calculate_properties#

Workflow for calculating shape properties.

Working location structure:

(name)
├── data
│   └── data.LOCATIONS
│       └── (name)_(key)_(seed).LOCATIONS.tar.xz
└── calculations
    └── calculations.PROPERTIES
        ├── (name)_(key)_(seed)_(tick).PROPERTIES.csv
        └── (name)_(key)_(seed)_(tick)_(region).PROPERTIES.csv

Data from data.LOCATIONS are used to calculate properties, which are saved to calculations.PROPERTIES.

If region is specified, the region is included in the output key. For calculations with offset but no chunking, the output key extension starts with .(offset). to specify the index offset. For calculations with chunking, the output key extension starts with .(offset).(chunk). to specify the index offset and chunk size.

Flows

run_flow

Main calculate properties flow.

run_flow(context: ContextConfig, series: SeriesConfig, parameters: ParametersConfig) → None[source]#: Main calculate properties flow.

Configs

`ContextConfig`	Context configuration for calculate properties flow.
`ParametersConfig`	Parameter configuration for calculate properties flow.
`SeriesConfig`	Series configuration for calculate properties flow.

class ContextConfig[source]#

Context configuration for calculate properties flow.

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

class ParametersConfig[source]#

Parameter configuration for calculate properties flow.

key: str#: Simulation key to calculate.

seed: int#: Simulation random seed to calculate.

tick: int#: Simulation tick to calculate.

offset: int = 0#: Index offset for skipped calculations.

chunk: int | None = None#: Number of indices to calculate, starting from offset.

region: str | None = None#: Subcellular region to calculate.

properties: list[str]#: List of shape properties to calculate.

class SeriesConfig[source]#

Series configuration for calculate properties flow.

name: str#: Name of the simulation series.