merge_bioscan_1m.py

#!/usr/bin/env python3
import os
import glob

def merge_files(parts_dir, output_file, base_filename):
    pattern = os.path.join(parts_dir, f"{base_filename}.part*")
    parts = sorted(glob.glob(pattern))
    if not parts:
        print("No files found")
        return

    print(f"found {len(parts)} files, merge to {output_file} ...")
    with open(output_file, 'wb') as outfile:
        for part in parts:
            print(f"Merging: {part} ...")
            with open(part, 'rb') as infile:
                while True:
                    data = infile.read(1024 * 1024)
                    if not data:
                        break
                    outfile.write(data)
    print(f"Merged: {output_file}")

if __name__ == '__main__':
    parts_dir = "data/BIOSCAN_1M/split_data/splitted_files"
    base_filename = "BioScan_data_in_splits.hdf5"
    output_file = "data/BIOSCAN_1M/split_data/BioScan_data_in_splits.hdf5"
    merge_files(parts_dir, output_file, base_filename)