PyDaymet: Daily climate data through Daymet#

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Warning

:rotating_light:Since the release of Daymet v4 R1 on November 2022, the URL of Daymet’s server has been changed. Therefore, only the latest version of PyDaymet (v0.13.7) is going to work, and previous versions will not work anymore.:rotating_light:

Features#

PyDaymet is a part of HyRiver software stack that is designed to aid in hydroclimate analysis through web services. This package provides access to climate data from Daymet V4 database using NetCDF Subset Service (NCSS). Both single pixel (using get_bycoords function) and gridded data (using get_bygeom) are supported which are returned as pandas.DataFrame and xarray.Dataset, respectively. Climate data is available for North America, Hawaii from 1980, and Puerto Rico from 1950 at three time scales: daily, monthly, and annual. Additionally, PyDaymet can compute Potential EvapoTranspiration (PET) using three methods: penman_monteith, priestley_taylor, and hargreaves_samani for both single pixel and gridded data.

You can find some example notebooks here.

Moreover, under the hood, PyDaymet uses AsyncRetriever for making requests asynchronously with persistent caching. This improves the reliability and speed of data retrieval significantly. AsyncRetriever caches all request/response pairs and upon making an already cached request, it will retrieve the responses from the cache if the server’s response is unchanged.

You can control the request/response caching behavior and verbosity of the package by setting the following environment variables:

  • HYRIVER_CACHE_NAME: Path to the caching SQLite database. It defaults to ./cache/aiohttp_cache.sqlite

  • HYRIVER_CACHE_EXPIRE: Expiration time for cached requests in seconds. It defaults to -1 (never expire).

  • HYRIVER_CACHE_DISABLE: Disable reading/writing from/to the cache. The default is false.

  • HYRIVER_VERBOSE: Enable verbose mode. The default is false.

For example, in your code before making any requests you can do:

import os

os.environ["HYRIVER_CACHE_NAME"] = "path/to/file.sqlite"
os.environ["HYRIVER_CACHE_EXPIRE"] = "3600"
os.environ["HYRIVER_CACHE_DISABLE"] = "true"

You can also try using PyDaymet without installing it on your system by clicking on the binder badge. A Jupyter Lab instance with the HyRiver stack pre-installed will be launched in your web browser, and you can start coding!

Moreover, requests for additional functionalities can be submitted via issue tracker.

Citation#

If you use any of HyRiver packages in your research, we appreciate citations:

@article{Chegini_2021,
    author = {Chegini, Taher and Li, Hong-Yi and Leung, L. Ruby},
    doi = {10.21105/joss.03175},
    journal = {Journal of Open Source Software},
    month = {10},
    number = {66},
    pages = {1--3},
    title = {{HyRiver: Hydroclimate Data Retriever}},
    volume = {6},
    year = {2021}
}

Installation#

You can install PyDaymet using pip after installing libgdal on your system (for example, in Ubuntu run sudo apt install libgdal-dev):

$ pip install pydaymet

Alternatively, PyDaymet can be installed from the conda-forge repository using Conda:

$ conda install -c conda-forge pydaymet

Quick start#

You can use PyDaymet using command-line or as a Python library. The commanda-line provides access to two functionality:

  • Getting gridded climate data: You must create a geopandas.GeoDataFrame that contains the geometries of the target locations. This dataframe must have four columns: id, start, end, geometry. The id column is used as filenames for saving the obtained climate data to a NetCDF (.nc) file. The start and end columns are starting and ending dates of the target period. Then, you must save the dataframe as a shapefile (.shp) or geopackage (.gpkg) with CRS attribute.

  • Getting single pixel climate data: You must create a CSV file that contains coordinates of the target locations. This file must have at four columns: id, start, end, lon, and lat. The id column is used as filenames for saving the obtained climate data to a CSV (.csv) file. The start and end columns are the same as the geometry command. The lon and lat columns are the longitude and latitude coordinates of the target locations.

$ pydaymet -h
Usage: pydaymet [OPTIONS] COMMAND [ARGS]...

Command-line interface for PyDaymet.

Options:
-h, --help  Show this message and exit.

Commands:
coords    Retrieve climate data for a list of coordinates.
geometry  Retrieve climate data for a dataframe of geometries.

The coords sub-command is as follows:

$ pydaymet coords -h
Usage: pydaymet coords [OPTIONS] FPATH

Retrieve climate data for a list of coordinates.

FPATH: Path to a csv file with four columns:
    - ``id``: Feature identifiers that daymet uses as the output netcdf filenames.
    - ``start``: Start time.
    - ``end``: End time.
    - ``lon``: Longitude of the points of interest.
    - ``lat``: Latitude of the points of interest.
    - ``time_scale``: (optional) Time scale, either ``daily`` (default), ``monthly`` or ``annual``.
    - ``pet``: (optional) Method to compute PET. Suppoerted methods are:
                ``penman_monteith``, ``hargreaves_samani``, ``priestley_taylor``, and ``none`` (default).
    - ``snow``: (optional) Separate snowfall from precipitation, default is ``False``.

Examples:
    $ cat coords.csv
    id,lon,lat,start,end,pet
    california,-122.2493328,37.8122894,2012-01-01,2014-12-31,hargreaves_samani
    $ pydaymet coords coords.csv -v prcp -v tmin

Options:
-v, --variables TEXT  Target variables. You can pass this flag multiple
                        times for multiple variables.
-s, --save_dir PATH   Path to a directory to save the requested files.
                        Extension for the outputs is .nc for geometry and .csv
                        for coords.
--disable_ssl         Pass to disable SSL certification verification.
-h, --help            Show this message and exit.

And, the geometry sub-command is as follows:

$ pydaymet geometry -h
Usage: pydaymet geometry [OPTIONS] FPATH

Retrieve climate data for a dataframe of geometries.

FPATH: Path to a shapefile (.shp) or geopackage (.gpkg) file.
This file must have four columns and contain a ``crs`` attribute:
    - ``id``: Feature identifiers that daymet uses as the output netcdf filenames.
    - ``start``: Start time.
    - ``end``: End time.
    - ``geometry``: Target geometries.
    - ``time_scale``: (optional) Time scale, either ``daily`` (default), ``monthly`` or ``annual``.
    - ``pet``: (optional) Method to compute PET. Suppoerted methods are:
                ``penman_monteith``, ``hargreaves_samani``, ``priestley_taylor``, and ``none`` (default).
    - ``snow``: (optional) Separate snowfall from precipitation, default is ``False``.

Examples:
    $ pydaymet geometry geo.gpkg -v prcp -v tmin

Options:
-v, --variables TEXT  Target variables. You can pass this flag multiple
                        times for multiple variables.
-s, --save_dir PATH   Path to a directory to save the requested files.
                        Extension for the outputs is .nc for geometry and .csv
                        for coords.
--disable_ssl         Pass to disable SSL certification verification.
-h, --help            Show this message and exit.

Now, let’s see how we can use PyDaymet as a library.

PyDaymet offers two functions for getting climate data; get_bycoords and get_bygeom. The arguments of these functions are identical except the first argument where the latter should be polygon and the former should be a coordinate (a tuple of length two as in (x, y)). The input geometry or coordinate can be in any valid CRS (defaults to EPSG:4326). The dates argument can be either a tuple of length two like (start_str, end_str) or a list of years like [2000, 2005]. It is noted that both functions have a pet flag for computing PET and a snow flag for separating snow from precipitation using Martinez and Gupta (2010) method. Additionally, we can pass time_scale to get daily, monthly or annual summaries. This flag by default is set to daily.

from pynhd import NLDI
import pydaymet as daymet

geometry = NLDI().get_basins("01031500").geometry[0]

var = ["prcp", "tmin"]
dates = ("2000-01-01", "2000-06-30")

daily = daymet.get_bygeom(geometry, dates, variables=var, pet="priestley_taylor", snow=True)
monthly = daymet.get_bygeom(geometry, dates, variables=var, time_scale="monthly")
https://raw.githubusercontent.com/hyriver/HyRiver-examples/main/notebooks/_static/daymet_grid.png

If the input geometry (or coordinate) is in a CRS other than EPSG:4326, we should pass it to the functions.

coords = (-1431147.7928, 318483.4618)
crs = "epsg:3542"
dates = ("2000-01-01", "2006-12-31")
annual = daymet.get_bycoords(coords, dates, variables=var, loc_crs=crs, time_scale="annual")
https://raw.githubusercontent.com/hyriver/HyRiver-examples/main/notebooks/_static/daymet_loc.png

Additionally, the get_bycoords function accepts a list of coordinates and by setting the to_xarray flag to True it can return the results as a xarray.Dataset instead of a pandas.DataFrame:

coords = [(-94.986, 29.973), (-95.478, 30.134)]
idx = ["P1", "P2"]
clm_ds = daymet.get_bycoords(coords, range(2000, 2021), coords_id=idx, to_xarray=True)

Also, we can use the potential_et function to compute PET by passing the daily climate data. We can either pass a pandas.DataFrame or a xarray.Dataset. Note that, penman_monteith and priestley_taylor methods have parameters that can be passed via the params argument, if any value other than the default values are needed. For example, default value of alpha for priestley_taylor method is 1.26 (humid regions), we can set it to 1.74 (arid regions) as follows:

pet_hs = daymet.potential_et(daily, methods="priestley_taylor", params={"alpha": 1.74})

Next, let’s get annual total precipitation for Hawaii and Puerto Rico for 2010.

hi_ext = (-160.3055, 17.9539, -154.7715, 23.5186)
pr_ext = (-67.9927, 16.8443, -64.1195, 19.9381)
hi = daymet.get_bygeom(hi_ext, 2010, variables="prcp", region="hi", time_scale="annual")
pr = daymet.get_bygeom(pr_ext, 2010, variables="prcp", region="pr", time_scale="annual")

Some example plots are shown below:

https://raw.githubusercontent.com/hyriver/HyRiver-examples/main/notebooks/_static/hi.png https://raw.githubusercontent.com/hyriver/HyRiver-examples/main/notebooks/_static/pr.png