scripts/download_jiggins_subset.py

# Built on Michelle's download script: https://huggingface.co./datasets/imageomics/Comparison-Subset-Jiggins/blob/977a934e1eef18f6b6152da430ac83ba6f7bd30f/download_jiggins_subset.py
# with modification of David's redo loop: https://github.com/Imageomics/data-fwg/blob/anomaly-data-challenge/HDR-anomaly-data-challenge/notebooks/download_images.ipynb
# and expanded logging and file checks. Further added checksum calculation for all downloaded images at end.

# Script to download Jiggins images from any of the master CSV files.
# Generates Checksum file for all images downloaded (<master filename>_checksums.csv).
# Logs image downloads and failures in json files (<master filename>_log.json & <master filename>_error_log.json).
# Logs record numbers and response codes as strings, not int64.

import requests
import shutil
import json

import pandas as pd
from checksum import get_checksums

from tqdm import tqdm
import os
import sys
import time
import argparse


EXPECTED_COLS = ["CAMID",
                 "X",
                 "Image_name",
                 "file_url",
                 "Taxonomic_Name",
                 "record_number",
                 "Dataset"
                 ]

REDO_CODE_LIST = [429, 500, 502, 503, 504]

# Reset to appropriate index if download gets interrupted.
STARTING_INDEX = 0


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 log_response(log_data, index, image, url, record_number, dataset, cam_id, response_code):
    # log status
    log_entry = {}
    log_entry["Image"] = image
    log_entry["file_url"] = url
    log_entry["record_number"] = str(record_number) #int64 has problems sometimes
    log_entry["dataset"] = dataset
    log_entry["CAMID"] = cam_id
    log_entry["Response_status"] = str(response_code)
    log_data[index] = log_entry

    return log_data


def update_log(log, index, filepath):
    # save logs
    with open(filepath, "a") as log_file:
        json.dump(log[index], log_file, indent = 4)
        log_file.write("\n")


def download_images(jiggins_data, image_folder, log_filepath, error_log_filepath):
    log_data = {}
    log_errors = {}

    for i in tqdm(range(0, len(jiggins_data))) : 
        # species will really be <Genus> <species> ssp. <subspecies>, where subspecies indicated
        species = jiggins_data["Taxonomic_Name"][i]
        image_name = jiggins_data["X"][i].astype(str) + "_" + jiggins_data["Image_name"][i]
        record_number = jiggins_data["record_number"][i]

        # download the image from url if not already downloaded
        # Will attempt to download everything in CSV (image_name is unique: <X>_<Image_name>), unless download restarted
        if os.path.exists(f"{image_folder}/{species}/{image_name}") != True:
            #get image from url
            url = jiggins_data["file_url"][i]
            dataset = jiggins_data["Dataset"][i]
            cam_id = jiggins_data["CAMID"][i]

            #download the image
            redo = True
            max_redos = 2
            while redo and max_redos > 0:
                try:
                    response = requests.get(url, stream=True)
                except Exception as e:
                    redo = True
                    max_redos -= 1
                    if max_redos <= 0:
                        log_errors = log_response(log_errors,
                                        index = i,
                                        image = species + "/" + image_name,
                                        url = url,
                                        record_number = record_number,
                                        dataset = dataset,
                                        cam_id = cam_id,
                                        response_code = str(e))
                        update_log(log = log_errors, index = i, filepath = error_log_filepath)
                        
                if response.status_code == 200:
                    redo = False
                    # log status
                    log_data = log_response(log_data,
                                        index = i,
                                        image = species + "/" + image_name,
                                        url = url,
                                        record_number = record_number,
                                        dataset = dataset,
                                        cam_id = cam_id,
                                        response_code = response.status_code
                                        )
                    update_log(log = log_data, index = i, filepath = log_filepath)
                    
                    #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)
                    
                    # save image to appropriate folder
                    with open(f"{image_folder}/{species}/{image_name}", "wb") as out_file:
                        shutil.copyfileobj(response.raw, out_file)
            
                # check for too many requests
                elif response.status_code in REDO_CODE_LIST:
                    redo = True
                    max_redos -= 1
                    if max_redos <= 0:
                        log_errors = log_response(log_errors,
                                        index = i,
                                        image = species + "/" + image_name,
                                        url = url,
                                        record_number = record_number,
                                        dataset = dataset,
                                        cam_id = cam_id,
                                        response_code = response.status_code)
                        update_log(log = log_errors, index = i, filepath = error_log_filepath)

                    else:
                        time.sleep(1)
                else: #other fail, eg. 404
                    redo = False
                    log_errors = log_response(log_errors,
                                            index = i,
                                            image = species + "/" + image_name,
                                            url = url,
                                            record_number = record_number,
                                            dataset = dataset,
                                            cam_id = cam_id,
                                            response_code = response.status_code)
                    update_log(log = log_errors, index = i, filepath = error_log_filepath)

            del response
    
        else:
            if i > STARTING_INDEX:
                # No need to print if download is restarted due to interruption (set STARTING_INDEX accordingly).
                print(f"duplicate image: {jiggins_data['X']}, {jiggins_data['Image_name']}, from record {record_number}")

    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 (folder of source CSV)
    log_filepath = csv_path.split(".")[0] + "_log.json"
    error_log_filepath = csv_path.split(".")[0] + "_error_log.json"

    #load csv 
    jiggins_data = pd.read_csv(csv_path, low_memory = False)

    # Check for required columns
    missing_cols = []
    for col in EXPECTED_COLS:
        if col not in list(jiggins_data.columns):
            missing_cols.append(col)
    if len(missing_cols) > 0:
        sys.exit(f"The CSV is missing column(s): {missing_cols}")

    #dowload images from urls
    download_images(jiggins_data, image_folder, log_filepath, error_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 logs are in {log_filepath} and {error_log_filepath}.")

    return

if __name__ == "__main__":
    main()