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Merge #77
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77: new datasets available r=Yujie-W a=Yujie-W

New data:
- V3 clumping index (monthly means)
- V1 vegetation cover fraction (annually data)

Fix:
- errors in README

Co-authored-by: Yujie Wang <[email protected]>
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bors[bot] and Yujie-W authored Feb 10, 2023
2 parents b437cc6 + c6e78be commit 7735f7b
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192 changes: 192 additions & 0 deletions Artifacts.toml
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Expand Up @@ -38,6 +38,14 @@ lazy = true
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Expand All @@ -46,6 +54,14 @@ lazy = true
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Expand Down Expand Up @@ -3542,6 +3558,182 @@ lazy = true
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[VCMAX_2X_1Y_V1]
git-tree-sha1 = "3c8a9cb068a1a242df4699dfbb6baaba9899eb84"
lazy = true
Expand Down
4 changes: 2 additions & 2 deletions Project.toml
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
name = "GriddingMachine"
uuid = "f20cf718-bf4d-4727-bc8f-485b1f283ac6"
authors = ["Yujie Wang"]
version = "0.2.8"
version = "0.2.9"

[deps]
Artifacts = "56f22d72-fd6d-98f1-02f0-08ddc0907c33"
Expand All @@ -23,7 +23,7 @@ DocStringExtensions = "0.8.5, 0.9.0"
HTTP = "0.9.14, 1.0.5"
JSON = "0.21.2"
NetcdfIO = "0.2.5"
PkgUtility = "0.2.0"
PkgUtility = "0.1.13, 0.2.0"
ProgressMeter = "1.7.1"
PyCall = "1.92.3"
julia = "1.6"
19 changes: 8 additions & 11 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -7,9 +7,6 @@
[dev-img]: https://img.shields.io/badge/docs-dev-blue.svg
[dev-url]: https://CliMA.github.io/GriddingMachine.jl/dev/

[rel-img]: https://img.shields.io/badge/docs-stable-blue.svg
[rel-url]: https://CliMA.github.io/GriddingMachine.jl/stable/

[st-img]: https://github.com/CliMA/GriddingMachine.jl/workflows/JuliaStable/badge.svg?branch=main
[st-url]: https://github.com/CliMA/GriddingMachine.jl/actions?query=branch%3A"main"++workflow%3A"JuliaStable"

Expand All @@ -32,9 +29,9 @@ Please cite our paper(s) when you use GriddingMachine:
## About
[`GriddingMachine.jl`][gm-url] includes a collection of global canopy propertie. To best utilize `Pkg.Artifacts` and FTP storage, [`GriddingMachine.jl`][gm-url] only supports julia 1.6 and above.

| Documentation | CI Status | Compatibility | Code Coverage |
|:------------------------------------------------|:----------------------|:------------------------|:------------------------|
| [![][dev-img]][dev-url] [![][rel-img]][rel-url] | [![][st-img]][st-url] | [![][min-img]][min-url] | [![][cov-img]][cov-url] |
| Documentation | CI Status | Compatibility | Code Coverage |
|:------------------------|:----------------------|:------------------------|:------------------------|
| [![][dev-img]][dev-url] | [![][st-img]][st-url] | [![][min-img]][min-url] | [![][cov-img]][cov-url] |


## Installation
Expand All @@ -59,15 +56,15 @@ See [`API`][gm-api] for more detailed information about how to use [`GriddingMac

To automatically download and query the file path of the dataset, use
```julia
julia> GriddingMachine.Collector;
julia> file_path = query_collection('VCMAX_2X_1Y_V1');
julia> using GriddingMachine.Collector;
julia> file_path = query_collection("VCMAX_2X_1Y_V1");
```

To request a partial dataset from the server without download the entire dataset, use
```julia
julia> GriddingMachine.Requestor;
julia> dat,std = request_LUT('VCMAX_2X_1Y_V1', 35.1, 115.2);
julia> dat,std = request_LUT('VCMAX_2X_1Y_V1', 35.1, 115.2; interpolation=true);
julia> using GriddingMachine.Requestor;
julia> dat,std = request_LUT("VCMAX_2X_1Y_V1", 35.1, 115.2);
julia> dat,std = request_LUT("VCMAX_2X_1Y_V1", 35.1, 115.2; interpolation=true);
```


Expand Down
3 changes: 0 additions & 3 deletions docs/make.jl
Original file line number Diff line number Diff line change
Expand Up @@ -30,9 +30,6 @@ if gen_preview
push!(pages, "Data Preview" => "generated/preview.md");
end

@info "Pages to generate:"
pretty_display!(pages);




Expand Down
1 change: 1 addition & 0 deletions docs/src/API.md
Original file line number Diff line number Diff line change
Expand Up @@ -30,6 +30,7 @@ Collector.soil_hydraulics_collection
Collector.surface_area_collection
Collector.tree_density_collection
Collector.vcmax_collection
Collector.vegetation_cover_fraction
Collector.wood_density_collection
```

Expand Down
2 changes: 1 addition & 1 deletion src/Blender.jl
Original file line number Diff line number Diff line change
Expand Up @@ -26,7 +26,7 @@ function truncate(data::Matrix{FT}, n::Int) where {FT<:AbstractFloat}

# create a new matrix to save the data
_mat = ones(FT, Int(size(data,1)/n), Int(size(data,2)/n)) .* FT(NaN);
for _i in 1:size(_mat,1), _j in 1:size(_mat,2)
for _i in axes(_mat,1), _j in axes(_mat,2)
_mat[_i,_j] = nanmean(data[(_i-1)*n+1:_i*n,(_j-1)*n+1:_j*n]);
end;

Expand Down
37 changes: 35 additions & 2 deletions src/Collector.jl
Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@ import Base: show
export GriddedCollection
export biomass_collection, canopy_height_collection, clumping_index_collection, elevation_collection, gpp_collection, lai_collection, land_mask_collection, latent_heat_collection,
leaf_chlorophyll_collection, leaf_drymass_collection, leaf_nitrogen_collection, leaf_phosphorus_collection, pft_collection, sif_collection, sil_collection, soil_color_collection,
soil_hydraulics_collection, sla_collection, surface_area_collection, tree_density_collection, vcmax_collection, wood_density_collection
soil_hydraulics_collection, sla_collection, surface_area_collection, tree_density_collection, vcmax_collection, vegetation_cover_fraction, wood_density_collection


# export public functions
Expand Down Expand Up @@ -152,6 +152,8 @@ Method to create a general dataset collection for clumping index. Supported data
- `240X_1Y_V1` [(He et al., 2012)](https://doi.org/10.1016/j.rse.2011.12.008)
- `2X_1Y_V1` [(regridded; He et al., 2012)](https://doi.org/10.1016/j.rse.2011.12.008)
- `2X_1Y_V2` [(Braghiere et al., 2019)](https://doi.org/10.1029/2018GB006135)
- `20X_1M_V3` [(Wei et al., 2019)](https://doi.org/10.1016/j.rse.2019.111296)
- `2X_1M_V3` [(regridded; Wei et al., 2019)](https://doi.org/10.1016/j.rse.2019.111296)
V2 dataset are classified for different plant functional types. The indices are Broadleaf, Needleleaf, C3 grasses, C4 grasses, and shrubland.
</summary>
Expand All @@ -174,10 +176,18 @@ V2 dataset are classified for different plant functional types. The indices are
number = {11},
pages = {1358--1369}
}
@article{wei2019global,
author = {Wei, Shanshan and Fang, Hongliang and Schaaf, Crystal B and He, Liming and Chen, Jing M},
year = {2019},
title = {Global 500 m clumping index product derived from MODIS BRDF data (2001--2017)},
journal = {Remote Sensing of Environment},
volume = {232},
pages = {111296}
}
```
</details>
"""
clumping_index_collection() = GriddedCollection("CI", ["240X_1Y_V1", "2X_1Y_V1", "2X_1Y_V2"], "2X_1Y_V1");
clumping_index_collection() = GriddedCollection("CI", ["240X_1Y_V1", "2X_1Y_V1", "2X_1Y_V2", "20X_1M_V3"], "2X_1Y_V1");


"""
Expand Down Expand Up @@ -822,6 +832,29 @@ Method to create a general dataset collection for Vcmax. Supported datasets are
vcmax_collection() = GriddedCollection("VCMAX", ["2X_1Y_V1", "2X_1Y_V2"], "2X_1Y_V2");


"""
vegetation_cover_fraction()
<details>
<summary>
Method to create a general dataset collection for vegetation cover fraction. Supported datasets are (click to view bibtex items)
- `MODIS_MOD44B_2X_1Y_V1` [(DiMiceli et al., 2022)](https://doi.org/10.5067/MODIS/MOD44B.061)
</summary>
```
@article{dimiceli2022modismod44b,
author = {DiMiceli, C. and Sohlberg, R. and Townshend, J.},
doi = {10.5067/MODIS/MOD44B.061},
year = {2022},
title = {MODIS/Terra Vegetation Continuous Fields Yearly L3 Global 250m SIN Grid V061},
journal = {NASA EOSDIS Land Processes DAAC}
}
```
</details>
"""
vegetation_cover_fraction() = GriddedCollection("VCF", ["MODIS_MOD44B_2X_1Y_$(_year)_V1" for _year in 2000:2021], "MODIS_MOD44B_2X_1Y_2021_V1");


"""
wood_density_collection()
Expand Down
1 change: 1 addition & 0 deletions test/runtests.jl
Original file line number Diff line number Diff line change
Expand Up @@ -29,6 +29,7 @@ using Test
surface_area_collection(),
tree_density_collection(),
vcmax_collection(),
vegetation_cover_fraction(),
wood_density_collection()];

@testset "Library" begin
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2 comments on commit 7735f7b

@Yujie-W
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Registration pull request created: JuliaRegistries/General/77444

After the above pull request is merged, it is recommended that a tag is created on this repository for the registered package version.

This will be done automatically if the Julia TagBot GitHub Action is installed, or can be done manually through the github interface, or via:

git tag -a v0.2.9 -m "<description of version>" 7735f7b08f0f3281ad6b879a03c603d1c0c15c96
git push origin v0.2.9

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