Add script to convert cell coordinates from plane to sphere

conda_package/docs/landice/visualization.rst

@@ -119,3 +119,29 @@ used to add grounding lines to maps as countours.
                          ax=ax,
                          cmap="plasma", times=[0])
     plot_map(data_path + files[0], "bedTopography", ax=ax, time=0)
+
+Converting Planar Coordinates for Spherical ParaView Rendering
+==============================================================
+
+The script ``landice/mesh_tools_li/convert_cell_coordinates_to_sphere.py``
+can be used to create a copy of a MALI file with ``xCell``, ``yCell`` and
+``zCell`` replaced by spherical coordinates for visualization in ParaView.
+
+The input file is never modified. By default, output is written to
+``<infile stem>_sphere<suffix>``.
+
+.. code-block:: bash
+
+    convert_cell_coordinates_to_sphere.py -i output_state_2015.nc
+
+You can also choose an explicit output file and optionally warp the surface
+to create 3d ice-sheet surface topography on the sphere
+using ``upperSurface`` (or ``thickness`` + ``bedTopography`` if 
+``upperSurface`` is not available).
+
+.. code-block:: bash
+
+    convert_cell_coordinates_to_sphere.py \
+        -i output_state_2015.nc \
+        -o output_state_2015_sphere.nc \
+        -w -s 100

landice/mesh_tools_li/convert_cell_coordinates_to_sphere.py

@@ -0,0 +1,98 @@
+#!/usr/bin/env python
+'''
+Script to allow plotting MALI output on a sphere in Paraview.
+This works by replacing x/y/zCell fields and modifying global attributes so
+Paraview will plot as a spherical mesh.  Paraview only uses those 3 fields for
+plotting.
+The script writes to a separate output file and leaves the input file unchanged.
+Note that the modified coordinates will make the file no longer compatible
+with MALI or many postprocessing tools, so this is meant as a modification
+for visualization in Paraview only.
+'''
+
+import argparse
+import shutil
+from pathlib import Path
+from netCDF4 import Dataset
+import numpy as np
+
+parser = argparse.ArgumentParser(
+    prog='convert_cell_coordinates_to_sphere.py',
+    description=__doc__,
+    formatter_class=argparse.RawDescriptionHelpFormatter)
+parser.add_argument("-i", "--infile", dest="infile", default="output.nc",
+                    help="input file to convert to spherical mesh convention")
+parser.add_argument("-o", "--outfile", dest="outfile", default=None,
+                    help="output file to write (default: <infile stem>_sphere<suffix>)")
+parser.add_argument("-r", dest="radius", type=float, default=6371220.,
+                    help="sphere radius to use (m)")
+parser.add_argument("-w", dest="warp_surface", action='store_true',
+                    help="warp surface by upperSurface variable. " \
+                         "Uses scale factor from -s" \
+                         "If upperSurface is not in file, will attempt " \
+                         "to calculate it from thickness and bedTopography. " \
+                         "Uses geometry from first time level only; it is not " \
+                         "possible to have scaling evolve in time with this method.")
+parser.add_argument("-s", dest="scale", type=float, default=100.,
+                    help="scale factor for warping surface")
+args = parser.parse_args()
+
+infile = Path(args.infile)
+if args.outfile is None:
+    outfile = infile.with_name(f'{infile.stem}_sphere{infile.suffix}')
+else:
+    outfile = Path(args.outfile)
+
+if infile.resolve() == outfile.resolve():
+    raise ValueError('Output file must be different from input file.')
+
+shutil.copyfile(infile, outfile)
+
+
+def compute_xyz(latCell_deg, lonCell_deg, radius):
+    '''
+    Copied from lonlat2xyz in mesh/creation/util.py
+    '''
+    lat_rad = np.radians(latCell_deg)
+    lon_rad = np.radians(lonCell_deg)
+
+    xCell = radius * np.cos(lat_rad) * np.cos(lon_rad)
+    yCell = radius * np.cos(lat_rad) * np.sin(lon_rad)
+    zCell = radius * np.sin(lat_rad)
+
+    return xCell, yCell, zCell
+
+
+with Dataset(outfile, "r+") as ds:
+    latCell = np.degrees(ds.variables["latCell"][:])
+    lonCell = np.degrees(ds.variables["lonCell"][:])
+
+    if args.warp_surface:
+        has_upper_surface = 'upperSurface' in ds.variables
+        has_thickness = 'thickness' in ds.variables
+        has_bed_topography = 'bedTopography' in ds.variables
+
+        if not (has_upper_surface or (has_thickness and has_bed_topography)):
+            raise ValueError(
+                "Cannot warp surface: provide 'upperSurface' or both "
+                "'thickness' and 'bedTopography'.")
+
+        if has_upper_surface:
+            sfc = ds.variables['upperSurface'][0,:]
+        else:
+            thickness = ds.variables['thickness'][0,:]
+            bedTopography = ds.variables['bedTopography'][0,:]
+            sfc = np.maximum(bedTopography + thickness,
+                             (1.0 - 910.0 / 1028.0) * thickness)
+        radius = args.radius + np.maximum(sfc, 0.0) * args.scale
+    else:
+        radius = args.radius
+    xCell, yCell, zCell = compute_xyz(latCell, lonCell, radius)
+
+    # Add to NetCDF file (assumes variables already exist)
+    ds.variables["xCell"][:] = xCell
+    ds.variables["yCell"][:] = yCell
+    ds.variables["zCell"][:] = zCell
+    # Update global attributes
+    ds.setncattr("on_a_sphere", "YES")
+    ds.setncattr("sphere_radius", args.radius)