"""Automated data download and IO."""
# Builtins
import glob
import os
import gzip
import lzma
import bz2
import hashlib
import shutil
import zipfile
import sys
import math
import logging
from functools import partial
import time
import fnmatch
import urllib.request
import urllib.error
from urllib.parse import urlparse
import socket
import multiprocessing as mp
from netrc import netrc
# External libs
import pandas as pd
import numpy as np
from shapely.ops import transform as shp_trafo
import shapely.geometry as shpg
import requests
# Optional libs
try:
import geopandas as gpd
except ImportError:
pass
try:
import salem
from salem import wgs84
except ImportError:
pass
try:
import rasterio
try:
# rasterio V > 1.0
from rasterio.merge import merge as merge_tool
except ImportError:
from rasterio.tools.merge import merge as merge_tool
except ImportError:
pass
try:
ModuleNotFoundError
except NameError:
ModuleNotFoundError = ImportError
# Locals
import oggm.cfg as cfg
from oggm.exceptions import (InvalidParamsError, NoInternetException,
DownloadVerificationFailedException,
DownloadCredentialsMissingException,
HttpDownloadError, HttpContentTooShortError,
InvalidDEMError)
# Module logger
logger = logging.getLogger('.'.join(__name__.split('.')[:-1]))
# Github repository and commit hash/branch name/tag name on that repository
# The given commit will be downloaded from github and used as source for
# all sample data
SAMPLE_DATA_GH_REPO = 'OGGM/oggm-sample-data'
SAMPLE_DATA_COMMIT = '5944d88bb8bdaed12988174fa036c7b603a05148'
CRU_SERVER = ('https://crudata.uea.ac.uk/cru/data/hrg/cru_ts_4.01/cruts'
'.1709081022.v4.01/')
HISTALP_SERVER = 'http://www.zamg.ac.at/histalp/download/grid5m/'
GDIR_URL = 'https://cluster.klima.uni-bremen.de/~fmaussion/gdirs/oggm_v1.1/'
DEMO_GDIR_URL = 'https://cluster.klima.uni-bremen.de/~fmaussion/demo_gdirs/'
CMIP5_URL = 'https://cluster.klima.uni-bremen.de/~nicolas/cmip5-ng/'
CHECKSUM_URL = 'https://cluster.klima.uni-bremen.de/data/downloads.sha256.xz'
CHECKSUM_VALIDATION_URL = CHECKSUM_URL + '.sha256'
# Web mercator proj constants
WEB_N_PIX = 256
WEB_EARTH_RADUIS = 6378137.
DEM_SOURCES = ['GIMP', 'ARCTICDEM', 'RAMP', 'TANDEM', 'AW3D30', 'MAPZEN',
'DEM3', 'ASTER', 'SRTM', 'REMA']
_RGI_METADATA = dict()
DEM3REG = {
'ISL': [-25., -13., 63., 67.], # Iceland
'SVALBARD': [9., 35.99, 75., 84.],
'JANMAYEN': [-10., -7., 70., 72.],
'FJ': [36., 68., 79., 90.], # Franz Josef Land
'FAR': [-8., -6., 61., 63.], # Faroer
'BEAR': [18., 20., 74., 75.], # Bear Island
'SHL': [-3., 0., 60., 61.], # Shetland
# Antarctica tiles as UTM zones, large files
'01-15': [-180., -91., -90, -60.],
'16-30': [-91., -1., -90., -60.],
'31-45': [-1., 89., -90., -60.],
'46-60': [89., 189., -90., -60.],
# Greenland tiles
'GL-North': [-72., -11., 76., 84.],
'GL-West': [-62., -42., 64., 76.],
'GL-South': [-52., -40., 59., 64.],
'GL-East': [-42., -17., 64., 76.]
}
# Function
tuple2int = partial(np.array, dtype=np.int64)
# Global Lock
lock = mp.Lock()
# Download verification dictionary
_dl_verify_data = None
def mkdir(path, reset=False):
"""Checks if directory exists and if not, create one.
Parameters
----------
reset: erase the content of the directory if exists
Returns
-------
the path
"""
if reset and os.path.exists(path):
shutil.rmtree(path)
try:
os.makedirs(path)
except FileExistsError:
pass
return path
def del_empty_dirs(s_dir):
"""Delete empty directories."""
b_empty = True
for s_target in os.listdir(s_dir):
s_path = os.path.join(s_dir, s_target)
if os.path.isdir(s_path):
if not del_empty_dirs(s_path):
b_empty = False
else:
b_empty = False
if b_empty:
os.rmdir(s_dir)
return b_empty
def findfiles(root_dir, endswith):
"""Finds all files with a specific ending in a directory
Parameters
----------
root_dir : str
The directory to search fo
endswith : str
The file ending (e.g. '.hgt'
Returns
-------
the list of files
"""
out = []
for dirpath, dirnames, filenames in os.walk(root_dir):
for filename in [f for f in filenames if f.endswith(endswith)]:
out.append(os.path.join(dirpath, filename))
return out
def _get_download_lock():
return lock
def get_dl_verify_data():
"""Returns a dictionary with all known download object hashes.
The returned dictionary resolves str: cache_obj_name
to a tuple (int: size, bytes: sha256).
"""
global _dl_verify_data
if _dl_verify_data is not None:
return _dl_verify_data
verify_file_path = os.path.join(cfg.CACHE_DIR, 'downloads.sha256.xz')
try:
with requests.get(CHECKSUM_VALIDATION_URL) as req:
req.raise_for_status()
verify_file_sha256 = req.text.split(maxsplit=1)[0]
verify_file_sha256 = bytearray.fromhex(verify_file_sha256)
except Exception as e:
verify_file_sha256 = None
logger.warning('Failed getting verification checksum: ' + repr(e))
def do_verify():
if os.path.isfile(verify_file_path) and verify_file_sha256:
sha256 = hashlib.sha256()
with open(verify_file_path, 'rb') as f:
for b in iter(lambda: f.read(0xFFFF), b''):
sha256.update(b)
if sha256.digest() != verify_file_sha256:
logger.warning('%s changed or invalid, deleting.'
% (verify_file_path))
os.remove(verify_file_path)
do_verify()
if not os.path.isfile(verify_file_path):
logger.info('Downloading %s to %s...'
% (CHECKSUM_URL, verify_file_path))
with requests.get(CHECKSUM_URL, stream=True) as req:
if req.status_code == 200:
with open(verify_file_path, 'wb') as f:
for b in req.iter_content(chunk_size=0xFFFF):
if b:
f.write(b)
logger.info('Done downloading.')
do_verify()
if not os.path.isfile(verify_file_path):
logger.warning('Downloading and verifiying checksums failed.')
return dict()
data = dict()
with lzma.open(verify_file_path, 'rb') as f:
for line in f:
line = line.decode('utf-8').strip()
if not line:
continue
elems = line.split(maxsplit=2)
data[elems[2]] = (int(elems[1]), bytearray.fromhex(elems[0]))
_dl_verify_data = data
logger.info('Successfully loaded verification data.')
return _dl_verify_data
def _call_dl_func(dl_func, cache_path):
"""Helper so the actual call to downloads can be overridden
"""
return dl_func(cache_path)
def _cached_download_helper(cache_obj_name, dl_func, reset=False):
"""Helper function for downloads.
Takes care of checking if the file is already cached.
Only calls the actual download function when no cached version exists.
"""
cache_dir = cfg.PATHS['dl_cache_dir']
cache_ro = cfg.PARAMS['dl_cache_readonly']
try:
# this is for real runs
fb_cache_dir = os.path.join(cfg.PATHS['working_dir'], 'cache')
check_fb_dir = False
except KeyError:
# Nothing have been set up yet, this is bad - use tmp
# This should happen on RO cluster only but still
fb_cache_dir = os.path.join(cfg.CACHE_DIR, 'cache')
check_fb_dir = True
if not cache_dir:
# Defaults to working directory: it must be set!
if not cfg.PATHS['working_dir']:
raise InvalidParamsError("Need a valid PATHS['working_dir']!")
cache_dir = fb_cache_dir
cache_ro = False
fb_path = os.path.join(fb_cache_dir, cache_obj_name)
if not reset and os.path.isfile(fb_path):
return fb_path
cache_path = os.path.join(cache_dir, cache_obj_name)
if not reset and os.path.isfile(cache_path):
return cache_path
if cache_ro:
if check_fb_dir:
# Add a manual check that we are caching sample data download
if 'oggm-sample-data' not in fb_path:
raise InvalidParamsError('Attempting to download something '
'with invalid global settings.')
cache_path = fb_path
if not cfg.PARAMS['has_internet']:
raise NoInternetException("Download required, but "
"`has_internet` is False.")
mkdir(os.path.dirname(cache_path))
try:
cache_path = _call_dl_func(dl_func, cache_path)
except BaseException:
if os.path.exists(cache_path):
os.remove(cache_path)
raise
return cache_path
def _verified_download_helper(cache_obj_name, dl_func, reset=False):
"""Helper function for downloads.
Verifies the size and hash of the downloaded file against the included
list of known static files.
Uses _cached_download_helper to perform the actual download.
"""
path = _cached_download_helper(cache_obj_name, dl_func, reset)
try:
dl_verify = cfg.PARAMS['dl_verify']
except KeyError:
dl_verify = True
if dl_verify and path is not None:
data = get_dl_verify_data()
if cache_obj_name not in data:
logger.warning('No known hash for %s' % cache_obj_name)
else:
# compute the hash
sha256 = hashlib.sha256()
with open(path, 'rb') as f:
for b in iter(lambda: f.read(0xFFFF), b''):
sha256.update(b)
sha256 = sha256.digest()
size = os.path.getsize(path)
# check
data = data[cache_obj_name]
if data[0] != size or data[1] != sha256:
err = '%s failed to verify!\nis: %s %s\nexpected: %s %s' % (
path, size, sha256.hex(), data[0], data[1].hex())
raise DownloadVerificationFailedException(msg=err, path=path)
logger.info('%s verified successfully.' % path)
return path
def _requests_urlretrieve(url, path, reporthook, auth=None, timeout=None):
"""Implements the required features of urlretrieve on top of requests
"""
chunk_size = 128 * 1024
chunk_count = 0
with requests.get(url, stream=True, auth=auth, timeout=timeout) as r:
if r.status_code != 200:
raise HttpDownloadError(r.status_code, url)
r.raise_for_status()
size = r.headers.get('content-length') or -1
size = int(size)
if reporthook:
reporthook(chunk_count, chunk_size, size)
with open(path, 'wb') as f:
for chunk in r.iter_content(chunk_size=chunk_size):
if not chunk:
continue
f.write(chunk)
chunk_count += 1
if reporthook:
reporthook(chunk_count, chunk_size, size)
if chunk_count * chunk_size < size:
raise HttpContentTooShortError()
def _classic_urlretrieve(url, path, reporthook, auth=None, timeout=None):
"""Thin wrapper around pythons urllib urlretrieve
"""
ourl = url
if auth:
u = urlparse(url)
if '@' not in u.netloc:
netloc = auth[0] + ':' + auth[1] + '@' + u.netloc
url = u._replace(netloc=netloc).geturl()
old_def_timeout = socket.getdefaulttimeout()
if timeout is not None:
socket.setdefaulttimeout(timeout)
try:
urllib.request.urlretrieve(url, path, reporthook)
except urllib.error.HTTPError as e:
raise HttpDownloadError(e.code, ourl)
except urllib.error.ContentTooShortError as e:
raise HttpContentTooShortError()
finally:
socket.setdefaulttimeout(old_def_timeout)
def _get_url_cache_name(url):
"""Returns the cache name for any given url.
"""
res = urlparse(url)
return res.netloc + res.path
def oggm_urlretrieve(url, cache_obj_name=None, reset=False,
reporthook=None, auth=None, timeout=None):
"""Wrapper around urlretrieve, to implement our caching logic.
Instead of accepting a destination path, it decided where to store the file
and returns the local path.
auth is expected to be either a tuple of ('username', 'password') or None.
"""
if cache_obj_name is None:
cache_obj_name = _get_url_cache_name(url)
def _dlf(cache_path):
logger.info("Downloading %s to %s..." % (url, cache_path))
try:
_requests_urlretrieve(url, cache_path, reporthook, auth, timeout)
except requests.exceptions.InvalidSchema:
_classic_urlretrieve(url, cache_path, reporthook, auth, timeout)
return cache_path
return _verified_download_helper(cache_obj_name, _dlf, reset)
def _progress_urlretrieve(url, cache_name=None, reset=False,
auth=None, timeout=None):
"""Downloads a file, returns its local path, and shows a progressbar."""
try:
from progressbar import DataTransferBar, UnknownLength
pbar = [None]
def _upd(count, size, total):
if pbar[0] is None:
pbar[0] = DataTransferBar()
if pbar[0].max_value is None:
if total > 0:
pbar[0].start(total)
else:
pbar[0].start(UnknownLength)
pbar[0].update(min(count * size, total))
sys.stdout.flush()
res = oggm_urlretrieve(url, cache_obj_name=cache_name, reset=reset,
reporthook=_upd, auth=auth, timeout=timeout)
try:
pbar[0].finish()
except BaseException:
pass
return res
except (ImportError, ModuleNotFoundError):
return oggm_urlretrieve(url, cache_obj_name=cache_name,
reset=reset, auth=auth, timeout=timeout)
def aws_file_download(aws_path, cache_name=None, reset=False):
with _get_download_lock():
return _aws_file_download_unlocked(aws_path, cache_name, reset)
def _aws_file_download_unlocked(aws_path, cache_name=None, reset=False):
"""Download a file from the AWS drive s3://astgtmv2/
**Note:** you need AWS credentials for this to work.
Parameters
----------
aws_path: path relative to s3://astgtmv2/
"""
while aws_path.startswith('/'):
aws_path = aws_path[1:]
if cache_name is not None:
cache_obj_name = cache_name
else:
cache_obj_name = 'astgtmv2/' + aws_path
def _dlf(cache_path):
raise NotImplementedError("Downloads from AWS are no longer supported")
return _verified_download_helper(cache_obj_name, _dlf, reset)
def file_downloader(www_path, retry_max=5, cache_name=None,
reset=False, auth=None, timeout=None):
"""A slightly better downloader: it tries more than once."""
local_path = None
retry_counter = 0
while retry_counter <= retry_max:
# Try to download
try:
retry_counter += 1
local_path = _progress_urlretrieve(www_path, cache_name=cache_name,
reset=reset, auth=auth,
timeout=timeout)
# if no error, exit
break
except HttpDownloadError as err:
# This works well for py3
if err.code == 404 or err.code == 300:
# Ok so this *should* be an ocean tile
return None
elif err.code >= 500 and err.code < 600:
logger.info("Downloading %s failed with HTTP error %s, "
"retrying in 10 seconds... %s/%s" %
(www_path, err.code, retry_counter, retry_max))
time.sleep(10)
continue
else:
raise
except HttpContentTooShortError as err:
logger.info("Downloading %s failed with ContentTooShortError"
" error %s, retrying in 10 seconds... %s/%s" %
(www_path, err.code, retry_counter, retry_max))
time.sleep(10)
continue
except DownloadVerificationFailedException as err:
if (cfg.PATHS['dl_cache_dir'] and
err.path.startswith(cfg.PATHS['dl_cache_dir']) and
cfg.PARAMS['dl_cache_readonly']):
if not cache_name:
cache_name = _get_url_cache_name(www_path)
cache_name = "GLOBAL_CACHE_INVALID/" + cache_name
retry_counter -= 1
logger.info("Global cache for %s is invalid!")
else:
try:
os.remove(err.path)
except FileNotFoundError:
pass
logger.info("Downloading %s failed with "
"DownloadVerificationFailedException\n %s\n"
"The file might have changed or is corrupted. "
"File deleted. Re-downloading... %s/%s" %
(www_path, err.msg, retry_counter, retry_max))
continue
except requests.ConnectionError as err:
if err.args[0].__class__.__name__ == 'MaxRetryError':
# if request tried often enough we don't have to do this
# this error does happen for not existing ASTERv3 files
return None
else:
# in other cases: try again
logger.info("Downloading %s failed with ConnectionError, "
"retrying in 10 seconds... %s/%s" %
(www_path, retry_counter, retry_max))
time.sleep(10)
continue
# See if we managed (fail is allowed)
if not local_path or not os.path.exists(local_path):
logger.warning('Downloading %s failed.' % www_path)
return local_path
def download_with_authentification(wwwfile, key):
""" Uses credentials from a local .netrc file to download files
This is function is currently used for TanDEM-X and ASTER
Parameters
----------
wwwfile : str
path to the file to download
key : str
the machine to to look at in the .netrc file
Returns
-------
"""
# Attempt to download without credentials first to hit the cache
try:
dest_file = file_downloader(wwwfile)
except HttpDownloadError:
dest_file = None
# Grab auth parameters
if not dest_file:
authfile = os.path.expanduser('~/.netrc')
if not os.path.isfile(authfile):
raise DownloadCredentialsMissingException(
(authfile, ' does not exist. Create and add credentials for ',
'TanDEM-X with `oggm_tdmdem90_login`. And use ',
'`oggm_nasa_earthdata_login` for ASTER data.'))
try:
netrc(authfile).authenticators(key)[0]
except TypeError:
raise DownloadCredentialsMissingException(
('Credentials for ', key, ' are not in ', authfile, '. Add ',
'credentials for TanDEM-X with `oggm_tdmdem90_login`. ',
'And use `oggm_nasa_earthdata_login` for ASTER data.'))
dest_file = file_downloader(
wwwfile, auth=(netrc(authfile).authenticators(key)[0],
netrc(authfile).authenticators(key)[2]))
return dest_file
def download_oggm_files():
with _get_download_lock():
return _download_oggm_files_unlocked()
def _download_oggm_files_unlocked():
"""Checks if the demo data is already on the cache and downloads it."""
zip_url = 'https://github.com/%s/archive/%s.zip' % \
(SAMPLE_DATA_GH_REPO, SAMPLE_DATA_COMMIT)
odir = os.path.join(cfg.CACHE_DIR)
sdir = os.path.join(cfg.CACHE_DIR,
'oggm-sample-data-%s' % SAMPLE_DATA_COMMIT)
# download only if necessary
if not os.path.exists(sdir):
ofile = file_downloader(zip_url)
with zipfile.ZipFile(ofile) as zf:
zf.extractall(odir)
assert os.path.isdir(sdir)
# list of files for output
out = dict()
for root, directories, filenames in os.walk(sdir):
for filename in filenames:
if filename in out:
# This was a stupid thing, and should not happen
# TODO: duplicates in sample data...
k = os.path.join(os.path.basename(root), filename)
assert k not in out
out[k] = os.path.join(root, filename)
else:
out[filename] = os.path.join(root, filename)
return out
def _download_srtm_file(zone):
with _get_download_lock():
return _download_srtm_file_unlocked(zone)
def _download_srtm_file_unlocked(zone):
"""Checks if the srtm data is in the directory and if not, download it.
"""
# extract directory
tmpdir = cfg.PATHS['tmp_dir']
mkdir(tmpdir)
outpath = os.path.join(tmpdir, 'srtm_' + zone + '.tif')
# check if extracted file exists already
if os.path.exists(outpath):
return outpath
# Did we download it yet?
wwwfile = ('http://srtm.csi.cgiar.org/wp-content/uploads/files/srtm_5x5/'
'TIFF/srtm_' + zone + '.zip')
dest_file = file_downloader(wwwfile)
# None means we tried hard but we couldn't find it
if not dest_file:
return None
# ok we have to extract it
if not os.path.exists(outpath):
with zipfile.ZipFile(dest_file) as zf:
zf.extractall(tmpdir)
# See if we're good, don't overfill the tmp directory
assert os.path.exists(outpath)
cfg.get_lru_handler(tmpdir).append(outpath)
return outpath
def _download_tandem_file(zone):
with _get_download_lock():
return _download_tandem_file_unlocked(zone)
def _download_tandem_file_unlocked(zone):
"""Checks if the tandem data is in the directory and if not, download it.
"""
# extract directory
tmpdir = cfg.PATHS['tmp_dir']
mkdir(tmpdir)
bname = zone.split('/')[-1] + '_DEM.tif'
wwwfile = ('https://download.geoservice.dlr.de/TDM90/files/'
'{}.zip'.format(zone))
outpath = os.path.join(tmpdir, bname)
# check if extracted file exists already
if os.path.exists(outpath):
return outpath
dest_file = download_with_authentification(wwwfile, 'geoservice.dlr.de')
# That means we tried hard but we couldn't find it
if not dest_file:
return None
elif not zipfile.is_zipfile(dest_file):
# If the TanDEM-X tile does not exist, a invalid file is created.
# See https://github.com/OGGM/oggm/issues/893 for more details
return None
# ok we have to extract it
if not os.path.exists(outpath):
with zipfile.ZipFile(dest_file) as zf:
for fn in zf.namelist():
if 'DEM/' + bname in fn:
break
with open(outpath, 'wb') as fo:
fo.write(zf.read(fn))
# See if we're good, don't overfill the tmp directory
assert os.path.exists(outpath)
cfg.get_lru_handler(tmpdir).append(outpath)
return outpath
def _download_dem3_viewpano(zone):
with _get_download_lock():
return _download_dem3_viewpano_unlocked(zone)
def _download_dem3_viewpano_unlocked(zone):
"""Checks if the DEM3 data is in the directory and if not, download it.
"""
# extract directory
tmpdir = cfg.PATHS['tmp_dir']
mkdir(tmpdir)
outpath = os.path.join(tmpdir, zone + '.tif')
extract_dir = os.path.join(tmpdir, 'tmp_' + zone)
mkdir(extract_dir, reset=True)
# check if extracted file exists already
if os.path.exists(outpath):
return outpath
# OK, so see if downloaded already
# some files have a newer version 'v2'
if zone in ['R33', 'R34', 'R35', 'R36', 'R37', 'R38', 'Q32', 'Q33', 'Q34',
'Q35', 'Q36', 'Q37', 'Q38', 'Q39', 'Q40', 'P31', 'P32', 'P33',
'P34', 'P35', 'P36', 'P37', 'P38', 'P39', 'P40']:
ifile = 'http://viewfinderpanoramas.org/dem3/' + zone + 'v2.zip'
elif zone in DEM3REG.keys():
# We prepared these files as tif already
ifile = ('https://cluster.klima.uni-bremen.de/~fmaussion/DEM/'
'DEM3_MERGED/{}.tif'.format(zone))
return file_downloader(ifile)
else:
ifile = 'http://viewfinderpanoramas.org/dem3/' + zone + '.zip'
dfile = file_downloader(ifile)
# None means we tried hard but we couldn't find it
if not dfile:
return None
# ok we have to extract it
with zipfile.ZipFile(dfile) as zf:
zf.extractall(extract_dir)
# Serious issue: sometimes, if a southern hemisphere URL is queried for
# download and there is none, a NH zip file is downloaded.
# Example: http://viewfinderpanoramas.org/dem3/SN29.zip yields N29!
# BUT: There are southern hemisphere files that download properly. However,
# the unzipped folder has the file name of
# the northern hemisphere file. Some checks if correct file exists:
if len(zone) == 4 and zone.startswith('S'):
zonedir = os.path.join(extract_dir, zone[1:])
else:
zonedir = os.path.join(extract_dir, zone)
globlist = glob.glob(os.path.join(zonedir, '*.hgt'))
# take care of the special file naming cases
if zone in DEM3REG.keys():
globlist = glob.glob(os.path.join(extract_dir, '*', '*.hgt'))
if not globlist:
# Final resort
globlist = (findfiles(extract_dir, '.hgt') or
findfiles(extract_dir, '.HGT'))
if not globlist:
raise RuntimeError("We should have some files here, but we don't")
# merge the single HGT files (can be a bit ineffective, because not every
# single file might be exactly within extent...)
rfiles = [rasterio.open(s) for s in globlist]
dest, output_transform = merge_tool(rfiles)
profile = rfiles[0].profile
if 'affine' in profile:
profile.pop('affine')
profile['transform'] = output_transform
profile['height'] = dest.shape[1]
profile['width'] = dest.shape[2]
profile['driver'] = 'GTiff'
with rasterio.open(outpath, 'w', **profile) as dst:
dst.write(dest)
for rf in rfiles:
rf.close()
# delete original files to spare disk space
for s in globlist:
os.remove(s)
del_empty_dirs(tmpdir)
# See if we're good, don't overfill the tmp directory
assert os.path.exists(outpath)
cfg.get_lru_handler(tmpdir).append(outpath)
return outpath
def _download_aster_file(zone):
with _get_download_lock():
return _download_aster_file_unlocked(zone)
def _download_aster_file_unlocked(zone):
"""Checks if the tandem data is in the directory and if not, download it.
"""
# extract directory
tmpdir = cfg.PATHS['tmp_dir']
mkdir(tmpdir)
wwwfile = ('https://e4ftl01.cr.usgs.gov/ASTER_B/ASTT/ASTGTM.003/'
'2000.03.01/{}.zip'.format(zone))
outpath = os.path.join(tmpdir, zone + '_dem.tif')
# check if extracted file exists already
if os.path.exists(outpath):
return outpath
# download from NASA Earthdata with credentials
dest_file = download_with_authentification(wwwfile,
'urs.earthdata.nasa.gov')
# That means we tried hard but we couldn't find it
if not dest_file:
return None
# ok we have to extract it
if not os.path.exists(outpath):
with zipfile.ZipFile(dest_file) as zf:
zf.extractall(tmpdir)
# See if we're good, don't overfill the tmp directory
assert os.path.exists(outpath)
cfg.get_lru_handler(tmpdir).append(outpath)
return outpath
def _download_topo_file_from_cluster(fname):
with _get_download_lock():
return _download_topo_file_from_cluster_unlocked(fname)
def _download_topo_file_from_cluster_unlocked(fname):
"""Checks if the special topo data is in the directory and if not,
download it from the cluster.
"""
# extract directory
tmpdir = cfg.PATHS['tmp_dir']
mkdir(tmpdir)
outpath = os.path.join(tmpdir, fname)
url = 'https://cluster.klima.uni-bremen.de/data/dems/'
url += fname + '.zip'
dfile = file_downloader(url)
if not os.path.exists(outpath):
logger.info('Extracting ' + fname + '.zip to ' + outpath + '...')
with zipfile.ZipFile(dfile) as zf:
zf.extractall(tmpdir)
# See if we're good, don't overfill the tmp directory
assert os.path.exists(outpath)
cfg.get_lru_handler(tmpdir).append(outpath)
return outpath
def _download_aw3d30_file(zone):
with _get_download_lock():
return _download_aw3d30_file_unlocked(zone)
def _download_aw3d30_file_unlocked(fullzone):
"""Checks if the AW3D30 data is in the directory and if not, download it.
"""
# extract directory
tmpdir = cfg.PATHS['tmp_dir']
mkdir(tmpdir)
# tarfiles are extracted in directories per each tile
tile = fullzone.split('/')[1]
demfile = os.path.join(tmpdir, tile, tile + '_AVE_DSM.tif')
# check if extracted file exists already
if os.path.exists(demfile):
return demfile
# Did we download it yet?
ftpfile = ('ftp://ftp.eorc.jaxa.jp/pub/ALOS/ext1/AW3D30/release_v1804/'
+ fullzone + '.tar.gz')
try:
dest_file = file_downloader(ftpfile, timeout=180)
except urllib.error.URLError:
# This error is raised if file is not available, could be water
return None
# None means we tried hard but we couldn't find it
if not dest_file:
return None
# ok we have to extract it
if not os.path.exists(demfile):
from oggm.utils import robust_tar_extract
dempath = os.path.dirname(demfile)
robust_tar_extract(dest_file, dempath)
# See if we're good, don't overfill the tmp directory
assert os.path.exists(demfile)
# this tarfile contains several files
for file in os.listdir(dempath):
cfg.get_lru_handler(tmpdir).append(os.path.join(dempath, file))
return demfile
def _download_mapzen_file(zone):
with _get_download_lock():
return _download_mapzen_file_unlocked(zone)
def _download_mapzen_file_unlocked(zone):
"""Checks if the mapzen data is in the directory and if not, download it.
"""
bucket = 'elevation-tiles-prod'
prefix = 'geotiff'
url = 'http://s3.amazonaws.com/%s/%s/%s' % (bucket, prefix, zone)
# That's all
return file_downloader(url, timeout=180)
def _get_centerline_lonlat(gdir):
"""Quick n dirty solution to write the centerlines as a shapefile"""
cls = gdir.read_pickle('centerlines')
olist = []
for j, cl in enumerate(cls[::-1]):
mm = 1 if j == 0 else 0
gs = gpd.GeoSeries()
gs['RGIID'] = gdir.rgi_id
gs['LE_SEGMENT'] = np.rint(np.max(cl.dis_on_line) * gdir.grid.dx)
gs['MAIN'] = mm
tra_func = partial(gdir.grid.ij_to_crs, crs=wgs84)
gs['geometry'] = shp_trafo(tra_func, cl.line)
olist.append(gs)
return olist
def get_prepro_gdir(rgi_version, rgi_id, border, prepro_level, demo_url=False):
with _get_download_lock():
return _get_prepro_gdir_unlocked(rgi_version, rgi_id, border,
prepro_level, demo_url)
def _get_prepro_gdir_unlocked(rgi_version, rgi_id, border, prepro_level,
demo_url=False):
# Prepro URL
url = DEMO_GDIR_URL if demo_url else GDIR_URL
url += 'RGI{}/'.format(rgi_version)
url += 'b_{:03d}/'.format(border)
url += 'L{:d}/'.format(prepro_level)
url += '{}/{}.tar' .format(rgi_id[:8], rgi_id[:11])
tar_base = file_downloader(url)
if tar_base is None:
raise RuntimeError('Could not find file at ' + url)
return tar_base
def srtm_zone(lon_ex, lat_ex):
"""Returns a list of SRTM zones covering the desired extent.
"""
# SRTM are sorted in tiles of 5 degrees
srtm_x0 = -180.
srtm_y0 = 60.
srtm_dx = 5.
srtm_dy = -5.
# quick n dirty solution to be sure that we will cover the whole range
mi, ma = np.min(lon_ex), np.max(lon_ex)
# int() to avoid Deprec warning:
lon_ex = np.linspace(mi, ma, int(np.ceil((ma - mi) + 3)))
mi, ma = np.min(lat_ex), np.max(lat_ex)
# int() to avoid Deprec warning
lat_ex = np.linspace(mi, ma, int(np.ceil((ma - mi) + 3)))
zones = []
for lon in lon_ex:
for lat in lat_ex:
dx = lon - srtm_x0
dy = lat - srtm_y0
assert dy < 0
zx = np.ceil(dx / srtm_dx)
zy = np.ceil(dy / srtm_dy)
zones.append('{:02.0f}_{:02.0f}'.format(zx, zy))
return list(sorted(set(zones)))
def _tandem_path(lon_tile, lat_tile):
# OK we have a proper tile now
# First folder level is sorted from S to N
level_0 = 'S' if lat_tile < 0 else 'N'
level_0 += '{:02d}'.format(abs(lat_tile))
# Second folder level is sorted from W to E, but in 10 steps
level_1 = 'W' if lon_tile < 0 else 'E'
level_1 += '{:03d}'.format(divmod(abs(lon_tile), 10)[0] * 10)
# Level 2 is formating, but depends on lat
level_2 = 'W' if lon_tile < 0 else 'E'
if abs(lat_tile) <= 60:
level_2 += '{:03d}'.format(abs(lon_tile))
elif abs(lat_tile) <= 80:
level_2 += '{:03d}'.format(divmod(abs(lon_tile), 2)[0] * 2)
else:
level_2 += '{:03d}'.format(divmod(abs(lon_tile), 4)[0] * 4)
# Final path
out = (level_0 + '/' + level_1 + '/' +
'TDM1_DEM__30_{}{}'.format(level_0, level_2))
return out
def tandem_zone(lon_ex, lat_ex):
"""Returns a list of TanDEM-X zones covering the desired extent.
"""
# Files are one by one tiles, so lets loop over them
# For higher lats they are stored in steps of 2 and 4. My code below
# is probably giving more files than needed but better safe than sorry
lat_tiles = np.arange(np.floor(lat_ex[0]), np.ceil(lat_ex[1]+1e-9),
dtype=np.int)
zones = []
for lat in lat_tiles:
if abs(lat) < 60:
l0 = np.floor(lon_ex[0])
l1 = np.floor(lon_ex[1])
elif abs(lat) < 80:
l0 = divmod(lon_ex[0], 2)[0] * 2
l1 = divmod(lon_ex[1], 2)[0] * 2
elif abs(lat) < 90:
l0 = divmod(lon_ex[0], 4)[0] * 4
l1 = divmod(lon_ex[1], 4)[0] * 4
lon_tiles = np.arange(l0, l1+1, dtype=np.int)
for lon in lon_tiles:
zones.append(_tandem_path(lon, lat))
return list(sorted(set(zones)))
def _aw3d30_path(lon_tile, lat_tile):
# OK we have a proper tile now
# Folders are sorted with N E S W in 5 degree steps
# But in N and E the lower boundary is indicated
# e.g. N060 contains N060 - N064
# e.g. E000 contains E000 - E004
# but S and W indicate the upper boundary:
# e.g. S010 contains S006 - S010
# e.g. W095 contains W091 - W095
# get letters
ns = 'S' if lat_tile < 0 else 'N'
ew = 'W' if lon_tile < 0 else 'E'
# get lat/lon
lon = abs(5 * np.floor(lon_tile/5))
lat = abs(5 * np.floor(lat_tile/5))
folder = '%s%.3d%s%.3d' % (ns, lat, ew, lon)
filename = '%s%.3d%s%.3d' % (ns, abs(lat_tile), ew, abs(lon_tile))
# Final path
out = folder + '/' + filename
return out
def aw3d30_zone(lon_ex, lat_ex):
"""Returns a list of AW3D30 zones covering the desired extent.
"""
# Files are one by one tiles, so lets loop over them
lon_tiles = np.arange(np.floor(lon_ex[0]), np.ceil(lon_ex[1]+1e-9),
dtype=np.int)
lat_tiles = np.arange(np.floor(lat_ex[0]), np.ceil(lat_ex[1]+1e-9),
dtype=np.int)
zones = []
for lon in lon_tiles:
for lat in lat_tiles:
zones.append(_aw3d30_path(lon, lat))
return list(sorted(set(zones)))
def _extent_to_polygon(lon_ex, lat_ex, to_crs=None):
if lon_ex[0] == lon_ex[1] and lat_ex[0] == lat_ex[1]:
out = shpg.Point(lon_ex[0], lat_ex[0])
else:
x = [lon_ex[0], lon_ex[1], lon_ex[1], lon_ex[0], lon_ex[0]]
y = [lat_ex[0], lat_ex[0], lat_ex[1], lat_ex[1], lat_ex[0]]
out = shpg.Polygon(np.array((x, y)).T)
if to_crs is not None:
out = salem.transform_geometry(out, to_crs=to_crs)
return out
def arcticdem_zone(lon_ex, lat_ex):
"""Returns a list of Arctic-DEM zones covering the desired extent.
"""
gdf = gpd.read_file(get_demo_file('ArcticDEM_Tile_Index_Rel7_by_tile.shp'))
p = _extent_to_polygon(lon_ex, lat_ex, to_crs=gdf.crs)
gdf = gdf.loc[gdf.intersects(p)]
return gdf.tile.values if len(gdf) > 0 else []
def rema_zone(lon_ex, lat_ex):
"""Returns a list of REMA-DEM zones covering the desired extent.
"""
gdf = gpd.read_file(get_demo_file('REMA_Tile_Index_Rel1.1.shp'))
p = _extent_to_polygon(lon_ex, lat_ex, to_crs=gdf.crs)
gdf = gdf.loc[gdf.intersects(p)]
return gdf.tile.values if len(gdf) > 0 else []
def dem3_viewpano_zone(lon_ex, lat_ex):
"""Returns a list of DEM3 zones covering the desired extent.
http://viewfinderpanoramas.org/Coverage%20map%20viewfinderpanoramas_org3.htm
"""
for _f in DEM3REG.keys():
if (np.min(lon_ex) >= DEM3REG[_f][0]) and \
(np.max(lon_ex) <= DEM3REG[_f][1]) and \
(np.min(lat_ex) >= DEM3REG[_f][2]) and \
(np.max(lat_ex) <= DEM3REG[_f][3]):
# test some weird inset files in Antarctica
if (np.min(lon_ex) >= -91.) and (np.max(lon_ex) <= -90.) and \
(np.min(lat_ex) >= -72.) and (np.max(lat_ex) <= -68.):
return ['SR15']
elif (np.min(lon_ex) >= -47.) and (np.max(lon_ex) <= -43.) and \
(np.min(lat_ex) >= -61.) and (np.max(lat_ex) <= -60.):
return ['SP23']
elif (np.min(lon_ex) >= 162.) and (np.max(lon_ex) <= 165.) and \
(np.min(lat_ex) >= -68.) and (np.max(lat_ex) <= -66.):
return ['SQ58']
# test some rogue Greenland tiles as well
elif (np.min(lon_ex) >= -72.) and (np.max(lon_ex) <= -66.) and \
(np.min(lat_ex) >= 76.) and (np.max(lat_ex) <= 80.):
return ['T19']
elif (np.min(lon_ex) >= -72.) and (np.max(lon_ex) <= -66.) and \
(np.min(lat_ex) >= 80.) and (np.max(lat_ex) <= 83.):
return ['U19']
elif (np.min(lon_ex) >= -66.) and (np.max(lon_ex) <= -60.) and \
(np.min(lat_ex) >= 80.) and (np.max(lat_ex) <= 83.):
return ['U20']
elif (np.min(lon_ex) >= -60.) and (np.max(lon_ex) <= -54.) and \
(np.min(lat_ex) >= 80.) and (np.max(lat_ex) <= 83.):
return ['U21']
elif (np.min(lon_ex) >= -54.) and (np.max(lon_ex) <= -48.) and \
(np.min(lat_ex) >= 80.) and (np.max(lat_ex) <= 83.):
return ['U22']
elif (np.min(lon_ex) >= -25.) and (np.max(lon_ex) <= -13.) and \
(np.min(lat_ex) >= 63.) and (np.max(lat_ex) <= 67.):
return ['ISL']
else:
return [_f]
# if the tile doesn't have a special name, its name can be found like this:
# corrected SRTMs are sorted in tiles of 6 deg longitude and 4 deg latitude
srtm_x0 = -180.
srtm_y0 = 0.
srtm_dx = 6.
srtm_dy = 4.
# quick n dirty solution to be sure that we will cover the whole range
mi, ma = np.min(lon_ex), np.max(lon_ex)
# TODO: Fabien, find out what Johannes wanted with this +3
# +3 is just for the number to become still a bit larger
# int() to avoid Deprec warning
lon_ex = np.linspace(mi, ma, int(np.ceil((ma - mi) / srtm_dy) + 3))
mi, ma = np.min(lat_ex), np.max(lat_ex)
# int() to avoid Deprec warning
lat_ex = np.linspace(mi, ma, int(np.ceil((ma - mi) / srtm_dx) + 3))
zones = []
for lon in lon_ex:
for lat in lat_ex:
dx = lon - srtm_x0
dy = lat - srtm_y0
zx = np.ceil(dx / srtm_dx)
# convert number to letter
zy = chr(int(abs(dy / srtm_dy)) + ord('A'))
if lat >= 0:
zones.append('%s%02.0f' % (zy, zx))
else:
zones.append('S%s%02.0f' % (zy, zx))
return list(sorted(set(zones)))
def aster_zone(lon_ex, lat_ex):
"""Returns a list of ASTGTMV3 zones covering the desired extent.
ASTER v3 tiles are 1 degree x 1 degree
N50 contains 50 to 50.9
E10 contains 10 to 10.9
S70 contains -69.99 to -69.0
W20 contains -19.99 to -19.0
"""
# adding small buffer for unlikely case where one lon/lat_ex == xx.0
lons = np.arange(np.floor(lon_ex[0]-1e-9), np.ceil(lon_ex[1]+1e-9))
lats = np.arange(np.floor(lat_ex[0]-1e-9), np.ceil(lat_ex[1]+1e-9))
zones = []
for lat in lats:
# north or south?
ns = 'S' if lat < 0 else 'N'
for lon in lons:
# east or west?
ew = 'W' if lon < 0 else 'E'
filename = 'ASTGTMV003_{}{:02.0f}{}{:03.0f}'.format(ns, abs(lat),
ew, abs(lon))
zones.append(filename)
return list(sorted(set(zones)))
def mapzen_zone(lon_ex, lat_ex, dx_meter=None, zoom=None):
"""Returns a list of AWS mapzen zones covering the desired extent.
For mapzen one has to specify the level of detail (zoom) one wants. The
best way in OGGM is to specify dx_meter of the underlying map and OGGM
will decide which zoom level works best.
"""
if dx_meter is None and zoom is None:
raise InvalidParamsError('Need either zoom level or dx_meter.')
bottom, top = lat_ex
left, right = lon_ex
ybound = 85.0511
if bottom <= -ybound:
bottom = -ybound
if top <= -ybound:
top = -ybound
if bottom > ybound:
bottom = ybound
if top > ybound:
top = ybound
if right >= 180:
right = 179.999
if left >= 180:
left = 179.999
if dx_meter:
# Find out the zoom so that we are close to the desired accuracy
lat = np.max(np.abs([bottom, top]))
zoom = int(np.ceil(math.log2((math.cos(lat * math.pi / 180) *
2 * math.pi * WEB_EARTH_RADUIS) /
(WEB_N_PIX * dx_meter))))
# According to this we should just always stay above 10 (sorry)
# https://github.com/tilezen/joerd/blob/master/docs/data-sources.md
zoom = 10 if zoom < 10 else zoom
# Code from planetutils
size = 2 ** zoom
xt = lambda x: int((x + 180.0) / 360.0 * size)
yt = lambda y: int((1.0 - math.log(math.tan(math.radians(y)) +
(1 / math.cos(math.radians(y))))
/ math.pi) / 2.0 * size)
tiles = []
for x in range(xt(left), xt(right) + 1):
for y in range(yt(top), yt(bottom) + 1):
tiles.append('/'.join(map(str, [zoom, x, str(y) + '.tif'])))
return tiles
[docs]def get_demo_file(fname):
"""Returns the path to the desired OGGM-sample-file.
If Sample data is not cached it will be downloaded from
https://github.com/OGGM/oggm-sample-data
Parameters
----------
fname : str
Filename of the desired OGGM-sample-file
Returns
-------
str
Absolute path to the desired file.
"""
d = download_oggm_files()
if fname in d:
return d[fname]
else:
return None
def get_cru_cl_file():
"""Returns the path to the unpacked CRU CL file (is in sample data)."""
download_oggm_files()
sdir = os.path.join(cfg.CACHE_DIR,
'oggm-sample-data-%s' % SAMPLE_DATA_COMMIT,
'cru')
fpath = os.path.join(sdir, 'cru_cl2.nc')
if os.path.exists(fpath):
return fpath
else:
with zipfile.ZipFile(fpath + '.zip') as zf:
zf.extractall(sdir)
assert os.path.exists(fpath)
return fpath
def get_wgms_files():
"""Get the path to the default WGMS-RGI link file and the data dir.
Returns
-------
(file, dir) : paths to the files
"""
download_oggm_files()
sdir = os.path.join(cfg.CACHE_DIR,
'oggm-sample-data-%s' % SAMPLE_DATA_COMMIT,
'wgms')
datadir = os.path.join(sdir, 'mbdata')
assert os.path.exists(datadir)
outf = os.path.join(sdir, 'rgi_wgms_links_20171101.csv')
outf = pd.read_csv(outf, dtype={'RGI_REG': object})
return outf, datadir
def get_glathida_file():
"""Get the path to the default GlaThiDa-RGI link file.
Returns
-------
file : paths to the file
"""
# Roll our own
download_oggm_files()
sdir = os.path.join(cfg.CACHE_DIR,
'oggm-sample-data-%s' % SAMPLE_DATA_COMMIT,
'glathida')
outf = os.path.join(sdir, 'rgi_glathida_links.csv')
assert os.path.exists(outf)
return outf
[docs]def get_rgi_dir(version=None, reset=False):
"""Path to the RGI directory.
If the RGI files are not present, download them.
Parameters
----------
version : str
'5', '6', defaults to None (linking to the one specified in cfg.PARAMS)
reset : bool
If True, deletes the RGI directory first and downloads the data
Returns
-------
str
path to the RGI directory
"""
with _get_download_lock():
return _get_rgi_dir_unlocked(version=version, reset=reset)
def _get_rgi_dir_unlocked(version=None, reset=False):
rgi_dir = cfg.PATHS['rgi_dir']
if version is None:
version = cfg.PARAMS['rgi_version']
if len(version) == 1:
version += '0'
# Be sure the user gave a sensible path to the RGI dir
if not rgi_dir:
raise InvalidParamsError('The RGI data directory has to be'
'specified explicitly.')
rgi_dir = os.path.abspath(os.path.expanduser(rgi_dir))
rgi_dir = os.path.join(rgi_dir, 'RGIV' + version)
mkdir(rgi_dir, reset=reset)
if version == '50':
dfile = 'http://www.glims.org/RGI/rgi50_files/rgi50.zip'
elif version == '60':
dfile = 'http://www.glims.org/RGI/rgi60_files/00_rgi60.zip'
elif version == '61':
dfile = 'https://cluster.klima.uni-bremen.de/data/rgi/rgi_61.zip'
elif version == '62':
dfile = 'https://cluster.klima.uni-bremen.de/~fmaussion/misc/rgi62.zip'
test_file = os.path.join(rgi_dir,
'*_rgi*{}_manifest.txt'.format(version))
if len(glob.glob(test_file)) == 0:
# if not there download it
ofile = file_downloader(dfile, reset=reset)
# Extract root
with zipfile.ZipFile(ofile) as zf:
zf.extractall(rgi_dir)
# Extract subdirs
pattern = '*_rgi{}_*.zip'.format(version)
for root, dirs, files in os.walk(cfg.PATHS['rgi_dir']):
for filename in fnmatch.filter(files, pattern):
zfile = os.path.join(root, filename)
with zipfile.ZipFile(zfile) as zf:
ex_root = zfile.replace('.zip', '')
mkdir(ex_root)
zf.extractall(ex_root)
# delete the zipfile after success
os.remove(zfile)
if len(glob.glob(test_file)) == 0:
raise RuntimeError('Could not find a manifest file in the RGI '
'directory: ' + rgi_dir)
return rgi_dir
[docs]def get_rgi_region_file(region, version=None, reset=False):
"""Path to the RGI region file.
If the RGI files are not present, download them.
Parameters
----------
region : str
from '01' to '19'
version : str
'5', '6', defaults to None (linking to the one specified in cfg.PARAMS)
reset : bool
If True, deletes the RGI directory first and downloads the data
Returns
-------
str
path to the RGI shapefile
"""
rgi_dir = get_rgi_dir(version=version, reset=reset)
f = list(glob.glob(rgi_dir + "/*/{}_*.shp".format(region)))
assert len(f) == 1
return f[0]
[docs]def get_rgi_glacier_entities(rgi_ids, version=None):
"""Get a list of glacier outlines selected from their RGI IDs.
Will download RGI data if not present.
Parameters
----------
rgi_ids : list of str
the glaciers you want the outlines for
version : str
the rgi version
Returns
-------
geopandas.GeoDataFrame
containing the desired RGI glacier outlines
"""
regions = [s.split('-')[1].split('.')[0] for s in rgi_ids]
if version is None:
version = rgi_ids[0].split('-')[0][-2:]
selection = []
for reg in sorted(np.unique(regions)):
sh = gpd.read_file(get_rgi_region_file(reg, version=version))
selection.append(sh.loc[sh.RGIId.isin(rgi_ids)])
# Make a new dataframe of those
selection = pd.concat(selection)
selection.crs = sh.crs # for geolocalisation
if len(selection) != len(rgi_ids):
raise RuntimeError('Could not find all RGI ids')
return selection
[docs]def get_rgi_intersects_dir(version=None, reset=False):
"""Path to the RGI directory containing the intersect files.
If the files are not present, download them.
Parameters
----------
version : str
'5', '6', defaults to None (linking to the one specified in cfg.PARAMS)
reset : bool
If True, deletes the intersects before redownloading them
Returns
-------
str
path to the directory
"""
with _get_download_lock():
return _get_rgi_intersects_dir_unlocked(version=version, reset=reset)
def _get_rgi_intersects_dir_unlocked(version=None, reset=False):
rgi_dir = cfg.PATHS['rgi_dir']
if version is None:
version = cfg.PARAMS['rgi_version']
if len(version) == 1:
version += '0'
# Be sure the user gave a sensible path to the RGI dir
if not rgi_dir:
raise InvalidParamsError('The RGI data directory has to be'
'specified explicitly.')
rgi_dir = os.path.abspath(os.path.expanduser(rgi_dir))
mkdir(rgi_dir)
dfile = 'https://cluster.klima.uni-bremen.de/data/rgi/'
dfile += 'RGI_V{}_Intersects.zip'.format(version)
if version == '62':
dfile = ('https://cluster.klima.uni-bremen.de/~fmaussion/misc/'
'rgi62_Intersects.zip')
odir = os.path.join(rgi_dir, 'RGI_V' + version + '_Intersects')
if reset and os.path.exists(odir):
shutil.rmtree(odir)
# A lot of code for backwards compat (sigh...)
if version in ['50', '60']:
test_file = os.path.join(odir, 'Intersects_OGGM_Manifest.txt')
if not os.path.exists(test_file):
# if not there download it
ofile = file_downloader(dfile, reset=reset)
# Extract root
with zipfile.ZipFile(ofile) as zf:
zf.extractall(odir)
if not os.path.exists(test_file):
raise RuntimeError('Could not find a manifest file in the RGI '
'directory: ' + odir)
else:
test_file = os.path.join(odir,
'*ntersect*anifest.txt'.format(version))
if len(glob.glob(test_file)) == 0:
# if not there download it
ofile = file_downloader(dfile, reset=reset)
# Extract root
with zipfile.ZipFile(ofile) as zf:
zf.extractall(odir)
# Extract subdirs
pattern = '*_rgi{}_*.zip'.format(version)
for root, dirs, files in os.walk(cfg.PATHS['rgi_dir']):
for filename in fnmatch.filter(files, pattern):
zfile = os.path.join(root, filename)
with zipfile.ZipFile(zfile) as zf:
ex_root = zfile.replace('.zip', '')
mkdir(ex_root)
zf.extractall(ex_root)
# delete the zipfile after success
os.remove(zfile)
if len(glob.glob(test_file)) == 0:
raise RuntimeError('Could not find a manifest file in the RGI '
'directory: ' + odir)
return odir
[docs]def get_rgi_intersects_region_file(region=None, version=None, reset=False):
"""Path to the RGI regional intersect file.
If the RGI files are not present, download them.
Parameters
----------
region : str
from '00' to '19', with '00' being the global file (deprecated).
From RGI version '61' onwards, please use `get_rgi_intersects_entities`
with a list of glaciers instead of relying to the global file.
version : str
'5', '6', '61'... defaults the one specified in cfg.PARAMS
reset : bool
If True, deletes the intersect file before redownloading it
Returns
-------
str
path to the RGI intersects shapefile
"""
if version is None:
version = cfg.PARAMS['rgi_version']
if len(version) == 1:
version += '0'
rgi_dir = get_rgi_intersects_dir(version=version, reset=reset)
if region == '00':
if version in ['50', '60']:
version = 'AllRegs'
region = '*'
else:
raise InvalidParamsError("From RGI version 61 onwards, please use "
"get_rgi_intersects_entities() instead.")
f = list(glob.glob(os.path.join(rgi_dir, "*", '*intersects*' + region +
'_rgi*' + version + '*.shp')))
assert len(f) == 1
return f[0]
[docs]def get_rgi_intersects_entities(rgi_ids, version=None):
"""Get a list of glacier intersects selected from their RGI IDs.
Parameters
----------
rgi_ids: list of str
list of rgi_ids you want to look for intersections for
version: str
'5', '6', '61'... defaults the one specified in cfg.PARAMS
Returns
-------
geopandas.GeoDataFrame
with the selected intersects
"""
if version is None:
version = cfg.PARAMS['rgi_version']
if len(version) == 1:
version += '0'
regions = [s.split('-')[1].split('.')[0] for s in rgi_ids]
selection = []
for reg in sorted(np.unique(regions)):
sh = gpd.read_file(get_rgi_intersects_region_file(reg,
version=version))
selection.append(sh.loc[sh.RGIId_1.isin(rgi_ids) |
sh.RGIId_2.isin(rgi_ids)])
# Make a new dataframe of those
selection = pd.concat(selection)
selection.crs = sh.crs # for geolocalisation
return selection
[docs]def get_cru_file(var=None):
"""Returns a path to the desired CRU baseline climate file.
If the file is not present, download it.
Parameters
----------
var : str
'tmp' for temperature
'pre' for precipitation
Returns
-------
str
path to the CRU file
"""
with _get_download_lock():
return _get_cru_file_unlocked(var)
def _get_cru_file_unlocked(var=None):
cru_dir = cfg.PATHS['cru_dir']
# Be sure the user gave a sensible path to the climate dir
if not cru_dir:
raise InvalidParamsError('The CRU data directory has to be'
'specified explicitly.')
cru_dir = os.path.abspath(os.path.expanduser(cru_dir))
mkdir(cru_dir)
# Be sure input makes sense
if var not in ['tmp', 'pre']:
raise InvalidParamsError('CRU variable {} does not exist!'.format(var))
# The user files may have different dates, so search for patterns
bname = 'cru_ts*.{}.dat.nc'.format(var)
search = glob.glob(os.path.join(cru_dir, bname))
if len(search) == 1:
ofile = search[0]
elif len(search) > 1:
raise RuntimeError('You seem to have more than one file in your CRU '
'directory: {}. Help me by deleting the one'
'you dont want to use anymore.'.format(cru_dir))
else:
# if not there download it
cru_filename = 'cru_ts4.01.1901.2016.{}.dat.nc'.format(var)
cru_url = CRU_SERVER + '{}/'.format(var) + cru_filename + '.gz'
dlfile = file_downloader(cru_url)
ofile = os.path.join(cru_dir, cru_filename)
with gzip.GzipFile(dlfile) as zf:
with open(ofile, 'wb') as outfile:
for line in zf:
outfile.write(line)
return ofile
[docs]def get_histalp_file(var=None):
"""Returns a path to the desired HISTALP baseline climate file.
If the file is not present, download it.
Parameters
----------
var : str
'tmp' for temperature
'pre' for precipitation
Returns
-------
str
path to the CRU file
"""
with _get_download_lock():
return _get_histalp_file_unlocked(var)
def _get_histalp_file_unlocked(var=None):
cru_dir = cfg.PATHS['cru_dir']
# Be sure the user gave a sensible path to the climate dir
if not cru_dir:
raise InvalidParamsError('The CRU data directory has to be'
'specified explicitly.')
cru_dir = os.path.abspath(os.path.expanduser(cru_dir))
mkdir(cru_dir)
# Be sure input makes sense
if var not in ['tmp', 'pre']:
raise InvalidParamsError('HISTALP variable {} '
'does not exist!'.format(var))
# File to look for
if var == 'tmp':
bname = 'HISTALP_temperature_1780-2014.nc'
else:
bname = 'HISTALP_precipitation_all_abs_1801-2014.nc'
search = glob.glob(os.path.join(cru_dir, bname))
if len(search) == 1:
ofile = search[0]
elif len(search) > 1:
raise RuntimeError('You seem to have more than one matching file in '
'your CRU directory: {}. Help me by deleting the '
'one you dont want to use anymore.'.format(cru_dir))
else:
# if not there download it
h_url = HISTALP_SERVER + bname + '.bz2'
dlfile = file_downloader(h_url)
ofile = os.path.join(cru_dir, bname)
with bz2.BZ2File(dlfile) as zf:
with open(ofile, 'wb') as outfile:
for line in zf:
outfile.write(line)
return ofile
def is_dem_source_available(source, lon_ex, lat_ex):
"""Checks if a DEM source is available for your purpose.
This is only a very rough check! It doesn't mean that the data really is
available, but at least it's worth a try.
Parameters
----------
source : str, required
the source you want to check for
lon_ex : tuple or int, required
a (min_lon, max_lon) tuple delimiting the requested area longitudes
lat_ex : tuple or int, required
a (min_lat, max_lat) tuple delimiting the requested area latitudes
Returns
-------
True or False
"""
from oggm.utils import tolist
lon_ex = tolist(lon_ex, length=2)
lat_ex = tolist(lat_ex, length=2)
def _in_grid(grid_json, lon, lat):
i, j = cfg.DATA['dem_grids'][grid_json].transform(lon, lat,
maskout=True)
return np.all(~ (i.mask | j.mask))
if source == 'GIMP':
return _in_grid('gimpdem_90m_v01.1.json', lon_ex, lat_ex)
elif source == 'ARCTICDEM':
return _in_grid('arcticdem_mosaic_100m_v3.0.json', lon_ex, lat_ex)
elif source == 'RAMP':
return _in_grid('AntarcticDEM_wgs84.json', lon_ex, lat_ex)
elif source == 'REMA':
return _in_grid('REMA_100m_dem.json', lon_ex, lat_ex)
elif source == 'TANDEM':
return True
elif source == 'AW3D30':
return np.min(lat_ex) > -60
elif source == 'MAPZEN':
return True
elif source == 'DEM3':
return True
elif source == 'ASTER':
return True
elif source == 'SRTM':
return np.max(np.abs(lat_ex)) < 60
elif source == 'USER':
return True
elif source is None:
return True
def default_dem_source(lon_ex, lat_ex, rgi_region=None, rgi_subregion=None):
"""Current default DEM source at a given location.
Parameters
----------
lon_ex : tuple or int, required
a (min_lon, max_lon) tuple delimiting the requested area longitudes
lat_ex : tuple or int, required
a (min_lat, max_lat) tuple delimiting the requested area latitudes
rgi_region : str, optional
the RGI region number (required for the GIMP DEM)
rgi_subregion : str, optional
the RGI subregion str (useful for RGI Reg 19)
Returns
-------
the chosen DEM source
"""
from oggm.utils import tolist
lon_ex = tolist(lon_ex, length=2)
lat_ex = tolist(lat_ex, length=2)
# GIMP is in polar stereographic, not easy to test if glacier is on the map
# It would be possible with a salem grid but this is a bit more expensive
# Instead, we are just asking RGI for the region
if rgi_region is not None and int(rgi_region) == 5:
return 'GIMP'
# ARCTIC DEM is not yet automatized
# If we have to automatise this one day, we should use the shapefile
# of the tiles, and then check for RGI region:
# use_without_check = ['03', '05', '06', '07', '09']
# to_test_on_shape = ['01', '02', '04', '08']
# Antarctica
if rgi_region is not None and int(rgi_region) == 19:
if rgi_subregion is None:
raise InvalidParamsError('Must specify subregion for Antarctica')
if rgi_subregion in ['19-01', '19-02', '19-03', '19-04', '19-05']:
# special case for some distant islands
return 'DEM3'
return 'RAMP'
# In high latitudes and an exceptional region in Eastern Russia, DEM3
# exceptional test for eastern russia:
if ((np.min(lat_ex) < -60.) or (np.max(lat_ex) > 60.) or
(np.min(lat_ex) > 59 and np.min(lon_ex) > 170)):
return 'DEM3'
# Everywhere else SRTM
return 'SRTM'
def get_topo_file(lon_ex, lat_ex, rgi_region=None, rgi_subregion=None,
dx_meter=None, zoom=None, source=None):
"""Path(s) to the DEM file(s) covering the desired extent.
If the needed files for covering the extent are not present, download them.
By default it will be referred to SRTM for [-60S; 60N], GIMP for Greenland,
RAMP for Antarctica, and a corrected DEM3 (viewfinderpanoramas.org)
elsewhere.
A user-specified data source can be given with the ``source`` keyword.
Parameters
----------
lon_ex : tuple or int, required
a (min_lon, max_lon) tuple delimiting the requested area longitudes
lat_ex : tuple or int, required
a (min_lat, max_lat) tuple delimiting the requested area latitudes
rgi_region : str, optional
the RGI region number (required for the GIMP DEM)
rgi_subregion : str, optional
the RGI subregion str (useful for RGI Reg 19)
dx_meter : float, required for source='MAPZEN'
the resolution of the glacier map (to decide the zoom level of mapzen)
zoom : int, optional
if you know the zoom already (for MAPZEN only)
source : str or list of str, optional
If you want to force the use of a certain DEM source. Available are:
- 'USER' : file set in cfg.PATHS['dem_file']
- 'SRTM' : http://srtm.csi.cgiar.org/
- 'GIMP' : https://bpcrc.osu.edu/gdg/data/gimpdem
- 'RAMP' : http://nsidc.org/data/docs/daac/nsidc0082_ramp_dem.gd.html
- 'REMA' : https://www.pgc.umn.edu/data/rema/
- 'DEM3' : http://viewfinderpanoramas.org/
- 'ASTER' : https://lpdaac.usgs.gov/products/astgtmv003/
- 'TANDEM' : https://geoservice.dlr.de/web/dataguide/tdm90/
- 'ARCTICDEM' : https://www.pgc.umn.edu/data/arcticdem/
- 'AW3D30' : https://www.eorc.jaxa.jp/ALOS/en/aw3d30
- 'MAPZEN' : https://registry.opendata.aws/terrain-tiles/
Returns
-------
tuple: (list with path(s) to the DEM file(s), data source str)
"""
from oggm.utils import tolist
lon_ex = tolist(lon_ex, length=2)
lat_ex = tolist(lat_ex, length=2)
if source is not None and not isinstance(source, str):
# check all user options
for s in source:
demf, source_str = get_topo_file(lon_ex, lat_ex,
rgi_region=rgi_region,
rgi_subregion=rgi_subregion,
source=s)
if demf[0]:
return demf, source_str
# Did the user specify a specific DEM file?
if 'dem_file' in cfg.PATHS and os.path.isfile(cfg.PATHS['dem_file']):
source = 'USER' if source is None else source
if source == 'USER':
return [cfg.PATHS['dem_file']], source
# Some logic to decide which source to take if unspecified
if source is None:
source = default_dem_source(lon_ex, lat_ex, rgi_region=rgi_region,
rgi_subregion=rgi_subregion)
if source not in DEM_SOURCES:
raise InvalidParamsError('`source` must be one of '
'{}'.format(DEM_SOURCES))
# OK go
files = []
if source == 'GIMP':
_file = _download_topo_file_from_cluster('gimpdem_90m_v01.1.tif')
files.append(_file)
if source == 'ARCTICDEM':
zones = arcticdem_zone(lon_ex, lat_ex)
for z in zones:
with _get_download_lock():
url = 'https://cluster.klima.uni-bremen.de/~fmaussion/'
url += 'DEM/ArcticDEM_100m_v3.0/'
url += '{}_100m_v3.0/{}_100m_v3.0_reg_dem.tif'.format(z, z)
files.append(file_downloader(url))
if source == 'RAMP':
_file = _download_topo_file_from_cluster('AntarcticDEM_wgs84.tif')
files.append(_file)
if source == 'REMA':
zones = rema_zone(lon_ex, lat_ex)
for z in zones:
with _get_download_lock():
url = 'https://cluster.klima.uni-bremen.de/~fmaussion/'
url += 'DEM/REMA_100m_v1.1/'
url += '{}_100m_v1.1/{}_100m_v1.1_reg_dem.tif'.format(z, z)
files.append(file_downloader(url))
if source == 'TANDEM':
zones = tandem_zone(lon_ex, lat_ex)
for z in zones:
files.append(_download_tandem_file(z))
if source == 'AW3D30':
zones = aw3d30_zone(lon_ex, lat_ex)
for z in zones:
files.append(_download_aw3d30_file(z))
if source == 'MAPZEN':
zones = mapzen_zone(lon_ex, lat_ex, dx_meter=dx_meter, zoom=zoom)
for z in zones:
files.append(_download_mapzen_file(z))
if source == 'ASTER':
zones = aster_zone(lon_ex, lat_ex)
for z in zones:
files.append(_download_aster_file(z))
if source == 'DEM3':
zones = dem3_viewpano_zone(lon_ex, lat_ex)
for z in zones:
files.append(_download_dem3_viewpano(z))
if source == 'SRTM':
zones = srtm_zone(lon_ex, lat_ex)
for z in zones:
files.append(_download_srtm_file(z))
# filter for None (e.g. oceans)
files = [s for s in files if s]
if files:
return files, source
else:
raise InvalidDEMError('Source: {2} no topography file available for '
'extent lat:{0}, lon:{1}!'.
format(lat_ex, lon_ex, source))
def get_cmip5_file(filename, reset=False):
"""Download a global CMIP5 file.
List of files: https://cluster.klima.uni-bremen.de/~nicolas/cmip5-ng/
Parameters
----------
filename : str
the file to download, e.g 'pr_ann_ACCESS1-3_rcp85_r1i1p1_g025.nc'
or 'tas_ann_ACCESS1-3_rcp45_r1i1p1_g025.nc'
reset : bool
force re-download of an existing file
Returns
-------
the path to the netCDF file
"""
prefix = filename.split('_')[0]
dfile = CMIP5_URL + prefix + '/' + filename
return file_downloader(dfile, reset=reset)
def get_ref_mb_glaciers_candidates(rgi_version=None):
"""Reads in the WGMS list of glaciers with available MB data.
Can be found afterwards (and extended) in cdf.DATA['RGIXX_ref_ids'].
"""
if rgi_version is None:
rgi_version = cfg.PARAMS['rgi_version']
if len(rgi_version) == 2:
# We might change this one day
rgi_version = rgi_version[:1]
key = 'RGI{}0_ref_ids'.format(rgi_version)
if key not in cfg.DATA:
flink, _ = get_wgms_files()
cfg.DATA[key] = flink['RGI{}0_ID'.format(rgi_version)].tolist()
return cfg.DATA[key]
[docs]def get_ref_mb_glaciers(gdirs):
"""Get the list of glaciers we have valid mass balance measurements for.
To be valid glaciers must have more than 5 years of measurements and
be land terminating. Therefore, the list depends on the time period of the
baseline climate data and this method selects them out of a list
of potential candidates (`gdirs` arg).
Parameters
----------
gdirs : list of :py:class:`oggm.GlacierDirectory` objects
list of glaciers to check for valid reference mass balance data
Returns
-------
ref_gdirs : list of :py:class:`oggm.GlacierDirectory` objects
list of those glaciers with valid reference mass balance data
See Also
--------
get_ref_mb_glaciers_candidates
"""
# Get the links
ref_ids = get_ref_mb_glaciers_candidates(gdirs[0].rgi_version)
# We remove tidewater glaciers and glaciers with < 5 years
ref_gdirs = []
for g in gdirs:
if g.rgi_id not in ref_ids or g.is_tidewater:
continue
try:
mbdf = g.get_ref_mb_data()
if len(mbdf) >= 5:
ref_gdirs.append(g)
except RuntimeError as e:
if 'Please process some climate data before call' in str(e):
raise
return ref_gdirs