group_colony_dynamics#

Workflow for grouping colony dynamics.

Working location structure:

(name)
├── analysis
│   ├── analysis.MEASURES
│   │   └── (name)_(key).MEASURES.csv
│   └── analysis.COLONIES
│       └── (name)_(key).COLONIES.csv
└── groups
    └── groups.COLONIES
        ├── (name).feature_distributions.(feature).json
        ├── (name).feature_temporal.(key).(feature).json
        ├── (name).neighbor_positions.(key).(seed).(tick).csv
        └── (name).neighbor_positions.(key).(seed).(tick).(feature).csv

Different groups use inputs from analysis.COLONIES and analysis.MEASURES. Grouped data are saved to groups.COLONIES.

Different groups can be visualized using the corresponding plotting workflow or loaded into alternative tools.

Flows

`run_flow`	Main group colony dynamics flow.
`run_flow_group_colony_contours`	Group colony dynamics subflow for colony contours.
`run_flow_group_feature_distributions`	Group colony dynamics subflow for feature distributions.
`run_flow_group_feature_temporal`	Group colony dynamics subflow for temporal features.
`run_flow_group_neighbor_positions`	Group colony dynamics subflow for neighbor positions.

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

Main group colony dynamics flow.

Calls the following subflows, if the group is specified:

run_flow_group_colony_contours()
run_flow_group_feature_distributions()
run_flow_group_feature_temporal()
run_flow_group_neighbor_positions()

run_flow_group_colony_contours(context: ContextConfig, series: SeriesConfig, parameters: ParametersConfigColonyContours) → None[source]#: Group colony dynamics subflow for colony contours.

run_flow_group_feature_distributions(context: ContextConfig, series: SeriesConfig, parameters: ParametersConfigFeatureDistributions) → None[source]#: Group colony dynamics subflow for feature distributions.

run_flow_group_feature_temporal(context: ContextConfig, series: SeriesConfig, parameters: ParametersConfigFeatureTemporal) → None[source]#: Group colony dynamics subflow for temporal features.

run_flow_group_neighbor_positions(context: ContextConfig, series: SeriesConfig, parameters: ParametersConfigNeighborPositions) → None[source]#: Group colony dynamics subflow for neighbor positions.

Configs

`ContextConfig`	Context configuration for group colony dynamics flow.
`ParametersConfig`	Parameter configuration for group colony dynamics flow.
`ParametersConfigColonyContours`	Parameter configuration for group colony dynamics subflow - colony contours.
`ParametersConfigFeatureDistributions`	Parameter configuration for group colony dynamics subflow - feature distributions.
`ParametersConfigFeatureTemporal`	Parameter configuration for group colony dynamics subflow - feature temporal.
`ParametersConfigNeighborPositions`	Parameter configuration for group colony dynamics subflow - neighbor positions.
`SeriesConfig`	Series configuration for group colony dynamics flow.

class ContextConfig[source]#

Context configuration for group colony dynamics flow.

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

class ParametersConfig[source]#

Parameter configuration for group colony dynamics flow.

groups: list[str]#: List of colony dynamics groups.

colony_contours: ParametersConfigColonyContours = ParametersConfigColonyContours(regions=['DEFAULT'], seed=0, time=0, ds=None, dt=None, projection='top', box=(1, 1, 1), slice_index=None)#: Parameters for group colony contours subflow.

feature_distributions: ParametersConfigFeatureDistributions = ParametersConfigFeatureDistributions(features=['degree', 'eccentricity', 'degree_centrality', 'closeness_centrality', 'betweenness_centrality'], bounds={'degree': [-1, 30], 'eccentricity': [-1, 15], 'degree_centrality': [-0.1, 1], 'closeness_centrality': [-0.1, 1], 'betweenness_centrality': [-0.1, 1]}, bandwidth={'degree': 1, 'eccentricity': 1, 'degree_centrality': 0.05, 'closeness_centrality': 0.05, 'betweenness_centrality': 0.05})#: Parameters for group feature distributions subflow.

feature_temporal: ParametersConfigFeatureTemporal = ParametersConfigFeatureTemporal(features=['degree', 'eccentricity', 'degree_centrality', 'closeness_centrality', 'betweenness_centrality', 'radius', 'diameter'])#: Parameters for group feature temporal subflow.

neighbor_positions: ParametersConfigNeighborPositions = ParametersConfigNeighborPositions(features=['depth', 'group'], seed=0, ticks=[0])#: Parameters for group neighbor positions subflow.

class ParametersConfigColonyContours[source]#

Parameter configuration for group colony dynamics subflow - colony contours.

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

seed: int = 0#: Simulation random seed to use for grouping colony contours.

time: int = 0#: Simulation time (in hours) to use for grouping colony contours.

ds: float | None = None#: Spatial scaling in units/um.

dt: float | None = None#: Temporal scaling in hours/tick.

projection: str = 'top'#: Selected colony projection.

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

slice_index: int | None = None#: Slice index along the colony projection axis.

class ParametersConfigFeatureDistributions[source]#

Parameter configuration for group colony dynamics subflow - feature distributions.

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

bounds: dict[str, list]#: Bounds for feature distributions.

bandwidth: dict[str, float]#: Bandwidths for feature distributions.

class ParametersConfigFeatureTemporal[source]#

Parameter configuration for group colony dynamics subflow - feature temporal.

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

class ParametersConfigNeighborPositions[source]#

Parameter configuration for group colony dynamics subflow - neighbor positions.

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

seed: int = 0#: Simulation seed to use for grouping neighbor positions.

ticks: list[int]#: Simulation ticks to use for grouping neighbor positions.

class SeriesConfig[source]#

Series configuration for group colony dynamics flow.

name: str#: Name of the simulation series.

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