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# (C) Copyright 2017- ECMWF.
#
# This software is licensed under the terms of the Apache Licence Version 2.0
# which can be obtained at http://www.apache.org/licenses/LICENSE-2.0.
#
# In applying this licence, ECMWF does not waive the privileges and immunities
# granted to it by virtue of its status as an intergovernmental organisation
# nor does it submit to any jurisdiction.
from inspect import signature
import sys
import numpy as np
import eccodes
from . import maths
from .temporary import temp_file
from . import indexdb as indexdb
from . import utils
BITS_PER_VALUE_FOR_WRITING = 24
class CodesHandle:
"""Wraps an ecCodes handle"""
MISSING_VALUE = 1e34
STRING = ("s", eccodes.codes_get_string, eccodes.codes_set_string)
LONG = ("l", eccodes.codes_get_long, eccodes.codes_set_long)
DOUBLE = ("d", eccodes.codes_get_double, eccodes.codes_set_double)
LONG_ARRAY = ("la", eccodes.codes_get_long_array, eccodes.codes_set_long_array)
DOUBLE_ARRAY = (
"da",
eccodes.codes_get_double_array,
eccodes.codes_set_double_array,
)
NATIVE = ("n", eccodes.codes_get, eccodes.codes_set)
NATIVE_ARRAY = ("na", eccodes.codes_get_array, eccodes.codes_set_array)
_STR_TYPES = {
v[0]: tuple(v[1:3])
for v in [STRING, LONG, DOUBLE, LONG_ARRAY, DOUBLE_ARRAY, NATIVE, NATIVE_ARRAY]
}
def __init__(self, handle, path, offset):
self.handle = handle
self.path = path
self.offset = offset
eccodes.codes_set(handle, "missingValue", CodesHandle.MISSING_VALUE)
def __del__(self):
# print("CodesHandle:release ", self)
eccodes.codes_release(self.handle)
def clone(self):
new_handle = eccodes.codes_clone(self.handle)
return CodesHandle(new_handle, None, None)
# def __str__(self):
# s = "CodesHandle("
# return s + str(self.handle) + "," + self.path + "," + str(self.offset) + ")"
def call_get_func(self, func, key, default=False):
try:
result = func(self.handle, key)
except Exception as exp:
if default != False:
return default
else:
raise exp
return result
def get_any(self, keys, key_type=None):
# single key with key_type specified
if key_type is not None:
assert isinstance(keys, str)
func = key_type[1]
return func(self.handle, keys)
# list of keys
else:
result = []
for key in keys:
key_type_str = "s"
parts = key.split(":")
if len(parts) == 2:
key, key_type_str = parts
if (
key_type_str == "n"
and eccodes.codes_get_size(self.handle, key) > 1
):
key_type_str = "na"
func = CodesHandle._STR_TYPES.get(key_type_str, None)[0]
result.append(self.call_get_func(func, key, default=None))
return result
def get_string(self, key):
return eccodes.codes_get_string(self.handle, key)
def get_long(self, key):
return eccodes.codes_get_long(self.handle, key)
def get_double(self, key):
return eccodes.codes_get_double(self.handle, key)
def get_long_array(self, key):
return eccodes.codes_get_long_array(self.handle, key)
def get_double_array(self, key):
return eccodes.codes_get_double_array(self.handle, key)
def get_values(self):
vals = eccodes.codes_get_values(self.handle)
if self.get_long("bitmapPresent"):
vals[vals == CodesHandle.MISSING_VALUE] = np.nan
return vals
def set_any(self, keys_and_vals, key_type=None):
for key, v in zip(keys_and_vals[0::2], keys_and_vals[1::2]):
if key_type is not None:
func = key_type[2]
else:
key_type_str = "s" # default is str
parts = key.split(":")
if len(parts) == 2:
key, key_type_str = parts
func = CodesHandle._STR_TYPES.get(key_type_str, None)[1]
func(self.handle, key, v)
def set_string(self, key, value):
eccodes.codes_set_string(self.handle, key, value)
def set_long(self, key, value):
eccodes.codes_set_long(self.handle, key, value)
def set_double(self, key, value):
eccodes.codes_set_double(self.handle, key, value)
def set_double_array(self, key, value):
eccodes.codes_set_double_array(self.handle, key, value)
def set_values(self, value):
# replace nans with missing values
values_nans_replaced = np.nan_to_num(
value, copy=True, nan=CodesHandle.MISSING_VALUE
)
self.set_long("bitsPerValue", BITS_PER_VALUE_FOR_WRITING)
self.set_double_array("values", values_nans_replaced)
def write(self, fout, path):
self.offset = fout.tell()
eccodes.codes_write(self.handle, fout)
if path:
self.path = path
class GribFile:
"""Encapsulates a GRIB file, giving access to an iteration of CodesHandles"""
def __init__(self, path):
self.path = path
self.file = open(path, "rb")
self.num_messages = eccodes.codes_count_in_file(self.file)
def __del__(self):
try:
# print("GribFile:close")
self.file.close()
except Exception:
pass
def __len__(self):
return self.num_messages
def __iter__(self):
return self
def __next__(self):
handle = self._next_handle()
if handle is None:
raise StopIteration()
return handle
def _next_handle(self):
offset = self.file.tell()
handle = eccodes.codes_new_from_file(self.file, eccodes.CODES_PRODUCT_GRIB)
if not handle:
return None
return CodesHandle(handle, self.path, offset)
class Field:
"""Encapsulates single GRIB message"""
def __init__(self, handle, gribfile, keep_values_in_memory=False, temp=None):
self.handle = handle
self.gribfile = gribfile
self.temp = temp
self.vals = None
self.keep_values_in_memory = keep_values_in_memory
def grib_get(self, *args, **kwargs):
return self.handle.get_any(*args, **kwargs)
def values(self):
if self.vals is None:
vals = self.handle.get_values()
if self.keep_values_in_memory:
self.vals = vals
else:
vals = self.vals
return vals
def latitudes(self):
return self.handle.get_double_array("latitudes")
def longitudes(self):
return self.handle.get_double_array("longitudes")
def grib_set(self, *args, **kwargs):
result = self.clone()
result.handle.set_any(*args, **kwargs)
return result
def encode_values(self, value):
self.handle.set_long("bitmapPresent", 1)
self.handle.set_values(value)
if not self.keep_values_in_memory:
self.vals = None
def write(self, fout, path, temp=None):
self.temp = temp # store a reference to the temp file object for persistence
self.handle.write(fout, path)
def grib_index(self):
return (self.handle.path, self.handle.offset)
# return (self.handle.path, self.grib_get("offset", key_type=CodesHandle.LONG))
def clone(self):
c = Field(
self.handle.clone(),
self.gribfile,
self.keep_values_in_memory,
)
c.vals = None
return c
def field_func(self, func):
"""Applies a function to all values, returning a new Field"""
result = self.clone()
result.vals = func(self.values())
result.encode_values(result.vals)
return result
def field_other_func(self, func, other, reverse_args=False):
"""Applies a function with something to all values, returning a new Field"""
result = self.clone()
if isinstance(other, Field):
other = other.values()
if reverse_args:
result.vals = func(other, self.values())
else:
result.vals = func(self.values(), other)
result.encode_values(result.vals)
return result
# decorator to implement math functions in Fieldset
def wrap_maths(cls):
def wrap_single_method(fn):
def wrapper(self):
return self.field_func(fn)
return wrapper
def wrap_double_method(fn, **opt):
def wrapper(self, *args):
return self.fieldset_other_func(fn, *args, **opt)
return wrapper
for name, it in cls.WRAP_MATHS_ATTRS.items():
if not isinstance(it, tuple):
it = (it, {})
fn, opt = it
n = len(signature(fn).parameters)
if n == 1:
setattr(cls, name, wrap_single_method(fn))
elif n == 2:
setattr(cls, name, wrap_double_method(fn, **opt))
return cls
@wrap_maths
class Fieldset:
"""A set of Fields, each of which can come from different GRIB files"""
WRAP_MATHS_ATTRS = {
"abs": maths.abs,
"acos": maths.acos,
"asin": maths.asin,
"atan": maths.atan,
"atan2": maths.atan2,
"cos": maths.cos,
"div": maths.floor_div,
"exp": maths.exp,
"log": maths.log,
"log10": maths.log10,
"mod": maths.mod,
"sgn": maths.sgn,
"sin": maths.sin,
"square": maths.square,
"sqrt": maths.sqrt,
"tan": maths.tan,
"__neg__": maths.neg,
"__pos__": maths.pos,
"__invert__": maths.not_func,
"__add__": maths.add,
"__radd__": (maths.add, {"reverse_args": True}),
"__sub__": maths.sub,
"__rsub__": (maths.sub, {"reverse_args": True}),
"__mul__": maths.mul,
"__rmul__": (maths.mul, {"reverse_args": True}),
"__truediv__": maths.div,
"__rtruediv__": (maths.div, {"reverse_args": True}),
"__pow__": maths.pow,
"__rpow__": (maths.pow, {"reverse_args": True}),
"__ge__": maths.ge,
"__gt__": maths.gt,
"__le__": maths.le,
"__lt__": maths.lt,
"__eq__": maths.eq,
"__ne__": maths.ne,
"__and__": maths.and_func,
"__or__": maths.or_func,
"bitmap": (maths.bitmap, {"use_first_from_other": True}),
"nobitmap": maths.nobitmap,
}
# QUALIFIER_MAP = {"float": "d"}
# INT_KEYS = ["Nx", "Ny", "number"]
def __init__(
self, path=None, fields=None, keep_values_in_memory=False, temporary=False
):
self.fields = []
self.count = 0
self.temporary = None
self._db = None
if (path is not None) and (fields is not None):
raise ValueError("Fieldset cannot take both path and fields")
if path:
if isinstance(path, list):
v = []
for p in path:
v.extend(utils.get_file_list(p))
path = v
else:
path = utils.get_file_list(path)
for p in path:
g = GribFile(p)
self.count = len(g)
for handle in g:
self.fields.append(Field(handle, p, keep_values_in_memory))
if temporary:
self.temporary = temp_file()
if fields:
self.fields = fields
def __len__(self):
return len(self.fields)
def __str__(self):
n = len(self)
s = "s" if n > 1 else ""
return f"Fieldset ({n} field{s})"
def _grib_get(self, *args, as_list=False, **kwargs):
ret = [x.grib_get(*args, **kwargs) for x in self.fields]
return ret if as_list else Fieldset._list_or_single(ret)
def grib_get_string(self, key):
return self._grib_get(key, key_type=CodesHandle.STRING)
def grib_get_long(self, key):
return self._grib_get(key, key_type=CodesHandle.LONG)
def grib_get_double(self, key):
return self._grib_get(key, key_type=CodesHandle.DOUBLE)
def grib_get_long_array(self, key):
return self._grib_get(key, key_type=CodesHandle.LONG_ARRAY)
def grib_get_double_array(self, key):
return self._grib_get(key, key_type=CodesHandle.DOUBLE_ARRAY)
def grib_get(self, keys, grouping="field"):
if grouping not in ["field", "key"]:
raise ValueError(f"grib_get: grouping must be field or key, not {grouping}")
ret = self._grib_get(keys, as_list=True)
if grouping == "key":
ret = list(map(list, zip(*ret))) # transpose lists of lists
return ret
def _grib_set(self, *args, **kwargs):
result = Fieldset(temporary=True)
path = result.temporary.path
with open(path, "wb") as fout:
for f in self.fields:
result._append_field(f.grib_set(*args, **kwargs))
result.fields[-1].write(fout, path, temp=result.temporary)
return result
def grib_set_string(self, keys_and_vals):
return self._grib_set(keys_and_vals, key_type=CodesHandle.STRING)
def grib_set_long(self, keys_and_vals):
return self._grib_set(keys_and_vals, key_type=CodesHandle.LONG)
def grib_set_double(self, keys_and_vals):
return self._grib_set(keys_and_vals, key_type=CodesHandle.DOUBLE)
def grib_set(self, keys_and_vals):
return self._grib_set(keys_and_vals)
# def grib_set_double_array(self, key, value):
# return self._grib_set_any(key, value, "grib_set_double_array")
def values(self):
v = [x.values() for x in self.fields]
return self._make_2d_array(v)
def set_values(self, values):
if isinstance(values, list):
list_of_arrays = values
else:
if len(values.shape) > 1:
list_of_arrays = [a for a in values]
else:
list_of_arrays = [values]
if len(list_of_arrays) != len(self.fields):
msg = str(len(list_of_arrays)) + " instead of " + str(len(self.fields))
raise ValueError("set_values has the wrong number of arrays: " + msg)
return self.fieldset_other_func(
maths.set_from_other, list_of_arrays, index_other=True
)
def write(self, path):
with open(path, "wb") as fout:
for f in self.fields:
f.write(fout, path)
def grib_index(self):
return [i.grib_index() for i in self.fields]
def _append_field(self, field):
self.fields.append(field)
self._db = None
def __getitem__(self, index):
try:
if isinstance(index, np.ndarray):
return Fieldset(fields=[self.fields[i] for i in index])
# # GRIB key
# elif isinstance(index, str):
# keyname = index
# qualifier = "n"
# parts = keyname.split(":")
# if len(parts) > 1:
# keyname = parts[0]
# qualifier = Fieldset.QUALIFIER_MAP[parts[1]]
# native_key = keyname + ":" + qualifier
# # print("native_key", native_key)
# value = self.grib_get([native_key])[0][0]
# # print(value)
# if value is None:
# raise IndexError
# if index in Fieldset.INT_KEYS:
# # print("int value:", int(value))
# return int(value)
# # if isinstance(value, float):
# # return int(value)
# return value
elif isinstance(index, str):
return self._get_db().select_with_name(index)
else:
return Fieldset(fields=self._always_list(self.fields[index]))
except IndexError as ide:
# print("This Fieldset contains", len(self), "fields; index is", index)
raise ide
def append(self, other):
self.fields = self.fields + other.fields
self._db = None
def merge(self, other):
result = Fieldset(fields=self.fields, temporary=True)
result.append(other)
return result
# def items(self):
# its = []
# for i in range(len(self)):
# its.append((i, Fieldset(fields=[self.fields[i]])))
# return its
# def to_dataset(self, via_file=True, **kwarg):
# # soft dependency on cfgrib
# try:
# import xarray as xr
# except ImportError: # pragma: no cover
# print("Package xarray not found. Try running 'pip install xarray'.")
# raise
# # dataset = xr.open_dataset(self.url(), engine="cfgrib", backend_kwargs=kwarg)
# if via_file:
# dataset = xr.open_dataset(self.url(), engine="cfgrib", backend_kwargs=kwarg)
# else:
# print("Using experimental cfgrib interface to go directly from Fieldset")
# dataset = xr.open_dataset(self, engine="cfgrib", backend_kwargs=kwarg)
# return dataset
def field_func(self, func):
"""Applies a function to all values in all fields"""
result = Fieldset(temporary=True)
with open(result.temporary.path, "wb") as fout:
for f in self.fields:
result._append_field(f.field_func(func))
result.fields[-1].write(
fout, result.temporary.path, temp=result.temporary
)
return result
def fieldset_other_func(
self,
func,
other,
reverse_args=False,
index_other=False,
use_first_from_other=False,
):
"""Applies a function to a fieldset and a scalar/fieldset, e.g. F+5"""
# print(
# f"Fieldset.fieldset_other_func() func={func}, other={other}, reverse_args={reverse_args}, index_other={index_other}, use_first_from_other={use_first_from_other}"
# )
def _process_one(f, g, result):
new_field = f.field_other_func(func, g, reverse_args=reverse_args)
result._append_field(new_field)
result.fields[-1].write(fout, result.temporary.path, temp=result.temporary)
result = Fieldset(temporary=True)
with open(result.temporary.path, "wb") as fout:
if isinstance(other, Fieldset):
if len(other) == len(self.fields):
for f, g in zip(self.fields, other.fields):
_process_one(f, g, result)
elif use_first_from_other:
for f in self.fields:
_process_one(f, other.fields[0], result)
else:
raise Exception(
f"Fieldsets must have the same number of fields for this operation! {len(self.fields)} != {len(other)}"
)
elif index_other:
for f, g in zip(self.fields, other):
_process_one(f, g, result)
else:
for f in self.fields:
_process_one(f, other, result)
return result
def base_date(self):
if len(self.fields) > 0:
result = []
for f in self.fields:
md = f.grib_get(["dataDate", "dataTime"])
result.append(
utils.date_from_ecc_keys(md[0], md[1]) if len(md) == 2 else None
)
return Fieldset._list_or_single(result)
def valid_date(self):
if len(self.fields) > 0:
result = []
for f in self.fields:
md = f.grib_get(["validityDate", "validityTime"])
result.append(
utils.date_from_ecc_keys(md[0], md[1]) if len(md) == 2 else None
)
return Fieldset._list_or_single(result)
def accumulate(self):
if len(self.fields) > 0:
result = [np.nan] * len(self.fields)
for i, f in enumerate(self.fields):
result[i] = np.sum(f.values())
return Fieldset._list_or_single(result)
def average(self):
if len(self.fields) > 0:
result = [np.nan] * len(self.fields)
for i, f in enumerate(self.fields):
result[i] = f.values().mean()
return Fieldset._list_or_single(result)
def maxvalue(self):
if len(self.fields) > 0:
result = np.array([np.nan] * len(self.fields))
for i, f in enumerate(self.fields):
result[i] = f.values().max()
return result.max()
def minvalue(self):
if len(self.fields) > 0:
result = np.array([np.nan] * len(self.fields))
for i, f in enumerate(self.fields):
result[i] = f.values().min()
return result.min()
def _make_single_result(self, v):
assert len(self) > 0
result = Fieldset(temporary=True)
with open(result.temporary.path, "wb") as fout:
f = self.fields[0].clone()
f.encode_values(v)
result._append_field(f)
result.fields[-1].write(fout, result.temporary.path, temp=result.temporary)
return result
def mean(self):
if len(self.fields) > 0:
v = self.fields[0].values()
for i in range(1, len(self.fields)):
v += self.fields[i].values()
v = v / len(self.fields)
return self._make_single_result(v)
else:
return None
def rms(self):
if len(self.fields) > 0:
v = np.square(self.fields[0].values())
for i in range(1, len(self.fields)):
v += np.square(self.fields[i].values())
v = np.sqrt(v / len(self.fields))
return self._make_single_result(v)
else:
return None
def stdev(self):
v = self._compute_var()
return self._make_single_result(np.sqrt(v)) if v is not None else None
def sum(self):
if len(self.fields) > 0:
v = self.fields[0].values()
for i in range(1, len(self.fields)):
v += self.fields[i].values()
return self._make_single_result(v)
else:
return None
def var(self):
v = self._compute_var()
return self._make_single_result(v) if v is not None else None
def _compute_var(self):
if len(self.fields) > 0:
v2 = self.fields[0].values()
v1 = np.square(v2)
for i in range(1, len(self.fields)):
v = self.fields[i].values()
v1 += np.square(v)
v2 += v
return v1 / len(self.fields) - np.square(v2 / len(self.fields))
def latitudes(self):
v = [x.latitudes() for x in self.fields]
return Fieldset._make_2d_array(v)
def longitudes(self):
v = [x.longitudes() for x in self.fields]
return Fieldset._make_2d_array(v)
def _lat_func(self, func, bitmap_poles=False):
result = Fieldset(temporary=True)
pole_limit = 90.0 - 1e-06
with open(result.temporary.path, "wb") as fout:
for f in self.fields:
lat = f.latitudes()
if bitmap_poles:
lat[np.fabs(lat) > pole_limit] = np.nan
v = func(np.deg2rad(lat))
c = f.clone()
c.encode_values(v)
result._append_field(c)
result.fields[-1].write(
fout, result.temporary.path, temp=result.temporary
)
return result
def coslat(self):
return self._lat_func(np.cos)
def sinlat(self):
return self._lat_func(np.sin)
def tanlat(self):
return self._lat_func(np.tan, bitmap_poles=True)
@staticmethod
def _list_or_single(lst):
return lst if len(lst) != 1 else lst[0]
@staticmethod
def _always_list(items):
return items if isinstance(items, list) else [items]
@staticmethod
def _make_2d_array(v):
"""Forms a 2D ndarray from a list of 1D ndarrays"""
v = Fieldset._list_or_single(v)
return np.stack(v, axis=0) if isinstance(v, list) else v
# TODO: add all the field_func functions
# TODO: add all field_field_func functions
# TODO: add all field_scalar_func functions
# TODO: add tests for all fieldset-fieldset methods:
# **, ==, !=, &, |
# TODO: allow these methods to be called as functions (?)
# TODO: function to write to single file if fields from different files
# TODO: optimise write() to copy file if exists
# TODO: to_dataset()
# TODO: pickling
# TODO: gribsetbits, default=24
def _get_db(self):
if self._db is None:
self._db = indexdb.FieldsetDb(fs=self)
assert self._db is not None
return self._db
def _unique_metadata(self, key):
return self._get_db().unique(key)
def select(self, *args, **kwargs):
if len(args) == 1 and isinstance(args[0], dict):
return self._get_db().select(**args[0])
else:
return self._get_db().select(**kwargs)
def describe(self, *args, **kwargs):
return self._get_db().describe(*args, **kwargs)
def ls(self, **kwargs):
return self._get_db().ls(**kwargs)
def sort(self, *args, **kwargs):
return self._get_db().sort(*args, **kwargs)
def deacc(self, **kwargs):
return utils.deacc(self, **kwargs)
def speed(self, *args):
if len(args) == 0:
u = self[0::2]
v = self[1::2]
if len(u) != len(v):
raise Exception(
f"Fieldsets must contain an even number of fields for this operation! len={len(self.fields)} is not even!"
)
return u.speed(v)
elif len(args) == 1:
other = args[0]
result = Fieldset(temporary=True)
param_ids = {
131: 10, # atmospheric wind
165: 207, # 10m wind
228246: 228249, # 100m wind
228239: 228241, # 200m wind
}
if len(self.fields) != len(other):
raise Exception(
f"Fieldsets must have the same number of fields for this operation! {len(self.fields)} != {len(other)}"
)
with open(result.temporary.path, "wb") as fout:
for f, g in zip(self.fields, other.fields):
sp = np.sqrt(np.square(f.values()) + np.square(g.values()))
c = f.clone()
c.encode_values(sp)
param_id_u = f.grib_get("paramId", CodesHandle.LONG)
param_id_sp = param_ids.get(param_id_u, None)
if param_id_sp is not None:
c = c.grib_set(["paramId", param_id_sp], CodesHandle.LONG)
result._append_field(c)
result.fields[-1].write(
fout, result.temporary.path, temp=result.temporary
)
return result
class FieldsetCF:
def __init__(self, fs):
self.fs = fs
def items(self):
its = []
for i in range(len(self.fs)):
its.append((i, FieldCF(self.fs[i])))
# print("FieldsetCF items: ", d)
return its
def __getitem__(self, index):
return FieldCF(self.fs[index])
class FieldCF:
QUALIFIER_MAP = {"float": "d"}
INT_KEYS = ["Nx", "Ny", "number"]
def __init__(self, fs):
self.fs = fs
def __getitem__(self, key):
keyname = key
qualifier = "n"
parts = key.split(":")
if len(parts) > 1:
keyname = parts[0]
qualifier = FieldCF.QUALIFIER_MAP[parts[1]]
native_key = keyname + ":" + qualifier
# print("native_key", native_key)
value = self.fs.grib_get([native_key])[0][0]
# print(value)
if value is None:
raise IndexError
if key in FieldCF.INT_KEYS:
# print("int value:", int(value))
return int(value)
# if isinstance(value, float):
# return int(value)
return value
def read(p):
return Fieldset(path=p)
# expose all Fieldset functions as a module level function
def _make_module_func(name):
def wrapped(fs, *args):
return getattr(fs, name)(*args)
return wrapped
module_obj = sys.modules[__name__]
for fn in dir(Fieldset):
if callable(getattr(Fieldset, fn)) and not fn.startswith("_"):
setattr(module_obj, fn, _make_module_func(fn))
def bind_functions(namespace, module_name=None):
"""Add to the module globals all metview functions except operators like: +, &, etc."""
namespace["read"] = read
for fn in dir(Fieldset):
if callable(getattr(Fieldset, fn)) and not fn.startswith("_"):
namespace[fn] = _make_module_func(fn)
namespace["Fieldset"] = Fieldset
|