diff --git a/launcers/all_statics/generate_mer_statics.sh b/launcers/all_statics/generate_mer_statics.sh index 53fea63..7bd6c89 100755 --- a/launcers/all_statics/generate_mer_statics.sh +++ b/launcers/all_statics/generate_mer_statics.sh @@ -63,6 +63,14 @@ process_domain () { if [ -f "${rcustom}" ]; then rbcs_options="${rbcs_options} -d ${rcustom}" fi + + # If there are rivers we also build the cosmetic mask + poetry run mitgcm_inputs cosmetic_mask -m "${domaindir}/meshmask.nc" \ + -r "${domaindir}/additional_variables.nc" \ + -o "${domaindir}/cmeshmask.nc" --mer + else + # No rivers? Then the cosmetic mask is equal to the original mask + cp -av "${domaindir}/meshmask.nc" "${domaindir}/cmeshmask.nc" fi poetry run mitgcm_inputs ob_indices \ diff --git a/poetry.lock b/poetry.lock index 3b3304b..d84aad8 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 2.1.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 2.3.2 and should not be changed by hand. [[package]] name = "aiofiles" @@ -80,14 +80,14 @@ tqdm = ">=4.65,<5.0" [[package]] name = "attrs" -version = "25.4.0" +version = "26.1.0" description = "Classes Without Boilerplate" optional = false python-versions = ">=3.9" groups = ["main"] files = [ - {file = "attrs-25.4.0-py3-none-any.whl", hash = "sha256:adcf7e2a1fb3b36ac48d97835bb6d8ade15b8dcce26aba8bf1d14847b57a3373"}, - {file = "attrs-25.4.0.tar.gz", hash = "sha256:16d5969b87f0859ef33a48b35d55ac1be6e42ae49d5e853b597db70c35c57e11"}, + {file = "attrs-26.1.0-py3-none-any.whl", hash = "sha256:c647aa4a12dfbad9333ca4e71fe62ddc36f4e63b2d260a37a8b83d2f043ac309"}, + {file = "attrs-26.1.0.tar.gz", hash = "sha256:d03ceb89cb322a8fd706d4fb91940737b6642aa36998fe130a9bc96c985eff32"}, ] [[package]] @@ -95,14 +95,15 @@ name = "bitsea" version = "0.1.0" description = "" optional = false -python-versions = "^3.9" +python-versions = "^3.11" groups = ["main"] files = [] develop = false [package.dependencies] +defusedxml = "^0.7.1" netcdf4 = 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mitgcm_inputs.bottom_fluxes import COMMAND_NAME as BFLUX_COMMAND_NAME from mitgcm_inputs.bottom_fluxes import main as bflux_main from mitgcm_inputs.bottom_fluxes import sub_arguments as bflux_sub_arguments +from mitgcm_inputs.cosmetic_mask import COMMAND_NAME as CMASK_COMMAND_NAME +from mitgcm_inputs.cosmetic_mask import main as cosmetic_mask_main +from mitgcm_inputs.cosmetic_mask import sub_arguments as cmask_sub_arguments from mitgcm_inputs.k_extinction import COMMAND_NAME as KEXT_COMMAND_NAME from mitgcm_inputs.k_extinction import main as kext_main from mitgcm_inputs.k_extinction import sub_arguments as kext_sub_arguments @@ -76,6 +79,7 @@ def argument(sys_argv=None): bflux_sub_arguments(subparsers) rbcs_sub_arguments(subparsers) ob_indices_sub_arguments(subparsers) + cmask_sub_arguments(subparsers) subparser = subparsers.add_parser( "FLUXES", @@ -107,7 +111,7 @@ def argument(sys_argv=None): return parser.parse_args() -def execute_all_commands(args: argparse.Namespace): +def execute_flux_commands(args: argparse.Namespace): mask_path = args.mask output_file = args.output @@ -183,11 +187,12 @@ def execute_all_commands(args: argparse.Namespace): CMD_MAP = { BFLUX_COMMAND_NAME: bflux_main, + CMASK_COMMAND_NAME: cosmetic_mask_main, SD_COMMAND_NAME: sd_main, KEXT_COMMAND_NAME: kext_main, RBCS_COMMAND_NAME: rbcs_main, OB_INDICES_COMMAND_NAME: ob_indices_main, - "FLUXES": execute_all_commands, + "FLUXES": execute_flux_commands, } diff --git a/src/mitgcm_inputs/cosmetic_mask/__init__.py b/src/mitgcm_inputs/cosmetic_mask/__init__.py new file mode 100644 index 0000000..339b371 --- /dev/null +++ b/src/mitgcm_inputs/cosmetic_mask/__init__.py @@ -0,0 +1,156 @@ +import argparse +import logging + +import numpy as np +import xarray as xr +from bitsea.commons.mask import MaskWithRivers +from bitsea.utilities.argparse_types import existing_file_path +from bitsea.utilities.argparse_types import path_inside_an_existing_dir + +from mitgcm_inputs.tools.read_mesh_mask import read_mesh_mask + +if __name__ == "__main__": + LOGGER = logging.getLogger() +else: + LOGGER = logging.getLogger(__name__) + + +COMMAND_NAME = "cosmetic_mask" + + +def sub_arguments(subparser): + parser = subparser.add_parser( + COMMAND_NAME, + help="Generate a new meshmask file that has no rivers and that can be " + "used to produce plots without the rivers stems", + ) + + parser.add_argument( + "-m", + "--mask", + required=True, + type=existing_file_path, + help="The meshmask file that defines the domain", + ) + + parser.add_argument( + "-r", + "--river-file", + required=False, + default=None, + type=existing_file_path, + help="An auxiliary file that contains a map that associates each " + "river cell with its river id. This file is useful only if this " + "information is not already stored in the meshmask file and if there " + "are rivers on the domain. If the rivers-positions file is not " + "provided, we will assume that the information about the rivers is " + 'stored inside the meshmask file (in a variable named "rivers")', + ) + + parser.add_argument( + "-o", + "--output", + required=True, + type=path_inside_an_existing_dir, + help="Path of the NetCDF output file to write", + ) + + parser.add_argument( + "--mer", + action="store_true", + help=""" + If this flag is set, this script will generate the meshmask in the + format used by the MER project. This format is CF-1.4 compliant. + """, + ) + + +def main(args: argparse.Namespace) -> int: + if args.cmd != COMMAND_NAME: + LOGGER.error( + "%s command has been invoked with command: %s", + COMMAND_NAME, + args.cmd, + ) + return 1 + + domain_mask = read_mesh_mask(args.mask) + + # On which file do we have the information about the cells occupied by + # the rivers? + if args.river_file is not None: + file_with_river = args.river_file + else: + file_with_river = args.mask + + with xr.open_dataset(file_with_river) as river_ds: + river_map = river_ds["rivers"].load() + + river_mask = MaskWithRivers( + grid=domain_mask.grid, + zlevels=domain_mask.zlevels, + mask_array=domain_mask[:], + river_positions=river_map, + ) + + if args.mer: + mesh_mask_coords = { + "depth": ( + ("depth",), + river_mask.zlevels, + { + "units": "m", + "positive": "down", + "standard_name": "depth", + "axis": "Z", + }, + ), + "latitude": ( + ("latitude",), + river_mask.lat, + { + "units": "degrees_north", + "standard_name": "latitude", + "axis": "Y", + }, + ), + "longitude": ( + ("longitude",), + river_mask.lon, + { + "units": "degrees_east", + "standard_name": "longitude", + "axis": "X", + }, + ), + } + e1t = xr.DataArray(data=river_mask.e1t, dims=("latitude", "longitude")) + e2t = xr.DataArray(data=river_mask.e2t, dims=("latitude", "longitude")) + e3t = xr.DataArray( + data=river_mask.e3t, dims=("depth", "latitude", "longitude") + ) + del_z = xr.DataArray( + data=river_mask.zlevels, + dims=("depth",), + ) + tmask = xr.DataArray( + data=np.asarray(river_mask, dtype=np.int8), + dims=("depth", "latitude", "longitude"), + ) + + mask_array = xr.Dataset( + data_vars={ + "e1t": e1t, + "e2t": e2t, + "e3t": e3t, + "delZ": del_z, + "tmask": tmask, + }, + coords=mesh_mask_coords, + attrs={"mer_mesh_mask_version": "1.0"}, + ) + mask_array.to_netcdf(args.output) + else: + river_mask.save_as_netcdf(args.output) + + return 0