actk.steps.diagnostic_sheets package¶

Submodules¶

actk.steps.diagnostic_sheets.diagnostic_sheets module¶

class actk.steps.diagnostic_sheets.diagnostic_sheets.DiagnosticSheetError(cell_id, error)[source]¶

Bases: tuple

Create new instance of DiagnosticSheetError(cell_id, error)

cell_id¶: Alias for field number 0

error¶: Alias for field number 1

class actk.steps.diagnostic_sheets.diagnostic_sheets.DiagnosticSheetResult(cell_id, save_path)[source]¶

Bases: tuple

Create new instance of DiagnosticSheetResult(cell_id, save_path)

cell_id¶: Alias for field number 0

save_path¶: Alias for field number 1

class actk.steps.diagnostic_sheets.diagnostic_sheets.DiagnosticSheets(direct_upstream_tasks: List[Step] = [<class 'actk.steps.single_cell_images.single_cell_images.SingleCellImages'>], filepath_columns=['DiagnosticSheetPath'], **kwargs)[source]¶

Bases: datastep.step.Step

run(dataset: Union[str, pathlib.Path, pandas.core.frame.DataFrame, dask.dataframe.core.DataFrame], max_cells: int = 200, metadata: Union[list, str, None] = 'FOVId', feature: Optional[str] = None, fig_width: Optional[int] = None, fig_height: Optional[int] = None, distributed_executor_address: Optional[str] = None, batch_size: Optional[int] = None, overwrite: bool = False, **kwargs)[source]¶

Provided a dataset of single cell all projection images, generate a diagnostic sheet grouped by desired metadata and feature

Parameters

dataset (Union[str, Path, pd.DataFrame, dd.DataFrame]) – The primary cell dataset to use for generating diagnistic sheet for a group of cells.

Required dataset columns: [“CellId”, “CellImage2DAllProjectionsPath”]
max_cells (int) – The maximum number of cells to display on a single diagnostic sheet. Deafult: 200
metadata (Optional[Union[list, str]]) – The metadata to group cells and generate a diagnostic sheet. For example, “FOVId” or “[“FOVId”, “ProteinDisplayName”]” Default: “FOVId”
feature (Optional[str]) – The name of the single cell feature to display. For example, “imsize_orig”.
fig_width (Optional[int]) – Width of the diagnostic sheet figure.
fig_height (Optional[int]) – Height of the diagnostic sheet figure.
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 DiagnosticSheetPath column added.

Return type

Path

Module contents¶

class actk.steps.diagnostic_sheets.DiagnosticSheets(direct_upstream_tasks: List[Step] = [<class 'actk.steps.single_cell_images.single_cell_images.SingleCellImages'>], filepath_columns=['DiagnosticSheetPath'], **kwargs)[source]¶