Merge pull request #1816 from OceanParcels/v/refactor-interp

Refactoring field interpolation and allow custom interpolation methods in Scipy mode

Author: VeckoTheGecko

parcels/_compat.py

@@ -17,3 +17,17 @@
     from sklearn.cluster import KMeans  # type: ignore[no-redef]
 except ModuleNotFoundError:
     pass
+
+
+def add_note(e: Exception, note: str, *, before=False) -> Exception:  # TODO: Remove once py3.10 support is dropped
+    """Implements something similar to PEP 678 but for python <3.11.
+
+    https://stackoverflow.com/a/75549200/15545258
+    """
+    args = e.args
+    if not args:
+        arg0 = note
+    else:
+        arg0 = f"{note}\n{args[0]}" if before else f"{args[0]}\n{note}"
+    e.args = (arg0,) + args[1:]
+    return e

parcels/_index_search.py

@@ -0,0 +1,337 @@
+from __future__ import annotations
+
+from typing import TYPE_CHECKING
+
+import numpy as np
+
+from parcels._typing import (
+    GridIndexingType,
+    InterpMethodOption,
+)
+from parcels.tools.statuscodes import (
+    FieldOutOfBoundError,
+    FieldOutOfBoundSurfaceError,
+    _raise_field_out_of_bound_error,
+    _raise_field_out_of_bound_surface_error,
+    _raise_field_sampling_error,
+)
+
+from .grid import GridType
+
+if TYPE_CHECKING:
+    from .field import Field
+    from .grid import Grid
+
+
+def search_indices_vertical_z(grid: Grid, gridindexingtype: GridIndexingType, z: float):
+    if grid.depth[-1] > grid.depth[0]:
+        if z < grid.depth[0]:
+            # Since MOM5 is indexed at cell bottom, allow z at depth[0] - dz where dz = (depth[1] - depth[0])
+            if gridindexingtype == "mom5" and z > 2 * grid.depth[0] - grid.depth[1]:
+                return (-1, z / grid.depth[0])
+            else:
+                _raise_field_out_of_bound_surface_error(z, None, None)
+        elif z > grid.depth[-1]:
+            # In case of CROCO, allow particles in last (uppermost) layer using depth[-1]
+            if gridindexingtype in ["croco"] and z < 0:
+                return (-2, 1)
+            _raise_field_out_of_bound_error(z, None, None)
+        depth_indices = grid.depth < z
+        if z >= grid.depth[-1]:
+            zi = len(grid.depth) - 2
+        else:
+            zi = depth_indices.argmin() - 1 if z > grid.depth[0] else 0
+    else:
+        if z > grid.depth[0]:
+            _raise_field_out_of_bound_surface_error(z, None, None)
+        elif z < grid.depth[-1]:
+            _raise_field_out_of_bound_error(z, None, None)
+        depth_indices = grid.depth > z
+        if z <= grid.depth[-1]:
+            zi = len(grid.depth) - 2
+        else:
+            zi = depth_indices.argmin() - 1 if z < grid.depth[0] else 0
+    zeta = (z - grid.depth[zi]) / (grid.depth[zi + 1] - grid.depth[zi])
+    while zeta > 1:
+        zi += 1
+        zeta = (z - grid.depth[zi]) / (grid.depth[zi + 1] - grid.depth[zi])
+    while zeta < 0:
+        zi -= 1
+        zeta = (z - grid.depth[zi]) / (grid.depth[zi + 1] - grid.depth[zi])
+    return (zi, zeta)
+
+
+def search_indices_vertical_s(
+    grid: Grid,
+    interp_method: InterpMethodOption,
+    time: float,
+    z: float,
+    y: float,
+    x: float,
+    ti: int,
+    yi: int,
+    xi: int,
+    eta: float,
+    xsi: float,
+):
+    if interp_method in ["bgrid_velocity", "bgrid_w_velocity", "bgrid_tracer"]:
+        xsi = 1
+        eta = 1
+    if time < grid.time[ti]:
+        ti -= 1
+    if grid._z4d:
+        if ti == len(grid.time) - 1:
+            depth_vector = (
+                (1 - xsi) * (1 - eta) * grid.depth[-1, :, yi, xi]
+                + xsi * (1 - eta) * grid.depth[-1, :, yi, xi + 1]
+                + xsi * eta * grid.depth[-1, :, yi + 1, xi + 1]
+                + (1 - xsi) * eta * grid.depth[-1, :, yi + 1, xi]
+            )
+        else:
+            dv2 = (
+                (1 - xsi) * (1 - eta) * grid.depth[ti : ti + 2, :, yi, xi]
+                + xsi * (1 - eta) * grid.depth[ti : ti + 2, :, yi, xi + 1]
+                + xsi * eta * grid.depth[ti : ti + 2, :, yi + 1, xi + 1]
+                + (1 - xsi) * eta * grid.depth[ti : ti + 2, :, yi + 1, xi]
+            )
+            tt = (time - grid.time[ti]) / (grid.time[ti + 1] - grid.time[ti])
+            assert tt >= 0 and tt <= 1, "Vertical s grid is being wrongly interpolated in time"
+            depth_vector = dv2[0, :] * (1 - tt) + dv2[1, :] * tt
+    else:
+        depth_vector = (
+            (1 - xsi) * (1 - eta) * grid.depth[:, yi, xi]
+            + xsi * (1 - eta) * grid.depth[:, yi, xi + 1]
+            + xsi * eta * grid.depth[:, yi + 1, xi + 1]
+            + (1 - xsi) * eta * grid.depth[:, yi + 1, xi]
+        )
+    z = np.float32(z)  # type: ignore # TODO: remove type ignore once we migrate to float64
+
+    if depth_vector[-1] > depth_vector[0]:
+        if z < depth_vector[0]:
+            _raise_field_out_of_bound_error(z, None, None)
+        elif z > depth_vector[-1]:
+            _raise_field_out_of_bound_error(z, None, None)
+        depth_indices = depth_vector < z
+        if z >= depth_vector[-1]:
+            zi = len(depth_vector) - 2
+        else:
+            zi = depth_indices.argmin() - 1 if z > depth_vector[0] else 0
+    else:
+        if z > depth_vector[0]:
+            _raise_field_out_of_bound_error(z, None, None)
+        elif z < depth_vector[-1]:
+            _raise_field_out_of_bound_error(z, None, None)
+        depth_indices = depth_vector > z
+        if z <= depth_vector[-1]:
+            zi = len(depth_vector) - 2
+        else:
+            zi = depth_indices.argmin() - 1 if z < depth_vector[0] else 0
+    zeta = (z - depth_vector[zi]) / (depth_vector[zi + 1] - depth_vector[zi])
+    while zeta > 1:
+        zi += 1
+        zeta = (z - depth_vector[zi]) / (depth_vector[zi + 1] - depth_vector[zi])
+    while zeta < 0:
+        zi -= 1
+        zeta = (z - depth_vector[zi]) / (depth_vector[zi + 1] - depth_vector[zi])
+    return (zi, zeta)
+
+
+def _search_indices_rectilinear(
+    field: Field, time: float, z: float, y: float, x: float, ti=-1, particle=None, search2D=False
+):
+    grid = field.grid
+
+    if grid.xdim > 1 and (not grid.zonal_periodic):
+        if x < grid.lonlat_minmax[0] or x > grid.lonlat_minmax[1]:
+            _raise_field_out_of_bound_error(z, y, x)
+    if grid.ydim > 1 and (y < grid.lonlat_minmax[2] or y > grid.lonlat_minmax[3]):
+        _raise_field_out_of_bound_error(z, y, x)
+
+    if grid.xdim > 1:
+        if grid.mesh != "spherical":
+            lon_index = grid.lon < x
+            if lon_index.all():
+                xi = len(grid.lon) - 2
+            else:
+                xi = lon_index.argmin() - 1 if lon_index.any() else 0
+            xsi = (x - grid.lon[xi]) / (grid.lon[xi + 1] - grid.lon[xi])
+            if xsi < 0:
+                xi -= 1
+                xsi = (x - grid.lon[xi]) / (grid.lon[xi + 1] - grid.lon[xi])
+            elif xsi > 1:
+                xi += 1
+                xsi = (x - grid.lon[xi]) / (grid.lon[xi + 1] - grid.lon[xi])
+        else:
+            lon_fixed = grid.lon.copy()
+            indices = lon_fixed >= lon_fixed[0]
+            if not indices.all():
+                lon_fixed[indices.argmin() :] += 360
+            if x < lon_fixed[0]:
+                lon_fixed -= 360
+
+            lon_index = lon_fixed < x
+            if lon_index.all():
+                xi = len(lon_fixed) - 2
+            else:
+                xi = lon_index.argmin() - 1 if lon_index.any() else 0
+            xsi = (x - lon_fixed[xi]) / (lon_fixed[xi + 1] - lon_fixed[xi])
+            if xsi < 0:
+                xi -= 1
+                xsi = (x - lon_fixed[xi]) / (lon_fixed[xi + 1] - lon_fixed[xi])
+            elif xsi > 1:
+                xi += 1
+                xsi = (x - lon_fixed[xi]) / (lon_fixed[xi + 1] - lon_fixed[xi])
+    else:
+        xi, xsi = -1, 0
+
+    if grid.ydim > 1:
+        lat_index = grid.lat < y
+        if lat_index.all():
+            yi = len(grid.lat) - 2
+        else:
+            yi = lat_index.argmin() - 1 if lat_index.any() else 0
+
+        eta = (y - grid.lat[yi]) / (grid.lat[yi + 1] - grid.lat[yi])
+        if eta < 0:
+            yi -= 1
+            eta = (y - grid.lat[yi]) / (grid.lat[yi + 1] - grid.lat[yi])
+        elif eta > 1:
+            yi += 1
+            eta = (y - grid.lat[yi]) / (grid.lat[yi + 1] - grid.lat[yi])
+    else:
+        yi, eta = -1, 0
+
+    if grid.zdim > 1 and not search2D:
+        if grid._gtype == GridType.RectilinearZGrid:
+            try:
+                (zi, zeta) = search_indices_vertical_z(field.grid, field.gridindexingtype, z)
+            except FieldOutOfBoundError:
+                _raise_field_out_of_bound_error(z, y, x)
+            except FieldOutOfBoundSurfaceError:
+                _raise_field_out_of_bound_surface_error(z, y, x)
+        elif grid._gtype == GridType.RectilinearSGrid:
+            (zi, zeta) = search_indices_vertical_s(field.grid, field.interp_method, time, z, y, x, ti, yi, xi, eta, xsi)
+    else:
+        zi, zeta = -1, 0
+
+    if not ((0 <= xsi <= 1) and (0 <= eta <= 1) and (0 <= zeta <= 1)):
+        _raise_field_sampling_error(z, y, x)
+
+    if particle:
+        particle.xi[field.igrid] = xi
+        particle.yi[field.igrid] = yi
+        particle.zi[field.igrid] = zi
+
+    return (zeta, eta, xsi, zi, yi, xi)
+
+
+def _search_indices_curvilinear(field: Field, time, z, y, x, ti=-1, particle=None, search2D=False):
+    if particle:
+        xi = particle.xi[field.igrid]
+        yi = particle.yi[field.igrid]
+    else:
+        xi = int(field.grid.xdim / 2) - 1
+        yi = int(field.grid.ydim / 2) - 1
+    xsi = eta = -1
+    grid = field.grid
+    invA = np.array([[1, 0, 0, 0], [-1, 1, 0, 0], [-1, 0, 0, 1], [1, -1, 1, -1]])
+    maxIterSearch = 1e6
+    it = 0
+    tol = 1.0e-10
+    if not grid.zonal_periodic:
+        if x < grid.lonlat_minmax[0] or x > grid.lonlat_minmax[1]:
+            if grid.lon[0, 0] < grid.lon[0, -1]:
+                _raise_field_out_of_bound_error(z, y, x)
+            elif x < grid.lon[0, 0] and x > grid.lon[0, -1]:  # This prevents from crashing in [160, -160]
+                _raise_field_out_of_bound_error(z, y, x)
+    if y < grid.lonlat_minmax[2] or y > grid.lonlat_minmax[3]:
+        _raise_field_out_of_bound_error(z, y, x)
+
+    while xsi < -tol or xsi > 1 + tol or eta < -tol or eta > 1 + tol:
+        px = np.array([grid.lon[yi, xi], grid.lon[yi, xi + 1], grid.lon[yi + 1, xi + 1], grid.lon[yi + 1, xi]])
+        if grid.mesh == "spherical":
+            px[0] = px[0] + 360 if px[0] < x - 225 else px[0]
+            px[0] = px[0] - 360 if px[0] > x + 225 else px[0]
+            px[1:] = np.where(px[1:] - px[0] > 180, px[1:] - 360, px[1:])
+            px[1:] = np.where(-px[1:] + px[0] > 180, px[1:] + 360, px[1:])
+        py = np.array([grid.lat[yi, xi], grid.lat[yi, xi + 1], grid.lat[yi + 1, xi + 1], grid.lat[yi + 1, xi]])
+        a = np.dot(invA, px)
+        b = np.dot(invA, py)
+
+        aa = a[3] * b[2] - a[2] * b[3]
+        bb = a[3] * b[0] - a[0] * b[3] + a[1] * b[2] - a[2] * b[1] + x * b[3] - y * a[3]
+        cc = a[1] * b[0] - a[0] * b[1] + x * b[1] - y * a[1]
+        if abs(aa) < 1e-12:  # Rectilinear cell, or quasi
+            eta = -cc / bb
+        else:
+            det2 = bb * bb - 4 * aa * cc
+            if det2 > 0:  # so, if det is nan we keep the xsi, eta from previous iter
+                det = np.sqrt(det2)
+                eta = (-bb + det) / (2 * aa)
+        if abs(a[1] + a[3] * eta) < 1e-12:  # this happens when recti cell rotated of 90deg
+            xsi = ((y - py[0]) / (py[1] - py[0]) + (y - py[3]) / (py[2] - py[3])) * 0.5
+        else:
+            xsi = (x - a[0] - a[2] * eta) / (a[1] + a[3] * eta)
+        if xsi < 0 and eta < 0 and xi == 0 and yi == 0:
+            _raise_field_out_of_bound_error(0, y, x)
+        if xsi > 1 and eta > 1 and xi == grid.xdim - 1 and yi == grid.ydim - 1:
+            _raise_field_out_of_bound_error(0, y, x)
+        if xsi < -tol:
+            xi -= 1
+        elif xsi > 1 + tol:
+            xi += 1
+        if eta < -tol:
+            yi -= 1
+        elif eta > 1 + tol:
+            yi += 1
+        (yi, xi) = _reconnect_bnd_indices(yi, xi, grid.ydim, grid.xdim, grid.mesh)
+        it += 1
+        if it > maxIterSearch:
+            print(f"Correct cell not found after {maxIterSearch} iterations")
+            _raise_field_out_of_bound_error(0, y, x)
+    xsi = max(0.0, xsi)
+    eta = max(0.0, eta)
+    xsi = min(1.0, xsi)
+    eta = min(1.0, eta)
+
+    if grid.zdim > 1 and not search2D:
+        if grid._gtype == GridType.CurvilinearZGrid:
+            try:
+                (zi, zeta) = search_indices_vertical_z(field.grid, field.gridindexingtype, z)
+            except FieldOutOfBoundError:
+                _raise_field_out_of_bound_error(z, y, x)
+        elif grid._gtype == GridType.CurvilinearSGrid:
+            (zi, zeta) = search_indices_vertical_s(field.grid, field.interp_method, time, z, y, x, ti, yi, xi, eta, xsi)
+    else:
+        zi = -1
+        zeta = 0
+
+    if not ((0 <= xsi <= 1) and (0 <= eta <= 1) and (0 <= zeta <= 1)):
+        _raise_field_sampling_error(z, y, x)
+
+    if particle:
+        particle.xi[field.igrid] = xi
+        particle.yi[field.igrid] = yi
+        particle.zi[field.igrid] = zi
+
+    return (zeta, eta, xsi, zi, yi, xi)
+
+
+def _reconnect_bnd_indices(yi: int, xi: int, ydim: int, xdim: int, sphere_mesh: bool):
+    if xi < 0:
+        if sphere_mesh:
+            xi = xdim - 2
+        else:
+            xi = 0
+    if xi > xdim - 2:
+        if sphere_mesh:
+            xi = 0
+        else:
+            xi = xdim - 2
+    if yi < 0:
+        yi = 0
+    if yi > ydim - 2:
+        yi = ydim - 2
+        if sphere_mesh:
+            xi = xdim - xi
+    return yi, xi