# coding=utf-8
"""Common utilities for multiple topics that are not big enough to have their own module"""
import datetime
import os
import time
import re
import shutil
import stat
import subprocess
import sys
import tarfile
import tempfile
from contextlib import contextmanager
import cf_units
import iris
import iris.exceptions
import netCDF4
import numpy as np
import six
import xxhash
from bscearth.utils.log import Log
from cdo import Cdo
from nco import Nco
from earthdiagnostics.constants import Basins
[docs]@contextmanager
def suppress_stdout():
"""Redirect the standard output to devnull"""
with open(os.devnull, "w") as devnull:
old_stdout = sys.stdout
sys.stdout = devnull
try:
yield
finally:
sys.stdout = old_stdout
[docs]class Utils(object):
"""Container class for miscellaneous utility methods"""
nco = Nco()
"""An instance of Nco class ready to be used"""
cdo = Cdo(env=os.environ)
"""An instance of Cdo class ready to be used"""
[docs] @staticmethod
def get_mask(basin, with_levels=False):
"""
Return the mask for the given basin
Parameters
----------
basin: Basin
Returns
-------
numpy.array
Raises
------
Exception: If mask.regions.nc is not available
"""
basin = Basins().parse(basin)
if basin != Basins().Global:
try:
if with_levels:
mask_handler = Utils.open_cdf('mask_regions.3d.nc')
mask = mask_handler.variables[basin.name][0, ...]
else:
mask_handler = Utils.open_cdf('mask_regions.nc')
mask = mask_handler.variables[basin.name][:, 0, :]
mask_handler.close()
except IOError:
raise Exception('File mask.regions.nc is required for basin {0}'.format(basin))
else:
mask_handler = Utils.open_cdf('mask.nc')
mask = mask_handler.variables['tmask'][0, 0, :]
mask_handler.close()
return np.squeeze(mask)
[docs] @staticmethod
def setminmax(filename, variable_list):
"""
Set the valid_max and valid_min values to the current max and min values on the file
Parameters
----------
filename: str
variable_list: str or iterable of str
"""
# noinspection PyTypeChecker
if isinstance(variable_list, six.string_types):
variable_list = variable_list.split()
Log.info('Getting max and min values for {0}', ' '.join(variable_list))
handler = Utils.open_cdf(filename)
for variable in variable_list:
var = handler.variables[variable]
values = [np.max(var), np.min(var)]
Utils.nco.ncatted(input=filename, output=filename,
options=('-h -a valid_max,{0},m,f,{1}'.format(variable, values[0]),))
Utils.nco.ncatted(input=filename, output=filename,
options=('-h -a valid_min,{0},m,f,{1}'.format(variable, values[1]),))
handler.close()
[docs] @staticmethod
def rename_variable(filepath, old_name, new_name, must_exist=True, rename_dimension=True):
"""
Rename variable from a NetCDF file
This function is just a wrapper around Utils.rename_variables
Parameters
----------
filepath: str
old_name: str
new_name: str
must_exist: bool, optional
See Also
--------
Utils.rename_variables
"""
Utils.rename_variables(filepath, {old_name: new_name}, must_exist, rename_dimension)
[docs] @staticmethod
def rename_variables(filepath, dic_names, must_exist=True, rename_dimension=True):
"""
Rename multiple variables from a NetCDF file
Parameters
----------
filepath: str
dic_names: dict of str: str
Gives the renaming to do in the form old_name: new_name
must_exist: bool, optional
Raises
-------
ValueError
If any original name is the same as the new
Exception
If any requested variable does not exist and must_exist is True
"""
for old, new in six.iteritems(dic_names):
if old == new:
raise ValueError('{0} original name is the same as the new')
original_handler = Utils.open_cdf(filepath)
original_names = set(original_handler.variables.keys()).union(original_handler.dimensions.keys())
if not any((True for x in dic_names.keys() if x in original_names)):
original_handler.close()
if must_exist:
raise Exception("Variables {0} does not exist in file {1}".format(','.join(dic_names.keys()), filepath))
return
temp = TempFile.get()
new_handler = Utils.open_cdf(temp, 'w')
for attribute in original_handler.ncattrs():
original = getattr(original_handler, attribute)
setattr(new_handler, attribute, Utils.convert_to_ascii_if_possible(original))
for dimension in original_handler.dimensions.keys():
Utils.copy_dimension(original_handler, new_handler, dimension,
new_names=dic_names, rename_dimension=rename_dimension)
for variable in original_handler.variables.keys():
Utils.copy_variable(original_handler, new_handler, variable,
new_names=dic_names, rename_dimension=rename_dimension)
original_handler.close()
new_handler.close()
Utils.move_file(temp, filepath)
[docs] @staticmethod
def check_netcdf_file(filepath):
"""
Check if a NetCDF file is well stored
This functions is used to check if a NetCDF file is corrupted. It prefers to raise a false postive than
to have false negatives.
Parameters
----------
filepath
Returns
-------
bool
"""
with suppress_stdout():
try:
handler = Utils.open_cdf(filepath)
if 'time' in handler.variables:
if handler.variables['time'].dimensions != ('time', ):
handler.close()
return False
handler.close()
iris.FUTURE.netcdf_promote = True
cubes = iris.load(filepath)
if len(cubes) == 0:
return False
except (iris.exceptions.IrisError, RuntimeError, OSError) as ex:
Log.debug('netCDF checks failed: {0}', ex)
return False
return True
[docs] @staticmethod
def get_file_variables(filename):
"""
Get all the variables in a file
Parameters
----------
filename
Returns
-------
iterable of str
"""
handler = Utils.open_cdf(filename)
variables = handler.variables.keys()
handler.close()
return variables
# noinspection PyPep8Naming
[docs] @staticmethod
def convert_to_ascii_if_possible(string, encoding='ascii'):
u"""
Convert an Unicode string to ASCII if all characters can be translated.
If a string can not be translated it is unchanged. It also automatically
replaces Bretonnière with Bretonniere
Parameters
----------
string: unicode
encoding: str, optional
Returns
-------
str
"""
# noinspection PyTypeChecker
if isinstance(string, six.string_types):
try:
return string.encode(encoding)
except UnicodeEncodeError:
if u'Bretonnière' in string:
string = string.replace(u'Bretonnière', 'Bretonniere')
return Utils.convert_to_ascii_if_possible(string, encoding)
return string
@staticmethod
def _rename_vars_directly(dic_names, filepath, handler, must_exist, rename_dimension):
for old_name, new_name in dic_names.items():
if rename_dimension:
if old_name in handler.dimensions:
handler.renameDimension(old_name, new_name)
elif must_exist:
raise Exception("Dimension {0} does not exist in file {1}".format(old_name, filepath))
if old_name in handler.variables:
if new_name not in handler.variables:
handler.renameVariable(old_name, new_name)
for var in handler.variables:
if hasattr(var, 'coordinates') and " {0} ".format(old_name) in var.coordinates:
new_coordinates = var.coordinates.replace(" {0} ".format(old_name),
" {0} ".format(new_name))
var.coordinates = Utils.convert_to_ascii_if_possible(new_coordinates)
elif must_exist:
raise Exception("Variable {0} does not exist in file {1}".format(old_name, filepath))
handler.sync()
[docs] @staticmethod
def copy_file(source, destiny, save_hash=False, use_stored_hash=True, retrials=3):
"""
Copy a file and compute a hash to check if the copy is equal to the source
Parameters
----------
source: str
destiny: str
save_hash: bool, optional
If True, stores a copy of the hash
use_stored_hash: bool, optional
If True, try to use the stored value of the source hash instead of computing it
retrials: int, optional
Minimum value is 1
See Also
--------
move_file
"""
dirname_path = os.path.dirname(destiny)
if dirname_path and not os.path.exists(dirname_path):
try:
os.makedirs(dirname_path)
Utils.give_group_write_permissions(dirname_path)
except OSError as ex:
# This can be due to a race condition. If directory already exists, we don have to do nothing
if not os.path.exists(dirname_path):
raise ex
hash_destiny = None
Log.debug('Hashing original file... {0}', datetime.datetime.now())
hash_original = Utils.get_file_hash(source, use_stored=use_stored_hash)
if retrials < 1:
retrials = 1
while hash_original != hash_destiny:
if retrials == 0:
raise Utils.CopyException('Can not copy {0} to {1}'.format(source, destiny))
Log.debug('Copying... {0}', datetime.datetime.now())
shutil.copyfile(source, destiny)
Log.debug('Hashing copy ... {0}', datetime.datetime.now())
hash_destiny = Utils.get_file_hash(destiny, save=save_hash)
retrials -= 1
Log.debug('Finished {0}', datetime.datetime.now())
[docs] @staticmethod
def move_file(source, destiny, save_hash=False, retrials=3):
"""
Move a file and compute a hash to check if the copy is equal to the source
It is just a call to Utils.copy_file followed bu
Parameters
----------
source: str
destiny: str
save_hash: bool, optional
If True, stores a copy of the hash
retrials: int, optional
Minimum value is 1
See Also
--------
copy_file
"""
Utils.copy_file(source, destiny, save_hash, retrials)
os.remove(source)
[docs] @staticmethod
def remove_file(path):
"""
Delete a file only if it previously exists
Parameters
----------
path: str
"""
if os.path.isfile(path):
os.remove(path)
[docs] @staticmethod
def copy_tree(source, destiny):
"""
Copy a full tree to a new location
Parameters
----------
source: str
destiny: str
See Also
--------
move_tree
"""
if not os.path.exists(destiny):
os.makedirs(destiny)
shutil.copystat(source, destiny)
lst = os.listdir(source)
for item in lst:
item_source = os.path.join(source, item)
item_destiny = os.path.join(destiny, item)
if os.path.isdir(item_source):
Utils.copy_tree(item_source, item_destiny)
else:
shutil.copy2(item_source, item_destiny)
[docs] @staticmethod
def move_tree(source, destiny):
"""
Move a tree to a new location
Parameters
----------
source: str
destiny: str
See Also
-------
copy_tree
"""
Utils.copy_tree(source, destiny)
time.sleep(2)
shutil.rmtree(source)
[docs] @staticmethod
def get_file_hash(filepath, use_stored=False, save=False):
"""
Get the xxHash hash for a given file
Parameters
----------
filepath: str
use_stored: bool, optional
If True, tries to use the stored hash before computing it
save: bool, optional
If True, saves the hash to a file
"""
if use_stored:
hash_file = Utils._get_hash_filename(filepath)
if os.path.isfile(hash_file):
hash_value = open(hash_file, 'r').readline()
return hash_value
blocksize = 104857600
hasher = xxhash.xxh64()
with open(filepath, 'rb') as afile:
buf = afile.read(blocksize)
while len(buf) > 0:
hasher.update(buf)
buf = afile.read(blocksize)
hash_value = hasher.hexdigest()
if save:
hash_file = open(Utils._get_hash_filename(filepath), 'w')
hash_file.write(hash_value)
hash_file.close()
return hash_value
@staticmethod
def _get_hash_filename(filepath):
folder = os.path.dirname(filepath)
filename = os.path.basename(filepath)
hash_file = os.path.join(folder, '.{0}.xxhash64.hash'.format(filename))
return hash_file
[docs] @staticmethod
def execute_shell_command(command, log_level=Log.DEBUG):
"""
Execute shell command
Writes the output to the log with the specified level
Parameters
----------
command: str or iterable of str
log_level: int, optional
Returns
-------
iterable of str
Standard output of the command
Raises
------
Utils.ExecutionError
If the command return value is non zero
"""
# noinspection PyTypeChecker
if isinstance(command, six.string_types):
command = command.split()
process = subprocess.Popen(command, stdout=subprocess.PIPE)
output = list()
comunicate = process.communicate()
for line in comunicate:
if not line:
continue
if six.PY3:
line = str(line, encoding='UTF-8')
if log_level != Log.NO_LOG:
Log.log.log(log_level, line)
output.append(line)
if process.returncode != 0:
raise Utils.ExecutionError('Error executing {0}\n Return code: {1}'.format(' '.join(command),
str(process.returncode)))
return output
_cpu_count = None
[docs] @staticmethod
def available_cpu_count():
"""Number of available virtual or physical CPUs on this system"""
if Utils._cpu_count is None:
try:
match = re.search(r'(?m)^Cpus_allowed:\s*(.*)$', open('/proc/self/status').read())
if match:
res = bin(int(match.group(1).replace(',', ''), 16)).count('1')
if res > 0:
Utils._cpu_count = res
except IOError:
try:
import multiprocessing
Utils._cpu_count = multiprocessing.cpu_count()
return Utils._cpu_count
except (ImportError, NotImplementedError):
Utils._cpu_count = -1
return Utils._cpu_count
[docs] @staticmethod
def convert2netcdf4(filetoconvert):
"""
Convert a file to NetCDF4
Conversion only performed if required. Deflation level set to 4 and shuffle activated.
Parameters
----------
filetoconvert: str
"""
if Utils._is_compressed_netcdf4(filetoconvert):
return
Log.debug('Reformatting to netCDF-4')
temp = TempFile.get()
Utils.execute_shell_command(["nccopy", "-4", "-d4", "-s", filetoconvert, temp])
shutil.move(temp, filetoconvert)
@classmethod
def _is_compressed_netcdf4(cls, filetoconvert):
ncdump_result = Utils.execute_shell_command('ncdump -hs {0}'.format(filetoconvert), Log.NO_LOG)
ncdump_result = ncdump_result[0].replace('\t', '').split('\n')
if any(':_Shuffle = "true"' in line for line in ncdump_result) and \
any(':_DeflateLevel = 4' in line for line in ncdump_result):
return True
return False
# noinspection PyPep8Naming
[docs] @staticmethod
def open_cdf(filepath, mode='a'):
"""
Open a NetCDF file
Parameters
----------
filepath: str
mode: str, optional
Returns
-------
netCDF4.Dataset
"""
return netCDF4.Dataset(filepath, mode)
[docs] @staticmethod
def get_datetime_from_netcdf(handler, time_variable='time'):
"""
Get time from NetCDF files
Parameters
----------
handler: netCDF4.Dataset
time_variable: str, optional
Returns
-------
numpy.array of Datetime
"""
var_time = handler.variables[time_variable]
nctime = var_time[:] # get values
units = var_time.units
try:
cal_temps = var_time.calendar
except AttributeError:
cal_temps = u"standard"
return netCDF4.num2date(nctime, units=units, calendar=cal_temps)
[docs] @staticmethod
def copy_variable(source, destiny, variable, must_exist=True, add_dimensions=False, new_names=None,
rename_dimension=True):
"""
Copy the given variable from source to destiny
Parameters
----------
source: netCDF4.Dataset
destiny: netCDF4.Dataset
variable: str
must_exist: bool, optional
add_dimensions: bool, optional
new_names: dict of str: str
Raises
------
Exception
If dimensions are not correct in the destiny file and add_dimensions is False
"""
if not must_exist and variable not in source.variables.keys():
return
if not new_names:
new_names = dict()
if variable in new_names:
new_name = new_names[variable]
else:
new_name = variable
if new_name in destiny.variables.keys():
return
translated_dimensions = Utils._copy_dimensions(add_dimensions, destiny, must_exist, new_names, rename_dimension,
source, variable)
if new_name in destiny.variables.keys():
# Just in case the variable we are copying match a dimension name
return
original_var = source.variables[variable]
new_var = destiny.createVariable(new_name, original_var.datatype, translated_dimensions)
Utils.copy_attributes(new_var, original_var)
if hasattr(new_var, 'coordinates'):
coords = [new_names[coord] if coord in new_names else coord for coord in new_var.coordinates.split(' ')]
new_var.coordinates = Utils.convert_to_ascii_if_possible(' '.join(coords))
new_var[:] = original_var[:]
@staticmethod
def _copy_dimensions(add_dimensions, destiny, must_exist, new_names, rename_dimension, source, variable):
if rename_dimension:
translated_dimensions = Utils._translate(source.variables[variable].dimensions, new_names)
else:
translated_dimensions = list(source.variables[variable].dimensions)
if not set(translated_dimensions).issubset(destiny.dimensions):
if not add_dimensions:
raise Exception('Variable {0} can not be added because dimensions does not match: '
'{1} {2}'.format(variable, translated_dimensions, destiny.dimensions))
for dimension in source.variables[variable].dimensions:
Utils.copy_dimension(source, destiny, dimension, must_exist, new_names, rename_dimension)
return translated_dimensions
[docs] @staticmethod
def copy_attributes(new_var, original_var, omitted_attributtes=None):
"""
Copy attributtes from one variable to another
Parameters
----------
new_var: netCDF4.Variable
original_var: netCDF4.Variable
omitted_attributtes: iterable of str
Collection of attributtes that should not be copied
"""
if omitted_attributtes is None:
omitted_attributtes = []
new_var.setncatts({k: Utils.convert_to_ascii_if_possible(original_var.getncattr(k))
for k in original_var.ncattrs() if k not in omitted_attributtes})
[docs] @staticmethod
def copy_dimension(source, destiny, dimension, must_exist=True, new_names=None, rename_dimension=False):
"""
Copy the given dimension from source to destiny, including dimension variables if present
Parameters
----------
source: netCDF4.Dataset
destiny: netCDF4.Dataset
dimension: str
must_exist: bool, optional
new_names: dict of str: str or None, optional
"""
if not must_exist and dimension not in source.dimensions.keys():
return
if not new_names or not rename_dimension:
new_names = dict()
if dimension in new_names:
new_name = new_names[dimension]
else:
new_name = dimension
if new_name in destiny.dimensions.keys():
return
if not new_name:
new_name = dimension
destiny.createDimension(new_name, source.dimensions[dimension].size)
if dimension in source.variables:
Utils.copy_variable(source, destiny, dimension,
new_names=new_names, rename_dimension=rename_dimension)
[docs] @staticmethod
def concat_variables(source, destiny, remove_source=False):
"""
Add variables from a nc file to another
Parameters
----------
source: str
destiny: str
remove_source: bool
if True, removes source file
"""
if os.path.exists(destiny):
handler_total = Utils.open_cdf(destiny)
handler_variable = Utils.open_cdf(source)
concatenated = dict()
for var in handler_variable.variables:
if var not in handler_total.variables:
Utils.copy_variable(handler_variable, handler_total, var, add_dimensions=True)
else:
variable = handler_variable.variables[var]
if 'time' not in variable.dimensions:
continue
concatenated[var] = np.concatenate((handler_total.variables[var][:], variable[:]),
axis=variable.dimensions.index('time'))
for var, array in six.iteritems(concatenated):
handler_total.variables[var][:] = array
handler_total.close()
handler_variable.close()
if remove_source:
os.remove(source)
else:
if remove_source:
Utils.move_file(source, destiny)
else:
shutil.copy(source, destiny)
Utils.convert2netcdf4(destiny)
[docs] class ExecutionError(Exception):
"""Exception to raise when a command execution fails"""
pass
@classmethod
def _translate(cls, dimensions, new_names):
translated = list()
for dim in dimensions:
if dim in new_names:
translated.append(new_names[dim])
else:
translated.append(dim)
return translated
[docs] @staticmethod
def create_folder_tree(path):
"""
Create a folder path with all parent directories if needed.
Parameters
----------
path: str
"""
if not os.path.exists(path):
# noinspection PyBroadException
try:
os.makedirs(path)
except OSError:
# This could happen if two threads are tying to create the folder.
# Let's check again for existence and rethrow if still not exists
if not os.path.isdir(path):
raise
[docs] @staticmethod
def give_group_write_permissions(path):
"""Give write permissions to the group"""
stats = os.stat(path)
if stats.st_mode & stat.S_IWGRP:
return
os.chmod(path, stats.st_mode | stat.S_IWGRP)
[docs] @staticmethod
def convert_units(var_handler, new_units, calendar=None, old_calendar=None):
"""
Convert units
Parameters
----------
var_handler: Dataset
new_units: str
calendar: str
old_calendar: str
"""
if new_units == var_handler.units:
return
if hasattr(var_handler, 'calendar'):
old_calendar = var_handler.calendar
new_unit = cf_units.Unit(new_units, calendar=calendar)
old_unit = cf_units.Unit(var_handler.units, calendar=old_calendar)
var_handler[:] = old_unit.convert(var_handler[:], new_unit, inplace=True)
if 'valid_min' in var_handler.ncattrs():
var_handler.valid_min = old_unit.convert(float(var_handler.valid_min), new_unit,
inplace=True)
if 'valid_max' in var_handler.ncattrs():
var_handler.valid_max = old_unit.convert(float(var_handler.valid_max), new_unit,
inplace=True)
var_handler.units = new_units
[docs] @staticmethod
def untar(files, destiny_path):
"""
Untar files to a given destiny
Parameters
----------
files: iterable of str
destiny_path: str
"""
for filepath in files:
Log.debug('Unpacking {0}', filepath)
tar = tarfile.open(filepath)
for file_compressed in tar.getmembers():
if file_compressed.isdir():
if os.path.isdir(os.path.join(destiny_path, file_compressed.name)):
continue
else:
if os.path.exists(os.path.join(destiny_path, file_compressed.name)):
os.remove(os.path.join(destiny_path, file_compressed.name))
tar.extract(file_compressed, destiny_path)
Log.debug('File {0} extracted', os.path.basename(file_compressed.name))
tar.close()
[docs] @staticmethod
def unzip(files, force=False):
"""
Unzip a list of files
files: str or iterable of str
force: bool, optional
if True, it will overwrite unzipped files
"""
# noinspection PyTypeChecker
if isinstance(files, six.string_types):
files = [files]
for filepath in files:
Log.debug('Unzipping {0}', filepath)
if force:
option = ' -f'
else:
option = ''
try:
Utils.execute_shell_command('gunzip{1} {0}'.format(filepath, option))
except Exception as ex:
raise Utils.UnzipException('Can not unzip {0}: {1}'.format(filepath, ex))
[docs] class UnzipException(Exception):
"""Exception raised when unzip fails"""
pass
[docs] class CopyException(Exception):
"""Exception raised when copy fails"""
pass
[docs]class TempFile(object):
"""Class to manage temporal files"""
autoclean = True
"""
If True, new temporary files are added to the list for future cleaning
"""
files = list()
"""
List of files to clean automatically
"""
scratch_folder = ''
"""
Scratch folder to create temporary files on it
"""
prefix = 'temp'
"""
Prefix for temporary filenames
"""
[docs] @staticmethod
def get(filename=None, clean=None, suffix='.nc'):
"""
Get a new temporal filename, storing it for automated cleaning
:param suffix:
:param filename: if it is not none, the function will use this filename instead of a random one
:type filename: str
:param clean: if true, stores filename for cleaning
:type clean: bool
:return: path to the temporal file
:rtype: str
"""
if clean is None:
clean = TempFile.autoclean
if filename:
path = os.path.join(TempFile.scratch_folder, filename)
else:
file_descriptor, path = tempfile.mkstemp(dir=TempFile.scratch_folder, prefix=TempFile.prefix, suffix=suffix)
path = str(path)
os.close(file_descriptor)
if clean:
TempFile.files.append(path)
return path
[docs] @staticmethod
def clean():
"""Remove all temporary files created with Tempfile until now"""
for temp_file in TempFile.files:
if os.path.exists(temp_file):
os.remove(temp_file)
TempFile.files = list()