Source code for locan.scripts.script_rois

#!/usr/bin/env python

"""
Define regions of interest with napari and save as roi files.

With this script you can choose a file name, open the localization file in napari.
Draw regions of interest as additional shapes in napari.
Upon closing napari each shape is taken as single roi and saved as _roi.yaml file.

To run the script::

    locan rois -f <file> -t <file type> -i <roi file indicator> --bin_size <>
    --rescale <string with tuple or rescale>

Try for instance::

    locan rois -f "locan/tests/test_data/five_blobs.txt" -t 1 -i "_roi" --bin_size 10

See Also
--------
locan.visualize.render_napari.utilities.select_by_drawing_napari
"""
from __future__ import annotations

import argparse
import os
from pathlib import Path
from typing import Any

import locan.locan_io.locdata.io_locdata as io
from locan.constants import FileType
from locan.data import metadata_pb2
from locan.dependencies import HAS_DEPENDENCY
from locan.gui.io import file_dialog
from locan.scripts.utilities import _type_converter_rescale
from locan.visualize.render_napari.utilities import select_by_drawing_napari

if HAS_DEPENDENCY["napari"]:
    import napari




def sc_draw_roi_napari(
    file_path: str | os.PathLike[Any] | None = None,
    file_type: int | str | FileType | metadata_pb2.Metadata = FileType.CUSTOM,
    roi_file_indicator: str = "_roi",
    **kwargs: Any,
) -> list[Path]:
    """
    Define regions of interest by drawing a boundary.

    Parameters
    ----------
    file_path
        File path to localization data.
    file_type
        Indicator for the file type.
        Integer or string should be according to locan.constants.FileType.
    roi_file_indicator
        Indicator to add to the localization file name and use as roi file
        name (with further extension .yaml).
    kwargs
        Other parameters passed to :func:`render_2d_napari`.

    Returns
    -------
    list[Path]
        File paths for all roi files
    """
    # choose file interactively
    if file_path is None:
        file_path = Path(file_dialog(message="choose file", filter="*.txt; *.csv")[0])
    else:
        file_path = Path(file_path)

    print(file_path)

    # load data
    dat = io.load_locdata(path=file_path, file_type=file_type)

    # set roi
    rois = select_by_drawing_napari(locdata=dat, **kwargs)
    napari.run()
    print(rois)

    # save roi
    roi_path_list = []
    for i, roi in enumerate(rois):
        roi_file = file_path.stem + roi_file_indicator + f"_{i}.yaml"
        roi_path = file_path.with_name(roi_file)
        roi_path_list.append(roi_path)
        roi.to_yaml(path=roi_path)

    return roi_path_list



def _add_arguments(parser: argparse.ArgumentParser) -> None:
    parser.add_argument(
        "-f",
        "--file",
        dest="file",
        type=str,
        default=None,
        help="File path to localization data.",
    )
    parser.add_argument(
        "-t",
        "--type",
        dest="type",
        type=int,
        default=2,
        help="Integer or string indicating the file type.",
    )
    parser.add_argument(
        "-i",
        "--indicator",
        dest="roi_file_indicator",
        type=str,
        default="_roi",
        help="Indicator to add to the localization file name and use as roi file name "
        "(with further extension .yaml).",
    )
    parser.add_argument(
        "--bin_size",
        dest="bin_size",
        type=float,
        default=50,
        help="Keyword passed to render function.",
    )
    parser.add_argument(
        "--rescale",
        dest="rescale",
        type=_type_converter_rescale,
        default="EQUALIZE",
        help="Rescale intensity values. Keyword passed to render_2d_napari function.",
    )




def main(args: list[str] | None = None) -> None:
    parser = argparse.ArgumentParser(description="Set roi by drawing a boundary.")
    _add_arguments(parser)
    returned_args = parser.parse_args(args)

    sc_draw_roi_napari(
        returned_args.file,
        returned_args.type,
        returned_args.roi_file_indicator,
        bin_size=returned_args.bin_size,
        rescale=returned_args.rescale,
    )



if __name__ == "__main__":
    main()