From a562b2cf7251c23b32d419cca139d0efefeb1cbb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Tobias=20H=C3=B6lzer?= Date: Fri, 24 Oct 2025 16:36:18 +0200 Subject: [PATCH] Finalize era5 and alphaearth --- pyproject.toml | 4 + steps/s1_0_alphaearth/alphaearth.py | 50 +- steps/s1_0_alphaearth/alphaearth.sh | 22 +- steps/s1_1_era5/era5.py | 749 ++++---- steps/s1_1_era5/era5.sh | 18 + uv.lock | 2542 +++++++++++++++------------ 6 files changed, 1993 insertions(+), 1392 deletions(-) create mode 100644 steps/s1_1_era5/era5.sh diff --git a/pyproject.toml b/pyproject.toml index 9f5d9b9..554864a 100755 --- a/pyproject.toml +++ b/pyproject.toml @@ -8,6 +8,7 @@ requires-python = ">=3.12" dependencies = [ "aiohttp>=3.12.11", "bokeh>=3.7.3", + "bottleneck>=1.6.0", "cartopy>=0.24.1", "cdsapi>=0.7.6", "cyclopts>=4.0.0", @@ -27,8 +28,11 @@ dependencies = [ "mapclassify>=2.9.0", "matplotlib>=3.10.3", "netcdf4>=1.7.2", + "numba>=0.62.1", + "numbagg>=0.9.3", "numpy>=2.3.0", "odc-geo[all]>=0.4.10", + "opt-einsum>=3.4.0", "pyarrow>=20.0.0", "requests>=2.32.3", "rich>=14.0.0", diff --git a/steps/s1_0_alphaearth/alphaearth.py b/steps/s1_0_alphaearth/alphaearth.py index c1838a7..2207b88 100644 --- a/steps/s1_0_alphaearth/alphaearth.py +++ b/steps/s1_0_alphaearth/alphaearth.py @@ -11,6 +11,7 @@ import geemap import geopandas as gpd import numpy as np import pandas as pd +import xarray as xr from rich import pretty, print, traceback from rich.progress import track @@ -26,7 +27,11 @@ EMBEDDINGS_DIR = DATA_DIR / "embeddings" EMBEDDINGS_DIR.mkdir(parents=True, exist_ok=True) -def cli(grid: Literal["hex", "healpix"], level: int, backup_intermediate: bool = False): +cli = cyclopts.App(name="alpha-earth") + + +@cli.command() +def download(grid: Literal["hex", "healpix"], level: int, backup_intermediate: bool = False): """Extract satellite embeddings from Google Earth Engine and map them to a grid. Args: @@ -93,8 +98,49 @@ def cli(grid: Literal["hex", "healpix"], level: int, backup_intermediate: bool = print(f"Saved embeddings for year {year} to {embeddings_file.resolve()}.") +@cli.command() +def combine_to_zarr(grid: Literal["hex", "healpix"], level: int): + """Combine yearly embeddings parquet files into a single zarr store. + + Args: + grid (Literal["hex", "healpix"]): The grid type to use. + level (int): The grid level to use. + + """ + embs = gpd.read_parquet(DATA_DIR / "embeddings" / f"permafrost_{grid}{level}_embeddings-2017.parquet") + # ? Converting cell IDs from hex strings to integers for xdggs compatibility + cells = [int(cid, 16) for cid in embs.cell_id.to_list()] + years = list(range(2017, 2025)) + aggs = ["median", "stdDev", "min", "max", "mean", "p1", "p5", "p25", "p75", "p95", "p99"] + bands = [f"A{str(i).zfill(2)}" for i in range(64)] + + a = xr.DataArray( + np.nan, + dims=("year", "cell", "band", "agg"), + coords={"year": years, "cell": cells, "band": bands, "agg": aggs}, + ) + # ? These attributes are needed for xdggs + a.cell.attrs = { + "grid_name": "h3" if grid == "hex" else "healpix", + "level": level, + } + if grid == "healpix": + a.cell.attrs["indexing_scheme"] = "nested" + + for year in track(years, total=len(years), description="Processing years..."): + embs = gpd.read_parquet(DATA_DIR / "embeddings" / f"permafrost_{grid}{level}_embeddings-{year}.parquet") + for band in bands: + for agg in aggs: + col = f"{band}_{agg}" + a.loc[{"band": band, "agg": agg, "year": year}] = embs[col].to_list() + + zarr_path = EMBEDDINGS_DIR / f"permafrost_{grid}{level}_embeddings.zarr" + a.to_zarr(zarr_path, consolidated=False, mode="w") + print(f"Saved combined embeddings to {zarr_path.resolve()}.") + + def main(): # noqa: D103 - cyclopts.run(cli) + cli() if __name__ == "__main__": diff --git a/steps/s1_0_alphaearth/alphaearth.sh b/steps/s1_0_alphaearth/alphaearth.sh index 32b5193..2f5cae6 100644 --- a/steps/s1_0_alphaearth/alphaearth.sh +++ b/steps/s1_0_alphaearth/alphaearth.sh @@ -1,9 +1,17 @@ #!/bin/bash -# uv run alpha-earth --grid hex --level 3 -uv run alpha-earth --grid hex --level 4 -uv run alpha-earth --grid hex --level 5 -uv run alpha-earth --grid healpix --level 6 -uv run alpha-earth --grid healpix --level 7 -uv run alpha-earth --grid healpix --level 8 -uv run alpha-earth --grid healpix --level 9 +# uv run alpha-earth download --grid hex --level 3 +# uv run alpha-earth download --grid hex --level 4 +# uv run alpha-earth download --grid hex --level 5 +# uv run alpha-earth download --grid healpix --level 6 +# uv run alpha-earth download --grid healpix --level 7 +# uv run alpha-earth download --grid healpix --level 8 +# uv run alpha-earth download --grid healpix --level 9 + +uv run alpha-earth combine-to-zarr --grid hex --level 3 +uv run alpha-earth combine-to-zarr --grid hex --level 4 +uv run alpha-earth combine-to-zarr --grid hex --level 5 +uv run alpha-earth combine-to-zarr --grid healpix --level 6 +uv run alpha-earth combine-to-zarr --grid healpix --level 7 +uv run alpha-earth combine-to-zarr --grid healpix --level 8 +uv run alpha-earth combine-to-zarr --grid healpix --level 9 diff --git a/steps/s1_1_era5/era5.py b/steps/s1_1_era5/era5.py index 508877c..83cdf7b 100644 --- a/steps/s1_1_era5/era5.py +++ b/steps/s1_1_era5/era5.py @@ -12,11 +12,12 @@ Variables of Interest: Naming patterns: - Instant Variables are downloaded already as statistically aggregated (lossy), therefore their names get the aggregation as suffix -- Accumulation Variables are downloaded as totals, their names stay the same +- Accumulation Variables are downloaded as totals (sum), their names stay the same Daily Variables (downloaded from hourly data): - t2m_max - t2m_min +- t2m_mean - snowc_mean - sde_mean - lblt_max @@ -25,80 +26,79 @@ Daily Variables (downloaded from hourly data): - sshf Derived Daily Variables: -- t2m_daily_avg -- t2m_daily_range -- t2m_daily_skew -- thawing_degree_days -- freezing_degree_days -- thawing_days -- freezing_days -- precipitation_occurrences -- snowfall_occurrences -- snow_isolation (snowc * sde) +- t2m_range [instant]: t2m_max - t2m_min +- t2m_avg [instant]: (t2m_max - t2m_min) / 2 +- t2m_skew [instant]: (t2m_mean - t2m_min) / t2m_range +- thawing_degree_days [accum]: (t2m_avg - 273.15).clip(min=0) +- freezing_degree_days [accum]: (273.15 - t2m_avg).clip(min=0) +- thawing_days [accum]: (t2m_avg > 273.15).astype(int) +- freezing_days [accum]: (t2m_avg < 273.15).astype(int) +- precipitation_occurrences [accum]: (tp > 0.001).astype(int) +- snowfall_occurrences [accum]: (sf > 0.001).astype(int) +- naive_snow_isolation [instant]: snowc_mean * sde_mean -Monthly Variables: -- t2m_monthly_max -- t2m_monthly_min -- tp_monthly_sum -- sf_monthly_sum -- snowc_monthly_mean -- sde_monthly_mean -- sshf_monthly_sum -- lblt_monthly_max -- t2m_monthly_avg -- t2m_monthly_range_avg -- t2m_monthly_skew_avg -- thawing_degree_days_monthly -- freezing_degree_days_monthly -- thawing_days_monthly -- freezing_days_monthly -- precipitation_occurrences_monthly TODO: Rename to precipitation_days_monthly? -- snowfall_occurrences_monthly TODO: Rename to snowfall_days_monthly? -- snow_isolation_monthly_mean -Yearly Variables: -- TODO +Monthly, Winter, Summer & Yearly Aggregations (Names don't change): +- instant variables: + - *_min -> min + - *_max -> max + - *_rest -> median +- accum variables: sum -# TODO Variables: -- Day of first thaw (yearly) -- Day of last thaw (yearly) -- Thawing period length (yearly) -- Freezing period length (yearly) +Derived & (from monthly) Aggregated Winter Variables: +- effective_snow_depth [instant]: (sde_mean * M + 1 - m).sum(M) / (m).sum(M),see also https://tc.copernicus.org/articles/11/989/2017/tc-11-989-2017.pdf + +Derived & (from daily) Aggregated Yearly Variables: +- day_of_first_thaw [yearly]: First day in year where t2m_daily_avg > 273.15 +- day_of_last_thaw [yearly]: Last day in year where t2m_daily_avg > 273.15 +- thawing_period_length [yearly]: day_of_last_thaw - day_of_first_thaw +- day_of_first_freeze [yearly]: First day in year where t2m_daily_avg < 273.15 +- day_of_last_freeze [yearly]: Last day in year where t2m_daily_avg < 273.15 + +About yearly aggregates: +- A year always starts on 1st October and ends on 30th September of the next year + to better capture the Arctic seasonal cycle. +- Thus year == 2020 means 1st Oct 2019 - 30th Sep 2020 +- Thus winter == 2020 means 1st Oct 2019 - 31th March 2020 +- Thus summer == 2020 means 1st April 2020 - 30th Sep 2020 Author: Tobias Hölzer -Date: 09. June 2025 +Date: June to October 2025 """ import os import time -from concurrent.futures import ProcessPoolExecutor, ThreadPoolExecutor, as_completed from pathlib import Path from typing import Literal import cyclopts import dask.distributed as dd import geopandas as gpd +import numpy as np import odc.geo import odc.geo.xr import pandas as pd import shapely import shapely.ops import xarray as xr -from numcodecs.zarr3 import Blosc from rich import pretty, print, traceback from rich.progress import track from shapely.geometry import LineString, Polygon +from zarr.codecs import BloscCodec traceback.install(show_locals=True, suppress=[cyclopts, xr, pd]) pretty.install() cli = cyclopts.App() -# TODO: Directly handle download on a grid level - this is more what the zarr access is indented to do - DATA_DIR = Path(os.environ.get("DATA_DIR", "data")) / "entropyc-rts" ERA5_DIR = DATA_DIR / "era5" DAILY_RAW_PATH = ERA5_DIR / "daily_raw.zarr" +DAILY_ENRICHED_PATH = ERA5_DIR / "daily_enriched.zarr" +MONTHLY_RAW_PATH = ERA5_DIR / "monthly_raw.zarr" +YEARLY_RAW_PATH = ERA5_DIR / "yearly_aligned.zarr" +SUMMER_RAW_PATH = ERA5_DIR / "summer_aligned.zarr" +WINTER_RAW_PATH = ERA5_DIR / "winter_aligned.zarr" def _get_grid_paths( @@ -119,16 +119,37 @@ max_time = "2024-12-31" today = time.strftime("%Y-%m-%d") -# ================ -# === Download === -# ================ +instants = { + "t2m_max", + "t2m_min", + "t2m_mean", + "snowc_mean", + "sde_mean", + "lblt_max", + "t2m_range", + "t2m_avg", + "t2m_skew", + "naive_snow_isolation", +} + +accums = { + "tp", + "sf", + "sshf", + "thawing_degree_days", + "freezing_degree_days", + "thawing_days", + "freezing_days", + "precipitation_occurrences", + "snowfall_occurrences", +} def create_encoding(ds: xr.Dataset): """Create compression encoding for zarr dataset storage. Creates Blosc compression configuration for all data variables and coordinates - in the dataset using zstd compression with level 9. + in the dataset using zstd compression with level 5. Args: ds (xr.Dataset): The xarray Dataset to create encoding for. @@ -138,10 +159,15 @@ def create_encoding(ds: xr.Dataset): """ # encoding = {var: {"compressors": BloscCodec(cname="zlib", clevel=9)} for var in ds.data_vars} - encoding = {var: {"compressors": Blosc(cname="zstd", clevel=9)} for var in [*ds.data_vars, *ds.coords]} + encoding = {var: {"compressors": BloscCodec(cname="zstd", clevel=5)} for var in [*ds.data_vars, *ds.coords]} return encoding +# ================ +# === Download === +# ================ + + def download_daily_aggregated(): """Download and aggregate ERA5 data to daily resolution. @@ -184,6 +210,7 @@ def download_daily_aggregated(): # Instant era5.t2m.resample(time="1D").max().rename("t2m_max"), era5.t2m.resample(time="1D").min().rename("t2m_min"), + era5.t2m.resample(time="1D").mean().rename("t2m_mean"), era5.snowc.resample(time="1D").mean().rename("snowc_mean"), era5.sde.resample(time="1D").mean().rename("sde_mean"), era5.lblt.resample(time="1D").max().rename("lblt_max"), @@ -197,6 +224,7 @@ def download_daily_aggregated(): # Assign attributes daily_raw["t2m_max"].attrs = {"long_name": "Daily maximum 2 metre temperature", "units": "K"} daily_raw["t2m_min"].attrs = {"long_name": "Daily minimum 2 metre temperature", "units": "K"} + daily_raw["t2m_mean"].attrs = {"long_name": "Daily mean 2 metre temperature", "units": "K"} daily_raw["tp"].attrs = {"long_name": "Daily total precipitation", "units": "m"} daily_raw["sf"].attrs = {"long_name": "Daily total snow fall", "units": "m"} daily_raw["snowc_mean"].attrs = {"long_name": "Daily mean snow cover", "units": "m"} @@ -227,6 +255,309 @@ def download(): print(f"Downloaded and aggregated ERA5 data to {DAILY_RAW_PATH.resolve()}.") +# ============================ +# === Temporal Aggregation === +# ============================ + + +def daily_enrich(): + """Enrich daily ERA5 data with derived climate variables. + + Loads downloaded daily ERA5 data and computes additional climate variables. + Creates derived variables including temperature statistics, degree days, and occurrence indicators. + + Derived variables include: + - Daily average and range temperature + - Temperature skewness + - Thawing and freezing degree days + - Thawing and freezing day counts + - Precipitation and snowfall occurrences + - Snow isolation index + + """ + daily = xr.open_zarr(DAILY_RAW_PATH, consolidated=False).set_coords("spatial_ref") + assert "time" in daily.dims, f"Expected dim 'time' to be in {daily.dims=}" + + # Formulas based on Groeke et. al. (2025) Stochastic Weather generation... + daily["t2m_avg"] = (daily.t2m_max + daily.t2m_min) / 2 + daily.t2m_avg.attrs = {"long_name": "Daily average 2 metre temperature", "units": "K"} + daily["t2m_range"] = daily.t2m_max - daily.t2m_min + daily.t2m_range.attrs = {"long_name": "Daily range of 2 metre temperature", "units": "K"} + daily["t2m_skew"] = (daily.t2m_mean - daily.t2m_min) / daily.t2m_range + daily.t2m_skew.attrs = {"long_name": "Daily skewness of 2 metre temperature"} + + daily["thawing_degree_days"] = (daily.t2m_avg - 273.15).clip(min=0) + daily.thawing_degree_days.attrs = {"long_name": "Thawing degree days", "units": "K"} + daily["freezing_degree_days"] = (273.15 - daily.t2m_avg).clip(min=0) + daily.freezing_degree_days.attrs = {"long_name": "Freezing degree days", "units": "K"} + + daily["thawing_days"] = (daily.t2m_avg > 273.15).astype(int) + daily.thawing_days.attrs = {"long_name": "Thawing days"} + daily["freezing_days"] = (daily.t2m_avg < 273.15).astype(int) + daily.freezing_days.attrs = {"long_name": "Freezing days"} + + daily["precipitation_occurrences"] = (daily.tp > 0).astype(int) + daily.precipitation_occurrences.attrs = {"long_name": "Precipitation occurrences"} + daily["snowfall_occurrences"] = (daily.sf > 0).astype(int) + daily.snowfall_occurrences.attrs = {"long_name": "Snowfall occurrences"} + + daily["naive_snow_isolation"] = daily.snowc_mean * daily.sde_mean + daily.naive_snow_isolation.attrs = {"long_name": "Naive snow isolation"} + + daily.to_zarr(DAILY_ENRICHED_PATH, mode="w", encoding=create_encoding(daily), consolidated=False) + + +def monthly_aggregate(): + """Aggregate enriched daily ERA5 data to monthly resolution. + + Takes the enriched daily ERA5 data and creates monthly aggregates using + appropriate statistical functions for each variable type. + Instant variables use min, max, or median aggregations, while accumulative + variables are summed over the month. + + The aggregated monthly data is saved to a zarr file for further processing. + + """ + daily = xr.open_zarr(DAILY_ENRICHED_PATH, consolidated=False) + assert "time" in daily.dims, f"Expected dim 'time' to be in {daily.dims=}" + daily = daily.sel(time=slice(min_time, max_time)) + + # Monthly instant aggregates + monthly_instants = [] + for var in instants: + if var.endswith("_min"): + agg = daily[var].resample(time="1ME").min().rename(var) + agg.attrs = daily[var].attrs + agg.attrs["long_name"] = f"Monthly minimum of {daily[var].attrs.get('long_name', var)}" + monthly_instants.append(agg) + elif var.endswith("_max"): + agg = daily[var].resample(time="1ME").max().rename(var) + agg.attrs = daily[var].attrs + agg.attrs["long_name"] = f"Monthly maximum of {daily[var].attrs.get('long_name', var)}" + monthly_instants.append(agg) + else: + agg = daily[var].resample(time="1ME").median().rename(var) + agg.attrs = daily[var].attrs + agg.attrs["long_name"] = f"Monthly median of {daily[var].attrs.get('long_name', var)}" + monthly_instants.append(agg) + + monthly_accums = [] + for var in accums: + agg = daily[var].resample(time="1ME").sum().rename(var) + agg.attrs = daily[var].attrs + monthly_accums.append(agg) + + monthly = xr.merge(monthly_instants + monthly_accums) + monthly = monthly.chunk({"time": len(monthly.time), "latitude": 64, "longitude": 64}) + monthly.to_zarr(MONTHLY_RAW_PATH, mode="w", encoding=create_encoding(monthly), consolidated=False) + + +def multi_monthly_aggregate(monthly: xr.Dataset, n: int = 12) -> xr.Dataset: + """Aggregate monthly ERA5 data to a multi-month resolution. + + Takes monthly aggregated data and creates multi-month aggregates using a shifted + calendar (October to September) to better capture Arctic seasonal patterns. + + Args: + monthly (xr.Dataset): The monthly aggregates + n (int, optional): Number of months to aggregate over. Defaults to 12. + + Returns: + xr.Dataset: The aggregated dataset + + """ + # Instants + multimonthly_instants = [] + for var in instants: + if var.endswith("_min"): + agg = monthly[var].resample(time=f"{n}MS", label="right").min().rename(var) + agg.attrs = monthly[var].attrs + agg.attrs["long_name"] = f"{n}-Monthly minimum of {monthly[var].attrs.get('long_name', var)}" + multimonthly_instants.append(agg) + elif var.endswith("_max"): + agg = monthly[var].resample(time=f"{n}MS", label="right").max().rename(var) + agg.attrs = monthly[var].attrs + agg.attrs["long_name"] = f"{n}-Monthly maximum of {monthly[var].attrs.get('long_name', var)}" + multimonthly_instants.append(agg) + else: + agg = monthly[var].resample(time=f"{n}MS", label="right").median().rename(var) + agg.attrs = monthly[var].attrs + agg.attrs["long_name"] = f"{n}-Monthly median of {monthly[var].attrs.get('long_name', var)}" + multimonthly_instants.append(agg) + + # Accums + multimonthly_accums = [] + for var in accums: + agg = monthly[var].resample(time=f"{n}MS", label="right").sum().rename(var) + agg.attrs = monthly[var].attrs + multimonthly_accums.append(agg) + + multimonthly = xr.merge(multimonthly_instants + multimonthly_accums) + + # Effective snow depth + m = np.resize(np.arange(1, n + 1), len(monthly.time)) + m = xr.DataArray(m, coords={"time": monthly.time}, dims=["time"]) + n_sum = n * (n + 1) // 2 + multimonthly["effective_snow_depth"] = (monthly.sde_mean * (n + 1 - m)).resample(time=f"{n}MS").sum().rename( + "effective_snow_depth" + ) / n_sum + multimonthly["effective_snow_depth"].attrs = { + "long_name": "Effective Snow Density", + "reference": "Slater et. al. (2017)", + "link": "https://tc.copernicus.org/articles/11/989/2017/tc-11-989-2017.pdf", + } + + multimonthly = multimonthly.chunk({"time": len(multimonthly.time), "latitude": 64, "longitude": 64}) + return multimonthly + + +def yearly_and_seasonal_aggregate(): + """Aggregate monthly ERA5 data to yearly resolution with seasonal splits. + + Takes monthly aggregated data and creates yearly aggregates using a shifted + calendar (October to September) to better capture Arctic seasonal patterns. + Creates separate aggregates for full year, winter (Oct-Apr), and summer + (May-Sep) periods. + + The first and last incomplete years are excluded from the analysis. + Winter months are defined as months 1-7 in the shifted calendar, + and summer months are 8-12. + + The final dataset includes yearly, winter, and summer aggregates for all + climate variables, saved to a zarr file. + + """ + monthly = xr.open_zarr(MONTHLY_RAW_PATH, consolidated=False).set_coords("spatial_ref") + assert "time" in monthly.dims, f"Expected dim 'time' to be in {monthly.dims=}" + + # "Shift" the calendar by slicing the first Jan-Sep and the last Oct-Dec months + first_year = monthly.time.dt.year.min().item() + last_year = monthly.time.dt.year.max().item() + monthly = monthly.sel(time=slice(f"{first_year}-10-01", f"{last_year}-09-30")) + + yearly = multi_monthly_aggregate(monthly, n=12) + yearly = derive_yearly_variables(yearly) + yearly.to_zarr(YEARLY_RAW_PATH, mode="w", encoding=create_encoding(yearly), consolidated=False) + + summer_winter = multi_monthly_aggregate(monthly, n=6) + + summer = summer_winter.sel(time=summer_winter.time.dt.month == 4) + summer.to_zarr(SUMMER_RAW_PATH, mode="w", encoding=create_encoding(summer), consolidated=False) + + winter = summer_winter.sel(time=summer_winter.time.dt.month == 10) + winter.to_zarr(WINTER_RAW_PATH, mode="w", encoding=create_encoding(winter), consolidated=False) + + +def derive_yearly_variables(yearly: xr.Dataset) -> xr.Dataset: + """Derive additional variables from daily data and add them to the yearly dataset. + + Args: + yearly (xr.Dataset): The yearly aggregated dataset to enrich. + + Returns: + xr.Dataset: The enriched yearly dataset with additional derived variables. + + """ + assert "time" in yearly.dims, f"Expected dim 'time' to be in {yearly.dims=}" + daily = xr.open_zarr(DAILY_ENRICHED_PATH, consolidated=False).set_coords("spatial_ref") + assert "time" in daily.dims, f"Expected dim 'time' to be in {daily.dims=}" + daily = daily.sel(time=slice(min_time, max_time)) + # ? Note: The functions do not really account for leap years + # n_days_in_year = daily.time.groupby("time.year").count().rename("n_days_in_year") + n_days_in_year = 365 + + # A mask to check which places never thaws + # Persist in memory because we need it twice and this dramatically reduces the Dask-Graph size + never_thaws = (daily.thawing_days.groupby("time.year").sum(dim="time") == 0).compute() + + # ? First and last thaw day is NOT calculated within the october-september year, but within the calendar year + # This results in a much more correct representation of thawing periods in regions where the last thawing day + # is between october and december. + # This assumes that the 01-01 is almost everywhere one of the coldest days in the year + first_thaw_day = daily.thawing_days.groupby("time.year").apply(lambda x: x.argmax(dim="time")) + 1 + first_thaw_day = first_thaw_day.where(~never_thaws).rename("day_of_first_thaw").rename(year="time") + first_thaw_day["time"] = pd.to_datetime([f"{y}-10-01" for y in first_thaw_day.time.values]) # noqa: PD011 + first_thaw_day.attrs = {"long_name": "Day of first thaw in year", "units": "day of year"} + yearly["day_of_first_thaw"] = first_thaw_day.sel(time=yearly.time) + + last_thaw_day = ( + n_days_in_year - daily.thawing_days[::-1].groupby("time.year").apply(lambda x: x.argmax(dim="time")) + 1 + ) + last_thaw_day = last_thaw_day.where(~never_thaws).rename("day_of_last_thaw").rename(year="time") + last_thaw_day["time"] = pd.to_datetime([f"{y}-10-01" for y in last_thaw_day.time.values]) # noqa: PD011 + last_thaw_day.attrs = {"long_name": "Day of last thaw in year", "units": "day of year"} + yearly["day_of_last_thaw"] = last_thaw_day.sel(time=yearly.time) + + yearly["thawing_period_length"] = (yearly.day_of_last_thaw - yearly.day_of_first_thaw).rename( + "thawing_period_length" + ) + yearly.thawing_period_length.attrs = {"long_name": "Thawing period length in year", "units": "days"} + + # ? First and last freeze day is NOT calculated within the october-september year, but within an july-june year + # This results, similar to the thawing days, in a much more correct representation of freezing periods in regions + # where the first freezing day is between july and september. + # This assumes that the 01-07 is almost everywhere one of the warmest days in the year + daily_shifted = daily.copy() + daily_shifted["time"] = pd.to_datetime(daily_shifted.time.values) + pd.DateOffset(months=6) + + # A mask to check which places never freeze + # Persist in memory because we need it twice and this dramatically reduces the Dask-Graph size + never_freezes = (daily_shifted.freezing_days.groupby("time.year").sum(dim="time") == 0).compute() + + first_freezing_day = daily_shifted.freezing_days.groupby("time.year").apply(lambda x: x.argmax(dim="time")) + 1 + first_freezing_day = first_freezing_day.where(~never_freezes).rename("day_of_first_freeze").rename(year="time") + first_freezing_day["time"] = pd.to_datetime([f"{y}-10-01" for y in first_freezing_day.time.values]) # noqa: PD011 + first_freezing_day.attrs = {"long_name": "Day of first freeze in year", "units": "day of year"} + yearly["day_of_first_freeze"] = first_freezing_day.sel(time=yearly.time) + + last_freezing_day = ( + n_days_in_year + - daily_shifted.freezing_days[::-1].groupby("time.year").apply(lambda x: x.argmax(dim="time")) + + 1 + ) + last_freezing_day = last_freezing_day.where(~never_freezes).rename("day_of_last_freeze").rename(year="time") + last_freezing_day["time"] = pd.to_datetime([f"{y}-10-01" for y in last_freezing_day.time.values]) # noqa: PD011 + last_freezing_day.attrs = {"long_name": "Day of last freeze in year", "units": "day of year"} + yearly["day_of_last_freeze"] = last_freezing_day.sel(time=yearly.time) + + yearly["freezing_period_length"] = (yearly.day_of_last_freeze - yearly.day_of_first_freeze).rename( + "freezing_period_length" + ) + yearly.freezing_period_length.attrs = {"long_name": "Freezing period length in year", "units": "days"} + + return yearly + + +@cli.command +def enrich(n_workers: int = 10, monthly: bool = True, yearly: bool = True, daily: bool = True): + """Enrich data and pPerform temporal aggregation of ERA5 data using Dask cluster. + + Creates a Dask cluster and runs both monthly and yearly aggregation + functions to generate temporally aggregated climate datasets. The + processing uses parallel workers for efficient computation. + + Args: + n_workers (int, optional): Number of Dask workers to use. Defaults to 10. + monthly (bool, optional): Whether to perform monthly aggregation. Defaults to True. + yearly (bool, optional): Whether to perform yearly aggregation. Defaults to True. + daily (bool, optional): Whether to perform daily enrichment. Defaults to True. + + """ + with ( + dd.LocalCluster(n_workers=n_workers, threads_per_worker=20, memory_limit="10GB") as cluster, + dd.Client(cluster) as client, + ): + print(client) + print(client.dashboard_link) + if daily: + daily_enrich() + if monthly: + monthly_aggregate() + if yearly: + yearly_and_seasonal_aggregate() + print("Enriched ERA5 data with additional features and aggregated it temporally.") + + # =========================== # === Spatial Aggregation === # =========================== @@ -250,26 +581,27 @@ def _split_antimeridian_cell(geom: Polygon) -> list[Polygon]: return list(polys.geoms) -def _check_geobox(geobox): - x, y = geobox.shape - return x > 1 and y > 1 +def _check_geom(geobox: odc.geo.geobox.GeoBox, geom: odc.geo.Geometry) -> bool: + enclosing = geobox.enclosing(geom) + x, y = enclosing.shape + if x <= 1 or y <= 1: + return False + roi: tuple[slice, slice] = geobox.overlap_roi(enclosing) + roix, roiy = roi + return (roix.stop - roix.start) > 1 and (roiy.stop - roiy.start) > 1 -def extract_cell_data(idx: int, geom: Polygon) -> xr.Dataset: +def extract_cell_data(yearly: xr.Dataset, geom: Polygon): """Extract ERA5 data for a specific grid cell geometry. Extracts and spatially averages ERA5 data within the bounds of a grid cell. Handles antimeridian-crossing cells by splitting them appropriately. Args: - idx (int): Index of the grid cell. + yearly (xr.Dataset): Yearly aggregated ERA5 dataset. geom (Polygon): Polygon geometry of the grid cell. - Returns: - xr.Dataset: The computed cell dataset - """ - daily_raw = xr.open_zarr(DAILY_RAW_PATH, consolidated=False).set_coords("spatial_ref") # cell.geometry is a shapely Polygon if not _crosses_antimeridian(geom): geoms = [geom] @@ -279,17 +611,16 @@ def extract_cell_data(idx: int, geom: Polygon) -> xr.Dataset: cell_data = [] for geom in geoms: geom = odc.geo.Geometry(geom, crs="epsg:4326") - if not _check_geobox(daily_raw.odc.geobox.enclosing(geom)): + if not _check_geom(yearly.odc.geobox, geom): continue - # TODO: use mean for instant variables, sum for accum variables - cell_data.append(daily_raw.odc.crop(geom).drop_vars("spatial_ref").mean(["latitude", "longitude"])) + cell_data.append(yearly.odc.crop(geom).drop_vars("spatial_ref").mean(["latitude", "longitude"])) if len(cell_data) == 0: return False elif len(cell_data) == 1: cell_data = cell_data[0] else: cell_data = xr.concat(cell_data, dim="part").mean("part") - cell_data = cell_data.expand_dims({"cell": [idx]}).compute() + cell_data = cell_data.compute() return cell_data @@ -297,8 +628,8 @@ def extract_cell_data(idx: int, geom: Polygon) -> xr.Dataset: def spatial_agg( grid: Literal["hex", "healpix"], level: int, + agg: Literal["summer", "winter", "yearly"] = "yearly", n_workers: int = 10, - executor: Literal["threads", "processes"] = "threads", ): """Perform spatial aggregation of ERA5 data to grid cells. @@ -309,267 +640,71 @@ def spatial_agg( Args: grid ("hex" | "healpix"): Grid type. level (int): Grid resolution level. + agg ("summer" | "winter" | "yearly"): Type of aggregation to perform. Defaults to yearly. n_workers (int, optional): Number of parallel workers to use. Defaults to 10. - executor ("threads" | "processes"): The type of parallel executor pool to use. Defaults to threads. """ gridname = f"permafrost_{grid}{level}" - daily_grid_path = _get_grid_paths("daily", grid, level) - grid = gpd.read_parquet(DATA_DIR / f"grids/{gridname}_grid.parquet") + agg_grid_path = _get_grid_paths(agg, grid, level) + grid_df = gpd.read_parquet(DATA_DIR / f"grids/{gridname}_grid.parquet") # Create an empty zarr array with the right dimensions - daily_raw = xr.open_zarr(DAILY_RAW_PATH, consolidated=False).set_coords("spatial_ref") - assert {"latitude", "longitude", "time"} == set(daily_raw.dims), ( - f"Expected dims ('latitude', 'longitude', 'time'), got {daily_raw.dims}" + if agg == "summer": + agg_data_path = SUMMER_RAW_PATH + elif agg == "winter": + agg_data_path = WINTER_RAW_PATH + elif agg == "yearly": + agg_data_path = YEARLY_RAW_PATH + else: + raise ValueError(f"Unknown aggregation type: {agg}") + agg_raw = ( + xr.open_zarr(agg_data_path, consolidated=False, decode_timedelta=False) + .set_coords("spatial_ref") + .drop_vars(["surface", "number", "depthBelowLandLayer"]) + .load() ) - assert daily_raw.odc.crs == "epsg:4326", f"Expected CRS 'epsg:4326', got {daily_raw.odc.crs}" - daily = ( - xr.zeros_like(daily_raw.isel(latitude=0, longitude=0)) - .expand_dims({"cell": [idx for idx, _ in grid.iterrows()]}) - .chunk({"cell": min(len(grid), 1000), "time": len(daily_raw.time)}) # ~50MB chunks + assert {"latitude", "longitude", "time"} == set(agg_raw.dims), ( + f"Expected dims ('latitude', 'longitude', 'time'), got {agg_raw.dims}" ) - daily.to_zarr(daily_grid_path, mode="w", consolidated=False, encoding=create_encoding(daily)) - print(f"Created empty zarr at {daily_grid_path.resolve()} with shape {daily.sizes}.") + assert agg_raw.odc.crs == "epsg:4326", f"Expected CRS 'epsg:4326', got {agg_raw.odc.crs}" - print(f"Starting spatial matching of {len(grid)} cells with {n_workers} workers...") - ExecutorCls = ThreadPoolExecutor if executor == "threads" else ProcessPoolExecutor - with ExecutorCls(max_workers=n_workers) as executor: - futures = { - executor.submit(extract_cell_data, idx, row.geometry): idx - for idx, row in grid.to_crs("epsg:4326").iterrows() - } - for future in track(as_completed(futures), total=len(futures), description="Processing cells"): - idx = futures[future] - try: - cell_data = future.result() - if not cell_data: - print(f"Cell {idx} did not overlap with ERA5 data.") - cell_data.to_zarr(daily_grid_path, region="auto", consolidated=False) - print(f"Successfully written cell {idx}") - except Exception as e: - print(f"{type(e)} processing cell {idx}: {e}") - print("Finished spatial matching.") + # Convert lons to -180 to 180 instead of 0 to 360 + agg_raw = agg_raw.assign_coords(longitude=(((agg_raw.longitude + 180) % 360) - 180)).sortby("longitude") + # ? Converting cell IDs from hex strings to integers for xdggs compatibility + cells = [int(cid, 16) for cid in grid_df.cell_id.to_list()] -# ============================ -# === Temporal Aggregation === -# ============================ - - -def daily_enrich(grid: Literal["hex", "healpix"], level: int) -> xr.Dataset: - """Enrich daily ERA5 data with derived climate variables. - - Loads spatially aligned ERA5 data and computes additional climate variables. - Creates derived variables including temperature statistics, degree days, and occurrence indicators. - - Derived variables include: - - Daily average and range temperature - - Temperature skewness - - Thawing and freezing degree days - - Thawing and freezing day counts - - Precipitation and snowfall occurrences - - Snow isolation index - - Args: - grid ("hex", "healpix"): Grid type. - level (int): Grid resolution level. - - Returns: - xr.Dataset: Enriched dataset with original and derived variables. - - """ - daily_grid_path = _get_grid_paths("daily", grid, level) - daily = xr.open_zarr(daily_grid_path, consolidated=False).set_coords("spatial_ref") - assert {"cell", "time"} == set(daily.dims), f"Expected dims ('cell', 'time'), got {daily.dims}" - - # Formulas based on Groeke et. al. (2025) Stochastic Weather generation... - daily["t2m_avg"] = (daily.t2m_max + daily.t2m_min) / 2 - daily.t2m_avg.attrs = {"long_name": "Daily average 2 metre temperature", "units": "K"} - daily["t2m_range"] = daily.t2m_max - daily.t2m_min - daily.t2m_range.attrs = {"long_name": "Daily range of 2 metre temperature", "units": "K"} - daily["t2m_skew"] = (daily.t2m_avg - daily.t2m_min) / daily.t2m_range - daily.t2m_skew.attrs = {"long_name": "Daily skewness of 2 metre temperature"} - - daily["thawing_degree_days"] = (daily.t2m_avg - 273.15).clip(min=0) - daily.thawing_degree_days.attrs = {"long_name": "Thawing degree days", "units": "K"} - daily["freezing_degree_days"] = (273.15 - daily.t2m_avg).clip(min=0) - daily.freezing_degree_days.attrs = {"long_name": "Freezing degree days", "units": "K"} - - daily["thawing_days"] = (daily.t2m_avg > 273.15).astype(int) - daily.thawing_days.attrs = {"long_name": "Thawing days"} - daily["freezing_days"] = (daily.t2m_avg < 273.15).astype(int) - daily.freezing_days.attrs = {"long_name": "Freezing days"} - - daily["precipitation_occurrences"] = (daily.tp > 0).astype(int) - daily.precipitation_occurrences.attrs = {"long_name": "Precipitation occurrences"} - daily["snowfall_occurrences"] = (daily.sf > 0).astype(int) - daily.snowfall_occurrences.attrs = {"long_name": "Snowfall occurrences"} - - daily["snow_isolation"] = daily.snowc_mean * daily.sde_mean - daily.snow_isolation.attrs = {"long_name": "Snow isolation"} - - return daily - - -def monthly_aggregate(grid: Literal["hex", "healpix"], level: int): - """Aggregate enriched daily ERA5 data to monthly resolution. - - Takes the enriched daily ERA5 data and creates monthly aggregates using - appropriate statistical functions for each variable type. Temperature - variables use min/max/mean, accumulation variables use sums, and derived - variables use appropriate aggregations. - - The aggregated monthly data is saved to a zarr file for further processing. - - Args: - grid ("hex", "healpix"): Grid type. - level (int): Grid resolution level. - - """ - daily = daily_enrich(grid, level) - assert {"cell", "time"} == set(daily.dims), f"Expected dims ('cell', 'time'), got {daily.dims}" - - # Monthly aggregates - monthly = xr.merge( - [ - # Original variables - daily.t2m_min.resample(time="1ME").min().rename("t2m_min"), - daily.t2m_max.resample(time="1ME").max().rename("t2m_max"), - daily.snowc_mean.resample(time="1ME").mean().rename("snowc_mean"), - daily.sde_mean.resample(time="1ME").mean().rename("sde_mean"), - daily.lblt_max.resample(time="1ME").max().rename("lblt_max"), - daily.tp.resample(time="1ME").sum().rename("tp"), - daily.sf.resample(time="1ME").sum().rename("sf"), - daily.sshf.resample(time="1ME").sum().rename("sshf"), - # Enriched variables - daily.t2m_avg.resample(time="1ME").mean().rename("t2m_avg"), - daily.t2m_range.resample(time="1ME").mean().rename("t2m_mean_range"), - daily.t2m_skew.resample(time="1ME").mean().rename("t2m_mean_skew"), - daily.thawing_degree_days.resample(time="1ME").sum().rename("thawing_degree_days"), - daily.freezing_degree_days.resample(time="1ME").sum().rename("freezing_degree_days"), - daily.thawing_days.resample(time="1ME").sum().rename("thawing_days"), - daily.freezing_days.resample(time="1ME").sum().rename("freezing_days"), - daily.precipitation_occurrences.resample(time="1ME").sum().rename("precipitation_occurrences"), - daily.snowfall_occurrences.resample(time="1ME").sum().rename("snowfall_occurrences"), - daily.snow_isolation.resample(time="1ME").mean().rename("snow_mean_isolation"), - ] + agg_aligned = ( + xr.zeros_like(agg_raw.isel(latitude=0, longitude=0).drop_vars(["latitude", "longitude"])) + .expand_dims({"cell_ids": cells}) + .chunk({"cell_ids": min(len(grid_df), 10000), "time": len(agg_raw.time)}) ) - monthly_grid_path = _get_grid_paths("monthly", grid, level) - monthly.to_zarr(monthly_grid_path, mode="w", encoding=create_encoding(monthly), consolidated=False) + agg_aligned.cell_ids.attrs = { + "grid_name": "h3" if grid == "hex" else grid, + "level": level, + } + if grid == "healpix": + agg_aligned.cell_ids.attrs["indexing_scheme"] = "nested" + from stopuhr import stopwatch -def yearly_aggregate(monthly: xr.Dataset) -> xr.Dataset: - """Aggregate monthly ERA5 data to yearly resolution. - - Takes monthly aggregated data and creates yearly aggregates using a shifted - calendar (October to September) to better capture Arctic seasonal patterns. - - Args: - monthly (xr.Dataset): The monthly aggregates - - Returns: - xr.Dataset: The aggregated dataset - - """ - return xr.merge( - [ - # Original variables - monthly.t2m_min.resample(time="1YE").min().rename("t2m_min"), - monthly.t2m_max.resample(time="1YE").max().rename("t2m_max"), - monthly.snowc_mean.resample(time="1YE").mean().rename("snowc_mean"), - monthly.sde_mean.resample(time="1YE").mean().rename("sde_mean"), - monthly.lblt_max.resample(time="1YE").max().rename("lblt_max"), - monthly.tp.resample(time="1YE").sum().rename("tp"), - monthly.sf.resample(time="1YE").sum().rename("sf"), - monthly.sshf.resample(time="1YE").sum().rename("sshf"), - # Enriched variables - monthly.t2m_avg.resample(time="1YE").mean().rename("t2m_avg"), - # TODO: Check if this is correct -> use daily / hourly data instead for range and skew? - monthly.t2m_mean_range.resample(time="1YE").mean().rename("t2m_mean_range"), - monthly.t2m_mean_skew.resample(time="1YE").mean().rename("t2m_mean_skew"), - monthly.thawing_degree_days.resample(time="1YE").sum().rename("thawing_degree_days"), - monthly.freezing_degree_days.resample(time="1YE").sum().rename("freezing_degree_days"), - monthly.thawing_days.resample(time="1YE").sum().rename("thawing_days"), - monthly.freezing_days.resample(time="1YE").sum().rename("freezing_days"), - monthly.precipitation_occurrences.resample(time="1YE").sum().rename("precipitation_occurrences"), - monthly.snowfall_occurrences.resample(time="1YE").sum().rename("snowfall_occurrences"), - monthly.snow_mean_isolation.resample(time="1YE").mean().rename("snow_mean_isolation"), - ] - ) - - -def yearly_and_seasonal_aggregate(grid: Literal["hex", "healpix"], level: int): - """Aggregate monthly ERA5 data to yearly resolution with seasonal splits. - - Takes monthly aggregated data and creates yearly aggregates using a shifted - calendar (October to September) to better capture Arctic seasonal patterns. - Creates separate aggregates for full year, winter (Oct-Apr), and summer - (May-Sep) periods. - - The first and last incomplete years are excluded from the analysis. - Winter months are defined as months 1-7 in the shifted calendar, - and summer months are 8-12. - - The final dataset includes yearly, winter, and summer aggregates for all - climate variables, saved to a zarr file. - - Args: - grid ("hex", "healpix"): Grid type. - level (int): Grid resolution level. - - """ - monthly_grid_path = _get_grid_paths("monthly", grid, level) - monthly = xr.open_zarr(monthly_grid_path, consolidated=False).set_coords("spatial_ref") - assert {"cell", "time"} == set(monthly.dims), f"Expected dims ('cell', 'time'), got {monthly.dims}" - - valid_years = slice(str(monthly.time.min().dt.year.item() + 1), str(monthly.time.max().dt.year.item())) - - # Summer aggregates - summer = yearly_aggregate(monthly.sel(time=monthly.time.dt.month.isin([5, 6, 7, 8, 9])).sel(time=valid_years)) - - # Yearly aggregates (shifted by +8 months to start in Oktober, first and last years will be cropped) - monthly_shifted = monthly.copy() - monthly_shifted["time"] = monthly_shifted.get_index("time") + pd.DateOffset(months=8) - monthly_shifted = monthly_shifted.sel(time=valid_years) - yearly = yearly_aggregate(monthly_shifted) - - # Winter aggregates (shifted by +8 months to start in Oktober, first and last years will be cropped) - monthly_shifted = monthly.copy().sel(time=monthly.time.dt.month.isin([1, 2, 3, 4, 10, 11, 12])) - monthly_shifted["time"] = monthly_shifted.get_index("time") + pd.DateOffset(months=8) - monthly_shifted = monthly_shifted.sel(time=valid_years) - winter = yearly_aggregate(monthly_shifted) - - yearly_grid_path = _get_grid_paths("yearly", grid, level) - yearly.to_zarr(yearly_grid_path, mode="w", encoding=create_encoding(yearly), consolidated=False) - - winter_grid_path = _get_grid_paths("winter", grid, level) - winter.to_zarr(winter_grid_path, mode="w", encoding=create_encoding(winter), consolidated=False) - - summer_grid_path = _get_grid_paths("summer", grid, level) - summer.to_zarr(summer_grid_path, mode="w", encoding=create_encoding(summer), consolidated=False) - - -@cli.command -def temporal_agg(n_workers: int = 10): - """Perform temporal aggregation of ERA5 data using Dask cluster. - - Creates a Dask cluster and runs both monthly and yearly aggregation - functions to generate temporally aggregated climate datasets. The - processing uses parallel workers for efficient computation. - - Args: - n_workers (int, optional): Number of Dask workers to use. Defaults to 10. - - """ - with ( - dd.LocalCluster(n_workers=n_workers, threads_per_worker=20, memory_limit="10GB") as cluster, - dd.Client(cluster) as client, + for _, row in track( + grid_df.to_crs("epsg:4326").iterrows(), + total=len(grid_df), + description="Spatially aggregating ERA5 data...", ): - print(client) - print(client.dashboard_link) - monthly_aggregate() - yearly_and_seasonal_aggregate() - print("Enriched ERA5 data with additional features and aggregated it temporally.") + cell_id = int(row.cell_id, 16) + with stopwatch("Extracting cell data", log=False): + cell_data = extract_cell_data(agg_raw, row.geometry) + if cell_data is False: + print(f"Warning: No data found for cell {cell_id}, skipping.") + continue + with stopwatch("Assigning cell data", log=False): + agg_aligned.loc[{"cell_ids": cell_id}] = cell_data + + agg_aligned.to_zarr(agg_grid_path, mode="w", consolidated=False, encoding=create_encoding(agg_aligned)) + print("Finished spatial matching.") + stopwatch.summary() if __name__ == "__main__": diff --git a/steps/s1_1_era5/era5.sh b/steps/s1_1_era5/era5.sh new file mode 100644 index 0000000..c2a49d6 --- /dev/null +++ b/steps/s1_1_era5/era5.sh @@ -0,0 +1,18 @@ +#!/bin/bash + +# uv run era5 download +# uv run era5 enrich + +# Can be summer, winter or yearly +agg=$1 + +echo "Running ERA5 spatial aggregation for aggregation type: $agg" + +uv run era5 spatial-agg --grid hex --level 3 --agg $agg +uv run era5 spatial-agg --grid hex --level 4 --agg $agg +uv run era5 spatial-agg --grid hex --level 5 --agg $agg + +uv run era5 spatial-agg --grid healpix --level 6 --agg $agg +uv run era5 spatial-agg --grid healpix --level 7 --agg $agg +uv run era5 spatial-agg --grid healpix --level 8 --agg $agg +uv run era5 spatial-agg --grid healpix --level 9 --agg $agg diff --git a/uv.lock b/uv.lock index 94aaf1a..468c96d 100755 --- a/uv.lock +++ b/uv.lock @@ -26,7 +26,7 @@ wheels = [ [[package]] name = "aiohttp" -version = "3.12.15" +version = "3.13.1" 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