Source code for

"""Dataset utilities."""
from __future__ import absolute_import

import os
import sys
import hashlib
import warnings
import requests
import pickle
import errno
import numpy as np

import pickle
import errno

from .graph_serialize import save_graphs, load_graphs, load_labels
from .tensor_serialize import save_tensors, load_tensors

from .. import backend as F

__all__ = ['loadtxt','download', 'check_sha1', 'extract_archive',
           'get_download_dir', 'Subset', 'split_dataset',
           'save_graphs', "load_graphs", "load_labels", "save_tensors", "load_tensors"]

def loadtxt(path, delimiter, dtype=None):
        import pandas as pd
        df = pd.read_csv(path, delimiter=delimiter, header=None)
        return df.values
    except ImportError:
        warnings.warn("Pandas is not installed, now using numpy.loadtxt to load data, "
                        "which could be extremely slow. Accelerate by installing pandas")
        return np.loadtxt(path, delimiter=delimiter)

def _get_dgl_url(file_url):
    """Get DGL online url for download."""
    dgl_repo_url = ''
    repo_url = os.environ.get('DGL_REPO', dgl_repo_url)
    if repo_url[-1] != '/':
        repo_url = repo_url + '/'
    return repo_url + file_url

[docs]def split_dataset(dataset, frac_list=None, shuffle=False, random_state=None): """Split dataset into training, validation and test set. Parameters ---------- dataset We assume ``len(dataset)`` gives the number of datapoints and ``dataset[i]`` gives the ith datapoint. frac_list : list or None, optional A list of length 3 containing the fraction to use for training, validation and test. If None, we will use [0.8, 0.1, 0.1]. shuffle : bool, optional By default we perform a consecutive split of the dataset. If True, we will first randomly shuffle the dataset. random_state : None, int or array_like, optional Random seed used to initialize the pseudo-random number generator. Can be any integer between 0 and 2**32 - 1 inclusive, an array (or other sequence) of such integers, or None (the default). If seed is None, then RandomState will try to read data from /dev/urandom (or the Windows analogue) if available or seed from the clock otherwise. Returns ------- list of length 3 Subsets for training, validation and test. """ from itertools import accumulate if frac_list is None: frac_list = [0.8, 0.1, 0.1] frac_list = np.asarray(frac_list) assert np.allclose(np.sum(frac_list), 1.), \ 'Expect frac_list sum to 1, got {:.4f}'.format(np.sum(frac_list)) num_data = len(dataset) lengths = (num_data * frac_list).astype(int) lengths[-1] = num_data - np.sum(lengths[:-1]) if shuffle: indices = np.random.RandomState( seed=random_state).permutation(num_data) else: indices = np.arange(num_data) return [Subset(dataset, indices[offset - length:offset]) for offset, length in zip(accumulate(lengths), lengths)]
[docs]def download(url, path=None, overwrite=True, sha1_hash=None, retries=5, verify_ssl=True, log=True): """Download a given URL. Codes borrowed from mxnet/gluon/ Parameters ---------- url : str URL to download. path : str, optional Destination path to store downloaded file. By default stores to the current directory with the same name as in url. overwrite : bool, optional Whether to overwrite the destination file if it already exists. By default always overwrites the downloaded file. sha1_hash : str, optional Expected sha1 hash in hexadecimal digits. Will ignore existing file when hash is specified but doesn't match. retries : integer, default 5 The number of times to attempt downloading in case of failure or non 200 return codes. verify_ssl : bool, default True Verify SSL certificates. log : bool, default True Whether to print the progress for download Returns ------- str The file path of the downloaded file. """ if path is None: fname = url.split('/')[-1] # Empty filenames are invalid assert fname, 'Can\'t construct file-name from this URL. ' \ 'Please set the `path` option manually.' else: path = os.path.expanduser(path) if os.path.isdir(path): fname = os.path.join(path, url.split('/')[-1]) else: fname = path assert retries >= 0, "Number of retries should be at least 0" if not verify_ssl: warnings.warn( 'Unverified HTTPS request is being made (verify_ssl=False). ' 'Adding certificate verification is strongly advised.') if overwrite or not os.path.exists(fname) or (sha1_hash and not check_sha1(fname, sha1_hash)): dirname = os.path.dirname(os.path.abspath(os.path.expanduser(fname))) if not os.path.exists(dirname): os.makedirs(dirname) while retries+1 > 0: # Disable pyling too broad Exception # pylint: disable=W0703 try: if log: print('Downloading %s from %s...' % (fname, url)) r = requests.get(url, stream=True, verify=verify_ssl) if r.status_code != 200: raise RuntimeError("Failed downloading url %s" % url) with open(fname, 'wb') as f: for chunk in r.iter_content(chunk_size=1024): if chunk: # filter out keep-alive new chunks f.write(chunk) if sha1_hash and not check_sha1(fname, sha1_hash): raise UserWarning('File {} is downloaded but the content hash does not match.' ' The repo may be outdated or download may be incomplete. ' 'If the "repo_url" is overridden, consider switching to ' 'the default repo.'.format(fname)) break except Exception as e: retries -= 1 if retries <= 0: raise e else: if log: print("download failed, retrying, {} attempt{} left" .format(retries, 's' if retries > 1 else '')) return fname
[docs]def check_sha1(filename, sha1_hash): """Check whether the sha1 hash of the file content matches the expected hash. Codes borrowed from mxnet/gluon/ Parameters ---------- filename : str Path to the file. sha1_hash : str Expected sha1 hash in hexadecimal digits. Returns ------- bool Whether the file content matches the expected hash. """ sha1 = hashlib.sha1() with open(filename, 'rb') as f: while True: data = if not data: break sha1.update(data) return sha1.hexdigest() == sha1_hash
[docs]def extract_archive(file, target_dir, overwrite=False): """Extract archive file. Parameters ---------- file : str Absolute path of the archive file. target_dir : str Target directory of the archive to be uncompressed. overwrite : bool, default True Whether to overwrite the contents inside the directory. By default always overwrites. """ if os.path.exists(target_dir) and not overwrite: return print('Extracting file to {}'.format(target_dir)) if file.endswith('.tar.gz') or file.endswith('.tar') or file.endswith('.tgz'): import tarfile with, 'r') as archive: archive.extractall(path=target_dir) elif file.endswith('.gz'): import gzip import shutil with, 'rb') as f_in: with open(file[:-3], 'wb') as f_out: shutil.copyfileobj(f_in, f_out) elif file.endswith('.zip'): import zipfile with zipfile.ZipFile(file, 'r') as archive: archive.extractall(path=target_dir) else: raise Exception('Unrecognized file type: ' + file)
[docs]def get_download_dir(): """Get the absolute path to the download directory. Returns ------- dirname : str Path to the download directory """ default_dir = os.path.join(os.path.expanduser('~'), '.dgl') dirname = os.environ.get('DGL_DOWNLOAD_DIR', default_dir) if not os.path.exists(dirname): os.makedirs(dirname) return dirname
def makedirs(path): try: os.makedirs(os.path.expanduser(os.path.normpath(path))) except OSError as e: if e.errno != errno.EEXIST and os.path.isdir(path): raise e
[docs]def save_info(path, info): """ Save dataset related information into disk. Parameters ---------- path : str File to save information. info : dict A python dict storing information to save on disk. """ with open(path, "wb" ) as pf: pickle.dump(info, pf)
[docs]def load_info(path): """ Load dataset related information from disk. Parameters ---------- path : str File to load information from. Returns ------- info : dict A python dict storing information loaded from disk. """ with open(path, "rb") as pf: info = pickle.load(pf) return info
def deprecate_property(old, new): warnings.warn('Property {} will be deprecated, please use {} instead.'.format(old, new)) def deprecate_function(old, new): warnings.warn('Function {} will be deprecated, please use {} instead.'.format(old, new)) def deprecate_class(old, new): warnings.warn('Class {} will be deprecated, please use {} instead.'.format(old, new)) def idx2mask(idx, len): """Create mask.""" mask = np.zeros(len) mask[idx] = 1 return mask def generate_mask_tensor(mask): """Generate mask tensor according to different backend For torch and tensorflow, it will create a bool tensor For mxnet, it will create a float tensor Parameters ---------- mask: numpy ndarray input mask tensor """ assert isinstance(mask, np.ndarray), "input for generate_mask_tensor" \ "should be an numpy ndarray" if F.backend_name == 'mxnet': return F.tensor(mask, dtype=F.data_type_dict['float32']) else: return F.tensor(mask, dtype=F.data_type_dict['bool'])
[docs]class Subset(object): """Subset of a dataset at specified indices Code adapted from PyTorch. Parameters ---------- dataset dataset[i] should return the ith datapoint indices : list List of datapoint indices to construct the subset """ def __init__(self, dataset, indices): self.dataset = dataset self.indices = indices
[docs] def __getitem__(self, item): """Get the datapoint indexed by item Returns ------- tuple datapoint """ return self.dataset[self.indices[item]]
[docs] def __len__(self): """Get subset size Returns ------- int Number of datapoints in the subset """ return len(self.indices)