import argparse
import shutil
from pathlib import Path

import pandas as pd
from tqdm import tqdm


def main(
    tiles_dirs, valid_tiles_summaries_path, output_tiles_folder, valid_tiles_csv_path,
):
    output_tiles_folder.mkdir(parents=True, exist_ok=True)

    summaries = []
    for tile_dir, summary_path in tqdm(
        zip(tiles_dirs, valid_tiles_summaries_path), total=len(tiles_dirs)
    ):
        summary = pd.read_csv(summary_path)
        summaries.append(summary)

        for i, row in summary.iterrows():
            filename = row["filename"]
            shutil.copy(Path(tile_dir) / filename, output_tiles_folder / filename)

    valid_tiles_all = pd.concat(summaries, ignore_index=True)
    valid_tiles_all.to_csv(valid_tiles_csv_path, index=False)


if __name__ == "__main__":
    parser = argparse.ArgumentParser(
        description="Copy valid tiles from respective folders to unique folder"
    )
    parser.add_argument(
        "--tiles_dirs", nargs="+", help="Directories where original tiles are"
    )
    parser.add_argument(
        "--valid_tiles_summaries_path",
        nargs="+",
        help="Paths of the valid tiles CSV summaries (one for each WSI)",
    )
    parser.add_argument(
        "--output_tiles_folder", type=str, help="Where to copy the tiles"
    )
    parser.add_argument(
        "--valid_tiles_csv_path",
        type=str,
        help="Path of the resulting CVS, "
        "as the concatenation of the tiles summaries provided",
    )

    args = parser.parse_args()

    tiles_dirs = args.tiles_dirs
    valid_tiles_summaries_path = args.valid_tiles_summaries_path
    output_tiles_folder = Path(args.output_tiles_folder)
    valid_tiles_csv_path = args.valid_tiles_csv_path

    assert len(tiles_dirs) == len(
        valid_tiles_summaries_path
    ), f"The number of tiles directories ({len(tiles_dirs)}) is different than "
    "the number of summaries ({valid_tiles_summaries_path})"

    main(
        tiles_dirs,
        valid_tiles_summaries_path,
        output_tiles_folder,
        valid_tiles_csv_path,
    )

a3527bdb12c25a9dbfc799496a0ef9a2d3b64986
<mask token>

<mask token>


def main(tiles_dirs, valid_tiles_summaries_path, output_tiles_folder,
    valid_tiles_csv_path):
    output_tiles_folder.mkdir(parents=True, exist_ok=True)
    summaries = []
    for tile_dir, summary_path in tqdm(zip(tiles_dirs,
        valid_tiles_summaries_path), total=len(tiles_dirs)):
        summary = pd.read_csv(summary_path)
        summaries.append(summary)
        for i, row in summary.iterrows():
            filename = row['filename']
            shutil.copy(Path(tile_dir) / filename, output_tiles_folder /
                filename)
    valid_tiles_all = pd.concat(summaries, ignore_index=True)
    valid_tiles_all.to_csv(valid_tiles_csv_path, index=False)


<mask token>

<mask token>


def main(tiles_dirs, valid_tiles_summaries_path, output_tiles_folder,
    valid_tiles_csv_path):
    output_tiles_folder.mkdir(parents=True, exist_ok=True)
    summaries = []
    for tile_dir, summary_path in tqdm(zip(tiles_dirs,
        valid_tiles_summaries_path), total=len(tiles_dirs)):
        summary = pd.read_csv(summary_path)
        summaries.append(summary)
        for i, row in summary.iterrows():
            filename = row['filename']
            shutil.copy(Path(tile_dir) / filename, output_tiles_folder /
                filename)
    valid_tiles_all = pd.concat(summaries, ignore_index=True)
    valid_tiles_all.to_csv(valid_tiles_csv_path, index=False)


if __name__ == '__main__':
    parser = argparse.ArgumentParser(description=
        'Copy valid tiles from respective folders to unique folder')
    parser.add_argument('--tiles_dirs', nargs='+', help=
        'Directories where original tiles are')
    parser.add_argument('--valid_tiles_summaries_path', nargs='+', help=
        'Paths of the valid tiles CSV summaries (one for each WSI)')
    parser.add_argument('--output_tiles_folder', type=str, help=
        'Where to copy the tiles')
    parser.add_argument('--valid_tiles_csv_path', type=str, help=
        'Path of the resulting CVS, as the concatenation of the tiles summaries provided'
        )
    args = parser.parse_args()
    tiles_dirs = args.tiles_dirs
    valid_tiles_summaries_path = args.valid_tiles_summaries_path
    output_tiles_folder = Path(args.output_tiles_folder)
    valid_tiles_csv_path = args.valid_tiles_csv_path
    assert len(tiles_dirs) == len(valid_tiles_summaries_path
        ), f'The number of tiles directories ({len(tiles_dirs)}) is different than '
    """the number of summaries ({valid_tiles_summaries_path})"""
    main(tiles_dirs, valid_tiles_summaries_path, output_tiles_folder,
        valid_tiles_csv_path)

import argparse
import shutil
from pathlib import Path
import pandas as pd
from tqdm import tqdm


def main(tiles_dirs, valid_tiles_summaries_path, output_tiles_folder,
    valid_tiles_csv_path):
    output_tiles_folder.mkdir(parents=True, exist_ok=True)
    summaries = []
    for tile_dir, summary_path in tqdm(zip(tiles_dirs,
        valid_tiles_summaries_path), total=len(tiles_dirs)):
        summary = pd.read_csv(summary_path)
        summaries.append(summary)
        for i, row in summary.iterrows():
            filename = row['filename']
            shutil.copy(Path(tile_dir) / filename, output_tiles_folder /
                filename)
    valid_tiles_all = pd.concat(summaries, ignore_index=True)
    valid_tiles_all.to_csv(valid_tiles_csv_path, index=False)


if __name__ == '__main__':
    parser = argparse.ArgumentParser(description=
        'Copy valid tiles from respective folders to unique folder')
    parser.add_argument('--tiles_dirs', nargs='+', help=
        'Directories where original tiles are')
    parser.add_argument('--valid_tiles_summaries_path', nargs='+', help=
        'Paths of the valid tiles CSV summaries (one for each WSI)')
    parser.add_argument('--output_tiles_folder', type=str, help=
        'Where to copy the tiles')
    parser.add_argument('--valid_tiles_csv_path', type=str, help=
        'Path of the resulting CVS, as the concatenation of the tiles summaries provided'
        )
    args = parser.parse_args()
    tiles_dirs = args.tiles_dirs
    valid_tiles_summaries_path = args.valid_tiles_summaries_path
    output_tiles_folder = Path(args.output_tiles_folder)
    valid_tiles_csv_path = args.valid_tiles_csv_path
    assert len(tiles_dirs) == len(valid_tiles_summaries_path
        ), f'The number of tiles directories ({len(tiles_dirs)}) is different than '
    """the number of summaries ({valid_tiles_summaries_path})"""
    main(tiles_dirs, valid_tiles_summaries_path, output_tiles_folder,
        valid_tiles_csv_path)

import argparse
import shutil
from pathlib import Path

import pandas as pd
from tqdm import tqdm


def main(
    tiles_dirs, valid_tiles_summaries_path, output_tiles_folder, valid_tiles_csv_path,
):
    output_tiles_folder.mkdir(parents=True, exist_ok=True)

    summaries = []
    for tile_dir, summary_path in tqdm(
        zip(tiles_dirs, valid_tiles_summaries_path), total=len(tiles_dirs)
    ):
        summary = pd.read_csv(summary_path)
        summaries.append(summary)

        for i, row in summary.iterrows():
            filename = row["filename"]
            shutil.copy(Path(tile_dir) / filename, output_tiles_folder / filename)

    valid_tiles_all = pd.concat(summaries, ignore_index=True)
    valid_tiles_all.to_csv(valid_tiles_csv_path, index=False)


if __name__ == "__main__":
    parser = argparse.ArgumentParser(
        description="Copy valid tiles from respective folders to unique folder"
    )
    parser.add_argument(
        "--tiles_dirs", nargs="+", help="Directories where original tiles are"
    )
    parser.add_argument(
        "--valid_tiles_summaries_path",
        nargs="+",
        help="Paths of the valid tiles CSV summaries (one for each WSI)",
    )
    parser.add_argument(
        "--output_tiles_folder", type=str, help="Where to copy the tiles"
    )
    parser.add_argument(
        "--valid_tiles_csv_path",
        type=str,
        help="Path of the resulting CVS, "
        "as the concatenation of the tiles summaries provided",
    )

    args = parser.parse_args()

    tiles_dirs = args.tiles_dirs
    valid_tiles_summaries_path = args.valid_tiles_summaries_path
    output_tiles_folder = Path(args.output_tiles_folder)
    valid_tiles_csv_path = args.valid_tiles_csv_path

    assert len(tiles_dirs) == len(
        valid_tiles_summaries_path
    ), f"The number of tiles directories ({len(tiles_dirs)}) is different than "
    "the number of summaries ({valid_tiles_summaries_path})"

    main(
        tiles_dirs,
        valid_tiles_summaries_path,
        output_tiles_folder,
        valid_tiles_csv_path,
    )
