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# Copyright (c) MONAI Consortium
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
import argparse
import os
import requests
from tqdm import tqdm
def download_files(url_dict, directory):
if not os.path.exists(directory):
os.makedirs(directory)
for key, url in url_dict.items():
if key == "nips_train.zip" or key == "nips_test.zip":
if not os.path.exists(os.path.join(directory, "nips_dataset")):
os.mkdir(os.path.join(directory, "nips_dataset"))
base_dir = os.path.join(directory, "nips_dataset")
elif key == "deepbacs.zip":
if not os.path.exists(os.path.join(directory, "deepbacs_dataset")):
os.mkdir(os.path.join(directory, "deepbacs_dataset"))
base_dir = os.path.join(directory, "deepbacs_dataset")
elif key == "livecell":
if not os.path.exists(os.path.join(directory, "livecell_dataset")):
os.mkdir(os.path.join(directory, "livecell_dataset"))
base_dir = os.path.join(directory, "livecell_dataset")
print(f"Downloading from {key}: {url}")
os.system(url + base_dir)
continue
try:
print(f"Downloading from {key}: {url}")
response = requests.get(url, stream=True, allow_redirects=True)
total_size = int(response.headers.get("content-length", 0))
# Extract the filename from the URL or use the key as the filename
filename = os.path.basename(key)
file_path = os.path.join(base_dir, filename)
# Write the content to a file in the specified directory with progress
with open(file_path, "wb") as file, tqdm(
desc=filename, total=total_size, unit="iB", unit_scale=True, unit_divisor=1024
) as bar:
for data in response.iter_content(chunk_size=1024):
size = file.write(data)
bar.update(size)
print(f"Saved to {file_path}")
except Exception as e:
print(f"Failed to download from {key} ({url}). Reason: {str(e)}")
def main():
parser = argparse.ArgumentParser(description="Process some integers.")
parser.add_argument("--dir", type=str, help="Directory to download files to", default="/set/the/path")
args = parser.parse_args()
directory = os.path.normpath(args.dir)
url_dict = {
"deepbacs.zip": "https://zenodo.org/records/5551009/files/DeepBacs_Data_Segmentation_StarDist_MIXED_dataset.zip?download=1",
"nips_test.zip": "https://zenodo.org/records/10719375/files/Testing.zip?download=1",
"nips_train.zip": "https://zenodo.org/records/10719375/files/Training-labeled.zip?download=1",
"livecell": "wget --recursive --no-parent --cut-dirs=0 --timestamping -i urls.txt --directory-prefix=",
# Add URLs with keys here
}
download_files(url_dict, directory)
if __name__ == "__main__":
main()
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