format flow - meshes.

seeds: list[int]#: Simulation seeds to use for converting to meshes.

frame_spec: tuple[int, int, int] = (0, 1153, 1152)#: Specification for simulation ticks to use for converting to meshes.

regions: list[str]#: List of subcellular regions.

box: tuple[int, int, int]#: Size of bounding box.

invert: bool = False#: True if mesh should have inverted faces, False otherwise.

class ParametersConfigProjections[source]#

Parameter configuration for convert ARCADE format flow - projections.

seeds: list[int]#: Simulation seeds to use for converting to projections.

frame_spec: tuple[int, int, int] = (0, 1153, 1152)#: Specification for simulation ticks to use for converting to projections.

regions: list[str]#: List of subcellular regions.

box: tuple[int, int, int]#: Size of bounding box.

ds: float = 1.0#: Spatial scaling in units/um.

dt: float = 1.0#: Temporal scaling in hours/tick.

scale: int = 100#: Size of scale bar (in um).

region_colors: dict[str, str]#: Colors for each cell region.

class ParametersConfigSimulariumObjects[source]#

Parameter configuration for convert ARCADE format flow - simularium objects.

seeds: list[int]#: Simulation seeds to use for converting to simularium.

frame_spec: tuple[int, int, int] = (0, 1153, 1152)#: Specification for simulation ticks to use for converting to simularium.

box: tuple[int, int, int]#: Size of bounding box.

ds: float = 1.0#: Spatial scaling in units/um.

dt: float = 1.0#: Temporal scaling in hours/tick.

phase_colors: dict[str, str]#: Colors for each cell cycle phase.

url: str = ''#: URL for object files.

group_size: int = 1#: Mesh group size.

class ParametersConfigSimulariumShapes[source]#

Parameter configuration for convert ARCADE format flow - simularium shapes.

seeds: list[int]#: Simulation seeds to use for converting to simularium.

frame_spec: tuple[int, int, int] = (0, 1153, 1152)#: Specification for simulation ticks to use for converting to simularium.

box: tuple[int, int, int]#: Size of bounding box.

ds: float = 1.0#: Spatial scaling in units/um.

dt: float = 1.0#: Temporal scaling in hours/tick.

phase_colors: dict[str, str]#: Colors for each cell cycle phase.

resolution: int = 0#: Number of voxels represented by a sphere (0 for single sphere per cell).

class SeriesConfig[source]#

Series configuration for convert ARCADE format flow.

name: str#: Name of the simulation series.

conditions: list[dict]#: List of series condition dictionaries (must include unique condition “key”).