Source code for brainglobe_atlasapi.atlas_generation.annotation_utils

"""Helper functions to read annotation metadata from common formats."""

from pathlib import Path




def split_label_text(name: str) -> str:
    """Split label text into name + acronym.

    If the label text ends with ')', extract the acronym inside parentheses.
    Otherwise, use the first letter as the acronym.
    """
    if name.endswith(")"):
        name, acronym = name.split("(")
        name = name[:-1]  # ignore trailing space
        acronym = acronym[:-1]  # ignore trailing )
    else:
        acronym = name[0]
    return name, acronym





def read_itk_labels(path: Path) -> dict:
    """Turn ITK label data from a file into a list of dictionaries."""
    labels = []
    with open(path) as labels_file:
        for line in labels_file:
            if not line.startswith("#"):
                raw_values = line.split(maxsplit=7)
                id = int(raw_values[0])
                rgb = tuple((int(r) for r in raw_values[1:4]))
                if raw_values[7][-1] == "\n":
                    raw_values[7] = raw_values[7][:-1]
                label_text = raw_values[7][1:-1]
                if label_text != "Clear Label":
                    name, acronym = split_label_text(label_text)
                    labels.append(
                        {
                            "id": id,
                            "name": name,
                            "rgb_triplet": rgb,
                            "acronym": acronym,
                        }
                    )
    return labels



ITK_SNAP_HEADER = """################################################
# ITK-SnAP Label Description File
# File format:
# IDX   -R-  -G-  -B-  -A--  VIS MSH  LABEL
# Fields:
#    IDX:   Zero-based index
#    -R-:   Red color component (0..255)
#    -G-:   Green color component (0..255)
#    -B-:   Blue color component (0..255)
#    -A-:   Label transparency (0.00 .. 1.00)
#    VIS:   Label visibility (0 or 1)
#    IDX:   Label mesh visibility (0 or 1)
#  LABEL:   Label description
################################################
"""

ITK_CLEAR_LABEL = '0 0 0 0 0 0 0 "Clear Label"\n'




def write_itk_labels(path: Path, labels):
    """Write ITK label data to a file."""
    with open(path, "w") as labels_file:
        labels_file.write(ITK_SNAP_HEADER)
        labels_file.write(ITK_CLEAR_LABEL)
        for label in labels:
            labels_file.write(
                f"{label['id']} "
                f"{label['rgb_triplet'][0]} "
                f"{label['rgb_triplet'][1]} "
                f"{label['rgb_triplet'][2]} 1.00 1 1 "
                f'"{label["name"] + " (" + label["acronym"] + ")"}"\n'
            )