process/process_iNaturalist.py

import json
import os
import shutil
from tqdm import tqdm
import argparse

def read_jsonl(path):
    data_list = []
    try:
        with open(path, "r", encoding="utf-8") as file:
            for line in tqdm(file, desc="Reading JSONL file"):
                data = json.loads(line)
                data_list.append(data)
        return data_list
    except FileNotFoundError:
        raise FileNotFoundError(f"Error: File {path} not found.")
    except json.JSONDecodeError:
        raise json.JSONDecodeError(f"Error: Invalid JSON format in file {path}.")
    except Exception as e:
        raise Exception(f"An unexpected error occurred while reading {path}: {e}")

def main():
    """
    Main function to process metadata and copy relevant files from iNaturalist test data.
    """
    # Set up argument parser
    parser = argparse.ArgumentParser(description="Process iNaturalist data.")
    parser.add_argument("--data_folder", type=str, required=True, help="Path to the iNaturalist test folder.")
    args = parser.parse_args()

    try:
        # Define the source folder containing the original files
        data_folder = args.data_folder
        
        meta_data = read_jsonl("meta_data.jsonl")

        # Copying iNaturalist test data in the metadata
        for data in tqdm(meta_data, desc="Copying iNaturalist test data"):
            if data["task_id"][0] == "BIU02":
                tmp_path = data["input_ts"]["path"]
                target_folder = os.path.dirname(tmp_path)
                
                # Create the target folder if it doesn't exist
                os.makedirs(target_folder, exist_ok=True)
                
                # Extract the file name and parent folder from the path
                data_name = os.path.basename(tmp_path).split("_")[-1]
                folder = os.path.basename(tmp_path).replace(data_name, "")[:-1]
                
                # Copy the file if it doesn't exist in the target path
                if not os.path.exists(tmp_path):
                    source_path = os.path.join(data_folder, os.path.join(folder, data_name))
                    try:
                        shutil.copy(source_path, tmp_path)
                    except FileNotFoundError:
                        print(f"Warning: Source file {source_path} not found. Skipping.")
                    except Exception as e:
                        print(f"Warning: Failed to copy {source_path} to {tmp_path}. Error: {e}")

    except Exception as e:
        print(f"An error occurred during execution: {e}")


if __name__ == "__main__":
    main()