actk.steps.standardize_fov_array package¶

Submodules¶

actk.steps.standardize_fov_array.standardize_fov_array module¶

class actk.steps.standardize_fov_array.standardize_fov_array.StandardizeFOVArray(filepath_columns=['StandardizedFOVPath'], **kwargs)[source]¶

Bases: datastep.step.Step

run(dataset: Union[str, pathlib.Path, pandas.core.frame.DataFrame, dask.dataframe.core.DataFrame], current_pixel_sizes: Optional[Tuple[float]] = (0.10833333333333332, 0.10833333333333332, 0.29), desired_pixel_sizes: Tuple[float] = (0.29, 0.29, 0.29), distributed_executor_address: Optional[str] = None, batch_size: Optional[int] = None, overwrite: bool = False, **kwargs) → pathlib.Path[source]¶

Convert a dataset of raw FOV images and their nucleus and membrane segmentations, into a single, standard order and shape, and normalized image.

Parameters

dataset (Union[str, Path, pd.DataFrame, dd.DataFrame]) – The dataset to use for generating standard order, normalized, image arrays.

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

current_pixel_sizes: Optional[Tuple[float]]: The current physical pixel sizes as a tuple of the raw image. Default: (0.10833333333333332, 0.10833333333333332, 0.29), though if None, uses (aicsimageio.AICSImage.get_physical_pixel_size on the raw image)
desired_pixel_sizes: Tuple[float]: The desired pixel size for to resize each image to in XYZ order. Default: (0.29, 0.29, 0.29)
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 StandardizedFOVPath column added.
Return type: Path

class actk.steps.standardize_fov_array.standardize_fov_array.StandardizeFOVArrayError(fov_id, error)[source]¶

Bases: tuple

Create new instance of StandardizeFOVArrayError(fov_id, error)

error¶: Alias for field number 1

fov_id¶: Alias for field number 0

class actk.steps.standardize_fov_array.standardize_fov_array.StandardizeFOVArrayResult(fov_id, path)[source]¶