parse_physicell_simulations#

Workflow for parsing PhysiCell simulations into tidy data.

Working location structure:

(name)
├── data
│   └── (name)_(key)_(seed).tar.xz
└── results
    └── (name)_(key)_(seed).csv

Data from data are parsed into results.

Flows

Main parse physicell simulations flow.

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

Configs

`ContextConfig`	Context configuration for parse physicell simulations flow.
`ParametersConfig`	Parameter configuration for parse physicell simulations flow.
`SeriesConfig`	Series configuration for parse physicell simulations flow.

class ContextConfig[source]#

Context configuration for parse physicell simulations flow.

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

manifest_location: str#: Location of manifest file (local path or S3 bucket).

class ParametersConfig[source]#

Parameter configuration for parse physicell simulations flow.

include_filters: list[str]#: List of Unix filename patterns for files to include in parsing.

exclude_filters: list[str]#: List of Unix filename patterns for files to exclude from parsing.

class SeriesConfig[source]#

Series configuration for parse physicell simulations flow.