Add script to convert cell coordinates from plane to sphere#675
Add script to convert cell coordinates from plane to sphere#675matthewhoffman wants to merge 5 commits intoMPAS-Dev:masterfrom
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Example of plotting ice speed from the MALI 4km AIS mesh on a sphere overlaid on bottom depth from MPAS-Ocean: |
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Using optional surface warping: 
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trhille
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Thanks for this very useful script, @matthewhoffman. I think we want to avoid editing files in-place because we can imagine a nightmare scenario in which someone inadvertently overwrites one of the mesh files in our database, so almost all of my comments have to do with that.
| from another file and set on_a_sphere back to NO. | ||
| 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 visuatlization in Paraview only. |
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| for visuatlization in Paraview only. | |
| for visualization in Paraview only. |
| 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 modifies the file in place, so be sure to make a copy first! |
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Let's get rid of this in favor of writing to a new output file. Otherwise we run the risk of someone inadvertently overwriting the mesh files in our database.
| bedTopography = ds.variables['bedTopography'][0,:] | ||
| sfc = np.maximum(bedTopography + thickness, | ||
| (1.0 - 910.0 / 1028.0) * thickness) | ||
| #sfc = thickness + np.minimum(bedTopography, 0.0) * 1028.0 / 910.0 |
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@trhille , thanks for the review - those are all good suggestions. Copilot implemented the requested changes and I tweaked them slightly. |
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Pull request overview
Adds a new landice utility script to rewrite MPAS/MALI cell-center coordinates into spherical XYZ (optionally with surface warping) so NetCDF output can be rendered on a sphere in ParaView, and documents the workflow in the landice visualization docs.
Changes:
- Add
convert_cell_coordinates_to_sphere.pyto copy an input NetCDF file and replacexCell/yCell/zCell, setting sphere-related global attributes. - Support optional surface warping based on
upperSurfaceorthickness + bedTopography. - Document usage in
conda_package/docs/landice/visualization.rst.
Reviewed changes
Copilot reviewed 2 out of 2 changed files in this pull request and generated 4 comments.
| File | Description |
|---|---|
landice/mesh_tools_li/convert_cell_coordinates_to_sphere.py |
New script to convert xCell/yCell/zCell to spherical coordinates (with optional warped radius) and set sphere attributes for ParaView rendering. |
conda_package/docs/landice/visualization.rst |
Adds a new section describing how to use the conversion script for spherical ParaView rendering. |
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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.
Enhance spherical coordinate conversion script: * don't overwrite input file * clean up to comments and docstring * addition of documentation section * error message when required fields are missing
Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
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Rebased because CI was stuck and I thought that might help. @trhille , I think this is ready to merge unless you see anything else. |
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. Plotting MALI output on a sphere allows it to be visualized with output from other E3SM components (e.g. MPAS-Ocean).
I placed it in landice/mesh_tools_li because it modifies a mesh, even though we are likely to primarily use it on output files.