add https://github.com/COSIMA/access-om2/blob/2911891/tools/make_salt…

…_sfc_restore.py

salt_sfc_restore_generation/make_salt_sfc_restore.py

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+#!/usr/bin/env python
+
+import numpy as np
+import sys
+import numba
+import os
+import argparse
+import netCDF4 as nc
+import shutil
+from scipy.ndimage.filters import uniform_filter
+from make_remap_weights import create_weights
+
+from esmgrids.mom_grid import MomGrid  # noqa
+from esmgrids.woa_grid import WoaGrid  # noqa
+
+"""
+Create MOM salt_sfc_restore.nc file from WOA
+"""
+
+def calc_regridding_err(weights, src, dest):
+    """
+    Calculate the regridding error.
+    """
+
+    EARTH_RADIUS = 6370997.0
+
+    with nc.Dataset(weights) as f:
+        try:
+            area_a = f.variables['area_a'][:]
+        except KeyError as e:
+            area_a = f.variables['src_grid_area'][:]
+        area_a = area_a.reshape(src.shape[0], src.shape[1])
+        area_a = area_a*EARTH_RADIUS**2
+
+        try:
+            area_b = f.variables['area_b'][:]
+        except KeyError as e:
+            area_b = f.variables['dst_grid_area'][:]
+        area_b = area_b.reshape(dest.shape[0], dest.shape[1])
+        area_b = area_b*EARTH_RADIUS**2
+
+        try:
+            frac_a = f.variables['frac_a'][:]
+        except KeyError as e:
+            frac_a = f.variables['src_grid_frac'][:]
+        frac_a = frac_a.reshape(src.shape[0], src.shape[1])
+
+        try:
+            frac_b = f.variables['frac_b'][:]
+        except KeyError as e:
+            frac_b = f.variables['dst_grid_frac'][:]
+        frac_b = frac_b.reshape(dest.shape[0], dest.shape[1])
+
+    # Calculation of totals here.
+    # http://www.earthsystemmodeling.org/esmf_releases/non_public/ESMF_5_3_0/ESMC_crefdoc/node3.html
+    src_tot = np.sum(src[:, :] * area_a[:, :] * frac_a[:, :])
+    dest_tot = np.sum(dest[:, :] * area_b[:, :])
+    rel_err = abs(src_tot - dest_tot) / dest_tot
+
+    return rel_err
+
+@numba.jit
+def apply_weights(src, dest_shape, n_s, n_b, row, col, s):
+    """
+    Apply ESMF regirdding weights.
+    """
+
+    dest = np.ndarray(dest_shape).flatten()
+    dest[:] = 0.0
+    src = src.flatten()
+
+    for i in range(n_s):
+        dest[row[i]-1] = dest[row[i]-1] + s[i]*src[col[i]-1]
+
+    return dest.reshape(dest_shape)
+
+
+def remap(src_data, weights, dest_shape):
+    """
+    Regrid a 2d field and see how it looks.
+    """
+
+    dest_data = np.ndarray(dest_shape)
+
+    with nc.Dataset(weights) as wf:
+        try:
+            n_s = wf.dimensions['n_s'].size
+        except KeyError as e:
+            n_s = wf.dimensions['num_links'].size
+        try:
+            n_b = wf.dimensions['n_b'].size
+        except KeyError as e:
+            n_b = wf.dimensions['dst_grid_size'].size
+        try:
+            row = wf.variables['row'][:]
+        except KeyError as e:
+            row = wf.variables['dst_address'][:]
+        try:
+            col = wf.variables['col'][:]
+        except KeyError as e:
+            col = wf.variables['src_address'][:]
+
+        s = wf.variables['S'][:]
+
+    dest_data[:, :] = apply_weights(src_data[:, :], dest_data.shape,
+                                    n_s, n_b, row, col, s)
+    return dest_data
+
+
+def smooth2d(src):
+
+    tmp_src = np.ndarray((src.shape[0] + 6, src.shape[1]))
+
+    # Window size
+    ws = 3
+
+    tmp_src[ws:-ws, :] = src[:, :]
+    tmp_src[:ws, :] = src[-ws:, :]
+    tmp_src[-ws:, :] = src[:3, :]
+
+    dest = uniform_filter(tmp_src, size=ws, mode='nearest')
+    return dest[ws:-ws, :]
+
+
+def main():
+
+    parser = argparse.ArgumentParser()
+    parser.add_argument('woa_input', help='The WOA input file.')
+    parser.add_argument('ocean_hgrid',
+                        help='The horizontal MOM grid definition to remap to')
+    parser.add_argument('old_salt_sfc_restore',
+                        help='The old salt sfc restoring file. Needed for metadata.')
+    parser.add_argument('output', help='salt_sfc_restore.nc file for MOM5')
+    parser.add_argument('--interpolation_weights', default=None,
+                        help='Interpolation weights, file if not given this will be created.')
+    parser.add_argument('--method', default='patch', help="""
+                        Interpolation method, passed to ESMF_RegridWeightGen.""")
+    parser.add_argument('--npes', default=None, help="""
+                        The number of PEs to use. Default is 1/2 of available.""")
+
+
+    args = parser.parse_args()
+
+    if args.npes is None:
+        import multiprocessing as mp
+        args.npes = mp.cpu_count() // 2
+
+    src_grid = WoaGrid(args.woa_input, calc_areas=False)
+    dest_grid = MomGrid.fromfile(args.ocean_hgrid, calc_areas=False)
+    dest_res = (dest_grid.num_lat_points, dest_grid.num_lon_points)
+
+    if args.interpolation_weights is None:
+        weights = create_weights(src_grid, dest_grid, args.npes, args.method)
+    else:
+        weights = args.interpolation_weights
+
+    with nc.Dataset(args.woa_input) as f:
+        src = f.variables['so'][:]
+
+    dest = np.zeros((src.shape[0], dest_res[0], dest_res[1]))
+
+    for t in range(src.shape[0]):
+        smooth_src = smooth2d(src[t, :, :])
+        dest[t, :, :] = remap(smooth_src, weights, dest_res)
+
+        if 'conserve' in args.method:
+            rel_err = calc_regridding_err(weights, smooth_src, dest[t, :, :])
+            print('relative error {}'.format(rel_err))
+            assert rel_err < 1e-14
+
+    shutil.copyfile(args.old_salt_sfc_restore, args.output)
+    with nc.Dataset(args.output, 'r+') as f:
+        f.variables['salt'][:] = dest
+
+if __name__ == '__main__':
+    sys.exit(main())