pygeohydro

A part of HyRiver software stack for accessing hydrology data through web services

https://github.com/hyriver/pygeohydro

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A part of HyRiver software stack for accessing hydrology data through web services

README.rst

.. image:: https://raw.githubusercontent.com/hyriver/HyRiver-examples/main/notebooks/_static/pygeohydro_logo.png
    :target: https://github.com/hyriver/HyRiver

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    :alt: JOSS

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    :target: https://github.com/hyriver/pydaymet/actions/workflows/test.yml
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    :target: https://github.com/hyriver/async-retriever/actions/workflows/test.yml
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    :target: https://github.com/hyriver/hydrosignatures/actions/workflows/test.yml
    :alt: Github Actions

================ ====================================================================
Package          Description
================ ====================================================================
PyNHD_           Navigate and subset NHDPlus (MR and HR) using web services
Py3DEP_          Access topographic data through National Map's 3DEP web service
PyGeoHydro_      Access NWIS, NID, WQP, eHydro, NLCD, CAMELS, and SSEBop databases
PyDaymet_        Access daily, monthly, and annual climate data via Daymet
PyGridMET_       Access daily climate data via GridMET
PyNLDAS2_        Access hourly NLDAS-2 data via web services
HydroSignatures_ A collection of tools for computing hydrological signatures
AsyncRetriever_  High-level API for asynchronous requests with persistent caching
PyGeoOGC_        Send queries to any ArcGIS RESTful-, WMS-, and WFS-based services
PyGeoUtils_      Utilities for manipulating geospatial, (Geo)JSON, and (Geo)TIFF data
================ ====================================================================

.. _PyGeoHydro: https://github.com/hyriver/pygeohydro
.. _AsyncRetriever: https://github.com/hyriver/async-retriever
.. _PyGeoOGC: https://github.com/hyriver/pygeoogc
.. _PyGeoUtils: https://github.com/hyriver/pygeoutils
.. _PyNHD: https://github.com/hyriver/pynhd
.. _Py3DEP: https://github.com/hyriver/py3dep
.. _PyDaymet: https://github.com/hyriver/pydaymet
.. _PyGridMET: https://github.com/hyriver/pygridmet
.. _PyNLDAS2: https://github.com/hyriver/pynldas2
.. _HydroSignatures: https://github.com/hyriver/hydrosignatures

PyGeoHydro: Retrieve Geospatial Hydrology Data
----------------------------------------------

.. image:: https://img.shields.io/pypi/v/pygeohydro.svg
    :target: https://pypi.python.org/pypi/pygeohydro
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Features
--------

PyGeoHydro (formerly named `hydrodata `__) is a part of
`HyRiver `__ software stack that
is designed to aid in hydroclimate analysis through web services. This package provides
access to some public web services that offer geospatial hydrology data. It has three
main modules: ``pygeohydro``, ``plot``, and ``helpers``.

PyGeoHydro supports the following datasets:

* `gNATSGO `__ for
  US soil properties.
* `SoilGrids `__
  for seamless global soil properties.
* `Derived Soil Properties `__
  for soil porosity, available water capacity, and field capacity across the US.
* `NWIS `__ for daily mean streamflow observations
  (returned as a ``pandas.DataFrame`` or ``xarray.Dataset`` with station attributes),
* `SensorThings API `__
  for accessing real-time data of USGS sensors.
* `CAMELS `__ for accessing streamflow
  observations (1980-2014) and basin-level attributes of 671 stations within CONUS.
* `Water Quality Portal `__ for accessing current and
  historical water quality data from more than 1.5 million sites across the US,
* `NID `__ for accessing the National Inventory of Dams
  web service,
* `HCDN 2009 `__ for identifying sites
  where human activity affects the natural flow of the watercourse,
* `NLCD 2021 `__ for land cover/land use, imperviousness
  descriptor, and canopy data. You can get data using both geometries and coordinates.
* `WBD `__ for accessing
  Hydrologic Unit (HU) polygon boundaries within the US (all HUC levels).
* `SSEBop `__ for daily actual
  evapotranspiration, for both single pixel and gridded data.
* `Irrigation Withdrawals `__ for estimated
  monthly water use for irrigation by 12-digit hydrologic unit in the CONUS for 2015
* `STN `__ for access USGS Short-Term Network (STN)
* `eHydro `__ for accessing USACE
  Hydrographic Surveys that includes topobathymetry data
* `NFHL `__ for accessing
  FEMA's National Flood Hazard Layer (NFHL) data.

Also, it includes several other functions:

* ``interactive_map``: Interactive map for exploring NWIS stations within a bounding box.
* ``cover_statistics``: Categorical statistics of land use/land cover data.
* ``overland_roughness``: Estimate overland roughness from land use/land cover data.
* ``streamflow_fillna``: Fill missing daily streamflow values with day-of-year averages.
  Streamflow observations must be at least for 10-year long.

The ``plot`` module includes two main functions:

* ``signatures``: Hydrologic signature graphs.
* ``cover_legends``: Official NLCD land cover legends for plotting a land cover dataset.
* ``descriptor_legends``: Color map and legends for plotting an imperviousness descriptor dataset.

The ``helpers`` module includes:

* ``nlcd_helper``: A roughness coefficients lookup table for each land cover and imperviousness
  descriptor type which is useful for overland flow routing among other applications.
* ``nwis_error``: A dataframe for finding information about NWIS requests' errors.

You can find some example notebooks `here `__.

Moreover, under the hood, PyGeoHydro uses
`PyGeoOGC `__ and
`AsyncRetriever `__ packages
for making requests in parallel and storing responses in chunks. This improves the
reliability and speed of data retrieval significantly.

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 for asynchronous HTTP
  requests. It defaults to ``./cache/aiohttp_cache.sqlite``
* ``HYRIVER_CACHE_NAME_HTTP``: Path to the caching SQLite database for HTTP requests.
  It defaults to ``./cache/http_cache.sqlite``
* ``HYRIVER_CACHE_EXPIRE``: Expiration time for cached requests in seconds. It defaults to
  one week.
* ``HYRIVER_CACHE_DISABLE``: Disable reading/writing from/to the cache. The default is false.
* ``HYRIVER_SSL_CERT``: Path to a SSL certificate file.

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

.. code-block:: python

    import os

    os.environ["HYRIVER_CACHE_NAME"] = "path/to/aiohttp_cache.sqlite"
    os.environ["HYRIVER_CACHE_NAME_HTTP"] = "path/to/http_cache.sqlite"
    os.environ["HYRIVER_CACHE_EXPIRE"] = "3600"
    os.environ["HYRIVER_CACHE_DISABLE"] = "true"
    os.environ["HYRIVER_SSL_CERT"] = "path/to/cert.pem"

You can also try using PyGeoHydro 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:

.. code-block:: bibtex

    @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 PyGeoHydro using ``pip`` after installing ``libgdal`` on your system
(for example, in Ubuntu run ``sudo apt install libgdal-dev``). Moreover, PyGeoHydro has an optional
dependency for using persistent caching, ``requests-cache``. We highly recommend installing
this package as it can significantly speed up send/receive queries. You don't have to change
anything in your code, since PyGeoHydro under-the-hood looks for ``requests-cache`` and
if available, it will automatically use persistent caching:

.. code-block:: console

    $ pip install pygeohydro

Alternatively, PyGeoHydro can be installed from the ``conda-forge`` repository
using `Conda `__:

.. code-block:: console

    $ conda install -c conda-forge pygeohydro

Quick start
-----------
We can obtain river topobathymetry data using the ``EHydro`` class. We can subset
the dataset either using a geometry or a bounding box, based on their ID, or SQL query:

.. code-block:: python

    from pygeohydro import EHydro

    ehydro = EHydro("points")
    topobathy = ehydro.bygeom((-122.53, 45.57, -122.52, 45.59))

We can explore the available NWIS stations within a bounding box using ``interactive_map``
function. It returns an interactive map and by clicking on a station some of the most
important properties of stations are shown.

.. code-block:: python

    import pygeohydro as gh

    bbox = (-69.5, 45, -69, 45.5)
    gh.interactive_map(bbox)

.. image:: https://raw.githubusercontent.com/hyriver/HyRiver-examples/main/notebooks/_static/interactive_map.png
    :target: https://github.com/hyriver/HyRiver-examples/blob/main/notebooks/nwis.ipynb
    :alt: Interactive Map

We can select all the stations within this boundary box that have daily mean streamflow data from
``2000-01-01`` to ``2010-12-31``:

.. code-block:: python

    from pygeohydro import NWIS

    nwis = NWIS()
    query = {
        "bBox": ",".join(f"{b:.06f}" for b in bbox),
        "hasDataTypeCd": "dv",
        "outputDataTypeCd": "dv",
    }
    info_box = nwis.get_info(query)
    dates = ("2000-01-01", "2010-12-31")
    stations = info_box[
        (info_box.begin_date <= dates[0]) & (info_box.end_date >= dates[1])
    ].site_no.tolist()

Then, we can get the daily streamflow data in mm/day (by default the values are in cms)
and plot them:

.. code-block:: python

    from pygeohydro import plot

    qobs = nwis.get_streamflow(stations, dates, mmd=True)
    plot.signatures(qobs)

By default, ``get_streamflow`` returns a ``pandas.DataFrame`` that has a ``attrs`` method
containing metadata for all the stations. You can access it like so ``qobs.attrs``.
Moreover, we can get the same data as ``xarray.Dataset`` as follows:

.. code-block:: python

    qobs_ds = nwis.get_streamflow(stations, dates, to_xarray=True)

This ``xarray.Dataset`` has two dimensions: ``time`` and ``station_id``. It has
10 variables including ``discharge`` with two dimensions while other variables
that are station attitudes are one dimensional.

We can also get instantaneous streamflow data using ``get_streamflow``. This method assumes
that the input dates are in UTC time zone and returns the data in UTC time zone as well.

.. code-block:: python

    date = ("2005-01-01 12:00", "2005-01-12 15:00")
    qobs = nwis.get_streamflow("01646500", date, freq="iv")

We can query USGS stations of type "stream" in Arizona using SensorThings API
as follows:

.. code-block:: python

    odata = {
        "filter": "properties/monitoringLocationType eq 'Stream' and properties/stateFIPS eq 'US:04'",
    }
    df = sensor.query_byodata(odata)

Irrigation withdrawals data can be obtained as follows:

.. code-block:: python

    irr = gh.irrigation_withdrawals()

We can get the CAMELS dataset as a ``geopandas.GeoDataFrame`` that includes geometry and
basin-level attributes of 671 natural watersheds within CONUS and their streamflow
observations between 1980-2014 as a ``xarray.Dataset``, like so:

.. code-block:: python

    attrs, qobs = gh.get_camels()

The ``WaterQuality`` has a number of convenience methods to retrieve data from the
web service. Since there are many parameter combinations that can be
used to retrieve data, a general method is also provided to retrieve data from
any of the valid endpoints. You can use ``get_json`` to retrieve stations info
as a ``geopandas.GeoDataFrame`` or ``get_csv`` to retrieve stations data as a
``pandas.DataFrame``. You can construct a dictionary of the parameters and pass
it to one of these functions. For more information on the parameters, please
consult the `Water Quality Data documentation `__.
For example, let's find all the stations within a bounding box that have Caffeine data:

.. code-block:: python

    from pynhd import WaterQuality

    bbox = (-92.8, 44.2, -88.9, 46.0)
    kwds = {"characteristicName": "Caffeine"}
    wq = WaterQuality()
    stations = wq.station_bybbox(bbox, kwds)

Or the same criterion but within a 30-mile radius of a point:

.. code-block:: python

    stations = wq.station_bydistance(-92.8, 44.2, 30, kwds)

Then we can get the data for all these stations the data like this:

.. code-block:: python

    sids = stations.MonitoringLocationIdentifier.tolist()
    caff = wq.data_bystation(sids, kwds)

.. image:: https://raw.githubusercontent.com/hyriver/HyRiver-examples/main/notebooks/_static/water_quality.png
    :target: https://github.com/hyriver/HyRiver-examples/blob/main/notebooks/water_quality.ipynb
    :alt: Water Quality

Moreover, we can get land use/land cove data using ``nlcd_bygeom`` or ``nlcd_bycoods`` functions,
percentages of land cover types using ``cover_statistics``, and overland roughness using
``overland_roughness``. The ``nlcd_bycoords`` function returns a ``geopandas.GeoDataFrame``
with the NLCD layers as columns and input coordinates as the ``geometry`` column. Moreover,
the ``nlcd_bygeom`` function accepts both a single geometry or a ``geopandas.GeoDataFrame``
as the input.

.. code-block:: python

    from pynhd import NLDI

    basins = NLDI().get_basins(["01031450", "01318500", "01031510"])
    lulc = gh.nlcd_bygeom(basins, 100, years={"cover": [2016, 2019]})
    stats = gh.cover_statistics(lulc["01318500"].cover_2016)
    roughness = gh.overland_roughness(lulc["01318500"].cover_2019)

.. image:: https://raw.githubusercontent.com/hyriver/HyRiver-examples/main/notebooks/_static/lulc.png
    :target: https://github.com/hyriver/HyRiver-examples/blob/main/notebooks/nlcd.ipynb
    :alt: Land Use/Land Cover

Next, let's use ``ssebopeta_bygeom`` to get actual ET data for a basin. Note that there's a
``ssebopeta_bycoords`` function that returns an ETA time series for a single coordinate.

.. code-block:: python

    geometry = NLDI().get_basins("01315500").geometry[0]
    eta = gh.ssebopeta_bygeom(geometry, dates=("2005-10-01", "2005-10-05"))

.. image:: https://raw.githubusercontent.com/hyriver/HyRiver-examples/main/notebooks/_static/eta.png
    :target: https://github.com/hyriver/HyRiver-examples/blob/main/notebooks/ssebop.ipynb
    :alt: Actual ET

Additionally, we can pull all the US dams data using ``NID``. Let's get dams that are within this
bounding box and have a maximum storage larger than 200 acre-feet.

.. code-block:: python

    nid = NID()
    dams = nid.get_bygeom((-65.77, 43.07, -69.31, 45.45), 4326)
    dams = nid.inventory_byid(dams.id.to_list())
    dams = dams[dams.maxStorage > 200]

We can get also all dams within CONUS with maximum storage larger than 2500 acre-feet:

.. code-block:: python

    conus_geom = gh.get_us_states("contiguous")

    dam_list = nid.get_byfilter([{"maxStorage": ["[2500 +inf]"]}])
    dams = nid.inventory_byid(dam_list[0].id.to_list(), stage_nid=True)

    conus_dams = dams[dams.stateKey.isin(conus_geom.STUSPS)].reset_index(drop=True)

.. image:: https://raw.githubusercontent.com/hyriver/HyRiver-examples/main/notebooks/_static/dams.png
    :target: https://github.com/hyriver/HyRiver-examples/blob/main/notebooks/nid.ipynb
    :alt: Dams


The ``WBD`` class allows us to get Hydrologic Unit (HU) polygon boundaries. Let's
get the two Hudson HUC4s:

.. code-block:: python

    from pygeohydro import WBD

    wbd = WBD("huc4")
    hudson = wbd.byids("huc4", ["0202", "0203"])


The ``NFHL`` class allows us to retrieve FEMA's National Flood Hazard Layer (NFHL) data.
Let's get the cross-section data for a small region in Vermont:

.. code-block:: python

    from pygeohydro import NFHL

    nfhl = NFHL("NFHL", "cross-sections")
    gdf_xs = nfhl.bygeom((-73.42, 43.28, -72.9, 43.52), geo_crs=4269)


Contributing
------------

Contributions are very welcomed. Please read
`CONTRIBUTING.rst `__
file for instructions.

Credits
-------

This package was created based on the `audreyr/cookiecutter-pypackage`__ project template.

__ https://github.com/audreyr/cookiecutter-pypackage

Owner

Citation (CITATION.cff)

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
- family-names: "Chegini"
  given-names: "Taher"
  orcid: "https://orcid.org/0000-0002-5430-6000"
- family-names: "Li"
  given-names: "Hong-Yi"
  orcid: "https://orcid.org/0000-0002-9807-3851"
- family-names: "Leung"
  given-names: "L. Ruby"
  orcid: "https://orcid.org/0000-0002-3221-9467"
title: "HyRiver: Hydroclimate Data Retriever"
version: 0.11
doi: 10.21105/joss.03175
date-released: 2021-10-27
url: "https://github.com/cheginit/HyRiver"
preferred-citation:
  type: article
  authors:
  - family-names: "Chegini"
    given-names: "Taher"
    orcid: "https://orcid.org/0000-0002-5430-6000"
  - family-names: "Li"
    given-names: "Hong-Yi"
    orcid: "https://orcid.org/0000-0002-9807-3851"
  - family-names: "Leung"
    given-names: "L. Ruby"
    orcid: "https://orcid.org/0000-0002-3221-9467"
  doi: "10.21105/joss.03175"
  journal: "Journal of Open Source Software"
  month: 10
  start: 1
  end: 3
  title: "HyRiver: Hydroclimate Data Retriever"
  issue: 66
  volume: 6
  year: 2021

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