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854
855 | class GrdcCaravan(HydroDataset):
"""GRDC-Caravan dataset class extending HydroDataset.
This class provides access to the GRDC-Caravan dataset, which contains
hydrological and meteorological data for watersheds globally.
This class uses a custom data reading implementation to support a newer
dataset version than the one supported by the underlying aquafetch library.
It overrides the download URLs and provides its own parsing and caching logic.
Attributes:
region: Geographic region identifier
download: Whether to download data automatically
"""
def __init__(
self,
uri: str,
region: Optional[str] = None,
download: bool = False,
cache_path: Optional[str] = None,
) -> None:
"""Initialize GRDC-Caravan dataset.
Args:
uri: Path to the data directory
region: Geographic region identifier (optional)
download: Whether to download data automatically (default: False)
cache_path: Path to the cache directory
"""
super().__init__(uri, cache_path=cache_path)
self.region = region
self.download = download
# cloud path: aqua_fetch cannot read S3, use cache_*_to_zarr instead
if str(uri).startswith("s3://"):
return
# Instantiate the custom class defined at module level
self.aqua_fetch = GRDCCaravan(uri)
# OSS relative paths (uploaded folder GRDCCaravan; nc extension is populated)
_EXT = "GRDCCaravan/GRDC_Caravan_extension_nc/GRDC_Caravan_extension_nc"
_ATTR_REL = f"{_EXT}/attributes/grdc"
_TS_REL = f"{_EXT}/timeseries/netcdf/grdc"
# AquaFetch GRDCCaravan.static_map
_STATIC_RENAME = {"area": "area_km2", "gauge_lat": "lat", "gauge_lon": "long"}
# AquaFetch GRDCCaravan.dyn_map resolved to cleaned names (others pass through)
_DYN_RENAME = {
"streamflow": "q_mm_obs",
"temperature_2m_mean": "airtemp_c_mean_2m",
"temperature_2m_min": "airtemp_c_2m_min",
"temperature_2m_max": "airtemp_c_2m_max",
"total_precipitation_sum": "pcp_mm",
}
def read_object_ids(self) -> np.ndarray:
if self._is_cloud():
fs = self._make_s3fs()
uri = str(self.data_source_dir).rstrip("/")
names = [p.split("/")[-1] for p in fs.ls(f"{uri}/{self._TS_REL}".removeprefix("s3://"))]
ids = sorted(n[:-3] for n in names if n.endswith(".nc"))
return np.array(ids)
return super().read_object_ids()
def cache_attributes_to_zarr(self) -> None:
import zarr
fs = self._make_s3fs()
uri = str(self.data_source_dir).rstrip("/")
base = f"{uri}/{self._ATTR_REL}"
def _read(fname):
with fs.open(f"{base}/{fname}".removeprefix("s3://")) as fh:
df = pd.read_csv(fh, index_col="gauge_id")
df.index = df.index.astype(str)
return df
other = _read("attributes_other_grdc.csv")
hydro = _read("attributes_hydroatlas_grdc.csv")
caravan = _read("attributes_caravan_grdc.csv")
static = pd.concat([other, hydro, caravan], axis=1)
static = static.loc[~static.index.duplicated(keep="first")]
static = static.rename(columns=self._STATIC_RENAME)
static.columns = self._clean_feature_names(list(static.columns))
static = static.loc[:, ~static.columns.duplicated(keep="first")]
zarr_name = self._attributes_cache_filename.replace(".nc", ".zarr")
out, opts = self._zarr_path_and_opts(zarr_name)
ids = static.index.tolist()
n = len(ids)
root = zarr.open_group(out, mode="w", storage_options=opts, zarr_format=2)
for col in static.columns:
vals = static[col].values.astype(str) if static[col].dtype == object else static[col].values
arr = root.create_array(col, shape=(n,), chunks=(n,), dtype=vals.dtype)
arr[:] = vals
arr.attrs["_ARRAY_DIMENSIONS"] = ["basin"]
basin_arr = root.create_array("basin", shape=(n,), chunks=(n,), dtype=str)
basin_arr[:] = ids
basin_arr.attrs["_ARRAY_DIMENSIONS"] = ["basin"]
root.attrs["coordinates"] = "basin"
self._write_zarr_units(root, "static")
print(f"Attributes zarr written to: {out}")
def cache_timeseries_to_zarr(self, batch_size: int = 200) -> None:
import zarr
import netCDF4 as nc4
fs = self._make_s3fs()
uri = str(self.data_source_dir).rstrip("/")
ts_base = f"{uri}/{self._TS_REL}"
stations = self.read_object_ids().tolist()
n = len(stations)
all_times = pd.date_range(self.default_t_range[0], self.default_t_range[1], freq="D")
nt = len(all_times)
times_ns = all_times.asi8
cleaned_var_lst = []
for info in self._dynamic_variable_mapping.values():
for s in info["sources"].values():
if s["specific_name"] not in cleaned_var_lst:
cleaned_var_lst.append(s["specific_name"])
zarr_name = self._timeseries_cache_filename.replace(".nc", ".zarr")
out, opts = self._zarr_path_and_opts(zarr_name)
chunk_t = min(nt, 365)
chunk_b = min(batch_size, n)
root = zarr.open_group(out, mode="a", storage_options=opts, zarr_format=2)
if "basin" not in root:
for vn in cleaned_var_lst:
arr = root.create_array(vn, shape=(n, nt), chunks=(chunk_b, chunk_t),
dtype="float64", fill_value=np.nan)
arr.attrs["_ARRAY_DIMENSIONS"] = ["basin", "time"]
time_arr = root.create_array("time", shape=(nt,), chunks=(chunk_t,), dtype="int64")
time_arr[:] = times_ns
time_arr.attrs["_ARRAY_DIMENSIONS"] = ["time"]
time_arr.attrs["units"] = "nanoseconds since 1970-01-01"
time_arr.attrs["calendar"] = "proleptic_gregorian"
basin_arr = root.create_array("basin", shape=(n,), chunks=(n,), dtype=str)
basin_arr[:] = stations
basin_arr.attrs["_ARRAY_DIMENSIONS"] = ["basin"]
prog = root.create_array("_progress", shape=(n,), chunks=(n,), dtype="int8", fill_value=0)
prog[:] = 0
prog.attrs["_ARRAY_DIMENSIONS"] = ["basin"]
root.attrs["coordinates"] = "basin time"
progress = root["_progress"]
n_batches = (n + batch_size - 1) // batch_size
for start in range(0, n, batch_size):
end = min(start + batch_size, n)
bnum = start // batch_size + 1
if all(progress[start:end]):
print(f"Batch {bnum}/{n_batches}: already done, skipping")
continue
print(f"Batch {bnum}/{n_batches}: {end-start} stations ...")
buffers = {vn: np.full((end - start, nt), np.nan) for vn in cleaned_var_lst}
for j, stn in enumerate(tqdm(stations[start:end], desc=f"batch {bnum}")):
path = f"{ts_base}/{stn}.nc".removeprefix("s3://")
try:
buf = fs.cat(path)
ds = xr.open_dataset(xr.backends.NetCDF4DataStore(
nc4.Dataset("inmem", memory=buf)))
df = ds.to_dataframe()
ds.close()
if "date" in df.index.names:
df.index = pd.to_datetime(df.index.get_level_values("date"))
df = df.rename(columns=self._DYN_RENAME)
df = df[~df.index.duplicated(keep="first")]
df.columns = self._clean_feature_names(list(df.columns))
df = df.reindex(all_times)
for vn in cleaned_var_lst:
if vn in df.columns:
buffers[vn][j] = pd.to_numeric(df[vn], errors="coerce").values
except Exception as e:
print(f" WARN {stn}: {e}")
for vn in cleaned_var_lst:
root[vn][start:end, :] = buffers[vn]
progress[start:end] = 1
print(f"Batch {bnum}/{n_batches}: done")
self._write_zarr_units(root, "dynamic")
print(f"Timeseries zarr written to: {out}")
@property
def _attributes_cache_filename(self):
return "grdc_caravan_attributes.nc"
@property
def _timeseries_cache_filename(self):
return "grdc_caravan_timeseries.nc"
@property
def default_t_range(self):
return ["1950-01-02", "2023-05-18"]
# get the information of features from grdc-caravan_data_description.pdf
# Static variable definitions based on inspected data
_subclass_static_definitions = {
"p_mean": {"specific_name": "p_mean", "unit": "mm/day"},
"area": {"specific_name": "area_km2", "unit": "km^2"},
}
# Dynamic variable mapping based on inspected data
_dynamic_variable_mapping = {
StandardVariable.STREAMFLOW: {
"default_source": "mm",
"sources": {
"mm": {"specific_name": "q_mm_obs", "unit": "mm/day"},
"cms": {"specific_name": "q_cms_obs", "unit": "m^3/s"},
},
},
StandardVariable.PRECIPITATION: {
"default_source": "era5",
"sources": {
"era5": {"specific_name": "pcp_mm", "unit": "mm/day"},
},
},
StandardVariable.TEMPERATURE_MAX: {
"default_source": "era5",
"sources": {
"era5": {"specific_name": "airtemp_c_2m_max", "unit": "°C"},
"dewpoint": {
"specific_name": "dewpoint_temperature_2m_max",
"unit": "°C",
},
},
},
StandardVariable.TEMPERATURE_MIN: {
"default_source": "era5",
"sources": {
"era5": {"specific_name": "airtemp_c_2m_min", "unit": "°C"},
"dewpoint": {
"specific_name": "dewpoint_temperature_2m_min",
"unit": "°C",
},
},
},
StandardVariable.TEMPERATURE_MEAN: {
"default_source": "era5",
"sources": {
"era5": {"specific_name": "airtemp_c_mean_2m", "unit": "°C"},
"dewpoint": {
"specific_name": "dewpoint_temperature_2m_mean",
"unit": "°C",
},
},
},
StandardVariable.POTENTIAL_EVAPOTRANSPIRATION: {
"default_source": "era5_land",
"sources": {
"era5_land": {
"specific_name": "potential_evaporation_sum_era5_land",
"unit": "mm/day",
},
"fao_pm": {
"specific_name": "potential_evaporation_sum_fao_penman_monteith",
"unit": "mm/day",
},
},
},
StandardVariable.SNOW_WATER_EQUIVALENT_MAX: {
"default_source": "era5",
"sources": {
"era5": {
"specific_name": "snow_depth_water_equivalent_max",
"unit": "m",
},
},
},
StandardVariable.SNOW_WATER_EQUIVALENT_MIN: {
"default_source": "era5",
"sources": {
"era5": {
"specific_name": "snow_depth_water_equivalent_min",
"unit": "m",
},
},
},
StandardVariable.SNOW_WATER_EQUIVALENT: {
"default_source": "era5",
"sources": {
"era5": {
"specific_name": "snow_depth_water_equivalent_mean",
"unit": "m",
},
},
},
StandardVariable.SOLAR_RADIATION_MAX: {
"default_source": "era5",
"sources": {
"era5": {
"specific_name": "surface_net_solar_radiation_max",
"unit": "W/m^2",
},
},
},
StandardVariable.SOLAR_RADIATION_MIN: {
"default_source": "era5",
"sources": {
"era5": {
"specific_name": "surface_net_solar_radiation_min",
"unit": "W/m^2",
},
},
},
StandardVariable.SOLAR_RADIATION: {
"default_source": "era5",
"sources": {
"era5": {
"specific_name": "surface_net_solar_radiation_mean",
"unit": "W/m^2",
},
},
},
StandardVariable.THERMAL_RADIATION_MAX: {
"default_source": "era5",
"sources": {
"era5": {
"specific_name": "surface_net_thermal_radiation_max",
"unit": "W/m^2",
},
},
},
StandardVariable.THERMAL_RADIATION_MIN: {
"default_source": "era5",
"sources": {
"era5": {
"specific_name": "surface_net_thermal_radiation_min",
"unit": "W/m^2",
},
},
},
StandardVariable.THERMAL_RADIATION: {
"default_source": "era5",
"sources": {
"era5": {
"specific_name": "surface_net_thermal_radiation_mean",
"unit": "W/m^2",
},
},
},
StandardVariable.SURFACE_PRESSURE_MAX: {
"default_source": "era5",
"sources": {
"era5": {"specific_name": "surface_pressure_max", "unit": "Pa"},
},
},
StandardVariable.SURFACE_PRESSURE_MIN: {
"default_source": "era5",
"sources": {
"era5": {"specific_name": "surface_pressure_min", "unit": "Pa"},
},
},
StandardVariable.SURFACE_PRESSURE: {
"default_source": "era5",
"sources": {
"era5": {"specific_name": "surface_pressure_mean", "unit": "Pa"},
},
},
StandardVariable.U_WIND_SPEED_MAX: {
"default_source": "era5",
"sources": {
"era5": {"specific_name": "u_component_of_wind_10m_max", "unit": "m/s"},
},
},
StandardVariable.U_WIND_SPEED_MIN: {
"default_source": "era5",
"sources": {
"era5": {"specific_name": "u_component_of_wind_10m_min", "unit": "m/s"},
},
},
StandardVariable.U_WIND_SPEED: {
"default_source": "era5",
"sources": {
"era5": {
"specific_name": "u_component_of_wind_10m_mean",
"unit": "m/s",
},
},
},
StandardVariable.V_WIND_SPEED_MAX: {
"default_source": "era5",
"sources": {
"era5": {"specific_name": "v_component_of_wind_10m_max", "unit": "m/s"},
},
},
StandardVariable.V_WIND_SPEED_MIN: {
"default_source": "era5",
"sources": {
"era5": {"specific_name": "v_component_of_wind_10m_min", "unit": "m/s"},
},
},
StandardVariable.V_WIND_SPEED: {
"default_source": "era5",
"sources": {
"era5": {
"specific_name": "v_component_of_wind_10m_mean",
"unit": "m/s",
},
},
},
StandardVariable.VOLUMETRIC_SOIL_WATER_LAYER1_MAX: {
"default_source": "era5",
"sources": {
"era5": {
"specific_name": "volumetric_soil_water_layer_1_max",
"unit": "m^3/m^3",
},
},
},
StandardVariable.VOLUMETRIC_SOIL_WATER_LAYER1_MIN: {
"default_source": "era5",
"sources": {
"era5": {
"specific_name": "volumetric_soil_water_layer_1_min",
"unit": "m^3/m^3",
},
},
},
StandardVariable.VOLUMETRIC_SOIL_WATER_LAYER1: {
"default_source": "era5",
"sources": {
"era5": {
"specific_name": "volumetric_soil_water_layer_1_mean",
"unit": "m^3/m^3",
},
},
},
StandardVariable.VOLUMETRIC_SOIL_WATER_LAYER2_MAX: {
"default_source": "era5",
"sources": {
"era5": {
"specific_name": "volumetric_soil_water_layer_2_max",
"unit": "m^3/m^3",
},
},
},
StandardVariable.VOLUMETRIC_SOIL_WATER_LAYER2_MIN: {
"default_source": "era5",
"sources": {
"era5": {
"specific_name": "volumetric_soil_water_layer_2_min",
"unit": "m^3/m^3",
},
},
},
StandardVariable.VOLUMETRIC_SOIL_WATER_LAYER2: {
"default_source": "era5",
"sources": {
"era5": {
"specific_name": "volumetric_soil_water_layer_2_mean",
"unit": "m^3/m^3",
},
},
},
StandardVariable.VOLUMETRIC_SOIL_WATER_LAYER3_MAX: {
"default_source": "era5",
"sources": {
"era5": {
"specific_name": "volumetric_soil_water_layer_3_max",
"unit": "m^3/m^3",
},
},
},
StandardVariable.VOLUMETRIC_SOIL_WATER_LAYER3_MIN: {
"default_source": "era5",
"sources": {
"era5": {
"specific_name": "volumetric_soil_water_layer_3_min",
"unit": "m^3/m^3",
},
},
},
StandardVariable.VOLUMETRIC_SOIL_WATER_LAYER3: {
"default_source": "era5",
"sources": {
"era5": {
"specific_name": "volumetric_soil_water_layer_3_mean",
"unit": "m^3/m^3",
},
},
},
StandardVariable.VOLUMETRIC_SOIL_WATER_LAYER4_MAX: {
"default_source": "era5",
"sources": {
"era5": {
"specific_name": "volumetric_soil_water_layer_4_max",
"unit": "m^3/m^3",
},
},
},
StandardVariable.VOLUMETRIC_SOIL_WATER_LAYER4_MIN: {
"default_source": "era5",
"sources": {
"era5": {
"specific_name": "volumetric_soil_water_layer_4_min",
"unit": "m^3/m^3",
},
},
},
StandardVariable.VOLUMETRIC_SOIL_WATER_LAYER4: {
"default_source": "era5",
"sources": {
"era5": {
"specific_name": "volumetric_soil_water_layer_4_mean",
"unit": "m^3/m^3",
},
},
},
}
def cache_timeseries_xrdataset(self, batch_size=200):
"""Cache timeseries to NetCDF in batches, one file per batch.
GRDC-Caravan has thousands of stations; fetching them all at once
exhausts memory, so we process ``batch_size`` stations at a time and
write each batch as ``batch{N}_grdc_caravan_timeseries.nc``.
"""
if not hasattr(self, "aqua_fetch"):
raise NotImplementedError("aqua_fetch attribute is required")
# Build mapping from specific variable names to units
unit_lookup = {}
if hasattr(self, "_dynamic_variable_mapping"):
for std_name, mapping_info in self._dynamic_variable_mapping.items():
for source, source_info in mapping_info["sources"].items():
unit_lookup[source_info["specific_name"]] = source_info["unit"]
gage_id_lst = self.read_object_ids().tolist()
total_stations = len(gage_id_lst)
original_var_lst = self.aqua_fetch.dynamic_features
cleaned_var_lst = self._clean_feature_names(original_var_lst)
var_name_mapping = dict(zip(original_var_lst, cleaned_var_lst))
n_batches = (total_stations + batch_size - 1) // batch_size
print(
f"Start batch processing {total_stations} stations, "
f"{batch_size} stations per batch ({n_batches} batches)"
)
self.cache_dir.mkdir(parents=True, exist_ok=True)
batch_num = 1
for batch_idx in range(0, total_stations, batch_size):
batch_end = min(batch_idx + batch_size, total_stations)
batch_stations = gage_id_lst[batch_idx:batch_end]
print(
f"\nProcessing batch {batch_num}/{n_batches} "
f"(stations {batch_idx}-{batch_end - 1})"
)
try:
batch_data = self.aqua_fetch.fetch_stations_features(
stations=batch_stations,
dynamic_features=original_var_lst,
static_features=None,
st=self.default_t_range[0],
en=self.default_t_range[1],
as_dataframe=False,
)
dynamic_data = (
batch_data[1] if isinstance(batch_data, tuple) else batch_data
)
new_data_vars = {}
time_coord = dynamic_data.coords["time"]
for original_var in tqdm(
original_var_lst,
desc=f"Variables (batch {batch_num})",
total=len(original_var_lst),
):
cleaned_var = var_name_mapping[original_var]
var_data = []
for station in batch_stations:
if station in dynamic_data.data_vars:
station_data = dynamic_data[station].sel(
dynamic_features=original_var
)
if "dynamic_features" in station_data.coords:
station_data = station_data.drop("dynamic_features")
var_data.append(station_data)
if var_data:
combined = xr.concat(var_data, dim="basin")
combined["basin"] = batch_stations
combined.attrs["units"] = unit_lookup.get(
cleaned_var, "unknown"
)
new_data_vars[cleaned_var] = combined
batch_ds = xr.Dataset(
data_vars=new_data_vars,
coords={"basin": batch_stations, "time": time_coord},
)
batch_filepath = self.cache_dir.joinpath(
f"batch{batch_num:03d}_grdc_caravan_timeseries.nc"
)
batch_ds.to_netcdf(batch_filepath)
print(f"Saved batch {batch_num} -> {batch_filepath}")
except Exception as e:
print(f"Batch {batch_num} processing failed: {e}")
import traceback
traceback.print_exc()
continue
batch_num += 1
print(f"\nAll batches processed! Total {batch_num - 1} batch files saved")
def read_ts_xrdataset(
self,
gage_id_lst: list = None,
t_range: list = None,
var_lst: list = None,
sources: dict = None,
**kwargs,
) -> xr.Dataset:
"""Read timeseries from the batch-saved cache (standard names + sources)."""
if self._is_cloud():
# cloud: base class opens the zarr and handles selection/renaming
return super().read_ts_xrdataset(
gage_id_lst=gage_id_lst, t_range=t_range,
var_lst=var_lst, sources=sources, **kwargs,
)
if (
not hasattr(self, "_dynamic_variable_mapping")
or not self._dynamic_variable_mapping
):
raise NotImplementedError(
"This dataset does not support the standardized variable mapping."
)
if var_lst is None:
var_lst = list(self._dynamic_variable_mapping.keys())
if t_range is None:
t_range = self.default_t_range
target_vars_to_fetch = []
rename_map = {}
for std_name in var_lst:
if std_name not in self._dynamic_variable_mapping:
raise ValueError(
f"'{std_name}' is not a recognized standard variable for this dataset."
)
mapping_info = self._dynamic_variable_mapping[std_name]
is_explicit_source = sources and std_name in sources
sources_to_use = []
if is_explicit_source:
provided_sources = sources[std_name]
if isinstance(provided_sources, list):
sources_to_use.extend(provided_sources)
else:
sources_to_use.append(provided_sources)
else:
sources_to_use.append(mapping_info["default_source"])
needs_suffix = is_explicit_source and len(sources_to_use) > 1
for source in sources_to_use:
if source not in mapping_info["sources"]:
raise ValueError(
f"Source '{source}' is not available for variable '{std_name}'."
)
actual_var_name = mapping_info["sources"][source]["specific_name"]
target_vars_to_fetch.append(actual_var_name)
output_name = f"{std_name}_{source}" if needs_suffix else std_name
rename_map[actual_var_name] = output_name
import glob
batch_pattern = str(self.cache_dir / "batch*_grdc_caravan_timeseries.nc")
batch_files = sorted(glob.glob(batch_pattern))
if not batch_files:
print("No batch cache files found, starting cache creation...")
self.cache_timeseries_xrdataset()
batch_files = sorted(glob.glob(batch_pattern))
if not batch_files:
raise FileNotFoundError("Cache creation failed, no batch files found")
if gage_id_lst is None:
gage_id_lst = self.read_object_ids().tolist()
gage_id_lst = [str(gid) for gid in gage_id_lst]
relevant_datasets = []
for batch_file in batch_files:
try:
ds_batch = xr.open_dataset(batch_file)
batch_basins = [str(b) for b in ds_batch.basin.values]
common_basins = list(set(gage_id_lst) & set(batch_basins))
if common_basins:
missing_vars = [
v for v in target_vars_to_fetch if v not in ds_batch.data_vars
]
if missing_vars:
ds_batch.close()
raise ValueError(
f"Batch {os.path.basename(batch_file)} missing variables: "
f"{missing_vars}"
)
ds_subset = ds_batch[target_vars_to_fetch]
ds_selected = ds_subset.sel(
basin=common_basins, time=slice(t_range[0], t_range[1])
)
relevant_datasets.append(ds_selected)
ds_batch.close()
except Exception as e:
print(f"Failed to read batch file {batch_file}: {e}")
continue
if not relevant_datasets:
raise ValueError(
f"Specified stations not found in any batch files: {gage_id_lst}"
)
if len(relevant_datasets) == 1:
final_ds = relevant_datasets[0]
else:
final_ds = xr.concat(relevant_datasets, dim="basin")
final_ds = final_ds.rename(rename_map)
existing_basins = [b for b in gage_id_lst if b in final_ds.basin.values]
if existing_basins:
final_ds = final_ds.sel(basin=existing_basins)
return final_ds
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