manual_script.py

import os
import sys
import json
import h5py
import numpy as np


def get_ds_dictionaries(name, node):  
    if isinstance(node, h5py.Dataset):
        try:
            dataset = np.array(node)
            metadata_dict[name] = json.loads(dataset[0].decode('utf-8'))
        except:
            pass


if __name__ == "__main__":

    try:
        if len(sys.argv) != 2:
            raise Exception("Please provide input directory name as an argument: python manual_script.py <directory_name>")

        input_dir = sys.argv[1]
        if not (os.path.exists(input_dir) and os.path.isdir(input_dir)):
            raise Exception(f"Directory with name '{input_dir}' does not exist.")

        for filename in os.listdir(input_dir):
            print("\n" + filename)
            metadata_dict = {}

            if filename.endswith(".prz"):
                try:
                    # using numpy because:
                    # h5py for .prz files gives error: 'Unable to open file (file signature not found)'

                    f = np.load(os.path.join(input_dir, filename), allow_pickle=True)

                    meta_data = f["meta_data"].tolist()
                    data_model = f["data_model"].tolist()

                    for dict in meta_data:
                        metadata_dict.update(dict)
                    for dict in data_model:
                        metadata_dict.update(dict)

                except Exception as e:
                    print(e)
                    pass

            elif filename.endswith(".emd"):
                try:
                    # using h5py because:
                    # numpy for .emd files  gives error: 'Cannot load file containing pickled data when allow_pickle=False'
                    # but when setting allow_pickle=True gives error: 'Failed to interpret file as a pickle'

                    f = h5py.File(os.path.join(input_dir, filename), "r")
                    f.visititems(get_ds_dictionaries)

                except Exception as e:
                    print(e)
                    pass

            else:
                print("Unsupported file format.")
                pass

            # create output directory if it doesn't exist
            output_dir = sys.argv[0].replace(".py", "_") + "metadata/"
            os.makedirs(output_dir, exist_ok=True)
            # save metadata as a json file
            with open(output_dir + filename.replace(" ", "_") + "_metadata.json", "w") as outfile:
                json.dump(metadata_dict, outfile, sort_keys=True, indent=4)

    except Exception as e:
        print(e)