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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.
import builtins
import datetime
from enum import Enum
import keyword
import logging
import os
import pkgutil
import signal
import tempfile
import cffi
import numpy as np
from metview.metviewpy.indexdb import FieldsetDb
from metview.dataset import Dataset
from metview.style import (
GeoView,
Style,
Visdef,
map_area_gallery,
map_style_gallery,
make_geoview,
)
from metview import plotting
from metview.metviewpy.ipython import is_ipython_active, import_widgets
from metview.metviewpy import utils
__version__ = "1.16.1"
# logging.basicConfig(level=logging.DEBUG, format="%(levelname)s - %(message)s")
LOG = logging.getLogger(__name__)
def string_from_ffi(s):
return ffi.string(s).decode("utf-8")
# -----------------------------------------------------------------------------
# Startup
# -----------------------------------------------------------------------------
class MetviewInvoker:
"""Starts a new Metview session on construction and terminates it on program exit"""
def __init__(self):
"""
Constructor - starts a Metview session and reads its environment information
Raises an exception if Metview does not respond within so-many seconds
"""
self.debug = os.environ.get("METVIEW_PYTHON_DEBUG", "0") == "1"
# check whether we're in a running Metview session
if "METVIEW_TITLE_PROD" in os.environ: # pragma: no cover
self.persistent_session = True
self.info_section = {"METVIEW_LIB": os.environ["METVIEW_LIB"]}
return
import atexit
import time
import subprocess
if self.debug: # pragma: no cover
print("MetviewInvoker: Invoking Metview")
self.persistent_session = False
self.metview_replied = False
self.metview_startup_timeout = int(
os.environ.get("METVIEW_PYTHON_START_TIMEOUT", "8")
) # seconds
# start Metview with command-line parameters that will let it communicate back to us
env_file = tempfile.NamedTemporaryFile(mode="rt")
pid = os.getpid()
# print('PYTHON:', pid, ' ', env_file.name, ' ', repr(signal.SIGUSR1))
signal.signal(signal.SIGUSR1, self.signal_from_metview)
# p = subprocess.Popen(['metview', '-edbg', 'tv8 -a', '-slog', '-python-serve',
# env_file.name, str(pid)], stdout=subprocess.PIPE)
metview_startup_cmd = os.environ.get("METVIEW_PYTHON_START_CMD", "metview")
metview_flags = [
metview_startup_cmd,
"-nocreatehome",
"-python-serve",
env_file.name,
str(pid),
]
if self.debug: # pragma: no cover
metview_flags.insert(2, "-slog")
print("Starting Metview using these command args:")
print(metview_flags)
try:
subprocess.Popen(metview_flags)
except Exception as exp: # pragma: no cover
if "METVIEW_PYTHON_ONLY" not in os.environ:
print(
"Could not run the Metview executable ('"
+ metview_startup_cmd
+ "'); "
"check that the binaries for Metview (version 5 at least) are installed "
"and are in the PATH."
)
raise exp
# wait for Metview to respond...
wait_start = time.time()
while not (self.metview_replied) and (
time.time() - wait_start < self.metview_startup_timeout
):
time.sleep(0.001)
if not (self.metview_replied): # pragma: no cover
raise Exception(
'Command "metview" did not respond within '
+ str(self.metview_startup_timeout)
+ " seconds. This timeout is configurable by setting "
"environment variable METVIEW_PYTHON_START_TIMEOUT in seconds. "
"At least Metview 5 is required, so please ensure it is in your PATH, "
"as earlier versions will not work with the Python interface."
)
self.read_metview_settings(env_file.name)
env_file.close()
# when the Python session terminates, we should destroy this object so that the Metview
# session is properly cleaned up. We can also do this in a __del__ function, but there can
# be problems with the order of cleanup - e.g. the 'os' module might be deleted before
# this destructor is called.
atexit.register(self.destroy)
def destroy(self):
"""Kills the Metview session. Raises an exception if it could not do it."""
if self.persistent_session: # pragma: no cover
return
if self.metview_replied:
if self.debug:
print("MetviewInvoker: Closing Metview")
metview_pid = self.info("EVENT_PID")
try:
os.kill(int(metview_pid), signal.SIGUSR1)
except Exception as exp:
print("Could not terminate the Metview process pid=" + metview_pid)
raise exp
def signal_from_metview(self, *args):
"""Called when Metview sends a signal back to Python to say that it's started"""
# print ('PYTHON: GOT SIGNAL BACK FROM METVIEW!')
self.metview_replied = True
def read_metview_settings(self, settings_file):
"""Parses the settings file generated by Metview and sets the corresponding env vars"""
import configparser
cf = configparser.ConfigParser()
cf.read(settings_file)
env_section = cf["Environment"]
for envar in env_section:
# print('set ', envar.upper(), ' = ', env_section[envar])
os.environ[envar.upper()] = env_section[envar]
self.info_section = cf["Info"]
def info(self, key):
"""Returns a piece of Metview information that was not set as an env var"""
return self.info_section[key]
def store_signal_handlers(self):
"""Stores the set of signal handlers that Metview will override"""
self.sigint = signal.getsignal(signal.SIGINT)
self.sighup = signal.getsignal(signal.SIGHUP)
self.sighquit = signal.getsignal(signal.SIGQUIT)
self.sigterm = signal.getsignal(signal.SIGTERM)
self.sigalarm = signal.getsignal(signal.SIGALRM)
def restore_signal_handlers(self):
"""Restores the set of signal handlers that Metview has overridden"""
signal.signal(signal.SIGINT, self.sigint)
signal.signal(signal.SIGHUP, self.sighup)
signal.signal(signal.SIGQUIT, self.sighquit)
signal.signal(signal.SIGTERM, self.sigterm)
signal.signal(signal.SIGALRM, self.sigalarm)
mi = MetviewInvoker()
try:
ffi = cffi.FFI()
ffi.cdef(pkgutil.get_data("metview", "metview.h").decode("ascii"))
mv_lib = mi.info("METVIEW_LIB")
# is there a more general way to add to a path to a list of paths?
os.environ["LD_LIBRARY_PATH"] = mv_lib + ":" + os.environ.get("LD_LIBRARY_PATH", "")
try:
# Linux / Unix systems
lib = ffi.dlopen(os.path.join(mv_lib, "libMvMacro.so"))
except OSError:
# MacOS systems
lib = ffi.dlopen(os.path.join(mv_lib, "libMvMacro"))
except Exception as exp: # pragma: no cover
print(
"Error loading Metview/libMvMacro. LD_LIBRARY_PATH="
+ os.environ.get("LD_LIBRARY_PATH", "")
)
raise exp
# The C/C++ code behind lib.p_init() will call marsinit(), which overrides various signal
# handlers. We don't necessarily want this when running a Python script - we should use
# the default Python behaviour for handling signals, so we save the current signals
# before calling p_init() and restore them after.
mi.store_signal_handlers()
lib.p_init()
mi.restore_signal_handlers()
# fix for binder-hosted notebooks, where PWD and os.cwd() do not seem to be in sync
os.putenv("PWD", os.getcwd())
# -----------------------------------------------------------------------------
# Classes to handle complex Macro types
# -----------------------------------------------------------------------------
class Value:
def __init__(self, val_pointer):
self.val_pointer = val_pointer
self.pickled = False
def push(self):
if self.val_pointer is None:
lib.p_push_nil()
else:
lib.p_push_value(self.val_pointer)
# if we steal a value pointer from a temporary Value object, we need to
# ensure that the Metview Value is not destroyed when the temporary object
# is destroyed by setting its pointer to None
def steal_val_pointer(self, other):
self.val_pointer = other.val_pointer
other.val_pointer = None
def set_temporary(self, flag):
lib.p_set_temporary(self.val_pointer, flag)
# enable a more object-oriented interface, e.g. a = fs.interpolate(10, 29.4)
def __getattr__(self, fname):
def call_func_with_self(*args, **kwargs):
return call(fname, self, *args, **kwargs)
return call_func_with_self
# on destruction, ensure that the Macro Value is also destroyed.
# note the exception - if the variable has been pickled, then there
# may be a temporary file that another process will want to use
# later, so in this case we do not destroy the Macro Value.
def __del__(self):
try:
if self.val_pointer is not None and lib is not None:
if not self.pickled:
lib.p_destroy_value(self.val_pointer)
self.val_pointer = None
except Exception as exp:
print("Could not destroy Metview variable ", self)
raise exp
class Request(dict, Value):
verb = "UNKNOWN"
def __init__(self, req, myverb=None):
if isinstance(req, Request): # copy an existing Request
self.xx = _request(req.get_verb(), req) # to avoid deletion of Macro object
self.val_pointer = self.xx.val_pointer
self.verb = req.get_verb()
self.update(req) # copy into dict
return
if myverb:
self.verb = myverb
if isinstance(req, dict):
self.create_new(self.verb, req)
return
# initialise from a Macro pointer
else:
Value.__init__(self, req)
self.verb = string_from_ffi(lib.p_get_req_verb(req))
super().update(self.to_dict()) # update dict
def __str__(self):
return "VERB: " + self.verb + super().__str__()
def to_dict(self):
keys = _keywords(self)
d = {}
for k in keys:
d[k] = self[k]
return d
# translate Python classes into Metview ones where needed - single parameter
def item_to_metview_style(self, key, value):
modified = False
delete_original_key = False
# bool -> on/off
if isinstance(value, bool):
conversion_dict = {True: "on", False: "off"}
value = conversion_dict[value]
modified = True
# class_ -> class (because 'class' is a Python keyword and cannot be
# used as a named parameter)
elif key == "class_":
key = "class"
delete_original_key = True
modified = True
return (key, value, modified, delete_original_key)
def set_verb(self, v):
self.verb = v
def get_verb(self):
return self.verb
def create_new(self, rverb, rdict):
r = definition() # new, empty definition
self.val_pointer = r.val_pointer
self.xx = r # to avoid deletion of Macro object
self.update(rdict) # will set all parameters via __setitem__
return
def push(self):
# if we have a pointer to a Metview Value, then use that because it's more
# complete than the dict
if self.val_pointer:
Value.push(self)
else:
self.create_new(self.verb, self)
lib.p_push_request(r)
def update(self, items, sub=""):
if sub:
if not isinstance(sub, str):
raise IndexError("sub argument should be a string")
subreq = self[sub.upper()]
if subreq:
subreq.update(items)
self[sub] = subreq
else:
raise IndexError("'" + sub + "' not a valid subrequest in " + str(self))
else:
for key in items:
self.__setitem__(key, items[key])
def __getitem__(self, index):
item = subset(self, index)
# subrequests can return '#' if not uppercase
if isinstance(item, str) and item == "#":
item = subset(self, index.upper())
return item
def __setitem__(self, index, value):
if (self.val_pointer) and (value is not None):
new_key, new_val, _, _ = self.item_to_metview_style(index, value)
push_arg(new_key)
push_arg(new_val)
lib.p_set_subvalue_from_arg_stack(self.val_pointer)
dict.__setitem__(self, new_key, new_val)
else:
dict.__setitem__(self, index, value)
def push_bytes(b):
lib.p_push_string(b)
def push_str(s):
push_bytes(s.encode("utf-8"))
def push_list(lst):
# ask Metview to create a new list, then add each element by
# pusing it onto the stack and asking Metview to pop it off
# and add it to the list
mlist = lib.p_new_list(len(lst))
for i, val in enumerate(lst):
push_arg(val)
lib.p_add_value_from_pop_to_list(mlist, i)
lib.p_push_list(mlist)
def push_date(d):
lib.p_push_datestring(np.datetime_as_string(d).encode("utf-8"))
def push_datetime(d):
lib.p_push_datestring(d.isoformat().encode("utf-8"))
def push_datetime_date(d):
s = d.isoformat() + "T00:00:00"
lib.p_push_datestring(s.encode("utf-8"))
def push_vector(npa):
# if this is a view with a non-contiguous step, make a copy so that
# we get contiguous data
if not npa.flags["C_CONTIGUOUS"]:
npa = npa.copy()
# convert numpy array to CData
dtype = npa.dtype
if dtype == np.float64: # can directly pass the data buffer
cffi_buffer = ffi.cast("double*", npa.ctypes.data)
lib.p_push_vector_from_double_array(cffi_buffer, npa.size, np.nan)
elif dtype == np.float32: # can directly pass the data buffer
cffi_buffer = ffi.cast("float*", npa.ctypes.data)
lib.p_push_vector_from_float32_array(cffi_buffer, npa.size, np.nan)
elif dtype == bool: # convert first to float32
f32_array = npa.astype(np.float32)
cffi_buffer = ffi.cast("float*", f32_array.ctypes.data)
lib.p_push_vector_from_float32_array(cffi_buffer, f32_array.size, np.nan)
elif dtype == int: # convert first to float64
f64_array = npa.astype(np.float64)
cffi_buffer = ffi.cast("double*", f64_array.ctypes.data)
lib.p_push_vector_from_double_array(cffi_buffer, f64_array.size, np.nan)
else:
raise TypeError(
"Only float32 and float64 numPy arrays can be passed to Metview, not ",
npa.dtype,
)
def push_style_object(s):
r = s.to_request()
if isinstance(r, list):
push_list(r)
else:
r.push()
def valid_date(*args, base=None, step=None, step_units=None):
if len(args) != 0:
return call("valid_date", *args)
else:
assert isinstance(base, datetime.datetime)
step = [] if step is None else step
step_units = datetime.timedelta(hours=1) if step_units is None else step_units
if not isinstance(step, list):
step = [step]
return [base + step_units * int(x) for x in step]
def sort(*args, **kwargs):
if "_cpp_implementation" in kwargs:
return call("sort", *args)
elif len(args) != 0 and isinstance(args[0], Fieldset):
if len(args) == 1:
return args[0].sort(**kwargs)
else:
args = args[1:]
return args[0].sort(*args, **kwargs)
else:
return call("sort", *args)
class File(Value):
def __init__(self, val_pointer):
Value.__init__(self, val_pointer)
class FileBackedValue(Value):
def __init__(self, val_pointer):
Value.__init__(self, val_pointer)
def write(self, filename):
return write(filename, self)
def url(self):
# ask Metview for the file relating to this data (Metview will write it if necessary)
return string_from_ffi(lib.p_data_path(self.val_pointer))
class FileBackedValueWithOperators(FileBackedValue):
def __init__(self, val_pointer):
FileBackedValue.__init__(self, val_pointer)
def __add__(self, other):
return add(self, other)
def __radd__(self, other):
return add(other, self)
def __sub__(self, other):
return sub(self, other)
def __rsub__(self, other):
return sub(other, self)
def __mul__(self, other):
return prod(self, other)
def __rmul__(other, self):
return prod(other, self)
def __truediv__(self, other):
return div(self, other)
def __rtruediv__(self, other):
return div(other, self)
def __pow__(self, other):
return power(self, other)
def __rpow__(self, other):
return power(other, self)
def __ge__(self, other):
return greater_equal_than(self, other)
def __gt__(self, other):
return greater_than(self, other)
def __le__(self, other):
return lower_equal_than(self, other)
def __lt__(self, other):
return lower_than(self, other)
def __eq__(self, other):
return equal(self, other)
def __ne__(self, other):
return met_not_eq(self, other)
def __pos__(self):
return self
def __neg__(self):
return 0.0 - self
def __abs__(self):
return self.abs()
def __and__(self, other):
return met_and(self, other)
def __rand__(self, other):
return met_and(other, self)
def __or__(self, other):
return met_or(self, other)
def __ror__(self, other):
return met_or(other, self)
def __invert__(self):
return met_not(self)
class ContainerValueIterator:
def __init__(self, data):
self.index = 0
self.data = data
def __iter__(self):
return self
def __next__(self):
if self.index >= len(self.data):
self.index = 0
raise StopIteration
else:
self.index += 1
return self.data[self.index - 1]
# ContainerValue
# val_pointer - pointer to a C++ Value
# macro_index_base - 0 or 1 - what do Macro indexing functions expect?
# element_types - the type of elements that the container contains
# support_slicing - does the container suppoer slicing?
class ContainerValue(Value):
def __init__(self, val_pointer, macro_index_base, element_types, support_slicing):
Value.__init__(self, val_pointer)
self.macro_index_base = macro_index_base
self.element_types = element_types
self.support_slicing = support_slicing
def __len__(self):
if self.val_pointer is None:
return 0
else:
return int(count(self))
def __getitem__(self, index):
if isinstance(index, slice):
if self.support_slicing:
indices = index.indices(len(self))
fields = [self[i] for i in range(*indices)]
if len(fields) == 0:
return None
else:
f = fields[0]
for i in range(1, len(fields)):
f = merge(f, fields[i])
return f
else:
raise IndexError(
"This object does not support extended slicing: " + str(self)
)
else: # normal index
if isinstance(index, str): # can have a string as an index
return subset(self, index)
elif isinstance(index, np.ndarray): # can have an array as an index
return subset(self, index + self.macro_index_base)
else:
c = int(count(self))
if index < 0: # negative index valid for range [-len..-1]
if index >= -c:
index = c + index
else:
raise IndexError("Index " + str(index) + " invalid ", self)
else:
if index > c - 1:
raise IndexError("Index " + str(index) + " invalid ", self)
return subset(
self, index + self.macro_index_base
) # numeric index: 0->1-based
def __setitem__(self, index, value):
if isinstance(value, self.element_types):
if isinstance(index, int):
index += self.macro_index_base
push_arg(index)
push_arg(value)
lib.p_set_subvalue_from_arg_stack(self.val_pointer)
else:
raise IndexError("Cannot assign ", value, " as element of ", self)
def __iter__(self):
return ContainerValueIterator(self)
class Fieldset(FileBackedValueWithOperators, ContainerValue):
def __init__(self, val_pointer=None, path=None, fields=None):
FileBackedValueWithOperators.__init__(self, val_pointer)
ContainerValue.__init__(
self,
val_pointer=val_pointer,
macro_index_base=1,
element_types=Fieldset,
support_slicing=True,
)
self._db = None
self._ds_param_info = None
self._label = ""
if (path is not None) and (fields is not None):
raise ValueError("Fieldset cannot take both path and fields")
if path is not None:
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)
# fill the 'fields' var - it will be used a few lines down
fields = [read(p) for p in path]
if fields is not None:
for f in fields:
self.append(f)
def append(self, other):
temp = merge(self, other)
if self.val_pointer is not None: # we will overwrite ourselves, so delete
lib.p_destroy_value(self.val_pointer)
self.steal_val_pointer(temp)
self._db = None
def to_dataset(self, **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)
return dataset
def index(self, path=""):
pass
def load_index(self, path):
pass
def _scan(self):
if self._db is None:
self._db = FieldsetDb(fs=self)
self._db.scan()
def _get_db(self):
if self._db is None:
self._db = FieldsetDb(fs=self)
assert self._db is not None
return self._db
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 apply_function_over_dim(self, dim, preserve_dims, func_to_run, name, **kwargs):
if len(self) == 0:
raise ValueError(f"Input to function {name} is an empty Fieldset")
if dim is None:
return func_to_run(self, **kwargs)
import itertools
if preserve_dims:
_preserve_dims = preserve_dims
else:
_preserve_dims = ["shortName", "level", "step", "number", "date", "time"]
if dim in _preserve_dims:
_preserve_dims.remove(dim)
dim_combos = {k: unique(self.grib_get_string(k)) for k in _preserve_dims}
keys, values = zip(*dim_combos.items())
perms = [dict(zip(keys, v)) for v in itertools.product(*values)]
# e.g. [{level=1000,shortName="t",date=20220101, time=6}, ...]
fieldsets_to_apply_function_to = [self.select(**x) for x in perms]
result = Fieldset(
fields=[
func_to_run(x, **kwargs)
for x in fieldsets_to_apply_function_to
if len(x) != 0
]
)
return result
def mean(self, dim=None, preserve_dims=None, missing=False):
return self.apply_function_over_dim(
dim, preserve_dims, met_mean, "mean", missing=missing
)
def sum(self, dim=None, preserve_dims=None, missing=False):
return self.apply_function_over_dim(
dim, preserve_dims, met_sum, "sum", missing=missing
)
def stdev(self, dim=None, preserve_dims=None, missing=False):
return self.apply_function_over_dim(dim, preserve_dims, met_stdev, "stdev")
@property
def ds_param_info(self):
if self._ds_param_info is None:
self._ds_param_info = FieldsetDb.make_param_info(self)
return self._ds_param_info
@property
def label(self):
if self._label is not None and self._label:
return self._label
elif self._db is not None:
return self._db.label
else:
return str()
@label.setter
def label(self, value):
if self._db is not None:
if self._db.label:
print(
f"Warning: cannot set label! It is already set on index database as {self._db.label}!"
)
return
else:
self._db.label = value
self._label = value
def _unique_metadata(self, key):
return self._get_db().unique(key)
def ds_style(self, plot_type="map"):
from metview import style
return style.get_db().style(self, plot_type=plot_type)
def ds_style_list(self, plot_type="map"):
from metview import style
return style.get_db().style_list(self, plot_type=plot_type)
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)} is not even!"
)
sp = u.speed(v)
sp._init_db_from(self)
return sp
else:
return call("speed", self, *args)
def deacc(self, **kwargs):
r = utils.deacc(self, **kwargs)
r._init_db_from(self)
return r
def convolve(self, *args, **kwargs):
return utils.convolve(self, *args, **kwargs)
def smooth_n_point(self, *args, **kwargs):
return utils.smooth_n_point(self, *args, **kwargs)
def smooth_gaussian(self, *args, **kwargs):
return utils.smooth_gaussian(self, *args, **kwargs)
def _init_db_from(self, other):
if self._db is None and other._db is not None:
self._db = FieldsetDb(self, other.label)
self._db.load()
def __getitem__(self, key):
if isinstance(key, str):
self._scan()
if self._db is not None:
return self._db.select_with_name(key)
return None
else:
return super().__getitem__(key)
def __getstate__(self):
# used for pickling
# we cannot (and do not want to) directly pickle the Value pointer
# so we remove it and put instead the path to the file
d = dict(self.__dict__)
del d["val_pointer"]
d["url_path"] = self.url()
self.pickled = True
return d
def __setstate__(self, state):
# used for un-pickling
# read the data from the pickled path
self.__dict__.update(state)
self.__init__(val_pointer=None, path=state["url_path"])
def __str__(self):
n = int(self.count())
s = "s"
if n == 1:
s = ""
return "Fieldset (" + str(n) + " field" + s + ")"
class Bufr(FileBackedValue):
def __init__(self, val_pointer):
FileBackedValue.__init__(self, val_pointer)
class Geopoints(FileBackedValueWithOperators, ContainerValue):
def __init__(self, val_pointer):
FileBackedValueWithOperators.__init__(self, val_pointer)
ContainerValue.__init__(
self,
val_pointer=val_pointer,
macro_index_base=0,
element_types=(np.ndarray, list),
support_slicing=False,
)
def to_dataframe(self):
try:
import pandas as pd
except ImportError: # pragma: no cover
print("Package pandas not found. Try running 'pip install pandas'.")
raise
# create a dictionary of columns (note that we do not include 'time'
# because it is incorporated into 'date')
cols = self.columns()
if "time" in cols:
cols.remove("time")
pddict = {}
for c in cols:
pddict[c] = self[c]
df = pd.DataFrame(pddict)
return df
class NetCDF(FileBackedValueWithOperators):
def __init__(self, val_pointer):
FileBackedValueWithOperators.__init__(self, val_pointer)
def to_dataset(self):
# soft dependency on xarray
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())
return dataset
class Odb(FileBackedValue):
def __init__(self, val_pointer):
FileBackedValue.__init__(self, val_pointer)
def to_dataframe(self):
try:
import pandas as pd
except ImportError: # pragma: no cover
print("Package pandas not found. Try running 'pip install pandas'.")
raise
cols = self.columns()
pddict = {}
for col in cols:
pddict[col] = self.values(col)
df = pd.DataFrame(pddict)
return df
class Table(FileBackedValue):
def __init__(self, val_pointer):
FileBackedValue.__init__(self, val_pointer)
def to_dataframe(self):
try:
import pandas as pd
except ImportError: # pragma: no cover
print("Package pandas not found. Try running 'pip install pandas'.")
raise
df = pd.read_csv(self.url())
return df
class GeopointSet(FileBackedValueWithOperators, ContainerValue):
def __init__(self, val_pointer):
FileBackedValueWithOperators.__init__(self, val_pointer)
ContainerValue.__init__(self, val_pointer, 1, Geopoints, False)
# -----------------------------------------------------------------------------
# Pushing data types to Macro
# -----------------------------------------------------------------------------
def dataset_to_fieldset(val, **kwarg):
# we try to import xarray as locally as possible to reduce startup time
# try to write the xarray as a GRIB file, then read into a fieldset
import xarray as xr
from cfgrib.xarray_to_grib import to_grib
if not isinstance(val, xr.core.dataset.Dataset):
raise TypeError(
"dataset_to_fieldset requires a variable of type xr.core.dataset.Dataset;"
" was supplied with ",
builtins.type(val),
)
f, tmp = tempfile.mkstemp(".grib")
os.close(f)
try:
# could add keys, e.g. grib_keys={'centre': 'ecmf'})
to_grib(val, tmp, **kwarg)
except:
print(
"Error trying to write xarray dataset to GRIB for conversion to Metview Fieldset"
)
raise
# TODO: tell Metview that this is a temporary file that should be deleted when no longer needed
fs = read(tmp)
fs.set_temporary(1)
return fs
def push_xarray_dataset(val):
fs = dataset_to_fieldset(val)
fs.push()
# try_to_push_complex_type exists as a separate function so that we don't have
# to import xarray at the top of the module - this saves some time on startup
def try_to_push_complex_type(val):
import xarray as xr
if isinstance(val, xr.core.dataset.Dataset):
push_xarray_dataset(val)
else:
raise TypeError(
"Cannot push this type of argument to Metview: ", builtins.type(val)
)
class ValuePusher:
"""Class to handle pushing values to the Macro library"""
def __init__(self):
# a set of pairs linking value types with functions to push them to Macro
# note that Request must come before dict, because a Request inherits from dict;
# this ordering requirement also means we should use list or tuple instead of a dict
self.funcs = (
(float, lambda n: lib.p_push_number(n)),
((int, np.number), lambda n: lib.p_push_number(float(n))),
(str, lambda n: push_str(n)),
(Request, lambda n: n.push()),
(dict, lambda n: Request(n).push()),
((list, tuple), lambda n: push_list(n)),
(type(None), lambda n: lib.p_push_nil()),
(FileBackedValue, lambda n: n.push()),
(np.datetime64, lambda n: push_date(n)),
(datetime.datetime, lambda n: push_datetime(n)),
(datetime.date, lambda n: push_datetime_date(n)),
(np.ndarray, lambda n: push_vector(n)),
(File, lambda n: n.push()),
(GeoView, lambda n: push_style_object(n)),
(Style, lambda n: push_style_object(n)),
(Visdef, lambda n: push_style_object(n)),
)
def push_value(self, val):
for typekey, typefunc in self.funcs:
if isinstance(val, typekey):
typefunc(val)
return 1
# if we haven't returned yet, then try the more complex types
try_to_push_complex_type(val)
return 1
vp = ValuePusher()
def push_arg(n):
return vp.push_value(n)
def dict_to_pushed_args(d):
# push each key and value onto the argument stack
for k, v in d.items():
push_str(k)
push_arg(v)
return 2 * len(d) # return the number of arguments generated
# -----------------------------------------------------------------------------
# Returning data types from Macro
# -----------------------------------------------------------------------------
def list_from_metview(val):
mlist = lib.p_value_as_list(val)
result = []
n = lib.p_list_count(mlist)
all_vectors = True
for i in range(0, n):
mval = lib.p_list_element_as_value(mlist, i)
v = value_from_metview(mval)
if all_vectors and not isinstance(v, np.ndarray):
all_vectors = False
result.append(v)
# if this is a list of vectors, then create a 2-D numPy array
if all_vectors and n > 0:
result = np.stack(result, axis=0)
# delete the Metview list - this will decrement the reference counts of its objects
lib.p_destroy_value(val)
return result
def datestring_from_metview(val):
mdate = string_from_ffi(lib.p_value_as_datestring(val))
dt = datetime.datetime.strptime(mdate, "%Y-%m-%dT%H:%M:%S")
lib.p_destroy_value(val)
return dt
def vector_from_metview(val):
vec = lib.p_value_as_vector(val, np.nan)
n = lib.p_vector_count(vec)
s = lib.p_vector_elem_size(vec)
if s == 4:
nptype = np.float32
b = lib.p_vector_float32_array(vec)
elif s == 8:
nptype = np.float64
b = lib.p_vector_double_array(vec)
else: # pragma: no cover
raise Exception("Metview vector data type cannot be handled: ", s)
bsize = n * s
c_buffer = ffi.buffer(b, bsize)
np_array = (
np.frombuffer(c_buffer, dtype=nptype)
).copy() # copy so that we can destroy
lib.p_destroy_value(val)
return np_array
def handle_error(val):
msg = string_from_ffi(lib.p_error_message(val))
if "Service" in msg and "Examiner" in msg:
return None
else:
return Exception("Metview error: " + (msg))
def string_from_metview(val):
s = string_from_ffi(lib.p_value_as_string(val))
lib.p_destroy_value(val)
return s
def number_from_metview(val):
n = lib.p_value_as_number(val)
lib.p_destroy_value(val)
return n
class MvRetVal(Enum):
tnumber = 0
tstring = 1
tgrib = 2
trequest = 3
tbufr = 4
tgeopts = 5
tlist = 6
tnetcdf = 7
tnil = 8
terror = 9
tdate = 10
tvector = 11
todb = 12
ttable = 13
tgptset = 14
tfile = 15
tunknown = 99
class ValueReturner:
"""Class to handle return values from the Macro library"""
def __init__(self):
self.funcs = {}
self.funcs[MvRetVal.tnumber.value] = lambda val: number_from_metview(val)
self.funcs[MvRetVal.tstring.value] = lambda val: string_from_metview(val)
self.funcs[MvRetVal.tgrib.value] = lambda val: Fieldset(val)
self.funcs[MvRetVal.trequest.value] = lambda val: Request(val)
self.funcs[MvRetVal.tbufr.value] = lambda val: Bufr(val)
self.funcs[MvRetVal.tgeopts.value] = lambda val: Geopoints(val)
self.funcs[MvRetVal.tlist.value] = lambda val: list_from_metview(val)
self.funcs[MvRetVal.tnetcdf.value] = lambda val: NetCDF(val)
self.funcs[MvRetVal.tnil.value] = lambda val: None
self.funcs[MvRetVal.terror.value] = lambda val: handle_error(val)
self.funcs[MvRetVal.tdate.value] = lambda val: datestring_from_metview(val)
self.funcs[MvRetVal.tvector.value] = lambda val: vector_from_metview(val)
self.funcs[MvRetVal.todb.value] = lambda val: Odb(val)
self.funcs[MvRetVal.ttable.value] = lambda val: Table(val)
self.funcs[MvRetVal.tgptset.value] = lambda val: GeopointSet(val)
self.funcs[MvRetVal.tfile.value] = lambda val: File(val)
def translate_return_val(self, val):
rt = lib.p_value_type(val)
try:
return self.funcs[rt](val)
except Exception:
# if the type is unknown, it might be a type that is actually stored
# as a request rather than as a MARS type, e.g. PNG
try:
if rt == 99:
rt = MvRetVal.trequest.value
return self.funcs[rt](val)
except Exception:
raise Exception(
"value_from_metview got an unhandled return type and could not convert to a Request: "
+ str(rt)
)
vr = ValueReturner()
def value_from_metview(val):
retval = vr.translate_return_val(val)
if isinstance(retval, Exception):
raise retval
return retval
# -----------------------------------------------------------------------------
#
# -----------------------------------------------------------------------------
def to_dataset(fs, *args, **kwargs):
return fs.to_dataset(args, kwargs)
def to_dataset(fs, *args, **kwargs):
return fs.to_dataset(args, kwargs)
# -----------------------------------------------------------------------------
# Creating and calling Macro functions
# -----------------------------------------------------------------------------
def _call_function(mfname, *args, **kwargs):
nargs = 0
for n in args:
actual_n_args = push_arg(n)
nargs += actual_n_args
merged_dict = {}
merged_dict.update(kwargs)
if len(merged_dict) > 0:
dn = dict_to_pushed_args(Request(merged_dict))
nargs += dn
lib.p_call_function(mfname.encode("utf-8"), nargs)
def make(mfname):
def wrapped(*args, **kwargs):
err = _call_function(mfname, *args, **kwargs)
if err:
pass # throw Exception
val = lib.p_result_as_value()
return value_from_metview(val)
return wrapped
def _make_function_for_object(name):
"""
Creates a function to invoke the method called name on obj. This will make it
possible to call some object methods as global functions. E.g.: if name="ls" and
f is a Fieldset we could invoke the ls() method as mv.ls(f) on top of f.ls()
"""
def fn(obj, *args, **kwargs):
return getattr(obj, name)(*args, **kwargs)
return fn
def bind_functions(namespace, module_name=None):
"""Add to the module globals all metview functions except operators like: +, &, etc."""
for metview_name in make("dictionary")():
if metview_name.isidentifier():
python_name = metview_name
# NOTE: we append a '_' to metview functions that clash with python reserved keywords
# as they cannot be used as identifiers, for example: 'in' -> 'in_'
if keyword.iskeyword(metview_name):
python_name += "_"
python_func = make(metview_name)
python_func.__name__ = python_name
python_func.__qualname__ = python_name
if module_name:
python_func.__module__ = module_name
namespace[python_name] = python_func
# else:
# print('metview function %r not bound to python' % metview_name)
# HACK: some functions are missing from the 'dictionary' call.
namespace["neg"] = make("neg")
namespace["nil"] = make("nil")
namespace["dialog"] = make("dialog")
namespace["div"] = div
namespace["mod"] = mod
namespace["string"] = make("string")
# override some functions that need special treatment
# FIXME: this needs to be more structured
namespace["plot"] = plot
namespace["setoutput"] = setoutput
namespace["metzoom"] = metzoom
namespace["version_info"] = version_info
namespace["merge"] = merge
namespace["dataset_to_fieldset"] = dataset_to_fieldset
namespace["valid_date"] = valid_date
namespace["sort"] = sort
namespace["load_dataset"] = Dataset.load_dataset
namespace["plot_maps"] = plotting.plot_maps
namespace["plot_diff_maps"] = plotting.plot_diff_maps
namespace["plot_xs"] = plotting.plot_xs
namespace["plot_xs_avg"] = plotting.plot_xs_avg
namespace["plot_stamp"] = plotting.plot_stamp
namespace["plot_rmse"] = plotting.plot_rmse
namespace["plot_cdf"] = plotting.plot_cdf
namespace["map_style_gallery"] = map_style_gallery
namespace["map_area_gallery"] = map_area_gallery
namespace["make_geoview"] = make_geoview
namespace["arguments"] = met_arguments
namespace["Fieldset"] = Fieldset
namespace["Request"] = Request
# some ui specific functions are prefixed with _. They will be exposed via the ui module!
for name in ["dialog", "any", "colour", "icon", "option_menu", "slider", "toggle"]:
namespace["_" + name] = namespace[name]
namespace.pop(name)
# add some object methods the to global namespace
for name in [
"to_dataset",
"to_dataframe",
"ls",
"describe",
"select",
"convolve",
"smooth_n_point",
"smooth_gaussian",
]:
namespace[name] = _make_function_for_object(name)
# some explicit bindings are used here
add = make("+")
call = make("call")
count = make("count")
definition = make("definition")
div = make("/")
download = make("download")
equal = make("=")
filter = make("filter")
greater_equal_than = make(">=")
greater_than = make(">")
_keywords = make("keywords")
lower_equal_than = make("<=")
lower_than = make("<")
met_mean = make("mean")
met_merge = make("&")
met_not_eq = make("<>")
met_plot = make("plot")
mod = make("mod")
nil = make("nil")
png_output = make("png_output")
power = make("^")
prod = make("*")
ps_output = make("ps_output")
read = make("read")
met_setoutput = make("setoutput")
metzoom = make("metzoom")
sub = make("-")
subset = make("[]")
met_stdev = make("stdev")
met_sum = make("sum")
met_and = make("and")
met_or = make("or")
met_not = make("not")
met_version_info = make("version_info")
_request = make("request")
unique = make("unique")
write = make("write")
# call the C++ version_info() function and add the version of the
# Python bindings to the resulting dict
def version_info():
binary_info = dict(met_version_info())
binary_info["metview_python_version"] = __version__
return binary_info
# wrapper so that we can merge a single value (just returns itself)
def merge(*args):
if len(args) == 1:
return args[0]
else:
return met_merge(*args)
# -----------------------------------------------------------------------------
# Particular code for calling the plot() command
# -----------------------------------------------------------------------------
class Plot:
has_pillow = None
padding = np.array([x * 40 for x in [-1, -1, 1, 1]])
def __init__(self):
self.plot_to_jupyter = False
self.plot_widget = True
self.jupyter_args = {}
self.called_once = False
self.setoutput_called_once = False
def __call__(self, *args, **kwargs):
# first time called? If we are in Jupyter and user did not specify,
# then plot inline to Jupyter by default
if not (self.called_once or self.setoutput_called_once):
if is_ipython_active():
setoutput("jupyter")
self.called_once = True
if self.plot_to_jupyter: # pragma: no cover
if self.plot_widget:
return plot_to_notebook(args, **kwargs)
else:
return plot_to_notebook_return_image(args, **kwargs)
else:
map_outputs = {
"png": png_output,
"ps": ps_output,
}
if "output_type" in kwargs:
output_function = map_outputs[kwargs["output_type"].lower()]
kwargs.pop("output_type")
met_plot(output_function(kwargs), *args)
else:
met_plot(*args)
# the Macro plot command returns an empty definition, but
# None is better for Python
return None
def crop_image(self, path):
if Plot.has_pillow is None:
try:
import PIL
Plot.has_pillow = True
except ImportError as e:
Plot.has_pillow = False
if Plot.has_pillow:
try:
from PIL import Image
from PIL import ImageOps
im = Image.open(path)
im.load()
# find inner part
im_invert = im.convert("RGB")
box = ImageOps.invert(im_invert).getbbox()
# crop to box
if box[2] - box[0] > 100 or box[3] - box[1] > 100:
box = list(np.asarray(box) + Plot.padding)
box = (
max(0, box[0]),
max(0, box[1]),
min(im.size[0], box[2]),
min(im.size[1], box[3]),
)
im_crop = im.crop(box)
im.close()
im_crop.save(path)
except Exception as e:
# print(f"ERROR={e}")
pass
plot = Plot()
# animate - only usable within Jupyter notebooks
# generates a widget allowing the user to select between plot frames
def plot_to_notebook(*args, **kwargs): # pragma: no cover
animation_mode = kwargs.get("animate", "auto") # True, False or "auto"
# create all the widgets first so that the 'waiting' label is at the bottom
image_widget = widgets.Image(
format="png"
# width=300,
# height=400,
)
image_widget.layout.visibility = "hidden"
waitl_widget = widgets.Label(value="Generating plots....")
display(image_widget, waitl_widget)
# plot all frames to a temporary directory owned by Metview to enure cleanup
tempdirpath = tempfile.mkdtemp(dir=os.environ.get("METVIEW_TMPDIR", None))
plot_path = os.path.join(tempdirpath, "plot")
met_setoutput(
png_output(
output_name=plot_path, output_file_minimal_width=3, **plot.jupyter_args
)
)
met_plot(*args)
(_, _, filenames) = next(os.walk(tempdirpath), (None, None, None))
if filenames is None:
waitl_widget.value = "No plots generated"
return
files = [os.path.join(tempdirpath, f) for f in sorted(filenames)]
for f in files:
plot.crop_image(f)
if (animation_mode == True) or (animation_mode == "auto" and len(filenames) > 1):
frame_widget = widgets.IntSlider(
value=1,
min=1,
max=1,
step=1,
description="Frame:",
disabled=False,
continuous_update=True,
readout=True,
)
play_widget = widgets.Play(
value=1,
min=1,
max=1,
step=1,
interval=500,
description="Play animation",
disabled=False,
)
speed_widget = widgets.IntSlider(
value=3,
min=1,
max=20,
step=1,
description="Speed",
disabled=False,
continuous_update=True,
readout=True,
)
widgets.jslink((play_widget, "value"), (frame_widget, "value"))
play_and_speed_widget = widgets.HBox([play_widget, speed_widget])
controls = widgets.VBox([frame_widget, play_and_speed_widget])
controls.layout.visibility = "hidden"
frame_widget.layout.width = "800px"
display(controls)
frame_widget.max = len(files)
frame_widget.description = "Frame (" + str(len(files)) + ") :"
play_widget.max = len(files)
def on_frame_change(change):
plot_frame(change["new"])
def on_speed_change(change):
play_widget.interval = 1500 / change["new"]
frame_widget.observe(on_frame_change, names="value")
speed_widget.observe(on_speed_change, names="value")
controls.layout.visibility = "visible"
def plot_frame(frame_index):
im_file = open(files[frame_index - 1], "rb")
imf = im_file.read()
im_file.close()
image_widget.value = imf
# everything is ready now, so plot the first frame, hide the
# 'waiting' label and reveal the plot and the frame slider
plot_frame(1)
waitl_widget.layout.visibility = "hidden"
image_widget.layout.visibility = "visible"
def plot_to_notebook_return_image(*args, **kwargs): # pragma: no cover
from IPython.display import Image
f, tmp = tempfile.mkstemp(".png")
os.close(f)
base, ext = os.path.splitext(tmp)
plot.jupyter_args.update(output_name=base, output_name_first_page_number="off")
met_setoutput(png_output(plot.jupyter_args))
met_plot(*args)
plot.crop_image(tmp)
image = Image(tmp)
os.unlink(tmp)
return image
# On a test system, importing IPython took approx 0.5 seconds, so to avoid that hit
# under most circumstances, we only import it when the user asks for Jupyter
# functionality. Since this occurs within a function, we need a little trickery to
# get the IPython functions into the global namespace so that the plot object can use them
def setoutput(*args, **kwargs):
plot.setoutput_called_once = True
if "jupyter" in args: # pragma: no cover
if is_ipython_active():
global widgets
plot.plot_to_jupyter = True
plot.plot_widget = kwargs.get("plot_widget", True)
if plot.plot_widget:
widgets = import_widgets()
if not widgets:
plot.plot_widget = False
if "plot_widget" in kwargs:
del kwargs["plot_widget"]
plot.jupyter_args = kwargs
else:
print(
"ERROR: setoutput('jupyter') was set, but we are not in a Jupyter environment"
)
raise (Exception("Could not set output to jupyter"))
else:
plot.plot_to_jupyter = False
met_setoutput(*args)
def met_arguments():
"""Emulate the Macro arguments() function"""
import sys
args = sys.argv[1:]
# these will all come in as strings; but Macro does a little processing on them
# in order to intelligently decide whether their types or string or number;
# creating a Request with these values will simulate this behaviour
args_dict = {i: i for i in args}
modified_args_dict = Request(args_dict).to_dict()
modified_args = [modified_args_dict[j] for j in modified_args_dict]
return modified_args
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