process_sample#

Workflow for processing image samples.

Working location structure:

(name)
├── plots
│   └── plots.SAMPLE
│       └── (name)_(key).SAMPLE.png
└── samples
    ├── samples.PROCESSED
    │   └── (name)_(key).PROCESSED.csv
    └── samples.RAW
        └── (name)_(key).RAW.csv

Samples to be processed are loaded from samples.RAW. Resulting processed sample(s) are placed into samples.PROCESSED and corresponding contact sheet(s) are placed into plots.SAMPLE. Note that these contact sheet(s) will overwrite existing contact sheets generated by the sample images task.

Flows

run_flow

Main process sample flow.

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

Configs

`ContextConfig`	Context configuration for process sample flow.
`ParametersConfig`	Parameter configuration for process sample flow.
`SeriesConfig`	Series configuration for process sample flow.

class ContextConfig[source]#

Context configuration for process sample flow.

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

class ParametersConfig[source]#

Parameter configuration for process sample flow.

key: str#: Sample key to process.

remove_unconnected: bool = True#: True to remove unconnected regions, False otherwise.

unconnected_threshold: float = 2.0#: Distance for removing unconnected regions.

unconnected_filter: str = 'connectivity'#: Filter type for assigning unconnected coordinates.

remove_edges: bool = True#: True to remove cells touching the edge of the bounds, False otherwise.

edge_threshold: int = 1#: Number of edge positions per axis needed to assign edge region.

edge_padding: float = 1.0#: Distance from axis limits to assign edge positions.

include_ids: list[int] | None = None#: List of ids to include.

exclude_ids: list[int] | None = None#: List of ids to exclude.

contact_sheet: bool = True#: True to save contact sheet of processed samples, False otherwise.

class SeriesConfig[source]#

Series configuration for process sample flow.

name: str#: Name of the simulation series.