Simplify and align dimensions and coordinates with netcdf Common Data Model #107
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Simplify and align with Common Data Model See corresponding PALEOboxes PR PALEOtoolkit/PALEOboxes.jl#151 TODO: this commit still includes old and now unused code Changes: - Add FixedCoord from PALEOboxes - generalized to handle 'bounds' ie Array size(2, ncells) as a simpler way of specifying cell edges (cf CF conventions) - OutputMemory now based on FieldRecord, not DataFrame - save / load to jld2 removed - updates to netcdf output format - Simpler and more generic get_array -> FieldArray from FieldRecord - replaces old approach using get_region
- remove old unused code - fix doc build
sjdaines
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to PALEOtoolkit/PALEOsediment.jl
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…s updates
See PRs:
PALEOtoolkit/PALEOboxes.jl#151
PALEOtoolkit/PALEOmodel.jl#107
Example of change needed from ReactionSedimentGridn1D do_sediment_setup_grid:
# attach coordinates to grid for output visualisation etc
if isdefined(PB, :set_coordinates!) # PALEOboxes >= 0.22
PB.set_coordinates!(rj.domain.grid, "cells", ["zmid", "zlower", "zupper"])
else
empty!(rj.domain.grid.z_coords)
push!(rj.domain.grid.z_coords, PB.FixedCoord("zmid", grid_vars.zmid, PB.get_variable(m, "zmid").attributes))
push!(rj.domain.grid.z_coords, PB.FixedCoord("zlower", grid_vars.zlower, PB.get_variable(m, "zlower").attributes))
push!(rj.domain.grid.z_coords, PB.FixedCoord("zupper", grid_vars.zupper, PB.get_variable(m, "zupper").attributes))
end
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sjdaines
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Dec 31, 2024
Simplify and tidy up FieldRecord and netcdf output
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Simplify and align with Common Data Model
See corresponding
PALEOboxesPR PALEOtoolkit/PALEOboxes.jl#151 (PALEOboxes v0.22).Closes #48
Changes:
FixedCoord, removed fromPALEOboxesArray size(2, ncells)as a simpler way of specifying cell edges (cf CF conventions)OutputMemorynow based onFieldRecord, notDataFrameget_array(fr::FieldRecord) -> FieldArrayget_regionThese changes should be non-breaking, except for models using 2D or 3D Cartesian grids.