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update data links, add docstrings, change data download parameter set…
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@gantian127
gantian127 committed Mar 16, 2024
1 parent 6a84ac3 commit 1ce3ea7
Showing 1 changed file with 62 additions and 37 deletions.
99 changes: 62 additions & 37 deletions src/bmi_dbseabed/dbseabed.py
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Original file line number Diff line number Diff line change
Expand Up @@ -6,82 +6,81 @@


class DbSeabed:
# TODO update the dict to add correct bmi names and links and units
# TODO update bmi names
DATA_SERVICES = {
"bathy": {
"name": "seafloor__water_depth ",
"link": "https://",
"units": "metres",
},
# "bathy": {
# "name": "seafloor__water_depth ",
# "link": "https://",
# "units": "metres",
# }, # TODO add bathymetry data link
"carbonate": {
"name": "surficial_seafloor_carbonate__content ",
"link": "https://files.isric.org/soilgrids/former/"
"2017-03-10/data/BDRICM_M_250m_ll.tif",
"link": "https://csdms.colorado.edu/pub/data/dbSEABED/gomex_crb_idw3d.tif",
"units": "percent",
},
"carbonate_unctn": {
"carbonate_totlsu": {
"name": "surficial_seafloor_carbonate__content_uncertainty ",
"link": "https://",
"link": "https://csdms.colorado.edu/pub/data/dbSEABED/gomex_crb_idw3d_TotlSU.tif",
"units": "percent",
},
"grainsize": {
"name": "surficial_seafloor_sediment__grainsize",
"link": "https://",
"link": "https://csdms.colorado.edu/pub/data/dbSEABED/gomex_grz_idw3d.tif",
"units": "phi",
},
"grainsize_unctn": {
"grainsize_totlsu": {
"name": "surficial_seafloor_sediment__grainsize_uncertainty",
"link": "https://",
"link": "https://csdms.colorado.edu/pub/data/dbSEABED/gomex_grz_idw3d_TotlSU.tif",
"units": "phi",
},
"gravel": {
"name": "surficial_seafloor_sediment_gravel__content",
"link": "https://",
"link": "https://csdms.colorado.edu/pub/data/dbSEABED/gomex_codaGVL_idw3d.tif",
"units": "percent",
},
"gravel_unctn": {
"gravel_totlsu": {
"name": "surficial_seafloor_sediment_gravel__content_uncertainty",
"link": "https://",
"link": "https://csdms.colorado.edu/pub/data/dbSEABED/gomex_codaGVL_TotlSU.tif",
"units": "percent",
},
"mud": {
"name": "surficial_seafloor_sediment_mud__content",
"link": "https://",
"link": "https://csdms.colorado.edu/pub/data/dbSEABED/gomex_codaMUD_idw3d.tif",
"units": "percent",
},
"mud_unctn": {
"mud_totlsu": {
"name": "surficial_seafloor_sediment_mud__content_uncertainty",
"link": "https://",
"link": "https://csdms.colorado.edu/pub/data/dbSEABED/gomex_codaMUD_TotlSU.tif",
"units": "percent",
},
"organic_carbon": {
"name": "surficial_seafloor_sediment_organic_carbon__content",
"link": "https://",
"link": "https://csdms.colorado.edu/pub/data/dbSEABED/gomex_ocbn_idw3d.tif",
"units": "percent",
},
"organic_carbon_unctn": {
"organic_carbon_totlsu": {
"name": "surficial_seafloor_sediment_organic_carbon__content_uncertainty",
"link": "https://",
"link": "https://csdms.colorado.edu/pub/data/dbSEABED/gomex_ocbn_idw3d_TotlSU.tif",
"units": "percent",
},
"rock": {
"name": "surficial_seafloor_exposed_rock__content",
"link": "https://",
"link": "https://csdms.colorado.edu/pub/data/dbSEABED/gomex_rck_idw3d.tif",
"units": "percent",
},
"rock_unctn": {
"rock_totlsu": {
"name": "surficial_seafloor_exposed_rock__content_uncertainty",
"link": "https://",
"link": "https://csdms.colorado.edu/pub/data/dbSEABED/gomex_rck_idw3d_TotlSU.tif",
"units": "percent",
},
"sand": {
"name": "surficial_seafloor_sediment_sand__content",
"link": "https://",
"link": "https://csdms.colorado.edu/pub/data/dbSEABED/gomex_codaSND_idw3d.tif",
"units": "percent",
},
"sand_unctn": {
"sand_totlsu": {
"name": "surficial_seafloor_sediment_sand__content_uncertainty",
"link": "https://",
"link": "https://csdms.colorado.edu/pub/data/dbSEABED/gomex_codaSND_TotlSU.tif",
"units": "percent",
},
}
Expand All @@ -100,6 +99,7 @@ def metadata(self):

@property
def data_services(self):
# Print data services information
string_list = []
for key, value in DbSeabed.DATA_SERVICES.items():
string_list.extend(
Expand All @@ -122,7 +122,22 @@ def get_data(
output,
local_file=False,
):
# TODO: add docstrings
"""
Get data from the remote server.
Args:
var_name: Variable name for dbSEABED datasets.
west: x coordinate of the lower left corner of the grid extent.
south: y coordinate of the lower left corner of the grid extent.
east: x coordinate of the upper right corner of the grid extent.
north: y coordinate of the upper right corner of the grid extent.
output: Output file path.
local_file: If True, load the local file without data download.
Returns:
rioxarray.Dataset: Dataset containing the dbSEABED dataset.
"""

# check var_name
if var_name not in DbSeabed.DATA_SERVICES.keys():
raise ValueError("Please provide a valid var_name value.")
Expand All @@ -135,18 +150,20 @@ def get_data(
)

# check output
if output[-4::] != ".tif":
if not output.endswith(".tif"):
raise ValueError(
"Please provide a valid output file name with .tif extension."
)

if local_file and os.path.isfile(output):
# load local data
dataset = rioxarray.open_rasterio(output)
dataset = rioxarray.open_rasterio(output, masked=True)

else:
# access and subset data from server
ori_data = rioxarray.open_rasterio(DbSeabed.DATA_SERVICES[var_name]["link"])
ori_data = rioxarray.open_rasterio(
DbSeabed.DATA_SERVICES[var_name]["link"], masked=True
)
dataset = ori_data.rio.clip_box(
minx=west,
miny=south,
Expand All @@ -155,9 +172,12 @@ def get_data(
)

# save the data as geotiff
dataset.rio.to_raster(raster_path=output, driver="GTiff")

dataset.close()
dataset.rio.to_raster(
raster_path=output,
driver="GTiff",
# dtype="float64",
recalc_transform=False,
)

# get resolution
geotrans = [
Expand All @@ -181,8 +201,13 @@ def get_data(
"variable_units": DbSeabed.DATA_SERVICES[var_name]["units"],
"service_url": DbSeabed.DATA_SERVICES[var_name]["link"],
"crs_wkt": crs_wkt,
"node_bounding_box": [west, north, east, south],
"grid_bounding_box": [round(value, 5) for value in dataset.rio.bounds()],
"node_bounding_box": [
dataset.x.values[0],
dataset.y.values[0],
dataset.x.values[-1],
dataset.y.values[-1],
],
"grid_bounding_box": dataset.rio.bounds(),
"grid_res": grid_res,
}

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