Source code for stlearn.adds.add_positions

from pathlib import Path

import pandas as pd
from anndata import AnnData




def positions(
    adata: AnnData,
    position_filepath: Path | str,
    scale_filepath: Path | str,
    quality: str = "low",
    copy: bool = False,
) -> AnnData | None:
    """\
    Adding spatial information into the Anndata object

    Parameters
    ----------
    adata
        Annotated data matrix.
    position_filepath
        Path to tissue_positions_list file.
    scale_filepath
        Path to scalefactors_json file.
    quality
        Choosing low or high resolution image.
    copy
        Return a copy instead of writing to adata.
    Returns
    -------
    Depending on `copy`, returns or updates `adata` with the following fields.
    **imagecol** and **imagerow** : `adata.obs` field
        Spatial information of the tissue image.
    """

    adata = adata.copy() if copy else adata

    tissue_positions = pd.read_csv(position_filepath, header=None)
    tissue_positions.columns = [
        "barcode",
        "tissue",
        "row",
        "col",
        "imagerow",
        "imagecol",
    ]
    import json

    with open(scale_filepath) as json_file:
        scale_factors = json.load(json_file)

    if quality == "low":
        tissue_positions["imagerow"] = (
            tissue_positions["imagerow"] * scale_factors["tissue_lowres_scalef"]
        )
        tissue_positions["imagecol"] = (
            tissue_positions["imagecol"] * scale_factors["tissue_lowres_scalef"]
        )
    elif quality == "high":
        tissue_positions["imagerow"] = (
            tissue_positions["imagerow"] * scale_factors["tissue_hires_scalef"]
        )
        tissue_positions["imagecol"] = (
            tissue_positions["imagecol"] * scale_factors["tissue_hires_scalef"]
        )

    tmp = adata.obs.merge(
        tissue_positions.reset_index().set_index(["barcode"]),
        left_index=True,
        right_index=True,
        how="left",
    ).reset_index()[["imagerow", "imagecol"]]

    adata.obs["imagerow"] = tmp["imagerow"].values
    adata.obs["imagecol"] = tmp["imagecol"].values

    return adata if copy else None