group_basic_metrics#

Workflow for grouping basic metrics.

Working location structure:

(name)
├── analysis
│   ├── analysis.BASIC_METRICS
│   │   └── (name)_(key).BASIC_METRICS.csv
│   └── analysis.POSITIONS
│       ├── (name)_(key)_(seed).POSITIONS.csv
│       └── (name)_(key)_(seed).POSITIONS.tar.xz
└── groups
    └── groups.BASIC_METRICS
        ├── (name).metrics_bins.(key).(time).(metric).csv
        ├── (name).metrics_distributions.(metric).json
        ├── (name).metrics_individuals.(key).(seed).(metric).json
        ├── (name).metrics_spatial.(key).(seed).(time).(metric).csv
        ├── (name).metrics_temporal.(key).(metric).json
        └── (name).population_counts.(time).csv

Different groups use inputs from results and analysis.POSITIONS. Grouped data are saved to groups.BASIC_METRICS.

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

Flows

`run_flow`	Main group basic metrics flow.
`run_flow_group_metrics_bins`	Group basic metrics subflow for binned metrics.
`run_flow_group_metrics_distributions`	Group basic metrics subflow for metrics distributions.
`run_flow_group_metrics_individuals`	Group basic metrics subflow for individual metrics.
`run_flow_group_metrics_spatial`	Group basic metrics subflow for spatial metrics.
`run_flow_group_metrics_temporal`	Group basic metrics subflow for temporal metrics.
`run_flow_group_population_counts`	Group basic metrics subflow for population counts.

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

Main group basic metrics flow.

Calls the following subflows, if the group is specified:

run_flow_group_metrics_bins()
run_flow_group_metrics_distributions()
run_flow_group_metrics_individuals()
run_flow_group_metrics_spatial()
run_flow_group_metrics_temporal()
run_flow_group_population_stats()

run_flow_group_metrics_bins(context: ContextConfig, series: SeriesConfig, parameters: ParametersConfigMetricsBins) → None[source]#: Group basic metrics subflow for binned metrics.

run_flow_group_metrics_distributions(context: ContextConfig, series: SeriesConfig, parameters: ParametersConfigMetricsDistributions) → None[source]#: Group basic metrics subflow for metrics distributions.

run_flow_group_metrics_individuals(context: ContextConfig, series: SeriesConfig, parameters: ParametersConfigMetricsIndividuals) → None[source]#: Group basic metrics subflow for individual metrics.

run_flow_group_metrics_spatial(context: ContextConfig, series: SeriesConfig, parameters: ParametersConfigMetricsSpatial) → None[source]#: Group basic metrics subflow for spatial metrics.

run_flow_group_metrics_temporal(context: ContextConfig, series: SeriesConfig, parameters: ParametersConfigMetricsTemporal) → None[source]#: Group basic metrics subflow for temporal metrics.

run_flow_group_population_counts(context: ContextConfig, series: SeriesConfig, parameters: ParametersConfigPopulationCounts) → None[source]#: Group basic metrics subflow for population counts.

Configs

`ContextConfig`	Context configuration for group basic metrics flow.
`ParametersConfig`	Parameter configuration for group basic metrics flow.
`ParametersConfigMetricsBins`	Parameter configuration for group basic metrics subflow - metrics bins.
`ParametersConfigMetricsDistributions`	Parameter configuration for group basic metrics subflow - metrics distributions.
`ParametersConfigMetricsIndividuals`	Parameter configuration for group basic metrics subflow - metrics individuals.
`ParametersConfigMetricsSpatial`	Parameter configuration for group basic metrics subflow - metrics spatial.
`ParametersConfigMetricsTemporal`	Parameter configuration for group basic metrics subflow - metrics temporal.
`ParametersConfigPopulationCounts`	Parameter configuration for group basic metrics subflow - population counts.
`SeriesConfig`	Series configuration for group basic metrics flow.

class ContextConfig[source]#

Context configuration for group basic metrics flow.

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

class ParametersConfig[source]#

Parameter configuration for group basic metrics flow.

groups: list[str]#: List of basic metrics groups.

metrics_bins: ParametersConfigMetricsBins = ParametersConfigMetricsBins(metrics=['count', 'volume', 'height'], seeds=[0], time=0, scale=1)#: Parameters for group metrics bins subflow.

metrics_distributions: ParametersConfigMetricsDistributions = ParametersConfigMetricsDistributions(metrics=['phase', 'volume', 'height'], seeds=[0], phases=['PROLIFERATIVE_G1', 'PROLIFERATIVE_S', 'PROLIFERATIVE_G2', 'PROLIFERATIVE_M', 'APOPTOTIC_EARLY', 'APOPTOTIC_LATE'], regions=['DEFAULT'], bounds={'volume.DEFAULT': [0, 6000], 'volume.NUCLEUS': [0, 2000], 'height.DEFAULT': [0, 21], 'height.NUCLEUS': [0, 21], 'phase.PROLIFERATIVE_G1': [0, 5], 'phase.PROLIFERATIVE_S': [0, 20], 'phase.PROLIFERATIVE_G2': [0, 40], 'phase.PROLIFERATIVE_M': [0, 2], 'phase.APOPTOTIC_EARLY': [0, 6], 'phase.APOPTOTIC_LATE': [0, 12]}, bandwidth={'volume.DEFAULT': 100, 'volume.NUCLEUS': 50, 'height.DEFAULT': 1, 'height.NUCLEUS': 1, 'phase.PROLIFERATIVE_G1': 0.25, 'phase.PROLIFERATIVE_S': 0.25, 'phase.PROLIFERATIVE_G2': 0.25, 'phase.PROLIFERATIVE_M': 0.25, 'phase.APOPTOTIC_EARLY': 0.25, 'phase.APOPTOTIC_LATE': 0.25}, threshold=0.2)#: Parameters for group metrics distributions subflow.

metrics_individuals: ParametersConfigMetricsIndividuals = ParametersConfigMetricsIndividuals(metrics=['volume', 'height'], seed=0, regions=['DEFAULT'])#: Parameters for group metrics individuals subflow.

metrics_spatial: ParametersConfigMetricsSpatial = ParametersConfigMetricsSpatial(metrics=['population', 'phase', 'volume', 'height'], seeds=[0], regions=['DEFAULT'], times=[0])#: Parameters for group metrics spatial subflow.

metrics_temporal: ParametersConfigMetricsTemporal = ParametersConfigMetricsTemporal(metrics=['count', 'population', 'phase', 'volume', 'height'], seeds=[0], regions=['DEFAULT'], populations=[1], phases=['PROLIFERATIVE_G1', 'PROLIFERATIVE_S', 'PROLIFERATIVE_G2', 'PROLIFERATIVE_M', 'APOPTOTIC_EARLY', 'APOPTOTIC_LATE'])#: Parameters for group metrics temporal subflow.

population_counts: ParametersConfigPopulationCounts = ParametersConfigPopulationCounts(seeds=[0], time=0)#: Parameters for group population counts subflow.

class ParametersConfigMetricsBins[source]#

Parameter configuration for group basic metrics subflow - metrics bins.

metrics: list[str]#: List of bin metrics.

seeds: list[int]#: Simulation seed(s) to use for grouping metric bins.

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

scale: float = 1#: Metric bin scaling.

class ParametersConfigMetricsDistributions[source]#

Parameter configuration for group basic metrics subflow - metrics distributions.

metrics: list[str]#: List of distribution metrics.

seeds: list[int]#: Simulation seed(s) to use for grouping metric distributions.

phases: list[str]#: List of cell cycle phases.

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

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

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

threshold: float = 0.2#: Threshold for separating phase durations (in hours).

class ParametersConfigMetricsIndividuals[source]#

Parameter configuration for group basic metrics subflow - metrics individuals.

metrics: list[str]#: List of individual metrics.

seed: int = 0#: Simulation seed to use for grouping individual metrics.

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

class ParametersConfigMetricsSpatial[source]#

Parameter configuration for group basic metrics subflow - metrics spatial.

metrics: list[str]#: List of spatial metrics.

seeds: list[int]#: Simulation seed(s) to use for grouping spatial metrics.

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

times: list[int]#: Simulation time(s) (in hours) to use for grouping spatial metrics.

class ParametersConfigMetricsTemporal[source]#

Parameter configuration for group basic metrics subflow - metrics temporal.

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

seeds: list[int]#: Simulation seed(s) to use for grouping temporal metrics.

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

populations: list[int]#: List of cell populations.

phases: list[str]#: List of cell cycle phases.

class ParametersConfigPopulationCounts[source]#

Parameter configuration for group basic metrics subflow - population counts.

seeds: list[int]#: Simulation seed(s) to use for grouping population counts.

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

class SeriesConfig[source]#

Series configuration for group basic metrics flow.

name: str#: Name of the simulation series.

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