calculate_image_properties#

Workflow for calculating shape properties from existing images.

Working location structure:

(name)
├── results
│   └── (name)_(key)_(seed).csv
└── calculations
    └── calculations.PROPERTIES
        ├── (name)_(key)_(seed)_(tick).PROPERTIES.csv
        └── (name)_(key)_(seed)_(tick)_(region).PROPERTIES.csv

Data from results are used to specify existing images, which are then used to calculate properties. Calculations are saved to calculations.PROPERTIES.

If region is specified, the region is included in the output key.

Flows

run_flow

Main calculate image properties flow.

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

Configs

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

class ContextConfig[source]#

Context configuration for calculate image properties flow.

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

class ParametersConfig[source]#

Parameter configuration for calculate image properties flow.

key: str#: Simulation key to calculate.

seed: int#: Simulation random seed to calculate.

tick: int#: Simulation tick to calculate.

channel: int#: Index of channel to calculate.

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

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

class SeriesConfig[source]#

Series configuration for calculate image properties flow.

name: str#: Name of the simulation series.