Cice grid generation (#6)

This change updates the workflow to generate a cice grid from a mom-supergrid file containing a tripolar grid. - fixes angle T - adds cf compliant variable names - add versioning to output - adds an end-end test COSIMA/om3-utils#5 describes full scope of changes --------- Co-authored-by: dougiesquire <[email protected]> Co-authored-by: Dougie Squire <[email protected]>
COSIMA · Apr 17, 2024 · 1b6837d · 1b6837d
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diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -1,7 +1,7 @@
 # This workflow will install Python dependencies, run tests and lint with a single version of Python
 # For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
 
-name: OM3Utils
+name: esmgrids
 
 on:
   push:

diff --git a/README.md b/README.md
@@ -1,6 +1,4 @@
-
-[![Code Health](https://landscape.io/github/DoublePrecision/esmgrids/master/landscape.svg?style=flat)](https://landscape.io/github/DoublePrecision/esmgrids/master)
-[![Build Status](https://travis-ci.org/DoublePrecision/esmgrids.svg?branch=master)](https://travis-ci.org/DoublePrecision/esmgrids)
+![Code Health](https://github.com/COSIMA/esmgrids/actions/workflows/ci.yml/badge.svg)
 
 # esmgrids
 
@@ -19,10 +17,6 @@ Grids currently supported:
 ## To run the tests
 
 ```
-conda env create -n grids python3
-source activate grids
-python -m pytest
+pip install '.[tests]'
+python -m pytest -m "not broken"
 ```
-
-Warning: this will download a rather large tarball of test inputs.
-
diff --git a/esmgrids/__init__.py b/esmgrids/__init__.py
@@ -0,0 +1,30 @@
+import re
+import warnings
+from importlib.metadata import version, PackageNotFoundError
+
+try:
+    __version__ = version("esmgrids")
+except PackageNotFoundError:
+    # package is not installed
+    pass
+
+
+def safe_version():
+    """
+    Returns the version, issuing a warning if there are revisions since the last tag
+    and an error if there are uncommitted changes
+
+    This function assumes the setuptools_scm default versioning scheme - see
+    https://setuptools-scm.readthedocs.io/en/latest/usage/#default-versioning-scheme
+    """
+    if re.match(r".*\d{8}$", __version__):
+        warnings.warn(
+            (
+                "There are uncommitted changes! Commit, push and release these changes before "
+                "generating any production files."
+            )
+        )
+    elif re.match(r".*dev.*", __version__):
+        warnings.warn(("There are unreleased commits! Do a release before generating any production files."))
+
+    return __version__
diff --git a/esmgrids/base_grid.py b/esmgrids/base_grid.py
@@ -1,7 +1,7 @@
 import numpy as np
 import netCDF4 as nc
 
-from .util import calc_area_of_polygons
+from esmgrids.util import calc_area_of_polygons
 
 
 class BaseGrid(object):

diff --git a/esmgrids/cice_grid.py b/esmgrids/cice_grid.py
@@ -1,13 +1,13 @@
 import numpy as np
 import netCDF4 as nc
 
-from .base_grid import BaseGrid
+from esmgrids.base_grid import BaseGrid
 
 
 class CiceGrid(BaseGrid):
 
     def __init__(self, **kwargs):
-        self.type = "Arakawa B"
+        self.type = "Arakawa B / C"
         self.full_name = "CICE"
 
         super(CiceGrid, self).__init__(**kwargs)
@@ -65,66 +65,95 @@ def fromfile(cls, h_grid_def, mask_file=None, description="CICE tripolar"):
             description=description,
         )
 
-    def write(self, grid_filename, mask_filename):
+    def _create_2d_nc_var(self, f, name):
+        return f.createVariable(
+            name,
+            "f8",
+            dimensions=("ny", "nx"),
+            compression="zlib",
+            complevel=1,
+        )
+
+    def write(self, grid_filename, mask_filename, metadata=None):
         """
-        Write out CICE grid to netcdf.
+        Write out CICE grid to netcdf
+
+        Parameters
+        ----------
+        grid_filename: str
+            The name of the grid file to write
+        mask_filename: str
+            The name of the mask file to write
+        metadata: dict
+            Any global or variable metadata attributes to add to the files being written
         """
 
+        # Grid file
         f = nc.Dataset(grid_filename, "w")
 
         # Create dimensions.
         f.createDimension("nx", self.num_lon_points)
+        # nx is the grid_longitude but doesn't have a value other than its index
         f.createDimension("ny", self.num_lat_points)
-        f.createDimension("nc", 4)
+        # ny is the grid_latitude but doesn't have a value other than its index
 
         # Make all CICE grid variables.
-        ulat = f.createVariable("ulat", "f8", dimensions=("ny", "nx"))
+        # names are based on https://cfconventions.org/Data/cf-standard-names/current/build/cf-standard-name-table.html
+        f.Conventions = "CF-1.6"
+
+        ulat = self._create_2d_nc_var(f, "ulat")
         ulat.units = "radians"
-        ulat.title = "Latitude of U points"
-        ulon = f.createVariable("ulon", "f8", dimensions=("ny", "nx"))
+        ulat.long_name = "Latitude of U points"
+        ulat.standard_name = "latitude"
+        ulon = self._create_2d_nc_var(f, "ulon")
         ulon.units = "radians"
-        ulon.title = "Longitude of U points"
-        tlat = f.createVariable("tlat", "f8", dimensions=("ny", "nx"))
+        ulon.long_name = "Longitude of U points"
+        ulon.standard_name = "longitude"
+        tlat = self._create_2d_nc_var(f, "tlat")
         tlat.units = "radians"
-        tlat.title = "Latitude of T points"
-        tlon = f.createVariable("tlon", "f8", dimensions=("ny", "nx"))
+        tlat.long_name = "Latitude of T points"
+        tlat.standard_name = "latitude"
+        tlon = self._create_2d_nc_var(f, "tlon")
         tlon.units = "radians"
-        tlon.title = "Longitude of T points"
-
-        if self.clon_t is not None:
-            clon_t = f.createVariable("clon_t", "f8", dimensions=("nc", "ny", "nx"))
-            clon_t.units = "radians"
-            clon_t.title = "Longitude of T cell corners"
-            clat_t = f.createVariable("clat_t", "f8", dimensions=("nc", "ny", "nx"))
-            clat_t.units = "radians"
-            clat_t.title = "Latitude of T cell corners"
-            clon_u = f.createVariable("clon_u", "f8", dimensions=("nc", "ny", "nx"))
-            clon_u.units = "radians"
-            clon_u.title = "Longitude of U cell corners"
-            clat_u = f.createVariable("clat_u", "f8", dimensions=("nc", "ny", "nx"))
-            clat_u.units = "radians"
-            clat_u.title = "Latitude of U cell corners"
-
-        htn = f.createVariable("htn", "f8", dimensions=("ny", "nx"))
+        tlon.long_name = "Longitude of T points"
+        tlon.standard_name = "longitude"
+
+        htn = self._create_2d_nc_var(f, "htn")
         htn.units = "cm"
-        htn.title = "Width of T cells on North side."
-        hte = f.createVariable("hte", "f8", dimensions=("ny", "nx"))
+        htn.long_name = "Width of T cells on North side."
+        htn.coordinates = "ulat tlon"
+        htn.grid_mapping = "crs"
+        hte = self._create_2d_nc_var(f, "hte")
         hte.units = "cm"
-        hte.title = "Width of T cells on East side."
+        hte.long_name = "Width of T cells on East side."
+        hte.coordinates = "tlat ulon"
+        hte.grid_mapping = "crs"
 
-        angle = f.createVariable("angle", "f8", dimensions=("ny", "nx"))
+        angle = self._create_2d_nc_var(f, "angle")
         angle.units = "radians"
-        angle.title = "Rotation angle of U cells."
-        angleT = f.createVariable("angleT", "f8", dimensions=("ny", "nx"))
+        angle.long_name = "Rotation angle of U cells."
+        angle.standard_name = "angle_of_rotation_from_east_to_x"
+        angle.coordinates = "ulat ulon"
+        angle.grid_mapping = "crs"
+        angleT = self._create_2d_nc_var(f, "angleT")
         angleT.units = "radians"
-        angleT.title = "Rotation angle of T cells."
+        angleT.long_name = "Rotation angle of T cells."
+        angleT.standard_name = "angle_of_rotation_from_east_to_x"
+        angleT.coordinates = "tlat tlon"
+        angleT.grid_mapping = "crs"
 
-        area_t = f.createVariable("tarea", "f8", dimensions=("ny", "nx"))
+        area_t = self._create_2d_nc_var(f, "tarea")
         area_t.units = "m^2"
-        area_t.title = "Area of T cells."
-        area_u = f.createVariable("uarea", "f8", dimensions=("ny", "nx"))
+        area_t.long_name = "Area of T cells."
+        area_t.standard_name = "cell_area"
+        area_t.coordinates = "tlat tlon"
+        area_t.grid_mapping = "crs"
+        area_u = self._create_2d_nc_var(f, "uarea")
         area_u.units = "m^2"
-        area_u.title = "Area of U cells."
+        area_u.long_name = "Area of U cells."
+        area_u.standard_name = "cell_area"
+        area_u.coordinates = "ulat ulon"
+        area_u.grid_mapping = "crs"
 
         area_t[:] = self.area_t[:]
         area_u[:] = self.area_u[:]
@@ -135,24 +164,43 @@ def write(self, grid_filename, mask_filename):
         ulat[:] = np.deg2rad(self.y_u)
         ulon[:] = np.deg2rad(self.x_u)
 
-        if self.clon_t is not None:
-            clon_t[:] = np.deg2rad(self.clon_t)
-            clat_t[:] = np.deg2rad(self.clat_t)
-            clon_u[:] = np.deg2rad(self.clon_u)
-            clat_u[:] = np.deg2rad(self.clat_u)
-
         # Convert from m to cm.
         htn[:] = self.dx_tn[:] * 100.0
         hte[:] = self.dy_te[:] * 100.0
 
         angle[:] = np.deg2rad(self.angle_u[:])
         angleT[:] = np.deg2rad(self.angle_t[:])
 
+        # Add the typical crs (i.e. WGS84/EPSG4326 , but in radians).
+        crs = f.createVariable("crs", "S1")
+        crs.crs_wkt = 'GEOGCS["WGS 84",DATUM["WGS_1984",SPHEROID["WGS 84",6378137,298.257223563,AUTHORITY["EPSG","7030"]],AUTHORITY["EPSG","6326"]],PRIMEM["Greenwich",0,AUTHORITY["EPSG","8901"]],UNIT["radians",1,AUTHORITY["EPSG","9122"]],AXIS["Latitude",NORTH],AXIS["Longitude",EAST],AUTHORITY["EPSG","4326"]]'
+
+        # Add global metadata
+        if metadata:
+            for attr, meta in metadata.items():
+                f.setncattr(attr, meta)
+
         f.close()
 
-        with nc.Dataset(mask_filename, "w") as f:
-            f.createDimension("nx", self.num_lon_points)
-            f.createDimension("ny", self.num_lat_points)
-            mask = f.createVariable("kmt", "f8", dimensions=("ny", "nx"))
-            # CICE uses 0 as masked, whereas internally we use 1 as masked.
-            mask[:] = 1 - self.mask_t
+        # Mask file
+        f = nc.Dataset(mask_filename, "w")
+
+        f.createDimension("nx", self.num_lon_points)
+        f.createDimension("ny", self.num_lat_points)
+        mask = self._create_2d_nc_var(f, "kmt")
+        mask.grid_mapping = "crs"
+        mask.standard_name = "sea_binary_mask"
+
+        # CICE uses 0 as masked, whereas internally we use 1 as masked.
+        mask[:] = 1 - self.mask_t
+
+        # Add the typical crs (i.e. WGS84/EPSG4326 , but in radians).
+        crs = f.createVariable("crs", "S1")
+        crs.crs_wkt = 'GEOGCS["WGS 84",DATUM["WGS_1984",SPHEROID["WGS 84",6378137,298.257223563,AUTHORITY["EPSG","7030"]],AUTHORITY["EPSG","6326"]],PRIMEM["Greenwich",0,AUTHORITY["EPSG","8901"]],UNIT["radians",1,AUTHORITY["EPSG","9122"]],AXIS["Latitude",NORTH],AXIS["Longitude",EAST],AUTHORITY["EPSG","4326"]]'
+
+        # Add global metadata
+        if metadata:
+            for attr, meta in metadata.items():
+                f.setncattr(attr, meta)
+
+        f.close()
diff --git a/esmgrids/cli.py b/esmgrids/cli.py
@@ -0,0 +1,40 @@
+import os
+import argparse
+
+from esmgrids import safe_version
+from esmgrids.util import md5sum
+from esmgrids.mom_grid import MomGrid
+from esmgrids.cice_grid import CiceGrid
+
+
+def cice_from_mom():
+    """Script for creating CICE grid files from MOM grid files"""
+
+    parser = argparse.ArgumentParser(description="Create CICE grid files from MOM grid files")
+    parser.add_argument("--ocean_hgrid", type=str, help="Input MOM ocean_hgrid.nc supergrid file")
+    parser.add_argument("--ocean_mask", type=str, help="Input MOM ocean_mask.nc mask file")
+    parser.add_argument("--cice_grid", type=str, default="grid.nc", help="Output CICE grid file")
+    parser.add_argument("--cice_kmt", type=str, default="kmt.nc", help="Output CICE kmt file")
+
+    args = parser.parse_args()
+    ocean_hgrid = os.path.abspath(args.ocean_hgrid)
+    ocean_mask = os.path.abspath(args.ocean_mask)
+    cice_grid = os.path.abspath(args.cice_grid)
+    cice_kmt = os.path.abspath(args.cice_kmt)
+
+    version = safe_version()
+    runcmd = (
+        f"Created using https://github.com/COSIMA/esmgrids {version}: "
+        f"cice_from_mom --ocean_hgrid={ocean_hgrid} --ocean_mask={ocean_mask} "
+        f"--cice_grid={cice_grid} --cice_kmt={cice_kmt}"
+    )
+    provenance_metadata = {
+        "inputfile": (
+            f"{ocean_hgrid} (md5 hash: {md5sum(ocean_hgrid)}), " f"{ocean_mask} (md5 hash: {md5sum(ocean_mask)})"
+        ),
+        "history": runcmd,
+    }
+
+    mom = MomGrid.fromfile(ocean_hgrid, mask_file=ocean_mask)
+    cice = CiceGrid.fromgrid(mom)
+    cice.write(cice_grid, cice_kmt, metadata=provenance_metadata)
diff --git a/esmgrids/mom_grid.py b/esmgrids/mom_grid.py
@@ -1,7 +1,7 @@
 import numpy as np
 import netCDF4 as nc
 
-from .base_grid import BaseGrid
+from esmgrids.base_grid import BaseGrid
 
 
 class MomGrid(BaseGrid):
@@ -86,9 +86,8 @@ def fromfile(cls, h_grid_def, v_grid_def=None, mask_file=None, calc_areas=True,
                 dy_ue = dy_ext[1::2, 3::2] + dy_ext[2::2, 3::2]
 
                 angle_dx = f.variables["angle_dx"][:]
-                # The angle of rotation is a corner cell centres and applies to
-                # both t and u cells.
-                angle_t = angle_dx[2::2, 2::2]
+
+                angle_t = angle_dx[1::2, 1::2]
                 angle_u = angle_dx[2::2, 2::2]
 
                 area = f.variables["area"][:]

diff --git a/esmgrids/util.py b/esmgrids/util.py
@@ -2,6 +2,7 @@
 import pyproj
 from shapely.geometry import shape
 
+
 proj_str = "+proj=laea +lat_0={} +lon_0={} +ellps=sphere"
 
 
@@ -39,3 +40,11 @@ def calc_area_of_polygons(clons, clats):
     assert np.min(areas) > 0
 
     return areas
+
+
+def md5sum(filename):
+    from hashlib import md5
+    from mmap import mmap, ACCESS_READ
+
+    with open(filename) as file, mmap(file.fileno(), 0, access=ACCESS_READ) as file:
+        return md5(file).hexdigest()
diff --git a/pyproject.toml b/pyproject.toml
@@ -22,7 +22,7 @@ dependencies = [
     "numpy",
     "netcdf4",
     "shapely",
-    "pyproj",
+    "pyproj"
 ]
 
 [build-system]
@@ -48,8 +48,13 @@ test = [
     "pytest",
     "pytest-cov",
     "sh",
+    "xarray",
+    "ocean_model_grid_generator@git+https://github.com/nikizadehgfdl/ocean_model_grid_generator@790069b31f9791864ccd514a2b8f53f385a0452e"
 ]
 
+[project.scripts]
+cice_from_mom = "esmgrids.cli:cice_from_mom"
+
 [tool.pytest.ini_options]
 addopts = ["--cov=esmgrids", "--cov-report=term", "--cov-report=xml"]
 testpaths = ["test"]