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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 copy
import datetime
import logging
import os
from pathlib import Path
from . import utils
import numpy as np
import pandas as pd
import yaml
# logging.basicConfig(level=logging.DEBUG)
# logging.basicConfig(level=logging.INFO)
LOG = logging.getLogger(__name__)
NEWER = True
class GribIndexer:
VECTOR_PARAMS = {
"wind10m": ["10u", "10v"],
"wind100m": ["100u", "100v"],
"wind200m": ["200u", "200v"],
"wind": ["u", "v"],
"wind3d": ["u", "v", "w"],
}
# tuple-> 0: ecCodes type, 1: pandas type, 2: Python type 3: use in duplicate check
DEFAULT_KEYS = {
"shortName": ("s", str, str, False),
"paramId": ("l", "Int32", int, False),
"date": ("l", "Int64", int, True),
"time": ("l", "Int64", int, True),
"step": ("l", "Int32", int, True),
"level": ("l", "Int32", int, True),
"typeOfLevel": ("s", str, str, False),
"number": ("s", str, str, True),
"experimentVersionNumber": ("s", str, str, False),
"marsClass": ("s", str, str, False),
"marsStream": ("s", str, str, False),
"marsType": ("s", str, str, False),
}
DEFAULT_ECC_KEYS = [f"{k}:{v[0]}" for k, v in DEFAULT_KEYS.items()]
BLOCK_KEYS = ["shortName", "typeOfLevel"]
DEFAULT_SORT_KEYS = [
"date",
"time",
"step",
"number",
"level",
"paramId",
]
DATE_KEYS = {
k: ("l", "Int64", int)
for k in ["date", "dataDate", "validityDate", "mars.date", "marsDate"]
}
TIME_KEYS = {
k: ("l", "Int64", int)
for k in ["time", "dataTime", "validityTime", "mars.time", "marsTime"]
}
DATETIME_KEYS = {
"_dateTime": ("date", "time"),
"_dataDateTime": ("dataDate", "dataTime"),
"_validityDateTime": ("validityDate", "validityTime"),
}
KEYS_TO_REPLACE = {
("type", "mars.type"): "marsType",
("stream", "mars.stream"): "marsStream",
("class", "mars.class", "class_"): "marsClass",
("perturbationNumber"): "number",
("mars.date", "marsDate"): "date",
("mars.time", "marsTime"): "time",
}
PREDEF_KEYS = copy.deepcopy(DEFAULT_KEYS)
PREDEF_KEYS.update(DATE_KEYS)
PREDEF_KEYS.update(TIME_KEYS)
PREDEF_PD_TYPES = {k: v[1] for k, v in PREDEF_KEYS.items()}
PREDEF_PT_TYPES = {k: v[2] for k, v in PREDEF_KEYS.items()}
def __init__(self, db):
self.db = db
assert self.db is not None
self.ref_column_count = None
self.keys = []
self.keys_ecc = []
for k, v in GribIndexer.DEFAULT_KEYS.items():
name = k
self.keys.append(name)
if v[0]:
name = f"{k}:{v[0]}"
self.keys_ecc.append(name)
self.keys_duplicate_check = [
k for k, v in GribIndexer.DEFAULT_KEYS.items() if v[3] == True
]
self.shortname_index = self.keys.index("shortName")
self.levtype_index = self.keys.index("typeOfLevel")
self.type_index = self.keys.index("marsType")
self.number_index = self.keys.index("number")
self.param_id_index = self.keys.index("paramId")
self.wind_check_index = []
for v in [
"date",
"time",
"step",
"level",
"typeOfLevel",
"level",
"number",
"experimentVersionNumber",
"marsClass",
"marsStream",
"marsType",
]:
self.wind_check_index.append(self.keys.index(v) + 1)
# self.block_key_index = [self.keys.index(v) for v in GribIndexer.BLOCK_KEYS]
self.pd_types = {k: v[1] for k, v in GribIndexer.DEFAULT_KEYS.items()}
self.pt_types = {k: v[2] for k, v in GribIndexer.DEFAULT_KEYS.items()}
def update_keys(self, keys):
ret = False
for k in keys:
name = k
# we do not add datetime keys (they are pseudo keys, and their value
# is always generated on the fly)
if name not in self.keys and name not in GribIndexer.DATETIME_KEYS:
self.keys.append(name)
p = GribIndexer.PREDEF_KEYS.get(name, ("", str, str))
ecc_name = name if p[0] == "" else name + ":" + p[0]
self.keys_ecc.append(ecc_name)
self.pd_types[name] = p[1]
self.pt_types[name] = p[2]
ret = True
return ret
def _check_duplicates(self, name, df):
dup = df.duplicated(subset=self.keys_duplicate_check)
first_dup = True
cnt = 0
for i, v in dup.items():
if v:
if first_dup:
LOG.error(
f"{name}: has duplicates for key group: {self.keys_duplicate_check}!"
)
first_dup = False
LOG.error(f" first duplicate: {df.iloc[i]}")
cnt += 1
if cnt > 1:
LOG.error(f" + {cnt-1} more duplicate(s)!")
def _build_vector_index(self, df, v_name, v_comp):
# LOG.debug(f"v_name={v_name} v_comp={v_comp}")
comp_num = len(v_comp)
# filter components belonging together
comp_df = []
for i, comp_name in enumerate(v_comp):
query = f"shortName == '{comp_name}'"
r = df.query(query, engine="python")
# if we do not use copy, the assignment below as:
# comp_df[0].loc[...
# generates the SettingWithCopyWarning warning!!!
if i == 0:
r = df.query(query, engine="python").copy()
else:
r = df.query(query, engine="python")
if r.empty:
return []
else:
comp_df.append(r)
assert comp_num == len(comp_df)
# pair up components within a 2D vector field. This
# version proved to be the fastest!
# LOG.debug(" pair up collected components:")
# print(f"v_name={v_name} {len(comp_df[1].index)}")
# print("view=", comp_df[0]._is_view)
r = []
used1 = np.full(len(comp_df[1].index), False, dtype="?")
comp_df[0].loc[:, "shortName"] = v_name
# 2D
if comp_num == 2:
for row0 in comp_df[0].itertuples(name=None):
i = 0
for row1 in comp_df[1].itertuples(name=None):
if not used1[i]:
b = True
for x in self.wind_check_index:
if row0[x] != row1[x]:
b = False
break
if b:
d = list(row0[1:])
d.extend(row1[-self.ref_column_count :])
r.append(d)
used1[i] = True
break
i += 1
# 3D
elif comp_num == 3:
used2 = np.full(len(comp_df[2].index), False, dtype="?")
for row0 in comp_df[0].itertuples(name=None):
i = 0
for row1 in comp_df[1].itertuples(name=None):
if not used1[i]:
b = True
for x in self.wind_check_index:
if row0[x] != row1[x]:
b = False
break
if b:
j = 0
for row2 in comp_df[2].itertuples(name=None):
if not used2[j]:
b = True
for x in self.wind_check_index:
if row0[x] != row2[x]:
b = False
break
if b:
d = list(row0[1:])
d.extend(row1[-self.ref_column_count :])
d.extend(row2[-self.ref_column_count :])
r.append(d)
used1[i] = True
used2[j] = True
j = -1
break
j += 1
if j == -1:
break
i += 1
return r
def _make_dataframe(self, data, sort=False, columns=None):
if columns is not None:
df = pd.DataFrame(data, columns=columns)
else:
df = pd.DataFrame(data)
for c in df.columns:
if self.pd_types.get(c, "") in ["Int32", "Int64"]:
df.fillna(value={c: np.nan}, inplace=True)
df = df.astype(self.pd_types)
if sort:
df = GribIndexer._sort_dataframe(df)
return df
@staticmethod
def _sort_dataframe(df, columns=None, ascending=True):
if columns is None:
columns = list(df.columns)
elif not isinstance(columns, list):
columns = [columns]
# mergesoft is a stable sorting algorithm
df = df.sort_values(by=columns, ascending=ascending, kind="mergesort")
df = df.reset_index(drop=True)
return df
def _write_dataframe(self, df, name, out_dir):
f_name = os.path.join(out_dir, f"{name}.csv.gz")
df.to_csv(path_or_buf=f_name, header=True, index=False, compression="gzip")
@staticmethod
def read_dataframe(key, dir_name):
# assert len(key) == len(GribIndexer.BLOCK_KEYS)
name = key
f_name = os.path.join(dir_name, f"{name}.csv.gz")
# LOG.debug("f_name={}".format(f_name))
return pd.read_csv(f_name, index_col=None, dtype=GribIndexer.PREDEF_PD_TYPES)
@staticmethod
def get_storage_key_list(dir_name):
r = []
# LOG.debug(f"dir_name={dir_name}")
suffix = ".csv.gz"
for f in utils.get_file_list(os.path.join(dir_name, f"*{suffix}")):
name = os.path.basename(f)
# LOG.debug(f"name={name}")
r.append(name[: -len(suffix)])
return r
@staticmethod
def is_key_wind(key):
return key in GribIndexer.VECTOR_PARAMS
@staticmethod
def _convert_query_value(v, col_type):
# print(f"v={v} {type(v)} {col_type}")
return v if col_type != "object" else str(v)
@staticmethod
def _check_datetime_in_filter_input(keys):
for k, v in GribIndexer.DATETIME_KEYS.items():
name = k[1:]
name_date = v[0]
name_time = v[1]
if keys.get(name, []) and (
keys.get(name_date, []) or keys.get(name_time, [])
):
raise Exception(
f"Cannot specify {name} together with {name_date} and {name_time}!"
)
@staticmethod
def _convert_filter_value(name, val):
"""
Analyse the filter key-value pairs and perform the necessary conversions
"""
valid_name = name.split(":")[0] if ":" in name else name
# datetime keys are pseudo keys, they start with _. Their value is converted to
# datetime. The key itself is not added to the scan!
if ("_" + valid_name) in GribIndexer.DATETIME_KEYS:
valid_name = "_" + valid_name
name_date = GribIndexer.DATETIME_KEYS[valid_name][0]
name_time = GribIndexer.DATETIME_KEYS[valid_name][1]
for i, t in enumerate(val):
val[i] = GribIndexer._to_datetime(name, t)
# print(f"t={t} -> {val[i]}")
# We add the date and time components with an empty value. So they will be
# added to the scan, but they will be ignored by the query. Conversely,
# the datetime key itself will be ignored in the scan, but will be used
# in the query.
return [("_" + name, val), (name_date, []), (name_time, [])]
# we convert dates to int
elif valid_name in GribIndexer.DATE_KEYS:
for i, t in enumerate(val):
d = GribIndexer._to_date(name, t)
# for daily climatologies dates where the year is missing the
# the a tuple is returned
if not isinstance(d, tuple):
val[i] = int(d.strftime("%Y%m%d"))
else:
val[i] = d[0] * 100 + d[1]
# we convert times to int
elif valid_name in GribIndexer.TIME_KEYS:
for i, t in enumerate(val):
val[i] = int(GribIndexer._to_time(name, t).strftime("%H%M"))
# print(f"t={t} -> {val[i]}")
else:
pt_type = GribIndexer.PREDEF_PT_TYPES.get(name, None)
# print(f"name={name} {pt_type}")
if pt_type is not None:
for i, t in enumerate(val):
val[i] = pt_type(t)
# print(f" t={t} -> {val[i]}")
# remap some names to the ones already in the default set of indexer keys
for k, v in GribIndexer.KEYS_TO_REPLACE.items():
if name in k:
name = v
return [(name, val)]
@staticmethod
def _to_datetime(param, val):
try:
if isinstance(val, datetime.datetime):
return val
elif isinstance(val, str):
return utils.date_from_str(val)
elif isinstance(val, (int, float)):
return utils.date_from_str(str(val))
else:
raise
except:
raise Exception(f"Invalid datetime value={val} specified for key={param}")
@staticmethod
def _to_date(param, val):
try:
if isinstance(val, datetime.datetime):
return val.date()
elif isinstance(val, datetime.date):
return val
elif isinstance(val, str):
d = utils.date_from_str(val)
return d.date() if not isinstance(d, tuple) else d
elif isinstance(val, (int, float)):
d = utils.date_from_str(str(val))
return d.date() if not isinstance(d, tuple) else d
else:
raise
except:
raise Exception(f"Invalid date value={val} specified for key={param}")
@staticmethod
def _to_time(param, val):
try:
if isinstance(val, (datetime.datetime)):
return val.time()
elif isinstance(val, datetime.time):
return val
elif isinstance(val, str):
return utils.time_from_str(val)
elif isinstance(val, int):
return utils.time_from_str(str(val))
else:
raise
except:
raise Exception(f"Invalid time value={val} specified for key={param}")
class FieldsetIndexer(GribIndexer):
def __init__(self, *args):
super().__init__(*args)
self.ref_column_count = 1
def scan(self, vector=False):
data = self._scan(self.db.fs, mapped_params=self.db.mapped_params)
if data:
df = self._make_dataframe(data, sort=False)
self.db.blocks["scalar"] = df
if vector:
self._scan_vector()
def _scan(self, fs, mapped_params={}):
LOG.info(f" scan fields ...")
data = {}
# print(f"fs_len={len(fs)}")
# print(f"keys_ecc={self.keys_ecc}")
if utils.is_fieldset_type(fs) and len(fs) > 0:
md_vals = fs.grib_get(self.keys_ecc, "key")
if mapped_params:
for i in range(len(fs)):
v = md_vals[self.param_id_index][i]
if v in mapped_params:
short_name = mapped_params[v]
md_vals[self.shortname_index][i] = short_name
assert len(self.keys) == len(self.keys_ecc)
data = {k: md_vals[i] for i, k in enumerate(self.keys)}
data["_msgIndex1"] = list(range(len(fs)))
LOG.info(f" {len(fs)} GRIB messages processed")
return data
def _scan_vector(self):
df = self.db.blocks["scalar"]
if df is not None and not df.empty:
for v_name, v_comp in GribIndexer.VECTOR_PARAMS.items():
r = self._build_vector_index(df, v_name, v_comp)
comp_num = len(v_comp)
if r:
cols = [*self.keys]
for i in range(comp_num):
cols.extend([f"_msgIndex{i+1}"])
w_df = self._make_dataframe(r, sort=False, columns=cols)
self.db.blocks[v_name] = w_df
# self._write_dataframe(w_df, v_name, out_dir)
else:
LOG.debug(" No paired fields found!")
continue
class ExperimentIndexer(GribIndexer):
def __init__(self, *args):
super().__init__(*args)
self.ref_column_count = 2
def scan(self):
out_dir = self.db.db_dir
Path(out_dir).mkdir(exist_ok=True, parents=True)
LOG.info(f"scan {self.db} out_dir={out_dir} ...")
data = {k: [] for k in [*self.keys, "_msgIndex1", "_fileIndex1"]}
input_files = []
# print(f"out_dir={out_dir}")
# merge existing experiment objects
if self.db.merge_conf:
ds = []
# simple merge
if isinstance(self.db.merge_conf, list):
for c_name in self.db.merge_conf:
ds.append(
{"data": db.dataset.find(c_name), "name": c_name, "ens": {}}
)
# explicit ENS merge
else:
assert "pf" in self.db.merge_conf
# control forecast
c_name = self.db.merge_conf.get("cf", "")
if c_name != "":
ds.append(
{
"data": self.db.dataset.find(c_name, comp="field"),
"name": c_name,
"ens": {"type": "cf", "number": 0},
}
)
for i, c_name in enumerate(self.db.merge_conf.get("pf", [])):
ds.append(
{
"data": self.db.dataset.find(c_name, comp="field"),
"name": c_name,
"ens": {"type": "pf", "number": i + 1},
}
)
for c in ds:
if c["data"] is None:
c_name = d["name"]
raise Exception(
f"Cannot merge experiments as {self.db}! Experiment {c_name} is not found!"
)
else:
input_files = self._scan_one(
input_dir=c["data"].path,
file_name_pattern=c["data"].file_name_pattern,
input_files=input_files,
mapped_params=self.db.mapped_params,
ens=c["ens"],
data=data,
rootdir_placeholder_value=c["data"].rootdir_placeholder_value,
rootdir_placeholder_token=self.db.ROOTDIR_PLACEHOLDER_TOKEN,
)
# index a single experiment
else:
input_files = self._scan_one(
input_dir=self.db.path,
file_name_pattern=self.db.file_name_pattern,
input_files=[],
mapped_params=self.db.mapped_params,
ens={},
data=data,
rootdir_placeholder_value=self.db.rootdir_placeholder_value,
rootdir_placeholder_token=self.db.ROOTDIR_PLACEHOLDER_TOKEN,
)
# print(f"input_files={input_files}")
if len(input_files) > 0 and len(data["shortName"]) > 0:
# write config file for input file list
LOG.info(f"generate datafiles.yaml ...")
f_name = os.path.join(out_dir, "datafiles.yaml")
r = yaml.dump(input_files, default_flow_style=False)
with open(f_name, "w") as f:
f.write(r)
self.db.input_files = input_files
# scalar
LOG.info(f"generate scalar fields index ...")
df = self._make_dataframe(data, sort=True)
self.db.blocks["scalar"] = df
self._write_dataframe(df, "scalar", out_dir)
# vector (2D)
LOG.info(f"generate vector fields index ...")
for v_name, v_comp in GribIndexer.VECTOR_PARAMS.items():
r = self._build_vector_index(df, v_name, v_comp)
comp_num = len(v_comp)
if r:
cols = [*self.keys]
for i in range(comp_num):
cols.extend([f"_msgIndex{i+1}", f"_fileIndex{i+1}"])
w_df = self._make_dataframe(r, sort=True, columns=cols)
# print(f"wind_len={len(w_df.index)}")
self.db.blocks[v_name] = w_df
self._write_dataframe(w_df, v_name, out_dir)
else:
LOG.debug(" No paired fields found!")
continue
def _scan_one(
self,
input_dir="",
file_name_pattern="",
input_files=[],
mapped_params={},
ens={},
data={},
rootdir_placeholder_value="",
rootdir_placeholder_token=None,
):
LOG.info("scan fields ...")
LOG.info(f" input_dir={input_dir} file_name_pattern={file_name_pattern}")
# print(f" input_dir={input_dir} file_name_pattern={file_name_pattern}")
# for f_path in glob.glob(f_pattern):
cnt = 0
input_files_tmp = []
for f_path in utils.get_file_list(
input_dir, file_name_pattern=file_name_pattern
):
# LOG.debug(f" f_path={f_path}")
fs = self.db.fieldset_class(path=f_path)
if utils.is_fieldset_type(fs) and len(fs) > 0:
cnt += 1
input_files_tmp.append(f_path)
file_index = len(input_files) + len(input_files_tmp) - 1
md_vals = fs.grib_get(self.keys_ecc, "key")
if mapped_params:
for i in range(len(fs)):
v = md_vals[self.param_id_index][i]
if v in mapped_params:
short_name = mapped_params[v]
md_vals[self.shortname_index][i] = short_name
if ens:
for i in range(len(fs)):
md_vals[self.type_index][i] = ens["type"]
md_vals[self.number_index][i] = ens["number"]
assert len(self.keys) == len(self.keys_ecc)
for i, c in enumerate(self.keys):
data[c].extend(md_vals[i])
data["_msgIndex1"].extend(list(range(len(fs))))
data["_fileIndex1"].extend([file_index] * len(fs))
# print({k: len(v) for k, v in data.items()})
if rootdir_placeholder_value:
input_files_tmp = [
x.replace(rootdir_placeholder_value, rootdir_placeholder_token)
for x in input_files_tmp
]
input_files.extend(input_files_tmp)
LOG.info(f" {cnt} GRIB files processed")
return input_files
def allowed_keys(self):
r = list(self.keys)
r.extend(GribIndexer.DATE_KEYS)
r.extend(GribIndexer.TIME_KEYS)
r.extend(list(GribIndexer.DATETIME_KEYS.keys()))
return set(r)
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