make_simulation_movies#

Workflow for making simulation movies.

Working location structure:

(name)
├── data
│   └── data.LOCATIONS
│       └── (name)_(key)_(seed).LOCATIONS.tar.xz
├── movies
│   ├── movies.CENTROIDS
│   │   ├── (name)_(key)_(seed).CENTROIDS.gif
│   │   └── (name)_(key)_(seed)
│   │       └── (frame).CENTROIDS.png
│   └── movies.SCAN
│       ├── (name)_(key)_(seed)_(view)_(frame).SCAN.gif
│       └── (name)_(key)_(seed)_(view)_(frame)
│           └── (index).SCAN.png
└── results
    └── (name)_(key)_(seed).csv

Different formats use inputs from results and data.LOCATIONS. Movies are saved to movies.

Flows

`run_flow`	Main make simulation movies flow.
`run_flow_make_centroids_movie`	Make simulation movies subflow for centroids.
`run_flow_make_scan_movie`	Make simulation movies subflow for scan.

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

Main make simulation movies flow.

Calls the following subflows, if the format is specified.

run_flow_make_centroids_movie()
run_flow_make_scan_movie()

run_flow_make_centroids_movie(context: ContextConfig, series: SeriesConfig, parameters: ParametersConfigCentroids) → None[source]#: Make simulation movies subflow for centroids.

run_flow_make_scan_movie(context: ContextConfig, series: SeriesConfig, parameters: ParametersConfigScan) → None[source]#: Make simulation movies subflow for scan.

Configs

`ContextConfig`	Context configuration for make simulation movies flow.
`ParametersConfig`	Parameter configuration for make simulation movies flow.
`ParametersConfigCentroids`	Parameter configuration for make simulation movies flow - centroids.
`ParametersConfigScan`	Parameter configuration for make simulation movies flow - scan.
`SeriesConfig`	Series configuration for make simulation movies flow.

class ContextConfig[source]#

Context configuration for make simulation movies flow.

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

class ParametersConfig[source]#

Parameter configuration for make simulation movies flow.

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

scan: ParametersConfigScan = ParametersConfigScan(seeds=[0], frame_spec=(0, 1153, 1152), index_spec=(0, 1, 1), regions=['DEFAULT'], box=(1, 1, 1), view='top', x_bounds=(0, 1), y_bounds=(0, 1), region_colors={'DEFAULT': '#FF00FF', 'NUCLEUS': '#00FFFF'})#: Parameters for scan movie subflow.

centroids: ParametersConfigCentroids = ParametersConfigCentroids(seeds=[0], frame_spec=(0, 1, 1), x_bounds=(0, 1), y_bounds=(0, 1), dt=1.0, window=0)#: Parameters for centroids movie subflow.

class ParametersConfigCentroids[source]#

Parameter configuration for make simulation movies flow - centroids.

seeds: list[int]#: Simulation seeds to use for creating centroid movies.

frame_spec: tuple[int, int, int] = (0, 1, 1)#: Specification for simulation ticks to use for creating centroid movies.

x_bounds: tuple[int, int]#: Size of x bounds.

y_bounds: tuple[int, int]#: Size of y bounds.

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

window: int = 0#: Window size for centroid tail.

class ParametersConfigScan[source]#

Parameter configuration for make simulation movies flow - scan.

seeds: list[int]#: Simulation seeds to use for creating scan movies.

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

index_spec: tuple[int, int, int] = (0, 1, 1)#: Specification for contour indices to use for creating scan movies.

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

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

view: str = 'top'#: Projection view.

x_bounds: tuple[int, int]#: Size of x bounds.

y_bounds: tuple[int, int]#: Size of y bounds.

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

class SeriesConfig[source]#

Series configuration for make simulation movies flow.

name: str#: Name of the simulation series.

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