Simplify and standardize dimensions and coordinates #151
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Simplify and align with Common Data Model
Overall design:
- dimensions now just have a name and a size
- coordinates can optionally be attached to a dimension
(currently this are separate Dicts etc)
- coordinates are specified by (coordinate) variable name
which is a "standard" PALEO variable.
Coordinate values then are looked up as needed
Changes:
- NamedDimension now just contains name, size.
Remove FixedCoord (simpler version now in PALEOmodel)
- add functions
get_dimensions
get_dimension
set_coordinates!
get_coordinates
- simplify grids
- remove coordinates, which can now be defined as "standard" PALEO variables
- remove get_region (similar functionality now in PALEOmodel)
- Experimental implementation of Julia CommonDataModel interface
in CommonDataModelExt extension.
sjdaines
added a commit
to PALEOtoolkit/PALEOmodel.jl
that referenced
this pull request
Dec 29, 2024
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
sjdaines
added a commit
to PALEOtoolkit/PALEOsediment.jl
that referenced
this pull request
Dec 30, 2024
…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
Move CommonDataModel extension changes to a separate PR
sjdaines
changed the title
sjdaines
referenced
this pull request
in PALEOtoolkit/PALEOmodel.jl
Dec 31, 2024
Simplify and tidy up FieldRecord and netcdf output
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Simplify and align with Common Data Model
Overall design:
Changes: