seagrass

A companion Python module (including Colab notebooks) for the University of Portsmouth seagrass project.

This package is still in development and is highly experimental, therefore the API is subject to frequent and significant change. Use with caution.

NOTE: This package currently holds no license and therefore cannot be copied, distributed, modified, or used for research outside the University of Portsmouth without express permission from the authors.

Installation

To install the seagrass Python package, run the following command from your bash terminal:

pip install git+https://github.com/Max-FM/seagrass.git

or alternatively from the cloned package directory run:

pip install .

Documentation (work in progress)

To generate html documentation pages locally, run the following command in your bash terminal (from the cloned package directory):

./generate_docs.sh

The documentation pages can then be found under docs/build/html.

Import JSON structure (experimental)

If importing data using the seagrass.raster.open_from_json method, the input json file needs to abide by the following example structure:

{
    "raster_filepath": "path/to/s2/data", OR ["path/to/s2/data_1", "path/to/s2/data_2", etc],
    "ground_truth_filepath": "path/to/ground/truth/data",
    "raster_bands": [1, 2, 3, 4, etc],
    "raster_scale": 10000,
    "ground_truth_nodata": -9999,
    "ground_truth_nodata_threshold": -1e6
}

Currently accepted arguments are:

• raster_filepath (str or list, required): Satellite image geoTIFF filepath OR list of satellite image geoTIFF filepaths if creating a mosaic.
• ground_truth_filepath (str, required): Ground truth geoTIFF filepath.
• raster_bands (list, optional): List of integers corresponding to the desired satellite image bands to consider when importing. If not included then all bands are considered.
• raster_scale (int, optional): Value to divide the satellite image pixels by to obtain the true pixel values. Defaults to 10000 if not included.
• ground_truth_nodata (int, optional): Integer value representing pixels containing no data. Defaults to None if not included.
• ground_truth_nodata_threshold (int or float, optional): Pixels with values less than the threshold will instead be set equal to ground_truth_nodata. Defaults to None if not included.