bmi-dbseabed 0.1.0

Fetch ocean seabed datasets from the dbSEABED system https://instaar.colorado.edu/~jenkinsc/dbseabed/

bmi_dbseabed

bmi_dbseabed provides a set of functions that allow downloading of the dataset from dbSEABED, a system for marine substrates datasets across the globe. This system uses very large amounts of diverse observational data and applies math methods to integrate/harmonize those and produces gridded data on the major properties of the seabed. The scope is the global ocean and across all depth zones.

The current page serves only the data for the Gulf of Mexico region. The entire collection of data is available at this webpage. Please note that the data will be updated from time to time, approximately annually.

bmi_dbseabed also includes a Basic Model Interface (BMI), which converts the dbSEABED datasets into a reusable, plug-and-play data component (pymt_dbseabed) for the PyMT modeling framework developed by Community Surface Dynamics Modeling System (CSDMS).

If you have any suggestion to improve the current function, please create a github issue here.

Install package

Stable Release

The bmi_dbseabed package and its dependencies can be installed with pip

$ pip install bmi_dbseabed

or with conda.

$ conda install -c conda-forge bmi_dbseabed

From Source

After downloading the source code, run the following command from top-level folder to install bmi_dbseabed.

$ pip install -e .

Quick Start

Below shows how to use two methods to download the datasets.

You can learn more details from the tutorial notebook.

Example 1: use DbSeabed class to download data (Recommended method)

import matplotlib.pyplot as plt
from bmi_dbseabed import DbSeabed

# get data from dbSEABED
dbseabed = DbSeabed()
data = dbseabed.get_data(
    var_name="carbonate",
    west=-98,
    south=18,
    east=-80,
    north=31,
    output="download.tif",
)

# show metadata
for key, value in dbseabed.metadata.items():
    print(f"{key}: {value}")


# plot data
data.plot(figsize=(9, 5))
plt.title("dbSEABED dataset (Carbonate in %)")

Example 2: use BmiDbSseabed class to download data (Demonstration of how to use BMI)

import matplotlib.pyplot as plt
import numpy as np

from bmi_dbseabed import BmiDbSeabed


# initiate a data component
data_comp = BmiDbSeabed()
data_comp.initialize("config_file.yaml")

# get variable info
var_name = data_comp.get_output_var_names()[0]
var_unit = data_comp.get_var_units(var_name)
var_location = data_comp.get_var_location(var_name)
var_type = data_comp.get_var_type(var_name)
var_grid = data_comp.get_var_grid(var_name)

print(f"{var_name=} \n{var_unit=} \n{var_location=} \n{var_type=} \n{var_grid=}")

# get variable grid info
grid_rank = data_comp.get_grid_rank(var_grid)

grid_size = data_comp.get_grid_size(var_grid)

grid_shape = np.empty(grid_rank, int)
data_comp.get_grid_shape(var_grid, grid_shape)

grid_spacing = np.empty(grid_rank)
data_comp.get_grid_spacing(var_grid, grid_spacing)

grid_origin = np.empty(grid_rank)
data_comp.get_grid_origin(var_grid, grid_origin)

print(f"{grid_rank=} \n{grid_size=} \n{grid_shape=} \n{grid_spacing=} \n{grid_origin=}")

# get variable data
data = np.empty(grid_size, var_type)
data_comp.get_value(var_name, data)
data_2D = data.reshape(grid_shape)

# get X, Y extent for plot
min_y, min_x = grid_origin
max_y = min_y + grid_spacing[0] * (grid_shape[0] - 1)
max_x = min_x + grid_spacing[1] * (grid_shape[1] - 1)
dy = grid_spacing[0] / 2
dx = grid_spacing[1] / 2
extent = [min_x - dx, max_x + dx, min_y - dy, max_y + dy]

# plot data
fig, ax = plt.subplots(1, 1, figsize=(9, 5))
im = ax.imshow(data_2D, extent=extent)
fig.colorbar(im)
plt.xlabel("X")
plt.ylabel("Y")
plt.title("dbSEABED dataset (Carbonate in %)")

# finalize data component
data_comp.finalize()