utils.py 17.9 KB
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# coding=utf-8
import hashlib
import shutil
import netCDF4
import re
import tempfile
from autosubmit.config.log import Log
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from earthdiagnostics.constants import Basins
    """
    Container class for miscellaneous utility methods
    """
    """An instance of Nco class ready to be used"""
    """An instance of Cdo class ready to be used"""
    @staticmethod
    def get_mask(basin):
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        """
        Returns a numpy array containing the mask for the given basin

        :param basin: basin to retrieve
        :type basin: Basin
        :return: mask
        :rtype: numpy.array
        """
        if basin != Basins.Global:
            mask_handler = Utils.openCdf('mask_regions.nc')
            mask = mask_handler.variables[basin.fullname][:, 0, :]
            mask_handler.close()
        else:
            mask_handler = Utils.openCdf('mask.nc')
            mask = np.asfortranarray(mask_handler.variables['tmask'][0, 0, :])
            mask_handler.close()
        return mask

    @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()

        Log.info('Getting max and min values for {0}', ' '.join(variable_list))
        handler = Utils.openCdf(filename)
            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()
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    @staticmethod
    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)
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    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
        """
        handler = Utils.openCdf(filepath)
        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()
            return
        handler.close()

        temp = TempFile.get()
        shutil.copyfile(filepath, temp)

        handler = Utils.openCdf(temp)
        for old_name, new_name in dic_names.items():
                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))

            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))
            handler.sync()

        try:
            Utils.execute_shell_command(['ncdump', '-h', temp])
        except Utils.ExecutionError:
            original_handler = Utils.openCdf(filepath)
            new_handler = Utils.openCdf(temp, 'w')
            for attribute in original_handler.ncattrs():
                setattr(new_handler, attribute, getattr(original_handler, attribute))

            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()

        Utils.move_file(temp, filepath)
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    @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
        """
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        if not os.path.exists(os.path.dirname(destiny)):
            try:
                os.makedirs(os.path.dirname(destiny))
            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(os.path.dirname(destiny)):
                    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)
        os.remove(source)

    @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 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
        """
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        blocksize = 65536
        hasher = hashlib.md5()
        with open(filepath, 'rb') as afile:
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            buf = afile.read(blocksize)
            while len(buf) > 0:
                hasher.update(buf)
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                buf = afile.read(blocksize)
        return hasher.hexdigest()
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    def execute_shell_command(command, log_level=Log.DEBUG):
        """
        Executes a sheel command
        :param command: command to execute

        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()
        if log_level != Log.NO_LOG:
            for line in comunicate:
                if not line:
                    continue
                Log.log.log(log_level, line)
                output.append(line)
            raise Utils.ExecutionError('Error executing {0}\n Return code: {1}', ' '.join(command), process.returncode)
        return output
    _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

    def convert2netcdf4(filetoconvert, force=True):
        """
        Checks if a file is in netCDF4 format and converts to netCDF4 if not

        :param force: if true, converts the file regardless of original encoding. Useful to make sure that a file has
                      deflation and shuffle activated
        :type force: bool
        :param filetoconvert: file to convert
        :type filetoconvert: str
        """
        if not force:
            handler = Utils.openCdf(filetoconvert)
            if handler.file_format == 'NETCDF4':
                handler.close()
                return
        Log.debug('Reformatting to netCDF-4')
        Utils.execute_shell_command(["nccopy", "-4", "-d4", "-s", filetoconvert, temp])
    # 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
        """
        nctime = handler.variables[time_variable][:]  # get values
        units = handler.variables[time_variable].units  # get unit  "days since 1950-01-01T00:00:00Z"

        try:
            cal_temps = handler.variables[time_variable].calendar
        except AttributeError:  # Attribute doesn't exist
            cal_temps = u"gregorian"  # or standard
        return netCDF4.num2date(nctime, units=units, calendar=cal_temps)

    @staticmethod
    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
        if not must_exist and variable not in source.variables.keys():
            return
        if variable in destiny.variables.keys():
            return

        if not new_names:
            new_names = dict()

        if variable in new_names:
            new_name = new_names[variable]
        else:
            new_name = variable
        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'.format(variable))
            for dimension in source.variables[variable].dimensions:
                Utils.copy_dimension(source, destiny, dimension, new_names, new_names)
            if variable 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)
        new_var.setncatts({k: original_var.getncattr(k) for k in original_var.ncattrs()})
        new_var[:] = original_var[:]

    @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 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)
            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, True)
    @staticmethod
    def expand_path(path):
        """
        Expands character ~ and system variables on the given path
        :param path: path to expand
        :type path: str
        :return: path after the expansion
        """
    class ExecutionError(Exception):
        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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class TempFile(object):
    """
    Class to manage temporal files
    """
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    autoclean = True
    """
    If True, new temporary files are added to the list for future cleaning
    """
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    files = list()
    """
    List of files to clean automatically
    """
    """
    Scratch folder to create temporary files on it
    """
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    prefix = 'temp'
    """
    Prefix for temporary filenames
    """
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    @staticmethod
    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

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        if filename:
            path = os.path.join(TempFile.scratch_folder, filename)
        else:
            fd, path = tempfile.mkstemp(dir=TempFile.scratch_folder, prefix=TempFile.prefix, suffix=suffix)
            os.close(fd)
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        if clean:
            TempFile.files.append(path)

        return path

    @staticmethod
    def clean():
        """
        Removes all temporary files created with Tempfile until now
        """
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        for temp_file in TempFile.files:
            if os.path.exists(temp_file):
                os.remove(temp_file)
        TempFile.files = list()