Source code for

"""Fetcher based on dipy."""

import os
import sys
import contextlib

from os.path import join as pjoin
from hashlib import md5
from shutil import copyfileobj

import tarfile
import zipfile

if sys.version_info[0] < 3:
    from urllib2 import urlopen
    from urllib.request import urlopen

# Set a user-writeable file-system location to put files:
if 'FURY_HOME' in os.environ:
    fury_home = os.environ['FURY_HOME']
    fury_home = pjoin(os.path.expanduser('~'), '.fury')

# The URL to the University of Washington Researchworks repository:

class FetcherError(Exception):

[docs]def update_progressbar(progress, total_length): """Show progressbar. Takes a number between 0 and 1 to indicate progress from 0 to 100%. """ # Try to set the bar_length according to the console size try: columns = os.popen('tput cols', 'r').read() bar_length = int(columns) - 46 if(not (bar_length > 1)): bar_length = 20 except Exception: # Default value if determination of console size fails bar_length = 20 block = int(round(bar_length * progress)) size_string = "{0:.2f} MB".format(float(total_length) / (1024 * 1024)) text = "\rDownload Progress: [{0}] {1:.2f}% of {2}".format( "#" * block + "-" * (bar_length - block), progress * 100, size_string) sys.stdout.write(text) sys.stdout.flush()
[docs]def copyfileobj_withprogress(fsrc, fdst, total_length, length=16 * 1024): copied = 0 while True: buf = if not buf: break fdst.write(buf) copied += len(buf) progress = float(copied) / float(total_length) update_progressbar(progress, total_length)
def _already_there_msg(folder): """Print a message indicating that a certain data-set is already in place.""" msg = 'Dataset is already in place. If you want to fetch it again ' msg += 'please first remove the folder %s ' % folder print(msg) def _get_file_md5(filename): """Compute the md5 checksum of a file""" md5_data = md5() with open(filename, 'rb') as f: for chunk in iter(lambda: * md5_data.block_size), b''): md5_data.update(chunk) return md5_data.hexdigest()
[docs]def check_md5(filename, stored_md5=None): """Compute the md5 of filename. check if it matches with the supplied string md5 Parameters ---------- filename : string Path to a file. md5 : string Known md5 of filename to check against. If None (default), checking is skipped """ if stored_md5 is not None: computed_md5 = _get_file_md5(filename) if stored_md5 != computed_md5: msg = """The downloaded file, %s, does not have the expected md5 checksum of "%s". Instead, the md5 checksum was: "%s". This could mean that something is wrong with the file or that the upstream file has been updated. You can try downloading the file again or updating to the newest version of Fury.""" % (filename, stored_md5, computed_md5) raise FetcherError(msg)
def _get_file_data(fname, url): with contextlib.closing(urlopen(url)) as opener: try: response_size = opener.headers['content-length'] except KeyError: response_size = None with open(fname, 'wb') as data: if(response_size is None): copyfileobj(opener, data) else: copyfileobj_withprogress(opener, data, response_size)
[docs]def fetch_data(files, folder, data_size=None): """Downloads files to folder and checks their md5 checksums. Parameters ---------- files : dictionary For each file in `files` the value should be (url, md5). The file will be downloaded from url if the file does not already exist or if the file exists but the md5 checksum does not match. folder : str The directory where to save the file, the directory will be created if it does not already exist. data_size : str, optional A string describing the size of the data (e.g. "91 MB") to be logged to the screen. Default does not produce any information about data size. Raises ------ FetcherError Raises if the md5 checksum of the file does not match the expected value. The downloaded file is not deleted when this error is raised. """ if not os.path.exists(folder): print("Creating new folder %s" % (folder)) os.makedirs(folder) if data_size is not None: print('Data size is approximately %s' % data_size) all_skip = True for f in files: url, md5 = files[f] fullpath = pjoin(folder, f) if os.path.exists(fullpath) and (_get_file_md5(fullpath) == md5): continue all_skip = False print('Downloading "%s" to %s' % (f, folder)) _get_file_data(fullpath, url) check_md5(fullpath, md5) if all_skip: _already_there_msg(folder) else: print("Files successfully downloaded to %s" % (folder))
def _make_fetcher(name, folder, baseurl, remote_fnames, local_fnames, md5_list=None, doc="", data_size=None, msg=None, unzip=False): """Create a new fetcher. Parameters ---------- name : str The name of the fetcher function. folder : str The full path to the folder in which the files would be placed locally. Typically, this is something like 'pjoin(fury_home, 'foo')' baseurl : str The URL from which this fetcher reads files remote_fnames : list of strings The names of the files in the baseurl location local_fnames : list of strings The names of the files to be saved on the local filesystem md5_list : list of strings, optional The md5 checksums of the files. Used to verify the content of the files. Default: None, skipping checking md5. doc : str, optional. Documentation of the fetcher. data_size : str, optional. If provided, is sent as a message to the user before downloading starts. msg : str, optional. A message to print to screen when fetching takes place. Default (None) is to print nothing unzip : bool, optional Whether to unzip the file(s) after downloading them. Supports zip, gz, and tar.gz files. Returns ------- fetcher : function A function that, when called, fetches data according to the designated inputs """ def fetcher(): files = {} for i, (f, n), in enumerate(zip(remote_fnames, local_fnames)): files[n] = (baseurl + f, md5_list[i] if md5_list is not None else None) fetch_data(files, folder, data_size) if msg is not None: print(msg) if unzip: for f in local_fnames: split_ext = os.path.splitext(f) if split_ext[-1] == '.gz' or split_ext[-1] == '.bz2': if os.path.splitext(split_ext[0])[-1] == '.tar': ar =, f)) ar.extractall(path=folder) ar.close() else: raise ValueError('File extension is not recognized') elif split_ext[-1] == '.zip': z = zipfile.ZipFile(pjoin(folder, f), 'r') z.extractall(folder) z.close() else: raise ValueError('File extension is not recognized') return files, folder fetcher.__name__ = name fetcher.__doc__ = doc return fetcher fetch_viz_icons = _make_fetcher("fetch_viz_icons", pjoin(fury_home, "icons"), UW_RW_URL + "1773/38478/", ['icomoon.tar.gz'], ['icomoon.tar.gz'], ['94a07cba06b4136b6687396426f1e380'], data_size="12KB", doc="Download icons for fury", unzip=True)
[docs]def read_viz_icons(style='icomoon', fname='infinity.png'): """Read specific icon from specific style. Parameters ---------- style : str Current icon style. Default is icomoon. fname : str Filename of icon. This should be found in folder HOME/.fury/style/. Default is infinity.png. Returns -------- path : str Complete path of icon. """ folder = pjoin(fury_home, 'icons', style) return pjoin(folder, fname)