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Source code for iris.fileformats.abf

# Copyright Iris contributors
#
# This file is part of Iris and is released under the LGPL license.
# See COPYING and COPYING.LESSER in the root of the repository for full
# licensing details.
"""
Provides ABF (and ABL) file format capabilities.

ABF and ABL files are satellite file formats defined by Boston University.
Including this module adds ABF and ABL loading to the session's capabilities.

The documentation for this file format can be found
`here <https://nasanex.s3.amazonaws.com/AVHRR/GIMMS/LAI3G/00README_V01.pdf>`_.

"""

import calendar
import datetime
import glob
import os.path

import numpy as np
import numpy.ma as ma

import iris
from iris._deprecation import warn_deprecated
from iris.coord_systems import GeogCS
from iris.coords import AuxCoord, DimCoord
import iris.fileformats
import iris.io.format_picker

wmsg = (
    "iris.fileformats.abf has been deprecated and will be removed in a "
    "future release. If you make use of this functionality, please contact "
    "the Iris Developers to discuss how to retain it (which may involve "
    "reversing the deprecation)."
)
warn_deprecated(wmsg)

X_SIZE = 4320
Y_SIZE = 2160


month_numbers = {
    "jan": 1,
    "feb": 2,
    "mar": 3,
    "apr": 4,
    "may": 5,
    "jun": 6,
    "jul": 7,
    "aug": 8,
    "sep": 9,
    "oct": 10,
    "nov": 11,
    "dec": 12,
}


[docs]class ABFField: """ A data field from an ABF (or ABL) file. Capable of creating a :class:`~iris.cube.Cube`. """ def __init__(self, filename): """ Create an ABFField object from the given filename. Args: * filename - An ABF filename. Example:: field = ABFField("AVHRRBUVI01.1985feba.abl") """ basename = os.path.basename(filename) if len(basename) != 24: raise ValueError( "ABFField expects a filename of 24 characters: " "{}".format(basename) ) self._filename = filename def __getattr__(self, key): # Do we need to load now? if key == "data" and "data" not in self.__dict__: self._read() try: return self.__dict__[key] except KeyError: raise AttributeError("ABFField has no attribute '{}'".format(key)) def _read(self): """Read the field from the given filename.""" basename = os.path.basename(self._filename) self.version = int(basename[9:11]) self.year = int(basename[12:16]) self.month = basename[16:19] self.period = basename[19:20] self.format = basename[21:24] self.month = month_numbers[self.month] # Data is 8 bit bigendian. data = np.fromfile(self._filename, dtype=">u1").reshape(X_SIZE, Y_SIZE) # Iris' preferred dimensional ordering is (y,x). data = data.transpose() # Flip, for a positive step through the Y dimension. data = data[::-1] # Any percentages greater than 100 represent missing data. data = ma.masked_greater(data, 100) # The default fill value is 999999(!), so we choose something # more sensible. NB. 999999 % 256 = 63 = bad. data.fill_value = 255 self.data = data
[docs] def to_cube(self): """Return a new :class:`~iris.cube.Cube` from this ABFField.""" cube = iris.cube.Cube(self.data) # Name. if self.format.lower() == "abf": cube.rename("FAPAR") elif self.format.lower() == "abl": cube.rename("leaf_area_index") else: msg = "Unknown ABF/ABL format: {}".format(self.format) raise iris.exceptions.TranslationError(msg) cube.units = "%" # Grid. step = 1.0 / 12.0 llcs = GeogCS(semi_major_axis=6378137.0, semi_minor_axis=6356752.31424) x_coord = DimCoord( np.arange(X_SIZE) * step + (step / 2) - 180, standard_name="longitude", units="degrees", coord_system=llcs, ) y_coord = DimCoord( np.arange(Y_SIZE) * step + (step / 2) - 90, standard_name="latitude", units="degrees", coord_system=llcs, ) x_coord.guess_bounds() y_coord.guess_bounds() cube.add_dim_coord(x_coord, 1) cube.add_dim_coord(y_coord, 0) # Time. if self.period == "a": start = 1 end = 15 elif self.period == "b": start = 16 end = calendar.monthrange(self.year, self.month)[1] else: raise iris.exceptions.TranslationError( "Unknown period: " "{}".format(self.period) ) start = datetime.date(year=self.year, month=self.month, day=start) end = datetime.date(year=self.year, month=self.month, day=end) # Convert to "days since 0001-01-01". # Iris will have proper datetime objects in the future. # This step will not be necessary. start = start.toordinal() - 1 end = end.toordinal() - 1 # TODO: Should we put the point in the middle of the period instead? cube.add_aux_coord( AuxCoord( start, standard_name="time", units="days since 0001-01-01", bounds=[start, end], ) ) # TODO: Do they only come from Boston? # Attributes. cube.attributes["source"] = "Boston University" return cube
[docs]def load_cubes(filespecs, callback=None): """ Loads cubes from a list of ABF filenames. Args: * filenames - list of ABF filenames to load Kwargs: * callback - a function that can be passed to :func:`iris.io.run_callback` .. note:: The resultant cubes may not be in the same order as in the file. """ if isinstance(filespecs, str): filespecs = [filespecs] for filespec in filespecs: for filename in glob.glob(filespec): field = ABFField(filename) cube = field.to_cube() # Were we given a callback? if callback is not None: cube = iris.io.run_callback(callback, cube, field, filename) if cube is None: continue yield cube