scripts/download_jiggins_subset.py

# Modified code from https://huggingface.co/datasets/imageomics/Comparison-Subset-Jiggins/blob/main/scripts/download_jiggins_subset.py
# For downloading Jiggins images from any of the master CSV files
# Generates Checksum file for all images download
# logs image download in json file

import requests
import shutil
import json

import pandas as pd
from checksum import get_checksums

from tqdm import tqdm
import os
import argparse


def parse_args():
    parser = argparse.ArgumentParser()
    parser.add_argument("--csv", required=True, help="Path to CSV file with urls.", nargs="?")
    parser.add_argument("--output", required=True, help="Main directory to download images into.", nargs="?")

    return parser.parse_args()


def update_log(log_data, index, image, url, response_code):
    # log status
    log_entry = {}
    log_entry["Image"] = image
    log_entry["zenodo_link"] = url
    log_entry["Response_status"] = response_code
    log_data[index] = log_entry

    return log_data


def download_images(csv_path, image_folder, log_filepath):
    #load csv 
    jiggins_data = pd.read_csv(csv_path)
    log_data = {}

    for i in tqdm(range(0, len(jiggins_data))) : 
        species = jiggins_data["Taxonomic_Name"][i]
        image_name = jiggins_data["X"][i].astype(str) + "_" + jiggins_data["Image_name"][i]

        #download the image from url is not already downloaded
        if os.path.exists(f"{image_folder}/{species}/{image_name}") != True:
            #get image from url
            url = jiggins_data["zenodo_link"][i]
            response = requests.get(url, stream=True)

            # log status
            log_data = update_log(log_data,
                                  index = i,
                                  image = species + "/" + image_name,
                                  url = url,
                                  response_code = response.status_code
                                  )
            
            #create the species appropriate folder if necessary
            if os.path.exists(f"{image_folder}/{species}") != True:
                os.makedirs(f"{image_folder}/{species}", exist_ok=False)

            #download the image
            if response.status_code == 200:
                with open(f"{image_folder}/{species}/{image_name}", "wb") as out_file:
                    shutil.copyfileobj(response.raw, out_file)
            del response
    
    with open(log_filepath, "w") as log_file:
        json.dump(log_data, log_file, indent = 4)

    return

def main():

    #get arguments from commandline
    args = parse_args() 
    csv_path = args.csv #path to our csv with urls to download images from
    image_folder = args.output  #folder where dataset will be downloaded to

    # log file location
    log_filepath = csv_path.split(".")[0] + "_log.json"

    #dowload images from urls
    download_images(csv_path, image_folder, log_filepath)

    # generate checksums and save CSV to same folder as CSV used for download
    checksum_path = csv_path.split(".")[0] + "_checksums.csv"
    get_checksums(image_folder, checksum_path)

    print(f"Images downloaded from {csv_path} to {image_folder}.")
    print(f"Checksums recorded in {checksum_path} and download log is in {log_filepath}.")

    return

if __name__ == "__main__":
    main()