actk.steps.raw package¶

Submodules¶

actk.steps.raw.raw module¶

class actk.steps.raw.raw.Raw(filepath_columns=['SourceReadPath', 'NucleusSegmentationReadPath', 'MembraneSegmentationReadPath'], metadata_columns=['FOVId'], **kwargs)[source]¶

Bases: datastep.step.Step

run(dataset: Union[str, pathlib.Path, pandas.core.frame.DataFrame, dask.dataframe.core.DataFrame], **kwargs)[source]¶

Simple passthrough to store the dataset in local_staging/raw. This does not copy any the image files to local_staging/raw, only the manifest. This is an optional step that will only run if you want to upload the raw data.

Parameters

dataset (Union[str, Path, pd.DataFrame, dd.DataFrame]) – The dataset to use for the rest of the pipeline run.

Required dataset columns: [“CellId”, “CellIndex”, “FOVId”, “SourceReadPath”, “NucleusSegmentationReadPath”, “MembraneSegmentationReadPath”, “ChannelIndexDNA”, “ChannelIndexMembrane”, “ChannelIndexStructure”, “ChannelIndexBrightfield”]

Returns

manifest_save_path – The path to the manifest in local_staging with the raw data.

Return type

Path

Module contents¶

class actk.steps.raw.Raw(filepath_columns=['SourceReadPath', 'NucleusSegmentationReadPath', 'MembraneSegmentationReadPath'], metadata_columns=['FOVId'], **kwargs)[source]¶