Py3DEP: Topographic data through 3DEP

PyPi Conda Version CodeCov Python Versions Downloads

CodeFactor black pre-commit Binder

Features

Py3DEP is a part of HyRiver software stack that is designed to aid in watershed analysis through web services. This package provides access to the 3DEP database which is a part of the National Map services. The 3DEP service has multi-resolution sources and depending on the user provided resolution, the data is resampled on the server-side based on all the available data sources. Py3DEP returns the requests as xarray dataset. Moreover, under-the-hood, this package uses requests-cache for persistent caching that can improve the performance significantly. The 3DEP web service includes the following layers:

  • DEM

  • Hillshade Gray

  • Aspect Degrees

  • Aspect Map

  • GreyHillshade Elevation Fill

  • Hillshade Multidirectional

  • Slope Map

  • Hillshade Elevation Tinted

  • Height Ellipsoidal

  • Contour 25

  • Contour Smoothed 25

Moreover, Py3DEP offers some additional utilities:

  • elevation_bygrid: For getting elevations of all the grid points in a 2D grid.

  • elevation_bycoords: For getting elevation of a list of x and y coordinates.

  • deg2mpm: For converting slope dataset from degree to meter per meter.

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!

Please note that since this project is in early development stages, while the provided functionalities should be stable, changes in APIs are possible in new releases. But we appreciate it if you give this project a try and provide feedback. Contributions are most welcome.

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

Installation

You can install Py3DEP using pip after installing libgdal on your system (for example, in Ubuntu run sudo apt install libgdal-dev). Moreover, Py3DEP 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 Py3DEP under-the-hood looks for requests-cache and if available, it will automatically use persistent caching:

$ pip install py3dep

Alternatively, Py3DEP can be installed from the conda-forge repository using Conda:

$ conda install -c conda-forge py3dep

Quick start

You can use Py3DEP using command-line or as a Python library. The command line interface provides access to two functionality:

  • Getting topographic data: You must create a geopandas.GeoDataFrame that contains the geometries of the target locations. This dataframe must have at least three columns: id, res, and geometry. The id column is used as filenames for saving the obtained topographic data to a NetCDF (.nc) file. The res column must be the target resolution in meter. Then, you must save the dataframe to a file with extensions such as .shp or .gpkg (whatever that geopandas.read_file can read).

  • Getting elevation: You must create a pandas.DataFrame that contains coordinates of the target locations. This dataframe must have at least two columns: x and y. The elevations are obtained using airmap service in meters. The data are saved as a csv file with the same filename as the input file with an _elevation appended, e.g., coords_elevation.csv.

$ py3dep --help
Usage: py3dep [OPTIONS] COMMAND [ARGS]...

Command-line interface for Py3DEP.

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

Commands:
coords    Retrieve topographic data for a list of coordinates.
geometry  Retrieve topographic data within geometries.

The coords sub-command is as follows:

$ py3dep coords -h
Usage: py3dep coords [OPTIONS] FPATH

Retrieve topographic data for a list of coordinates.

FPATH: Path to a csv file with two columns named ``lon`` and ``lat``.

Examples:
    $ cat coords.csv
    lon,lat
    -122.2493328,37.8122894
    $ py3dep coords coords.csv -q airmap -s topo_dir

Options:
-q, --query_source [airmap|tnm|tep]
                                Source of the elevation data.
-s, --save_dir PATH             Path to a directory to save the requested
                                files. Extension for the outputs is either
                                `.nc` for geometry or `.csv` for coords.

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

And, the geometry sub-command is as follows:

$ py3dep geometry -h
Usage: py3dep geometry [OPTIONS] FPATH

Retrieve topographic data within geometries.

FPATH: Path to a shapefile (.shp) or geopackage (.gpkg) file.
This file must have three columns and contain a ``crs`` attribute:
    - ``id``: Feature identifiers that py3dep uses as the output netcdf/csv filenames.
    - ``res``: Target resolution in meters.
    - ``geometry``: A Polygon or MultiPloygon.

Examples:
    $ py3dep geometry ny_geom.gpkg -l "Slope Map" -l DEM -s topo_dir

Options:
-l, --layers [DEM|Hillshade Gray|Aspect Degrees|Aspect Map|GreyHillshade_elevationFill|Hillshade Multidirectional|Slope Map|Slope Degrees|Hillshade Elevation Tinted|Height Ellipsoidal|Contour 25|Contour Smoothed 25]
                                Target topographic data layers
-s, --save_dir PATH             Path to a directory to save the requested
                                files.Extension for the outputs is either
                                `.nc` for geometry or `.csv` for coords.

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

Now, let’s see how we can use Py3DEP as a library.

Py3DEP accepts Shapely’s Polygon or a bounding box (a tuple of length four) as an input geometry. We can use PyNHD to get a watershed’s geometry, then use it to get the DEM and slope in meters/meters from Py3DEP using get_map function.

The get_map has a resolution argument that sets the target resolution in meters. Note that the highest available resolution throughout the CONUS is about 10 m, though higher resolutions are available in limited parts of the US. Note that the input geometry can be in any valid spatial reference (geo_crs argument). The crs argument, however, is limited to CRS:84, EPSG:4326, and EPSG:3857 since 3DEP only supports these spatial references.

import py3dep
from pynhd import NLDI

geom = NLDI().get_basins("01031500").geometry[0]
dem = py3dep.get_map("DEM", geom, resolution=30, geo_crs="epsg:4326", crs="epsg:3857")
slope = py3dep.get_map("Slope Degrees", geom, resolution=30)
slope = py3dep.deg2mpm(slope)
https://raw.githubusercontent.com/cheginit/HyRiver-examples/main/notebooks/_static/dem_slope.png

We can use rioxarray package to save the obtained dataset as a raster file:

import rioxarray

dem.rio.to_raster("dem_01031500.tif")

Moreover, we can get the elevations of set of x- and y- coordinates on a grid. For example, let’s get the minimum temperature data within this watershed from Daymet using PyDaymet then add the elevation as a new variable to the dataset:

import pydaymet as daymet
import xarray as xr
import numpy as np

clm = daymet.get_bygeom(geometry, ("2005-01-01", "2005-01-31"), variables="tmin")
elev = py3dep.elevation_bygrid(clm.x.values, clm.y.values, clm.crs, clm.res[0] * 1000)
attrs = clm.attrs
clm = xr.merge([clm, elev])
clm["elevation"] = clm.elevation.where(~np.isnan(clm.isel(time=0).tmin), drop=True)
clm.attrs.update(attrs)

Now, let’s get street network data using osmnx package and add elevation data for its nodes using elevation_bycoords function.

import osmnx as ox

G = ox.graph_from_place("Piedmont, California, USA", network_type="drive")
x, y = nx.get_node_attributes(G, "x").values(), nx.get_node_attributes(G, "y").values()
elevation = py3dep.elevation_bycoords(zip(x, y), crs="epsg:4326")
nx.set_node_attributes(G, dict(zip(G.nodes(), elevation)), "elevation")
https://raw.githubusercontent.com/cheginit/HyRiver-examples/main/notebooks/_static/street_elev.png