Add download and checksum scripts.

scripts/checksum.py

@@ -0,0 +1,32 @@
+import argparse
+import os
+import hashlib
+import csv
+from tqdm import tqdm
+
+def md5_checksum(file_path):
+    hash_md5 = hashlib.md5()
+    with open(file_path, "rb") as f:
+        for chunk in iter(lambda: f.read(4096), b""):
+            hash_md5.update(chunk)
+    return hash_md5.hexdigest()
+
+def get_checksums(input_directory, output_filepath):
+    with open(output_filepath, 'w', newline='') as csvfile:
+        writer = csv.writer(csvfile)
+        writer.writerow(["filepath", "filename", "md5"])
+        for root, dirs, files in os.walk(input_directory):
+            n_files = len(files)
+            for name in tqdm(files, total=n_files, desc="MD5ing"):
+                file_path = os.path.join(root, name)
+                checksum = md5_checksum(file_path)
+                writer.writerow([file_path, name, checksum])
+        print(f"Checksums written to {output_filepath}")
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(description="Generate MD5 checksums for files in a directory")
+    parser.add_argument("--input-directory", required=True, help="Directory to traverse for files")
+    parser.add_argument("--output-filepath", required=True, help="Filepath for the output CSV file")
+    args = parser.parse_args()
+    get_checksums(args.input_directory, args.output_filepath)
+

scripts/download_jiggins_subset.py

@@ -0,0 +1,98 @@
+# 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()