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import subprocess
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import numpy as np
from bscearth.utils.log import Log
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from cdo import Cdo, CDOException
from cfunits import Units
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from nco import Nco
from contextlib import contextmanager
import sys
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@contextmanager
def suppress_stdout():
with open(os.devnull, "w") as devnull:
old_stdout = sys.stdout
sys.stdout = devnull
try:
yield
finally:
sys.stdout = old_stdout
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class Utils(object):
"""
Container class for miscellaneous utility methods
"""
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nco = Nco()
"""An instance of Nco class ready to be used"""
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cdo = Cdo()
"""An instance of Cdo class ready to be used"""
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@staticmethod
def get_mask(basin):
"""
Returns a numpy array containing the mask for the given basin
:param basin: basin to retrieve
:type basin: Basin
:return: mask
:rtype: numpy.array
"""
basin = Basins().parse(basin)
if basin != Basins().Global:
try:
mask_handler = Utils.openCdf('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.openCdf('mask.nc')
mask = mask_handler.variables['tmask'][0, 0, :]
mask_handler.close()
return mask
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@staticmethod
def setminmax(filename, variable_list):
"""
Sets the valid_max and valid_min values to the current max and min values on the file
:param filename: path to file
:type filename: str
:param variable_list: list of variables in which valid_min and valid_max will be set
:type variable_list: str | list
"""
if isinstance(variable_list, basestring):
variable_list = variable_list.split()
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Log.info('Getting max and min values for {0}', ' '.join(variable_list))
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for variable in variable_list:
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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]),))
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Utils.nco.ncatted(input=filename, output=filename,
options=('-h -a valid_min,{0},m,f,{1}'.format(variable, values[1]),))
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def rename_variable(filepath, old_name, new_name, must_exist=True, rename_dimension=False):
"""
Rename multiple variables from a NetCDF file
:param filepath: path to file
:type filepath: str
:param old_name: variable's name to change
:type old_name: str
:param new_name: new name
:type new_name: str
:param must_exist: if True, the function will raise an exception if the variable name does not exist
:type must_exist: bool
:param rename_dimension: if True, also rename dimensions with the same name
:type rename_dimension: bool
"""
Utils.rename_variables(filepath, {old_name: new_name}, must_exist, rename_dimension)
def rename_variables(filepath, dic_names, must_exist=True, rename_dimension=False):
"""
Rename multiple variables from a NetCDF file
:param filepath: path to file
:type filepath: str
:param dic_names: dictionary containing old names as keys and new names as values
:type dic_names: dict
:param must_exist: if True, the function will raise an exception if the variable name does not exist
:type must_exist: bool
:param rename_dimension: if True, also rename dimensions with the same name
:type rename_dimension: bool
"""
for old, new in dic_names.iteritems():
if old == new:
raise ValueError('{0} original name is the same as the new')
handler = Utils.openCdf(filepath)
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original_names = set(handler.variables.keys()).union(handler.dimensions.keys())
if not any((True for x in dic_names.keys() if x in original_names)):
handler.close()
if must_exist:
raise Exception("Variables {0} does not exist in file {1}".format(','.join(dic_names.keys()), filepath))
return
handler.close()
temp = TempFile.get()
shutil.copyfile(filepath, temp)
handler = Utils.openCdf(temp)
error = False
try:
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Utils._rename_vars_directly(dic_names, filepath, handler, must_exist, rename_dimension)
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handler.close()
if not Utils.check_netcdf_file(temp):
error = True
if error:
Log.debug('First attemp to rename failed. Using secondary rename method for netCDF')
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Utils._rename_vars_by_creating_new_file(dic_names, filepath, temp)
Utils.move_file(temp, filepath)
@staticmethod
def check_netcdf_file(filepath):
with suppress_stdout():
try:
Utils.cdo.showvar(input=filepath)
except CDOException:
return False
return True
@staticmethod
def get_file_variables(filename):
handler = Utils.openCdf(filename)
variables = handler.variables.keys()
handler.close()
return variables
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@staticmethod
def _rename_vars_by_creating_new_file(dic_names, filepath, temp):
original_handler = Utils.openCdf(filepath)
new_handler = Utils.openCdf(temp, 'w')
for attribute in original_handler.ncattrs():
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original = getattr(original_handler, attribute)
setattr(new_handler, attribute, Utils.convert_to_ASCII_if_possible(original))
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for dimension in original_handler.dimensions.keys():
Utils.copy_dimension(original_handler, new_handler, dimension, new_names=dic_names)
for variable in original_handler.variables.keys():
Utils.copy_variable(original_handler, new_handler, variable, new_names=dic_names)
original_handler.close()
new_handler.close()
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@staticmethod
def convert_to_ASCII_if_possible(string, encoding='ascii'):
if isinstance(string, basestring):
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)
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return string
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@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)
elif must_exist:
raise Exception("Variable {0} does not exist in file {1}".format(old_name, filepath))
handler.sync()
def copy_file(source, destiny):
Copies a file from source to destiny, creating dirs if necessary
:param source: path to source
:type source: str
:param destiny: path to destiny
:type destiny: str
"""
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
hash_original = Utils.get_file_hash(source)
retrials = 5
while hash_original != hash_destiny:
if retrials == 0:
raise Exception('Can not move {0} to {1}'.format(source, destiny))
shutil.copyfile(source, destiny)
hash_destiny = Utils.get_file_hash(destiny)
@staticmethod
def move_file(source, destiny):
"""
Moves a file from source to destiny, creating dirs if necessary
:param source: path to source
:type source: str
:param destiny: path to destiny
:type destiny: str
"""
Utils.copy_file(source, destiny)
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@staticmethod
def remove_file(path):
"""
Removes a file, checking before if its exists
:param path: path to file
:type path: str
"""
if os.path.isfile(path):
os.remove(path)
@staticmethod
def copy_tree(source, destiny):
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)
@staticmethod
def move_tree(source, destiny):
Utils.copy_tree(source, destiny)
shutil.rmtree(source)
@staticmethod
def get_file_hash(filepath):
"""
Returns the MD5 hash for the given filepath
:param filepath: path to the file to compute hash on
:type filepath:str
:return: file's MD5 hash
:rtype: str
"""
hasher = hashlib.md5()
with open(filepath, 'rb') as afile:
while len(buf) > 0:
hasher.update(buf)
@staticmethod
def execute_shell_command(command, log_level=Log.DEBUG):
"""
Executes a sheel command
:param command: command to execute
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Log.info('Detailed time for diagnostic class')
:param log_level: log level to use for command output
:type log_level: int
:return: command output
:rtype: list
"""
if isinstance(command, basestring):
command = command.split()
process = subprocess.Popen(command, stdout=subprocess.PIPE)
output = list()
comunicate = process.communicate()
for line in comunicate:
if not line:
continue
if log_level != Log.NO_LOG:
output.append(line)
if process.returncode != 0:
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raise Utils.ExecutionError('Error executing {0}\n Return code: {1}'.format(' '.join(command),
process.returncode))
_cpu_count = None
@staticmethod
def available_cpu_count():
"""
Number of available virtual or physical CPUs on this systemx
"""
if Utils._cpu_count is None:
try:
m = re.search(r'(?m)^Cpus_allowed:\s*(.*)$',
open('/proc/self/status').read())
if m:
res = bin(int(m.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
@staticmethod
def convert2netcdf4(filetoconvert):
"""
Checks if a file is in netCDF4 format and converts to netCDF4 if not
:param filetoconvert: file to convert
:type filetoconvert: str
"""
if Utils._is_compressed_netcdf4(filetoconvert):
return
Log.debug('Reformatting to netCDF-4')
temp = TempFile.get()
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Utils.execute_shell_command(["nccopy", "-4", "-d4", "-s", filetoconvert, temp])
shutil.move(temp, filetoconvert)
@classmethod
def _is_compressed_netcdf4(cls, filetoconvert):
is_compressed = True
handler = Utils.openCdf(filetoconvert)
if not handler.file_format == 'NETCDF4':
is_compressed = False
else:
ncdump_result = Utils.execute_shell_command('ncdump -hs {0}'.format(filetoconvert), Log.NO_LOG)
ncdump_result = ncdump_result[0].replace('\t', '').split('\n')
for var in handler.variables:
if not '{0}:_DeflateLevel = 4 ;'.format(var) in ncdump_result:
is_compressed = False
break
if not '{0}:_Shuffle = "true" ;'.format(var) in ncdump_result:
is_compressed = False
break
handler.close()
return is_compressed
# noinspection PyPep8Naming
@staticmethod
def openCdf(filepath, mode='a'):
"""
Opens a netCDF file and returns a handler to it
:param filepath: path to the file
:type filepath: str
:param mode: mode to open the file. By default, a (append)
:type mode: str
:return: handler to the file
:rtype: netCDF4.Dataset
"""
return netCDF4.Dataset(filepath, mode)
@staticmethod
def get_datetime_from_netcdf(handler, time_variable='time'):
"""
Gets a datetime array from a netCDF file
:param handler: file to read
:type handler: netCDF4.Dataset
:param time_variable: variable to read, by default 'time'
:type time_variable: str
:return: Datetime numpy array created from the values stored at the netCDF file
:rtype: np.array
"""
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var_time = handler.variables[time_variable]
nctime = var_time[:] # get values
units = var_time.units
try:
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cal_temps = var_time.calendar
except AttributeError:
cal_temps = u"standard"
return netCDF4.num2date(nctime, units=units, calendar=cal_temps)
def copy_variable(source, destiny, variable, must_exist=True, add_dimensions=False, new_names=None):
"""
Copies the given variable from source to destiny
:param add_dimensions: if it's true, dimensions required by the variable will be automatically added to the
file. It will also add the dimension variable
:type add_dimensions: bool
:param source: origin file
:type source: netCDF4.Dataset
:param destiny: destiny file
:type destiny: netCDF4.Dataset
:param variable: variable to copy
:type variable: str
:param must_exist: if false, does not raise an error uf variable does not exist
:type must_exist: bool
:param new_names: dictionary containing variables to rename and new name as key-value pairs
:type new_names: dict
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._translate(source.variables[variable].dimensions, new_names)
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)
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)
new_var[:] = original_var[:]
@staticmethod
def copy_attributes(new_var, original_var, omitted_attributtes=None):
if omitted_attributtes is None:
omitted_attributtes = []
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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})
@staticmethod
def copy_dimension(source, destiny, dimension, must_exist=True, new_names=None):
"""
Copies the given dimension from source to destiny, including dimension variables if present
:param new_names: dictionary containing variables to rename and new name as key-value pairs
:type new_names: dict
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:param source: origin file
:type source: netCDF4.Dataset
:param destiny: destiny file
:type destiny: netCDF4.Dataset
:param dimension: variable to copy
:type dimension: str
:param must_exist: if false, does not raise an error uf variable does not exist
:type must_exist: bool
:return:
"""
if not must_exist and dimension not in source.dimensions.keys():
return
if not new_names:
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)
@staticmethod
def concat_variables(source, destiny, remove_source=False):
"""
Add variables from a nc file to another
:param source: path to source file
:type source: str
:param destiny: path to destiny file
:type destiny: str
:param remove_source: if True, removes source file
:type remove_source: bool
"""
if os.path.exists(destiny):
handler_total = Utils.openCdf(destiny)
handler_variable = Utils.openCdf(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 concatenated.iteritems():
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)
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
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@staticmethod
def create_folder_tree(path):
"""
Createas a fodle path will and parent directories if needed.
:param path: folder's path
:type path: str
"""
if not os.path.exists(path):
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try:
os.makedirs(path)
except:
# Here we can have a race condition. Let's check again for existence and rethrow if still not exists
if not os.path.isdir(path):
raise
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@staticmethod
def give_group_write_permissions(path):
st = os.stat(path)
if st.st_mode & stat.S_IWGRP:
return
os.chmod(path, st.st_mode | stat.S_IWGRP)
@staticmethod
def convert_units(var_handler, new_units):
if new_units == var_handler.units:
return
new_unit = Units(new_units)
old_unit = Units(var_handler.units)
var_handler[:] = Units.conform(var_handler[:], old_unit, new_unit, inplace=True)
if 'valid_min' in var_handler.ncattrs():
var_handler.valid_min = Units.conform(float(var_handler.valid_min), old_unit, new_unit,
inplace=True)
if 'valid_max' in var_handler.ncattrs():
var_handler.valid_max = Units.conform(float(var_handler.valid_max), old_unit, new_unit,
inplace=True)
var_handler.units = new_units
def untar(files, destiny_path):
"""
Untar files to a given destiny
:param files: files to unzip
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:type files: list[Any] | Tuple[Any]
:param destiny_path: path to destination folder
:type 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)
tar.close()
"""
Unzip a list of files
:param files: files to unzip
:type files: list | str
:param force: if True, it will overwrite unzipped files
:type force: bool
"""
if isinstance(files, basestring):
files = [files]
for filepath in files:
Log.debug('Unzipping {0}', filepath)
if force:
option = ' -f'
else:
option = ''
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))
class UnzipException(Exception):
"""
Excpetion raised when unzip fails
"""
"""
Class to manage temporal files
"""
"""
If True, new temporary files are added to the list for future cleaning
"""
"""
List of files to clean automatically
"""
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scratch_folder = ''
"""
Scratch folder to create temporary files on it
"""
"""
Prefix for temporary filenames
"""
def get(filename=None, clean=None, suffix='.nc'):
"""
Gets a new temporal filename, storing it for automated cleaning
: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:
fd, path = tempfile.mkstemp(dir=TempFile.scratch_folder, prefix=TempFile.prefix, suffix=suffix)
if clean:
TempFile.files.append(path)
return path
@staticmethod
def clean():
"""
Removes 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()