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Diffstat (limited to 'src/python/gudhi/datasets/remote.py')
| -rw-r--r-- | src/python/gudhi/datasets/remote.py | 206 |
1 files changed, 206 insertions, 0 deletions
diff --git a/src/python/gudhi/datasets/remote.py b/src/python/gudhi/datasets/remote.py new file mode 100644 index 00000000..8b3baef4 --- /dev/null +++ b/src/python/gudhi/datasets/remote.py @@ -0,0 +1,206 @@ +# This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT. +# See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details. +# Author(s): Hind Montassif +# +# Copyright (C) 2021 Inria +# +# Modification(s): +# - YYYY/MM Author: Description of the modification + +from os.path import join, exists, expanduser +from os import makedirs, remove + +from urllib.request import urlretrieve +import hashlib +import shutil + +import numpy as np + +def get_data_home(data_home = None): + """ + Return the path of the remote datasets directory. + This folder is used to store remotely fetched datasets. + By default the datasets directory is set to a folder named 'gudhi_data' in the user home folder. + Alternatively, it can be set by giving an explicit folder path. The '~' symbol is expanded to the user home folder. + If the folder does not already exist, it is automatically created. + + Parameters + ---------- + data_home : string + The path to remote datasets directory. Default is `None`, meaning that the data home directory will be set to "~/gudhi_data". + + Returns + ------- + data_home: string + The path to remote datasets directory. + """ + if data_home is None: + data_home = join("~", "gudhi_data") + data_home = expanduser(data_home) + makedirs(data_home, exist_ok=True) + return data_home + + +def clear_data_home(data_home = None): + """ + Delete the data home cache directory and all its content. + + Parameters + ---------- + data_home : string, default is None. + The path to remote datasets directory. If `None`, the default directory to be removed is set to "~/gudhi_data". + """ + data_home = get_data_home(data_home) + shutil.rmtree(data_home) + +def _checksum_sha256(file_path): + """ + Compute the file checksum using sha256. + + Parameters + ---------- + file_path: string + Full path of the created file. + + Returns + ------- + The hex digest of file_path. + """ + sha256_hash = hashlib.sha256() + chunk_size = 4096 + with open(file_path,"rb") as f: + # Read and update hash string value in blocks of 4K + while True: + buffer = f.read(chunk_size) + if not buffer: + break + sha256_hash.update(buffer) + return sha256_hash.hexdigest() + +def _fetch_remote(url, filename, dirname, file_checksum = None, accept_license = False): + """ + Fetch the wanted dataset from the given url and save it in file_path. + + Parameters + ---------- + url : string + The url to fetch the dataset from. + filename : string + The name to give to downloaded file. + dirname : string + The directory to save the file to. + file_checksum : string + The file checksum using sha256 to check against the one computed on the downloaded file. + Default is 'None', which means the checksum is not checked. + accept_license : boolean + Flag to specify if user accepts the file LICENSE and prevents from printing the corresponding license terms. + Default is False. + + Returns + ------- + file_path: string + Full path of the created file. + + Raises + ------ + IOError + If the computed SHA256 checksum of file does not match the one given by the user. + """ + + file_path = join(dirname, filename) + + # Get the file + urlretrieve(url, file_path) + + if file_checksum is not None: + checksum = _checksum_sha256(file_path) + if file_checksum != checksum: + # Remove file and raise error + remove(file_path) + raise IOError("{} has a SHA256 checksum : {}, " + "different from expected : {}." + "The file may be corrupted or the given url may be wrong !".format(file_path, checksum, file_checksum)) + + # Print license terms unless accept_license is set to True + if not accept_license: + license_file = join(dirname, "LICENSE") + if exists(license_file) and (file_path != license_file): + with open(license_file, 'r') as f: + print(f.read()) + + return file_path + +def _get_archive_and_dir(dirname, filename, label): + if dirname is None: + dirname = join(get_data_home(dirname), label) + makedirs(dirname, exist_ok=True) + else: + dirname = get_data_home(dirname) + + archive_path = join(dirname, filename) + + return archive_path, dirname + +def fetch_spiral_2d(filename = "spiral_2d.npy", dirname = None): + """ + Fetch spiral_2d dataset remotely. + + Parameters + ---------- + filename : string + The name to give to downloaded file. Default is "spiral_2d.npy". + dirname : string + The directory to save the file to. Default is None, meaning that the downloaded file will be put in "~/gudhi_data/points/spiral_2d". + + Returns + ------- + points: numpy array + Array of shape (114562, 2). + """ + file_url = "https://raw.githubusercontent.com/GUDHI/gudhi-data/main/points/spiral_2d/spiral_2d.npy" + file_checksum = '88312ffd6df2e2cb2bde9c0e1f962d7d644c6f58dc369c7b377b298dacdc4eaf' + + archive_path, dirname = _get_archive_and_dir(dirname, filename, "points/spiral_2d") + + if not exists(archive_path): + file_path_pkl = _fetch_remote(file_url, filename, dirname, file_checksum) + + return np.load(file_path_pkl, mmap_mode='r') + else: + return np.load(archive_path, mmap_mode='r') + +def fetch_bunny(filename = "bunny.npy", dirname = None, accept_license = False): + """ + Fetch Stanford bunny dataset remotely and its LICENSE file. + This dataset contains 35947 vertices. + + Parameters + ---------- + filename : string + The name to give to downloaded file. Default is "bunny.npy". + dirname : string + The directory to save the file to. Default is None, meaning that the downloaded files will be put in "~/gudhi_data/points/bunny". + accept_license : boolean + Flag to specify if user accepts the file LICENSE and prevents from printing the corresponding license terms. + Default is False. + + Returns + ------- + points: numpy array + Array of shape (35947, 3). + """ + + file_url = "https://raw.githubusercontent.com/GUDHI/gudhi-data/main/points/bunny/bunny.npy" + file_checksum = '13f7842ebb4b45370e50641ff28c88685703efa5faab14edf0bb7d113a965e1b' + license_url = "https://raw.githubusercontent.com/GUDHI/gudhi-data/main/points/bunny/LICENSE" + license_checksum = 'b763dbe1b2fc6015d05cbf7bcc686412a2eb100a1f2220296e3b4a644c69633a' + + archive_path, dirname = _get_archive_and_dir(dirname, filename, "points/bunny") + + if not exists(archive_path): + license_path = _fetch_remote(license_url, "LICENSE", dirname, license_checksum) + file_path_pkl = _fetch_remote(file_url, filename, dirname, file_checksum, accept_license) + + return np.load(file_path_pkl, mmap_mode='r') + else: + return np.load(archive_path, mmap_mode='r') |