actk.steps.single_cell_features package¶

Submodules¶

actk.steps.single_cell_features.single_cell_features module¶

class actk.steps.single_cell_features.single_cell_features.SingleCellFeatures(direct_upstream_tasks=[<class 'actk.steps.standardize_fov_array.standardize_fov_array.StandardizeFOVArray'>], filepath_columns=['CellFeaturesPath'], **kwargs)[source]¶

Bases: datastep.step.Step

run(dataset: Union[str, pathlib.Path, pandas.core.frame.DataFrame, dask.dataframe.core.DataFrame], cell_ceiling_adjustment: int = 0, distributed_executor_address: Optional[str] = None, batch_size: Optional[int] = None, overwrite: bool = False, **kwargs)[source]¶

Provided a dataset generate a features JSON file for each cell.

Parameters

dataset (Union[str, Path, pd.DataFrame, dd.DataFrame]) – The primary cell dataset to use for generating features JSON for each cell.

Required dataset columns: [“CellId”, “CellIndex”, “FOVId”, “StandardizedFOVPath”]
cell_ceiling_adjustment (int) – The adjust to use for raising the cell shape ceiling. If <= 0, this will be ignored and cell data will be selected but not adjusted. Default: 0
distributed_executor_address (Optional[str]) – An optional executor address to pass to some computation engine. Default: None
batch_size (Optional[int]) – An optional batch size to process n features at a time. Default: None (Process all at once)
overwrite (bool) – If this step has already partially or completely run, should it overwrite the previous files or not. Default: False (Do not overwrite or regenerate files)

Returns

manifest_save_path – Path to the produced manifest with the CellFeaturesPath column added.

Return type

Path

class actk.steps.single_cell_features.single_cell_features.SingleCellFeaturesError(cell_id, error)[source]¶

Bases: tuple

Create new instance of SingleCellFeaturesError(cell_id, error)

cell_id¶: Alias for field number 0

error¶: Alias for field number 1

class actk.steps.single_cell_features.single_cell_features.SingleCellFeaturesResult(cell_id, path)[source]¶