bmi-topography 0.3.2

Fetch and cache NASA SRTM land elevation data

bmi-topography

bmi-topography is a Python library for fetching and caching NASA Shuttle Radar Topography Mission (SRTM) land elevation data using the OpenTopography REST API.

The bmi-topography library provides access to the following global raster datasets:

• SRTM GL3 (90m)
• SRTM GL1 (30m)
• SRTM GL1 (Ellipsoidal)

The library includes an API and a CLI that accept the dataset type, a latitude-longitude bounding box, and the output file format. Data are downloaded from OpenTopography and cached locally. The cache is checked before downloading new data. Data from a cached file can optionally be loaded into an xarray DataArray using the experimental open_rasterio method.

The bmi-topography API is wrapped with a Basic Model Interface (BMI), which provides a standard set of functions for coupling with data or models that also expose a BMI. More information on the BMI can found in its documentation.

Installation

Install the latest stable release of bmi-topography with pip:

pip install bmi-topography

or with conda:

conda install -c conda-forge bmi-topography

The bmi-topography library can also be built and installed from source. The library uses several other open source libraries, so a convenient way of building and installing it is within a conda environment. After cloning or downloading the bmi-topography repository, change into the repository directory and set up a conda environment with the included environment file:

conda env create --file=environment.yml

Then build and install bmi-topography from source with

make install

Examples

A brief example of using the bmi-topography API is given in the following steps.

Start a Python session and import the Topography class:

>>> from bmi_topography import Topography

For convenience, a set of default parameter values for Topography are included in the class definition. Copy these and modify them with custom values:

>>> params = Topography.DEFAULT.copy()
>>> params["south"] = 39.75
>>> params["north"] = 40.25
>>> params["west"] = -105.25
>>> params["east"] = -104.75
>>> params
{'dem_type': 'SRTMGL3',
 'south': 39.75,
 'north': 40.25,
 'west': -105.25,
 'east': -104.75,
 'output_format': 'GTiff',
 'cache_dir': '~/.bmi_topography'}

These coordinate values represent an area around Boulder, Colorado.

Make a instance of Topography with these parameters:

>>> boulder = Topography(**params)

then fetch the data from OpenTopography:

>>> boulder.fetch()
PosixPath('/Users/mpiper/.bmi_topography/SRTMGL3_39.75_-105.25_40.25_-104.75.tif')

This step might take a few moments, and it will increase for requests of larger areas. Note that the file has been saved to a local cache directory.

Load the data into an xarray DataArray for further work:

>>> boulder.load()
<xarray.DataArray 'SRTMGL3' (band: 1, y: 600, x: 600)>
[360000 values with dtype=int16]
Coordinates:
  * band     (band) int64 1
  * y        (y) float64 40.25 40.25 40.25 40.25 ... 39.75 39.75 39.75 39.75
  * x        (x) float64 -105.3 -105.2 -105.2 -105.2 ... -104.8 -104.8 -104.8
Attributes:
    transform:      (0.000833333333333144, 0.0, -105.25041666668365, 0.0, -0....
    crs:            +init=epsg:4326
    res:            (0.000833333333333144, 0.000833333333333144)
    is_tiled:       1
    nodatavals:     (0.0,)
    scales:         (1.0,)
    offsets:        (0.0,)
    AREA_OR_POINT:  Area
    units:          meters
    location:       node

For examples with more detail, see the two Jupyter Notebooks, Python script, and shell script included in the examples directory of the bmi-topography repository.

User and developer documentation for bmi-topography is available at https://bmi-topography.readthedocs.io.

Changes for bmi-topography

0.3.2 (2021-04-23)

• Add citation recommendation with DOI
• Fix typos, update text in example notebooks
• Create CREDITS.md and rearrange docs

0.3.1 (2021-03-04)

• Install with conda
• Include shell script demonstrating CLI

0.3 (2021-02-25)

• Update README with overview and install instructions
• Write documentation

0.2 (2021-02-24)

• Implement BMI for Topography class from template generated by bmipy-render
• Include sample config file and Jupyter Notebook to demo BMI
• Add CI with GitHub Actions

0.1.1 (2021-02-22)

• Add Makefile rule to test upload to TestPyPI
• Test upload to TestPyPI

0.1 (2021-02-22)

• Create base library that calls OpenTopography API
• Create CLI for library
• Write tests for library and CLI
• Include demo Jupyter Notebook for library

Contributing

Contributions are welcome, and they are greatly appreciated! Every little bit helps, and credit will always be given.

You can contribute in many ways:

Types of Contributions

Report Bugs

Report bugs at https://github.com/csdms/bmi-topography/issues.

If you are reporting a bug, please include:

• Your operating system name and version.
• Any details about your local setup that might be helpful in troubleshooting.
• Detailed steps to reproduce the bug.

Fix Bugs

Look through the GitHub issues for bugs. Anything tagged with "bug" and "help wanted" is open to whoever wants to implement it.

Implement Features

Look through the GitHub issues for features. Anything tagged with "enhancement" and "help wanted" is open to whoever wants to implement it.

Write Documentation

bmi-topography could always use more documentation, whether as part of the official docs, in docstrings, or even on the web in blog posts, articles, and such.

Submit Feedback

The best way to send feedback is to file an issue at https://github.com/csdms/bmi-topography/issues.

If you are proposing a feature:

• Explain in detail how it would work.
• Keep the scope as narrow as possible, to make it easier to implement.
• Remember that this is a volunteer-driven project, and that contributions are welcome :)

Get Started!

Ready to contribute? Here's how to set up bmi-topography for local development.

1. Fork the bmi-topography repo on GitHub.

2. Clone your fork locally:

   $ git clone [e-mail]:your_name_here/bmi-topography.git
   

3. Install your local copy into a conda environment. A conda enviroment file is supplied at the root of the repository. Assuming you have conda installed, this is how you set up your fork for local development:

   $ cd bmi-topography
   $ conda env create --file=environment.yml
   $ conda activate topography
   $ make install
   

4. Create a branch for local development:

   $ git checkout -b name-of-your-bugfix-or-feature
   

   Now you can make your changes locally.

5. When you're done making changes, check that your changes pass flake8 and the tests:

   $ make lint
   $ make test
   

   Both flake8 and pytest are included in the environment.

6. Commit your changes and push your branch to GitHub:

   $ git add .
   $ git commit -m "Your detailed description of your changes."
   $ git push origin name-of-your-bugfix-or-feature
   

7. Submit a pull request through the GitHub website.

Pull Request Guidelines

Before you submit a pull request, check that it meets these guidelines:

1. The pull request should include tests.
2. If the pull request adds functionality, the docs should be updated. Put your new functionality into a function with a docstring, and add the feature to the list in README.rst.
3. The pull request need only work with Python >= 3.8.

Deploying

A reminder for the maintainers on how to deploy. To make a new release, you will need to have zest.releaser installed, which can be installed with pip,

$ pip install zest.releaser[recommended]

Make sure all your changes are committed (including an entry in CHANGES.md). Then run,

$ fullrelease

This will create a new tag and alert the bmi-topography feedstock on conda-forge that there is a new release.

Citation

If you use bmi-topography, please cite it with:

Piper, M (2021). CSDMS Topography data component (v0.3.1). Zenodo. http://doi.org/10.5281/zenodo.4608653

Credits

Project lead

• Mark Piper

Acknowledgments

This work is supported by the National Science Foundation under Award No. 2026951, EarthCube Capabilities: Cloud-Based Accessible and Reproducible Modeling for Water and Sediment Research.

MIT License

Copyright (c) 2021 Community Surface Dynamics Modeling System

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.