bmi-geotiff 0.2.3

Access data and metadata in a GeoTIFF file through an API or a BMI

bmi-geotiff

Access data (and metadata) from a GeoTIFF file through an API or a BMI.

The bmi-geotiff library accepts a filepath or an URL to a GeoTIFF file. Data are loaded into an xarray DataArray using the experimental open_rasterio method. The 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-geotiff with pip:

pip install bmi-geotiff

or with conda:

conda install -c conda-forge bmi-geotiff

Alternately, the bmi-geotiff library can 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-geotiff 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-geotiff from source with

make install

Examples

A brief example of using the bmi-geotiff API is given in the following steps. The example is derived from a similar example in the xarray documentation.

Start a Python session and import the GeoTiff class:

>>> from bmi_geotiff import GeoTiff

For convenience, let's use a test image from the rasterio project:

>>> url = "https://github.com/mapbox/rasterio/raw/master/tests/data/RGB.byte.tif"

Make an instance of GeoTiff with this URL:

>>> g = GeoTiff(url)

This step might take a few moments as the data are pulled from GitHub.

The data have been loaded into an xarray DataArray, which can be accessed through the da property:

>>> print(g.da)
<xarray.DataArray (band: 3, y: 718, x: 791)>
[1703814 values with dtype=uint8]
Coordinates:
  * band     (band) int64 1 2 3
  * y        (y) float64 2.827e+06 2.826e+06 2.826e+06 ... 2.612e+06 2.612e+06
  * x        (x) float64 1.021e+05 1.024e+05 1.027e+05 ... 3.389e+05 3.392e+05
Attributes:
    transform:      (300.0379266750948, 0.0, 101985.0, 0.0, -300.041782729805...
    crs:            +init=epsg:32618
    res:            (300.0379266750948, 300.041782729805)
    is_tiled:       0
    nodatavals:     (0.0, 0.0, 0.0)
    scales:         (1.0, 1.0, 1.0)
    offsets:        (0.0, 0.0, 0.0)
    AREA_OR_POINT:  Area

Display the image with the xarray.plot.imshow method.

>>> import matplotlib.pyplot as plt
>>> g.da.plot.imshow()
>>> plt.show()

For examples with more detail, see the Jupyter Notebooks and Python scripts included in the examples directory of the bmi-geotiff repository.

Documentation for bmi-geotiff is available at https://bmi-geotiff.readthedocs.io.

Changes for bmi-geotiff

0.2.3 (2021-05-09)

• Modify how the BMI treats the projection string variable (#7)

0.2.2 (2021-05-05)

• Fix shapes in BMI (#6)

0.2.1 (2021-05-05)

• Add DOI and CITATION document
• Remove dimensions of length 1 (#5)

0.2 (2021-04-22)

• Add user and API documentation, deplot to Read the Docs (#3)
• Set up CI tasks using GitHub Actions (#4)

0.1 (2021-04-16)

• Create base library that uses xarray
• Write tests for library
• Implement BMI for GeoTiff class from template generated by bmipy-render
• Make demo Jupyter Notebooks

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-geotiff/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-geotiff 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-geotiff/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-geotiff for local development.

1. Fork the bmi-geotiff repo on GitHub.

2. Clone your fork locally:

   $ git clone [e-mail]:your_name_here/bmi-geotiff.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-geotiff
   $ conda env create --file=environment.yml
   $ conda activate geotiff
   $ 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-geotiff feedstock on conda-forge that there is a new release.

Citation

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

Piper, M (2021). CSDMS GeoTIFF data component (v0.2). Zenodo. http://doi.org/10.5281/zenodo.4721475.

Credits

Project lead

• Mark Piper

Acknowledgments

This work is supported by the National Science Foundation under Award No. 1831623, Community Facility Support: The Community Surface Dynamics Modeling System (CSDMS).

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.