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reformat_label_files.py 3.71 KiB
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import pandas as pd


"""reformat itksnap_label_description_2022.txt"""


def reformat_allen_label(inputpath, outputpath):
    df = pd.read_csv(
        inputpath,
        sep=" ",
        header=None,
        names=["row", "r", "g", "b", "a", "VIS", "MSH", "name"],
    )

    # this is to reformat the name to allenID
    df[["name", "idx"]] = df["name"].str.split(" - ", expand=True)
    # this is to add on "root" as this was missing from the Allen file
    df = df.append(
        {
            "idx": 0,
            "name": "background",
            "r": 255,
            "g": 255,
            "b": 255,
            "a": 1.0,
            "VIS": 1.0,
            "MSH": 1.0,
        },
        ignore_index=True,
    )

    df
    reordered_df = df.loc[:, ["idx", "r", "g", "b", "a", "VIS", "MSH", "name", "row"]]
    reordered_df.to_csv(outputpath, index=False)


reformat_allen_label(
    "../annotation_volumes/itksnap_label_description_2022.txt",
    "../annotation_volumes/allen2022_colours_updated.csv",
)


"""reformat AllenMouseBrain_atlas_CCF_2017.label, add clear label to first row"""


def reformat_label(inputpath, outputpath):
    df = pd.read_csv(
        inputpath,
        sep="\t",
        header=None,
        skiprows=15,
        names=["idx", "r", "g", "b", "a", "VIS", "MSH", "name"],
    )
    df_clear = pd.DataFrame(
        {
            "idx": 0,
            "name": "Clear Label",
            "r": 0,
            "g": 0,
            "b": 0,
            "a": 1.0,
            "VIS": 1.0,
            "MSH": 1.0,
        },
        index=[0],
    )
    df = pd.concat([df_clear, df])
    df.to_csv(outputpath, index=False)


reformat_label(
    "../annotation_volumes/AllenMouseBrain_Atlas_CCF_2017.label",
    "../annotation_volumes/allen2017_colours.csv",
)


"""reformat AllenMouseBrain_atlas_CCF_2015.label, add clear label to first row"""


def reformat_label(inputpath, outputpath):
    df = pd.read_csv(
        inputpath,
        sep="\t",
        header=None,
        skiprows=15,
        names=["idx", "r", "g", "b", "a", "VIS", "MSH", "name"],
    )
    df_clear = pd.DataFrame(
        {
            "idx": 0,
            "name": "Clear Label",
            "r": 0,
            "g": 0,
            "b": 0,
            "a": 1.0,
            "VIS": 1.0,
            "MSH": 1.0,
        },
        index=[0],
    )
    df = pd.concat([df_clear, df])
    # df = df.append({"idx": 0, "name": "Clear Label", "r": 0, "g": 0, "b": 0, "a": 1.0, "VIS":1.0, "MSH":1.0}, ignore_index=True)
    df.to_csv(outputpath, index=False)


reformat_label(
    "../annotation_volumes/AllenMouseBrain_Atlas_CCF_2015.label",
    "../annotation_volumes/allen2015_colours.csv",
)


"""reformat WHS_rat_atlas"""


def reformat_WHS_label(inputpath, outputpath):
    df = pd.read_csv(
        inputpath,
        sep="\s+",
        header=None,
        skiprows=15,
        names=["idx", "r", "g", "b", "a", "VIS", "MSH", "name"],
    )
    # df = df.append({"idx": 0, "name": "Clear Label", "r": 0, "g": 0, "b": 0, "a": 1.0, "VIS":1.0, "MSH":1.0}, ignore_index=True)
    df_clear = pd.DataFrame(
        {
            "idx": 0,
            "name": "Clear Label",
            "r": 0,
            "g": 0,
            "b": 0,
            "a": 1.0,
            "VIS": 1.0,
            "MSH": 1.0,
        },
        index=[0],
    )
    df = pd.concat([df_clear, df])
    df.to_csv(outputpath, index=False)


reformat_WHS_label(
    "../annotation_volumes/WHS_SD_rat_atlas_v4.label",
    "../annotation_volumes/WHS_v4_colours.csv",
)
reformat_WHS_label(
    "../annotation_volumes/WHS_Atlas_Rat_Brain_v3.label",
    "../annotation_volumes/WHS_v3_colours.csv",
)
reformat_WHS_label(
    "../annotation_volumes/WHS_Atlas_Rat_Brain_v2.label",
    "../annotation_volumes/WHS_v2_colours.csv",
)